Accuracy of the unified approach in maternally influenced traits--illustrated by a simulation study in the honey bee (Apis mellifera).

PubMed

Gupta, Pooja; Reinsch, Norbert; Spötter, Andreas; Conrad, Tim; Bienefeld, Kaspar

2013-05-06

The honey bee is an economically important species. With a rapid decline of the honey bee population, it is necessary to implement an improved genetic evaluation methodology. In this study, we investigated the applicability of the unified approach and its impact on the accuracy of estimation of breeding values for maternally influenced traits on a simulated dataset for the honey bee. Due to the limitation to the number of individuals that can be genotyped in a honey bee population, the unified approach can be an efficient strategy to increase the genetic gain and to provide a more accurate estimation of breeding values. We calculated the accuracy of estimated breeding values for two evaluation approaches, the unified approach and the traditional pedigree based approach. We analyzed the effects of different heritabilities as well as genetic correlation between direct and maternal effects on the accuracy of estimation of direct, maternal and overall breeding values (sum of maternal and direct breeding values). The genetic and reproductive biology of the honey bee was accounted for by taking into consideration characteristics such as colony structure, uncertain paternity, overlapping generations and polyandry. In addition, we used a modified numerator relationship matrix and a realistic genome for the honey bee. For all values of heritability and correlation, the accuracy of overall estimated breeding values increased significantly with the unified approach. The increase in accuracy was always higher for the case when there was no correlation as compared to the case where a negative correlation existed between maternal and direct effects. Our study shows that the unified approach is a useful methodology for genetic evaluation in honey bees, and can contribute immensely to the improvement of traits of apicultural interest such as resistance to Varroa or production and behavioural traits. In particular, the study is of great interest for cases where negative correlation between maternal and direct effects and uncertain paternity exist, thus, is of relevance for other species as well. The study also provides an important framework for simulating genomic and pedigree datasets that will prove to be helpful for future studies.

Estimates of direct and maternal (co)variance components as well as genetic parameters of growth traits in Nellore sheep.

PubMed

I, Satish Kumar; C, Vijaya Kumar; G, Gangaraju; Nath, Sapna; A K, Thiruvenkadan

2017-10-01

In the present study, (co)variance components and genetic parameters in Nellore sheep were obtained by restricted maximum likelihood (REML) method using six different animal models with various combinations of direct and maternal genetic effects for birth weight (BW), weaning weight (WW), 6-month weight (6MW), 9-month weight (9MW) and 12-month weight (YW). Evaluated records of 2075 lambs descended from 69 sires and 478 dams over a period of 8 years (2007-2014) were collected from the Livestock Research Station, Palamaner, India. Lambing year, sex of lamb, season of lambing and parity of dam were the fixed effects in the model, and ewe weight was used as a covariate. Best model for each trait was determined by log-likelihood ratio test. Direct heritability for BW, WW, 6MW, 9MW and YW were 0.08, 0.03, 0.12, 0.16 and 0.10, respectively, and their corresponding maternal heritabilities were 0.07, 0.10, 0.09, 0.08 and 0.11. The proportions of maternal permanent environment variance to phenotypic variance (Pe 2 ) were 0.07, 0.10, 0.07, 0.06 and 0.10 for BW, WW, 6MW, 9MW and YW, respectively. The estimates of direct genetic correlations among the growth traits were positive and ranged from 0.44(BW-WW) to 0.96(YW-9MW), and the estimates of phenotypic and environmental correlations were found to be lower than those of genetic correlations. Exclusion of maternal effects in the model resulted in biased estimates of genetic parameters in Nellore sheep. Hence, to implement optimum breeding strategies for improvement of traits in Nellore sheep, maternal effects should be considered.

Genetic and Environmental Influences on Pulmonary Function and Muscle Strength: The Chinese Twin Study of Aging.

PubMed

Tian, Xiaocao; Xu, Chunsheng; Wu, Yili; Sun, Jianping; Duan, Haiping; Zhang, Dongfeng; Jiang, Baofa; Pang, Zengchang; Li, Shuxia; Tan, Qihua

2017-02-01

Genetic and environmental influences on predictors of decline in daily functioning, including forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC), handgrip, and five-times-sit-to-stand test (FTSST), have not been addressed in the aging Chinese population. We performed classical twin modeling on FEV1, FVC, handgrip, and FTSST in 379 twin pairs (240 MZ and 139 DZ) with median age of 50 years (40-80 years). Data were analyzed by fitting univariate and bivariate twin models to estimate the genetic and environmental influences on these measures of physical function. Heritability was moderate for FEV1, handgrip, and FTSST (55-60%) but insignificant for FVC. Only FVC showed moderate control, with shared environmental factors accounting for about 50% of the total variance. In contrast, all measures of pulmonary function and muscle strength showed modest influences from the unique environment (40-50%). Bivariate analysis showed highly positive genetic correlations between FEV1 and FVC (r G = 1.00), and moderately negative genetic correlations between FTSST and FEV1 (r G = -0.33) and FVC (r G = -0.42). FEV1 and FVC, as well as FEV1 and handgrip, displayed high common environmental correlations (r C = 1.00), and there were moderate correlations between FVC and handgrip (r C = 0.44). FEV1 and FVC showed high unique environmental correlations (r E = 0.76) and low correlations between handgrip and FEV1 (r E = 0.17), FVC (r E = 0.14), and FTSST (r E = -0.13) with positive or negative direction. We conclude that genetic factors contribute significantly to the individual differences in common indicators of daily functioning (FEV1, handgrip, and FTSST). FEV1 and FVC were genetically and environmentally correlated. Pulmonary function and FTSST may share similar sets of genes but in the negative direction. Pulmonary function and muscle strength may have a shared environmental background.

Rapid independent trait evolution despite a strong pleiotropic genetic correlation.

PubMed

Conner, Jeffrey K; Karoly, Keith; Stewart, Christy; Koelling, Vanessa A; Sahli, Heather F; Shaw, Frank H

2011-10-01

Genetic correlations are the most commonly studied of all potential constraints on adaptive evolution. We present a comprehensive test of constraints caused by genetic correlation, comparing empirical results to predictions from theory. The additive genetic correlation between the filament and the corolla tube in wild radish flowers is very high in magnitude, is estimated with good precision (0.85 ± 0.06), and is caused by pleiotropy. Thus, evolutionary changes in the relative lengths of these two traits should be constrained. Still, artificial selection produced rapid evolution of these traits in opposite directions, so that in one replicate relative to controls, the difference between them increased by six standard deviations in only nine generations. This would result in a 54% increase in relative fitness on the basis of a previous estimate of natural selection in this population, and it would produce the phenotypes found in the most extreme species in the family Brassicaceae in less than 100 generations. These responses were within theoretical expectations and were much slower than if the genetic correlation was zero; thus, there was evidence for constraint. These results, coupled with comparable results from other species, show that evolution can be rapid despite the constraints caused by genetic correlations.

Selection on parental performance opposes selection for larger body mass in a wild population of blue tits.

PubMed

Thomson, Caroline E; Bayer, Florian; Crouch, Nicholas; Farrell, Samantha; Heap, Elizabeth; Mittell, Elizabeth; Zurita-Cassinello, Mar; Hadfield, Jarrod D

2017-03-01

There is abundant evidence in many taxa for positive directional selection on body size, and yet little evidence for microevolutionary change. In many species, variation in body size is partly determined by the actions of parents, so a proposed explanation for stasis is the presence of a negative genetic correlation between direct and parental effects. Consequently, selecting genes for increased body size would result in a correlated decline in parental effects, reducing body size in the following generation. We show that these arguments implicitly assume that parental care is cost free, and that including a cost alters the predicted genetic architectures needed to explain stasis. Using a large cross-fostered population of blue tits, we estimate direct selection on parental effects for body mass, and show it is negative. Negative selection is consistent with a cost to parental care, mainly acting through a reduction in current fecundity rather than survival. Under these conditions, evolutionary stasis is possible for moderately negative genetic correlations between direct and parental effects. This is in contrast to the implausibly extreme correlations needed when care is assumed to be cost-free. Thus, we highlight the importance of accounting correctly for complete selection acting on traits across generations. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Direct and indirect selection on flowering time, water-use efficiency (WUE, δ 13C), and WUE plasticity to drought in Arabidopsis thaliana

PubMed Central

Kenney, Amanda M; McKay, John K; Richards, James H; Juenger, Thomas E

2014-01-01

Flowering time and water-use efficiency (WUE) are two ecological traits that are important for plant drought response. To understand the evolutionary significance of natural genetic variation in flowering time, WUE, and WUE plasticity to drought in Arabidopsis thaliana, we addressed the following questions: (1) How are ecophysiological traits genetically correlated within and between different soil moisture environments? (2) Does terminal drought select for early flowering and drought escape? (3) Is WUE plasticity to drought adaptive and/or costly? We measured a suite of ecophysiological and reproductive traits on 234 spring flowering accessions of A. thaliana grown in well-watered and season-ending soil drying treatments, and quantified patterns of genetic variation, correlation, and selection within each treatment. WUE and flowering time were consistently positively genetically correlated. WUE was correlated with WUE plasticity, but the direction changed between treatments. Selection generally favored early flowering and low WUE, with drought favoring earlier flowering significantly more than well-watered conditions. Selection for lower WUE was marginally stronger under drought. There were no net fitness costs of WUE plasticity. WUE plasticity (per se) was globally neutral, but locally favored under drought. Strong genetic correlation between WUE and flowering time may facilitate the evolution of drought escape, or constrain independent evolution of these traits. Terminal drought favored drought escape in these spring flowering accessions of A. thaliana. WUE plasticity may be favored over completely fixed development in environments with periodic drought. PMID:25512847

Genetic relationships between growth and carcass traits and profitability in Japanese Brown cattle.

PubMed

Kahi, A K; Oguni, T; Sumio, Y; Hirooka, H

2007-02-01

The objectives of this study were 1) to examine the genetic relationship between growth and carcass traits and carcass price (CaP) and profitability in Japanese Brown cattle, 2) to estimate economic values of carcass and growth traits as regression coefficients of price and profit traits on growth and carcass traits using a multiple regression model, and 3) to compare direct and indirect predictions of the genetic merit of profit obtained from multitrait analysis and selection index, respectively. Growth and carcass traits considered in this study were ADG during the feedlot period, CWT, LM area (LMA), rib thickness (RT), subcutaneous fat thickness (SFT), and marbling score (MS). Carcass price was evaluated as a price trait independent of its influence on profit. Profit traits were defined as 1) net income per year (PROF1), 2) net income per year/energy requirement (PROF2), and 3) net income per year minus feed costs (PROF3). Correlations between direct and indirect predictions were estimated based on EBV of sires and dams with progeny records. The heritability estimate for CaP was 0.41. The heritability estimates for profit traits were high and were 0.62, 0.66, and 0.60 for PROF1, PROF2, and PROF3, respectively. The genetic correlations between CaP and ADG, CWT, LMA, RT, SFT, and MS were 0.19, 0.14, 0.30, 0.38, -0.11, and 0.98, respectively. Among the profit traits, PROF1 had the greatest genetic correlations with growth and carcass traits. The correlations with ADG, CWT, LMA, RT, SFT, and MS were 0.30, 0.21, 0.24, 0.39, -0.01, and 0.69, respectively. These estimates indicate that use of profit traits as a selection criterion may promote desirable correlated responses in growth and carcass traits. The economic values for growth and carcass traits estimated relative to CaP and each profit trait differed because of the apparent differences in the description of these traits. The correlations between EBV for the same profit traits from direct and indirect predictions were high and ranged from 0.818 to 0.846 based on EBV of sires and from 0.786 to 0.798 based on EBV of dams. The strong correlations between direct and indirect predictions for profit indicate that there is no advantage to selecting directly for profit compared with an index with all of the component traits.

Genetic conflict between sexual signalling and juvenile survival in the three-spined stickleback.

PubMed

Kim, Sin-Yeon; Velando, Alberto

2016-02-29

Secondary sexual traits and mating preferences may evolve in part because the offspring of attractive males inherit attractiveness and other genetically correlated traits such as fecundity and viability. A problem regarding these indirect genetic mechanisms is how sufficient genetic variation in the traits subject to sexual selection is maintained within a population. Here we explored the additive genetic correlations between carotenoid-based male ornament colouration, female fecundity and juvenile survival rate in the three-spined stickleback (Gasterosteus aculeatus) to test the possibility that attractiveness genes reduce important fitness components in the bearers not expressing the sexual trait. Male sexual attractiveness (i.e., red nuptial colouration) as well as female fecundity and juvenile viability showed heritable variations in the three-spined stickleback. Thus, females can gain indirect benefits by mating with an attractive male. There was a strong positive genetic correlation between female fecundity and juvenile viability. However, red sexual signal of male sticklebacks was negatively genetically correlated with juvenile survival, suggesting genetic conflict between attractiveness and viability. There was no significant correlation between attractiveness of brothers and fecundity of sisters, suggesting no intra-locus sexual conflict. The negative effects of mating with a colourful male on offspring viability may contribute to maintaining the heritable variation under strong directional sexual selection. The strength of indirect sexual selection may be weaker than previously thought due to the hidden genetic conflicts.

Plumage condition in laying hens: genetic parameters for direct and indirect effects in two purebred layer lines.

PubMed

Brinker, Tessa; Bijma, Piter; Visscher, Jeroen; Rodenburg, T Bas; Ellen, Esther D

2014-05-29

Feather pecking is a major welfare issue in laying hen industry that leads to mortality. Due to a ban on conventional cages in the EU and on beak trimming in some countries of the EU, feather pecking will become an even bigger problem. Its severity depends both on the victim receiving pecking and on its group mates inflicting pecking (indirect effects), which together determine plumage condition of the victim. Plumage condition may depend, therefore, on both the direct genetic effect of an individual itself and on the indirect genetic effects of its group mates. Here, we present estimated genetic parameters for direct and indirect effects on plumage condition of different body regions in two purebred layer lines, and estimates of genetic correlations between body regions. Feather condition scores (FCS) were recorded at 40 weeks of age for neck, back, rump and belly and these four scores were added-up into a total FCS. A classical animal model and a direct-indirect effects model were used to estimate genetic parameters for FCS. In addition, a bivariate model with mortality (0/1) was used to account for mortality before recording FCS. Due to mortality during the first 23 weeks of laying, 5363 (for W1) and 5089 (for WB) FCS records were available. Total heritable variance for FCS ranged from 1.5% to 9.8% and from 9.8% to 53.6% when estimated respectively with the classical animal and the direct-indirect effects model. The direct-indirect effects model had a significantly higher likelihood. In both lines, 70% to 94% of the estimated total heritable variation in FCS was due to indirect effects. Using bivariate analysis of FCS and mortality did not affect estimates of genetic parameters. Genetic correlations were high between adjacent regions for FCS on neck, back, and rump but moderate to low for belly with other regions. Our results show that 70% to 94% of the heritable variation in FCS relates to indirect effects, indicating that methods of genetic selection that include indirect genetic effects offer perspectives to improve plumage condition in laying hens. This, in turn could reduce a major welfare problem.

Hemiclonal analysis of interacting phenotypes in male and female Drosophila melanogaster

PubMed Central

2014-01-01

Background Identifying the sources of variation in mating interactions between males and females is important because this variation influences the strength and/or the direction of sexual selection that populations experience. While the origins and effects of variation in male attractiveness and ornamentation have received much scrutiny, the causes and consequences of intraspecific variation in females have been relatively overlooked. We used cytogenetic cloning techniques developed for Drosophila melanogaster to create “hemiclonal” males and females with whom we directly observed sexual interaction between individuals of different known genetic backgrounds and measured subsequent reproductive outcomes. Using this approach, we were able to quantify the genetic contribution of each mate to the observed phenotypic variation in biologically important traits including mating speed, copulation duration, and subsequent offspring production, as well as measure the magnitude and direction of intersexual genetic correlation between female choosiness and male attractiveness. Results We found significant additive genetic variation contributing to mating speed that can be attributed to male genetic identity, female genetic identity, but not their interaction. Furthermore we found that phenotypic variation in copulation duration had a significant male-associated genetic component. Female genetic identity and the interaction between male and female genetic identity accounted for a substantial amount of the observed phenotypic variation in egg size. Although previous research predicts a trade-off between egg size and fecundity, this was not evident in our results. We found a strong negative genetic correlation between female choosiness and male attractiveness, a result that suggests a potentially important role for sexually antagonistic alleles in sexual selection processes in our population. Conclusion These results further our understanding of sexual selection because they identify that genetic identity plays a significant role in phenotypic variation in female behaviour and fecundity. This variation may be potentially due to ongoing sexual conflict found between the sexes for interacting phenotypes. Our unexpected observation of a negative correlation between female choosiness and male attractiveness highlights the need for more explicit theoretical models of genetic covariance to investigate the coevolution of female choosiness and male attractiveness. PMID:24884361

Correlation not Causation: The Relationship between Personality Traits and Political Ideologies

PubMed Central

Verhulst, Brad; Eaves, Lindon J.; Hatemi, Peter K.

2013-01-01

The assumption in the personality and politics literature is that a person's personality motivates them to develop certain political attitudes later in life. This assumption is founded on the simple correlation between the two constructs and the observation that personality traits are genetically influenced and develop in infancy, whereas political preferences develop later in life. Work in psychology, behavioral genetics, and recently political science, however, has demonstrated that political preferences also develop in childhood and are equally influenced by genetic factors. These findings cast doubt on the assumed causal relationship between personality and politics. Here we test the causal relationship between personality traits and political attitudes using a direction of causation structural model on a genetically informative sample. The results suggest that personality traits do not cause people to develop political attitudes; rather, the correlation between the two is a function of an innate common underlying genetic factor. PMID:22400142

Correlation not causation: the relationship between personality traits and political ideologies.

PubMed

Verhulst, Brad; Eaves, Lindon J; Hatemi, Peter K

2012-01-01

The assumption in the personality and politics literature is that a person's personality motivates them to develop certain political attitudes later in life. This assumption is founded on the simple correlation between the two constructs and the observation that personality traits are genetically influenced and develop in infancy, whereas political preferences develop later in life. Work in psychology, behavioral genetics, and recently political science, however, has demonstrated that political preferences also develop in childhood and are equally influenced by genetic factors. These findings cast doubt on the assumed causal relationship between personality and politics. Here we test the causal relationship between personality traits and political attitudes using a direction of causation structural model on a genetically informative sample. The results suggest that personality traits do not cause people to develop political attitudes; rather, the correlation between the two is a function of an innate common underlying genetic factor.

Genetic correlations between mature cow weight and productive and reproductive traits in Nellore cattle.

PubMed

Regatieri, I C; Boligon, A A; Baldi, F; Albuquerque, L G

2012-08-29

We investigated genetic associations between mature cow weight (MW) and weaning weight (WW), yearling weight (YW), weight gain from birth to weaning (GBW), weight gain from weaning to yearling (GWY), weaning hip height (WHH), yearling hip height (YHH), scrotal circumference (SC), and age at first calving (AFC). Data from 127,104 Nellore animals born between 1993 and 2006, belonging to Agropecuária Jacarezinho Ltda., were analyzed. (Co)variance components were obtained by the restricted maximum likelihood method, applying an animal model in a multi-traits analysis. The model included direct genetic and residual effects as random effects, the fixed effects of contemporary group, and the linear and quadratic effects of animal age at recording (except for AFC, GBW, and GWY) and age of cow at calving as covariates (except for MW). The numbers of days from birth to weaning and from weaning to yearling were included as covariates for GBW and GWY, respectively. Estimated direct heritabilities were 0.43 ± 0.02 (MW), 0.33 ± 0.01 (WW), 0.36 ± 0.01 (YW), 0.28 ± 0.02 (GBW), 0.31 ± 0.01 (GWY), 0.44 ± 0.02 (WHH), 0.48 ± 0.02 (YHH), 0.44 ± 0.01 (SC), and 0.16 ± 0.03 (AFC). Genetic correlations between MW and productive traits were positive and of medium to high magnitude (ranging from 0.47 ± 0.03 to 0.71 ± 0.01). A positive and low genetic correlation was observed between MW and SC (0.24 ± 0.04). A negative genetic correlation (-0.19 ± 0.03) was estimated between MW and AFC. Selection to increase weight or weight gains at any age, as well as hip height, will change MW in the same direction. Selection for higher SC may lead to a long-term increase in MW. The AFC can be included in selection indices to improve the reproductive performance of beef cattle without significant changes in MW.

Genetic correlations between body weight change and reproduction traits in Merino ewes depend on age.

PubMed

Rose, G; Mulder, H A; van der Werf, J H J; Thompson, A N; van Arendonk, J A M

2014-08-01

Merino sheep in Australia experience periods of variable feed supply. Merino sheep can be bred to be more resilient to this variation by losing less BW when grazing poor quality pasture and gaining more BW when grazing good quality pasture. Therefore, selection on BW change might be economically attractive but correlations with other traits in the breeding objective need to be known. The genetic correlations (rg) between BW, BW change, and reproduction were estimated using records from approximately 7,350 fully pedigreed Merino ewes managed at Katanning in Western Australia. Number of lambs and total weight of lambs born and weaned were measured on approximately 5,300 2-yr-old ewes, approximately 4,900 3-yr-old ewes, and approximately 3,600 4-yr-old ewes. On a proportion of these ewes BW change was measured: approximately 1,950 2-yr-old ewes, approximately 1,500 3-yr-old ewes, and approximately 1,100 4-yr-old ewes. The BW measurements were for 3 periods. The first period was during mating period over 42 d on poor pasture. The second period was during pregnancy over 90 d for ewes that got pregnant on poor and medium quality pasture. The third period was during lactation over 130 d for ewes that weaned a lamb on good quality pasture. Genetic correlations between weight change and reproduction were estimated within age classes. Genetic correlations were tested to be significantly greater magnitude than 0 using likelihood ratio tests. Nearly all BW had significant positive genetic correlations with all reproduction traits. In 2-yr-old ewes, BW change during the mating period had a positive genetic correlation with number of lambs weaned (rg = 0.58); BW change during pregnancy had a positive genetic correlation with total weight of lambs born (rg = 0.33) and a negative genetic correlation with number of lambs weaned (rg = -0.49). All other genetic correlations were not significantly greater magnitude than 0 but estimates of genetic correlations for 3-yr-old ewes were generally consistent with these findings. The direction of the genetic correlations mostly coincided with the energy requirements of the ewes and the stage of maturity of the ewes. In conclusion, optimized selection strategies on BW changes to increase resilience will depend on the genetic correlations with reproduction and are dependent on age.

Estimation of Genetic Parameters from Longitudinal Records of Body Weight of Berkshire Pigs

PubMed Central

Lee, Dong-Hee; Do, Chang-Hee

2012-01-01

Direct and maternal genetic heritabilities and their correlations with body weight at 5 stages in the life span of purebred Berkshire pigs, from birth to harvest, were estimated to scrutinize body weight development with the records for 5,088 purebred Berkshire pigs in a Korean farm, using the REML based on an animal model. Body weights were measured at birth (Birth), at weaning (Weaning: mean 22.9 d), at the beginning of a performance test (On: mean 72.7 d), at the end of a performance test (Off: mean 152.4 d), and at harvest (Finish: mean 174.3 d). Ordinary polynomials and Legendre with order 1, 2, and 3 were adopted to adjust body weight with age in the multivariate animal models. Legendre with order 3 fitted best concerning prediction error deviation (PED) and yielded the lowest AIC for multivariate analysis of longitudinal body weights. Direct genetic correlations between body weight at Birth and body weight at Weaning, On, Off, and Finish were 0.48, 0.36, 0.10, and 0.10, respectively. The estimated maternal genetic correlations of body weight at Finish with body weight at Birth, Weaning, On, and Off were 0.39, 0.49, 0.65, and 0.90, respectively. Direct genetic heritabilities progressively increased from birth to harvest and were 0.09, 0.11, 0.20, 0.31, and 0.43 for body weight at Birth, Weaning, On, Off, and Finish, respectively. Maternal genetic heritabilities generally decreased and were 0.26, 0.34, 0.15, 0.10, and 0.10 for body weight at Birth, Weaning, On, Off, and Finish, respectively. As pigs age, maternal genetic effects on growth are reduced and pigs begin to rely more on the expression of their own genes. Although maternal genetic effects on body weight may not be large, they are sustained through life. PMID:25049624

Direct multitrait selection realizes the highest genetic response for ratio traits.

PubMed

Zetouni, L; Henryon, M; Kargo, M; Lassen, J

2017-05-01

For a number of traits the phenotype considered to be the goal trait is a combination of 2 or more traits, like methane (CH) emission (CH/kg of milk). Direct selection on CH4 emission defined as a ratio is problematic, because it is uncertain whether the improvement comes from an improvement in milk yield, a decrease in CH emission or both. The goal was to test different strategies on selecting for 2 antagonistic traits- improving milk yield while decreasing methane emissions. The hypothesis was that to maximize genetic gain for a ratio trait, the best approach is to select directly for the component traits rather than using a ratio trait or a trait where 1 trait is corrected for the other as the selection criteria. Stochastic simulation was used to mimic a dairy cattle population. Three scenarios were tested, which differed in selection criteria but all selecting for increased milk yield: 1) selection based on a multitrait approach using the correlation structure between the 2 traits, 2) the ratio of methane to milk and 3) gross methane phenotypically corrected for milk. Four correlation sets were tested in all scenarios, to access robustness of the results. An average genetic gain of 66 kg of milk per yr was obtained in all scenarios, but scenario 1 had the best response for decreased methane emissions, with a genetic gain of 24.8 l/yr, while scenarios 2 and 3 had genetic gains of 27.1 and 27.3 kg/yr. The results found were persistent across correlation sets. These results confirm the hypothesis that to obtain the highest genetic gain a multitrait selection is a better approach than selecting for the ratio directly. The results are exemplified for a methane and milk scenario but can be generalized to other situations where combined traits need to be improved.

Genetic and Environmental Basis in Phenotype Correlation Between Physical Function and Cognition in Aging Chinese Twins.

PubMed

Xu, Chunsheng; Zhang, Dongfeng; Tian, Xiaocao; Wu, Yili; Pang, Zengchang; Li, Shuxia; Tan, Qihua

2017-02-01

Although the correlation between cognition and physical function has been well studied in the general population, the genetic and environmental nature of the correlation has been rarely investigated. We conducted a classical twin analysis on cognitive and physical function, including forced expiratory volume in one second (FEV1), forced vital capacity (FVC), handgrip strength, five-times-sit-to-stand test (FTSST), near visual acuity, and number of teeth lost in 379 complete twin pairs. Bivariate twin models were fitted to estimate the genetic and environmental correlation between physical and cognitive function. Bivariate analysis showed mildly positively genetic correlations between cognition and FEV1, r G = 0.23 [95% CI: 0.03, 0.62], as well as FVC, r G = 0.35 [95% CI: 0.06, 1.00]. We found that FTSST and cognition presented very high common environmental correlation, r C = -1.00 [95% CI: -1.00, -0.57], and low but significant unique environmental correlation, r E = -0.11 [95% CI: -0.22, -0.01], all in the negative direction. Meanwhile, near visual acuity and cognition also showed unique environmental correlation, r E = 0.16 [95% CI: 0.03, 0.27]. We found no significantly genetic correlation for cognition with handgrip strength, FTSST, near visual acuity, and number of teeth lost. Cognitive function was genetically related to pulmonary function. The FTSST and cognition shared almost the same common environmental factors but only part of the unique environmental factors, both with negative correlation. In contrast, near visual acuity and cognition may positively share part of the unique environmental factors.

Genetic and phenotypic relationships of feeding behavior and temperament with performance, feed efficiency, ultrasound, and carcass merit of beef cattle.

PubMed

Nkrumah, J D; Crews, D H; Basarab, J A; Price, M A; Okine, E K; Wang, Z; Li, C; Moore, S S

2007-10-01

Feeding behavior and temperament may be useful in genetic evaluations either as indicator traits for other economically relevant traits or because the behavior traits may have a direct economic value. We determined the variation in feeding behavior and temperament of beef cattle sired by Angus, Charolais, or Hybrid bulls and evaluated their associations with performance, efficiency, and carcass merit. The behavior traits were daily feeding duration, feeding head down (HD) time, feeding frequency (FF), and flight speed (FS, as a measure of temperament). A pedigree file of 813 animals forming 28 paternal half-sib families with about 20 progeny per sire was used. Performance, feeding behavior, and efficiency records were available on 464 animals of which 381 and 302 had records on carcass merit and flight speed, respectively. Large SE reflect the number of animals used. Direct heritability estimates were 0.28 +/- 0.12 for feeding duration, 0.33 +/- 0.12 for HD, 0.38 +/- 0.13 for FF, and 0.49 +/- 0.18 for FS. Feeding duration had a weak positive genetic (r(g)) correlation with HD (r(g) = 0.25 +/- 0.32) and FS (r(g) = 0.42 +/- 0.26) but a moderate negative genetic correlation with FF (r(g) = -0.40 +/- 0.30). Feeding duration had positive phenotypic (r(p)) and genetic correlations with DMI (r(p) = 0.27; r(g) = 0.56 +/- 0.20) and residual feed intake (RFI; r(p) = 0.49; r(g) = 0.57 +/- 0.28) but was unrelated phenotypically with feed conversion ratio [FCR; which is the reciprocal of the efficiency of growth (G:F)]. Feeding duration was negatively correlated with FCR (r(g) = -0.25 +/- 0.29). Feeding frequency had a moderate to high negative genetic correlation with DMI (r(g) = -0.74 +/- 0.15), FCR (r(g) = -0.52 +/- 0.21), and RFI (r(g) = -0.77 +/- 0.21). Flight speed was negatively correlated phenotypically with DMI (r(p) = -0.35) but was unrelated phenotypically with FCR or RFI. On the other hand, FS had a weak negative genetic correlation with DMI (r(g) = -0.11 +/- 0.26), a moderate genetic correlation with FCR (r(g) = 0.40 +/- 0.26), and a negative genetic correlation with RFI (r(g) = -0.59 +/- 0.45). The results indicate that behavior traits may contribute to the variation in the efficiency of growth of beef cattle, and there are potential correlated responses to selection to improve efficiency. Feeding behavior and temperament may need to be included in the definition of beef cattle breeding goals, and approaches such as the culling of unmanageable cattle and the introduction of correct handling facilities or early life provision of appropriate experiences to improve handling will be useful.

Additive genetic variation in the craniofacial skeleton of baboons (genus Papio) and its relationship to body and cranial size.

PubMed

Joganic, Jessica L; Willmore, Katherine E; Richtsmeier, Joan T; Weiss, Kenneth M; Mahaney, Michael C; Rogers, Jeffrey; Cheverud, James M

2018-02-01

Determining the genetic architecture of quantitative traits and genetic correlations among them is important for understanding morphological evolution patterns. We address two questions regarding papionin evolution: (1) what effect do body and cranial size, age, and sex have on phenotypic (V P ) and additive genetic (V A ) variation in baboon crania, and (2) how might additive genetic correlations between craniofacial traits and body mass affect morphological evolution? We use a large captive pedigreed baboon sample to estimate quantitative genetic parameters for craniofacial dimensions (EIDs). Our models include nested combinations of the covariates listed above. We also simulate the correlated response of a given EID due to selection on body mass alone. Covariates account for 1.2-91% of craniofacial V P . EID V A decreases across models as more covariates are included. The median genetic correlation estimate between each EID and body mass is 0.33. Analysis of the multivariate response to selection reveals that observed patterns of craniofacial variation in extant baboons cannot be attributed solely to correlated response to selection on body mass, particularly in males. Because a relatively large proportion of EID V A is shared with body mass variation, different methods of correcting for allometry by statistically controlling for size can alter residual V P patterns. This may conflate direct selection effects on craniofacial variation with those resulting from a correlated response to body mass selection. This shared genetic variation may partially explain how selection for increased body mass in two different papionin lineages produced remarkably similar craniofacial phenotypes. © 2017 Wiley Periodicals, Inc.

Direct and maternal genetic relationships between calving ease, gestation length, milk production, fertility, type, and lifespan of Holstein-Friesian primiparous cows.

PubMed

Eaglen, S A E; Coffey, M P; Woolliams, J A; Wall, E

2013-06-01

As the emphasis in cattle breeding is shifting from traits that increase income toward traits that reduce costs, national breeding indices are expanding to include functional traits such as calving ease (CE). However, one issue is the lack of knowledge of genetic relationships between CE and other dairy traits. The same can be said about gestation length (GL), a potential novel selection trait with considerable heritabilities and possible genetic relationships with the calving process. This study aimed to estimate the genetic relationships between CE, GL, and other dairy traits of interest using a national data set of 31,053 primiparous cow performance records, as well as to separate direct and maternal genetic effects. Chosen dairy traits included fertility (calving interval, days to first service, nonreturn rate after 56 d, number of inseminations per conception), milk production (milk yield at d 110 in milk, accumulated 305-d milk yield, accumulated 305-d fat yield, accumulated 305-d protein yield), type (udder depth, chest width, rump width, rump angle, mammary composition, stature, body depth), and lifespan traits (functional days of productive life). To allow the separation of direct and maternal genetic effects, a random sire of the calf effect was included in the multi-trait linear trivariate sire models fitted using ASReml. Significant results showed that easily born individuals were genetically prone to high milk yield and reduced fertility in first lactation. Difficult calving primiparous cows were likely associated with being high-producing, wide and deep animals, with a reduced ability to subsequently conceive. Individuals that were born relatively early were associated with good genetic merit for milk production. Finally, individuals carrying their offspring longer were genetically associated with being wide and large animals that were themselves born relatively early. The study shows that it is feasible and valuable to separate direct and maternal effects when estimating genetic correlations between calving and other dairy traits. Furthermore, gestation length is best used as an indicator trait for lowly heritable calving traits, rather than as a novel selection trait. As estimated direct and maternal genetic correlations differ, we can conclude that genetic relationships between CE, GL, and traits of interest are present, but caution is required if these traits are implemented in national breeding indices. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

In search of genetic constraints limiting the evolution of egg size: direct and correlated responses to artificial selection on a prenatal maternal effector.

PubMed

Pick, J L; Hutter, P; Tschirren, B

2016-06-01

Maternal effects are an important force in nature, but the evolutionary dynamics of the traits that cause them are not well understood. Egg size is known to be a key mediator of prenatal maternal effects with an established genetic basis. In contrast to theoretical expectations for fitness-related traits, there is a large amount of additive genetic variation in egg size observed in natural populations. One possible mechanism for the maintenance of this variation is through genetic constraints caused by a shared genetic basis among traits. Here we created replicated, divergent selection lines for maternal egg investment in Japanese quail (Coturnix japonica) to quantify the role of genetic constraints in the evolution of egg size. We found that egg size responds rapidly to selection, accompanied by a strong response in all egg components. Initially, we observed a correlated response in body size, but this response declined over time, showing that egg size and body size can evolve independently. Furthermore, no correlated response in fecundity (measured as the proportion of days on which a female laid an egg) was observed. However, the response to selection was asymmetrical, with egg size plateauing after one generation of selection in the high but not the low investment lines. We attribute this pattern to the presence of genetic asymmetries, caused by directional dominance or unequal allele frequencies. Such asymmetries may contribute to the evolutionary stasis in egg size observed in natural populations, despite a positive association between egg size and fitness.

In search of genetic constraints limiting the evolution of egg size: direct and correlated responses to artificial selection on a prenatal maternal effector

PubMed Central

Pick, J L; Hutter, P; Tschirren, B

2016-01-01

Maternal effects are an important force in nature, but the evolutionary dynamics of the traits that cause them are not well understood. Egg size is known to be a key mediator of prenatal maternal effects with an established genetic basis. In contrast to theoretical expectations for fitness-related traits, there is a large amount of additive genetic variation in egg size observed in natural populations. One possible mechanism for the maintenance of this variation is through genetic constraints caused by a shared genetic basis among traits. Here we created replicated, divergent selection lines for maternal egg investment in Japanese quail (Coturnix japonica) to quantify the role of genetic constraints in the evolution of egg size. We found that egg size responds rapidly to selection, accompanied by a strong response in all egg components. Initially, we observed a correlated response in body size, but this response declined over time, showing that egg size and body size can evolve independently. Furthermore, no correlated response in fecundity (measured as the proportion of days on which a female laid an egg) was observed. However, the response to selection was asymmetrical, with egg size plateauing after one generation of selection in the high but not the low investment lines. We attribute this pattern to the presence of genetic asymmetries, caused by directional dominance or unequal allele frequencies. Such asymmetries may contribute to the evolutionary stasis in egg size observed in natural populations, despite a positive association between egg size and fitness. PMID:26956564

From sweaty towels to genetic stats: stalking athletes for their genetic information.

PubMed

Suter, Sonia M

2012-12-01

With recent advances in genetics, sports fans may soon have access to a new category of statistics: genetic information. With patented correlations between genetics and athletics, and with the emergence of a growing and unregulated market in direct-to-consumer ("DTC") genetic testing, fans may be able to obtain an athlete's genetic information on their own, as long as they can access any item that may have some DNA on it. In some jurisdictions, they may even be able to do so legally, notwithstanding the potential harms to the athletes and their privacy.

Genotype by production environment interaction for birth and weaning weights in a population of composite beef cattle.

PubMed

Santana, M L; Eler, J P; Bignardi, A B; Ferraz, J B S

2014-03-01

The objectives of the present study were: (1) to evaluate the importance of genotype × production environment interaction for the genetic evaluation of birth weight (BW) and weaning weight (WW) in a population of composite beef cattle in Brazil, and (2) to investigate the importance of sire × contemporary group interaction (S × CG) to model G × E and improve the accuracy of prediction in routine genetic evaluations of this population. Analyses were performed with one, two (favorable and unfavorable) or three (favorable, intermediate, unfavorable) different definitions of production environments. Thus, BW and WW records of animals in a favorable environment were assigned to either trait 1, in an intermediate environment to trait 2 or in an unfavorable environment to trait 3. The (co)variance components were estimated using Gibbs sampling in single-, bi- or three-trait animal models according to the definition of number of production environments. In general, the estimates of genetic parameters for BW and WW were similar between environments. The additive genetic correlations between production environments were close to unity for BW; however, when examining the highest posterior density intervals, the correlation between favorable and unfavorable environments reached a value of only 0.70, a fact that may lead to changes in the ranking of sires across environments. The posterior mean genetic correlation between direct effects was 0.63 in favorable and unfavorable environments for WW. When S × CG was included in two- or three-trait analyses, all direct genetic correlations were close to unity, suggesting that there was no evidence of a genotype × production environment interaction. Furthermore, the model including S × CG contributed to prevent overestimation of the accuracy of breeding values of sires, provided a lower error of prediction for both direct and maternal breeding values, lower squared bias, residual variance and deviance information criterion than the model omitting S × CG. Thus, the model that included S × CG can therefore be considered the best model on the basis of these criteria. The genotype × production environment interaction should not be neglected in the genetic evaluation of BW and WW in the present population of beef cattle. The inclusion of S × CG in the model is a feasible and plausible alternative to model the effects of G × E in the genetic evaluations.

Understanding the Relative Contributions of Direct Environmental Effects and Passive Genotype-Environment Correlations in the Association between Familial Risk Factors and Child Disruptive Behavior Disorders

PubMed Central

Bornovalova, Marina A.; Cummings, Jenna R.; Hunt, Elizabeth; Blazei, Ryan; Malone, Steve; Iacono, William G.

2013-01-01

Background: Previous work reports an association between familial risk factors stemming from parental characteristics and offspring disruptive behavior disorders (DBDs). This association may reflect a) the direct effects of familial environment, and b) a passive gene-environment correlation, wherein the parents provide both the genes and the environment. The current study examined the contributions of direct environmental influences and passive gene-environment correlations by comparing the effects of familial risk factors on child DBDs in genetically related (biological) and non-related (adoptive) families. Method: Participants were 402 adoptive and 204 biological families. Familial environment was defined as maternal and paternal maladaptive parenting and antisociality, marital conflict, and divorce; offspring DBDs included attention deficit/hyperactivity disorder, conduct disorder, and oppositional defiant disorder. Mixed-level regressions estimated the main effects of familial environment, adoption status, and the familial environment by adoption status interaction term, which tested for a presence of passive gene-environment correlations. Results: There was a main effect of maternal and paternal maladaptive parenting and marital discord on child DBDs, indicating a direct environmental effect. There was no direct environmental effect of maternal or paternal antisociality, but maternal and paternal antisociality had stronger associations with child DBDs in biological families than adoptive families, indicating the presence of a passive gene-environment correlation. Conclusions: Many familial risk factors affected children equally across genetically-related and non-related families, providing evidence for direct environmental effects. The relationship of parental antisociality and offspring DBDs was best explained by a passive gene-environment correlation, where a general vulnerability toward externalizing psychopathology is passed down by the parents to the children. PMID:23714724

Gene-environment correlation in the development of adolescent substance abuse: selection effects of child personality and mediation via contextual risk factors.

PubMed

Hicks, Brian M; Johnson, Wendy; Durbin, C Emily; Blonigen, Daniel M; Iacono, William G; McGue, Matt

2013-02-01

We used a longitudinal twin design to examine selection effects of personality traits at age 11 on high-risk environmental contexts at age 14 and the extent to which these contexts mediated risk for substance abuse at age 17. Socialization at age 11 (willingness to follow rules and endorse conventional values) predicted exposure to contextual risk at age 14. Contextual risk partially mediated the effect of socialization on substance abuse, though socialization also had a direct effect. In contrast, boldness at age 11 (social engagement and assurance, thrill seeking, and stress resilience) also predicted substance abuse directly but was unrelated to contextual risk. There was substantial overlap in the genetic and shared environmental influences on socialization and contextual risk, and genetic risk in socialization contributed to substance abuse indirectly via increased exposure to contextual risk. This suggests that active gene-environment correlations related to individual differences in socialization contributed to an early, high-risk developmental trajectory for adolescent substance abuse. In contrast, boldness appeared to index an independent and direct genetic risk factor for adolescent substance abuse.

Genetic evaluations for growth heat tolerance in Angus cattle.

PubMed

Bradford, H L; Fragomeni, B O; Bertrand, J K; Lourenco, D A L; Misztal, I

2016-10-01

The objectives were to assess the impact of heat stress and to develop a model for genetic evaluation of growth heat tolerance in Angus cattle. The American Angus Association provided weaning weight (WW) and yearling weight (YW) data, and records from the Upper South region were used because of the hot climatic conditions. Heat stress was characterized by a weaning (yearling) heat load function defined as the mean temperature-humidity index (THI) units greater than 75 (70) for 30 (150) d prior to the weigh date. Therefore, a weaning (yearling) heat load of 5 units corresponded to 80 (75) for the corresponding period prior to the weigh date. For all analyses, 82,669 WW and 69,040 YW were used with 3 ancestral generations in the pedigree. Univariate models were a proxy for the Angus growth evaluation, and reaction norms using 2 B-splines for heat load were fit separately for weaning and yearling heat loads. For both models, random effects included direct genetic, maternal genetic, maternal permanent environment (WW only), and residual. Fixed effects included a linear age covariate, age-of-dam class (WW only), and contemporary group for both models and fixed regressions on the B-splines in the reaction norm. Direct genetic correlations for WW were strong for modest heat load differences but decreased to less than 0.50 for large differences. Reranking of proven sires occurred for only WW direct effects for the reaction norms with extreme heat load differences. Conversely, YW results indicated little effect of heat stress on genetic merit. Therefore, weaning heat tolerance was a better candidate for developing selection tools. Maternal heritabilities were consistent across heat loads, and maternal genetic correlations were greater than 0.90 for nearly all heat load combinations. No evidence existed for a genotype × environment interaction for the maternal component of growth. Overall, some evidence exists for phenotypic plasticity for the direct genetic effects of WW, but traditional national cattle evaluations are likely adequately ranking sires for nonextreme environmental conditions.

An analysis of indirect genetic effects on adult body weight of the Pacific white shrimp Litopenaeus vannamei at low rearing density.

PubMed

Luan, Sheng; Luo, Kun; Chai, Zhan; Cao, Baoxiang; Meng, Xianhong; Lu, Xia; Liu, Ning; Xu, Shengyu; Kong, Jie

2015-12-14

Our aim was to estimate the genetic parameters for the direct genetic effect (DGE) and indirect genetic effects (IGE) on adult body weight in the Pacific white shrimp. IGE is the heritable effect of an individual on the trait values of its group mates. To examine IGE on body weight, 4725 shrimp from 105 tagged families were tested in multiple small test groups (MSTG). Each family was separated into three groups (15 shrimp per group) that were randomly assigned to 105 concrete tanks with shrimp from two other families. To estimate breeding values, one large test group (OLTG) in a 300 m(2) circular concrete tank was used for the communal rearing of 8398 individuals from 105 families. Body weight was measured after a growth-test period of more than 200 days. Variance components for body weight in the MSTG programs were estimated using an animal model excluding or including IGE whereas variance components in the OLTG programs were estimated using a conventional animal model that included only DGE. The correlation of DGE between MSTG and OLTG programs was estimated by a two-trait animal model that included or excluded IGE. Heritability estimates for body weight from the conventional animal model in MSTG and OLTG programs were 0.26 ± 0.13 and 0.40 ± 0.06, respectively. The log likelihood ratio test revealed significant IGE on body weight. Total heritable variance was the sum of direct genetic variance (43.5%), direct-indirect genetic covariance (2.1%), and indirect genetic variance (54.4%). It represented 73% of the phenotypic variance and was more than two-fold greater than that (32%) obtained by using a classical heritability model for body weight. Correlations of DGE on body weight between MSTG and OLTG programs were intermediate regardless of whether IGE were included or not in the model. Our results suggest that social interactions contributed to a large part of the heritable variation in body weight. Small and non-significant direct-indirect genetic correlations implied that neutral or slightly cooperative heritable interactions, rather than competition, were dominant in this population but this may be due to the low rearing density.

Soil properties drive a negative correlation between species diversity and genetic diversity in a tropical seasonal rainforest

PubMed Central

Xu, Wumei; Liu, Lu; He, Tianhua; Cao, Min; Sha, Liqing; Hu, Yuehua; Li, Qiaoming; Li, Jie

2016-01-01

A negative species-genetic diversity correlation (SGDC) could be predicted by the niche variation hypothesis, whereby an increase in species diversity within community reduces the genetic diversity of the co-occurring species because of the reduction in average niche breadth; alternatively, competition could reduce effective population size and therefore genetic diversity of the species within community. We tested these predictions within a 20 ha tropical forest dynamics plot (FDP) in the Xishuangbanna tropical seasonal rainforest. We established 15 plots within the FDP and investigated the soil properties, tree diversity, and genetic diversity of a common tree species Beilschmiedia roxburghiana within each plot. We observed a significant negative correlation between tree diversity and the genetic diversity of B. roxburghiana within the communities. Using structural equation modeling, we further determined that the inter-plot environmental characteristics (soil pH and phosphorus availability) directly affected tree diversity and that the tree diversity within the community determined the genetic diversity of B. roxburghiana. Increased soil pH and phosphorus availability might promote the coexistence of more tree species within community and reduce genetic diversity of B. roxburghiana for the reduced average niche breadth; alternatively, competition could reduce effective population size and therefore genetic diversity of B. roxburghiana within community. PMID:26860815

Soil properties drive a negative correlation between species diversity and genetic diversity in a tropical seasonal rainforest.

PubMed

Xu, Wumei; Liu, Lu; He, Tianhua; Cao, Min; Sha, Liqing; Hu, Yuehua; Li, Qiaoming; Li, Jie

2016-02-10

A negative species-genetic diversity correlation (SGDC) could be predicted by the niche variation hypothesis, whereby an increase in species diversity within community reduces the genetic diversity of the co-occurring species because of the reduction in average niche breadth; alternatively, competition could reduce effective population size and therefore genetic diversity of the species within community. We tested these predictions within a 20 ha tropical forest dynamics plot (FDP) in the Xishuangbanna tropical seasonal rainforest. We established 15 plots within the FDP and investigated the soil properties, tree diversity, and genetic diversity of a common tree species Beilschmiedia roxburghiana within each plot. We observed a significant negative correlation between tree diversity and the genetic diversity of B. roxburghiana within the communities. Using structural equation modeling, we further determined that the inter-plot environmental characteristics (soil pH and phosphorus availability) directly affected tree diversity and that the tree diversity within the community determined the genetic diversity of B. roxburghiana. Increased soil pH and phosphorus availability might promote the coexistence of more tree species within community and reduce genetic diversity of B. roxburghiana for the reduced average niche breadth; alternatively, competition could reduce effective population size and therefore genetic diversity of B. roxburghiana within community.

Genetic and Environmental Influences on Writing and their Relations to Language and Reading

PubMed Central

Olson, Richard K.; Hulslander, Jacqueline; Christopher, Micaela; Keenan, Janice M.; Wadsworth, Sally J.; Willcutt, Erik G.; Pennington, Bruce F.; DeFries, John C.

2011-01-01

Identical and fraternal twins (N = 540, age 8 to 18 years) were tested on three different measures of writing (Woodcock-Johnson III Tests of Achievement-Writing Samples and Writing Fluency; Handwriting Copy from the Group Diagnostic Reading and Aptitude Achievement Tests), three different language skills (Phonological Awareness, Rapid Naming, and Vocabulary), and three different reading skills (Word Recognition, Spelling, and Reading Comprehension). Substantial genetic influence was found on two of the writing measures, Writing Samples and Handwriting Copy, and all of the language and reading measures. Shared environment influences were generally not significant, except for vocabulary. Non-shared environment estimates, including measurement error, were significant for all variables. Genetic influences among the writing measures were significantly correlated (highest between the speeded measures Writing Fluency and Handwriting Copy), but there were also significant independent genetic influences between Copy and Samples and between Fluency and Samples. Genetic influences on writing were significantly correlated with genetic influences on all of the language and reading skills, but significant independent genetic influences were also found for Copy and Samples, whose genetic correlations were significantly less than 1.0 with the reading and language skills. The genetic correlations varied significantly in strength depending on the overlap between the writing, language, and reading task demands. We discuss implications of our results for education, limitations of the study, and new directions for research on writing and its relations to language and reading. PMID:21842316

Genetic parameter estimation for pre- and post-weaning traits in Brahman cattle in Brazil.

PubMed

Vargas, Giovana; Buzanskas, Marcos Eli; Guidolin, Diego Gomes Freire; Grossi, Daniela do Amaral; Bonifácio, Alexandre da Silva; Lôbo, Raysildo Barbosa; da Fonseca, Ricardo; Oliveira, João Ademir de; Munari, Danísio Prado

2014-10-01

Beef cattle producers in Brazil use body weight traits as breeding program selection criteria due to their great economic importance. The objectives of this study were to evaluate different animal models, estimate genetic parameters, and define the most fitting model for Brahman cattle body weight standardized at 120 (BW120), 210 (BW210), 365 (BW365), 450 (BW450), and 550 (BW550) days of age. To estimate genetic parameters, single-, two-, and multi-trait analyses were performed using the animal model. The likelihood ratio test was verified between all models. For BW120 and BW210, additive direct genetic, maternal genetic, maternal permanent environment, and residual effects were considered, while for BW365 and BW450, additive direct genetic, maternal genetic, and residual effects were considered. Finally, for BW550, additive direct genetic and residual effects were considered. Estimates of direct heritability for BW120 were similar in all analyses; however, for the other traits, multi-trait analysis resulted in higher estimates. The maternal heritability and proportion of maternal permanent environmental variance to total variance were minimal in multi-trait analyses. Genetic, environmental, and phenotypic correlations were of high magnitude between all traits. Multi-trait analyses would aid in the parameter estimation for body weight at older ages because they are usually affected by a lower number of animals with phenotypic information due to culling and mortality.

Mapping eQTL Networks with Mixed Graphical Markov Models

PubMed Central

Tur, Inma; Roverato, Alberto; Castelo, Robert

2014-01-01

Expression quantitative trait loci (eQTL) mapping constitutes a challenging problem due to, among other reasons, the high-dimensional multivariate nature of gene-expression traits. Next to the expression heterogeneity produced by confounding factors and other sources of unwanted variation, indirect effects spread throughout genes as a result of genetic, molecular, and environmental perturbations. From a multivariate perspective one would like to adjust for the effect of all of these factors to end up with a network of direct associations connecting the path from genotype to phenotype. In this article we approach this challenge with mixed graphical Markov models, higher-order conditional independences, and q-order correlation graphs. These models show that additive genetic effects propagate through the network as function of gene–gene correlations. Our estimation of the eQTL network underlying a well-studied yeast data set leads to a sparse structure with more direct genetic and regulatory associations that enable a straightforward comparison of the genetic control of gene expression across chromosomes. Interestingly, it also reveals that eQTLs explain most of the expression variability of network hub genes. PMID:25271303

Heritabilities of Directional Asymmetry in the Fore- and Hindlimbs of Rabbit Fetuses

PubMed Central

Breno, Matteo; Bots, Jessica; Van Dongen, Stefan

2013-01-01

Directional asymmetry (DA), where at the population level symmetry differs from zero, has been reported in a wide range of traits and taxa, even for traits in which symmetry is expected to be the target of selection such as limbs or wings. In invertebrates, DA has been suggested to be non-adaptive. In vertebrates, there has been a wealth of research linking morphological asymmetry to behavioural lateralisation. On the other hand, the prenatal expression of DA and evidences for quantitative genetic variation for asymmetry may suggest it is not solely induced by differences in mechanic loading between sides. We estimate quantitative genetic variation of fetal limb asymmetry in a large dataset of rabbits. Our results showed a low but highly significant level of DA that is partially under genetic control for all traits, with forelimbs displaying higher levels of asymmetry. Genetic correlations were positive within limbs, but negative across bones of fore and hind limbs. Environmental correlations were positive for all, but smaller across fore and hind limbs. We discuss our results in light of the existence and maintenance of DA in locomotory traits. PMID:24130770

Multilocus approaches for the measurement of selection on correlated genetic loci.

PubMed

Gompert, Zachariah; Egan, Scott P; Barrett, Rowan D H; Feder, Jeffrey L; Nosil, Patrik

2017-01-01

The study of ecological speciation is inherently linked to the study of selection. Methods for estimating phenotypic selection within a generation based on associations between trait values and fitness (e.g. survival) of individuals are established. These methods attempt to disentangle selection acting directly on a trait from indirect selection caused by correlations with other traits via multivariate statistical approaches (i.e. inference of selection gradients). The estimation of selection on genotypic or genomic variation could also benefit from disentangling direct and indirect selection on genetic loci. However, achieving this goal is difficult with genomic data because the number of potentially correlated genetic loci (p) is very large relative to the number of individuals sampled (n). In other words, the number of model parameters exceeds the number of observations (p ≫ n). We present simulations examining the utility of whole-genome regression approaches (i.e. Bayesian sparse linear mixed models) for quantifying direct selection in cases where p ≫ n. Such models have been used for genome-wide association mapping and are common in artificial breeding. Our results show they hold promise for studies of natural selection in the wild and thus of ecological speciation. But we also demonstrate important limitations to the approach and discuss study designs required for more robust inferences. © 2016 John Wiley & Sons Ltd.

Genetic parameters for carcass traits and body weight using a Bayesian approach in the Canchim cattle.

PubMed

Meirelles, S L C; Mokry, F B; Espasandín, A C; Dias, M A D; Baena, M M; de A Regitano, L C

2016-06-10

Correlation between genetic parameters and factors such as backfat thickness (BFT), rib eye area (REA), and body weight (BW) were estimated for Canchim beef cattle raised in natural pastures of Brazil. Data from 1648 animals were analyzed using multi-trait (BFT, REA, and BW) animal models by the Bayesian approach. This model included the effects of contemporary group, age, and individual heterozygosity as covariates. In addition, direct additive genetic and random residual effects were also analyzed. Heritability estimated for BFT (0.16), REA (0.50), and BW (0.44) indicated their potential for genetic improvements and response to selection processes. Furthermore, genetic correlations between BW and the remaining traits were high (P > 0.50), suggesting that selection for BW could improve REA and BFT. On the other hand, genetic correlation between BFT and REA was low (P = 0.39 ± 0.17), and included considerable variations, suggesting that these traits can be jointly included as selection criteria without influencing each other. We found that REA and BFT responded to the selection processes, as measured by ultrasound. Therefore, selection for yearling weight results in changes in REA and BFT.

Colour ornamentation in the blue tit: quantitative genetic (co)variances across sexes

PubMed Central

Charmantier, A; Wolak, M E; Grégoire, A; Fargevieille, A; Doutrelant, C

2017-01-01

Although secondary sexual traits are commonly more developed in males than females, in many animal species females also display elaborate ornaments or weaponry. Indirect selection on correlated traits in males and/or direct sexual or social selection in females are hypothesized to drive the evolution and maintenance of female ornaments. Yet, the relative roles of these evolutionary processes remain unidentified, because little is known about the genetic correlation that might exist between the ornaments of both sexes, and few estimates of sex-specific autosomal or sex-linked genetic variances are available. In this study, we used two wild blue tit populations with 9 years of measurements on two colour ornaments: one structurally based (blue crown) and one carotenoid based (yellow chest). We found significant autosomal heritability for the chromatic part of the structurally based colouration in both sexes, whereas carotenoid chroma was heritable only in males, and the achromatic part of both colour patches was mostly non heritable. Power limitations, which are probably common among most data sets collected so far in wild populations, prevented estimation of sex-linked genetic variance. Bivariate analyses revealed very strong cross-sex genetic correlations in all heritable traits, although the strength of these correlations was not related to the level of sexual dimorphism. In total, our results suggest that males and females share a majority of their genetic variation underlying colour ornamentation, and hence the evolution of these sex-specific traits may depend greatly on correlated responses to selection in the opposite sex. PMID:27577691

Geographical gradients in selection can reveal genetic constraints for evolutionary responses to ocean acidification

PubMed Central

Gaitán-Espitia, Juan Diego; Marshall, Dustin; Dupont, Sam; Bacigalupe, Leonardo D.; Bodrossy, Levente; Hobday, Alistair J.

2017-01-01

Geographical gradients in selection can shape different genetic architectures in natural populations, reflecting potential genetic constraints for adaptive evolution under climate change. Investigation of natural pH/pCO2 variation in upwelling regions reveals different spatio-temporal patterns of natural selection, generating genetic and phenotypic clines in populations, and potentially leading to local adaptation, relevant to understanding effects of ocean acidification (OA). Strong directional selection, associated with intense and continuous upwellings, may have depleted genetic variation in populations within these upwelling regions, favouring increased tolerances to low pH but with an associated cost in other traits. In contrast, diversifying or weak directional selection in populations with seasonal upwellings or outside major upwelling regions may have resulted in higher genetic variances and the lack of genetic correlations among traits. Testing this hypothesis in geographical regions with similar environmental conditions to those predicted under climate change will build insights into how selection may act in the future and how populations may respond to stressors such as OA. PMID:28148831

Genetic analysis of growth traits in Polled Nellore cattle raised on pasture in tropical region using Bayesian approaches.

PubMed

Lopes, Fernando Brito; Magnabosco, Cláudio Ulhôa; Paulini, Fernanda; da Silva, Marcelo Corrêa; Miyagi, Eliane Sayuri; Lôbo, Raysildo Barbosa

2013-01-01

Components of (co)variance and genetic parameters were estimated for adjusted weights at ages 120 (W120), 240 (W240), 365 (W365) and 450 (W450) days of Polled Nellore cattle raised on pasture and born between 1987 and 2010. Analyses were performed using an animal model, considering fixed effects: herd-year-season of birth and calf sex as contemporary groups and the age of cow as a covariate. Gibbs Samplers were used to estimate (co)variance components, genetic parameters and additive genetic effects, which accounted for great proportion of total variation in these traits. High direct heritability estimates for the growth traits were revealed and presented mean 0.43, 0.61, 0.72 and 0.67 for W120, W240, W365 and W450, respectively. Maternal heritabilities were 0.07 and 0.08 for W120 and W240, respectively. Direct additive genetic correlations between the weight at 120, 240, 365 and 450 days old were strong and positive. These estimates ranged from 0.68 to 0.98. Direct-maternal genetic correlations were negative for W120 and W240. The estimates ranged from -0.31 to -0.54. Estimates of maternal heritability ranged from 0.056 to 0.092 for W120 and from 0.064 to 0.096 for W240. This study showed that genetic progress is possible for the growth traits we studied, which is a novel and favorable indicator for an upcoming and promising Polled Zebu breed in Tropical regions. Maternal effects influenced the performance of weight at 120 and 240 days old. These effects should be taken into account in genetic analyses of growth traits by fitting them as a genetic or a permanent environmental effect, or even both. In general, due to a medium-high estimate of environmental (co)variance components, management and feeding conditions for Polled Nellore raised at pasture in tropical regions of Brazil needs improvement and growth performance can be enhanced.

Conservation genetics of whales and dolphins.

PubMed

Hoelzel, A R

1992-08-01

Whales and dolphins (cetaceans) are found in all the world's oceans and in some of the major rivers, yet little is known about the distribution and behaviour of many species. At the same time, cetaceans are under threat from a variety of pressures including direct and indirect takes, pollution, and competition for habitat and prey. To ensure their long-term survival it will be necessary to preserve genetic diversity through the identification and protection of differentiated populations, the assessment of variation within local populations, and through a better understanding of reproductive and dispersal behaviour. The application of molecular genetic techniques is helping to provide answers to some of these previously intractable questions. Early results suggest few consistent patterns. Obvious geographic boundaries correlate to genetic distance in some species, and not in others. Furthermore, morphological variation within species can be fairly extensive without correlating to genetic distance, or relatively minor between morphotypes that are as genetically distinct as some species. These examples emphasize the need for further study.

Gene-Environment Correlation in the Development of Adolescent Substance Abuse: Selection Effects of Child Personality and Mediation via Contextual Risk Factors

PubMed Central

Hicks, Brian M.; Johnson, Wendy; Durbin, C. Emily; Blonigen, Daniel M.; Iacono, William G.; McGue, Matt

2012-01-01

We used a longitudinal twin design to examine selection effects of personality traits at age 11 on high-risk environmental contexts at age 14, and the extent to which these contexts mediated risk for substance abuse at age 17. Socialization at age 11—willingness to follow rules and endorse conventional values—predicted exposure to contextual risk at age 14. Contextual risk partially mediated the effect of socialization on substance abuse, though socialization also had a direct effect. In contrast, boldness at age 11—social engagement and assurance, thrill-seeking, and stress resilience— also predicted substance abuse directly, but was unrelated to contextual risk. There was substantial overlap in the genetic and shared environmental influences on socialization and contextual risk, and genetic risk in socialization contributed to substance abuse indirectly via increased exposure to contextual risk. This suggests that active gene-environment correlations related to individual differences in socialization contributed to an early, high-risk developmental trajectory for adolescent substance abuse. In contrast, boldness appeared to index an independent and direct genetic risk factor for adolescent substance abuse. PMID:23398757

The genetic basis for cognitive ability, memory, and depression symptomatology in middle-aged and elderly chinese twins.

PubMed

Xu, Chunsheng; Sun, Jianping; Ji, Fuling; Tian, Xiaocao; Duan, Haiping; Zhai, Yaoming; Wang, Shaojie; Pang, Zengchang; Zhang, Dongfeng; Zhao, Zhongtang; Li, Shuxia; Hjelmborg, Jacob V B; Christensen, Kaare; Tan, Qihua

2015-02-01

The genetic influences on aging-related phenotypes, including cognition and depression, have been well confirmed in the Western populations. We performed the first twin-based analysis on cognitive performance, memory and depression status in middle-aged and elderly Chinese twins, representing the world's largest and most rapidly aging population. The sample consisted of 384 twin pairs with a median age of 50 years. Cognitive function was measured using the Montreal Cognitive Assessment (MoCA) scale; memory was assessed using the revised Wechsler Adult Intelligence scale; depression symptomatology was evaluated by the self-reported 30-item Geriatric Depression (GDS-30)scale. Both univariate and multivariate twin models were fitted to the three phenotypes with full and nested models and compared to select the best fitting models. Univariate analysis showed moderate-to-high genetic influences with heritability 0.44 for cognition and 0.56 for memory. Multivariate analysis by the reduced Cholesky model estimated significant genetic (rG = 0.69) and unique environmental (rE = 0.25) correlation between cognitive ability and memory. The model also estimated weak but significant inverse genetic correlation for depression with cognition (-0.31) and memory (-0.28). No significant unique environmental correlation was found for depression with other two phenotypes. In conclusion, there can be a common genetic architecture for cognitive ability and memory that weakly correlates with depression symptomatology, but in the opposite direction.

Integrating Gene Expression with Summary Association Statistics to Identify Genes Associated with 30 Complex Traits.

PubMed

Mancuso, Nicholas; Shi, Huwenbo; Goddard, Pagé; Kichaev, Gleb; Gusev, Alexander; Pasaniuc, Bogdan

2017-03-02

Although genome-wide association studies (GWASs) have identified thousands of risk loci for many complex traits and diseases, the causal variants and genes at these loci remain largely unknown. Here, we introduce a method for estimating the local genetic correlation between gene expression and a complex trait and utilize it to estimate the genetic correlation due to predicted expression between pairs of traits. We integrated gene expression measurements from 45 expression panels with summary GWAS data to perform 30 multi-tissue transcriptome-wide association studies (TWASs). We identified 1,196 genes whose expression is associated with these traits; of these, 168 reside more than 0.5 Mb away from any previously reported GWAS significant variant. We then used our approach to find 43 pairs of traits with significant genetic correlation at the level of predicted expression; of these, eight were not found through genetic correlation at the SNP level. Finally, we used bi-directional regression to find evidence that BMI causally influences triglyceride levels and that triglyceride levels causally influence low-density lipoprotein. Together, our results provide insight into the role of gene expression in the susceptibility of complex traits and diseases. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Testing for biases in selection on avian reproductive traits and partitioning direct and indirect selection using quantitative genetic models.

PubMed

Reed, Thomas E; Gienapp, Phillip; Visser, Marcel E

2016-10-01

Key life history traits such as breeding time and clutch size are frequently both heritable and under directional selection, yet many studies fail to document microevolutionary responses. One general explanation is that selection estimates are biased by the omission of correlated traits that have causal effects on fitness, but few valid tests of this exist. Here, we show, using a quantitative genetic framework and six decades of life-history data on two free-living populations of great tits Parus major, that selection estimates for egg-laying date and clutch size are relatively unbiased. Predicted responses to selection based on the Robertson-Price Identity were similar to those based on the multivariate breeder's equation (MVBE), indicating that unmeasured covarying traits were not missing from the analysis. Changing patterns of phenotypic selection on these traits (for laying date, linked to climate change) therefore reflect changing selection on breeding values, and genetic constraints appear not to limit their independent evolution. Quantitative genetic analysis of correlational data from pedigreed populations can be a valuable complement to experimental approaches to help identify whether apparent associations between traits and fitness are biased by missing traits, and to parse the roles of direct versus indirect selection across a range of environments. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Correlational selection leads to genetic integration of body size and an attractive plumage trait in dark-eyed juncos.

PubMed

McGlothlin, Joel W; Parker, Patricia G; Nolan, Val; Ketterson, Ellen D

2005-03-01

When a trait's effect on fitness depends on its interaction with other traits, the resultant selection is correlational and may lead to the integration of functionally related traits. In relation to sexual selection, when an ornamental trait interacts with phenotypic quality to determine mating success, correlational sexual selection should generate genetic correlations between the ornament and quality, leading to the evolution of honest signals. Despite its potential importance in the evolution of signal honesty, correlational sexual selection has rarely been measured in natural populations. In the dark-eyed junco (Junco hyemalis), males with experimentally elevated values of a plumage trait (whiteness in the tail or "tail white") are more attractive to females and dominant in aggressive encounters over resources. We used restricted maximum-likelihood analysis of a long-term dataset to measure the heritability of tail white and two components of body size (wing length and tail length), as well as genetic correlations between pairs of these traits. We then used multiple regression to assess directional, quadratic, and correlational selection as they acted on tail white and body size via four components of lifetime fitness (juvenile and adult survival, mating success, and fecundity). We found a positive genetic correlation between tail white and body size (as measured by wing length), which indicates past correlational selection. Correlational selection, which was largely due to sexual selection on males, was also found to be currently acting on the same pair of traits. Larger males with whiter tails sired young with more females, most likely due to a combination of female choice, which favors males with whiter tails, and male-male competition, which favors both tail white and larger body size. To our knowledge, this is the first study to show both genetic correlations between sexually selected traits and currently acting correlational sexual selection, and we suggest that correlational sexual selection frequently may be an important mechanism for maintaining the honesty of sexual signals.

Evaluation of mature cow weight: genetic correlations with traits used in selection indices, correlated responses, and genetic trends in Nelore cattle.

PubMed

Boligon, A A; Carvalheiro, R; Albuquerque, L G

2013-01-01

Genetic correlations of selection indices and the traits considered in these indices with mature weight (MW) of Nelore females and correlated responses were estimated to determine whether current selection practices will result in an undesired correlated response in MW. Genetic trends for weaning and yearling indices and MW were also estimated. Data from 612,244 Nelore animals born between 1984 and 2010, belonging to different beef cattle evaluation programs from Brazil and Paraguay, were used. The following traits were studied: weaning conformation (WC), weaning precocity (WP), weaning muscling (WM), yearling conformation (YC), yearling precocity (YP), yearling muscling (YM), weaning and yearling indices, BW gain from birth to weaning (BWG), postweaning BW gain (PWG), scrotal circumference (SC), and MW. The variance and covariance components were estimated by Bayesian inference in a multitrait analysis, including all traits in the same analysis, using a nonlinear (threshold) animal model for visual scores and a linear animal model for the other traits. The mean direct heritabilities were 0.21±0.007 (WC), 0.22±0.007 (WP), 0.20±0.007 (WM), 0.43±0.005 (YC), 0.40±0.005 (YP), 0.40±0.005 (YM), 0.17±0.003 (BWG), 0.21±0.004 (PWG), 0.32±0.001 (SC), and 0.44±0.018 (MW). The genetic correlations between MW and weaning and yearling indices were positive and of medium magnitude (0.30±0.01 and 0.31±0.01, respectively). The genetic changes in weaning index, yearling index, and MW, expressed as units of genetic SD per year, were 0.26, 0.27, and 0.01, respectively. The genetic trend for MW was nonsignificant, suggesting no negative correlated response. The selection practice based on the use of sires with high final index giving preference for those better ranked for yearling precocity and muscling than for conformation generates only a minimal correlated response in MW.

Direct and correlated responses to artificial selection on male mating frequency in the stalk-eyed fly Cyrtodiopsis dalmanni.

PubMed

Rogers, D W; Baker, R H; Chapman, T; Denniff, M; Pomiankowski, A; Fowler, K

2005-05-01

Traditionally it was thought that fitness-related traits such as male mating frequency, with a history of strong directional selection, should have little additive genetic variance and thus respond asymmetrically to bidirectional artificial selection. However, recent findings and theory suggest that a balance between selection for increased male mating frequency and opposing selection pressures on physiologically linked traits will cause male mating frequency to have high additive genetic variation and hence respond symmetrically to selection. We tested these hypotheses in the stalk-eyed fly, Cyrtodiopsis dalmanni, in which males hold harems comprising many females and so have the opportunity to mate at extremely high frequencies. We subjected male stalk-eyed flies to artificial selection for increased ('high') and decreased ('low') mating frequency in the presence of ecologically realistic, high numbers of females. High line males mated significantly more often than control or low line males. The direct response to selection was approximately symmetric in the high and low lines, revealing high additive genetic variation for, and no significant genetic constraints on, increased male mating frequency in C. dalmanni. In order to investigate trade-offs that might constrain male mating frequency under natural conditions we examined correlated responses to artificial selection. We measured accessory gland length, testis length and eyespan after 7 and 14 generations of selection. High line males had significantly larger accessory glands than low line males. No consistent correlated responses to selection were found in testis length or eyespan. Our results suggest that costs associated with the production and maintenance of large accessory glands, although yet to be identified, are likely to be a major constraint on mating frequency in natural populations of C. dalmanni.

Genetic correlations between wellbeing, depression and anxiety symptoms and behavioral responses to the emotional faces task in healthy twins.

PubMed

Routledge, Kylie M; Williams, Leanne M; Harris, Anthony W F; Schofield, Peter R; Clark, C Richard; Gatt, Justine M

2018-06-01

Currently there is a very limited understanding of how mental wellbeing versus anxiety and depression symptoms are associated with emotion processing behaviour. For the first time, we examined these associations using a behavioural emotion task of positive and negative facial expressions in 1668 healthy adult twins. Linear mixed model results suggested faster reaction times to happy facial expressions was associated with higher wellbeing scores, and slower reaction times with higher depression and anxiety scores. Multivariate twin modelling identified a significant genetic correlation between depression and anxiety symptoms and reaction time to happy facial expressions, in the absence of any significant correlations with wellbeing. We also found a significant negative phenotypic relationship between depression and anxiety symptoms and accuracy for identifying neutral emotions, although the genetic or environment correlations were not significant in the multivariate model. Overall, the phenotypic relationships between speed of identifying happy facial expressions and wellbeing on the one hand, versus depression and anxiety symptoms on the other, were in opposing directions. Twin modelling revealed a small common genetic correlation between response to happy faces and depression and anxiety symptoms alone, suggesting that wellbeing and depression and anxiety symptoms show largely independent relationships with emotion processing at the behavioral level. Copyright © 2018 Elsevier B.V. All rights reserved.

Genetic relationships between body condition score and reproduction traits in Canadian Holstein and Ayrshire first-parity cows.

PubMed

Bastin, C; Loker, S; Gengler, N; Sewalem, A; Miglior, F

2010-05-01

The objective of this study was to investigate the genetic relationship between body condition score (BCS) and reproduction traits for first-parity Canadian Ayrshire and Holstein cows. Body condition scores were collected by field staff several times over the lactation in herds from Québec, and reproduction records (including both fertility and calving traits) were extracted from the official database used for the Canadian genetic evaluation of those herds. For each breed, six 2-trait animal models were run; they included random regressions that allowed the estimation of genetic correlations between BCS over the lactation and reproduction traits that are measured as a single lactation record. Analyses were undertaken on data from 108 Ayrshire herds and 342 Holstein herds. Average daily heritabilities of BCS were close to 0.13 for both breeds; these relatively low estimates might be explained by the high variability among herds and BCS evaluators. Genetic correlations between BCS and interval fertility traits (days from calving to first service, days from first service to conception, and days open) were negative and ranged between -0.77 and -0.58 for Ayrshire and between -0.31 and -0.03 for Holstein. Genetic correlations between BCS and 56-d nonreturn rate at first insemination were positive and moderate. The trends of these genetic correlations over the lactation suggest that a genetically low BCS in early lactation would increase the number of days that the primiparous cow was not pregnant and would decrease the chances of the primiparous cow to conceive at first service. Genetic correlations between BCS and calving traits were generally the strongest at calving and decreased with increasing days in milk. The correlation between BCS at calving and maternal calving ease was 0.21 for Holstein and 0.31 for Ayrshire and emphasized the relationship between fat cows around calving and dystocia. Genetic correlations between calving traits and BCS during the subsequent lactation were moderate and favorable, indicating that primiparous cows with a genetically high BCS over the lactation would have a greater chance of producing a calf that survived (maternal calf survival) and would transmit the genes that allowed the calf to be born more easily (maternal calving ease) and to survive (direct calving ease). Copyright 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Parent-offspring conflict and the genetic trade-offs shaping parental investment.

PubMed

Kölliker, Mathias; Boos, Stefan; Wong, Janine W Y; Röllin, Lilian; Stucki, Dimitri; Raveh, Shirley; Wu, Min; Meunier, Joël

2015-04-16

The genetic conflict between parents and their offspring is a cornerstone of kin selection theory and the gene-centred view of evolution, but whether it actually occurs in natural systems remains an open question. Conflict operates only if parenting is driven by genetic trade-offs between offspring performance and the parent's ability to raise additional offspring, and its expression critically depends on the shape of these trade-offs. Here we investigate the occurrence and nature of genetic conflict in an insect with maternal care, the earwig Forficula auricularia. Specifically, we test for a direct response to experimental selection on female future reproduction and correlated responses in current offspring survival, developmental rate and growth. The results demonstrate genetic trade-offs that differ in shape before and after hatching. Our study not only provides direct evidence for parent-offspring conflict but also highlights that conflict is not inevitable and critically depends on the genetic trade-offs shaping parental investment.

Genomic Model with Correlation Between Additive and Dominance Effects.

PubMed

Xiang, Tao; Christensen, Ole Fredslund; Vitezica, Zulma Gladis; Legarra, Andres

2018-05-09

Dominance genetic effects are rarely included in pedigree-based genetic evaluation. With the availability of single nucleotide polymorphism markers and the development of genomic evaluation, estimates of dominance genetic effects have become feasible using genomic best linear unbiased prediction (GBLUP). Usually, studies involving additive and dominance genetic effects ignore possible relationships between them. It has been often suggested that the magnitude of functional additive and dominance effects at the quantitative trait loci are related, but there is no existing GBLUP-like approach accounting for such correlation. Wellmann and Bennewitz showed two ways of considering directional relationships between additive and dominance effects, which they estimated in a Bayesian framework. However, these relationships cannot be fitted at the level of individuals instead of loci in a mixed model and are not compatible with standard animal or plant breeding software. This comes from a fundamental ambiguity in assigning the reference allele at a given locus. We show that, if there has been selection, assigning the most frequent as the reference allele orients the correlation between functional additive and dominance effects. As a consequence, the most frequent reference allele is expected to have a positive value. We also demonstrate that selection creates negative covariance between genotypic additive and dominance genetic values. For parameter estimation, it is possible to use a combined additive and dominance relationship matrix computed from marker genotypes, and to use standard restricted maximum likelihood (REML) algorithms based on an equivalent model. Through a simulation study, we show that such correlations can easily be estimated by mixed model software and accuracy of prediction for genetic values is slightly improved if such correlations are used in GBLUP. However, a model assuming uncorrelated effects and fitting orthogonal breeding values and dominant deviations performed similarly for prediction. Copyright © 2018, Genetics.

Genetic correlations between intraocular pressure, blood pressure and primary open-angle glaucoma: a multi-cohort analysis.

PubMed

Aschard, Hugues; Kang, Jae H; Iglesias, Adriana I; Hysi, Pirro; Cooke Bailey, Jessica N; Khawaja, Anthony P; Allingham, R Rand; Ashley-Koch, Allison; Lee, Richard K; Moroi, Sayoko E; Brilliant, Murray H; Wollstein, Gadi; Schuman, Joel S; Fingert, John H; Budenz, Donald L; Realini, Tony; Gaasterland, Terry; Scott, William K; Singh, Kuldev; Sit, Arthur J; Igo, Robert P; Song, Yeunjoo E; Hark, Lisa; Ritch, Robert; Rhee, Douglas J; Gulati, Vikas; Haven, Shane; Vollrath, Douglas; Zack, Donald J; Medeiros, Felipe; Weinreb, Robert N; Cheng, Ching-Yu; Chasman, Daniel I; Christen, William G; Pericak-Vance, Margaret A; Liu, Yutao; Kraft, Peter; Richards, Julia E; Rosner, Bernard A; Hauser, Michael A; Klaver, Caroline C W; vanDuijn, Cornelia M; Haines, Jonathan; Wiggs, Janey L; Pasquale, Louis R

2017-11-01

Primary open-angle glaucoma (POAG) is the most common chronic optic neuropathy worldwide. Epidemiological studies show a robust positive relation between intraocular pressure (IOP) and POAG and modest positive association between IOP and blood pressure (BP), while the relation between BP and POAG is controversial. The International Glaucoma Genetics Consortium (n=27 558), the International Consortium on Blood Pressure (n=69 395), and the National Eye Institute Glaucoma Human Genetics Collaboration Heritable Overall Operational Database (n=37 333), represent genome-wide data sets for IOP, BP traits and POAG, respectively. We formed genome-wide significant variant panels for IOP and diastolic BP and found a strong relation with POAG (odds ratio and 95% confidence interval: 1.18 (1.14-1.21), P=1.8 × 10 -27 ) for the former trait but no association for the latter (P=0.93). Next, we used linkage disequilibrium (LD) score regression, to provide genome-wide estimates of correlation between traits without the need for additional phenotyping. We also compared our genome-wide estimate of heritability between IOP and BP to an estimate based solely on direct measures of these traits in the Erasmus Rucphen Family (ERF; n=2519) study using Sequential Oligogenic Linkage Analysis Routines (SOLAR). LD score regression revealed high genetic correlation between IOP and POAG (48.5%, P=2.1 × 10 -5 ); however, genetic correlation between IOP and diastolic BP (P=0.86) and between diastolic BP and POAG (P=0.42) were negligible. Using SOLAR in the ERF study, we confirmed the minimal heritability between IOP and diastolic BP (P=0.63). Overall, IOP shares genetic basis with POAG, whereas BP has limited shared genetic correlation with IOP or POAG.

Body composition and energetic efficiency in two lines of mice selected for rapid growth rate and their F1 crosses.

PubMed

Eisen, E J; Bakker, H; Nagai, J

1977-01-01

Correlated responses to selection for increased growth rate were compared in two mouse populations (M16 and H6) of distinct genetic origin. Traits studied were body composition, feed intake, constituent gains and energetic efficiency. When compared with their respective controls (ICR and C2) at 6 and 9 weeks of age, body weight increased more in M16 (57%and 69 % of the control mean) than in H6 (40 % and 34%). The M16 showed correlated responses in fat percent of 2.6% (P <.05), 8.4% (P <.01) and 11.2% (P <.01) at 3, 6 and 9 weeks, respectively, whereas corresponding values in H6 were -2.4% (P <.05), 3.3% (P <.05) and 2.09 % (P >.05). The correlated responses in fat percent were 2.7 and 4.7 times higher in M16 than H6 at 6 and 9 weeks. The regression of ln fat weight on ln empty body weight was larger in M16 (P <.05) compared to ICR and larger (P <.01) in H6 compared to C2. Both M16 and H8 exhibited positive correlated responses from 3 to 6 weeks of age in feed intake and gain and efficiency in fat, protein, calories and ash; fat and caloric gain and efficiency exhibited higher correlated responses in M16 than H6. During the 6- to 9-week interval, the M16 population continued to evince positive correlated responses in gains and efficiencies of fat, protein and calories, whereas H6 did not. Several possible explanations are presented to account for the differences in correlated responses between the selected populations. Partitioning of correlated response differences between M16 and H6 into average direct and average maternal genetic effects indicated that average direct genetic effects, favoring M16, were responsible for the major difference between the selected populations. Direct heterosis in F1 crosses of the selected populations were generally not significant, although there was a tendency for fat percent and fat weight to show heterosis.

Bayesian analyses of genetic parameters for growth traits in Nellore cattle raised on pasture.

PubMed

Lopes, F B; Ferreira, J L; Lobo, R B; Rosa, G J M

2017-07-06

This study was carried out to investigate (co)variance components and genetic parameters for growth traits in beef cattle using a multi-trait model by Bayesian methods. Genetic and residual (co)variances and parameters were estimated for weights at standard ages of 120 (W120), 210 (W210), 365 (W365), and 450 days (W450), and for pre- and post-weaning daily weight gain (preWWG and postWWG) in Nellore cattle. Data were collected over 16 years (1993-2009), and all animals were raised on pasture in eight farms in the North of Brazil that participate in the National Association of Breeders and Researchers. Analyses were run by the Bayesian approach using Gibbs sampler. Additive direct heritabilities for W120, W210, W365, and W450 and for preWWG and postWWG were 0.28 ± 0.013, 0.32 ± 0.002, 0.31 ± 0.002, 0.50 ± 0.026, 0.61 ± 0.047, and 0.79 ± 0.055, respectively. The estimates of maternal heritability were 0.32 ± 0.012, 0.29 ± 0.004, 0.30 ± 0.005, 0.25 ± 0.015, 0.23 ± 0.017, and 0.22 ± 0.016, respectively, for W120, W210, W365, and W450 and for preWWG and postWWG. The estimates of genetic direct additive correlation among all traits were positive and ranged from 0.25 ± 0.03 (preWWG and postWWG) to 0.99 ± 0.00 (W210 and preWWG). The moderate to high estimates of heritability and genetic correlation for weights and daily weight gains at different ages is suggestive of genetic improvement in these traits by selection at an appropriate age. Maternal genetic effects seemed to be significant across the traits. When the focus is on direct and maternal effects, W210 seems to be a good criterium for the selection of Nellore cattle considering the importance of this breed as a major breed of beef cattle not only in Northern Brazil but all regions covered by tropical pastures. As in this study the genetic correlations among all traits were high, the selection based on weaning weight might be a good choice because at this age there are two important effects (maternal and direct genetic effects). In contrast, W120 should be preferred when the objective is improving the maternal ability of the dams. Furthermore, selection for postWWG can be used if the animals show both heavier weaning weights and high growth rate after weaning because it is possible to shorten the time between weaning and slaughter based on weaning weight, postWWG, and desired weight at the time of slaughter.

Genetic parameters for carcass and meat quality traits and their relationships to liveweight and wool production in hogget Merino rams.

PubMed

Greeff, J C; Safari, E; Fogarty, N M; Hopkins, D L; Brien, F D; Atkins, K D; Mortimer, S I; van der Werf, J H J

2008-06-01

Genetic parameters for carcass and meat quality traits of about 18-month-old Merino rams (n = 5870), the progeny of 543 sires from three research resource flocks, were estimated. The estimates of heritability for hot carcass weight (HCW) and the various fat and muscle dimension measurements were moderate and ranged from 0.20 to 0.37. The brightness of meat (colour L*, 0.18 +/- 0.03 standard error) and meat pH (0.22 +/- 0.03) also had moderate estimates of heritability, although meat relative redness (colour a*, 0.10 +/- 0.03) and relative yellowness (colour b*, 0.10 +/- 0.03) were lower. Heritability estimates for live weights were moderate and ranged from 0.29 to 0.41 with significant permanent maternal environmental effects (0.13 to 0.10). The heritability estimates for the hogget wool traits were moderate to high and ranged from 0.27 to 0.60. The ultrasound measurements of fat depth (FATUS) and eye muscle depth (EMDUS) on live animals were highly genetically correlated with the corresponding carcass measurements (0.69 +/- 0.09 FATC and 0.77 +/- 0.07 EMD). Carcass tissue depth (FATGR) had moderate to low genetic correlations with carcass muscle measurements [0.18 +/- 0.10 EMD and 0.05 +/- 0.10 eye muscle area (EMA)], while those with FATC were negative. The genetic correlation between EMD and eye muscle width (EMW) was 0.41 +/- 0.08, while EMA was highly correlated with EMD (0.89 +/- 0.0) and EMW (0.78 +/- 0.04). The genetic correlations for muscle colour with muscle measurements were moderately negative, while those with fat measurements were close to zero. Meat pH was positively correlated with muscle measurements (0.14 to 0.17) and negatively correlated with fat measurements (-0.06 to -0.18). EMDUS also showed a similar pattern of correlations to EMD with meat quality indicator traits, although FATUS had positive correlations with these traits which were generally smaller than their standard error. The genetic correlations among the meat colour traits were high and positive while those with meat pH were high and negative, which were all in the favourable direction. Generally, phenotypic correlations were similar or slightly lower than the corresponding genetic correlations. There were generally small to moderate negative genetic correlations between clean fleece weight (CFW) and carcass fat traits while those with muscle traits were close to zero. As the Merino is already a relatively lean breed, this implies that particular attention should be given to this relationship in Merino breeding programmes to prevent the reduction of fat reserves as a correlated response to selection for increased fleece weight. The ultrasound scan traits generally showed a similar pattern to the corresponding carcass fat and muscle traits. There was a small unfavourable genetic correlation between CFW and meat pH (0.19 +/- 0.07).

Genetic effects and correlations between production and fertility traits and their dependency on the lactation-stage in Holstein Friesians

PubMed Central

2012-01-01

Background This study focused on the dynamics of genome-wide effects on five milk production and eight fertility traits as well as genetic correlations between the traits. For 2,405 Holstein Friesian bulls, estimated breeding values (EBVs) were used. The production traits were additionally assessed in 10-day intervals over the first 60 lactation days, as this stage is physiologically the most crucial time in milk production. Results SNPs significantly affecting the EBVs of the production traits could be separated into three groups according to the development of the size of allele effects over time: 1) increasing effects for all traits; 2) decreasing effects for all traits; and 3) increasing effects for all traits except fat yield. Most of the significant markers were found within 22 haplotypes spanning on average 135,338 bp. The DGAT1 region showed high density of significant markers, and thus, haplotype blocks. Further functional candidate genes are proposed for haplotype blocks of significant SNPs (KLHL8, SICLEC12, AGPAT6 and NID1). Negative genetic correlations were found between yield and fertility traits, whilst content traits showed positive correlations with some fertility traits. Genetic correlations became stronger with progressing lactation. When correlations were estimated within genotype classes, correlations were on average 0.1 units weaker between production and fertility traits when the yield increasing allele was present in the genotype. Conclusions This study provides insight into the expression of genetic effects during early lactation and suggests possible biological explanations for the presented time-dependent effects. Even though only three markers were found with effects on fertility, the direction of genetic correlations within genotype classes between production and fertility traits suggests that alleles increasing the milk production do not affect fertility in a more negative way compared to the decreasing allele. PMID:23244492

The genetic overlap between schizophrenia and height.

PubMed

Bacanu, Silviu-Alin; Chen, Xianging; Kendler, Kenneth S

2013-12-01

Epidemiological studies suggest that height and schizophrenia risk are inversely correlated. These findings might arise because i) height and schizophrenia share genetic variants and ii) the effects of these shared variants are in opposite direction for the two traits. We use genome wide association data to empirically evaluate these hypotheses. We find that variants which impact on height and risk for schizophrenia are distributed across several genomic regions and the directions of effect vary, some consistent and others inconsistent with the direction expected from the phenotypic data. Moreover, signals that were in and not in accord with the phenotypic data aggregated in distinct biological pathways. © 2013 Elsevier B.V. All rights reserved.

Geographical gradients in selection can reveal genetic constraints for evolutionary responses to ocean acidification.

PubMed

Gaitán-Espitia, Juan Diego; Marshall, Dustin; Dupont, Sam; Bacigalupe, Leonardo D; Bodrossy, Levente; Hobday, Alistair J

2017-02-01

Geographical gradients in selection can shape different genetic architectures in natural populations, reflecting potential genetic constraints for adaptive evolution under climate change. Investigation of natural pH/pCO 2 variation in upwelling regions reveals different spatio-temporal patterns of natural selection, generating genetic and phenotypic clines in populations, and potentially leading to local adaptation, relevant to understanding effects of ocean acidification (OA). Strong directional selection, associated with intense and continuous upwellings, may have depleted genetic variation in populations within these upwelling regions, favouring increased tolerances to low pH but with an associated cost in other traits. In contrast, diversifying or weak directional selection in populations with seasonal upwellings or outside major upwelling regions may have resulted in higher genetic variances and the lack of genetic correlations among traits. Testing this hypothesis in geographical regions with similar environmental conditions to those predicted under climate change will build insights into how selection may act in the future and how populations may respond to stressors such as OA. © 2017 The Author(s).

Health Orientation, Knowledge, and Attitudes toward Genetic Testing and Personalized Genomic Services: Preliminary Data from an Italian Sample.

PubMed

Oliveri, Serena; Masiero, Marianna; Arnaboldi, Paola; Cutica, Ilaria; Fioretti, Chiara; Pravettoni, Gabriella

2016-01-01

Objective . The study aims at assessing personality tendencies and orientations that could be closely correlated with knowledge, awareness, and interest toward undergoing genetic testing. Methods. A sample of 145 subjects in Italy completed an online survey, investigating demographic data, health orientation, level of perceived knowledge about genetic risk, genetic screening, and personal attitudes toward direct to consumer genetic testing (DTCGT). Results . Results showed that respondents considered genetic assessment to be helpful for disease prevention, but they were concerned that results could affect their life planning with little clinical utility. Furthermore, a very high percentage of respondents (67%) had never heard about genetic testing directly available to the public. Data showed that personality tendencies, such as personal health consciousness, health internal control, health esteem, and confidence, motivation to avoid unhealthiness and motivation for healthiness affected the uptake of genetic information and the interest in undergoing genetic testing. Conclusions . Public knowledge and attitudes toward genetic risk and genetic testing among European countries, along with individual personality and psychological tendencies that could affect these attitudes, remain unexplored. The present study constitutes one of the first attempts to investigate how such personality tendencies could motivation to undergo genetic testing and engagement in lifestyle changes.

Health Orientation, Knowledge, and Attitudes toward Genetic Testing and Personalized Genomic Services: Preliminary Data from an Italian Sample

PubMed Central

Arnaboldi, Paola; Cutica, Ilaria; Fioretti, Chiara

2016-01-01

Objective. The study aims at assessing personality tendencies and orientations that could be closely correlated with knowledge, awareness, and interest toward undergoing genetic testing. Methods. A sample of 145 subjects in Italy completed an online survey, investigating demographic data, health orientation, level of perceived knowledge about genetic risk, genetic screening, and personal attitudes toward direct to consumer genetic testing (DTCGT). Results. Results showed that respondents considered genetic assessment to be helpful for disease prevention, but they were concerned that results could affect their life planning with little clinical utility. Furthermore, a very high percentage of respondents (67%) had never heard about genetic testing directly available to the public. Data showed that personality tendencies, such as personal health consciousness, health internal control, health esteem, and confidence, motivation to avoid unhealthiness and motivation for healthiness affected the uptake of genetic information and the interest in undergoing genetic testing. Conclusions. Public knowledge and attitudes toward genetic risk and genetic testing among European countries, along with individual personality and psychological tendencies that could affect these attitudes, remain unexplored. The present study constitutes one of the first attempts to investigate how such personality tendencies could motivation to undergo genetic testing and engagement in lifestyle changes. PMID:28105428

Genetic parameters estimation for preweaning traits and their relationship with reproductive, productive and morphological traits in alpaca.

PubMed

Cruz, A; Cervantes, I; Burgos, A; Morante, R; Gutiérrez, J P

2017-05-01

The aim of this study was to estimate the genetic parameters for preweaning traits and their relationship with reproductive, productive and morphological traits in alpacas. The data were collected from 2001 to 2015 in the Pacomarca experimental farm. The data set contained data from 4330 females and 3788 males corresponding to 6396 and 1722 animals for Huacaya and Suri variants, respectively. The number of records for Huacaya and Suri variants were 5494 and 1461 for birth weight (BW), 5429 and 1431 for birth withers height (BH), 3320 and 896 for both weaning weight (WW) and average daily gain (DG) from birth to weaning, 3317 and 896 for weaning withers height (WH), and 5514 and 1474 for survival to weaning. The reproductive traits analyzed were age at first calving and calving interval. The fiber traits were fiber diameter (FD), standard deviation of FD (SD), comfort factor and coefficient of variation of FD and the morphological traits studied were density, crimp in Huacaya and lock structure in Suri, head, coverage and balance. Regarding preweaning traits, model of analysis included additive, maternal and residual random effects for all traits, with sex, coat color, number of calving, month-year and contemporary group as systematic effects, and age at weaning as linear covariate for WW and WH. The most relevant direct heritabilities for Huacaya and Suri were 0.50 and 0.34 for WW, 0.36 and 0.66 for WH, 0.45 and 0.20 for DG, respectively. Maternal heritabilities were 0.25 and 0.38 for BW, 0.18 and 0.32 for BH, 0.29 and 0.39 for WW, 0.19 and 0.26 for WH, 0.27 and 0.36 for DG, respectively. Direct genetic correlations within preweaning traits were high and favorable and lower between direct and maternal genetic effects. The genetic correlations of preweaning traits with fiber traits were moderate and unfavorable. With morphological traits they were high and positive for Suri but not for Huacaya and favorable for direct genetic effect but unfavorable for maternal genetic effect with reproductive traits. If the selection objective was meat production, the selection would have to be based on the direct genetic effect for WW but not on the maternal genetic effect that has been shown to have less relevance. Other weaning traits such as WH or DG would be indirectly selected.

Genetic analysis of a red tilapia (Oreochromis spp.) population undergoing three generations of selection for increased body weight at harvest.

PubMed

Hamzah, Azhar; Thoa, Ngo Phu; Nguyen, Nguyen Hong

2017-11-01

Quantitative genetic analysis was performed on 10,919 data records collected over three generations from the selection programme for increased body weight at harvest in red tilapia (Oreochromis spp.). They were offspring of 224 sires and 226 dams (50 sires and 60 dams per generation, on average). Linear mixed models were used to analyse body traits (weight, length, width and depth), whereas threshold generalised models assuming probit distribution were employed to examine genetic inheritance of survival rate, sexual maturity and body colour. The estimates of heritability for traits studied (body weight, standard length, body width, body depth, body colour, early sexual maturation and survival) across statistical models were moderate to high (0.13-0.45). Genetic correlations among body traits and survival were high and positive (0.68-0.96). Body length and width exhibited negative genetic correlations with body colour (- 0.47 to - 0.25). Sexual maturity was genetically correlated positively with measurements of body traits (weight and length). Direct and correlated genetic responses to selection were measured as estimated breeding values in each generation and expressed in genetic standard deviation units (σ G ). The cumulative improvement achieved for harvest body weight was 1.72 σ G after three generations or 12.5% per generation when the gain was expressed as a percentage of the base population. Selection for improved body weight also resulted in correlated increase in other body traits (length, width and depth) and survival rate (ranging from 0.25 to 0.81 genetic standard deviation units). Avoidance of black spot parent matings also improved the overall red colour of the selected population. It is concluded that the selective breeding programme for red tilapia has succeeded in achieving significant genetic improvement for a range of commercially important traits in this species, and the large genetic variation in body colour and survival also shows that there are prospects for future improvement of these traits in this population of red tilapia.

Analysis of genetic correlations of hip height with selection indices and mature weight in Nelore cattle.

PubMed

Boligon, A A; Carvalheiro, R; Ayres, D R; Albuquerque, L G

2013-02-01

Body size is directly related to the productive and reproductive performance of beef cattle raised under free-range conditions. In an attempt to better plan selection criteria, avoiding extremes in body size, this study estimated the heritabilities and genetic correlations of yearling hip height (YH) and mature hip height (MH) with selection indices obtained at weaning (WI) and yearling (YI) and mature weight (MW). Data from 102,373 Nelore animals born between 1984 and 2010, which belong to 263 farms that participate in genetic evaluation programmes of beef cattle conducted in Brazil and Paraguay, were used. The (co)variance components and genetic parameters were estimated by Bayesian inference in multi-trait analysis using an animal model. The mean heritabilities for YH, MH and MW were 0.56 ± 0.06, 0.47 ± 0.02 and 0.42 ± 0.02, respectively. The genetic correlation of YH with WI (0.13 ± 0.01) and YI (0.11 ± 0.01) was practically zero, whereas a higher correlation was observed with MW (0.22 ± 0.03). Positive genetic correlations of medium magnitude were estimated between MH and WI and YI (0.23 ± 0.01 and 0.43 ± 0.02, respectively). On the other hand, a high genetic correlation (0.68 ± 0.03) was observed between the indicator traits of mature body size (MH and MW). Considering the top 20 % of sire (896 sires) in terms of breeding values for the yearling index, the rank sire correlations between breeding values for MH and MW was 0.62. In general, the results indicate that selection based on WI and YI should not lead to important changes in YH. However, an undesired correlated response in mature cow height is expected, particularly when selection is performed using YI. Therefore, changes in the body structure of Nelore females can be obtained when MH and MW is used as a selection criterion for cows.

Growth of Mashona cattle on range in Zimbabwe. II. Estimates of genetic parameters and predicted response to selection.

PubMed

Tawonezvi, H P

1989-08-01

For 1,456 Mashona calves sired by 88 bulls heritability estimates from paternal half-sibs were 0.44 +/- 0.11 for birth weight, 0.38 +/- 0.10 for 205-day weaning weight, 0.39 +/- 0.10 for 18-month weight, 0.37 +/- 0.10 for pre-weaning daily liveweight gain and 0.41 +/- 0.11 for daily gain from weaning to 18 months of age. Genetic correlations were relatively low for birth weight with weaning weight (0.42 +/- 0.18), 18-month weight (0.56 +/- 0.16), pre-weaning gain (0.33 +/- 0.19) and post-weaning gain (0.36 +/- 0.19). Higher genetic correlations were observed for pre-weaning gain with weaning weight (0.98 +/- 0.01) and 18-month weight (0.59 +/- 0.14) and for 18-month weight with weaning weight (0.67 +/- 0.12) and post-weaning gain (0.73 +/- 0.10). Post-weaning daily gain was not significantly correlated genetically with both pre-weaning gain (-0.11 +/- 0.22) and weaning weight (-0.03 +/- 0.22). With 10% retention of males and 60% of females expected genetic improvements per generation from direct selection for weaning weight or 18-month weight were 8.11 kg and 12.12 kg respectively. These improvements would be reduced by 18% and 35% if selection indices were used to produce no correlated change in birth weight.

Genetic correlations and sex-specific adaptation in changing environments.

PubMed

Connallon, Tim; Hall, Matthew D

2016-10-01

Females and males have conflicting evolutionary interests. Selection favors the evolution of different phenotypes within each sex, yet divergence between the sexes is constrained by the shared genetic basis of female and male traits. Current theory predicts that such "sexual antagonism" should be common: manifesting rapidly during the process of adaptation, and slow in its resolution. However, these predictions apply in temporally stable environments. Environmental change has been shown empirically to realign the direction of selection acting on shared traits and thereby alleviate signals of sexually antagonistic selection. Yet there remains no theory for how common sexual antagonism should be in changing environments. Here, we analyze models of sex-specific evolutionary divergence under directional and cyclic environmental change, and consider the impact of genetic correlations on long-run patterns of sex-specific adaptation. We find that environmental change often aligns directional selection between the sexes, even when they have divergent phenotypic optima. Nevertheless, some forms of environmental change generate persistent sexually antagonistic selection that is difficult to resolve. Our results reinforce recent empirical observations that changing environmental conditions alleviate conflict between males and females. They also generate new predictions regarding the scope for sexually antagonistic selection and its resolution in changing environments. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Positive correlation between genetic diversity and fitness in a large, well-connected metapopulation.

PubMed

Vandewoestijne, Sofie; Schtickzelle, Nicolas; Baguette, Michel

2008-11-05

Theory predicts that lower dispersal, and associated gene flow, leads to decreased genetic diversity in small isolated populations, which generates adverse consequences for fitness, and subsequently for demography. Here we report for the first time this effect in a well-connected natural butterfly metapopulation with high population densities at the edge of its distribution range. We demonstrate that: (1) lower genetic diversity was coupled to a sharp decrease in adult lifetime expectancy, a key component of individual fitness; (2) genetic diversity was positively correlated to the number of dispersing individuals (indicative of landscape functional connectivity) and adult population size; (3) parameters inferred from capture-recapture procedures (population size and dispersal events between patches) correlated much better with genetic diversity than estimates usually used as surrogates for population size (patch area and descriptors of habitat quality) and dispersal (structural connectivity index). Our results suggest that dispersal is a very important factor maintaining genetic diversity. Even at a very local spatial scale in a metapopulation consisting of large high-density populations interconnected by considerable dispersal rates, genetic diversity can be decreased and directly affect the fitness of individuals. From a biodiversity conservation perspective, this study clearly shows the benefits of both in-depth demographic and genetic analyses. Accordingly, to ensure the long-term survival of populations, conservation actions should not be blindly based on patch area and structural isolation. This result may be especially pertinent for species at their range margins, particularly in this era of rapid environmental change.

Results from six generations of selection for intramuscular fat in Duroc swine using real-time ultrasound. II. Genetic parameters and trends.

PubMed

Schwab, C R; Baas, T J; Stalder, K J

2010-01-01

Design of breeding programs requires knowledge of variance components that exist for traits included in specific breeding goals and the genetic relationships that exist among traits of economic importance. A study was conducted to evaluate direct and correlated genetic responses to selection for intramuscular fat (IMF) and to estimate genetic parameters for economically important traits in Duroc swine. Forty gilts were purchased from US breeders and randomly mated for 2 generations to boars available in regional boar studs to develop a base population of 56 litters. Littermate pairs of gilts from this population were randomly assigned to a select line (SL) or control line (CL) and mated to the same boar to establish genetic ties between lines. In the SL, the top 10 boars and 75 gilts were selected based on IMF EBV obtained from a bivariate animal model that included IMF evaluated on the carcass and IMF predicted via ultrasound. One boar from each sire family and 50 to 60 gilts representing all sire families were randomly selected to maintain the CL. Carcass and ultrasound IMF were both moderately heritable (0.31 and 0.38, respectively). Moderate to high genetic relationships were estimated among carcass backfat and meat quality measures of IMF, Instron tenderness, and objective loin muscle color. Based on estimates obtained in this study, more desirable genetic merit for pH is associated with greater genetic value for loin color, tenderness, and sensory characteristics. Intramuscular fat measures obtained on the carcass and predicted using ultrasound technology were highly correlated (r(g) = 0.86 from a 12-trait analysis; r(g) = 0.90 from a 5-trait analysis). Estimated genetic relationships among IMF measures and other traits evaluated were generally consistent. Intramuscular fat measures were also genetically associated with Instron tenderness and flavor score in a desirable direction. Direct genetic response in IMF measures observed in the SL corresponded to a significant decrease in EBV for carcass loin muscle area (-0.90 cm(2) per generation) and an increase in carcass backfat EBV (0.98 mm per generation). Selection for IMF has led to more desirable EBV for objective tenderness and has had an adverse effect on additive genetic merit for objective loin color.

Genetic Analysis of Growth Traits in Polled Nellore Cattle Raised on Pasture in Tropical Region Using Bayesian Approaches

PubMed Central

Lopes, Fernando Brito; Magnabosco, Cláudio Ulhôa; Paulini, Fernanda; da Silva, Marcelo Corrêa; Miyagi, Eliane Sayuri; Lôbo, Raysildo Barbosa

2013-01-01

Components of (co)variance and genetic parameters were estimated for adjusted weights at ages 120 (W120), 240 (W240), 365 (W365) and 450 (W450) days of Polled Nellore cattle raised on pasture and born between 1987 and 2010. Analyses were performed using an animal model, considering fixed effects: herd-year-season of birth and calf sex as contemporary groups and the age of cow as a covariate. Gibbs Samplers were used to estimate (co)variance components, genetic parameters and additive genetic effects, which accounted for great proportion of total variation in these traits. High direct heritability estimates for the growth traits were revealed and presented mean 0.43, 0.61, 0.72 and 0.67 for W120, W240, W365 and W450, respectively. Maternal heritabilities were 0.07 and 0.08 for W120 and W240, respectively. Direct additive genetic correlations between the weight at 120, 240, 365 and 450 days old were strong and positive. These estimates ranged from 0.68 to 0.98. Direct-maternal genetic correlations were negative for W120 and W240. The estimates ranged from −0.31 to −0.54. Estimates of maternal heritability ranged from 0.056 to 0.092 for W120 and from 0.064 to 0.096 for W240. This study showed that genetic progress is possible for the growth traits we studied, which is a novel and favorable indicator for an upcoming and promising Polled Zebu breed in Tropical regions. Maternal effects influenced the performance of weight at 120 and 240 days old. These effects should be taken into account in genetic analyses of growth traits by fitting them as a genetic or a permanent environmental effect, or even both. In general, due to a medium-high estimate of environmental (co)variance components, management and feeding conditions for Polled Nellore raised at pasture in tropical regions of Brazil needs improvement and growth performance can be enhanced. PMID:24040412

The mediating effect of parental neglect on adolescent and young adult anti-sociality: a longitudinal study of twins and their parents.

PubMed

Eaves, Lindon J; Prom, Elizabeth C; Silberg, Judy L

2010-07-01

The causes of correlation between parental treatment and offspring behavior are ambiguous since genetic and social factors are correlated in typical family studies. The problem is complicated by the need to characterize the effects of genes and environment on both juvenile and adult behavioral outcomes. A model is developed for the resemblance between juvenile and adult twins and their parents that allows some of these effects to be resolved. Data on childhood adversity, parental anti-social behavior, and longitudinal adult and juvenile anti-social behavior were obtained from 1,412 families of adolescent and young adult twins. A structural model is fitted that allows for the effects of genetic and social transmission of information from parents to children. Environmental effects of parents may be mediated through measured features of the home environment. Parameters were estimated by diagonal weighted least squares applied to the 33 distinct polychoric correlations between relatives and between variables within and between ages. Sub-hypotheses were tested. Results confirmed that effects of genes and environment were both highly significant. Genetic effects were large in juveniles and largely age and sex-specific. Approximately 30% of the variation due to the shared environment was due to the effect of childhood adversity. The remaining shared environmental effects are unexplained. Adversity is affected significantly by maternal anti-social behavior. The correlation between paternal ASP and adversity may be explained by antisocial fathers selecting (or creating) antisocial mothers. All significant environmental effects of parental ASP are mediated through the measure of adversity. Though transmission of ASP is both genetic and social, passive genotype-environment correlation is very small. Assortative mating for ASP has barely detectable consequence for the genetic correlation between siblings. The longitudinal study of twins and their parents makes it possible to demonstrate there is a direct causal effect of childhood adversity on child conduct disorder over and above any indirect genetic correlation.

Spectral reflectance indices as a selection criterion for yield improvement in wheat

NASA Astrophysics Data System (ADS)

Babar, Md. Ali

2005-11-01

Scope and methods of study. Yield in wheat ( Triticum aestivum L.) is a complex trait and influenced by many environmental factors, and yield improvement is a daunting task for wheat breeders. Spectral reflectance indices (SRIs) have been used to study different physiological traits in wheat. SRIs have the potential to differentiate genotypes for grain yield. SRIs strongly associated with grain yield can be used to achieve effective genetic gain in wheat under different environments. Three experiments (15 adapted genotypes, 25 and 36 random sister lines derived from two different crosses) under irrigated conditions, and three experiments (each with 30 advanced genotypes) under water-limited conditions were conducted in three successive years in Northwest Mexico at the CIMMYT (International Maize and wheat Improvement Center) experimental station. SRIs and different agronomic data were collected for three years, and biomass was harvested for two years. Phenotypic and genetic correlations between SRIs and grain yield, between SRIs and biomass, realized and broad sense heritability, direct and correlated selection responses for grain yield, and SRIs were calculated. Findings and conclusion. Seven SRIs were calculated, and three near infrared based indices (WI, NWI-1 and NWI-2) showed higher level of genetic and phenotypic correlations with grain yield, yield components and biomass than other SRIs (PRI, RNDVI, GNDVI, and SR) under both irrigated and water limiting environments. Moderate to high realized and broad sense heritability, and selection response were demonstrated by the three NIR based indices. High efficiency of correlated response for yield estimation was demonstrated by the three NIR based indices. The ratio between the correlated response to grain yield based on the three NIR based indices and direct selection response for grain yield was very close to one. The NIR based indices showed very high accuracy in selecting superior genotypes for grain yield under both well-watered and water-limited conditions. These results demonstrated that effective genetic gain in grain yield improvement can be achieved by making selections with the three NIR based indices.

Restricted maximum likelihood estimation of genetic principal components and smoothed covariance matrices

PubMed Central

Meyer, Karin; Kirkpatrick, Mark

2005-01-01

Principal component analysis is a widely used 'dimension reduction' technique, albeit generally at a phenotypic level. It is shown that we can estimate genetic principal components directly through a simple reparameterisation of the usual linear, mixed model. This is applicable to any analysis fitting multiple, correlated genetic effects, whether effects for individual traits or sets of random regression coefficients to model trajectories. Depending on the magnitude of genetic correlation, a subset of the principal component generally suffices to capture the bulk of genetic variation. Corresponding estimates of genetic covariance matrices are more parsimonious, have reduced rank and are smoothed, with the number of parameters required to model the dispersion structure reduced from k(k + 1)/2 to m(2k - m + 1)/2 for k effects and m principal components. Estimation of these parameters, the largest eigenvalues and pertaining eigenvectors of the genetic covariance matrix, via restricted maximum likelihood using derivatives of the likelihood, is described. It is shown that reduced rank estimation can reduce computational requirements of multivariate analyses substantially. An application to the analysis of eight traits recorded via live ultrasound scanning of beef cattle is given. PMID:15588566

Accuracies of genomic breeding values in American Angus beef cattle using K-means clustering for cross-validation.

PubMed

Saatchi, Mahdi; McClure, Mathew C; McKay, Stephanie D; Rolf, Megan M; Kim, JaeWoo; Decker, Jared E; Taxis, Tasia M; Chapple, Richard H; Ramey, Holly R; Northcutt, Sally L; Bauck, Stewart; Woodward, Brent; Dekkers, Jack C M; Fernando, Rohan L; Schnabel, Robert D; Garrick, Dorian J; Taylor, Jeremy F

2011-11-28

Genomic selection is a recently developed technology that is beginning to revolutionize animal breeding. The objective of this study was to estimate marker effects to derive prediction equations for direct genomic values for 16 routinely recorded traits of American Angus beef cattle and quantify corresponding accuracies of prediction. Deregressed estimated breeding values were used as observations in a weighted analysis to derive direct genomic values for 3570 sires genotyped using the Illumina BovineSNP50 BeadChip. These bulls were clustered into five groups using K-means clustering on pedigree estimates of additive genetic relationships between animals, with the aim of increasing within-group and decreasing between-group relationships. All five combinations of four groups were used for model training, with cross-validation performed in the group not used in training. Bivariate animal models were used for each trait to estimate the genetic correlation between deregressed estimated breeding values and direct genomic values. Accuracies of direct genomic values ranged from 0.22 to 0.69 for the studied traits, with an average of 0.44. Predictions were more accurate when animals within the validation group were more closely related to animals in the training set. When training and validation sets were formed by random allocation, the accuracies of direct genomic values ranged from 0.38 to 0.85, with an average of 0.65, reflecting the greater relationship between animals in training and validation. The accuracies of direct genomic values obtained from training on older animals and validating in younger animals were intermediate to the accuracies obtained from K-means clustering and random clustering for most traits. The genetic correlation between deregressed estimated breeding values and direct genomic values ranged from 0.15 to 0.80 for the traits studied. These results suggest that genomic estimates of genetic merit can be produced in beef cattle at a young age but the recurrent inclusion of genotyped sires in retraining analyses will be necessary to routinely produce for the industry the direct genomic values with the highest accuracy.

Accuracies of genomic breeding values in American Angus beef cattle using K-means clustering for cross-validation

PubMed Central

2011-01-01

Background Genomic selection is a recently developed technology that is beginning to revolutionize animal breeding. The objective of this study was to estimate marker effects to derive prediction equations for direct genomic values for 16 routinely recorded traits of American Angus beef cattle and quantify corresponding accuracies of prediction. Methods Deregressed estimated breeding values were used as observations in a weighted analysis to derive direct genomic values for 3570 sires genotyped using the Illumina BovineSNP50 BeadChip. These bulls were clustered into five groups using K-means clustering on pedigree estimates of additive genetic relationships between animals, with the aim of increasing within-group and decreasing between-group relationships. All five combinations of four groups were used for model training, with cross-validation performed in the group not used in training. Bivariate animal models were used for each trait to estimate the genetic correlation between deregressed estimated breeding values and direct genomic values. Results Accuracies of direct genomic values ranged from 0.22 to 0.69 for the studied traits, with an average of 0.44. Predictions were more accurate when animals within the validation group were more closely related to animals in the training set. When training and validation sets were formed by random allocation, the accuracies of direct genomic values ranged from 0.38 to 0.85, with an average of 0.65, reflecting the greater relationship between animals in training and validation. The accuracies of direct genomic values obtained from training on older animals and validating in younger animals were intermediate to the accuracies obtained from K-means clustering and random clustering for most traits. The genetic correlation between deregressed estimated breeding values and direct genomic values ranged from 0.15 to 0.80 for the traits studied. Conclusions These results suggest that genomic estimates of genetic merit can be produced in beef cattle at a young age but the recurrent inclusion of genotyped sires in retraining analyses will be necessary to routinely produce for the industry the direct genomic values with the highest accuracy. PMID:22122853

From cow to cheese: genetic parameters of the flavour fingerprint of cheese investigated by direct-injection mass spectrometry (PTR-ToF-MS).

PubMed

Bergamaschi, Matteo; Cecchinato, Alessio; Biasioli, Franco; Gasperi, Flavia; Martin, Bruno; Bittante, Giovanni

2016-11-16

Volatile organic compounds determine important quality traits in cheese. The aim of this work was to infer genetic parameters of the profile of volatile compounds in cheese as revealed by direct-injection mass spectrometry of the headspace gas from model cheeses that were produced from milk samples from individual cows. A total of 1075 model cheeses were produced using raw whole-milk samples that were collected from individual Brown Swiss cows. Single spectrometry peaks and a combination of these peaks obtained by principal component analysis (PCA) were analysed. Using a Bayesian approach, we estimated genetic parameters for 240 individual spectrometry peaks and for the first ten principal components (PC) extracted from them. Our results show that there is some genetic variability in the volatile compound fingerprint of these model cheeses. Most peaks were characterized by a substantial heritability and for about one quarter of the peaks, heritability (up to 21.6%) was higher than that of the best PC. Intra-herd heritability of the PC ranged from 3.6 to 10.2% and was similar to heritabilities estimated for milk fat, specific fatty acids, somatic cell count and some coagulation parameters in the same population. We also calculated phenotypic correlations between PC (around zero as expected), the corresponding genetic correlations (from -0.79 to 0.86) and correlations between herds and sampling-processing dates (from -0.88 to 0.66), which confirmed that there is a relationship between cheese flavour and the dairy system in which cows are reared. This work reveals the existence of a link between the cow's genetic background and the profile of volatile compounds in cheese. Analysis of the relationships between the volatile organic compound (VOC) content and the sensory characteristics of cheese as perceived by the consumer, and of the genetic basis of these relationships could generate new knowledge that would open up the possibility of controlling and improving the sensory properties of cheese through genetic selection of cows. More detailed investigations are necessary to connect VOC with the sensory properties of cheese and gain a better understanding of the significance of these new phenotypes.

Estimation of genetic parameters related to eggshell strength using random regression models.

PubMed

Guo, J; Ma, M; Qu, L; Shen, M; Dou, T; Wang, K

2015-01-01

This study examined the changes in eggshell strength and the genetic parameters related to this trait throughout a hen's laying life using random regression. The data were collected from a crossbred population between 2011 and 2014, where the eggshell strength was determined repeatedly for 2260 hens. Using random regression models (RRMs), several Legendre polynomials were employed to estimate the fixed, direct genetic and permanent environment effects. The residual effects were treated as independently distributed with heterogeneous variance for each test week. The direct genetic variance was included with second-order Legendre polynomials and the permanent environment with third-order Legendre polynomials. The heritability of eggshell strength ranged from 0.26 to 0.43, the repeatability ranged between 0.47 and 0.69, and the estimated genetic correlations between test weeks was high at > 0.67. The first eigenvalue of the genetic covariance matrix accounted for about 97% of the sum of all the eigenvalues. The flexibility and statistical power of RRM suggest that this model could be an effective method to improve eggshell quality and to reduce losses due to cracked eggs in a breeding plan.

Genetic signatures of natural selection in a model invasive ascidian

NASA Astrophysics Data System (ADS)

Lin, Yaping; Chen, Yiyong; Yi, Changho; Fong, Jonathan J.; Kim, Won; Rius, Marc; Zhan, Aibin

2017-03-01

Invasive species represent promising models to study species’ responses to rapidly changing environments. Although local adaptation frequently occurs during contemporary range expansion, the associated genetic signatures at both population and genomic levels remain largely unknown. Here, we use genome-wide gene-associated microsatellites to investigate genetic signatures of natural selection in a model invasive ascidian, Ciona robusta. Population genetic analyses of 150 individuals sampled in Korea, New Zealand, South Africa and Spain showed significant genetic differentiation among populations. Based on outlier tests, we found high incidence of signatures of directional selection at 19 loci. Hitchhiking mapping analyses identified 12 directional selective sweep regions, and all selective sweep windows on chromosomes were narrow (~8.9 kb). Further analyses indentified 132 candidate genes under selection. When we compared our genetic data and six crucial environmental variables, 16 putatively selected loci showed significant correlation with these environmental variables. This suggests that the local environmental conditions have left significant signatures of selection at both population and genomic levels. Finally, we identified “plastic” genomic regions and genes that are promising regions to investigate evolutionary responses to rapid environmental change in C. robusta.

Direct and maternal genetic effects for preweaning growth in Retinta cattle estimated by a longitudinal approach throughout the calving trajectory of the cow.

PubMed

Morales, R; Menéndez-Buxadera, A; Avilés, C; Molina, A

2013-12-01

The direct and maternal genetic effects were estimated for the preweaning growth of Retinta calves with a multitrait model across parities, using a longitudinal approach with random regression models (RRM). The 120 (P120) and 180 days (P180) weights (5972 calves) were considered as different traits in each calving. The heritability of direct effect across parities was on average 0.37 for P120 and 0.58 for P180, slightly higher than the estimates by univariate (0.30 and 0.56) and bivariate models (0.30 and 0.51, respectively). The heritability for maternal effects was 0.16 for P120 and 0.26 for P180 and very similar by uni- (0.16 and 0.23) and multivariate model (0.16 and 0.22, respectively). The correlation between direct and maternal effects by RRM showed a pronounced antagonism -0.64 for P120 and -0.78 for P180), likewise uni- (-0.62 and -0.72) and multivariate case (-0.64 and -0.74, respectively). The preweaning weights should be considered as different traits across parities, because the genetic correlations were different from unity. The RRM also allowed us to estimate all the parameters throughout the calving trajectory of the cow. The use of multiple traits RRM across parities can provide very useful information for the breeding programmes. © 2013 Blackwell Verlag GmbH.

The Three-Factor Eating Questionnaire, body mass index, and responses to sweet and salty fatty foods: a twin study of genetic and environmental associations.

PubMed

Keskitalo, Kaisu; Tuorila, Hely; Spector, Tim D; Cherkas, Lynn F; Knaapila, Antti; Kaprio, Jaakko; Silventoinen, Karri; Perola, Markus

2008-08-01

The relation between body weight and energy-dense foods remains unclear. We estimated the effects of genetic and environmental factors on cognitive and emotional aspects of dieting behavior, body mass index (BMI), and responses to fatty foods and on their relations. A total of 1326 adult twin persons (aged 17-82 y; 17% M and 83% F) from the United Kingdom and Finland completed the revised version of the Three-Factor Eating Questionnaire (TFEQ-R18) and reported the liking and use-frequency of 4 sweet-and-fatty and salty-and-fatty food items (6 items in the United Kingdom and 5 items in Finland). Genetic modeling was done by using linear structural equations. Heritability estimates were calculated separately for the countries and sexes; they were 26-63% for cognitive restraint, 45-69% for uncontrolled eating, and 9-45% for emotional eating, respectively. Of the variation in liking and use-frequency of fatty foods, 24-54% was attributed to interindividual genetic differences. No significant correlations were observed between BMI and fatty food use or liking. However, BMI was positively (mostly genetically) correlated (genetic r = 0.16-0.51) with all of the dieting behaviors, and they correlated with fatty food use and liking ratings. Uncontrolled eating was both genetically and environmentally associated with liking for salty-and-fatty foods (genetic and environmental r = 0.16), and emotional eating was genetically associated with liking for sweet-and-fatty foods (genetic r = 0.31). The relation between BMI and diet appears to be mediated through dieting behaviors. Dietary counseling should focus on unhealthy dieting behaviors rather than only on direct advice on food use.

Genetic parameters of milk production traits and fatty acid contents in milk for Holstein cows in parity 1-3.

PubMed

Bastin, C; Soyeurt, H; Gengler, N

2013-04-01

The objective of this study was to estimate genetic parameters of milk, fat, and protein yields, fat and protein contents, somatic cell count, and 17 groups and individual milk fatty acid (FA) contents predicted by mid-infrared spectrometry for first-, second- and third-parity Holstein cows. Edited data included records collected in the Walloon region of Belgium from 37,768 cows in parity 1,22,566 cows in parity 2 and 8221 in parity 3. A total of 69 (23 traits for three parities) single-trait random regression animal test-day models were run. Approximate genetic correlations among traits were inferred from pairwise regressions among estimated breeding values of cow having observations. Heritability and genetic correlation estimates from this study reflected the origins of FA: de novo synthetized or originating from the diet and the body fat mobilization. Averaged daily heritabilities of FA contents in milk ranged between 0.18 and 0.47. Average daily genetic correlations (averaged across days in milk and parities) among groups and individual FA contents in milk ranged between 0.31 and 0.99. The genetic variability of FAs in combination with the moderate to high heritabilities indicated that FA contents in milk could be changed by genetic selection; however, desirable direction of change in these traits remains unclear and should be defined with respect to all issues of importance related to milk FA. © 2012 Blackwell Verlag GmbH.

Shared Etiology of Psychotic Experiences and Depressive Symptoms in Adolescence: A Longitudinal Twin Study

PubMed Central

Eley, Thalia C.; McGuire, Philip; Plomin, Robert; Cardno, Alastair G.; Freeman, Daniel; Ronald, Angelica

2016-01-01

Psychotic disorders and major depression, both typically adult-onset conditions, often co-occur. At younger ages psychotic experiences and depressive symptoms are often reported in the community. We used a genetically sensitive longitudinal design to investigate the relationship between psychotic experiences and depressive symptoms in adolescence. A representative community sample of twins from England and Wales was employed. Self-rated depressive symptoms, paranoia, hallucinations, cognitive disorganization, grandiosity, anhedonia, and parent-rated negative symptoms were collected when the twins were age 16 (N = 9618) and again on a representative subsample 9 months later (N = 2873). Direction and aetiology of associations were assessed using genetically informative cross-lagged models. Depressive symptoms were moderately correlated with paranoia, hallucinations, and cognitive disorganization. Lower correlations were observed between depression and anhedonia, and depression and parent-rated negative symptoms. Nonsignificant correlations were observed between depression and grandiosity. Largely the same genetic effects influenced depression and paranoia, depression and hallucinations, and depression and cognitive disorganization. Modest overlap in environmental influences also played a role in the associations. Significant bi-directional longitudinal associations were observed between depression and paranoia. Hallucinations and cognitive disorganization during adolescence were found to impact later depression, even after controlling for earlier levels of depression. Our study shows that psychotic experiences and depression, as traits in the community, have a high genetic overlap in mid-adolescence. Future research should test the prediction stemming from our longitudinal results, namely that reducing or ameliorating positive and cognitive psychotic experiences in adolescence would decrease later depressive symptoms. PMID:26994398

Genetic parameters for lactose and its correlation with other milk production traits and fitness traits in pasture-based production systems.

PubMed

Haile-Mariam, M; Pryce, J E

2017-05-01

Lactose is a major component of milk (typically around 5% of composition) that is not usually directly considered in national genetic improvement programs of dairy cattle. Daily test-day lactose yields and percentage data from pasture-based seasonal calving herds in Australia were analyzed to assess if lactose content can be used for predicting fitness traits and if an additional benefit is achieved by including lactose yield in selecting for milk yield traits. Data on lactose percentage collected from 2007 to 2014, from about 600 herds, were used to estimated genetic parameters for lactose percentage and lactose yield and correlations with other milk yield traits, somatic cell count (SCC), calving interval (CIV), and survival. Daily test-day data were analyzed using bivariate random regression models. In addition, multi-trait models were also performed mainly to assess the value of lactose to predict fitness traits. The heritability of lactose percentage (0.25 to 0.37) was higher than lactose yield (0.11 to 0.20) in the first parity. Genetically, the correlation of lactose percentage with protein percentage varied from 0.3 at the beginning of lactation to -0.24 at the end of the lactation in the first parity. Similar patterns in genetic correlations were also observed in the second and third parity. At all levels (i.e., genetic, permanent environmental, and residual), the correlation between milk yield and lactose yield was close to 1. The genetic and permanent environmental correlations between lactose percentage and SCC were stronger in the second and third parity and toward the end of the lactation (-0.35 to -0.50) when SCC levels are at their maximum. The genetic correlation between lactose percentage in the first 120 d and CIV (-0.23) was similar to correlation of CIV with protein percentage (-0.28), another component trait with the potential to predict fertility. Furthermore, the correlations of estimated breeding values of lactose percentage and estimated breeding values of traits such as survival, fertility, SCC, and angularity suggest that the value of lactose percentage as a predictor of fitness traits is weak. The results also suggest that including lactose yield as a trait into the breeding objective is of limited value due to the high positive genetic correlation between lactose yield and protein yield, the trait highly emphasized in Australia. However, recording lactose percentage as part of the routine milk recording system will enable the Australian dairy industry to respond quickly to any future changes and market signals. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Positive correlation between genetic diversity and fitness in a large, well-connected metapopulation

PubMed Central

Vandewoestijne, Sofie; Schtickzelle, Nicolas; Baguette, Michel

2008-01-01

Background Theory predicts that lower dispersal, and associated gene flow, leads to decreased genetic diversity in small isolated populations, which generates adverse consequences for fitness, and subsequently for demography. Here we report for the first time this effect in a well-connected natural butterfly metapopulation with high population densities at the edge of its distribution range. Results We demonstrate that: (1) lower genetic diversity was coupled to a sharp decrease in adult lifetime expectancy, a key component of individual fitness; (2) genetic diversity was positively correlated to the number of dispersing individuals (indicative of landscape functional connectivity) and adult population size; (3) parameters inferred from capture-recapture procedures (population size and dispersal events between patches) correlated much better with genetic diversity than estimates usually used as surrogates for population size (patch area and descriptors of habitat quality) and dispersal (structural connectivity index). Conclusion Our results suggest that dispersal is a very important factor maintaining genetic diversity. Even at a very local spatial scale in a metapopulation consisting of large high-density populations interconnected by considerable dispersal rates, genetic diversity can be decreased and directly affect the fitness of individuals. From a biodiversity conservation perspective, this study clearly shows the benefits of both in-depth demographic and genetic analyses. Accordingly, to ensure the long-term survival of populations, conservation actions should not be blindly based on patch area and structural isolation. This result may be especially pertinent for species at their range margins, particularly in this era of rapid environmental change. PMID:18986515

A hybrid correlation analysis with application to imaging genetics

NASA Astrophysics Data System (ADS)

Hu, Wenxing; Fang, Jian; Calhoun, Vince D.; Wang, Yu-Ping

2018-03-01

Investigating the association between brain regions and genes continues to be a challenging topic in imaging genetics. Current brain region of interest (ROI)-gene association studies normally reduce data dimension by averaging the value of voxels in each ROI. This averaging may lead to a loss of information due to the existence of functional sub-regions. Pearson correlation is widely used for association analysis. However, it only detects linear correlation whereas nonlinear correlation may exist among ROIs. In this work, we introduced distance correlation to ROI-gene association analysis, which can detect both linear and nonlinear correlations and overcome the limitation of averaging operations by taking advantage of the information at each voxel. Nevertheless, distance correlation usually has a much lower value than Pearson correlation. To address this problem, we proposed a hybrid correlation analysis approach, by applying canonical correlation analysis (CCA) to the distance covariance matrix instead of directly computing distance correlation. Incorporating CCA into distance correlation approach may be more suitable for complex disease study because it can detect highly associated pairs of ROI and gene groups, and may improve the distance correlation level and statistical power. In addition, we developed a novel nonlinear CCA, called distance kernel CCA, which seeks the optimal combination of features with the most significant dependence. This approach was applied to imaging genetic data from the Philadelphia Neurodevelopmental Cohort (PNC). Experiments showed that our hybrid approach produced more consistent results than conventional CCA across resampling and both the correlation and statistical significance were increased compared to distance correlation analysis. Further gene enrichment analysis and region of interest (ROI) analysis confirmed the associations of the identified genes with brain ROIs. Therefore, our approach provides a powerful tool for finding the correlation between brain imaging and genomic data.

Genes influence young children's human figure drawings and their association with intelligence a decade later.

PubMed

Arden, Rosalind; Trzaskowski, Maciej; Garfield, Victoria; Plomin, Robert

2014-10-01

Drawing is ancient; it is the only childhood cognitive behavior for which there is any direct evidence from the Upper Paleolithic. Do genes influence individual differences in this species-typical behavior, and is drawing related to intelligence (g) in modern children? We report on the first genetically informative study of children's figure drawing. In a study of 7,752 pairs of twins, we found that genetic differences exert a greater influence on children's figure drawing at age 4 than do between-family environmental differences. Figure drawing was as heritable as g at age 4 (heritability of .29 for both). Drawing scores at age 4 correlated significantly with g at age 4 (r = .33, p < .001, n = 14,050) and with g at age 14 (r = .20, p < .001, n = 4,622). The genetic correlation between drawing at age 4 and g at age 14 was .52, 95% confidence interval = [.31, .75]. Individual differences in this widespread behavior have an important genetic component and a significant genetic link with g. © The Author(s) 2014.

Evolutionary responses of tree phenology to the combined effects of assortative mating, gene flow and divergent selection

PubMed Central

Soularue, J-P; Kremer, A

2014-01-01

The timing of bud burst (TBB) in temperate trees is a key adaptive trait, the expression of which is triggered by temperature gradients across the landscape. TBB is strongly correlated with flowering time and is therefore probably mediated by assortative mating. We derived theoretical predictions and realized numerical simulations of evolutionary changes in TBB in response to divergent selection and gene flow in a metapopulation. We showed that the combination of the environmental gradient of TBB and assortative mating creates contrasting genetic clines, depending on the direction of divergent selection. If divergent selection acts in the same direction as the environmental gradient (cogradient settings), genetic clines are established and inflated by assortative mating. Conversely, under divergent selection of the same strength but acting in the opposite direction (countergradient selection), genetic clines are slightly constrained. We explored the consequences of these dynamics for population maladaptation, by monitoring pollen swamping. Depending on the direction of divergent selection with respect to the environmental gradient, pollen filtering owing to assortative mating either facilitates or impedes adaptation in peripheral populations. PMID:24924591

Dietary Differentiation and the Evolution of Population Genetic Structure in a Highly Mobile Carnivore

PubMed Central

Pilot, Małgorzata; Jędrzejewski, Włodzimierz; Sidorovich, Vadim E.; Meier-Augenstein, Wolfram; Hoelzel, A. Rus

2012-01-01

Recent studies on highly mobile carnivores revealed cryptic population genetic structures correlated to transitions in habitat types and prey species composition. This led to the hypothesis that natal-habitat-biased dispersal may be responsible for generating population genetic structure. However, direct evidence for the concordant ecological and genetic differentiation between populations of highly mobile mammals is rare. To address this we analyzed stable isotope profiles (δ 13C and δ 15N values) for Eastern European wolves (Canis lupus) as a quantifiable proxy measure of diet for individuals that had been genotyped in an earlier study (showing cryptic genetic structure), to provide a quantitative assessment of the relationship between individual foraging behavior and genotype. We found a significant correlation between genetic distances and dietary differentiation (explaining 46% of the variation) in both the marginal test and crucially, when geographic distance was accounted for as a co-variable. These results, interpreted in the context of other possible mechanisms such as allopatry and isolation by distance, reinforce earlier studies suggesting that diet and associated habitat choice are influencing the structuring of populations in highly mobile carnivores. PMID:22768075

The genetic architecture of sexual conflict: male harm and female resistance in Callosobruchus maculatus.

PubMed

Gay, L; Brown, E; Tregenza, T; Pincheira-Donoso, D; Eady, P E; Vasudev, R; Hunt, J; Hosken, D J

2011-02-01

Males harm females during mating in a range of species. This harm is thought to evolve because it is directly or indirectly beneficial to the male, despite being costly to his mate. The resulting sexually antagonistic selection can cause sexual arms races. For sexually antagonistic co-evolution to occur, there must be genetic variation for traits involved in female harming and susceptibility to harm, but even then intersexual genetic correlations could facilitate or impede sexual co-evolution. Male Callosobruchus maculatus harm their mates during copulation by damaging the female's reproductive tract. However, there have been no investigations of the genetic variation in damage or in female susceptibility to damage, nor has the genetic covariance between these characters been assessed. Here, we use a full-sib/half-sib breeding design to show that male damage is heritable, whereas female susceptibility to damage is much less so. There is also a substantial positive genetic correlation between the two, suggesting that selection favouring damaging males will increase the prevalence of susceptible females. We also provide evidence consistent with intralocus sexual conflict in this species. © 2010 The Authors. Journal of Evolutionary Biology © 2010 European Society For Evolutionary Biology.

Genetic parameter estimates among scale activity score and farrowing disposition with reproductive traits in swine.

PubMed

Schneider, J F; Rempel, L A; Rohrer, G A; Brown-Brandl, T M

2011-11-01

The primary objective of this study was to determine if certain behavior traits were genetically correlated with reproduction. If 1 or both of the behavior traits were found to be correlated, a secondary objective was to determine if the behavior traits could be useful in selecting for more productive females. A scale activity score taken at 5 mo of age and a farrowing disposition score taken at farrowing were selected as the behavioral traits. Scale activity score ranged from 1 to 5 and farrowing disposition ranged from 1 to 3. Reproductive traits included age at puberty, number born alive, number born dead, litter birth weight, average piglet birth weight, number weaned, litter weaning weight, average weaning weight, wean-to-estrus interval, ovulation rate including gilts, and postweaning ovulation rate. Genetic correlations between scale activity score and reproduction ranged from -0.79 to 0.61. Three of the correlations, number born alive (P < 0.01), average piglet birth weight (P < 0.001), and wean-to-estrus interval (P = 0.014), were statistically significant but included both favorable and antagonistic correlations. In contrast, all but 1 of the farrowing disposition correlations was favorable and ranged from -0.66 to 0.67. Although only the correlation with litter birth weight was significant (P = 0.018), the consistent favorable direction of all farrowing disposition correlations, except average weaning weight, shows a potential for inclusion of farrowing disposition into a selection program.

Longitudinal analyses of correlated response efficiencies of fillet traits in Nile tilapia.

PubMed

Turra, E M; Fernandes, A F A; de Alvarenga, E R; Teixeira, E A; Alves, G F O; Manduca, L G; Murphy, T W; Silva, M A

2018-03-01

Recent studies with Nile tilapia have shown divergent results regarding the possibility of selecting on morphometric measurements to promote indirect genetic gains in fillet yield (FY). The use of indirect selection for fillet traits is important as these traits are only measurable after harvesting. Random regression models are a powerful tool in association studies to identify the best time point to measure and select animals. Random regression models can also be applied in a multiple trait approach to analyze indirect response to selection, which would avoid the need to sacrifice candidate fish. Therefore, the aim of this study was to investigate the genetic relationships between several body measurements, weight and fillet traits throughout the growth period and to evaluate the possibility of indirect selection for fillet traits in Nile tilapia. Data were collected from 2042 fish and was divided into two subsets. The first subset was used to estimate genetic parameters, including the permanent environmental effect for BW and body measurements (8758 records for each body measurement, as each fish was individually weighed and measured a maximum of six times). The second subset (2042 records for each trait) was used to estimate genetic correlations and heritabilities, which enabled the calculation of correlated response efficiencies between body measurements and the fillet traits. Heritability estimates across ages ranged from 0.05 to 0.5 for height, 0.02 to 0.48 for corrected length (CL), 0.05 to 0.68 for width, 0.08 to 0.57 for fillet weight (FW) and 0.12 to 0.42 for FY. All genetic correlation estimates between body measurements and FW were positive and strong (0.64 to 0.98). The estimates of genetic correlation between body measurements and FY were positive (except for CL at some ages), but weak to moderate (-0.08 to 0.68). These estimates resulted in strong and favorable correlated response efficiencies for FW and positive, but moderate for FY. These results indicate the possibility of achieving indirect genetic gains for FW and by selecting for morphometric traits, but low efficiency for FY when compared with direct selection.

Genetic questions for environmental studies. Differential parenting and psychopathology in adolescence.

PubMed

Reiss, D; Hetherington, E M; Plomin, R; Howe, G W; Simmens, S J; Henderson, S H; O'Connor, T J; Bussell, D A; Anderson, E R; Law, T

1995-11-01

Recent genetic evidence suggests that the most important environmental influences on normal and pathologic development are those that are not shared by siblings in the same family. We sought to determine the relationship between differences in parenting styles and depressive symptoms and antisocial behavior in adolescence, and to compare the influence of these nonshared experiences with genetic influences. We studied 708 families with at least two same-sexed adolescent siblings who were monozygotic twins (93 families), dizygotic twins (99 families), ordinary siblings (95 families), full siblings in step families (181 families), half siblings in step families (110 families), and genetically unrelated siblings in step families (130 families). Data on parenting style were collected by questionnaire and by video recording of interaction between parents and children. Almost 60% of variance in adolescent antisocial behavior and 37% of variance in depressive symptoms could be accounted for by conflictual and negative parental behavior directed specifically at the adolescent. In contrast, when a parent directed harsh, aggressive, explosive, and inconsistent parenting toward the sibling, we found less psychopathologic outcome in the adolescent. Parenting behavior directed specifically at each child in the family is a major correlate of symptoms in adolescents. Furthermore, harsh parental behavior directed at a sibling may have protective effects for adolescents, a phenomenon we call the "siblin barricade."

Heritability, covariation and natural selection on 24 traits of common evening primrose (Oenothera biennis) from a field experiment.

PubMed

Johnson, M T J; Agrawal, A A; Maron, J L; Salminen, J-P

2009-06-01

This study explored genetic variation and co-variation in multiple functional plant traits. Our goal was to characterize selection, heritabilities and genetic correlations among different types of traits to gain insight into the evolutionary ecology of plant populations and their interactions with insect herbivores. In a field experiment, we detected significant heritable variation for each of 24 traits of Oenothera biennis and extensive genetic covariance among traits. Traits with diverse functions formed several distinct groups that exhibited positive genetic covariation with each other. Genetic variation in life-history traits and secondary chemistry together explained a large proportion of variation in herbivory (r(2) = 0.73). At the same time, selection acted on lifetime biomass, life-history traits and two secondary compounds of O. biennis, explaining over 95% of the variation in relative fitness among genotypes. The combination of genetic covariances and directional selection acting on multiple traits suggests that adaptive evolution of particular traits is constrained, and that correlated evolution of groups of traits will occur, which is expected to drive the evolution of increased herbivore susceptibility. As a whole, our study indicates that an examination of genetic variation and covariation among many different types of traits can provide greater insight into the evolutionary ecology of plant populations and plant-herbivore interactions.

Genetic evaluation and selection response for growth in meat-type quail through random regression models using B-spline functions and Legendre polynomials.

PubMed

Mota, L F M; Martins, P G M A; Littiere, T O; Abreu, L R A; Silva, M A; Bonafé, C M

2018-04-01

The objective was to estimate (co)variance functions using random regression models (RRM) with Legendre polynomials, B-spline function and multi-trait models aimed at evaluating genetic parameters of growth traits in meat-type quail. A database containing the complete pedigree information of 7000 meat-type quail was utilized. The models included the fixed effects of contemporary group and generation. Direct additive genetic and permanent environmental effects, considered as random, were modeled using B-spline functions considering quadratic and cubic polynomials for each individual segment, and Legendre polynomials for age. Residual variances were grouped in four age classes. Direct additive genetic and permanent environmental effects were modeled using 2 to 4 segments and were modeled by Legendre polynomial with orders of fit ranging from 2 to 4. The model with quadratic B-spline adjustment, using four segments for direct additive genetic and permanent environmental effects, was the most appropriate and parsimonious to describe the covariance structure of the data. The RRM using Legendre polynomials presented an underestimation of the residual variance. Lesser heritability estimates were observed for multi-trait models in comparison with RRM for the evaluated ages. In general, the genetic correlations between measures of BW from hatching to 35 days of age decreased as the range between the evaluated ages increased. Genetic trend for BW was positive and significant along the selection generations. The genetic response to selection for BW in the evaluated ages presented greater values for RRM compared with multi-trait models. In summary, RRM using B-spline functions with four residual variance classes and segments were the best fit for genetic evaluation of growth traits in meat-type quail. In conclusion, RRM should be considered in genetic evaluation of breeding programs.

Genetic overlap between endometriosis and endometrial cancer: evidence from cross-disease genetic correlation and GWAS meta-analyses.

PubMed

Painter, Jodie N; O'Mara, Tracy A; Morris, Andrew P; Cheng, Timothy H T; Gorman, Maggie; Martin, Lynn; Hodson, Shirley; Jones, Angela; Martin, Nicholas G; Gordon, Scott; Henders, Anjali K; Attia, John; McEvoy, Mark; Holliday, Elizabeth G; Scott, Rodney J; Webb, Penelope M; Fasching, Peter A; Beckmann, Matthias W; Ekici, Arif B; Hein, Alexander; Rübner, Matthias; Hall, Per; Czene, Kamila; Dörk, Thilo; Dürst, Matthias; Hillemanns, Peter; Runnebaum, Ingo; Lambrechts, Diether; Amant, Frederic; Annibali, Daniela; Depreeuw, Jeroen; Vanderstichele, Adriaan; Goode, Ellen L; Cunningham, Julie M; Dowdy, Sean C; Winham, Stacey J; Trovik, Jone; Hoivik, Erling; Werner, Henrica M J; Krakstad, Camilla; Ashton, Katie; Otton, Geoffrey; Proietto, Tony; Tham, Emma; Mints, Miriam; Ahmed, Shahana; Healey, Catherine S; Shah, Mitul; Pharoah, Paul D P; Dunning, Alison M; Dennis, Joe; Bolla, Manjeet K; Michailidou, Kyriaki; Wang, Qin; Tyrer, Jonathan P; Hopper, John L; Peto, Julian; Swerdlow, Anthony J; Burwinkel, Barbara; Brenner, Hermann; Meindl, Alfons; Brauch, Hiltrud; Lindblom, Annika; Chang-Claude, Jenny; Couch, Fergus J; Giles, Graham G; Kristensen, Vessela N; Cox, Angela; Zondervan, Krina T; Nyholt, Dale R; MacGregor, Stuart; Montgomery, Grant W; Tomlinson, Ian; Easton, Douglas F; Thompson, Deborah J; Spurdle, Amanda B

2018-05-01

Epidemiological, biological, and molecular data suggest links between endometriosis and endometrial cancer, with recent epidemiological studies providing evidence for an association between a previous diagnosis of endometriosis and risk of endometrial cancer. We used genetic data as an alternative approach to investigate shared biological etiology of these two diseases. Genetic correlation analysis of summary level statistics from genomewide association studies (GWAS) using LD Score regression revealed moderate but significant genetic correlation (r g  = 0.23, P = 9.3 × 10 -3 ), and SNP effect concordance analysis provided evidence for significant SNP pleiotropy (P = 6.0 × 10 -3 ) and concordance in effect direction (P = 2.0 × 10 -3 ) between the two diseases. Cross-disease GWAS meta-analysis highlighted 13 distinct loci associated at P ≤ 10 -5 with both endometriosis and endometrial cancer, with one locus (SNP rs2475335) located within PTPRD associated at a genomewide significant level (P = 4.9 × 10 -8 , OR = 1.11, 95% CI = 1.07-1.15). PTPRD acts in the STAT3 pathway, which has been implicated in both endometriosis and endometrial cancer. This study demonstrates the value of cross-disease genetic analysis to support epidemiological observations and to identify biological pathways of relevance to multiple diseases. © 2018 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

File Compression and Expansion of the Genetic Code by the use of the Yin/Yang Directions to find its Sphered Cube

PubMed Central

Castro-Chavez, Fernando

2014-01-01

Objective The objective of this article is to demonstrate that the genetic code can be studied and represented in a 3-D Sphered Cube for bioinformatics and for education by using the graphical help of the ancient “Book of Changes” or I Ching for the comparison, pair by pair, of the three basic characteristics of nucleotides: H-bonds, molecular structure, and their tautomerism. Methods The source of natural biodiversity is the high plasticity of the genetic code, analyzable with a reverse engineering of its 2-D and 3-D representations (here illustrated), but also through the classical 64-hexagrams of the ancient I Ching, as if they were the 64-codons or words of the genetic code. Results In this article, the four elements of the Yin/Yang were found by correlating the 3×2=6 sets of Cartesian comparisons of the mentioned properties of nucleic acids, to the directionality of their resulting blocks of codons grouped according to their resulting amino acids and/or functions, integrating a 384-codon Sphered Cube whose function is illustrated by comparing six brain peptides and a promoter of osteoblasts from Humans versus Neanderthal, as well as to Negadi’s work on the importance of the number 384 within the genetic code. Conclusions Starting with the codon/anticodon correlation of Nirenberg, published in full here for the first time, and by studying the genetic code and its 3-D display, the buffers of reiteration within codons codifying for the same amino acid, displayed the two long (binary number one) and older Yin/Yang arrows that travel in opposite directions, mimicking the parental DNA strands, while annealing to the two younger and broken (binary number zero) Yin/Yang arrows, mimicking the new DNA strands; the graphic analysis of the of the genetic code and its plasticity was helpful to compare compatible sequences (human compatible to human versus neanderthal compatible to neanderthal), while further exploring the wondrous biodiversity of nature for educational purposes. PMID:25340175

Genetic signatures of natural selection in a model invasive ascidian

PubMed Central

Lin, Yaping; Chen, Yiyong; Yi, Changho; Fong, Jonathan J.; Kim, Won; Rius, Marc; Zhan, Aibin

2017-01-01

Invasive species represent promising models to study species’ responses to rapidly changing environments. Although local adaptation frequently occurs during contemporary range expansion, the associated genetic signatures at both population and genomic levels remain largely unknown. Here, we use genome-wide gene-associated microsatellites to investigate genetic signatures of natural selection in a model invasive ascidian, Ciona robusta. Population genetic analyses of 150 individuals sampled in Korea, New Zealand, South Africa and Spain showed significant genetic differentiation among populations. Based on outlier tests, we found high incidence of signatures of directional selection at 19 loci. Hitchhiking mapping analyses identified 12 directional selective sweep regions, and all selective sweep windows on chromosomes were narrow (~8.9 kb). Further analyses indentified 132 candidate genes under selection. When we compared our genetic data and six crucial environmental variables, 16 putatively selected loci showed significant correlation with these environmental variables. This suggests that the local environmental conditions have left significant signatures of selection at both population and genomic levels. Finally, we identified “plastic” genomic regions and genes that are promising regions to investigate evolutionary responses to rapid environmental change in C. robusta. PMID:28266616

RECENT ADVANCES OF GENETIC ANCESTRY TESTING IN BIOMEDICAL RESEARCH AND DIRECT TO CONSUMER TESTING

PubMed Central

Via, Marc; Ziv, Elad; Burchard, Esteban González

2010-01-01

In the post-Human Genome Project era, the debate on the concept of race/ethnicity and its implications for biomedical research are dependent on two critical issues: whether and how to classify individuals and whether biological factors play a role in health disparities. The advent of reliable estimates of genetic (or biogeographic) ancestry has provided this debate with a quantitative and more objective tool. The estimation of genetic ancestry allows investigators to control for population stratification in association studies and helps to detect biological causation behind population-specific differences in disease and drug response. New techniques such as admixture mapping can specifically detect population-specific risk alleles for a disease in admixed populations. However, researchers have to be mindful of the correlation between genetic ancestry and socioeconomic and environmental factors that could underlie these differences. More importantly, researchers must avoid the stigmatization of individuals based on perceived or real genetic risks. The latter point will become increasingly sensitive as several “for profit companies” are offering ancestry and genetic testing directly to consumers and the consequences of the spread of the services of these companies is still unforeseeable. PMID:19793051

Shared Etiology of Psychotic Experiences and Depressive Symptoms in Adolescence: A Longitudinal Twin Study.

PubMed

Zavos, Helena M S; Eley, Thalia C; McGuire, Philip; Plomin, Robert; Cardno, Alastair G; Freeman, Daniel; Ronald, Angelica

2016-09-01

Psychotic disorders and major depression, both typically adult-onset conditions, often co-occur. At younger ages psychotic experiences and depressive symptoms are often reported in the community. We used a genetically sensitive longitudinal design to investigate the relationship between psychotic experiences and depressive symptoms in adolescence. A representative community sample of twins from England and Wales was employed. Self-rated depressive symptoms, paranoia, hallucinations, cognitive disorganization, grandiosity, anhedonia, and parent-rated negative symptoms were collected when the twins were age 16 (N = 9618) and again on a representative subsample 9 months later (N = 2873). Direction and aetiology of associations were assessed using genetically informative cross-lagged models. Depressive symptoms were moderately correlated with paranoia, hallucinations, and cognitive disorganization. Lower correlations were observed between depression and anhedonia, and depression and parent-rated negative symptoms. Nonsignificant correlations were observed between depression and grandiosity. Largely the same genetic effects influenced depression and paranoia, depression and hallucinations, and depression and cognitive disorganization. Modest overlap in environmental influences also played a role in the associations. Significant bi-directional longitudinal associations were observed between depression and paranoia. Hallucinations and cognitive disorganization during adolescence were found to impact later depression, even after controlling for earlier levels of depression. Our study shows that psychotic experiences and depression, as traits in the community, have a high genetic overlap in mid-adolescence. Future research should test the prediction stemming from our longitudinal results, namely that reducing or ameliorating positive and cognitive psychotic experiences in adolescence would decrease later depressive symptoms. © The Author 2016. Published by Oxford University Press on behalf of the Maryland Psychiatric Research Center.

Genetic evaluation of recombinant inbred lines of rice (Oryza sativa L.) for grain zinc concentrations, yield related traits and identification of associated SSR markers.

PubMed

Bekele, Berhanu D; Naveen, G K; Rakhi, S; Shashidhar, H E

2013-12-01

The objectives of the present study were to evaluate genetic variability parameters, correlations that exist for grain Zn concentration and yield related traits and identification of SSR markers linked to these traits in rice. One hundred seventy six Recombinant Inbred Lines (RILs) of Azucena X Moromutant were grown at University of Agricultural Sciences, Bangalore in augmented experimental design during wet seasons of 2010 and 2011. The study revealed significant genetic variability for all the traits. Grain yield per plant and grain zinc concentration showed higher phenotypic and genotypic co-efficient of variation. Significant positive correlation was observed for grain yield per plant with number of productive tillers per plant (r = 0.5) and number of tillers per plant (r = 0.4). Grain zinc concentration showed negative correlation with grain yield per plant (r = - 0.27). The path-coefficient analysis indicated the positive direct effect of number of productive tillers per plant on grain yield per plant (0.514). Grain zinc concentration showed negative direct effect on grain yield per plant (-0.186). Single-marker analysis using 26 SSR markers on RILs mapping population showed that RM212, RM263, RM6832, RM152, RM21, RM234 and RM3331 had association with grain zinc concentration and other yield related traits. But validation of these markers on fifty two rice genotypes showed that only three markers RM263, RM152 and RM21 had association with grain zinc concentration. Therefore, the genetic information generated and molecular markers identified from this study could be used for zinc biofortification programmes in rice.

A test of the facultative calibration/reactive heritability model of extraversion

PubMed Central

Haysom, Hannah J.; Mitchem, Dorian G.; Lee, Anthony J.; Wright, Margaret J.; Martin, Nicholas G.; Keller, Matthew C.; Zietsch, Brendan P.

2015-01-01

A model proposed by Lukaszewski and Roney (2011) suggests that each individual’s level of extraversion is calibrated to other traits that predict the success of an extraverted behavioural strategy. Under ‘facultative calibration’, extraversion is not directly heritable, but rather exhibits heritability through its calibration to directly heritable traits (“reactive heritability”). The current study uses biometrical modelling of 1659 identical and non-identical twins and their siblings to assess whether the genetic variation in extraversion is calibrated to variation in facial attractiveness, intelligence, height in men and body mass index (BMI) in women. Extraversion was significantly positively correlated with facial attractiveness in both males (r=.11) and females (r=.18), but correlations between extraversion and the other variables were not consistent with predictions. Further, twin modelling revealed that the genetic variation in facial attractiveness did not account for a substantial proportion of the variation in extraversion in either males (2.4%) or females (0.5%). PMID:26880866

Determining the Effect of Natural Selection on Linked Neutral Divergence across Species

PubMed Central

Phung, Tanya N.; Lohmueller, Kirk E.

2016-01-01

A major goal in evolutionary biology is to understand how natural selection has shaped patterns of genetic variation across genomes. Studies in a variety of species have shown that neutral genetic diversity (intra-species differences) has been reduced at sites linked to those under direct selection. However, the effect of linked selection on neutral sequence divergence (inter-species differences) remains ambiguous. While empirical studies have reported correlations between divergence and recombination, which is interpreted as evidence for natural selection reducing linked neutral divergence, theory argues otherwise, especially for species that have diverged long ago. Here we address these outstanding issues by examining whether natural selection can affect divergence between both closely and distantly related species. We show that neutral divergence between closely related species (e.g. human-primate) is negatively correlated with functional content and positively correlated with human recombination rate. We also find that neutral divergence between distantly related species (e.g. human-rodent) is negatively correlated with functional content and positively correlated with estimates of background selection from primates. These patterns persist after accounting for the confounding factors of hypermutable CpG sites, GC content, and biased gene conversion. Coalescent models indicate that even when the contribution of ancestral polymorphism to divergence is small, background selection in the ancestral population can still explain a large proportion of the variance in divergence across the genome, generating the observed correlations. Our findings reveal that, contrary to previous intuition, natural selection can indirectly affect linked neutral divergence between both closely and distantly related species. Though we cannot formally exclude the possibility that the direct effects of purifying selection drive some of these patterns, such a scenario would be possible only if more of the genome is under purifying selection than currently believed. Our work has implications for understanding the evolution of genomes and interpreting patterns of genetic variation. PMID:27508305

Determining the Effect of Natural Selection on Linked Neutral Divergence across Species.

PubMed

Phung, Tanya N; Huber, Christian D; Lohmueller, Kirk E

2016-08-01

A major goal in evolutionary biology is to understand how natural selection has shaped patterns of genetic variation across genomes. Studies in a variety of species have shown that neutral genetic diversity (intra-species differences) has been reduced at sites linked to those under direct selection. However, the effect of linked selection on neutral sequence divergence (inter-species differences) remains ambiguous. While empirical studies have reported correlations between divergence and recombination, which is interpreted as evidence for natural selection reducing linked neutral divergence, theory argues otherwise, especially for species that have diverged long ago. Here we address these outstanding issues by examining whether natural selection can affect divergence between both closely and distantly related species. We show that neutral divergence between closely related species (e.g. human-primate) is negatively correlated with functional content and positively correlated with human recombination rate. We also find that neutral divergence between distantly related species (e.g. human-rodent) is negatively correlated with functional content and positively correlated with estimates of background selection from primates. These patterns persist after accounting for the confounding factors of hypermutable CpG sites, GC content, and biased gene conversion. Coalescent models indicate that even when the contribution of ancestral polymorphism to divergence is small, background selection in the ancestral population can still explain a large proportion of the variance in divergence across the genome, generating the observed correlations. Our findings reveal that, contrary to previous intuition, natural selection can indirectly affect linked neutral divergence between both closely and distantly related species. Though we cannot formally exclude the possibility that the direct effects of purifying selection drive some of these patterns, such a scenario would be possible only if more of the genome is under purifying selection than currently believed. Our work has implications for understanding the evolution of genomes and interpreting patterns of genetic variation.

Signal trait sexual dimorphism and mutual sexual selection in Drosophila serrata.

PubMed

Chenoweth, Stephen F; Blows, Mark W

2003-10-01

The evolution of sexual dimorphism may occur when natural and sexual selection result in different optimum trait values for males and females. Perhaps the most prominent examples of sexual dimorphism occur in sexually selected traits, for which males usually display exaggerated trait levels, while females may show reduced expression of the trait. In some species, females also exhibit secondary sexual traits that may either be a consequence of a correlated response to sexual selection on males or direct sexual selection for female secondary sexual traits. In this experiment, we simultaneously measure the intersex genetic correlations and the relative strength of sexual selection on males and females for a set of cuticular hydrocarbons in Drosophila serrata. There was significant directional sexual selection on both male and female cuticular hydrocarbons: the strength of sexual selection did not differ among the sexes but males and females preferred different cuticular hydrocarbons. In contrast with many previous studies of sexual dimorphism, intersex genetic correlations were low. The evolution of sexual dimorphism in D. serrata appears to have been achieved by sex-limited expression of traits controlled by genes on the X chromosome and is likely to be in its final stages.

Genetic parameters for racing records in trotters using linear and generalized linear models.

PubMed

Suontama, M; van der Werf, J H J; Juga, J; Ojala, M

2012-09-01

Heritability and repeatability and genetic and phenotypic correlations were estimated for trotting race records with linear and generalized linear models using 510,519 records on 17,792 Finnhorses and 513,161 records on 25,536 Standardbred trotters. Heritability and repeatability were estimated for single racing time and earnings traits with linear models, and logarithmic scale was used for racing time and fourth-root scale for earnings to correct for nonnormality. Generalized linear models with a gamma distribution were applied for single racing time and with a multinomial distribution for single earnings traits. In addition, genetic parameters for annual earnings were estimated with linear models on the observed and fourth-root scales. Racing success traits of single placings, winnings, breaking stride, and disqualifications were analyzed using generalized linear models with a binomial distribution. Estimates of heritability were greatest for racing time, which ranged from 0.32 to 0.34. Estimates of heritability were low for single earnings with all distributions, ranging from 0.01 to 0.09. Annual earnings were closer to normal distribution than single earnings. Heritability estimates were moderate for annual earnings on the fourth-root scale, 0.19 for Finnhorses and 0.27 for Standardbred trotters. Heritability estimates for binomial racing success variables ranged from 0.04 to 0.12, being greatest for winnings and least for breaking stride. Genetic correlations among racing traits were high, whereas phenotypic correlations were mainly low to moderate, except correlations between racing time and earnings were high. On the basis of a moderate heritability and moderate to high repeatability for racing time and annual earnings, selection of horses for these traits is effective when based on a few repeated records. Because of high genetic correlations, direct selection for racing time and annual earnings would also result in good genetic response in racing success.

IMPLICATIONS OF MATING PATTERNS FOR CONSERVATION OF THE ENDANGERED PLANT ERIOGONUM OVALIFOLIUM VAR. VINEUM (POLYGONACEAE). (R826102)

EPA Science Inventory

Mating patterns have direct application to: conservation because of their influence on structuring genetic diversity within and among populations and on maintaining that diversity over time. We measured population and family outcrossing rates, biparental inbreeding correlation of...

Interactive effects of genotype x environment on the live weight of GIFT Nile tilapias.

PubMed

Oliveira, Sheila N DE; Ribeiro, Ricardo P; Oliveira, Carlos A L DE; Alexandre, Luiz; Oliveira, Aline M S; Lopera-Barrero, Nelson M; Santander, Victor F A; Santana, Renan A C

2017-01-01

In this paper, the existence of a genotype x environment interaction for the average daily weight in GIFT Nile tilapia (Oreochromis niloticus) in different regions in the state of Paraná (Brazil) was analyzed. The heritability results were high in the uni-characteristic analysis: 0.71, 0.72 and 0.67 for the cities of Palotina (PL), Floriano (FL) and Diamond North (DN), respectively. Genetic correlations estimated in bivariate analyzes were weak with values between 0.12 for PL-FL, 0.06 for PL and 0.23 for DN-FL-DN. The Spearman correlation values were low, which indicated a change in ranking in the selection of animals in different environments in the study. There was heterogeneity in the phenotypic variance among the three regions and heterogeneity in the residual variance between PL and DN. The direct genetic gain was greater for the region with a DN value gain of 198.24 g/generation, followed by FL (98.73 g/generation) and finally PL (98.73 g/generation). The indirect genetic gains were lower than 0.37 and greater than 0.02 g/generation. The evidence of the genotype x environment interaction was verified, which indicated the phenotypic heterogeneity of the variances among the three regions, weak genetic correlation and modified rankings in the different environments.

Sparse models for correlative and integrative analysis of imaging and genetic data

PubMed Central

Lin, Dongdong; Cao, Hongbao; Calhoun, Vince D.

2014-01-01

The development of advanced medical imaging technologies and high-throughput genomic measurements has enhanced our ability to understand their interplay as well as their relationship with human behavior by integrating these two types of datasets. However, the high dimensionality and heterogeneity of these datasets presents a challenge to conventional statistical methods; there is a high demand for the development of both correlative and integrative analysis approaches. Here, we review our recent work on developing sparse representation based approaches to address this challenge. We show how sparse models are applied to the correlation and integration of imaging and genetic data for biomarker identification. We present examples on how these approaches are used for the detection of risk genes and classification of complex diseases such as schizophrenia. Finally, we discuss future directions on the integration of multiple imaging and genomic datasets including their interactions such as epistasis. PMID:25218561

Geographic variation in advertisement calls of a Microhylid frog - testing the role of drift and ecology.

PubMed

Lee, Ko-Huan; Shaner, Pei-Jen L; Lin, Yen-Po; Lin, Si-Min

2016-05-01

Acoustic signals for mating are important traits that could drive population differentiation and speciation. Ecology may play a role in acoustic divergence through direct selection (e.g., local adaptation to abiotic environment), constraint of correlated traits (e.g., acoustic traits linked to another trait under selection), and/or interspecific competition (e.g., character displacement). However, genetic drift alone can also drive acoustic divergence. It is not always easy to differentiate the role of ecology versus drift in acoustic divergence. In this study, we tested the role of ecology and drift in shaping geographic variation in the advertisement calls of Microhyla fissipes. We examined three predictions based on ecological processes: (1) the correlation between temperature and call properties across M. fissipes populations; (2) the correlation between call properties and body size across M. fissipes populations; and (3) reproductive character displacement (RCD) in call properties between M. fissipes populations that are sympatric with and allopatric to a congener M. heymonsi. To test genetic drift, we examined correlations among call divergence, geographic distance, and genetic distance across M. fissipes populations. We recorded the advertisement calls from 11 populations of M. fissipes in Taiwan, five of which are sympatrically distributed with M. heymonsi. We found geographic variation in both temporal and spectral properties of the advertisement calls of M. fissipes. However, the call properties were not correlated with local temperature or the callers' body size. Furthermore, we did not detect RCD. By contrast, call divergence, geographic distance, and genetic distance between M. fissipes populations were all positively correlated. The comparisons between phenotypic Q st (P st) and F st values did not show significant differences, suggesting a role of drift. We concluded that genetic drift, rather than ecological processes, is the more likely driver for the geographic variation in the advertisement calls of M. fissipes.

Parametric correlation functions to model the structure of permanent environmental (co)variances in milk yield random regression models.

PubMed

Bignardi, A B; El Faro, L; Cardoso, V L; Machado, P F; Albuquerque, L G

2009-09-01

The objective of the present study was to estimate milk yield genetic parameters applying random regression models and parametric correlation functions combined with a variance function to model animal permanent environmental effects. A total of 152,145 test-day milk yields from 7,317 first lactations of Holstein cows belonging to herds located in the southeastern region of Brazil were analyzed. Test-day milk yields were divided into 44 weekly classes of days in milk. Contemporary groups were defined by herd-test-day comprising a total of 2,539 classes. The model included direct additive genetic, permanent environmental, and residual random effects. The following fixed effects were considered: contemporary group, age of cow at calving (linear and quadratic regressions), and the population average lactation curve modeled by fourth-order orthogonal Legendre polynomial. Additive genetic effects were modeled by random regression on orthogonal Legendre polynomials of days in milk, whereas permanent environmental effects were estimated using a stationary or nonstationary parametric correlation function combined with a variance function of different orders. The structure of residual variances was modeled using a step function containing 6 variance classes. The genetic parameter estimates obtained with the model using a stationary correlation function associated with a variance function to model permanent environmental effects were similar to those obtained with models employing orthogonal Legendre polynomials for the same effect. A model using a sixth-order polynomial for additive effects and a stationary parametric correlation function associated with a seventh-order variance function to model permanent environmental effects would be sufficient for data fitting.

Caste load and the evolution of reproductive skew.

PubMed

Holman, Luke

2014-01-01

Reproductive skew theory seeks to explain how reproduction is divided among group members in animal societies. Existing theory is framed almost entirely in terms of selection, though nonadaptive processes must also play some role in the evolution of reproductive skew. Here I propose that a genetic correlation between helper fecundity and breeder fecundity may frequently constrain the evolution of reproductive skew. This constraint is part of a wider phenomenon that I term "caste load," which is defined as the decline in mean fitness caused by caste-specific selection pressures, that is, differential selection on breeding and nonbreeding individuals. I elaborate the caste load hypothesis using quantitative and population genetic arguments and individual-based simulations. Although selection can sometimes erode genetic correlations and resolve caste load, this may be constrained when mutations have similar pleiotropic effects on breeder and helper traits. I document evidence for caste load, identify putative genomic adaptations to it, and suggest future research directions. The models highlight the value of considering adaptation within the boundaries imposed by genetic architecture and incidentally reaffirm that monogamy promotes the evolutionary transition to eusociality.

Shared genetic aetiology of puberty timing between sexes and with health-related outcomes

PubMed Central

Day, Felix R.; Bulik-Sullivan, Brendan; Hinds, David A.; Finucane, Hilary K.; Murabito, Joanne M.; Tung, Joyce Y.; Ong, Ken K.; Perry, John R.B.

2015-01-01

Understanding of the genetic regulation of puberty timing has come largely from studies of rare disorders and population-based studies in women. Here, we report the largest genomic analysis for puberty timing in 55,871 men, based on recalled age at voice breaking. Analysis across all genomic variants reveals strong genetic correlation (0.74, P=2.7 × 10−70) between male and female puberty timing. However, some loci show sex-divergent effects, including directionally opposite effects between sexes at the SIM1/MCHR2 locus (Pheterogeneity=1.6 × 10−12). We find five novel loci for puberty timing (P<5 × 10−8), in addition to nine signals in men that were previously reported in women. Newly implicated genes include two retinoic acid-related receptors, RORB and RXRA, and two genes reportedly disrupted in rare disorders of puberty, LEPR and KAL1. Finally, we identify genetic correlations that indicate shared aetiologies in both sexes between puberty timing and body mass index, fasting insulin levels, lipid levels, type 2 diabetes and cardiovascular disease. PMID:26548314

Shared genetic aetiology of puberty timing between sexes and with health-related outcomes.

PubMed

Day, Felix R; Bulik-Sullivan, Brendan; Hinds, David A; Finucane, Hilary K; Murabito, Joanne M; Tung, Joyce Y; Ong, Ken K; Perry, John R B

2015-11-09

Understanding of the genetic regulation of puberty timing has come largely from studies of rare disorders and population-based studies in women. Here, we report the largest genomic analysis for puberty timing in 55,871 men, based on recalled age at voice breaking. Analysis across all genomic variants reveals strong genetic correlation (0.74, P=2.7 × 10(-70)) between male and female puberty timing. However, some loci show sex-divergent effects, including directionally opposite effects between sexes at the SIM1/MCHR2 locus (Pheterogeneity=1.6 × 10(-12)). We find five novel loci for puberty timing (P<5 × 10(-8)), in addition to nine signals in men that were previously reported in women. Newly implicated genes include two retinoic acid-related receptors, RORB and RXRA, and two genes reportedly disrupted in rare disorders of puberty, LEPR and KAL1. Finally, we identify genetic correlations that indicate shared aetiologies in both sexes between puberty timing and body mass index, fasting insulin levels, lipid levels, type 2 diabetes and cardiovascular disease.

Genetic selection for ovulation rate and litter size in rabbits: Estimation of genetic parameters and direct and correlated responses.

PubMed

Ziadi, C; Mocé, M L; Laborda, P; Blasco, A; Santacreu, M A

2013-07-01

The aim of this work was to estimate direct and correlated responses in survival rates in an experiment of selection for ovulation rate (OR) and litter size (LS) in a line of rabbits (OR_LS). From generation 0 to 6 (first selection period), females were selected only for second gestation OR estimated by laparoscopy. From generation 7 to 13 (second selection period), a 2-stage selection for OR and LS was performed. In stage 1, females having the greatest OR at second gestation were selected. In stage 2, selection was for the greatest average LS of the first 2 parities of the females selected in stage 1. Total selection pressure in females was about 30%. The line had approximately 17 males and 75 females per generation. Traits recorded were OR estimated as the number of corpora lutea in both ovaries, number of implanted embryos (IE) estimated as the number of implantation sites, LS estimated as total number of rabbits born recorded at each parity, embryo survival (ES) estimated as IE/OR, fetal survival (FS) estimated as LS/IE, and prenatal survival (PS) estimated as LS/OR. Data were analyzed using Bayesian methodology. The estimated heritabilities of LS, OR, IE, ES, FS, and PS were 0.07, 0.21, 0.10, 0.07, 0.12, and 0.16, respectively. Direct and correlated responses from this study were estimated in each period of selection as the difference between the average genetic values of last and first generation. In the first selection period, OR increased 1.36 ova, but no correlated response was observed in LS due to a decrease on FS. Correlated responses for IE, ES, FS, and PS in the first selection period were 1.11, 0.00, -0.04, and -0.01, respectively. After 7 generations of 2-stage selection for OR and LS, OR increased 1.0 ova and response in LS was 0.9 kits. Correlated responses for IE, ES, FS, and PS in the second selection period were 1.14, 0.02, 0.02, and 0.07, respectively. Two-stage selection for OR and LS can be a promising procedure to improve LS in rabbits.

Statistical power and utility of meta-analysis methods for cross-phenotype genome-wide association studies.

PubMed

Zhu, Zhaozhong; Anttila, Verneri; Smoller, Jordan W; Lee, Phil H

2018-01-01

Advances in recent genome wide association studies (GWAS) suggest that pleiotropic effects on human complex traits are widespread. A number of classic and recent meta-analysis methods have been used to identify genetic loci with pleiotropic effects, but the overall performance of these methods is not well understood. In this work, we use extensive simulations and case studies of GWAS datasets to investigate the power and type-I error rates of ten meta-analysis methods. We specifically focus on three conditions commonly encountered in the studies of multiple traits: (1) extensive heterogeneity of genetic effects; (2) characterization of trait-specific association; and (3) inflated correlation of GWAS due to overlapping samples. Although the statistical power is highly variable under distinct study conditions, we found the superior power of several methods under diverse heterogeneity. In particular, classic fixed-effects model showed surprisingly good performance when a variant is associated with more than a half of study traits. As the number of traits with null effects increases, ASSET performed the best along with competitive specificity and sensitivity. With opposite directional effects, CPASSOC featured the first-rate power. However, caution is advised when using CPASSOC for studying genetically correlated traits with overlapping samples. We conclude with a discussion of unresolved issues and directions for future research.

Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes.

PubMed

Seligmann, Hervé; Warthi, Ganesh

2017-01-01

A new codon property, codon directional asymmetry in nucleotide content (CDA), reveals a biologically meaningful genetic code dimension: palindromic codons (first and last nucleotides identical, codon structure XZX) are symmetric (CDA = 0), codons with structures ZXX/XXZ are 5'/3' asymmetric (CDA = - 1/1; CDA = - 0.5/0.5 if Z and X are both purines or both pyrimidines, assigning negative/positive (-/+) signs is an arbitrary convention). Negative/positive CDAs associate with (a) Fujimoto's tetrahedral codon stereo-table; (b) tRNA synthetase class I/II (aminoacylate the 2'/3' hydroxyl group of the tRNA's last ribose, respectively); and (c) high/low antiparallel (not parallel) betasheet conformation parameters. Preliminary results suggest CDA-whole organism associations (body temperature, developmental stability, lifespan). Presumably, CDA impacts spatial kinetics of codon-anticodon interactions, affecting cotranslational protein folding. Some synonymous codons have opposite CDA sign (alanine, leucine, serine, and valine), putatively explaining how synonymous mutations sometimes affect protein function. Correlations between CDA and tRNA synthetase classes are weaker than between CDA and antiparallel betasheet conformation parameters. This effect is stronger for mitochondrial genetic codes, and potentially drives mitochondrial codon-amino acid reassignments. CDA reveals information ruling nucleotide-protein relations embedded in reversed (not reverse-complement) sequences (5'-ZXX-3'/5'-XXZ-3').

Evolution of floral display in Eichhornia paniculata (Pontederiaceae): direct and correlated responses to selection on flower size and number.

PubMed

Worley, A C; Barrett, S C

2000-10-01

Trade-offs between flower size and number seem likely to influence the evolution of floral display and are an important assumption of several theoretical models. We assessed floral trade-offs by imposing two generations of selection on flower size and number in a greenhouse population of bee-pollinated Eichhornia paniculata. We established a control line and two replicate selection lines of 100 plants each for large flowers (S+), small flowers (S-), and many flowers per inflorescence (N+). We compared realized heritabilities and genetic correlations with estimates based on restricted-maximum-likelihood (REML) analysis of pedigrees. Responses to selection confirmed REML heritability estimates (flower size, h2 = 0.48; daily flower number, h2 = 0.10; total flower number, h2 = 0.23). Differences in nectar, pollen, and ovule production between S+ and S- lines supported an overall divergence in investment per flower. Both realized and REML estimates of the genetic correlation between daily and total flower number were r = 1.0. However, correlated responses to selection were inconsistent in their support of a trade-off. In both S- lines, correlated increases in flower number indicated a genetic correlation of r = -0.6 between flower size and number. In contrast, correlated responses in N+ and S+ lines were not significant, although flower size decreased in one N+ line. In addition, REML estimates of genetic correlations between flower size and number were positive, and did not differ from zero when variation in leaf area and age at first flowering were taken into account. These results likely reflect the combined effects of variation in genes controlling the resources available for flowering and genes with opposing effects on flower size and number. Our results suggest that the short-term evolution of floral display is not necessarily constrained by trade-offs between flower size and number, as is often assumed.

Genetic evaluation of weekly body weight in Japanese quail using random regression models.

PubMed

Karami, K; Zerehdaran, S; Tahmoorespur, M; Barzanooni, B; Lotfi, E

2017-02-01

1. A total of 11 826 records from 2489 quails, hatched between 2012 and 2013, were used to estimate genetic parameters for BW (body weight) of Japanese quail using random regression models. Weekly BW was measured from hatch until 49 d of age. WOMBAT software (University of New England, Australia) was used for estimating genetic and phenotypic parameters. 2. Nineteen models were evaluated to identify the best orders of Legendre polynomials. A model with Legendre polynomial of order 3 for additive genetic effect, order 3 for permanent environmental effects and order 1 for maternal permanent environmental effects was chosen as the best model. 3. According to the best model, phenotypic and genetic variances were higher at the end of the rearing period. Although direct heritability for BW reduced from 0.18 at hatch to 0.12 at 7 d of age, it gradually increased to 0.42 at 49 d of age. It indicates that BW at older ages is more controlled by genetic components in Japanese quail. 4. Phenotypic and genetic correlations between adjacent periods except hatching weight were more closely correlated than remote periods. The present results suggested that BW at earlier ages, especially at hatch, are different traits compared to BW at older ages. Therefore, BW at earlier ages could not be used as a selection criterion for improving BW at slaughter age.

Genetic parameters and path analysis in cowpea genotypes grown in the Cerrado/Pantanal ecotone.

PubMed

Lopes, K V; Teodoro, P E; Silva, F A; Silva, M T; Fernandes, R L; Rodrigues, T C; Faria, T C; Corrêa, A M

2017-05-18

Estimating genetic parameters in plant breeding allows us to know the population potential for selecting and designing strategies that can maximize the achievement of superior genotypes. The objective of this study was to evaluate the genetic potential of a population of 20 cowpea genotypes by estimating genetic parameters and path analysis among the traits to guide the selection strategies. The trial was conducted in randomized block design with four replications. Its morphophysiological components, components of green grain production and dry grain yield were estimated from genetic use and correlations between the traits. Phenotypic correlations were deployed through path analysis into direct and indirect effects of morphophysiological traits and yield components on dry grain yield. There were significant differences (P < 0.01) between the genotypes for most the traits, indicating the presence of genetic variability in the population and the possibility of practicing selection. The population presents the potential for future genetic breeding studies and is highly promising for the selection of traits dry grain yield, the number of grains per pod, and hundred grains mass. A number of grains per green pod is the main determinant trait of dry grain yield that is also influenced by the cultivar cycle and that the selection for the dry grain yield can be made indirectly by selecting the green pod mass and green pod length.

Mendelian randomization analysis associates increased serum urate, due to genetic variation in uric acid transporters, with improved renal function.

PubMed

Hughes, Kim; Flynn, Tanya; de Zoysa, Janak; Dalbeth, Nicola; Merriman, Tony R

2014-02-01

Increased serum urate predicts chronic kidney disease independent of other risk factors. The use of xanthine oxidase inhibitors coincides with improved renal function. Whether this is due to reduced serum urate or reduced production of oxidants by xanthine oxidase or another physiological mechanism remains unresolved. Here we applied Mendelian randomization, a statistical genetics approach allowing disentangling of cause and effect in the presence of potential confounding, to determine whether lowering of serum urate by genetic modulation of renal excretion benefits renal function using data from 7979 patients of the Atherosclerosis Risk in Communities and Framingham Heart studies. Mendelian randomization by the two-stage least squares method was done with serum urate as the exposure, a uric acid transporter genetic risk score as instrumental variable, and estimated glomerular filtration rate and serum creatinine as the outcomes. Increased genetic risk score was associated with significantly improved renal function in men but not in women. Analysis of individual genetic variants showed the effect size associated with serum urate did not correlate with that associated with renal function in the Mendelian randomization model. This is consistent with the possibility that the physiological action of these genetic variants in raising serum urate correlates directly with improved renal function. Further studies are required to understand the mechanism of the potential renal function protection mediated by xanthine oxidase inhibitors.

Evolution of resistance and tolerance to herbivores: testing the trade-off hypothesis.

PubMed

Kariñho-Betancourt, Eunice; Núñez-Farfán, Juan

2015-01-01

Background. To cope with their natural enemies, plants rely on resistance and tolerance as defensive strategies. Evolution of these strategies among natural population can be constrained by the absence of genetic variation or because of the antagonistic genetic correlation (trade-off) between them. Also, since plant defenses are integrated by several traits, it has been suggested that trade-offs might occur between specific defense traits. Methodology/Principal Findings. We experimentally assessed (1) the presence of genetic variance in tolerance, total resistance, and leaf trichome density as specific defense trait, (2) the extent of natural selection acting on plant defenses, and (3) the relationship between total resistance and leaf trichome density with tolerance to herbivory in the annual herb Datura stramonium. Full-sib families of D. stramonium were either exposed to natural herbivores (control) or protected from them by a systemic insecticide. We detected genetic variance for leaf trichome density, and directional selection acting on this character. However, we did not detect a negative significant correlation between tolerance and total resistance, or between tolerance and leaf trichome density. We argue that low levels of leaf damage by herbivores precluded the detection of a negative genetic correlation between plant defense strategies. Conclusions/Significance. This study provides empirical evidence of the independent evolution of plant defense strategies, and a defensive role of leaf trichomes. The pattern of selection should favor individuals with high trichomes density. Also, because leaf trichome density reduces damage by herbivores and possess genetic variance in the studied population, its evolution is not constrained.

Evolution of resistance and tolerance to herbivores: testing the trade-off hypothesis

PubMed Central

Kariñho-Betancourt, Eunice

2015-01-01

Background. To cope with their natural enemies, plants rely on resistance and tolerance as defensive strategies. Evolution of these strategies among natural population can be constrained by the absence of genetic variation or because of the antagonistic genetic correlation (trade-off) between them. Also, since plant defenses are integrated by several traits, it has been suggested that trade-offs might occur between specific defense traits. Methodology/Principal Findings. We experimentally assessed (1) the presence of genetic variance in tolerance, total resistance, and leaf trichome density as specific defense trait, (2) the extent of natural selection acting on plant defenses, and (3) the relationship between total resistance and leaf trichome density with tolerance to herbivory in the annual herb Datura stramonium. Full-sib families of D. stramonium were either exposed to natural herbivores (control) or protected from them by a systemic insecticide. We detected genetic variance for leaf trichome density, and directional selection acting on this character. However, we did not detect a negative significant correlation between tolerance and total resistance, or between tolerance and leaf trichome density. We argue that low levels of leaf damage by herbivores precluded the detection of a negative genetic correlation between plant defense strategies. Conclusions/Significance. This study provides empirical evidence of the independent evolution of plant defense strategies, and a defensive role of leaf trichomes. The pattern of selection should favor individuals with high trichomes density. Also, because leaf trichome density reduces damage by herbivores and possess genetic variance in the studied population, its evolution is not constrained. PMID:25780756

Oral and Craniofacial Clinical Signs Associated to Genetic Conditions in Human Identification Part I: A Review

PubMed Central

Ayoub, Fouad; Aoun, Nicole; el Husseini, Hassan; Jassar, Houssam; Sayah, Fida; Salameh, Ziad

2015-01-01

Background: Forensic dentistry is one of the most reliable methods used in human identification when other technique as fingerprint, DNA, visual identification cannot be used. Genetic disorders have several manifestations that can target the intra-oral cavity, the cranio-facial area or any location in the human body. Materials and Methods: A literature search of the scientific database (Medline and Science Direct) for the years 1990 to 2014 was carried out to find out all the available papers that indicate oral, cranio-facial signs, genetic and human identification. Results: A table with 10 genetic conditions was described with oral and cranio-facial signs that can help forensic specialist in human identification. Conclusion: This review showed a correlation between genetics, facial and intra-oral signs that would help forensic ondontologist in the identification procedures. PMID:26028912

Genotype by environment interaction effects in genetic evaluation of preweaning gain for Line 1 Hereford cattle from Miles City, Montana.

PubMed

MacNeil, M D; Cardoso, F F; Hay, E

2017-09-01

It has long been recognized that genotype × environment interaction potentially influences genetic evaluation of beef cattle. However, this recognition has largely been ignored in systems for national cattle evaluation. The objective of this investigation was to determine if direct and maternal genetic effects on preweaning gain would be reranked depending on an environmental gradient as determined by year effects. Data used were from the 76-yr selection experiment with the Line 1 Hereford cattle raised at Miles City, MT. The data comprised recorded phenotypes from 7,566 animals and an additional 1,862 ancestral records included in the pedigree. The presence of genotype × environment interaction was examined using reaction norms wherein year effects on preweaning gain were hypothesized to linearly influence the EBV. Estimates of heritability for direct and maternal effects, given the average environment, were 10 ± 2 and 26 ± 3%, respectively. In an environment that is characterized by the 5th (95th) percentile of the distribution of year effects, the corresponding estimates of heritability were 18 ± 3 (22 ± 3%) and 30 ± 3% (30 ± 3%), respectively. Rank correlations of direct and maternal EBV appropriate to the 5th and 95th percentiles of the year effects were 0.67 and 0.92, respectively. In the average environment, the genetic trends were 255 ± 1 g/yr for direct effects and 557 ± 3 g/yr for maternal effects. In the fifth percentile environment, the corresponding estimates of genetic trend were 271 ± 1 and 540 ± 3 g/yr, respectively, and in the 95th percentile environment, they were 236 ± 1 and 578 ± 3 g/yr, respectively. Linear genetic trends in environmental sensitivity were observed for both the direct (-8.06 × 10 ± 0.49 × 10) and maternal (8.72 × 10 ± 0.43 × 10) effects. Therefore, changing systems of national cattle evaluation to more fully account for potential genotype × environment interaction would improve the assessment of breeding stock, particularly for direct effects. Estimates of environmental sensitivity parameters could also facilitate identification of genetic limitations to production.

Quantitative genetics of age at reproduction in wild swans: Support for antagonistic pleiotropy models of senescence

PubMed Central

Charmantier, Anne; Perrins, Christopher; McCleery, Robin H.; Sheldon, Ben C.

2006-01-01

Why do individuals stop reproducing after a certain age, and how is this age determined? The antagonistic pleiotropy theory for the evolution of senescence predicts that increased early-life performance should be accompanied by earlier (or faster) senescence. Hence, an individual that has started to breed early should also lose its reproductive capacities early. We investigate here the relationship between age at first reproduction (AFR) and age at last reproduction (ALR) in a free-ranging mute swan (Cygnus olor) population monitored for 36 years. Using multivariate analyses on the longitudinal data, we show that both traits are strongly selected in opposite directions. Analysis of the phenotypic covariance between these characters shows that individuals vary in their inherent quality, such that some individuals have earlier AFR and later ALR than expected. Quantitative genetic pedigree analyses show that both traits possess additive genetic variance but also that AFR and ALR are positively genetically correlated. Hence, although both traits display heritable variation and are under opposing directional selection, their evolution is constrained by a strong evolutionary tradeoff. These results are consistent with the theory that increased early-life performance comes with faster senescence because of genetic tradeoffs. PMID:16618935

Natural selection and inheritance of breeding time and clutch size in the collared flycatcher.

PubMed

Sheldon, B C; Kruuk, L E B; Merilä, J

2003-02-01

Many characteristics of organisms in free-living populations appear to be under directional selection, possess additive genetic variance, and yet show no evolutionary response to selection. Avian breeding time and clutch size are often-cited examples of such characters. We report analyses of inheritance of, and selection on, these traits in a long-term study of a wild population of the collared flycatcher Ficedula albicollis. We used mixed model analysis with REML estimation ("animal models") to make full use of the information in complex multigenerational pedigrees. Heritability of laying date, but not clutch size, was lower than that estimated previously using parent-offspring regressions, although for both traits there was evidence of substantial additive genetic variance (h2 = 0.19 and 0.29, respectively). Laying date and clutch size were negatively genetically correlated (rA = -0.41 +/- 0.09), implying that selection on one of the traits would cause a correlated response in the other, but there was little evidence to suggest that evolution of either trait would be constrained by correlations with other phenotypic characters. Analysis of selection on these traits in females revealed consistent strong directional fecundity selection for earlier breeding at the level of the phenotype (beta = -0.28 +/- 0.03), but little evidence for stabilising selection on breeding time. We found no evidence that clutch size was independently under selection. Analysis of fecundity selection on breeding values for laying date, estimated from an animal model, indicated that selection acts directly on additive genetic variance underlying breeding time (beta = -0.20 +/- 0.04), but not on clutch size (beta = 0.03 +/- 0.05). In contrast, selection on laying date via adult female survival fluctuated in sign between years, and was opposite in sign for selection on phenotypes (negative) and breeding values (positive). Our data thus suggest that any evolutionary response to selection on laying date is partially constrained by underlying life-history trade-offs, and illustrate the difficulties in using purely phenotypic measures and incomplete fitness estimates to assess evolution of life-history trade-offs. We discuss some of the difficulties associated with understanding the evolution of laying date and clutch size in natural populations.

Molecular insight into the association between cartilage regeneration and ear wound healing in genetic mouse models: targeting new genes in regeneration.

PubMed

Rai, Muhammad Farooq; Schmidt, Eric J; McAlinden, Audrey; Cheverud, James M; Sandell, Linda J

2013-11-06

Tissue regeneration is a complex trait with few genetic models available. Mouse strains LG/J and MRL are exceptional healers. Using recombinant inbred strains from a large (LG/J, healer) and small (SM/J, nonhealer) intercross, we have previously shown a positive genetic correlation between ear wound healing, knee cartilage regeneration, and protection from osteoarthritis. We hypothesize that a common set of genes operates in tissue healing and articular cartilage regeneration. Taking advantage of archived histological sections from recombinant inbred strains, we analyzed expression of candidate genes through branched-chain DNA technology directly from tissue lysates. We determined broad-sense heritability of candidates, Pearson correlation of candidates with healing phenotypes, and Ward minimum variance cluster analysis for strains. A bioinformatic assessment of allelic polymorphisms within and near candidate genes was also performed. The expression of several candidates was significantly heritable among strains. Although several genes correlated with both ear wound healing and cartilage healing at a marginal level, the expression of four genes representing DNA repair (Xrcc2, Pcna) and Wnt signaling (Axin2, Wnt16) pathways was significantly positively correlated with both phenotypes. Cluster analysis accurately classified healers and nonhealers for seven out of eight strains based on gene expression. Specific sequence differences between LG/J and SM/J were identified as potential causal polymorphisms. Our study suggests a common genetic basis between tissue healing and osteoarthritis susceptibility. Mapping genetic variations causing differences in diverse healing responses in multiple tissues may reveal generic healing processes in pursuit of new therapeutic targets designed to induce or enhance regeneration and, potentially, protection from osteoarthritis.

Female mating preferences and offspring survival: testing hypotheses on the genetic basis of mate choice in a wild lekking bird.

PubMed

Sardell, Rebecca J; Kempenaers, Bart; Duval, Emily H

2014-02-01

Indirect benefits of mate choice result from increased offspring genetic quality and may be important drivers of female behaviour. 'Good-genes-for-viability' models predict that females prefer mates of high additive genetic value, such that offspring survival should correlate with male attractiveness. Mate choice may also vary with genetic diversity (e.g. heterozygosity) or compatibility (e.g. relatedness), where the female's genotype influences choice. The relative importance of these nonexclusive hypotheses remains unclear. Leks offer an excellent opportunity to test their predictions, because lekking males provide no material benefits and choice is relatively unconstrained by social limitations. Using 12 years of data on lekking lance-tailed manakins, Chiroxiphia lanceolata, we tested whether offspring survival correlated with patterns of mate choice. Offspring recruitment weakly increased with father attractiveness (measured as reproductive success, RS), suggesting attractive males provide, if anything, only minor benefits via offspring viability. Both male RS and offspring survival until fledging increased with male heterozygosity. However, despite parent-offspring correlation in heterozygosity, offspring survival was unrelated to its own or maternal heterozygosity or to parental relatedness, suggesting survival was not enhanced by heterozygosity per se. Instead, offspring survival benefits may reflect inheritance of specific alleles or nongenetic effects. Although inbreeding depression in male RS should select for inbreeding avoidance, mates were not less related than expected under random mating. Although mate heterozygosity and relatedness were correlated, selection on mate choice for heterozygosity appeared stronger than that for relatedness and may be the primary mechanism maintaining genetic variation in this system despite directional sexual selection. © 2014 John Wiley & Sons Ltd.

Genetic parameter estimates for carcass traits and visual scores including or not genomic information.

PubMed

Gordo, D G M; Espigolan, R; Tonussi, R L; Júnior, G A F; Bresolin, T; Magalhães, A F Braga; Feitosa, F L; Baldi, F; Carvalheiro, R; Tonhati, H; de Oliveira, H N; Chardulo, L A L; de Albuquerque, L G

2016-05-01

The objective of this study was to determine whether visual scores used as selection criteria in Nellore breeding programs are effective indicators of carcass traits measured after slaughter. Additionally, this study evaluated the effect of different structures of the relationship matrix ( and ) on the estimation of genetic parameters and on the prediction accuracy of breeding values. There were 13,524 animals for visual scores of conformation (CS), finishing precocity (FP), and muscling (MS) and 1,753, 1,747, and 1,564 for LM area (LMA), backfat thickness (BF), and HCW, respectively. Of these, 1,566 animals were genotyped using a high-density panel containing 777,962 SNP. Six analyses were performed using multitrait animal models, each including the 3 visual scores and 1 carcass trait. For the visual scores, the model included direct additive genetic and residual random effects and the fixed effects of contemporary group (defined by year of birth, management group at yearling, and farm) and the linear effect of age of animal at yearling. The same model was used for the carcass traits, replacing the effect of age of animal at yearling with the linear effect of age of animal at slaughter. The variance and covariance components were estimated by the REML method in analyses using the numerator relationship matrix () or combining the genomic and the numerator relationship matrices (). The heritability estimates for the visual scores obtained with the 2 methods were similar and of moderate magnitude (0.23-0.34), indicating that these traits should response to direct selection. The heritabilities for LMA, BF, and HCW were 0.13, 0.07, and 0.17, respectively, using matrix and 0.29, 0.16, and 0.23, respectively, using matrix . The genetic correlations between the visual scores and carcass traits were positive, and higher correlations were generally obtained when matrix was used. Considering the difficulties and cost of measuring carcass traits postmortem, visual scores of CS, FP, and MS could be used as selection criteria to improve HCW, BF, and LMA. The use of genomic information permitted the detection of greater additive genetic variability for LMA and BF. For HCW, the high magnitude of the genetic correlations with visual scores was probably sufficient to recover genetic variability. The methods provided similar breeding value accuracies, especially for the visual scores.

Genetic Testing as a New Standard for Clinical Diagnosis of Color Vision Deficiencies.

PubMed

Davidoff, Candice; Neitz, Maureen; Neitz, Jay

2016-09-01

The genetics underlying inherited color vision deficiencies is well understood: causative mutations change the copy number or sequence of the long (L), middle (M), or short (S) wavelength sensitive cone opsin genes. This study evaluated the potential of opsin gene analyses for use in clinical diagnosis of color vision defects. We tested 1872 human subjects using direct sequencing of opsin genes and a novel genetic assay that characterizes single nucleotide polymorphisms (SNPs) using the MassArray system. Of the subjects, 1074 also were given standard psychophysical color vision tests for a direct comparison with current clinical methods. Protan and deutan deficiencies were classified correctly in all subjects identified by MassArray as having red-green defects. Estimates of defect severity based on SNPs that control photopigment spectral tuning correlated with estimates derived from Nagel anomaloscopy. The MassArray assay provides genetic information that can be useful in the diagnosis of inherited color vision deficiency including presence versus absence, type, and severity, and it provides information to patients about the underlying pathobiology of their disease. The MassArray assay provides a method that directly analyzes the molecular substrates of color vision that could be used in combination with, or as an alternative to current clinical diagnosis of color defects.

Multicollinearity in spatial genetics: separating the wheat from the chaff using commonality analyses.

PubMed

Prunier, J G; Colyn, M; Legendre, X; Nimon, K F; Flamand, M C

2015-01-01

Direct gradient analyses in spatial genetics provide unique opportunities to describe the inherent complexity of genetic variation in wildlife species and are the object of many methodological developments. However, multicollinearity among explanatory variables is a systemic issue in multivariate regression analyses and is likely to cause serious difficulties in properly interpreting results of direct gradient analyses, with the risk of erroneous conclusions, misdirected research and inefficient or counterproductive conservation measures. Using simulated data sets along with linear and logistic regressions on distance matrices, we illustrate how commonality analysis (CA), a detailed variance-partitioning procedure that was recently introduced in the field of ecology, can be used to deal with nonindependence among spatial predictors. By decomposing model fit indices into unique and common (or shared) variance components, CA allows identifying the location and magnitude of multicollinearity, revealing spurious correlations and thus thoroughly improving the interpretation of multivariate regressions. Despite a few inherent limitations, especially in the case of resistance model optimization, this review highlights the great potential of CA to account for complex multicollinearity patterns in spatial genetics and identifies future applications and lines of research. We strongly urge spatial geneticists to systematically investigate commonalities when performing direct gradient analyses. © 2014 John Wiley & Sons Ltd.

Genetic Testing as a New Standard for Clinical Diagnosis of Color Vision Deficiencies

PubMed Central

Davidoff, Candice; Neitz, Maureen; Neitz, Jay

2016-01-01

Purpose The genetics underlying inherited color vision deficiencies is well understood: causative mutations change the copy number or sequence of the long (L), middle (M), or short (S) wavelength sensitive cone opsin genes. This study evaluated the potential of opsin gene analyses for use in clinical diagnosis of color vision defects. Methods We tested 1872 human subjects using direct sequencing of opsin genes and a novel genetic assay that characterizes single nucleotide polymorphisms (SNPs) using the MassArray system. Of the subjects, 1074 also were given standard psychophysical color vision tests for a direct comparison with current clinical methods. Results Protan and deutan deficiencies were classified correctly in all subjects identified by MassArray as having red–green defects. Estimates of defect severity based on SNPs that control photopigment spectral tuning correlated with estimates derived from Nagel anomaloscopy. Conclusions The MassArray assay provides genetic information that can be useful in the diagnosis of inherited color vision deficiency including presence versus absence, type, and severity, and it provides information to patients about the underlying pathobiology of their disease. Translational Relevance The MassArray assay provides a method that directly analyzes the molecular substrates of color vision that could be used in combination with, or as an alternative to current clinical diagnosis of color defects. PMID:27622081

Local Genetic Correlation Gives Insights into the Shared Genetic Architecture of Complex Traits.

PubMed

Shi, Huwenbo; Mancuso, Nicholas; Spendlove, Sarah; Pasaniuc, Bogdan

2017-11-02

Although genetic correlations between complex traits provide valuable insights into epidemiological and etiological studies, a precise quantification of which genomic regions disproportionately contribute to the genome-wide correlation is currently lacking. Here, we introduce ρ-HESS, a technique to quantify the correlation between pairs of traits due to genetic variation at a small region in the genome. Our approach requires GWAS summary data only and makes no distributional assumption on the causal variant effect sizes while accounting for linkage disequilibrium (LD) and overlapping GWAS samples. We analyzed large-scale GWAS summary data across 36 quantitative traits, and identified 25 genomic regions that contribute significantly to the genetic correlation among these traits. Notably, we find 6 genomic regions that contribute to the genetic correlation of 10 pairs of traits that show negligible genome-wide correlation, further showcasing the power of local genetic correlation analyses. Finally, we report the distribution of local genetic correlations across the genome for 55 pairs of traits that show putative causal relationships. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Matching genetics with oceanography: directional gene flow in a Mediterranean fish species.

PubMed

Schunter, C; Carreras-Carbonell, J; Macpherson, E; Tintoré, J; Vidal-Vijande, E; Pascual, A; Guidetti, P; Pascual, M

2011-12-01

Genetic connectivity and geographic fragmentation are two opposing mechanisms determining the population structure of species. While the first homogenizes the genetic background across populations the second one allows their differentiation. Therefore, knowledge of processes affecting dispersal of marine organisms is crucial to understand their genetic distribution patterns and for the effective management of their populations. In this study, we use genetic analyses of eleven microsatellites in combination with oceanographic satellite and dispersal simulation data to determine distribution patterns for Serranus cabrilla, a ubiquitous demersal broadcast spawner, in the Mediterranean Sea. Pairwise population F(ST) values ranged between -0.003 and 0.135. Two genetically distinct clusters were identified, with a clear division located between the oceanographic discontinuities at the Ibiza Channel (IC) and the Almeria-Oran Front (AOF), revealing an admixed population in between. The Balearic Front (BF) also appeared to dictate population structure. Directional gene flow on the Spanish coast was observed as S. cabrilla dispersed from west to east over the AOF, from north to south on the IC and from south of the IC towards the Balearic Islands. Correlations between genetic and oceanographic data were highly significant. Seasonal changes in current patterns and the relationship between ocean circulation patterns and spawning season may also play an important role in population structure around oceanographic fronts. © 2011 Blackwell Publishing Ltd.

Genetic and environmental contributions to children's prosocial behavior: brief review and new evidence from a reanalysis of experimental twin data.

PubMed

Knafo-Noam, Ariel; Vertsberger, Dana; Israel, Salomon

2018-04-01

Children's prosocial behaviors show considerable variability. Here we discuss the genetic and environmental contributions to individual differences in children's prosocial behavior. Twin research systematically shows, at least from the age of 3 years, a genetic contribution to individual differences in prosocial behavior, both questionnaire-based and observed. This finding is demonstrated across a wide variety of cultures. We discuss the possibility that different prosocial behaviors have different genetic etiologies. A re-analysis of past twin data shows that sharing and comforting are affected by overlapping genetic factors at age 3.5 years. In contrast, the association between helping and comforting is attributed to environmental factors. The few molecular genetic studies of children's prosocial behavior are reviewed, and we point out genome-wide and polygenic methods as a key future direction. Finally, we discuss the interplay of genetic and environmental factors, focusing on both gene×environment interactions and gene-environment correlations. Copyright © 2017 Elsevier Ltd. All rights reserved.

Analyzing Population Genetics Using the Mitochondrial Control Region and Bioinformatics

ERIC Educational Resources Information Center

Sato, Takumi; Phillips, Bonnie; Latourelle, Sandra M.; Elwess, Nancy L.

2010-01-01

The 14-base pair hypervariable region in mitochondrial DNA (mtDNA) of Asian populations, specifically Japanese and Chinese students at Plattsburgh State University, was examined. Previous research on this 14-base pair region showed it to be susceptible to mutations and as a result indicated direct correlation with specific ethnic populations.…

Geographical structuring of Trypanosoma cruzi populations from Chilean Triatoma infestans triatomines and their genetic relationship with other Latino American counterparts

PubMed Central

Venegas, J; Rojas, T; DÍaz, F; Miranda, S; Jercic, M I; González, C; Coñoepán, W; Pichuantes, S; RodrÍguez, J; Gajardo, M; Sánchez, G

2011-01-01

In order to obtain more information about the population structure of Chilean Trypanosoma cruzi, and their genetic relationship with other Latino American counterparts, we performed the study of T. cruzi samples detected in the midgut content of Triatoma infestans insects from three endemic regions of Chile. The genetic characteristics of these samples were analysed using microsatellite markers and PCR conditions that allow the detection of predominant T. cruzi clones directly in triatomine midgut content. Population genetic analyses using the Fisher’s exact method, analysis of molecular variance (AMOVA) and the determination of FST showed that the northern T. cruzi population sample was genetically differentiated from the two southern population counterparts. Further analysis showed that the cause of this genetic differentiation was the asymmetrical distribution of TcIII T. cruzi predominant clones. Considering all triatomines from the three regions, the most frequent predominant lineages were TcIII (38%), followed by TcI (34%) and hybrid (8%). No TcII lineage was observed along the predominant T. cruzi clones. The best phylogenetic reconstruction using the shared allelic genetic distance was concordant with the population genetic analysis and tree topology previously described studying foreign samples. The correlation studies showed that the lineage TcIII from the III region was genetically differentiated from the other two, and this differentiation was correlated with geographical distance including Chilean and mainly Brazilian samples. It will be interesting to investigate whether this geographical structure may be related with different clinical manifestation of Chagas disease. PMID:22325822

Genetic dissection of adaptive form and function in rapidly speciating cichlid fishes.

PubMed

Henning, Frederico; Machado-Schiaffino, Gonzalo; Baumgarten, Lukas; Meyer, Axel

2017-05-01

Genes of major phenotypic effects and strong genetic correlations can facilitate adaptation, direct selective responses, and potentially lead to phenotypic convergence. However, the preponderance of this type of genetic architecture in repeatedly evolved adaptations remains unknown. Using hybrids between Haplochromis chilotes (thick-lipped) and Pundamilia nyererei (thin-lipped) we investigated the genetics underlying hypertrophied lips and elongated heads, traits that evolved repeatedly in cichlids. At least 25 loci of small-to-moderate and mainly additive effects were detected. Phenotypic variation in lip and head morphology was largely independent. Although several QTL overlapped for lip and head morphology traits, they were often of opposite effects. The distribution of effect signs suggests strong selection on lips. The fitness implications of several detected loci were demonstrated using a laboratory assay testing for the association between genotype and variation in foraging performance. The persistence of low fitness alleles in head morphology appears to be maintained through antagonistic pleiotropy/close linkage with positive-effect lip morphology alleles. Rather than being based on few major loci with strong positive genetic correlations, our results indicate that the evolution of the Lake Victoria thick-lipped ecomorph is the result of selection on numerous loci distributed throughout the genome. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Genetic relationship between growth and reproductive traits in Nellore cattle.

PubMed

Santana, M L; Eler, J P; Ferraz, J B S; Mattos, E C

2012-04-01

The objective of this study was to evaluate the genetic relationship between postweaning weight gain (PWG), heifer pregnancy (HP), scrotal circumference (SC) at 18 months of age, stayability at 6 years of age (STAY) and finishing visual score at 18 months of age (PREC), and to determine the potential of these traits as selection criteria for the genetic improvement of growth and reproduction in Nellore cattle. The HP was defined as the observation that a heifer conceived and remained pregnant, which was assessed by rectal palpation at 60 days. The STAY was defined as whether or not a cow calved every year up to the age of 6 years, given that she was provided the opportunity to breed. The Bayesian linear-threshold analysis via the Gibbs sampler was used to estimate the variance and covariance components applying a multitrait model. Posterior mean estimates of direct heritability were 0.15 ± 0.00, 0.42 ± 0.02, 0.49 ± 0.01, 0.11 ± 0.01 and 0.19 ± 0.00 for PWG, HP, SC, STAY and PREC, respectively. The genetic correlations between traits ranged from 0.17 to 0.62. The traits studied generally have potential for use as selection criteria in genetic breeding programs. The genetic correlations between all traits show that selection for one of these traits does not imply the loss of the others.

The potential for using canopy spectral reflectance as an indirect selection tool for yield improvement in winter wheat

NASA Astrophysics Data System (ADS)

Prasad, Bishwajit

Scope and methods of study. Complementing breeding effort by deploying alternative methods of identifying higher yielding genotypes in a wheat breeding program is important for obtaining greater genetic gains. Spectral reflectance indices (SRI) are one of the many indirect selection tools that have been reported to be associated with different physiological process of wheat. A total of five experiments (a set of 25 released cultivars from winter wheat breeding programs of the U.S. Great Plains and four populations of randomly derived recombinant inbred lines having 25 entries in each population) were conducted in two years under Great Plains winter wheat rainfed environments at Oklahoma State University research farms. Grain yield was measured in each experiment and biomass was measured in three experiments at three growth stages (booting, heading, and grainfilling). Canopy spectral reflectance was measured at three growth stages and eleven SRI were calculated. Correlation (phenotypic and genetic) between grain yield and SRI, biomass and SRI, heritability (broad sense) of the SRI and yield, response to selection and correlated response, relative selection efficiency of the SRI, and efficiency in selecting the higher yielding genotypes by the SRI were assessed. Findings and conclusions. The genetic correlation coefficients revealed that the water based near infrared indices (WI and NWI) were strongly associated with grain yield and biomass production. The regression analysis detected a linear relationship between the water based indices with grain yield and biomass. The two newly developed indices (NWI-3 and NWI-4) gave higher broad sense heritability than grain yield, higher direct response to selection compared to grain yield, correlated response equal to or higher than direct response for grain yield, relative selection efficiency greater than one, and higher efficiency in selecting higher yielding genotypes. Based on the overall genetic analysis required to establish any trait as an efficient indirect selection tool, the water based SRI (especially NWI-3 and NWI-4) have the potential to complement the classical breeding effort for selecting genotypes with higher yield potential in a winter wheat breeding program.

Genotype by region and season interactions on weaning weight in United States Angus cattle.

PubMed

Williams, J L; Lukaszewicz, M; Bertrand, J K; Misztal, I

2012-10-01

The objective of this study was to determine if weaning weight performance is genetically consistent across different environments in the United States. The American Angus Association provided weight and pedigree data. Weaning weights observed in the Southeast (SoE) and Northwest (NW) were the focus of this study, as these regions are perceived as opposite extremes in climate. The 2 most represented calving seasons in each region were fall and winter in the SoE and winter and spring in the NW. The original data were edited to remove weaning weight records outside of 3 SD from the respective region-season mean, contemporary groups smaller than 20, and single-sire contemporary groups. The final dataset included 884,465 weaning weight records with 64,907 from fall-born calves in the SoE, 74,820 from winter-born calves in the SoE, 346,724 from winter-born calves in the NW and 398,014 from spring-born calves in the NW. Weaning weights of calves born in different region-season classes adjusted to 205 d of age were considered different but genetically correlated traits in a multivariate analysis. The sole fixed effect was weaning contemporary group and random effects included direct, maternal, maternal permanent environment, and a residual. Direct heritability estimates differed little across environments: 0.31 and 0.35 for weight in fall- and winter-born calves in the SoE, and 0.29 and 0.32 for winter- and spring-born calves in NW. Maternal heritability estimates ranged from 0.12 in the NW to 0.16 the SoE. Genetic correlations spanned from 0.69 to 0.93 among direct effects and from 0.65 to 0.95 among maternal effects. All heritability estimates had small (0.01 to 0.04) SE. The most distinct environments appeared to be winter in SoE and spring in NW (correlations of 0.69 and 0.65 for the direct and maternal effects). Different choices of sires for different environments might be justified to achieve the growth performance expected.

Genetic analyses of partial egg production in Japanese quail using multi-trait random regression models.

PubMed

Karami, K; Zerehdaran, S; Barzanooni, B; Lotfi, E

2017-12-01

1. The aim of the present study was to estimate genetic parameters for average egg weight (EW) and egg number (EN) at different ages in Japanese quail using multi-trait random regression (MTRR) models. 2. A total of 8534 records from 900 quail, hatched between 2014 and 2015, were used in the study. Average weekly egg weights and egg numbers were measured from second until sixth week of egg production. 3. Nine random regression models were compared to identify the best order of the Legendre polynomials (LP). The most optimal model was identified by the Bayesian Information Criterion. A model with second order of LP for fixed effects, second order of LP for additive genetic effects and third order of LP for permanent environmental effects (MTRR23) was found to be the best. 4. According to the MTRR23 model, direct heritability for EW increased from 0.26 in the second week to 0.53 in the sixth week of egg production, whereas the ratio of permanent environment to phenotypic variance decreased from 0.48 to 0.1. Direct heritability for EN was low, whereas the ratio of permanent environment to phenotypic variance decreased from 0.57 to 0.15 during the production period. 5. For each trait, estimated genetic correlations among weeks of egg production were high (from 0.85 to 0.98). Genetic correlations between EW and EN were low and negative for the first two weeks, but they were low and positive for the rest of the egg production period. 6. In conclusion, random regression models can be used effectively for analysing egg production traits in Japanese quail. Response to selection for increased egg weight would be higher at older ages because of its higher heritability and such a breeding program would have no negative genetic impact on egg production.

Genetic association between body energy measured throughout lactation and fertility in dairy cattle.

PubMed

Banos, G; Coffey, M P

2010-02-01

The objective of this study was to quantify the genetic association of body energy assessed throughout lactation with a cow's fertility. Nine direct and indirect body energy traits were defined at different stages of lactation. Four were daily records of energy balance, energy content, cumulative effective energy (CEE) and body condition score (BCS) calculated between lactation days 4 and 311. The other five traits included duration of negative energy balance (DNEB), rate of recovery during DNEB (RNEB), sum of negative energy balance (SNEB), nadir of energy content (NEC) and number of days from calving to NEC. Of these traits, energy balance, DNEB, RNEB and SNEB were primarily based on individual cow feed intake and milk yield, and considered direct measures of body energy. The other traits were calculated from body lipid and protein changes, predicted from BCS and live weight profiles, and were considered indirect measures of body energy. Fertility was defined by number of days between calving and commencement of luteal activity (DLA), first observed oestrus (DH) and conception (DC), and number of services per conception. A total of 957 cows in their first four lactations were considered in the study. Genetic models fitted cubic splines to define longitudinal traits (energy balance, energy content, CEE and BCS) and calculate heritability and genetic correlation with fertility. Daily heritability estimate ranges were 0.10 to 0.34, 0.35 to 0.61, 0.32 to 0.53 and 0.24 to 0.56 for energy balance, energy content, CEE and BCS, respectively, and, in most cases, tended to increase towards the middle of lactation and remain relatively stable thereafter. Of the other body energy traits, heritability of NEC (0.44) was the most notable. Statistically significant (P < 0.05) genetic correlations of DH with daily energy balance, energy content, CEE and BCS ranged from -0.16 to -0.28, -0.35 to -0.48, -0.16 to -0.26 and -0.37 to -0.44, respectively. For DC, respective estimates were -0.28 to -0.64, -0.37 to -0.60, -0.30 to -0.48 and -0.29 to -0.53. For DLA, they ranged from -0.47 to -0.56 with energy content and from -0.50 to -0.74 with BCS. Of special interest was the genetic correlation of NEC with DH (-0.54) and DC (-0.48). Results suggest that indirect measures of body energy have the strongest genetic association with cow fertility. NEC and early lactation (circa day 50) BCS and energy content are the most useful traits for selection in terms of the correlated improvement in a cow's capacity to resume her reproductive activity post partum.

Molecular genetic analysis of the F11 gene in 14 Turkish patients with factor XI deficiency: identification of novel and recurrent mutations and their inheritance within families.

PubMed

Colakoglu, Seyma; Bayhan, Turan; Tavil, Betül; Keskin, Ebru Yılmaz; Cakir, Volkan; Gümrük, Fatma; Çetin, Mualla; Aytaç, Selin; Berber, Ergul

2018-01-01

Factor XI (FXI) deficiency is an autosomal bleeding disease associated with genetic defects in the F11 gene which cause decreased FXI levels or impaired FXI function. An increasing number of mutations has been reported in the FXI mutation database, most of which affect the serine protease domain of the protein. FXI is a heterogeneous disorder associated with a variable bleeding tendency and a variety of causative F11 gene mutations. The molecular basis of FXI deficiency in 14 patients from ten unrelated families in Turkey was analysed to establish genotype-phenotype correlations and inheritance of the mutations in the patients' families. Fourteen index cases with a diagnosis of FXI deficiency and family members of these patients were enrolled into the study. The patients' F11 genes were amplified by polymerase chain reaction and subjected to direct DNA sequencing analysis. The findings were analysed statistically using bivariate correlations, Pearson's correlation coefficient and the nonparametric Mann-Whitney test. Direct DNA sequencing analysis of the F11 genes revealed that all of the 14 patients had a F11 gene mutation. Eight different mutations were identified in the apple 1, apple 2 or serine protease domains, except one which was a splice site mutation. Six of the mutations were recurrent. Two of the mutations were novel missense mutations, p.Val522Gly and p.Cys581Arg, within the catalytic domain. The p.Trp519Stop mutation was observed in two families whereas all the other mutations were specific to a single family. Identification of mutations confirmed the genetic heterogeneity of FXI deficiency. Most of the patients with mutations did not have any bleeding complications, whereas some had severe bleeding symptoms. Genetic screening for F11 gene mutations is important to decrease the mortality and morbidity rate associated with FXI deficiency, which can be life-threatening if bleeding occurs in tissues with high fibrinolytic activity.

Elimination of a genetic correlation between the sexes via artificial correlational selection.

PubMed

Delph, Lynda F; Steven, Janet C; Anderson, Ingrid A; Herlihy, Christopher R; Brodie, Edmund D

2011-10-01

Genetic correlations between the sexes can constrain the evolution of sexual dimorphism and be difficult to alter, because traits common to both sexes share the same genetic underpinnings. We tested whether artificial correlational selection favoring specific combinations of male and female traits within families could change the strength of a very high between-sex genetic correlation for flower size in the dioecious plant Silene latifolia. This novel selection dramatically reduced the correlation in two of three selection lines in fewer than five generations. Subsequent selection only on females in a line characterized by a lower between-sex genetic correlation led to a significantly lower correlated response in males, confirming the potential evolutionary impact of the reduced correlation. Although between-sex genetic correlations can potentially constrain the evolution of sexual dimorphism, our findings reveal that these constraints come not from a simple conflict between an inflexible genetic architecture and a pattern of selection working in opposition to it, but rather a complex relationship between a changeable correlation and a form of selection that promotes it. In other words, the form of selection on males and females that leads to sexual dimorphism may also promote the genetic phenomenon that limits sexual dimorphism. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Shared genetic variance between obesity and white matter integrity in Mexican Americans.

PubMed

Spieker, Elena A; Kochunov, Peter; Rowland, Laura M; Sprooten, Emma; Winkler, Anderson M; Olvera, Rene L; Almasy, Laura; Duggirala, Ravi; Fox, Peter T; Blangero, John; Glahn, David C; Curran, Joanne E

2015-01-01

Obesity is a chronic metabolic disorder that may also lead to reduced white matter integrity, potentially due to shared genetic risk factors. Genetic correlation analyses were conducted in a large cohort of Mexican American families in San Antonio (N = 761, 58% females, ages 18-81 years; 41.3 ± 14.5) from the Genetics of Brain Structure and Function Study. Shared genetic variance was calculated between measures of adiposity [(body mass index (BMI; kg/m(2)) and waist circumference (WC; in)] and whole-brain and regional measurements of cerebral white matter integrity (fractional anisotropy). Whole-brain average and regional fractional anisotropy values for 10 major white matter tracts were calculated from high angular resolution diffusion tensor imaging data (DTI; 1.7 × 1.7 × 3 mm; 55 directions). Additive genetic factors explained intersubject variance in BMI (heritability, h (2) = 0.58), WC (h (2) = 0.57), and FA (h (2) = 0.49). FA shared significant portions of genetic variance with BMI in the genu (ρG = -0.25), body (ρG = -0.30), and splenium (ρG = -0.26) of the corpus callosum, internal capsule (ρG = -0.29), and thalamic radiation (ρG = -0.31) (all p's = 0.043). The strongest evidence of shared variance was between BMI/WC and FA in the superior fronto-occipital fasciculus (ρG = -0.39, p = 0.020; ρG = -0.39, p = 0.030), which highlights region-specific variation in neural correlates of obesity. This may suggest that increase in obesity and reduced white matter integrity share common genetic risk factors.

Genetic and environmental influences on non-specific neck pain in early adolescence: A classical twin study

PubMed Central

Ståhl, Minna K; El-Metwally, Ashraf A; Mikkelsson, Marja K; Salminen, Jouko J; Pulkkinen, Lea R; Rose, Richard J; Kaprio, Jaakko A

2012-01-01

Background Prevalence of neck pain has increased among adolescents. The origins of adult chronic neck pain may lie in late childhood, but for early prevention, more information is needed about its aetiology. We investigated the relative roles of genetic and environmental factors in early adolescent neck pain with a classic twin study. Methods Frequency of neck pain was assessed with a validated pain questionnaire in a population-based sample of nearly 1800 pairs of 11–12-year-old Finnish twins. Twin pair similarity for neck pain was quantified by polychoric correlations, and variance components were estimated with biometric structural equation modelling. Results Prevalence of neck pain reported at least once monthly was 38% and at least once weekly 16%, with no significant differences between gender or zygosity. A greater polychoric correlation in liability to neck pain was found in monozygotic (0.67) than for dizygotic pairs (0.38), suggesting strong genetic influences. Model-fitting indicated that 68% (95% CI 62 to 74) of the variation in liability to neck pain could be attributed to genetic effects, with the remainder attributed to unshared environmental effects. No evidence for sex-specific genetic effects or for sex differences in the magnitude of genetic effects was found. Conclusions Genetic and unique environmental factors seem to play the most important roles in liability to neck pain in early adolescence. Future research should be directed to identifying pathways for genetic influences on neck pain and in exploring effectiveness of interventions that target already identified environmental risk factors. PMID:23139100

Genetic response to selection for weaning weight or yearling weight or yearling weight and muscle score in Hereford cattle: efficiency of gain, growth, and carcass characteristics.

PubMed

Koch, R M; Cundiff, L V; Gregory, K E; Van Vleck, L D

2004-03-01

An experiment involving crosses among selection and control lines was conducted to partition direct and maternal additive genetic response to 20 yr of selection for 1) weaning weight, 2) yearling weight, and 3) index of yearling weight and muscle score. Selection response was evaluated for efficiency of gain, growth from birth through market weight, and carcass characteristics. Heritability and genetic correlations among traits were estimated using animal model analyses. Over a time-constant interval, selected lines were heavier, gained more weight, consumed more ME, and had more gain/ME than the control. Over a weight-constant interval, selected lines required fewer days, consumed less ME, had more efficient gains, and required less energy for maintenance than control. Direct and maternal responses were estimated from reciprocal crosses among unselected sires and dams of control and selection lines. Most of the genetic response to selection in all three lines was associated with direct genetic effects, and the highest proportion was from postweaning gain. Indirect responses of carcass characteristics to selection over the 20 yr were increased weight of carcasses that had more lean meat, produced with less feed per unit of gain. At a constant carcass weight, selected lines had 1.32 to 1.85% more retail product and 1.62 to 2.24% less fat trim and 10/100 to 25/100 degrees less marbling than control. At a constant age, heritability of direct and maternal effects and correlations between them were as follows: market weight, 0.36, 0.14, and 0.10; carcass weight, 0.26, 0.15, and 0.03; longissimus muscle area, 0.33, 0.00, and 0.00; marbling, 0.36, 0.07, and -0.35; fat thickness, 0.41, 0.05, and -0.18; percentage of kidney, pelvic, and heart fat, 0.12, 0.08, and -0.76; percentage of retail product, 0.46, 0.05, and -0.29; retail product weight, 0.44, 0.08, -0.14; and muscle score, 0.37, 0.14, and -0.54. Selection criteria in all lines improved efficiency of postweaning gain and increased the amount of salable lean meat on an age- or weight-constant basis, but carcasses had slightly lower marbling scores.

The genetic correlation between height and IQ: shared genes or assortative mating?

PubMed

Keller, Matthew C; Garver-Apgar, Christine E; Wright, Margaret J; Martin, Nicholas G; Corley, Robin P; Stallings, Michael C; Hewitt, John K; Zietsch, Brendan P

2013-04-01

Traits that are attractive to the opposite sex are often positively correlated when scaled such that scores increase with attractiveness, and this correlation typically has a genetic component. Such traits can be genetically correlated due to genes that affect both traits ("pleiotropy") and/or because assortative mating causes statistical correlations to develop between selected alleles across the traits ("gametic phase disequilibrium"). In this study, we modeled the covariation between monozygotic and dizygotic twins, their siblings, and their parents (total N = 7,905) to elucidate the nature of the correlation between two potentially sexually selected traits in humans: height and IQ. Unlike previous designs used to investigate the nature of the height-IQ correlation, the present design accounts for the effects of assortative mating and provides much less biased estimates of additive genetic, non-additive genetic, and shared environmental influences. Both traits were highly heritable, although there was greater evidence for non-additive genetic effects in males. After accounting for assortative mating, the correlation between height and IQ was found to be almost entirely genetic in nature. Model fits indicate that both pleiotropy and assortative mating contribute significantly and about equally to this genetic correlation.

Selection of Drought Tolerant Maize Hybrids Using Path Coefficient Analysis and Selection Index.

PubMed

Dao, Abdalla; Sanou, Jacob; V S Traore, Edgar; Gracen, Vernon; Danquah, Eric Y

2017-01-01

In drought-prone environments, direct selection for yield is not adequate because of the variable environment and genotype x environment interaction. Therefore, the use of secondary traits in addition to yield has been suggested. The relative usefulness of secondary traits as indirect selection criteria for maize grain yield is determined by the magnitudes of their genetic variance, heritability and genetic correlation with the grain yield. Forty eight testcross hybrids derived from lines with different genetic background and geographical origins plus 7 checks were evaluated in both well-watered and water-stressed conditions over two years for grain yield and secondary traits to determine the most appropriate secondary traits and select drought tolerant hybrids. Study found that broad-sense heritability of grain yield and Ear Per Plant (EPP) increased under drought stress. Ear aspect (EASP) and ear height (EHT) had larger correlation coefficients and direct effect on grain yield but in opposite direction, negative and positive respectively. Traits like, EPP, Tassel Size (TS) and Plant Recovery (PR) contributed to increase yield via EASP by a large negative indirect effect. Under drought stress, EHT had positive and high direct effect and negative indirect effect via plant height on grain yield indicating that the ratio between ear and plant heights (R-EPH) was associated to grain yield. Path coefficient analysis showed that traits EPP, TS, PR, EASP, R-EPH were important secondary traits in the present experiment. These traits were used in a selection index to classify hybrids according to their performance under drought. The selection procedure included also a Relative Decrease in Yield (RDY) index. Some secondary traits reported as significant selection criteria for selection under drought stress were not finally established in the present study. This is because the relationship between grain and secondary traits can be affected by various factors including germplasm, environment and applied statistical analysis. Therefore, different traits and selection procedure should be applied in the selection process of drought tolerant genotypes for diverse genetic materials and growing conditions.

Genetic structure of the world's polar bear populations.

PubMed

Paetkau, D; Amstrup, S C; Born, E W; Calvert, W; Derocher, A E; Garner, G W; Messier, F; Stirling, I; Taylor, M K; Wiig, O; Strobeck, C

1999-10-01

We studied genetic structure in polar bear (Ursus maritimus) populations by typing a sample of 473 individuals spanning the species distribution at 16 highly variable microsatellite loci. No genetic discontinuities were found that would be consistent with evolutionarily significant periods of isolation between groups. Direct comparison of movement data and genetic data from the Canadian Arctic revealed a highly significant correlation. Genetic data generally supported existing population (management unit) designations, although there were two cases where genetic data failed to differentiate between pairs of populations previously resolved by movement data. A sharp contrast was found between the minimal genetic structure observed among populations surrounding the polar basin and the presence of several marked genetic discontinuities in the Canadian Arctic. The discontinuities in the Canadian Arctic caused the appearance of four genetic clusters of polar bear populations. These clusters vary in total estimated population size from 100 to over 10 000, and the smallest may merit a relatively conservative management strategy in consideration of its apparent isolation. We suggest that the observed pattern of genetic discontinuities has developed in response to differences in the seasonal distribution and pattern of sea ice habitat and the effects of these differences on the distribution and abundance of seals.

Genetic structure of the world's polar bear populations

USGS Publications Warehouse

Paetkau, David; Amstrup, Steven C.; Born, E.W.; Calvert, W.; Derocher, A.E.; Garner, G.W.; Messier, F.; Stirling, I.; Taylor, M.K.; Wiig, O.; Strobeck, C.

1999-01-01

We studied genetic structure in polar bear (Ursus maritimus) populations by typing a sample of 473 individuals spanning the species distribution at 16 highly variable microsatellite loci. No genetic discontinuities were found that would be consistent with evolutionarily significant periods of isolation between groups. Direct comparison of movement data and genetic data from the Canadian Arctic revealed a highly significant correlation. Genetic data generally supported existing population (management unit) designations, although there were two cases where genetic data failed to differentiate between pairs of populations previously resolved by movement data. A sharp contrast was found between the minimal genetic structure observed among populations surrounding the polar basin and the presence of several marked genetic discontinuities in the Canadian Arctic. The discontinuities in the Canadian Arctic caused the appearance of four genetic clusters of polar bear populations. These clusters vary in total estimated population size from 100 to over 10 000, and the smallest may merit a relatively conservative management strategy in consideration of its apparent isolation. We suggest that the observed pattern of genetic discontinuities has developed in response to differences in the seasonal distribution and pattern of sea ice habitat and the effects of these differences on the distribution and abundance of seals.

Site-to-site genetic correlations and their implications on breeding zone size and optimum number of progeny test sites for Coastal Douglas-fir.

Treesearch

G.R. Johnson

1997-01-01

Type B genetic correlations were used to examine the relation among geographic differences between sites and their site-to-site genetic (Type B) correlations. Examination of six local breeding zones in Oregon indicated that breeding zones were, for the most part, not too large because few environmental variables were correlated with Type B genetic correlations. The...

HDL cholesterol and bone mineral density: Is there a genetic link?

PubMed Central

Ackert-Bicknell, Cheryl L.

2011-01-01

Overwhelming evidence has linked cardiovascular disease and osteoporosis, but the shared root cause of these two diseases of the elderly remains unknown. Low levels of high-density lipoprotein cholesterol (HDL) and bone mineral density (BMD) are risk factors for cardiovascular disease and osteoporosis respectively. A number of correlation studies have attempted to determine if there is a relationship between serum HDL and BMD but these studies are confounded by a number of variables including age, diet, genetic background, gender and hormonal status. Collectively, these data suggest that there is a relationship between these two phenotypes, but that the nature of this relationship is context specific. Studies in mice plainly demonstrate that genetic loci for BMD and HDL co-map and transgenic mouse models have been used to show that a single gene can affect both serum HDL and BMD. Work completed to date has demonstrated that HDL can interact directly with both osteoblasts and osteoclasts, but no direct evidence links bone back to the regulation of HDL levels. Understanding the genetic relationship between BMD and HDL has huge implications for understanding the clinical relationship between CVD and osteoporosis and for the development of safe treatment options for both diseases. PMID:21810493

Genetic parameters and genetic trends in the Chinese × European Tiameslan composite pig line. II. Genetic trends

PubMed Central

Zhang, Siqing; Bidanel, Jean-Pierre; Burlot, Thierry; Legault, Christian; Naveau, Jean

2000-01-01

The Tiameslan line was created between 1983 and 1985 by mating Meishan × Jiaxing crossbred Chinese boars with sows from the Laconie composite male line. The Tiameslan line has been selected since then on an index combining average backfat thickness (ABT) and days from 20 to 100 kg (DT). Direct and correlated responses to 11 years of selection were estimated using BLUP methodology applied to a multiple trait animal model. A total of 11 traits were considered, i.e.: ABT, DT, body weight at 4 (W4w), 8 (W8w) and 22 (W22w) weeks of age, teat number (TEAT), number of good teats (GTEAT), total number of piglets born (TNB), born alive (NBA) and weaned (NW) per litter, and birth to weaning survival rate (SURV). Performance data from a total of 4 881 males and 4 799 females from 1 341 litters were analysed. The models included both direct and maternal effects for ABT, W4w and W8w. Male and female performances were considered as different traits for W22w, DT and ABT. Genetic parameters estimated in another paper (Zhang et al., Genet. Sel. Evol. 32 (2000) 41-56) were used to perform the analyses. Favourable phenotypic (ΔP) and direct genetic trends (ΔGd) were obtained for post-weaning growth traits and ABT. Trends for maternal effects were limited. Phenotypic and genetic trends were larger in females than in males for ABT (e.g. ΔGd = -0.48 vs. -0.38 mm/year), were larger in males for W22w (ΔGd = 0.90 vs. 0.58 kg/year) and were similar in both sexes for DT (ΔGd = -0.54 vs. -0.55 day/year). Phenotypic and genetic trends were slightly favourable for W4w, W8w, TEAT and GTEAT and close to zero for reproductive traits. PMID:14736407

Rapid changes in genetic architecture of behavioural syndromes following colonization of a novel environment.

PubMed

Karlsson Green, K; Eroukhmanoff, F; Harris, S; Pettersson, L B; Svensson, E I

2016-01-01

Behavioural syndromes, that is correlated behaviours, may be a result from adaptive correlational selection, but in a new environmental setting, the trait correlation might act as an evolutionary constraint. However, knowledge about the quantitative genetic basis of behavioural syndromes, and the stability and evolvability of genetic correlations under different ecological conditions, is limited. We investigated the quantitative genetic basis of correlated behaviours in the freshwater isopod Asellus aquaticus. In some Swedish lakes, A. aquaticus has recently colonized a novel habitat and diverged into two ecotypes, presumably due to habitat-specific selection from predation. Using a common garden approach and animal model analyses, we estimated quantitative genetic parameters for behavioural traits and compared the genetic architecture between the ecotypes. We report that the genetic covariance structure of the behavioural traits has been altered in the novel ecotype, demonstrating divergence in behavioural correlations. Thus, our study confirms that genetic correlations behind behaviours can change rapidly in response to novel selective environments. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Adoptive Parent Hostility and Children’s Peer Behavior Problems: Examining the Role of Genetically-Informed Child Attributes on Adoptive Parent Behavior

PubMed Central

Elam, Kit K.; Harold, Gordon T.; Neiderhiser, Jenae M.; Reiss, David; Shaw, Daniel S.; Natsuaki, Misaki N.; Gaysina, Darya; Barrett, Doug; Leve, Leslie D.

2014-01-01

Socially disruptive behavior during peer interactions in early childhood is detrimental to children’s social, emotional, and academic development. Few studies have investigated the developmental underpinnings of children’s socially disruptive behavior using genetically-sensitive research designs that allow examination of parent-on-child and child-on-parent (evocative genotype-environment correlation) effects when examining family process and child outcome associations. Using an adoption-at-birth design, the present study controlled for passive genotype-environment correlation and directly examined evocative genotype-environment correlation (rGE) while examining the associations between family processes and children’s peer behavior. Specifically, the present study examined the evocative effect of genetic influences underlying toddler low social motivation on mother-child and father-child hostility, and the subsequent influence of parent hostility on disruptive peer behavior during the preschool period. Participants were 316 linked triads of birth mothers, adoptive parents, and adopted children. Path analysis showed that birth mother low behavioral motivation predicted toddler low social motivation, which predicted both adoptive mother-child and father-child hostility, suggesting the presence of an evocative genotype-environment association. In addition, both mother-child and father-child hostility predicted children’s later disruptive peer behavior. Results highlight the importance of considering genetically-influenced child attributes on parental hostility that in turn link to later child social behavior. Implications for intervention programs focusing on early family processes and the precursors of disrupted child social development are discussed. PMID:24364829

Genetic analysis of calf health in Charolais beef cattle.

PubMed

Vinet, A; Leclerc, H; Marquis, F; Phocas, F

2018-04-14

The objective of this study was to investigate the factors that influence calf health and survival in Charolais cattle. Data from 2,740 calves, originating from 16 French farms and observed from birth until 30 d of age, were analyzed using models that took account of direct genetic, maternal genetic, and common environmental effects. Both direct and maternal genetic parameters were estimated for birth weight (BW), calving ease (CE), neonatal vitality (NV), survival at 30 d (Surv), and umbilical infection and diarrhea at different ages (0 to 5 d: Umb1 and Diar1; 6 to 20 d: Umb2 and Diar2; and 21 to 30 d: Umb3 and Diar3). The heritability values for direct and maternal genetic effects were, 0.026 (SE = 0.027) and 0.096 (SE = 0.042) for Surv, 0.280 (SE = 0.063) and 0.063 (SE = 0.038) for BW, 0.129 (SE = 0.041) and 0 for CE, 0.073 (SE = 0.035) and 0 for NV, 0.071 (SE = 0.038) and 0.017 (SE = 0.026) for Umb1, 0 and 0.082 (SE = 0.029) for Umb2, 0 and 0.044 (SE = 0.030) for Diar1, 0.016 (SE = 0.022) and 0.012 (SE = 0.026) for Diar2, and 0.016 (SE = 0.028) and 0 for Diar3, respectively. Significant genetic variability in beef cattle was thus revealed for five calf health traits: NV, Surv, Diar1, Umb1, and Umb2. In addition, for three traits (Surv, Diar1, and Umb2), maternal genetic effects clearly contributed more to health performance than direct genetic effects. Estimates of genetic correlation between traits varied markedly (from 0 to 1 in absolute values) depending on the traits in question, the age for a given trait, and the type (direct or maternal) of the genetic effects considered. These results suggest that not all health traits in Charolais cattle can be improved simultaneously, and breeders will therefore have to prioritize certain traits of interest in their breeding objectives. Overall, our results demonstrate the potential utility of collecting and integrating data on calf diseases, NV and survival in future beef cattle breeding programs. To ensure appropriate biological and genetic evaluations of calf health performance, it is important to accurately describe the phenotypes for diarrhea and umbilical infections (in terms of age ranges) and account for maternal genetic and common environmental effects that explain calf health performance traits. Further investigation and improved data collection are now necessary to maximize the efficiency of breeding schemes designed to simultaneously improve production and health traits.

An analysis of the metabolic theory of the origin of the genetic code

NASA Technical Reports Server (NTRS)

Amirnovin, R.; Bada, J. L. (Principal Investigator)

1997-01-01

A computer program was used to test Wong's coevolution theory of the genetic code. The codon correlations between the codons of biosynthetically related amino acids in the universal genetic code and in randomly generated genetic codes were compared. It was determined that many codon correlations are also present within random genetic codes and that among the random codes there are always several which have many more correlations than that found in the universal code. Although the number of correlations depends on the choice of biosynthetically related amino acids, the probability of choosing a random genetic code with the same or greater number of codon correlations as the universal genetic code was found to vary from 0.1% to 34% (with respect to a fairly complete listing of related amino acids). Thus, Wong's theory that the genetic code arose by coevolution with the biosynthetic pathways of amino acids, based on codon correlations between biosynthetically related amino acids, is statistical in nature.

Understanding the relative contributions of direct environmental effects and passive genotype-environment correlations in the association between familial risk factors and child disruptive behavior disorders.

PubMed

Bornovalova, M A; Cummings, J R; Hunt, E; Blazei, R; Malone, S; Iacono, W G

2014-03-01

Previous work reports an association between familial risk factors stemming from parental characteristics and offspring disruptive behavior disorders (DBDs). This association may reflect (a) the direct effects of familial environment and (b) a passive gene-environment correlation (r(GE)), wherein the parents provide both the genes and the environment. The current study examined the contributions of direct environmental influences and passive r(GE) by comparing the effects of familial risk factors on child DBDs in genetically related (biological) and non-related (adoptive) families. Participants were 402 adoptive and 204 biological families. Familial environment was defined as maternal and paternal maladaptive parenting and antisociality, marital conflict and divorce; offspring DBDs included attention deficit hyperactivity disorder (ADHD), conduct disorder (CD) and oppositional defiant disorder (ODD). Mixed-level regressions estimated the main effects of familial environment, adoption status and the familial environment by adoption status interaction term, which tested for the presence of passive r(GE). There was a main effect of maternal and paternal maladaptive parenting and marital discord on child DBDs, indicating a direct environmental effect. There was no direct environmental effect of maternal or paternal antisociality, but maternal and paternal antisociality had stronger associations with child DBDs in biological families than adoptive families, indicating the presence of a passive r(GE). Many familial risk factors affected children equally across genetically related and non-related families, providing evidence for direct environmental effects. The relationship of parental antisociality and offspring DBDs was best explained by a passive r(GE), where a general vulnerability toward externalizing psychopathology is passed down by the parents to the children.

Biological causal links on physiological and evolutionary time scales.

PubMed

Karmon, Amit; Pilpel, Yitzhak

2016-04-26

Correlation does not imply causation. If two variables, say A and B, are correlated, it could be because A causes B, or that B causes A, or because a third factor affects them both. We suggest that in many cases in biology, the causal link might be bi-directional: A causes B through a fast-acting physiological process, while B causes A through a slowly accumulating evolutionary process. Furthermore, many trained biologists tend to consistently focus at first on the fast-acting direction, and overlook the slower process in the opposite direction. We analyse several examples from modern biology that demonstrate this bias (codon usage optimality and gene expression, gene duplication and genetic dispensability, stem cell division and cancer risk, and the microbiome and host metabolism) and also discuss an example from linguistics. These examples demonstrate mutual effects between the fast physiological processes and the slow evolutionary ones. We believe that building awareness of inference biases among biologists who tend to prefer one causal direction over another could improve scientific reasoning.

Combining Population Structure with Historic Abitoic Processes to Better Understand Species and Community Range Shifts in Response to Climate Change

NASA Astrophysics Data System (ADS)

Graham, N. M.

2015-12-01

The evolution and speciation of plants is directly tied to the environment as the constrained stages of dispersal creates strong genetic differentiation among populations. This can result in differing genetic patterns between nuclear and chloroplast loci, where genes are inherited differently and dispersed via separate vectors. By developing distribution models based on genetic patterns found within a species, it is possible to begin understanding the influence of historic geomorphic and/or climatic processes on population evolution. If genetic patterns of the current range correlate with specific patterns of climate variability within the Pleistocene, it is possible that future shifts in species distribution in response to climate change can be more accurately modelled due to the historic signature that is found within inherited genes. Preliminary genetic analyses of Linanthus dichotomus, an annual herb distributed across California, suggests that the current taxonomic treatment does not accurately depict how this species is evolving. Genetic patterns of chloroplast genes suggest that populations are more correlated with biogeography than what the current nomenclature states. Additionally, chloroplast and nuclear genes show discrepancies in the dispersal across the landscape, suggesting pollinator driven gene flow overcoming seed dispersal boundaries. By comparing discrepancies between pollinator and seed induced gene flow we may be able to gain insight into historical pollinator communities within the Pleistocene. This information can then be applied to projected climate models to more accurately understand how species and/or communities will respond to a changing environment.

Quantitative genetics of ultrasonic advertisement signalling in the lesser waxmoth Achroia grisella (Lepidoptera: pyralidae).

PubMed

Collins, R D; Jang, Y; Reinhold, K; Greenfield, M D

1999-12-01

Males of the lesser waxmoth Achroia grisella (Lepidoptera: Pyralidae) produce ultrasonic advertisement signals attractive to females within several metres. Previous studies showed that females prefer male signals that are louder, delivered at a faster rate, and have a greater asynchrony between pulses produced by the right and left wings. These three signal characters vary considerably within populations but are repeatable within individuals. Breeding experiments employing half-sib designs were conducted on both collectively and individually reared moths to determine genetic variance within and covariance among these signal characters. Heritabilities of all signal characters were significant among collectively reared moths. Heritabilities for signal rate and right-left wing asynchrony interval were not significant, however, among individually reared moths, suggesting the presence of significant nonadditive genetic variance or common environmental variation. Development time was also significantly heritable, but only under individual rearing. The only significant genetic correlation was between signal rate and length of the right-left wing asynchrony and this was negative. Our findings on heritability of signal characters are consistent with a coevolutionary sexual selection mechanism, but the absence of signal x development genetic correlation fails to support specifically a good-genes mechanism. The variation in heritability among conditions suggests that environmental variance may be high, and may render selection on signal characters by female choice ineffective. Thus, additive genetic variance for these characters may be maintained in the presence of directional female choice.

Reparametrization-based estimation of genetic parameters in multi-trait animal model using Integrated Nested Laplace Approximation.

PubMed

Mathew, Boby; Holand, Anna Marie; Koistinen, Petri; Léon, Jens; Sillanpää, Mikko J

2016-02-01

A novel reparametrization-based INLA approach as a fast alternative to MCMC for the Bayesian estimation of genetic parameters in multivariate animal model is presented. Multi-trait genetic parameter estimation is a relevant topic in animal and plant breeding programs because multi-trait analysis can take into account the genetic correlation between different traits and that significantly improves the accuracy of the genetic parameter estimates. Generally, multi-trait analysis is computationally demanding and requires initial estimates of genetic and residual correlations among the traits, while those are difficult to obtain. In this study, we illustrate how to reparametrize covariance matrices of a multivariate animal model/animal models using modified Cholesky decompositions. This reparametrization-based approach is used in the Integrated Nested Laplace Approximation (INLA) methodology to estimate genetic parameters of multivariate animal model. Immediate benefits are: (1) to avoid difficulties of finding good starting values for analysis which can be a problem, for example in Restricted Maximum Likelihood (REML); (2) Bayesian estimation of (co)variance components using INLA is faster to execute than using Markov Chain Monte Carlo (MCMC) especially when realized relationship matrices are dense. The slight drawback is that priors for covariance matrices are assigned for elements of the Cholesky factor but not directly to the covariance matrix elements as in MCMC. Additionally, we illustrate the concordance of the INLA results with the traditional methods like MCMC and REML approaches. We also present results obtained from simulated data sets with replicates and field data in rice.

Genetic effects influencing risk for major depressive disorder in China and Europe.

PubMed

Bigdeli, T B; Ripke, S; Peterson, R E; Trzaskowski, M; Bacanu, S-A; Abdellaoui, A; Andlauer, T F M; Beekman, A T F; Berger, K; Blackwood, D H R; Boomsma, D I; Breen, G; Buttenschøn, H N; Byrne, E M; Cichon, S; Clarke, T-K; Couvy-Duchesne, B; Craddock, N; de Geus, E J C; Degenhardt, F; Dunn, E C; Edwards, A C; Fanous, A H; Forstner, A J; Frank, J; Gill, M; Gordon, S D; Grabe, H J; Hamilton, S P; Hardiman, O; Hayward, C; Heath, A C; Henders, A K; Herms, S; Hickie, I B; Hoffmann, P; Homuth, G; Hottenga, J-J; Ising, M; Jansen, R; Kloiber, S; Knowles, J A; Lang, M; Li, Q S; Lucae, S; MacIntyre, D J; Madden, P A F; Martin, N G; McGrath, P J; McGuffin, P; McIntosh, A M; Medland, S E; Mehta, D; Middeldorp, C M; Milaneschi, Y; Montgomery, G W; Mors, O; Müller-Myhsok, B; Nauck, M; Nyholt, D R; Nöthen, M M; Owen, M J; Penninx, B W J H; Pergadia, M L; Perlis, R H; Peyrot, W J; Porteous, D J; Potash, J B; Rice, J P; Rietschel, M; Riley, B P; Rivera, M; Schoevers, R; Schulze, T G; Shi, J; Shyn, S I; Smit, J H; Smoller, J W; Streit, F; Strohmaier, J; Teumer, A; Treutlein, J; Van der Auwera, S; van Grootheest, G; van Hemert, A M; Völzke, H; Webb, B T; Weissman, M M; Wellmann, J; Willemsen, G; Witt, S H; Levinson, D F; Lewis, C M; Wray, N R; Flint, J; Sullivan, P F; Kendler, K S

2017-03-28

Major depressive disorder (MDD) is a common, complex psychiatric disorder and a leading cause of disability worldwide. Despite twin studies indicating its modest heritability (~30-40%), extensive heterogeneity and a complex genetic architecture have complicated efforts to detect associated genetic risk variants. We combined single-nucleotide polymorphism (SNP) summary statistics from the CONVERGE and PGC studies of MDD, representing 10 502 Chinese (5282 cases and 5220 controls) and 18 663 European (9447 cases and 9215 controls) subjects. We determined the fraction of SNPs displaying consistent directions of effect, assessed the significance of polygenic risk scores and estimated the genetic correlation of MDD across ancestries. Subsequent trans-ancestry meta-analyses combined SNP-level evidence of association. Sign tests and polygenic score profiling weakly support an overlap of SNP effects between East Asian and European populations. We estimated the trans-ancestry genetic correlation of lifetime MDD as 0.33; female-only and recurrent MDD yielded estimates of 0.40 and 0.41, respectively. Common variants downstream of GPHN achieved genome-wide significance by Bayesian trans-ancestry meta-analysis (rs9323497; log 10 Bayes Factor=8.08) but failed to replicate in an independent European sample (P=0.911). Gene-set enrichment analyses indicate enrichment of genes involved in neuronal development and axonal trafficking. We successfully demonstrate a partially shared polygenic basis of MDD in East Asian and European populations. Taken together, these findings support a complex etiology for MDD and possible population differences in predisposing genetic factors, with important implications for future genetic studies.

Genetic effects influencing risk for major depressive disorder in China and Europe

PubMed Central

Bigdeli, T B; Ripke, S; Peterson, R E; Trzaskowski, M; Bacanu, S-A; Abdellaoui, A; Andlauer, T F M; Beekman, A T F; Berger, K; Blackwood, D H R; Boomsma, D I; Breen, G; Buttenschøn, H N; Byrne, E M; Cichon, S; Clarke, T-K; Couvy-Duchesne, B; Craddock, N; de Geus, E J C; Degenhardt, F; Dunn, E C; Edwards, A C; Fanous, A H; Forstner, A J; Frank, J; Gill, M; Gordon, S D; Grabe, H J; Hamilton, S P; Hardiman, O; Hayward, C; Heath, A C; Henders, A K; Herms, S; Hickie, I B; Hoffmann, P; Homuth, G; Hottenga, J-J; Ising, M; Jansen, R; Kloiber, S; Knowles, J A; Lang, M; Li, Q S; Lucae, S; MacIntyre, D J; Madden, P A F; Martin, N G; McGrath, P J; McGuffin, P; McIntosh, A M; Medland, S E; Mehta, D; Middeldorp, C M; Milaneschi, Y; Montgomery, G W; Mors, O; Müller-Myhsok, B; Nauck, M; Nyholt, D R; Nöthen, M M; Owen, M J; Penninx, B W J H; Pergadia, M L; Perlis, R H; Peyrot, W J; Porteous, D J; Potash, J B; Rice, J P; Rietschel, M; Riley, B P; Rivera, M; Schoevers, R; Schulze, T G; Shi, J; Shyn, S I; Smit, J H; Smoller, J W; Streit, F; Strohmaier, J; Teumer, A; Treutlein, J; Van der Auwera, S; van Grootheest, G; van Hemert, A M; Völzke, H; Webb, B T; Weissman, M M; Wellmann, J; Willemsen, G; Witt, S H; Levinson, D F; Lewis, C M; Wray, N R; Flint, J; Sullivan, P F; Kendler, K S

2017-01-01

Major depressive disorder (MDD) is a common, complex psychiatric disorder and a leading cause of disability worldwide. Despite twin studies indicating its modest heritability (~30–40%), extensive heterogeneity and a complex genetic architecture have complicated efforts to detect associated genetic risk variants. We combined single-nucleotide polymorphism (SNP) summary statistics from the CONVERGE and PGC studies of MDD, representing 10 502 Chinese (5282 cases and 5220 controls) and 18 663 European (9447 cases and 9215 controls) subjects. We determined the fraction of SNPs displaying consistent directions of effect, assessed the significance of polygenic risk scores and estimated the genetic correlation of MDD across ancestries. Subsequent trans-ancestry meta-analyses combined SNP-level evidence of association. Sign tests and polygenic score profiling weakly support an overlap of SNP effects between East Asian and European populations. We estimated the trans-ancestry genetic correlation of lifetime MDD as 0.33; female-only and recurrent MDD yielded estimates of 0.40 and 0.41, respectively. Common variants downstream of GPHN achieved genome-wide significance by Bayesian trans-ancestry meta-analysis (rs9323497; log10 Bayes Factor=8.08) but failed to replicate in an independent European sample (P=0.911). Gene-set enrichment analyses indicate enrichment of genes involved in neuronal development and axonal trafficking. We successfully demonstrate a partially shared polygenic basis of MDD in East Asian and European populations. Taken together, these findings support a complex etiology for MDD and possible population differences in predisposing genetic factors, with important implications for future genetic studies. PMID:28350396

Genetic influences on adolescent sexual behavior: Why genes matter for environmentally oriented researchers.

PubMed

Harden, K Paige

2014-03-01

There are dramatic individual differences among adolescents in how and when they become sexually active adults, and early sexual activity is frequently cited as a cause of concern for scientists, policymakers, and the general public. Understanding the causes and developmental impact of adolescent sexual activity can be furthered by considering genes as a source of individual differences. Quantitative behavioral genetics (i.e., twin and family studies) and candidate gene association studies now provide clear evidence for the genetic underpinnings of individual differences in adolescent sexual behavior and related phenotypes. Genetic influences on sexual behavior may operate through a variety of direct and indirect mechanisms, including pubertal development, testosterone levels, and dopaminergic systems. Genetic differences may be systematically associated with exposure to environments that are commonly treated as causes of sexual behavior (gene-environment correlation). Possible gene-environment correlations pose a serious challenge for interpreting the results of much behavioral research. Multivariate, genetically informed research on adolescent sexual behavior compares twins and family members as a form of quasi experiment: How do twins who differ in their sexual experiences differ in their later development? The small but growing body of genetically informed research has already challenged dominant assumptions regarding the etiology and sequelae of adolescent sexual behavior, with some studies indicating possible positive effects of teenage sexuality. Studies of Gene × Environment interaction may further elucidate the mechanisms by which genes and environments combine to shape the development of sexual behavior and its psychosocial consequences. Overall, the existence of heritable variation in adolescent sexual behavior has profound implications for environmentally oriented theory and research.

Meta-analysis suggests choosy females get sexy sons more than "good genes".

PubMed

Prokop, Zofia M; Michalczyk, Łukasz; Drobniak, Szymon M; Herdegen, Magdalena; Radwan, Jacek

2012-09-01

Female preferences for specific male phenotypes have been documented across a wide range of animal taxa, including numerous species where males contribute only gametes to offspring production. Yet, selective pressures maintaining such preferences are among the major unknowns of evolutionary biology. Theoretical studies suggest that preferences can evolve if they confer genetic benefits in terms of increased attractiveness of sons ("Fisherian" models) or overall fitness of offspring ("good genes" models). These two types of models predict, respectively, that male attractiveness is heritable and genetically correlated with fitness. In this meta-analysis, we draw general conclusions from over two decades worth of empirical studies testing these predictions (90 studies on 55 species in total). We found evidence for heritability of male attractiveness. However, attractiveness showed no association with traits directly associated with fitness (life-history traits). Interestingly, it did show a positive correlation with physiological traits, which include immunocompetence and condition. In conclusion, our results support "Fisherian" models of preference evolution, while providing equivocal evidence for "good genes." We pinpoint research directions that should stimulate progress in our understanding of the evolution of female choice. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Characterization of Gladiolus Germplasm Using Morphological, Physiological, and Molecular Markers.

PubMed

Singh, Niraj; Pal, Ashish K; Roy, R K; Tewari, S K; Tamta, Sushma; Rana, T S

2018-04-01

Estimation of variability and genetic relationships among breeding materials is one of the important strategies in crop improvement programs. Morphological (plant height, spike length, a number of florets/spike), physiological (chlorophyll content, chlorophyll fluorescence, and rapid light curve parameters) and Directed amplification of minisatellite DNA (DAMD) markers were used to investigate the relationships among 50 Gladiolus cultivars. Cluster analysis based on morphological data, physiological characteristics, molecular markers, and cumulative data discriminated all cultivars into seven, five, seven, and six clusters in the unweighted pair-group method using arithmetic mean (UPGMA) dendrogram, respectively. The results of the principal coordinate analysis (PCoA) also supported UPGMA clustering. Variations among the Gladiolus cultivars at phenotypic level could be due to the changes in physiology, environmental conditions, and genetic variability. DAMD analysis using 10 primers produced 120 polymorphic bands with 80% polymorphism showing polymorphic information content (PIC = 0.28), Marker index (MI = 3.37), Nei's gene diversity (h = 0.267), and Shannon's information index (I = 0.407). Plant height showed a positive significant correlation with Spike length and Number of florets/spike (r = 0.729, p < 0.001 and r = 0.448, p = 0.001 respectively). Whereas, Spike length showed positive significant correlation with Number of florets/spike (r = 0.688, p < 0.001) and Chlorophyll content showed positive significant correlation with Electron transport rate (r = 0.863, p < 0.001). Based on significant morphological variations, high physiological performance, high genetic variability, and genetic distances between cultivars, we have been able to identify diverse cultivars of Gladiolus that could be the potential source as breeding material for further genetic improvement in this ornamental crop.

Genetic Evaluation of Dual-Purpose Buffaloes (Bubalus bubalis) in Colombia Using Principal Component Analysis

PubMed Central

Agudelo-Gómez, Divier; Pineda-Sierra, Sebastian; Cerón-Muñoz, Mario Fernando

2015-01-01

Genealogy and productive information of 48621 dual-purpose buffaloes born in Colombia between years 1996 and 2014 was used. The following traits were assessed using one-trait models: milk yield at 270 days (MY270), age at first calving (AFC), weaning weight (WW), and weights at the following ages: first year (W12), 18 months (W18), and 2 years (W24). Direct additive genetic and residual random effects were included in all the traits. Maternal permanent environmental and maternal additive genetic effects were included for WW and W12. The fixed effects were: contemporary group (for all traits), sex (for WW, W12, W18, and W24), parity (for WW, W12, and MY270). Age was included as covariate for WW, W12, W18 and W24. Principal component analysis (PCA) was conducted using the genetic values of 133 breeding males whose breeding-value reliability was higher than 50% for all the traits in order to define the number of principal components (PC) which would explain most of the variation. The highest heritabilities were for W18 and MY270, and the lowest for AFC; with 0.53, 0.23, and 0.17, respectively. The first three PCs represented 66% of the total variance. Correlation of the first PC with meat production traits was higher than 0.73, and it was -0.38 with AFC. Correlations of the second PC with maternal genetic component traits for WW and W12 were above 0.75. The third PC had 0.84 correlation with MY270. PCA is an alternative approach for analyzing traits in dual-purpose buffaloes and reduces the dimension of the traits. PMID:26230093

Shared genetic variance between obesity and white matter integrity in Mexican Americans

PubMed Central

Spieker, Elena A.; Kochunov, Peter; Rowland, Laura M.; Sprooten, Emma; Winkler, Anderson M.; Olvera, Rene L.; Almasy, Laura; Duggirala, Ravi; Fox, Peter T.; Blangero, John; Glahn, David C.; Curran, Joanne E.

2015-01-01

Obesity is a chronic metabolic disorder that may also lead to reduced white matter integrity, potentially due to shared genetic risk factors. Genetic correlation analyses were conducted in a large cohort of Mexican American families in San Antonio (N = 761, 58% females, ages 18–81 years; 41.3 ± 14.5) from the Genetics of Brain Structure and Function Study. Shared genetic variance was calculated between measures of adiposity [(body mass index (BMI; kg/m2) and waist circumference (WC; in)] and whole-brain and regional measurements of cerebral white matter integrity (fractional anisotropy). Whole-brain average and regional fractional anisotropy values for 10 major white matter tracts were calculated from high angular resolution diffusion tensor imaging data (DTI; 1.7 × 1.7 × 3 mm; 55 directions). Additive genetic factors explained intersubject variance in BMI (heritability, h2 = 0.58), WC (h2 = 0.57), and FA (h2 = 0.49). FA shared significant portions of genetic variance with BMI in the genu (ρG = −0.25), body (ρG = −0.30), and splenium (ρG = −0.26) of the corpus callosum, internal capsule (ρG = −0.29), and thalamic radiation (ρG = −0.31) (all p's = 0.043). The strongest evidence of shared variance was between BMI/WC and FA in the superior fronto-occipital fasciculus (ρG = −0.39, p = 0.020; ρG = −0.39, p = 0.030), which highlights region-specific variation in neural correlates of obesity. This may suggest that increase in obesity and reduced white matter integrity share common genetic risk factors. PMID:25763009

Variance and covariance estimates for weaning weight of Senepol cattle.

PubMed

Wright, D W; Johnson, Z B; Brown, C J; Wildeus, S

1991-10-01

Variance and covariance components were estimated for weaning weight from Senepol field data for use in the reduced animal model for a maternally influenced trait. The 4,634 weaning records were used to evaluate 113 sires and 1,406 dams on the island of St. Croix. Estimates of direct additive genetic variance (sigma 2A), maternal additive genetic variance (sigma 2M), covariance between direct and maternal additive genetic effects (sigma AM), permanent maternal environmental variance (sigma 2PE), and residual variance (sigma 2 epsilon) were calculated by equating variances estimated from a sire-dam model and a sire-maternal grandsire model, with and without the inverse of the numerator relationship matrix (A-1), to their expectations. Estimates were sigma 2A, 139.05 and 138.14 kg2; sigma 2M, 307.04 and 288.90 kg2; sigma AM, -117.57 and -103.76 kg2; sigma 2PE, -258.35 and -243.40 kg2; and sigma 2 epsilon, 588.18 and 577.72 kg2 with and without A-1, respectively. Heritability estimates for direct additive (h2A) were .211 and .210 with and without A-1, respectively. Heritability estimates for maternal additive (h2M) were .47 and .44 with and without A-1, respectively. Correlations between direct and maternal (IAM) effects were -.57 and -.52 with and without A-1, respectively.

Heterozygosity-fitness correlations in a wild mammal population: accounting for parental and environmental effects.

PubMed

Annavi, Geetha; Newman, Christopher; Buesching, Christina D; Macdonald, David W; Burke, Terry; Dugdale, Hannah L

2014-06-01

HFCs (heterozygosity-fitness correlations) measure the direct relationship between an individual's genetic diversity and fitness. The effects of parental heterozygosity and the environment on HFCs are currently under-researched. We investigated these in a high-density U.K. population of European badgers (Meles meles), using a multimodel capture-mark-recapture framework and 35 microsatellite loci. We detected interannual variation in first-year, but not adult, survival probability. Adult females had higher annual survival probabilities than adult males. Cubs with more heterozygous fathers had higher first-year survival, but only in wetter summers; there was no relationship with individual or maternal heterozygosity. Moist soil conditions enhance badger food supply (earthworms), improving survival. In dryer years, higher indiscriminate mortality rates appear to mask differential heterozygosity-related survival effects. This paternal interaction was significant in the most supported model; however, the model-averaged estimate had a relative importance of 0.50 and overlapped zero slightly. First-year survival probabilities were not correlated with the inbreeding coefficient (f); however, small sample sizes limited the power to detect inbreeding depression. Correlations between individual heterozygosity and inbreeding were weak, in line with published meta-analyses showing that HFCs tend to be weak. We found support for general rather than local heterozygosity effects on first-year survival probability, and g2 indicated that our markers had power to detect inbreeding. We emphasize the importance of assessing how environmental stressors can influence the magnitude and direction of HFCs and of considering how parental genetic diversity can affect fitness-related traits, which could play an important role in the evolution of mate choice.

Direct-to-consumer genetic testing: an assessment of genetic counselors' knowledge and beliefs

PubMed Central

Hock, Kathryn T.; Christensen, Kurt D.; Yashar, Beverly M.; Roberts, J. Scott; Gollust, Sarah E.; Uhlmann, Wendy R.

2013-01-01

Purpose Direct-to-consumer genetic testing is a new means of obtaining genetic testing outside of a traditional clinical setting. This study assesses genetic counselors’ experience, knowledge, and beliefs regarding direct-to-consumer genetic testing for tests that would currently be offered in genetics clinics. Methods Members of the National Society of Genetic Counselors completed a web-administered survey in February 2008. Results Response rate was 36%; the final data analysis included 312 respondents. Eighty-three percent of respondents had two or fewer inquiries about direct-to-consumer genetic testing, and 14% had received requests for test interpretation or discussion. Respondents believed that genetic counselors have a professional obligation to be knowledgeable about direct-to-consumer genetic testing (55%) and interpret results (48%). Fifty-one percent of respondents thought genetic testing should be limited to a clinical setting; 56% agreed direct-to-consumer genetic testing is acceptable if genetic counseling is provided. More than 70% of respondents would definitely or possibly consider direct-to-consumer testing for patients who (1) have concerns about genetic discrimination, (2) want anonymous testing, or (3) have geographic constraints. Conclusions Results indicate that genetic counselors have limited patient experiences with direct-to-consumer genetic testing and are cautiously considering if and under what circumstances this approach should be used PMID:21233722

Variation and evolution of male sex combs in Drosophila: nature of selection response and theories of genetic variation for sexual traits.

PubMed

Ahuja, Abha; Singh, Rama S

2008-05-01

We investigated the genetic architecture of variation in male sex comb bristle number, a rapidly evolving secondary sexual character of Drosophila. Twenty-four generations of divergent artificial selection for sex comb bristle number in a heterogeneous population of Drosophila melanogaster resulted in a significant response that was more pronounced in the direction of low bristle numbers. We observed a strong positive correlated response to selection in the corresponding female transverse bristle row. The correlated response in male abdominal and sternopleural bristle numbers, on the other hand, did not follow the same pattern as sex comb bristle number differences between selection lines. Relaxation-of-selection experiments along with mate choice and fecundity assays using the selection lines developed demonstrated the action of stabilizing selection on sex comb bristle number. Our results show (1) substantial genetic variation underlying sex comb bristle number variation; (2) a weak relationship between the sex comb and developmentally related, non-sex bristle systems; and (3) that sexual selection may be a driving force in sex comb evolution, indicating the potential of sex combs to diversify rapidly during population differentiation and speciation. We discuss the implications of these results for theories of genetic variation in display and nondisplay male sex traits.

The danger within: the role of genetic, behavioural and ecological factors in population persistence of colour polymorphic species.

PubMed

Bolton, Peri E; Rollins, Lee A; Griffith, Simon C

2015-06-01

Polymorphic species have been the focus of important work in evolutionary biology. It has been suggested that colour polymorphic species have specific evolutionary and population dynamics that enable them to persist through environmental changes better than less variable species. We suggest that recent empirical and theoretical work indicates that polymorphic species may be more vulnerable to extinction than previously thought. This vulnerability arises because these species often have a number of correlated sexual, behavioural, life history and ecological traits, which can have a simple genetic underpinning. When exacerbated by environmental change, these alternate strategies can lead to conflict between morphs at the genomic and population levels, which can directly or indirectly affect population and evolutionary dynamics. In this perspective, we identify a number of ways in which the nature of the correlated traits, their underpinning genetic architecture, and the inevitable interactions between colour morphs can result in a reduction in population fitness. The principles illustrated here apply to all kinds of discrete polymorphism (e.g. behavioural syndromes), but we focus primarily on colour polymorphism because they are well studied. We urge further empirical investigation of the genetic architecture and interactions in polymorphic species to elucidate the impact on population fitness. © 2015 John Wiley & Sons Ltd.

Heterozygosity-based assortative mating in blue tits (Cyanistes caeruleus): implications for the evolution of mate choice

PubMed Central

García-Navas, Vicente; Ortego, Joaquín; Sanz, Juan José

2009-01-01

The general hypothesis of mate choice based on non-additive genetic traits suggests that individuals would gain important benefits by choosing genetically dissimilar mates (compatible mate hypothesis) and/or more heterozygous mates (heterozygous mate hypothesis). In this study, we test these hypotheses in a socially monogamous bird, the blue tit (Cyanistes caeruleus). We found no evidence for a relatedness-based mating pattern, but heterozygosity was positively correlated between social mates, suggesting that blue tits may base their mating preferences on partner's heterozygosity. We found evidence that the observed heterozygosity-based assortative mating could be maintained by both direct and indirect benefits. Heterozygosity reflected individual quality in both sexes: egg production and quality increased with female heterozygosity while more heterozygous males showed higher feeding rates during the brood-rearing period. Further, estimated offspring heterozygosity correlated with both paternal and maternal heterozygosity, suggesting that mating with heterozygous individuals can increase offspring genetic quality. Finally, plumage crown coloration was associated with male heterozygosity, and this could explain unanimous mate preferences for highly heterozygous and more ornamented individuals. Overall, this study suggests that non-additive genetic traits may play an important role in the evolution of mating preferences and offers empirical support to the resolution of the lek paradox from the perspective of the heterozygous mate hypothesis. PMID:19474042

Genetic determinants of anti-malarial acquired immunity in a large multi-centre study.

PubMed

Shelton, Jennifer M G; Corran, Patrick; Risley, Paul; Silva, Nilupa; Hubbart, Christina; Jeffreys, Anna; Rowlands, Kate; Craik, Rachel; Cornelius, Victoria; Hensmann, Meike; Molloy, Sile; Sepulveda, Nuno; Clark, Taane G; Band, Gavin; Clarke, Geraldine M; Spencer, Christopher C A; Kerasidou, Angeliki; Campino, Susana; Auburn, Sarah; Tall, Adama; Ly, Alioune Badara; Mercereau-Puijalon, Odile; Sakuntabhai, Anavaj; Djimdé, Abdoulaye; Maiga, Boubacar; Touré, Ousmane; Doumbo, Ogobara K; Dolo, Amagana; Troye-Blomberg, Marita; Mangano, Valentina D; Verra, Frederica; Modiano, David; Bougouma, Edith; Sirima, Sodiomon B; Ibrahim, Muntaser; Hussain, Ayman; Eid, Nahid; Elzein, Abier; Mohammed, Hiba; Elhassan, Ahmed; Elhassan, Ibrahim; Williams, Thomas N; Ndila, Carolyne; Macharia, Alexander; Marsh, Kevin; Manjurano, Alphaxard; Reyburn, Hugh; Lemnge, Martha; Ishengoma, Deus; Carter, Richard; Karunaweera, Nadira; Fernando, Deepika; Dewasurendra, Rajika; Drakeley, Christopher J; Riley, Eleanor M; Kwiatkowski, Dominic P; Rockett, Kirk A

2015-08-28

Many studies report associations between human genetic factors and immunity to malaria but few have been reliably replicated. These studies are usually country-specific, use small sample sizes and are not directly comparable due to differences in methodologies. This study brings together samples and data collected from multiple sites across Africa and Asia to use standardized methods to look for consistent genetic effects on anti-malarial antibody levels. Sera, DNA samples and clinical data were collected from 13,299 individuals from ten sites in Senegal, Mali, Burkina Faso, Sudan, Kenya, Tanzania, and Sri Lanka using standardized methods. DNA was extracted and typed for 202 Single Nucleotide Polymorphisms with known associations to malaria or antibody production, and antibody levels to four clinical grade malarial antigens [AMA1, MSP1, MSP2, and (NANP)4] plus total IgE were measured by ELISA techniques. Regression models were used to investigate the associations of clinical and genetic factors with antibody levels. Malaria infection increased levels of antibodies to malaria antigens and, as expected, stable predictors of anti-malarial antibody levels included age, seasonality, location, and ethnicity. Correlations between antibodies to blood-stage antigens AMA1, MSP1 and MSP2 were higher between themselves than with antibodies to the (NANP)4 epitope of the pre-erythrocytic circumsporozoite protein, while there was little or no correlation with total IgE levels. Individuals with sickle cell trait had significantly lower antibody levels to all blood-stage antigens, and recessive homozygotes for CD36 (rs321198) had significantly lower anti-malarial antibody levels to MSP2. Although the most significant finding with a consistent effect across sites was for sickle cell trait, its effect is likely to be via reducing a microscopically positive parasitaemia rather than directly on antibody levels. However, this study does demonstrate a framework for the feasibility of combining data from sites with heterogeneous malaria transmission levels across Africa and Asia with which to explore genetic effects on anti-malarial immunity.

Laboratory Estimates of Heritabilities and Genetic Correlations in Nature

PubMed Central

Riska, B.; Prout, T.; Turelli, M.

1989-01-01

A lower bound on heritability in a natural environment can be determined from the regression of offspring raised in the laboratory on parents raised in nature. An estimate of additive genetic variance in the laboratory is also required. The estimated lower bounds on heritabilities can sometimes be used to demonstrate a significant genetic correlation between two traits in nature, if their genetic and phenotypic correlations in nature have the same sign, and if sample sizes are large, and heritabilities and phenotypic and genetic correlations are high. PMID:2515111

Genetic confirmation for a central role for TNFα in the direct action of thyroid stimulating hormone on the skeleton

PubMed Central

Sun, Li; Zhu, Ling-Ling; Lu, Ping; Yuen, Tony; Li, Jianhua; Ma, Risheng; Baliram, Ramkumarie; Moonga, Surinder S.; Liu, Peng; Zallone, Alberta; New, Maria I.; Davies, Terry F.; Zaidi, Mone

2013-01-01

Clinical data showing correlations between low thyroid-stimulating hormone (TSH) levels and high bone turnover markers, low bone mineral density, and an increased risk of osteoporosis-related fractures are buttressed by mouse genetic and pharmacological studies identifying a direct action of TSH on the skeleton. Here we show that the skeletal actions of TSH deficiency are mediated, in part, through TNFα. Compound mouse mutants generated by genetically deleting the Tnfα gene on a Tshr−/− (homozygote) or Tshr+/− (heterozygote) background resulted in full rescue of the osteoporosis, low bone formation, and hyperresorption that accompany TSH deficiency. Studies using ex vivo bone marrow cell cultures showed that TSH inhibits and stimulates TNFα production from macrophages and osteoblasts, respectively. TNFα, in turn, stimulates osteoclastogenesis but also enhances the production in bone marrow of a variant TSHβ. This locally produced TSH suppresses osteoclast formation in a negative feedback loop. We speculate that TNFα elevations due to low TSH signaling in human hyperthyroidism contribute to the bone loss that has traditionally been attributed solely to high thyroid hormone levels. PMID:23716650

Investigating yellow dung fly body size evolution in the field: Response to climate change?

PubMed

Blanckenhorn, Wolf U

2015-08-01

Uncovering genetic responses to selection in wild populations typically requires tracking individuals over generations and use of animal models. Our group monitored the body size of one Swiss Yellow Dung Fly (Scathophaga stercoraria; Diptera: Scathophagidae) field population over 15 years, including intermittent common-garden rearing in the laboratory to assess body size with minimized environmental and maximized genetic variation. Contrary to expectations based on repeated heritability and phenotypic selection assessments over the years (reported elsewhere), field body sizes declined by >10% and common-garden laboratory sizes by >5% from 1993 to 2009. Our results confirm the temperature-size rule (smaller when warmer) and, albeit entirely correlational, could be mediated by climate change, as over this period mean temperature at the site increased by 0.5°C, although alternative systematic environmental changes cannot be entirely excluded. Monitoring genetic responses to selection in wild invertebrate populations is thus possible, though indirect, and wild populations may evolve in directions not consistent with strongly positive directional selection favoring large body size. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Testing the link between population genetic differentiation and clade diversification in Costa Rican orchids.

PubMed

Kisel, Yael; Moreno-Letelier, Alejandra C; Bogarín, Diego; Powell, Martyn P; Chase, Mark W; Barraclough, Timothy G

2012-10-01

Species population genetics could be an important factor explaining variation in clade species richness. Here, we use newly generated amplified fragment length polymorphism (AFLP) data to test whether five pairs of sister clades of Costa Rican orchids that differ greatly in species richness also differ in average neutral genetic differentiation within species, expecting that if the strength of processes promoting differentiation within species is phylogenetically heritable, then clades with greater genetic differentiation should diversify more. Contrary to expectation, neutral genetic differentiation does not correlate directly with total diversification in the clades studied. Neutral genetic differentiation varies greatly among species and shows no heritability within clades. Half of the variation in neutral genetic differentiation among populations can be explained by ecological variables, and species-level traits explain the most variation. Unexpectedly, we find no isolation by distance in any species, but genetic differentiation is greater between populations occupying different niches. This pattern corresponds with those observed for microscopic eukaryotes and could reflect effective widespread dispersal of tiny and numerous orchid seeds. Although not providing a definitive answer to whether population genetics processes affect clade diversification, this work highlights the potential for addressing new macroevolutionary questions using a comparative population genetic approach. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Congruence-Incongruence Patterns in Alpha-1 Antitrypsin Deficiency Couples’ Genetic Determinist Beliefs and Perceived Control over Genes: Implications for Clinical and Public Health Genomic Communication

PubMed Central

Smith, Rachel A.; Hong, Soo Jung; Worthington, Amber

2015-01-01

Genomics makes possible the isolation of multiple genes as co-factors that increase, but do not determine, risk for many adult-onset medical conditions, including alpha-1 antitrypsin deficiency (AATD). Those diagnosed with an adult-onset medical condition, such as AATD, are often married and make decisions about testing and care as a couple. We examined genetic essentialist and threat beliefs, focusing on beliefs about the genetic contribution to disease susceptibility and severity, as well as perceptions of control related to genes and health for married couples (N =59), in which one spouse has been tested for genetic mutations associated with AATD. The intraclass correlation for spouses’ beliefs about genetic essentialism was strong and statistically significant, but the associations for their other beliefs were not. Incongruence between AATD participants and their spouses regarding genes’ influence on disease severity directly related to incongruent perceptions of control and genetic contribution to disease susceptibility. Results revealed an inverse relationship to AATD participants’ perceptions of behavioral control and a direct relationship to their beliefs about genes’ influence on disease severity. This suggests a pattern of incongruence in which AATD participants have low levels of perceived control over genes’ influence on health and high levels of perceived genetic influence on disease severity compared to spouses. With public health communication efforts lagging behind the science of genomics, insights regarding the congruence or incongruence associated with married couples’ beliefs about genes’ influence on disease afford pathways to guide clinical and public health communication about genomics. PMID:25413221

Congruence-Incongruence Patterns in Alpha-1 Antitrypsin Deficiency Couples' Genetic Determinist Beliefs and Perceived Control over Genes: Implications for Clinical and Public Health Genomic Communication.

PubMed

Parrott, Roxanne L; Smith, Rachel A; Hong, Soo Jung; Worthington, Amber

2015-06-01

Genomics makes possible the isolation of multiple genes as co-factors that increase, but do not determine, risk for many adult-onset medical conditions, including alpha-1 antitrypsin deficiency (AATD). Those diagnosed with an adult-onset medical condition, such as AATD, are often married and make decisions about testing and care as a couple. We examined genetic essentialist and threat beliefs, focusing on beliefs about the genetic contribution to disease susceptibility and severity, as well as perceptions of control related to genes and health for married couples (N =59), in which one spouse has been tested for genetic mutations associated with AATD. The intraclass correlation for spouses' beliefs about genetic essentialism was strong and statistically significant, but the associations for their other beliefs were not. Incongruence between AATD participants and their spouses regarding genes' influence on disease severity directly related to incongruent perceptions of control and genetic contribution to disease susceptibility. Results revealed an inverse relationship to AATD participants' perceptions of behavioral control and a direct relationship to their beliefs about genes' influence on disease severity. This suggests a pattern of incongruence in which AATD participants have low levels of perceived control over genes' influence on health and high levels of perceived genetic influence on disease severity compared to spouses. With public health communication efforts lagging behind the science of genomics, insights regarding the congruence or incongruence associated with married couples' beliefs about genes' influence on disease afford pathways to guide clinical and public health communication about genomics.

Common genetic variants explain the majority of the correlation between height and intelligence: the generation Scotland study.

PubMed

Marioni, Riccardo E; Batty, G David; Hayward, Caroline; Kerr, Shona M; Campbell, Archie; Hocking, Lynne J; Porteous, David J; Visscher, Peter M; Deary, Ian J

2014-03-01

Greater height and higher intelligence test scores are predictors of better health outcomes. Here, we used molecular (single-nucleotide polymorphism) data to estimate the genetic correlation between height and general intelligence (g) in 6,815 unrelated subjects (median age 57, IQR 49-63) from the Generation Scotland: Scottish Family Health Study cohort. The phenotypic correlation between height and g was 0.16 (SE 0.01). The genetic correlation between height and g was 0.28 (SE 0.09) with a bivariate heritability estimate of 0.71. Understanding the molecular basis of the correlation between height and intelligence may help explain any shared role in determining health outcomes. This study identified a modest genetic correlation between height and intelligence with the majority of the phenotypic correlation being explained by shared genetic influences.

Genetic selection for lifetime reproductive performance.

PubMed

Clutter, A C

2009-01-01

Genetic improvement of sow lifetime reproductive performance has value from both the economic perspectives of pork producers and the pork industry, but also from the perspective of ethical and animal welfare concerns by the general public. Genetic potential for piglets produced from individual litters is a primary determinant of lifetime prolificacy, but females must be able to sustain productivity without injury or death beyond the achievement of positive net present value. Evidence exists for between- and within-line genetic variation in sow lifetime performance, suggesting that improvements may be made by both line choices and genetic selection within lines. However, some of the same barriers to accurate within-line selection that apply to individual litter traits also present challenges to genetic selection for sow lifetime prolificacy: generally low heritabilites, sex-limited expression, expression after the age that animals are typically selected, and unfavorable genetic correlations with other traits in the profit function. In addition, there is an inherent conflict within the genetic nucleus herds where selections take place between the goal of shortened generation interval to accelerate genetic progress and the expression of sow lifetime traits. A proliferation in the industry of commercial multipliers with direct genetic ties and routine record flows to genetic nucleus herds provides a framework for accurate estimates of relevant genetic variances and covariances, and estimation of breeding values for sow lifetime traits that can be used in genetic selection.

Evolutionary Determinants of Genetic Variation in Susceptibility to Infectious Diseases in Humans

PubMed Central

Baker, Christi; Antonovics, Janis

2012-01-01

Although genetic variation among humans in their susceptibility to infectious diseases has long been appreciated, little focus has been devoted to identifying patterns in levels of variation in susceptibility to different diseases. Levels of genetic variation in susceptibility associated with 40 human infectious diseases were assessed by a survey of studies on both pedigree-based quantitative variation, as well as studies on different classes of marker alleles. These estimates were correlated with pathogen traits, epidemiological characteristics, and effectiveness of the human immune response. The strongest predictors of levels of genetic variation in susceptibility were disease characteristics negatively associated with immune effectiveness. High levels of genetic variation were associated with diseases with long infectious periods and for which vaccine development attempts have been unsuccessful. These findings are consistent with predictions based on theoretical models incorporating fitness costs associated with the different types of resistance mechanisms. An appreciation of these observed patterns will be a valuable tool in directing future research given that genetic variation in disease susceptibility has large implications for vaccine development and epidemiology. PMID:22242158

Molecular Basis and Genetic Modifiers of Thalassemia.

PubMed

Mettananda, Sachith; Higgs, Douglas R

2018-04-01

Thalassemia is a disorder of hemoglobin characterized by reduced or absent production of one of the globin chains in human red blood cells with relative excess of the other. Impaired synthesis of β-globin results in β-thalassemia, whereas defective synthesis of α-globin leads to α-thalassemia. Despite being a monogenic disorder, thalassemia exhibits remarkable clinical heterogeneity that is directly related to the intracellular imbalance between α- and β-like globin chains. Novel insights into the genetic modifiers have contributed to the understanding of the correlation between genotype and phenotype and are being explored as therapeutic pathways to cure this life-limiting disease. Copyright © 2017 Elsevier Inc. All rights reserved.

Genetic and environmental factors affecting perinatal and preweaning survival of D'man lambs.

PubMed

Boujenane, Ismaïl; Chikhi, Abdelkader; Lakcher, Oumaïma; Ibnelbachyr, Mustapha

2013-08-01

This study examined the viability of 4,554 D'man lambs born alive at Errachidia research station in south-eastern Morocco between 1988 and 2009. Lamb survival to 1, 10, 30 and 90 days old was 0.95, 0.93, 0.93 and 0.92, respectively. The majority of deaths (85.7%) occurred before 10 days of age. Type and period of birth both had a significant effect on lamb survival traits, whereas age of dam and sex of lamb did not. The study revealed a curvilinear relationship between lamb's birth weight and survival traits from birth to 90 days, with optimal birth weights for maximal perinatal and preweaning survival varying according to type of birth from 2.6 to 3.5 kg. Estimation of variance components, using an animal model including direct and maternal genetic effects, the permanent maternal environment as well as fixed effects, showed that direct and maternal heritability estimates for survival traits between birth and 90 days were mostly low and varied from 0.01 to 0.10; however, direct heritability for survival at 1 day from birth was estimated at 0.63. Genetic correlations between survival traits and birth weight were positive and low to moderate. It was concluded that survival traits of D'man lambs between birth and 90 days could be improved through selection, but genetic progress would be low. However, the high proportion of the residual variance to total variance reinforces the need to improve management and lambing conditions.

Genetic influences on the cognitive biases associated with anxiety and depression symptoms in adolescents.

PubMed

Zavos, Helena M S; Rijsdijk, Frühling V; Gregory, Alice M; Eley, Thalia C

2010-07-01

There is a substantial overlap between genes affecting anxiety and depression. Both anxiety and depression are associated with cognitive biases such as anxiety sensitivity and attributional style. Little, however, is known about the relationship between these variables and whether these too are genetically correlated. Self-reports of anxiety sensitivity, anxiety symptoms, attributional style and depression symptoms were obtained for over 1300 adolescent twin and sibling pairs at two time points. The magnitude of genetic and environmental influences on the measures was examined. Strongest associations were found between anxiety sensitivity and anxiety ratings at both measurement times (r=.70, .72) and between anxiety and depression (r=.62 at both time points). Correlations between the cognitive biases were modest at time 1 (r=-.12) and slightly larger at time 2 (r=-.31). All measures showed moderate genetic influence. Generally genetic correlations reflected phenotypic correlations. Thus the highest genetic correlations were between anxiety sensitivity and anxiety ratings (.86, .87) and between anxiety and depression ratings (.77, .71). Interestingly, depression ratings also showed a high genetic correlation with anxiety sensitivity (.70, .76). Genetic correlations between the cognitive bias measures were moderate (-.31, -.46). The sample consists primarily of twins, there are limitations associated with the twin design. Cognitive biases associated with depression and anxiety are not as genetically correlated as anxiety and depression ratings themselves. Further research into the cognitive processes related to anxiety and depression will facilitate understanding of the relationship between bias and symptoms.

Neuronal boost to evolutionary dynamics.

PubMed

de Vladar, Harold P; Szathmáry, Eörs

2015-12-06

Standard evolutionary dynamics is limited by the constraints of the genetic system. A central message of evolutionary neurodynamics is that evolutionary dynamics in the brain can happen in a neuronal niche in real time, despite the fact that neurons do not reproduce. We show that Hebbian learning and structural synaptic plasticity broaden the capacity for informational replication and guided variability provided a neuronally plausible mechanism of replication is in place. The synergy between learning and selection is more efficient than the equivalent search by mutation selection. We also consider asymmetric landscapes and show that the learning weights become correlated with the fitness gradient. That is, the neuronal complexes learn the local properties of the fitness landscape, resulting in the generation of variability directed towards the direction of fitness increase, as if mutations in a genetic pool were drawn such that they would increase reproductive success. Evolution might thus be more efficient within evolved brains than among organisms out in the wild.

Methylation interactions in Arabidopsis hybrids require RNA-directed DNA methylation and are influenced by genetic variation

PubMed Central

Zhang, Qingzhu; Wang, Dong; Lang, Zhaobo; He, Li; Yang, Lan; Zeng, Liang; Li, Yanqiang; Zhao, Cheng; Huang, Huan; Zhang, Heng; Zhang, Huiming; Zhu, Jian-Kang

2016-01-01

DNA methylation is a conserved epigenetic mark in plants and many animals. How parental alleles interact in progeny to influence the epigenome is poorly understood. We analyzed the DNA methylomes of Arabidopsis Col and C24 ecotypes, and their hybrid progeny. Hybrids displayed nonadditive DNA methylation levels, termed methylation interactions, throughout the genome. Approximately 2,500 methylation interactions occurred at regions where parental DNA methylation levels are similar, whereas almost 1,000 were at differentially methylated regions in parents. Methylation interactions were characterized by an abundance of 24-nt small interfering RNAs. Furthermore, dysfunction of the RNA-directed DNA methylation pathway abolished methylation interactions but did not affect the increased biomass observed in hybrid progeny. Methylation interactions correlated with altered genetic variation within the genome, suggesting that they may play a role in genome evolution. PMID:27382183

Genetic improvement of feed conversion ratio via indirect selection against lipid deposition in farmed rainbow trout (Oncorhynchus mykiss Walbaum).

PubMed

Kause, Antti; Kiessling, Anders; Martin, Samuel A M; Houlihan, Dominic; Ruohonen, Kari

2016-11-01

In farmed fish, selective breeding for feed conversion ratio (FCR) may be possible via indirectly selecting for easily-measured indicator traits correlated with FCR. We tested the hypothesis that rainbow trout with low lipid% have genetically better FCR, and that lipid% may be genetically related to retention efficiency of macronutrients, making lipid% a useful indicator trait. A quantitative genetic analysis was used to quantify the benefit of replacing feed intake in a selection index with one of three lipid traits: body lipid%, muscle lipid% or viscera% weight of total body weight (reflecting visceral lipid). The index theory calculations showed that simultaneous selection for weight gain and against feed intake (direct selection to improve FCR) increased the expected genetic response in FCR by 1·50-fold compared with the sole selection for growth. Replacing feed intake in the selection index with body lipid%, muscle lipid% or viscera% increased genetic response in FCR by 1·29-, 1·49- and 1·02-fold, respectively, compared with the sole selection for growth. Consequently, indirect selection for weight gain and against muscle lipid% was almost as effective as direct selection for FCR. Fish with genetically low body and muscle lipid% were more efficient in turning ingested protein into protein weight gain. Both physiological and genetic mechanisms promote the hypothesis that low-lipid% fish are more efficient. These results highlight that in breeding programmes of rainbow trout, control of lipid deposition improves not only FCR but also protein-retention efficiency. This improves resource efficiency of aquaculture and reduces nutrient load to the environment.

Genetic parameters of pelt character, feed efficiency and size traits in Finnish blue fox (Vulpes lagopus).

PubMed

Kempe, R; Koskinen, N; Strandén, I

2013-12-01

Pelt character traits (size, quality, colour clarity, darkness) are important economic traits in blue fox breeding. Better feed efficiency (FE) is another economically important and new breeding goal for fur animals. The purpose of this study was to determine the correlations between pelt character traits, FE and size traits and to estimate genetic parameters for pelt character traits. Pelt size (pSIcm ) had a high positive genetic correlation with animal grading size (gSI), final body weight (BWFin), body length and daily gain (DG), and a moderate correlation with body condition score (BCS). Animal body length and BCS (describing fatness) were considered as genetically different traits. Genetic correlations between pelt quality and size traits were estimated without precision and did not differ from zero, but colour clarity (pCL) had a low antagonistic genetic correlation with FE. Pelt size and DG had a favourable genetic correlation with FE but a fairly high unfavourable genetic correlation with dry matter feed intake. The current emphasis on selection for larger animal and pelt size improves FE indirectly, but selection for larger pelt size favours fast-growing and fat individuals and simultaneously increases feed intake. The detected genetic connections between FE, size, feed intake and pCL should be taken into account in the Finnish blue fox breeding programme. © 2013 Blackwell Verlag GmbH.

Genome-Wide Associations between Genetic and Epigenetic Variation Influence mRNA Expression and Insulin Secretion in Human Pancreatic Islets

PubMed Central

Olsson, Anders H.; Volkov, Petr; Bacos, Karl; Dayeh, Tasnim; Hall, Elin; Nilsson, Emma A.; Ladenvall, Claes; Rönn, Tina; Ling, Charlotte

2014-01-01

Genetic and epigenetic mechanisms may interact and together affect biological processes and disease development. However, most previous studies have investigated genetic and epigenetic mechanisms independently, and studies examining their interactions throughout the human genome are lacking. To identify genetic loci that interact with the epigenome, we performed the first genome-wide DNA methylation quantitative trait locus (mQTL) analysis in human pancreatic islets. We related 574,553 single nucleotide polymorphisms (SNPs) with genome-wide DNA methylation data of 468,787 CpG sites targeting 99% of RefSeq genes in islets from 89 donors. We identified 67,438 SNP-CpG pairs in cis, corresponding to 36,783 SNPs (6.4% of tested SNPs) and 11,735 CpG sites (2.5% of tested CpGs), and 2,562 significant SNP-CpG pairs in trans, corresponding to 1,465 SNPs (0.3% of tested SNPs) and 383 CpG sites (0.08% of tested CpGs), showing significant associations after correction for multiple testing. These include reported diabetes loci, e.g. ADCY5, KCNJ11, HLA-DQA1, INS, PDX1 and GRB10. CpGs of significant cis-mQTLs were overrepresented in the gene body and outside of CpG islands. Follow-up analyses further identified mQTLs associated with gene expression and insulin secretion in human islets. Causal inference test (CIT) identified SNP-CpG pairs where DNA methylation in human islets is the potential mediator of the genetic association with gene expression or insulin secretion. Functional analyses further demonstrated that identified candidate genes (GPX7, GSTT1 and SNX19) directly affect key biological processes such as proliferation and apoptosis in pancreatic β-cells. Finally, we found direct correlations between DNA methylation of 22,773 (4.9%) CpGs with mRNA expression of 4,876 genes, where 90% of the correlations were negative when CpGs were located in the region surrounding transcription start site. Our study demonstrates for the first time how genome-wide genetic and epigenetic variation interacts to influence gene expression, islet function and potential diabetes risk in humans. PMID:25375650

Molecular genetic contributions to socioeconomic status and intelligence

PubMed Central

Marioni, Riccardo E.; Davies, Gail; Hayward, Caroline; Liewald, Dave; Kerr, Shona M.; Campbell, Archie; Luciano, Michelle; Smith, Blair H.; Padmanabhan, Sandosh; Hocking, Lynne J.; Hastie, Nicholas D.; Wright, Alan F.; Porteous, David J.; Visscher, Peter M.; Deary, Ian J.

2014-01-01

Education, socioeconomic status, and intelligence are commonly used as predictors of health outcomes, social environment, and mortality. Education and socioeconomic status are typically viewed as environmental variables although both correlate with intelligence, which has a substantial genetic basis. Using data from 6815 unrelated subjects from the Generation Scotland study, we examined the genetic contributions to these variables and their genetic correlations. Subjects underwent genome-wide testing for common single nucleotide polymorphisms (SNPs). DNA-derived heritability estimates and genetic correlations were calculated using the ‘Genome-wide Complex Trait Analyses’ (GCTA) procedures. 21% of the variation in education, 18% of the variation in socioeconomic status, and 29% of the variation in general cognitive ability was explained by variation in common SNPs (SEs ~ 5%). The SNP-based genetic correlations of education and socioeconomic status with general intelligence were 0.95 (SE 0.13) and 0.26 (0.16), respectively. There are genetic contributions to intelligence and education with near-complete overlap between common additive SNP effects on these traits (genetic correlation ~ 1). Genetic influences on socioeconomic status are also associated with the genetic foundations of intelligence. The results are also compatible with substantial environmental contributions to socioeconomic status. PMID:24944428

Molecular genetic contributions to socioeconomic status and intelligence.

PubMed

Marioni, Riccardo E; Davies, Gail; Hayward, Caroline; Liewald, Dave; Kerr, Shona M; Campbell, Archie; Luciano, Michelle; Smith, Blair H; Padmanabhan, Sandosh; Hocking, Lynne J; Hastie, Nicholas D; Wright, Alan F; Porteous, David J; Visscher, Peter M; Deary, Ian J

2014-05-01

Education, socioeconomic status, and intelligence are commonly used as predictors of health outcomes, social environment, and mortality. Education and socioeconomic status are typically viewed as environmental variables although both correlate with intelligence, which has a substantial genetic basis. Using data from 6815 unrelated subjects from the Generation Scotland study, we examined the genetic contributions to these variables and their genetic correlations. Subjects underwent genome-wide testing for common single nucleotide polymorphisms (SNPs). DNA-derived heritability estimates and genetic correlations were calculated using the 'Genome-wide Complex Trait Analyses' (GCTA) procedures. 21% of the variation in education, 18% of the variation in socioeconomic status, and 29% of the variation in general cognitive ability was explained by variation in common SNPs (SEs ~ 5%). The SNP-based genetic correlations of education and socioeconomic status with general intelligence were 0.95 (SE 0.13) and 0.26 (0.16), respectively. There are genetic contributions to intelligence and education with near-complete overlap between common additive SNP effects on these traits (genetic correlation ~ 1). Genetic influences on socioeconomic status are also associated with the genetic foundations of intelligence. The results are also compatible with substantial environmental contributions to socioeconomic status.

Carcass traits of young bulls in dual-purpose cattle: genetic parameters and genetic correlations with veal calf, type and production traits.

PubMed

Croué, I; Fouilloux, M N; Saintilan, R; Ducrocq, V

2017-06-01

The profitability of dual-purpose breeding farms can be increased through genetic improvement of carcass traits. To develop a genetic evaluation of carcass traits of young bulls, breed-specific genetic parameters were estimated in three French dual-purpose breeds. Genetic correlations between these traits and veal calf, type and milk production traits were also estimated. Slaughter performances of 156 226 Montbeliarde, 160 361 Normande and 8691 Simmental young bulls were analyzed with a multitrait animal model. In the three breeds, heritabilities were moderate for carcass weight (0.12 to 0.19±0.01 to 0.04) and carcass conformation (0.21 to 0.26±0.01 to 0.04) and slightly lower for age at slaughter (0.08 to 0.17±0.01 to 0.03). For all three breeds, genetic correlations between carcass weight and carcass conformation were moderate and favorable (0.30 to 0.52±0.03 to 0.13). They were strong and favorable (-0.49 to -0.71±0.05 to 0.15) between carcass weight and age at slaughter. Between age at slaughter and carcass conformation, they were low and unfavorable to moderate and favorable (-0.25 to 0.10±0.06 to 0.18). Heavier young bulls tend to be better conformed and slaughtered earlier. Genetic correlations between corresponding young bulls and veal production traits were moderate and favorable (0.32 to 0.70±0.03 to 0.09), implying that selecting sires for veal calf production leads to select sires producing better young bulls. Genetic correlations between young bull carcass weight and cow size were moderately favorable (0.22 to 0.45±0.04 to 0.10). Young bull carcass conformation had moderate and favorable genetic correlations (0.11 to 0.24±0.04 to 0.10) with cow width but moderate and unfavorable genetic correlations (-0.21 to -0.36±0.03 to 0.08) with cow height. Taller cows tended to produce heavier young bulls and thinner cows to produce less conformed ones. Genetic correlations between carcass traits of young bulls and cow muscularity traits were low to moderate and favorable. Finally, genetic correlations between carcass traits of young bulls and milk production traits were low and unfavorable to moderate and favorable. These results indicate the existence for all three breeds of genetic variability for the genetic improvement of carcass traits of young bulls as well as favorable genetic correlations for their simultaneous selection and no strong unfavorable correlation with milk production traits.

Reducing bias in maintenance energy expected progeny difference by accounting for selection on weaning and yearling weights.

PubMed

Williams, J L; Garrick, D J; Speidel, S E

2009-05-01

Maintenance energy requirements of cattle can be predicted from published equations utilizing metabolic BW and milk production potential. Metabolic BW is a function of BW at a constant fat percentage or BCS. Pedigree and performance records can be used in random regression models to predict genetic merit for metabolic BW and milk production potentials. The purpose of this study was to present a methodology for predicting mature cow maintenance energy EPD using mature cow BW and BCS and accounting for prior selection of replacement females at weaning and yearling ages. Variance components were obtained for direct and maternal effects on weaning weight, direct effects on postweaning BW gain, and direct coefficients for random regression on mature weights (MW) adjusted for BCS. These BW were transformed into metabolic BW by taking BW to the power of 0.75, variance components were estimated for metabolic BW, and were then used to predict breeding values from which cow maintenance energy EPD could be derived. Data used in this analysis were obtained from the Red Angus Association of America and limited to herds with MW and corresponding BCS observations. The data set included 52,338 BW records on 21,103 individuals. Weaning and yearling contemporaries to those with MW observations, but with no MW records themselves, were included to account for selection occurring before maturity. Heritability estimates for weaning weight direct, weaning weight maternal, and postweaning BW gain were 0.18 +/- 0.02, 0.16 +/- 0.02, and 0.18 +/- 0.02, respectively. Mature BW observed at 2, 3, 4, 5, and 6 yr of age had heritability estimates of 0.45 +/- 0.03, 0.44 +/- 0.03, 0.49 +/- 0.03, 0.66 +/- 0.04, and 0.62 +/- 0.05, respectively. Correlations between weaning weight direct and MW ranged from 0.65 +/- 0.07 to 0.82 +/- 0.04, and correlations between MW at different ages ranged from 0.95 +/- 0.03 to 0.99 +/- 0.01. The genetic correlations between postweaning BW gain and MW ranged from 0.48 +/- 0.06 to 0.59 +/- 0.06. The 15-yr genetic increase in metabolic BW was 3.6 kg(0.75), greater than the value of 0.23 kg(0.75) obtained from the same data ignoring weaning and yearling contemporaries with unobserved MW, the approach currently used in the derivation of cow maintenance EPD published by the Red Angus Association of America.

Genetic Influences on Adolescent Sexual Behavior: Why Genes Matter for Environmentally-Oriented Researchers

PubMed Central

Harden, K. Paige

2013-01-01

There are dramatic individual differences among adolescents in how and when they become sexually active adults, and “early” sexual activity is frequently cited as a cause of concern for scientists, policymakers, and the general public. Understanding the causes and developmental impact of adolescent sexual activity can be furthered by considering genes as a source of individual differences. Quantitative behavioral genetics (i.e., twin and family studies) and candidate gene association studies now provide clear evidence for the genetic underpinnings of individual differences in adolescent sexual behavior and related phenotypes. Genetic influences on sexual behavior may operate through a variety of direct and indirect mechanisms, including pubertal development, testosterone levels, and dopaminergic systems. Genetic differences may be systematically associated with exposure to environments that are commonly treated as causes of sexual behavior (gene-environment correlation). Possible gene-environment correlations pose a serious challenge for interpreting the results of much behavioral research. Multivariate, genetically-informed research on adolescent sexual behavior compares twins and family members as a form of “quasi-experiment”: How do twins who differ in their sexual experiences differ in their later development? The small but growing body of genetically-informed research has already challenged dominant assumptions regarding the etiology and sequelae of adolescent sexual behavior, with some studies indicating possible positive effects of teenage sexuality. Studies of gene × environment interaction may further elucidate the mechanisms by which genes and environments combine to shape the development of sexual behavior and its psychosocial consequences. Overall, the existence of heritable variation in adolescent sexual behavior has profound implications for environmentally-oriented theory and research. PMID:23855958

Investigating the genetic relationship between Alzheimer's disease and cancer using GWAS summary statistics.

PubMed

Feng, Yen-Chen Anne; Cho, Kelly; Lindstrom, Sara; Kraft, Peter; Cormack, Jean; Liang, Liming; Driver, Jane A

2017-10-01

Growing evidence from both epidemiology and basic science suggest an inverse association between Alzheimer's disease (AD) and cancer. We examined the genetic relationship between AD and various cancer types using GWAS summary statistics from the IGAP and GAME-ON consortia. Sample size ranged from 9931 to 54,162; SNPs were imputed to the 1000 Genomes European panel. Our results based on cross-trait LD Score regression showed a significant positive genetic correlation between AD and five cancers combined (colon, breast, prostate, ovarian, lung; r g  = 0.17, P = 0.04), and specifically with breast cancer (ER-negative and overall; r g  = 0.21 and 0.18, P = 0.035 and 0.034) and lung cancer (adenocarcinoma, squamous cell carcinoma and overall; r g  = 0.31, 0.38 and 0.30, P = 0.029, 0.016, and 0.006). Estimating the genetic correlation in specific functional categories revealed mixed positive and negative signals, notably stronger at annotations associated with increased enhancer activity. This suggests a role of gene expression regulators in the shared genetic etiology between AD and cancer, and that some shared variants modulate disease risk concordantly while others have effects in opposite directions. Due to power issues, we did not detect cross-phenotype associations at individual SNPs. This genetic overlap is not likely driven by a handful of major loci. Our study is the first to examine the co-heritability of AD and cancer leveraging large-scale GWAS results. The functional categories highlighted in this study need further investigation to illustrate the details of the genetic sharing and to bridge between different levels of associations.

Molecular genetic analysis of the F11 gene in 14 Turkish patients with factor XI deficiency: identification of novel and recurrent mutations and their inheritance within families

PubMed Central

Colakoglu, Seyma; Bayhan, Turan; Tavil, Betül; Keskin, Ebru Yılmaz; Cakir, Volkan; Gümrük, Fatma; Çetin, Mualla; Aytaç, Selin; Berber, Ergul

2018-01-01

Background Factor XI (FXI) deficiency is an autosomal bleeding disease associated with genetic defects in the F11 gene which cause decreased FXI levels or impaired FXI function. An increasing number of mutations has been reported in the FXI mutation database, most of which affect the serine protease domain of the protein. FXI is a heterogeneous disorder associated with a variable bleeding tendency and a variety of causative F11 gene mutations. The molecular basis of FXI deficiency in 14 patients from ten unrelated families in Turkey was analysed to establish genotype-phenotype correlations and inheritance of the mutations in the patients’ families. Material and methods Fourteen index cases with a diagnosis of FXI deficiency and family members of these patients were enrolled into the study. The patients’ F11 genes were amplified by polymerase chain reaction and subjected to direct DNA sequencing analysis. The findings were analysed statistically using bivariate correlations, Pearson’s correlation coefficient and the nonparametric Mann-Whitney test. Results Direct DNA sequencing analysis of the F11 genes revealed that all of the 14 patients had a F11 gene mutation. Eight different mutations were identified in the apple 1, apple 2 or serine protease domains, except one which was a splice site mutation. Six of the mutations were recurrent. Two of the mutations were novel missense mutations, p.Val522Gly and p.Cys581Arg, within the catalytic domain. The p.Trp519Stop mutation was observed in two families whereas all the other mutations were specific to a single family. Discussion Identification of mutations confirmed the genetic heterogeneity of FXI deficiency. Most of the patients with mutations did not have any bleeding complications, whereas some had severe bleeding symptoms. Genetic screening for F11 gene mutations is important to decrease the mortality and morbidity rate associated with FXI deficiency, which can be life-threatening if bleeding occurs in tissues with high fibrinolytic activity. PMID:27723456

What Is Direct-to-Consumer Genetic Testing?

MedlinePlus

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Unraveling the intrafamilial correlations and heritability of tumor types in MEN1: a Groupe d'étude des Tumeurs Endocrines study.

PubMed

Thevenon, J; Bourredjem, A; Faivre, L; Cardot-Bauters, C; Calender, A; Le Bras, M; Giraud, S; Niccoli, P; Odou, M F; Borson-Chazot, F; Barlier, A; Lombard-Bohas, C; Clauser, E; Tabarin, A; Pasmant, E; Chabre, O; Castermans, E; Ruszniewski, P; Bertherat, J; Delemer, B; Christin-Maitre, S; Beckers, A; Guilhem, I; Rohmer, V; Goichot, B; Caron, P; Baudin, E; Chanson, P; Groussin, L; Du Boullay, H; Weryha, G; Lecomte, P; Schillo, F; Bihan, H; Archambeaud, F; Kerlan, V; Bourcigaux, N; Kuhn, J M; Vergès, B; Rodier, M; Renard, M; Sadoul, J L; Binquet, C; Goudet, P

2015-12-01

MEN1, which is secondary to the mutation of the MEN1 gene, is a rare autosomal-dominant disease that predisposes mutation carriers to endocrine tumors. Most studies demonstrated the absence of direct genotype-phenotype correlations. The existence of a higher risk of death in the Groupe d'étude des Tumeurs Endocrines-cohort associated with a mutation in the JunD interacting domain suggests heterogeneity across families in disease expressivity. This study aims to assess the existence of modifying genetic factors by estimating the intrafamilial correlations and heritability of the six main tumor types in MEN1. The study included 797 patients from 265 kindred and studied seven phenotypic criteria: parathyroid and pancreatic neuroendocrine tumors (NETs) and pituitary, adrenal, bronchial, and thymic (thNET) tumors and the presence of metastasis. Intrafamilial correlations and heritability estimates were calculated from family tree data using specific validated statistical analysis software. Intrafamilial correlations were significant and decreased along parental degrees distance for pituitary, adrenal and thNETs. The heritability of these three tumor types was consistently strong and significant with 64% (s.e.m.=0.13; P<0.001) for pituitary tumor, 65% (s.e.m.=0.21; P<0.001) for adrenal tumors, and 97% (s.e.m.=0.41; P=0.006) for thNETs. The present study shows the existence of modifying genetic factors for thymus, adrenal, and pituitary MEN1 tumor types. The identification of at-risk subgroups of individuals within cohorts is the first step toward personalization of care. Next generation sequencing on this subset of tumors will help identify the molecular basis of MEN1 variable genetic expressivity. © 2015 European Society of Endocrinology.

Smoking and caffeine consumption: a genetic analysis of their association.

PubMed

Treur, Jorien L; Taylor, Amy E; Ware, Jennifer J; Nivard, Michel G; Neale, Michael C; McMahon, George; Hottenga, Jouke-Jan; Baselmans, Bart M L; Boomsma, Dorret I; Munafò, Marcus R; Vink, Jacqueline M

2017-07-01

Smoking and caffeine consumption show a strong positive correlation, but the mechanism underlying this association is unclear. Explanations include shared genetic/environmental factors or causal effects. This study employed three methods to investigate the association between smoking and caffeine. First, bivariate genetic models were applied to data of 10 368 twins from the Netherlands Twin Register in order to estimate genetic and environmental correlations between smoking and caffeine use. Second, from the summary statistics of meta-analyses of genome-wide association studies on smoking and caffeine, the genetic correlation was calculated by LD-score regression. Third, causal effects were tested using Mendelian randomization analysis in 6605 Netherlands Twin Register participants and 5714 women from the Avon Longitudinal Study of Parents and Children. Through twin modelling, a genetic correlation of r0.47 and an environmental correlation of r0.30 were estimated between current smoking (yes/no) and coffee use (high/low). Between current smoking and total caffeine use, this was r0.44 and r0.00, respectively. LD-score regression also indicated sizeable genetic correlations between smoking and coffee use (r0.44 between smoking heaviness and cups of coffee per day, r0.28 between smoking initiation and coffee use and r0.25 between smoking persistence and coffee use). Consistent with the relatively high genetic correlations and lower environmental correlations, Mendelian randomization provided no evidence for causal effects of smoking on caffeine or vice versa. Genetic factors thus explain most of the association between smoking and caffeine consumption. These findings suggest that quitting smoking may be more difficult for heavy caffeine consumers, given their genetic susceptibility. © 2016 The Authors.Addiction Biology published by John Wiley & Sons Ltd on behalf of Society for the Study of Addiction.

Smoking and caffeine consumption: a genetic analysis of their association

PubMed Central

Taylor, Amy E.; Ware, Jennifer J.; Nivard, Michel G.; Neale, Michael C.; McMahon, George; Hottenga, Jouke‐Jan; Baselmans, Bart M. L.; Boomsma, Dorret I.; Munafò, Marcus R.; Vink, Jacqueline M.

2016-01-01

Abstract Smoking and caffeine consumption show a strong positive correlation, but the mechanism underlying this association is unclear. Explanations include shared genetic/environmental factors or causal effects. This study employed three methods to investigate the association between smoking and caffeine. First, bivariate genetic models were applied to data of 10 368 twins from the Netherlands Twin Register in order to estimate genetic and environmental correlations between smoking and caffeine use. Second, from the summary statistics of meta‐analyses of genome‐wide association studies on smoking and caffeine, the genetic correlation was calculated by LD‐score regression. Third, causal effects were tested using Mendelian randomization analysis in 6605 Netherlands Twin Register participants and 5714 women from the Avon Longitudinal Study of Parents and Children. Through twin modelling, a genetic correlation of r0.47 and an environmental correlation of r0.30 were estimated between current smoking (yes/no) and coffee use (high/low). Between current smoking and total caffeine use, this was r0.44 and r0.00, respectively. LD‐score regression also indicated sizeable genetic correlations between smoking and coffee use (r0.44 between smoking heaviness and cups of coffee per day, r0.28 between smoking initiation and coffee use and r0.25 between smoking persistence and coffee use). Consistent with the relatively high genetic correlations and lower environmental correlations, Mendelian randomization provided no evidence for causal effects of smoking on caffeine or vice versa. Genetic factors thus explain most of the association between smoking and caffeine consumption. These findings suggest that quitting smoking may be more difficult for heavy caffeine consumers, given their genetic susceptibility. PMID:27027469

Genetic parameters for lamb birth weight, survival and death risk traits.

PubMed

Everett-Hincks, J M; Mathias-Davis, H C; Greer, G J; Auvray, B A; Dodds, K G

2014-07-01

This paper reports genetic parameters for lamb survival and mortality traits on sheep farms in New Zealand. Lamb survival and mortality records were obtained from 38 flocks (103,357 lambs) from 5 yr of lambing data (2007 to 2011) and include many breeds and their crosses (predominantly Romney, Perendale, Coopworth, and Texel). A number of models were tested, all including environmental weather effects and investigating the random environmental effect of dam and litter (dam/year) as well as logit transformation for binary traits. Total heritability (direct + maternal) estimates were low for lamb viability at birth (0.01), lamb death risk to dystocia (0.01), and lamb death risk to starvation exposure (0.01) from birth to 3 d of age in an analysis accounting for direct and maternal genetic effects and the maternal environmental effects. Lamb survival heritabilities reported are very low (total heritabilities range from 0.02 to 0.06). The total heritabilities for the lamb death risk traits are lower than reported estimates of survival to 3 d of age or to weaning suggesting selection for the postmortem traits are not warranted at this time within these flocks. The total heritability for lamb birth weight was moderate (0.38) and the genetic correlations with the lamb death risk traits suggested that directional selection on lamb birth weight would have an effect on survival, although it is likely to have a nonlinear effect and therefore an optimum birth weight at which survival is maximized. This study has also shown that the total heritabilities may be overestimated when not accounting for maternal genetic and environment effects and in particular not accounting for the random environmental effect of litter (dam/year).

Genetic and epigenetic differences associated with environmental gradients in replicate populations of two salt marsh perennials.

PubMed

Foust, C M; Preite, V; Schrey, A W; Alvarez, M; Robertson, M H; Verhoeven, K J F; Richards, C L

2016-04-01

While traits and trait plasticity are partly genetically based, investigating epigenetic mechanisms may provide more nuanced understanding of the mechanisms underlying response to environment. Using AFLP and methylation-sensitive AFLP, we tested the hypothesis that differentiation to habitats along natural salt marsh environmental gradients occurs at epigenetic, but not genetic loci in two salt marsh perennials. We detected significant genetic and epigenetic structure among populations and among subpopulations, but we found multilocus patterns of differentiation to habitat type only in epigenetic variation for both species. In addition, more epigenetic than genetic loci were correlated with habitat in both species. When we analysed genetic and epigenetic variation simultaneously with partial Mantel, we found no correlation between genetic variation and habitat and a significant correlation between epigenetic variation and habitat in Spartina alterniflora. In Borrichia frutescens, we found significant correlations between epigenetic and/or genetic variation and habitat in four of five populations when populations were analysed individually, but there was no significant correlation between genetic or epigenetic variation and habitat when analysed jointly across the five populations. These analyses suggest that epigenetic mechanisms are involved in the response to salt marsh habitats, but also that the relationships among genetic and epigenetic variation and habitat vary by species. Site-specific conditions may also cloud our ability to detect response in replicate populations with similar environmental gradients. Future studies analysing sequence data and the correlation between genetic variation and DNA methylation will be powerful to identify the contributions of genetic and epigenetic response to environmental gradients. © 2016 John Wiley & Sons Ltd.

Multiple-trait estimates of genetic parameters for metabolic disease traits, fertility disorders, and their predictors in Canadian Holsteins.

PubMed

Jamrozik, J; Koeck, A; Kistemaker, G J; Miglior, F

2016-03-01

Producer-recorded health data for metabolic disease traits and fertility disorders on 35,575 Canadian Holstein cows were jointly analyzed with selected indicator traits. Metabolic diseases included clinical ketosis (KET) and displaced abomasum (DA); fertility disorders were metritis (MET) and retained placenta (RP); and disease indicators were fat-to-protein ratio, milk β-hydroxybutyrate, and body condition score (BCS) in the first lactation. Traits in first and later (up to fifth) lactations were treated as correlated in the multiple-trait (13 traits in total) animal linear model. Bayesian methods with Gibbs sampling were implemented for the analysis. Estimates of heritability for disease incidence were low, up to 0.06 for DA in first lactation. Among disease traits, the environmental herd-year variance constituted 4% of the total variance for KET and less for other traits. First- and later-lactation disease traits were genetically correlated (from 0.66 to 0.72) across all traits, indicating different genetic backgrounds for first and later lactations. Genetic correlations between KET and DA were relatively strong and positive (up to 0.79) in both first- and later-lactation cows. Genetic correlations between fertility disorders were slightly lower. Metritis was strongly genetically correlated with both metabolic disease traits in the first lactation only. All other genetic correlations between metabolic and fertility diseases were statistically nonsignificant. First-lactation KET and MET were strongly positively correlated with later-lactation performance for these traits due to the environmental herd-year effect. Indicator traits were moderately genetically correlated (from 0.30 to 0.63 in absolute values) with both metabolic disease traits in the first lactation. Smaller and mostly nonsignificant genetic correlations were among indicators and metabolic diseases in later lactations. The only significant genetic correlations between indicators and fertility disorders were those between BCS and MET in both first and later lactations. Results indicated a limited value of a joint genetic evaluation model for metabolic disease traits and fertility disorders in Canadian Holsteins. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Assessing the potential for an ongoing arms race within and between the sexes: selection and heritable variation.

PubMed

Friberg, Urban; Lew, Timothy A; Byrne, Phillip G; Rice, William R

2005-07-01

In promiscuous species, sexual selection generates two opposing male traits: offense (acquiring new mates and supplanting stored sperm) and defense (enforcing fidelity on one's mates and preventing sperm displacement when this fails). Coevolution between these traits requires both additive genetic variation and associated natural selection. Previous work with Drosophila melanogaster found autosomal genetic variation for these traits among inbred lines from a mixture of populations, but only nonheritable genetic variation was found within a single outbred population. These results do not support ongoing antagonistic coevolution between offense and defense, nor between either of these male traits and female reproductive characters. Here we use a new method (hemiclonal analysis) to study genomewide genetic variation in a large outbred laboratory population of D. melanogaster. Hemiclonal analysis estimates the additive genetic variation among random, genomewide haplotypes taken from a large, outbred, locally adapted laboratory population and determines the direction of the selection gradient on this variation. In contrast to earlier studies, we found low but biologically significant heritable variation for defensive and offensive offspring production as well as all their components (P1, fidelity, P2, and remating). Genetic correlations between these traits were substantially different from those reported for inbred lines. A positive genetic correlation was found between defense and offense, demonstrating that some shared genes influence both traits. In addition to this common variation, evidence for unique genetic variation for each trait was also found, supporting an ongoing coevolutionary arms race between defense and offense. Reproductive conflict between males can strongly influence female fitness. Correspondingly, we found genetic variation in both defense and offense that affected female fitness. No evidence was found for intersexual conflict in the context of male defense, but we found substantial intersexual conflict in the context of male offensive sperm competitive ability. These results indicate that conflict between competing males also promotes an associated arms race between the sexes.

Genetic and environmental correlations between subjective wellbeing and experience of life events in adolescence.

PubMed

Wootton, Robyn E; Davis, Oliver S P; Mottershaw, Abigail L; Wang, R Adele H; Haworth, Claire M A

2017-09-01

Some life events appear heritable due to the genetic influence on related behaviours. Shared genetic influence between negative behaviours and negative life events has previously been established. This study investigated whether subjective wellbeing and positive life events were genetically associated. Participants in the Twins Early Development Study (aged 16.32 ± .68 years) completed subjective wellbeing and life events assessments via two separate studies (overlapping N for wellbeing and life events measures ranged from 3527 to 9350). We conducted bivariate twin models between both positive and negative life events with subjective wellbeing and related positive psychological traits including subjective happiness, life satisfaction, optimism, hopefulness and gratitude measured at 16 years. Results suggested that the heritability of life events can partially be explained by shared genetic influences with the wellbeing indicators. Wellbeing traits were positively genetically correlated with positive life events and negatively correlated with negative life events (except curiosity where there was no correlation). Those positive traits that drive behaviour (grit and ambition) showed the highest genetic correlation with life events, whereas the reflective trait gratitude was less correlated. This suggests that gene-environment correlations might explain the observed genetic association between life events and wellbeing. Inheriting propensity for positive traits might cause you to seek environments that lead to positive life events and avoid environments which make negative life events more likely.

Prediction accuracy of direct and indirect approaches, and their relationships with prediction ability of calibration models.

PubMed

Belay, T K; Dagnachew, B S; Boison, S A; Ådnøy, T

2018-03-28

Milk infrared spectra are routinely used for phenotyping traits of interest through links developed between the traits and spectra. Predicted individual traits are then used in genetic analyses for estimated breeding value (EBV) or for phenotypic predictions using a single-trait mixed model; this approach is referred to as indirect prediction (IP). An alternative approach [direct prediction (DP)] is a direct genetic analysis of (a reduced dimension of) the spectra using a multitrait model to predict multivariate EBV of the spectral components and, ultimately, also to predict the univariate EBV or phenotype for the traits of interest. We simulated 3 traits under different genetic (low: 0.10 to high: 0.90) and residual (zero to high: ±0.90) correlation scenarios between the 3 traits and assumed the first trait is a linear combination of the other 2 traits. The aim was to compare the IP and DP approaches for predictions of EBV and phenotypes under the different correlation scenarios. We also evaluated relationships between performances of the 2 approaches and the accuracy of calibration equations. Moreover, the effect of using different regression coefficients estimated from simulated phenotypes (β p ), true breeding values (β g ), and residuals (β r ) on performance of the 2 approaches were evaluated. The simulated data contained 2,100 parents (100 sires and 2,000 cows) and 8,000 offspring (4 offspring per cow). Of the 8,000 observations, 2,000 were randomly selected and used to develop links between the first and the other 2 traits using partial least square (PLS) regression analysis. The different PLS regression coefficients, such as β p , β g , and β r , were used in subsequent predictions following the IP and DP approaches. We used BLUP analyses for the remaining 6,000 observations using the true (co)variance components that had been used for the simulation. Accuracy of prediction (of EBV and phenotype) was calculated as a correlation between predicted and true values from the simulations. The results showed that accuracies of EBV prediction were higher in the DP than in the IP approach. The reverse was true for accuracy of phenotypic prediction when using β p but not when using β g and β r , where accuracy of phenotypic prediction in the DP was slightly higher than in the IP approach. Within the DP approach, accuracies of EBV when using β g were higher than when using β p only at the low genetic correlation scenario. However, we found no differences in EBV prediction accuracy between the β p and β g in the IP approach. Accuracy of the calibration models increased with an increase in genetic and residual correlations between the traits. Performance of both approaches increased with an increase in accuracy of the calibration models. In conclusion, the DP approach is a good strategy for EBV prediction but not for phenotypic prediction, where the classical PLS regression-based equations or the IP approach provided better results. The Authors. Published by FASS Inc. and Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).

Genetic parameters of egg quality traits in long-term pedigree recorded Japanese quail.

PubMed

Sari, M; Tilki, M; Saatci, M

2016-08-01

This study was conducted to determine the genetic parameters of internal and external quality traits of Japanese quail eggs. Two statistical models were used in the calculation of genetic parameters and variance components. While 286 eggs were used based on model 1, 1,524 eggs were used based on model 2. Genetic parameters of the first eggs were calculated with direct genetic effect included in the analysis as random factors by using model 1. Model 2 was used for all eggs (5 to 6 eggs from each hen for six rearing groups). As different from model 1, their permanent environmental effects were also included in the model 2. Heritability of egg weight, egg length, egg width, shape index, shell weight, shell thickness, and shell ratio among the external quality traits of the eggs was respectively found to be 0.44, 0.53, 0.51, 0.70, 0.19, 0.16, and 0.05, respectively, according to model 1. These values were found to be 0.46, 0.40, 0.74, 0.48, 0.60, 0.28, and 0.21, respectively, according to model 2. Yolk weight, yolk diameter, yolk height, yolk index, yolk ratio, albumen weight, albumen height, albumen ratio, and Haugh unit values among the internal quality traits of the egg were found to be 0.22, 0.32, 0.02, 0.16, 0.19, 0.34, 0.19, 0.17, and 0.17, respectively, according to model 1. These internal quality traits were found to be 0.27, 0.18, 0.38, 0.06, 0.20, 0.41, 0.15, 0.15, and 0.12, respectively, according to model 2. Consequently, in this study, strong genetic correlations were detected between albumen height and Haugh unit, and also between albumen height and albumen weight. Additionally, a high and positive correlation was observed between some yolk traits (yolk weight and diameter) and albumen traits (weight and height). All these genetic correlations can be used to improve egg quality with a selection according to albumen weight. © 2016 Poultry Science Association Inc.

Genetic parameters of mid-infrared methane predictions and their relationships with milk production traits in Holstein cattle.

PubMed

Kandel, P B; Vanrobays, M-L; Vanlierde, A; Dehareng, F; Froidmont, E; Gengler, N; Soyeurt, H

2017-07-01

Many countries have pledged to reduce greenhouse gases. In this context, the dairy sector is one of the identified sectors to adapt production circumstances to address socio-environmental constraints due to its large carbon footprint related to CH 4 emission. This study aimed mainly to estimate (1) the genetic parameters of 2 milk mid-infrared-based CH 4 proxies [predicted daily CH 4 emission (PME, g/d), and log-transformed predicted CH 4 intensity (LMI)] and (2) their genetic correlations with milk production traits [milk (MY), fat (FY), and protein (PY) yields] from first- and second-parity Holstein cows. A total of 336,126 and 231,400 mid-infrared CH 4 phenotypes were collected from 56,957 and 34,992 first- and second-parity cows, respectively. The PME increased from the first to the second lactation (433 vs. 453 g/d) and the LMI decreased (2.93 vs. 2.86). We used 20 bivariate random regression test-day models to estimate the variance components. Moderate heritability values were observed for both CH 4 traits, and those values decreased slightly from the first to the second lactation (0.25 ± 0.01 and 0.22 ± 0.01 for PME; 0.18 ± 0.01 and 0.17 ± 0.02 for LMI). Lactation phenotypic and genetic correlations were negative between PME and MY in both first and second lactations (-0.07 vs. -0.07 and -0.19 vs. -0.24, respectively). More close scrutiny revealed that relative increase of PME was lower with high MY levels even reverting to decrease, and therefore explaining the negative correlations, indicating that higher producing cows could be a mitigation option for CH 4 emission. The PME phenotypic correlations were almost equal to 0 with FY and PY for both lactations. However, the genetic correlations between PME and FY were slightly positive (0.11 and 0.12), whereas with PY the correlations were slightly negative (-0.05 and -0.04). Both phenotypic and genetic correlations between LMI and MY or PY or FY were always relatively highly negative (from -0.21 to -0.88). As the genetic correlations between PME and LMI were strong (0.71 and 0.72 in first and second lactation), the selection of one trait would also strongly influence the other trait. However, in animal breeding context, PME, as a direct quantity CH 4 proxy, would be preferred to LMI, which is a ratio trait of PME with a trait already in the index. The range of PME sire estimated breeding values were 22.1 and 29.41 kg per lactation in first and second parity, respectively. Further studies must be conducted to evaluate the effect of the introduction of PME in a selection index on the other traits already included in this index, such as, for instance, fertility or longevity. The Authors. Published by the Federation of Animal Science Societies and Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).

Children with Prader-Willi syndrome vs. Williams syndrome: indirect effects on parents during a jigsaw puzzle task.

PubMed

Ly, T M; Hodapp, R M

2005-12-01

Genetic disorders predispose individuals to exhibit characteristic behaviours, which in turn elicit particular behaviours from others. In response to the strength of Prader-Willi syndrome (PWS) and weakness of Williams syndrome (WS) in visual-spatial tasks such as jigsaw puzzles, parents' behaviours can be affected by their child's level of puzzle ability or syndrome diagnosis. Children were asked to complete two jigsaw puzzles (one with the experimenter and the other with the parent) for 5 min each. Frequencies of parental helping and reinforcement behaviours, along with ratings of parental directiveness, were examined as parents interacted with their children on a jigsaw puzzle task. Within each aetiological group, correlates of parental behaviours with child characteristics were also examined. Compared to parents of children with PWS, parents of children with WS engaged in a more directive style of interaction, and provided more help and reinforcement. Relative to parents of children with higher puzzle abilities (from both aetiologies), parents of children with lower abilities also showed the same pattern. Both the child's aetiology and puzzle abilities were important in predicting parents' directiveness and helping and reinforcement behaviours. Within the PWS group, parents' behaviours correlated negatively with the child's puzzle abilities and general cognitive functioning; no such relations occurred in the WS group. Parents' behaviours were affected by both the child's diagnosis and actual puzzle abilities, suggesting important implications for understanding and intervening with parents and children with different genetic syndromes.

Genetic parameters of infectious bovine keratoconjunctivitis and its relationship with weight and parasite infestations in Australian tropical Bos taurus cattle.

PubMed

Ali, Abdirahman A; O'Neill, Christopher J; Thomson, Peter C; Kadarmideen, Haja N

2012-07-27

Infectious bovine keratoconjunctivitis (IBK) or 'pinkeye' is an economically important ocular disease that significantly impacts animal performance. Genetic parameters for IBK infection and its genetic and phenotypic correlations with cattle tick counts, number of helminth (unspecified species) eggs per gram of faeces and growth traits in Australian tropically adapted Bos taurus cattle were estimated. Animals were clinically examined for the presence of IBK infection before and after weaning when the calves were 3 to 6 months and 15 to 18 months old, respectively and were also recorded for tick counts, helminth eggs counts as an indicator of intestinal parasites and live weights at several ages including 18 months. Negative genetic correlations were estimated between IBK incidence and weight traits for animals in pre-weaning and post-weaning datasets. Genetic correlations among weight measurements were positive, with moderate to high values. Genetic correlations of IBK incidence with tick counts were positive for the pre-weaning and negative for the post-weaning datasets but negative with helminth eggs counts for the pre-weaning dataset and slightly positive for the post-weaning dataset. Genetic correlations between tick and helminth eggs counts were moderate and positive for both datasets. Phenotypic correlations of IBK incidence with helminth eggs per gram of faeces were moderate and positive for both datasets, but were close to zero for both datasets with tick counts. Our results suggest that genetic selection against IBK incidence in tropical cattle is feasible and that calves genetically prone to acquire IBK infection could also be genetically prone to have a slower growth. The positive genetic correlations among weight traits and between tick and helminth eggs counts suggest that they are controlled by common genes (with pleiotropic effects). Genetic correlations between IBK incidence and tick and helminth egg counts were moderate and opposite between pre-weaning and post-weaning datasets, suggesting that the environmental and (or) maternal effects differ between these two growth phases. This preliminary study provides estimated genetic parameters for IBK incidence, which could be used to design selection and breeding programs for tropical adaptation in beef cattle.

Genetic parameters of infectious bovine keratoconjunctivitis and its relationship with weight and parasite infestations in Australian tropical Bos taurus cattle

PubMed Central

2012-01-01

Background Infectious bovine keratoconjunctivitis (IBK) or ‘pinkeye’ is an economically important ocular disease that significantly impacts animal performance. Genetic parameters for IBK infection and its genetic and phenotypic correlations with cattle tick counts, number of helminth (unspecified species) eggs per gram of faeces and growth traits in Australian tropically adapted Bos taurus cattle were estimated. Methods Animals were clinically examined for the presence of IBK infection before and after weaning when the calves were 3 to 6 months and 15 to 18 months old, respectively and were also recorded for tick counts, helminth eggs counts as an indicator of intestinal parasites and live weights at several ages including 18 months. Results Negative genetic correlations were estimated between IBK incidence and weight traits for animals in pre-weaning and post-weaning datasets. Genetic correlations among weight measurements were positive, with moderate to high values. Genetic correlations of IBK incidence with tick counts were positive for the pre-weaning and negative for the post-weaning datasets but negative with helminth eggs counts for the pre-weaning dataset and slightly positive for the post-weaning dataset. Genetic correlations between tick and helminth eggs counts were moderate and positive for both datasets. Phenotypic correlations of IBK incidence with helminth eggs per gram of faeces were moderate and positive for both datasets, but were close to zero for both datasets with tick counts. Conclusions Our results suggest that genetic selection against IBK incidence in tropical cattle is feasible and that calves genetically prone to acquire IBK infection could also be genetically prone to have a slower growth. The positive genetic correlations among weight traits and between tick and helminth eggs counts suggest that they are controlled by common genes (with pleiotropic effects). Genetic correlations between IBK incidence and tick and helminth egg counts were moderate and opposite between pre-weaning and post-weaning datasets, suggesting that the environmental and (or) maternal effects differ between these two growth phases. This preliminary study provides estimated genetic parameters for IBK incidence, which could be used to design selection and breeding programs for tropical adaptation in beef cattle. PMID:22839739

Parental knowledge is an environmental influence on adolescent externalizing.

PubMed

Marceau, Kristine; Narusyte, Jurgita; Lichtenstein, Paul; Ganiban, Jody M; Spotts, Erica L; Reiss, David; Neiderhiser, Jenae M

2015-02-01

There is evidence both that parental monitoring is an environmental influence serving to diminish adolescent externalizing problems and that this association may be driven by adolescents' characteristics via genetic and/or environmental mechanisms, such that adolescents with fewer problems tell their parents more, and therefore appear to be better monitored. Without information on how parents' and children's genes and environments influence correlated parent and child behaviors, it is impossible to clarify the mechanisms underlying this association. The present study used the Extended Children of Twins model to distinguish types of gene-environment correlation and direct environmental effects underlying associations between parental knowledge and adolescent (age 11-22 years) externalizing behavior with a Swedish sample of 909 twin parents and their adolescent offspring and a US-based sample of 405 White adolescent siblings and their parents. Results suggest that more parental knowledge is associated with less adolescent externalizing via a direct environmental influence independent of any genetic influences. There was no evidence of a child-driven explanation of the association between parental knowledge and adolescent externalizing problems. In this sample of adolescents, parental knowledge exerted an environmental influence on adolescent externalizing after accounting for genetic influences of parents and adolescents. Because the association between parenting and child development originates in the parent, treatment for adolescent externalizing must not only include parents but should also focus on altering their parental style. Thus, findings suggest that teaching parents better knowledge-related monitoring strategies is likely to help reduce externalizing problems in adolescents. © 2014 The Authors. Journal of Child Psychology and Psychiatry. © 2014 Association for Child and Adolescent Mental Health.

Parental Knowledge is an Environmental Influence on Adolescent Externalizing

PubMed Central

Marceau, Kristine; Narusyte, Jurgita; Lichtenstein, Paul; Ganiban, Jody M.; Spotts, Erica L.; Reiss, David; Neiderhiser, Jenae M.

2014-01-01

Background There is evidence both that parental monitoring is an environmental influence serving to diminish adolescent externalizing problems and that this association may be driven by adolescents’ characteristics via genetic and/or environmental mechanisms, such that adolescents with fewer problems tell their parents more, and therefore appear to be better monitored. Without information on how parents’ and children’s genes and environments influence correlated parent and child behaviors, it is impossible to clarify the mechanisms underlying this association. Method The present study used the Extended Children of Twins model to distinguish types of gene-environment correlation and direct environmental effects underlying associations between parental knowledge and adolescent (age 11-22 years) externalizing behavior with a Swedish sample of 909 twin parents and their adolescent offspring and a US-based sample of 405 White adolescent siblings and their parents. Results Results suggest that more parental knowledge is associated with less adolescent externalizing via a direct environmental influence independent of any genetic influences. There was no evidence of a child-driven explanation of the association between parental knowledge and adolescent externalizing problems. Conclusions In this sample of adolescents, parental knowledge exerted an environmental influence on adolescent externalizing after accounting for genetic influences of parents and adolescents. Because the association between parenting and child development originates in the parent, treatment for adolescent externalizing must not only include parents but should focus on altering their parental style. Thus, findings suggest that teaching parents better knowledge-related monitoring strategies is likely to help reduce externalizing problems in adolescents. PMID:24975929

Why do measures of normal and disordered personality correlate? A study of genetic comorbidity.

PubMed

Jang, K L; Livesley, W J

1999-01-01

The genetic and environmental correlations between measures of normal (NEO-FFI) and abnormal personality (Dimensional Assessment of Personality Pathology: DAPP-BQ) were estimated in a sample of 545 volunteer general population twin pairs (269 monozygotic and 276 dizygotic pairs). The largest genetic correlations were observed between the 18 DAPP-BQ dimensions and NEO-FFI neuroticism (range = .05 to .81; median = .48), extraversion (range = -.65 to .33; median = -.28), agreeableness (range = -.65 to .00; median = -.38), and conscientiousness (range = -.76 to .52; median = -.31). The smallest genetic correlations were found between the DAPP-BQ dimensions and NEO-FFI openness (range = -.17 to .20; median = -.04). The environmental correlations are lower in magnitude but show the same pattern of correlations between DAPP-BQ and NEO-FFI scales. These results indicate that these two scales share a common broad-based genetic architecture, whereas the environmental influences show greater scale specificity.

Chaotic homes and school achievement: a twin study

PubMed Central

Hanscombe, Ken B; Haworth, Claire MA; Davis, Oliver SP; Jaffee, Sara R; Plomin, Robert

2011-01-01

Background Chaotic homes predict poor school performance. Given that it is known that genes affect both children's experience of household chaos and their school achievement, to what extent is the relationship between high levels of noise and environmental confusion in the home, and children's school performance, mediated by heritable child effects? This is the first study to explore the genetic and environmental pathways between household chaos and academic performance. Method Children's perceptions of family chaos at ages 9 and 12 and their school performance at age 12 were assessed in more than 2,300 twin pairs. The use of child-specific measures in a multivariate genetic analysis made it possible to investigate the genetic and environmental origins of the covariation between children's experience of chaos in the home and their school achievement. Results Children's experience of family chaos and their school achievement were significantly correlated in the expected negative direction (r = −.26). As expected, shared environmental factors explained a large proportion (63%) of the association. However, genetic factors accounted for a significant proportion (37%) of the association between children's experience of household chaos and their school performance. Conclusions The association between chaotic homes and poor performance in school, previously assumed to be entirely environmental in origin, is in fact partly genetic. How children's home environment affects their academic achievement is not simply in the direction environment → child → outcome. Instead, genetic factors that influence children's experience of the disordered home environment also affect how well they do at school. The relationship between the child, their environment and their performance at school is complex: both genetic and environmental factors play a role. PMID:21675992

Human Facial Shape and Size Heritability and Genetic Correlations.

PubMed

Cole, Joanne B; Manyama, Mange; Larson, Jacinda R; Liberton, Denise K; Ferrara, Tracey M; Riccardi, Sheri L; Li, Mao; Mio, Washington; Klein, Ophir D; Santorico, Stephanie A; Hallgrímsson, Benedikt; Spritz, Richard A

2017-02-01

The human face is an array of variable physical features that together make each of us unique and distinguishable. Striking familial facial similarities underscore a genetic component, but little is known of the genes that underlie facial shape differences. Numerous studies have estimated facial shape heritability using various methods. Here, we used advanced three-dimensional imaging technology and quantitative human genetics analysis to estimate narrow-sense heritability, heritability explained by common genetic variation, and pairwise genetic correlations of 38 measures of facial shape and size in normal African Bantu children from Tanzania. Specifically, we fit a linear mixed model of genetic relatedness between close and distant relatives to jointly estimate variance components that correspond to heritability explained by genome-wide common genetic variation and variance explained by uncaptured genetic variation, the sum representing total narrow-sense heritability. Our significant estimates for narrow-sense heritability of specific facial traits range from 28 to 67%, with horizontal measures being slightly more heritable than vertical or depth measures. Furthermore, for over half of facial traits, >90% of narrow-sense heritability can be explained by common genetic variation. We also find high absolute genetic correlation between most traits, indicating large overlap in underlying genetic loci. Not surprisingly, traits measured in the same physical orientation (i.e., both horizontal or both vertical) have high positive genetic correlations, whereas traits in opposite orientations have high negative correlations. The complex genetic architecture of facial shape informs our understanding of the intricate relationships among different facial features as well as overall facial development. Copyright © 2017 by the Genetics Society of America.

Evolution of resistance to a multiple-herbivore community: genetic correlations, diffuse coevolution, and constraints on the plant's response to selection.

PubMed

Wise, Michael J; Rausher, Mark D

2013-06-01

Although plants are generally attacked by a community of several species of herbivores, relatively little is known about the strength of natural selection for resistance in multiple-herbivore communities-particularly how the strength of selection differs among herbivores that feed on different plant organs or how strongly genetic correlations in resistance affect the evolutionary responses of the plant. Here, we report on a field study measuring natural selection for resistance in a diverse community of herbivores of Solanum carolinense. Using linear phenotypic-selection analyses, we found that directional selection acted to increase resistance to seven species. Selection was strongest to increase resistance to fruit feeders, followed by flower feeders, then leaf feeders. Selection favored a decrease in resistance to a stem borer. Bootstrapping analyses showed that the plant population contained significant genetic variation for each of 14 measured resistance traits and significant covariances in one-third of the pairwise combinations of resistance traits. These genetic covariances reduced the plant's overall predicted evolutionary response for resistance against the herbivore community by about 60%. Diffuse (co)evolution was widespread in this community, and the diffuse interactions had an overwhelmingly constraining (rather than facilitative) effect on the plant's evolution of resistance. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Genetic parameters for chronic progressive lymphedema in Belgian Draught Horses.

PubMed

De Keyser, K; Janssens, S; Peeters, L M; Foqué, N; Gasthuys, F; Oosterlinck, M; Buys, N

2014-12-01

Genetic parameters for chronic progressive lymphedema (CPL)-associated traits in Belgian Draught Horses were estimated, using a multitrait animal model. Clinical scores of CPL in the four limbs/horse (CPLclin ), skinfold thickness and hair samples (hair diameter) were studied. Due to CPLclin uncertainty in younger horses (progressive CPL character), a restricted data set (D_3+) was formed, excluding records from horses under 3 years from the complete data set (D_full). Age, gender, coat colour and limb hair pigmentation were included as fixed, permanent environment and date of recording as random effects. Higher CPLclin certainty (D_3+) increased heritability coefficients of, and genetic correlations between traits, with CPLclin heritabilities (SE) for the respective data sets: 0.11 (0.06) and 0.26 (0.05). A large proportion of the CPLclin variance was attributed to the permanent environmental effect in D_full, but less in D_3+. Date of recording explained a proportion of variance from 0.09 ± 0.03 to 0.61 ± 0.08. Additive genetic correlations between CPLclin and both skinfold thickness and hair diameter showed the latter two traits cannot be used as a direct diagnostic aid for CPL. Due to the relatively low heritability of CPLclin , selection should focus on estimated breeding values (from repeated clinical examinations) to reduce CPL occurrence in the Belgian Draught Horse. © 2014 Blackwell Verlag GmbH.

Correlation of genetic and clinical findings in Spanish patients with X-linked juvenile retinoschisis.

PubMed

Riveiro-Alvarez, Rosa; Trujillo-Tiebas, Maria-Jose; Gimenez-Pardo, Ascension; Garcia-Hoyos, Maria; Lopez-Martinez, Miguel-Angel; Aguirre-Lamban, Jana; Garcia-Sandoval, Blanca; Vazquez-Fernandez del Pozo, Silvia; Cantalapiedra, Diego; Avila-Fernandez, Almudena; Baiget, Montserrat; Ramos, Carmen; Ayuso, Carmen

2009-09-01

X-linked juvenile retinoschisis (XLRS) is one of the most common causes of juvenile macular degeneration in males, characterized by microcystic changes, splitting within the inner retinal layer (schisis), and the presence of vitreous veils. This study was conducted to describe and further correlate specific genetic variation in Spanish patients with XLRS with clinical characteristics and additional ophthalmic complications. The study was performed in 34 Spanish families with XLRS, comprising 51 affected males. Thorough clinical ophthalmic and electrophysiological examinations were performed. The coding regions of the RS1 gene were amplified by polymerase chain reaction and directly sequenced. Haplotype analyses were also performed. Twenty different mutations were identified. Ten of the 20 were novel and 3 were de novo mutational events. The most common mutation (p.Gln154Arg; 6/20) presented a common haplotype. RS1 variants did not correlate with ophthalmic findings and were not associated with additional ophthalmic complications. The prevalent p.Gln154Arg mutation is first reported in this work and presents a common origin in Spanish patients with XLRS. In addition, de novo mutations mainly occur in CG dinucleotides. Despite the large mutational spectrum and variable phenotypes, no genotype-phenotype correlations were found. Identifying the causative mutation is helpful in confirming diagnosis and counseling, but cannot provide a prognosis.

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions.

PubMed

Hoban, Sean; Kelley, Joanna L; Lotterhos, Katie E; Antolin, Michael F; Bradburd, Gideon; Lowry, David B; Poss, Mary L; Reed, Laura K; Storfer, Andrew; Whitlock, Michael C

2016-10-01

Uncovering the genetic and evolutionary basis of local adaptation is a major focus of evolutionary biology. The recent development of cost-effective methods for obtaining high-quality genome-scale data makes it possible to identify some of the loci responsible for adaptive differences among populations. Two basic approaches for identifying putatively locally adaptive loci have been developed and are broadly used: one that identifies loci with unusually high genetic differentiation among populations (differentiation outlier methods) and one that searches for correlations between local population allele frequencies and local environments (genetic-environment association methods). Here, we review the promises and challenges of these genome scan methods, including correcting for the confounding influence of a species' demographic history, biases caused by missing aspects of the genome, matching scales of environmental data with population structure, and other statistical considerations. In each case, we make suggestions for best practices for maximizing the accuracy and efficiency of genome scans to detect the underlying genetic basis of local adaptation. With attention to their current limitations, genome scan methods can be an important tool in finding the genetic basis of adaptive evolutionary change.

Genome-wide association analysis of secondary imaging phenotypes from the Alzheimer's disease neuroimaging initiative study.

PubMed

Zhu, Wensheng; Yuan, Ying; Zhang, Jingwen; Zhou, Fan; Knickmeyer, Rebecca C; Zhu, Hongtu

2017-02-01

The aim of this paper is to systematically evaluate a biased sampling issue associated with genome-wide association analysis (GWAS) of imaging phenotypes for most imaging genetic studies, including the Alzheimer's Disease Neuroimaging Initiative (ADNI). Specifically, the original sampling scheme of these imaging genetic studies is primarily the retrospective case-control design, whereas most existing statistical analyses of these studies ignore such sampling scheme by directly correlating imaging phenotypes (called the secondary traits) with genotype. Although it has been well documented in genetic epidemiology that ignoring the case-control sampling scheme can produce highly biased estimates, and subsequently lead to misleading results and suspicious associations, such findings are not well documented in imaging genetics. We use extensive simulations and a large-scale imaging genetic data analysis of the Alzheimer's Disease Neuroimaging Initiative (ADNI) data to evaluate the effects of the case-control sampling scheme on GWAS results based on some standard statistical methods, such as linear regression methods, while comparing it with several advanced statistical methods that appropriately adjust for the case-control sampling scheme. Copyright © 2016 Elsevier Inc. All rights reserved.

Genetic parameters for milk, fat and protein yields in Murrah buffaloes (Bubalus bubalis Artiodactyla, Bovidae)

PubMed Central

2010-01-01

The objective of the present study was to estimate genetic parameters for test-day milk, fat and protein yields and 305-day-yields in Murrah buffaloes. 4,757 complete lactations of Murrah buffaloes were analyzed. Co-variance components were estimated by the restricted maximum likelihood method. The models included additive direct genetic and permanent environmental effects as random effects, and the fixed effects of contemporary group, milking number and age of the cow at calving as linear and quadratic covariables. Contemporary groups were defined by herd-year-month of test for test-day yields and by herd-year-season of calving for 305-day yields. The heritability estimates obtained by two-trait analysis ranged from 0.15 to 0.24 for milk, 0.16 to 0.23 for protein and 0.13 to 0.22 for fat, yields. Genetic and phenotypic correlations were all positive. The observed population additive genetic variation indicated that selection might be an effective tool in changing population means in milk, fat and protein yields. PMID:21637608

Genetic and environmental influences on restrained eating behavior

PubMed Central

Schur, Ellen; Noonan, Carolyn; Polivy, Janet; Goldberg, Jack; Buchwald, Dedra

2009-01-01

Objective We examined the relative contributions of genetic and environmental influences to restrained eating. Methods Restrained eating was assessed by the Restraint Scale in a survey mailed to all twins enrolled in the University of Washington Twin Registry. We used structural equation modeling to estimate genetic and non-genetic contributions to restrained eating. Results 1,196 monozygotic, 456 same-sex dizygotic twins, and 447 opposite-sex twins were included in analyses. Restraint Scale scores were more closely correlated in monozygotic twins (rmale = 0.55, rfemale = 0.55) than in same-sex dizygotic twins (rmale = 0.31, rfemale = 0.19). Based on structural equation modeling, the estimated heritability for restrained eating, adjusted for BMI and sex, was 43% (95% confidence interval 35–50%). There was little evidence for common environmental effects. Conclusion These results indicate an inherited component to restrained eating. Genes could influence restrained eating directly or through inherited mediators such as personality factors or tendencies to gain weight. PMID:19658171

Transmission of biology and culture among post-contact Native Americans on the western Great Plains.

PubMed

Lycett, Stephen J; von Cramon-Taubadel, Noreen

2016-08-12

The transmission of genes and culture between human populations has major implications for understanding potential correlations between history, biological, and cultural variation. Understanding such dynamics in 19th century, post-contact Native Americans on the western Great Plains is especially challenging given passage of time, complexity of known dynamics, and difficulties of determining genetic patterns in historical populations for whom, even today, genetic data for their descendants are rare. Here, biometric data collected under the direction of Franz Boas from communities penecontemporaneous with the classic bison-hunting societies, were used as a proxy for genetic variation and analyzed together with cultural data. We show that both gene flow and "culture flow" among populations on the High Plains were mediated by geography, fitting a model of isolation-by-distance. Moreover, demographic and cultural exchange among these communities largely overrode the visible signal of the prior millennia of cultural and genetic histories of these populations.

To grow or not to grow: Hair morphogenesis and human genetic hair disorders

PubMed Central

Duverger, Olivier; Morasso, Maria I.

2014-01-01

Mouse models have greatly helped in elucidating the molecular mechanisms involved in hair formation and regeneration. Recent publications have reviewed the genes involved in mouse hair development based on the phenotype of transgenic, knockout and mutant animal models. While much of this information has been instrumental in determining molecular aspects of human hair development and cycling, mice exhibit a specific pattern of hair morphogenesis and hair distribution throughout the body that cannot be directly correlated to human hair. In this mini-review, we discuss specific aspects of human hair follicle development and present an up-to-date summary of human genetic disorders associated with abnormalities in hair follicle morphogenesis, structure or regeneration. PMID:24361867

Continuity of Genetic and Environmental Influences on Cognition across the Life Span: A Meta-Analysis of Longitudinal Twin and Adoption Studies

PubMed Central

Tucker-Drob, Elliot M.; Briley, Daniel A.

2014-01-01

The longitudinal rank-order stability of cognitive ability increases dramatically over the lifespan. Multiple theoretical perspectives have proposed that genetic and/or environmental mechanisms underlie the longitudinal stability of cognition, and developmental trends therein. However, the patterns of stability of genetic and environmental influences on cognition over the lifespan largely remain poorly understood. We searched for longitudinal studies of cognition that reported raw genetically-informative longitudinal correlations or parameter estimates from longitudinal behavior genetic models. We identified 150 combinations of time points and measures from 15 independent longitudinal samples. In total, longitudinal data came from 4,538 monozygotic twin pairs raised together, 7,777 dizygotic twin pairs raised together, 34 monozygotic twin pairs raised apart, 78 dizygotic twin pairs raised apart, 141 adoptive sibling pairs, and 143 non-adoptive sibling pairs, ranging in age from infancy through late adulthood. At all ages, cross-time genetic correlations and shared environmental correlations were substantially larger than cross-time nonshared environmental correlations. Cross-time correlations for genetic and shared environmental components were low during early childhood, increased sharply over child development, and remained relatively high from adolescence through late adulthood. Cross-time correlations for nonshared environmental components were low across childhood and increased gradually to moderate magnitudes in adulthood. Increasing phenotypic stability over child development was almost entirely mediated by genetic factors. Time-based decay of genetic and shared environmental stability was more pronounced earlier in child development. Results are interpreted in reference to theories of gene-environment interaction and correlation. PMID:24611582

[Correlation between genetic differences of mates and pathogenicity of Schistosoma japonicum in definitive host].

PubMed

Wen-Qiao, Huang; Yuan-Jian, Zhu; Da-Bing, Lv; Xia, Zhou; Ying-Nan, Yang; Hong-Xiang, Zhu-Ge

2016-05-24

To explore the correlation between the genetic dissimilarity and heterozygosity of mates and the pathogenicity of Schistosoma japonicum in the definitive host. By using seven microsatellite loci markers, S. japonicum genotyping of sixteen pairs randomly mated was performed, the genetic dissimilarity and heterozygosity were calculated between the mates, and the correlation between the genetic dissimilarity and heterozygosity of the mates and the pathogenicity of S. japonicum in the definitive host was evaluated. There was a significant correlation between the genetic similarity of S. japonicum mates and the mean number of eggs per worm pair in the liver and intestinal tissue ( r = 0.501 6, P < 0.05; r = 0.796 5, P < 0.01, respectively) and the hatching rate of deposited eggs in the liver ( r = 0.508 3, P < 0.05), respectively. There was no correlation between the genetic similarity of the mates and hepatosplenomegaly per worm pair ( r = 0.109 5, P > 0.05; r = 0.265 3, P > 0.05, respectively) and the average diameter of granuloma in the liver ( r = -0.272 7, P > 0.05), respectively. There was no correlation between the heterozygosity of the mates and all the pathological parameters of S. japonicum in the definitive host ( P > 0.05). There is the correlation between the genetic dissimilarity of the mates and the pathogenicity of S. japonicum in the definitive host, and the genetic dissimilarity is greater, pathogenicity is weaker. There is no correlation between heterozygosity of the mates and the pathogenicity of S. japonicum in the definitive host.

DISSCO: direct imputation of summary statistics allowing covariates

PubMed Central

Xu, Zheng; Duan, Qing; Yan, Song; Chen, Wei; Li, Mingyao; Lange, Ethan; Li, Yun

2015-01-01

Background: Imputation of individual level genotypes at untyped markers using an external reference panel of genotyped or sequenced individuals has become standard practice in genetic association studies. Direct imputation of summary statistics can also be valuable, for example in meta-analyses where individual level genotype data are not available. Two methods (DIST and ImpG-Summary/LD), that assume a multivariate Gaussian distribution for the association summary statistics, have been proposed for imputing association summary statistics. However, both methods assume that the correlations between association summary statistics are the same as the correlations between the corresponding genotypes. This assumption can be violated in the presence of confounding covariates. Methods: We analytically show that in the absence of covariates, correlation among association summary statistics is indeed the same as that among the corresponding genotypes, thus serving as a theoretical justification for the recently proposed methods. We continue to prove that in the presence of covariates, correlation among association summary statistics becomes the partial correlation of the corresponding genotypes controlling for covariates. We therefore develop direct imputation of summary statistics allowing covariates (DISSCO). Results: We consider two real-life scenarios where the correlation and partial correlation likely make practical difference: (i) association studies in admixed populations; (ii) association studies in presence of other confounding covariate(s). Application of DISSCO to real datasets under both scenarios shows at least comparable, if not better, performance compared with existing correlation-based methods, particularly for lower frequency variants. For example, DISSCO can reduce the absolute deviation from the truth by 3.9–15.2% for variants with minor allele frequency <5%. Availability and implementation: http://www.unc.edu/∼yunmli/DISSCO. Contact: yunli@med.unc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25810429

DISSCO: direct imputation of summary statistics allowing covariates.

PubMed

Xu, Zheng; Duan, Qing; Yan, Song; Chen, Wei; Li, Mingyao; Lange, Ethan; Li, Yun

2015-08-01

Imputation of individual level genotypes at untyped markers using an external reference panel of genotyped or sequenced individuals has become standard practice in genetic association studies. Direct imputation of summary statistics can also be valuable, for example in meta-analyses where individual level genotype data are not available. Two methods (DIST and ImpG-Summary/LD), that assume a multivariate Gaussian distribution for the association summary statistics, have been proposed for imputing association summary statistics. However, both methods assume that the correlations between association summary statistics are the same as the correlations between the corresponding genotypes. This assumption can be violated in the presence of confounding covariates. We analytically show that in the absence of covariates, correlation among association summary statistics is indeed the same as that among the corresponding genotypes, thus serving as a theoretical justification for the recently proposed methods. We continue to prove that in the presence of covariates, correlation among association summary statistics becomes the partial correlation of the corresponding genotypes controlling for covariates. We therefore develop direct imputation of summary statistics allowing covariates (DISSCO). We consider two real-life scenarios where the correlation and partial correlation likely make practical difference: (i) association studies in admixed populations; (ii) association studies in presence of other confounding covariate(s). Application of DISSCO to real datasets under both scenarios shows at least comparable, if not better, performance compared with existing correlation-based methods, particularly for lower frequency variants. For example, DISSCO can reduce the absolute deviation from the truth by 3.9-15.2% for variants with minor allele frequency <5%. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Methods for meta-analysis of multiple traits using GWAS summary statistics.

PubMed

Ray, Debashree; Boehnke, Michael

2018-03-01

Genome-wide association studies (GWAS) for complex diseases have focused primarily on single-trait analyses for disease status and disease-related quantitative traits. For example, GWAS on risk factors for coronary artery disease analyze genetic associations of plasma lipids such as total cholesterol, LDL-cholesterol, HDL-cholesterol, and triglycerides (TGs) separately. However, traits are often correlated and a joint analysis may yield increased statistical power for association over multiple univariate analyses. Recently several multivariate methods have been proposed that require individual-level data. Here, we develop metaUSAT (where USAT is unified score-based association test), a novel unified association test of a single genetic variant with multiple traits that uses only summary statistics from existing GWAS. Although the existing methods either perform well when most correlated traits are affected by the genetic variant in the same direction or are powerful when only a few of the correlated traits are associated, metaUSAT is designed to be robust to the association structure of correlated traits. metaUSAT does not require individual-level data and can test genetic associations of categorical and/or continuous traits. One can also use metaUSAT to analyze a single trait over multiple studies, appropriately accounting for overlapping samples, if any. metaUSAT provides an approximate asymptotic P-value for association and is computationally efficient for implementation at a genome-wide level. Simulation experiments show that metaUSAT maintains proper type-I error at low error levels. It has similar and sometimes greater power to detect association across a wide array of scenarios compared to existing methods, which are usually powerful for some specific association scenarios only. When applied to plasma lipids summary data from the METSIM and the T2D-GENES studies, metaUSAT detected genome-wide significant loci beyond the ones identified by univariate analyses. Evidence from larger studies suggest that the variants additionally detected by our test are, indeed, associated with lipid levels in humans. In summary, metaUSAT can provide novel insights into the genetic architecture of a common disease or traits. © 2017 WILEY PERIODICALS, INC.

Variances and correlations of milk production, fertility, longevity, and type traits over time in Australian Holstein cattle.

PubMed

Haile-Mariam, M; Pryce, J E

2015-10-01

When using historical data, it is often assumed that the genetic correlation of the same trait recorded at different time points is reasonably close to 1. However, selection and possible changes in trait definitions means that this may not necessarily be the case. Regularly monitoring genetic parameters over time is important, as changes could reduce the accuracy of genetic evaluations. About 20 yr (1993 to 2012) of data on milk yield as well as functional and type traits from Australian Holstein dairy cattle were analyzed to assess changes in genetic correlations within and among traits over time by considering 2 traits at a time using linear random regression (RR) and multitrait (MT) models. Both residual and genetic variances for milk yield traits and calving interval (CI) increased over time, with the highest increase observed for protein yield. For most type traits some fluctuations over time were noted in both the residual and additive genetic variances. Genetic correlations among survival (i.e., from first to second lactation), milk yield traits, CI, and some type traits varied over time. The genetic correlation of the same trait (e.g., protein yield, fat yield, and some type traits) measured in different years was also less than 1.0 (0.1-0.9), which is likely to be due to selection or changes in trait definitions. Estimates of parameters from the RR model were generally similar to those from MT models that considered the same trait recorded in different year groups as different traits. However, in the case of survival and CI (i.e., lowly heritable traits), the genetic correlations over time obtained from the MT model were lower (0.21 to 0.75) than those from the RR models (0.9-1.0). Genetic correlations of survival with milk, fat, and protein yields declined from ~0.4 to 0.5 at the beginning of the study period (1993/94) to zero or negative at the end (2009/10), whereas the correlation between CI and milk yield became more unfavorable and increased from 0.3 to 0.5 over the same time period. The same pattern was observed for the genetic correlation between survival and CI, which also became more unfavorable over time and increased from 0.67 to 0.87 in absolute value. The genetic correlations of survival with type traits, such as angularity and body depth, decreased from near zero to negative (-0.3 to -0.4). But genetic correlations between pin set and survival showed less variation (0.2-0.3) over time. Similarly the genetic correlation of CI with body depth and angularity became more antagonistic over time. Over time the importance of traits such as milk yield and overall type as criteria for culling decreased, whereas the importance of fertility and possible disease incidence increased, implying that there has been a switch from voluntary to involuntary reasons dominating culling decisions. Changes in genetic correlations of the same trait and among traits over time have important implications on the accuracy of prediction of traits, such as survival and CI, which often rely on other traits as predictors and ultimately on the accuracy of genetic evaluations (traditional and genomic), and also the prediction of response to selection. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Predicting age-age genetic correlations in tree-breeding programs: a case study of Pinus taeda L.

Treesearch

D.P. Gwaze; F.E. Bridgwater; T.D. Byram; J.A. Woolliams; C.G. Williams

2000-01-01

A meta-analysis of 520 parents and 51,439 individuals was used to develop two equations for predicting age-age genetic correlations in Pinus taeda L. Genetic and phenotypic family mean correlations and heritabilities were estimated for ages ranging from 2 to 25 years on 31...

Effects of selection for blood serum IGF-I concentration on reproductive performance of female Angus beef cattle.

PubMed

Zhang, X; Davis, M E; Moeller, S J; Ottobre, J S

2013-09-01

Reproductive performance of animals affects lifetime productivity. However, improvement of reproductive traits via direct selection is generally slow due to low heritability. Therefore, identification of indicator traits for reproductive performance may enhance genetic response. Previous studies showed that serum IGF-I concentration is a candidate indicator for growth and reproductive traits. The objective of our study was to estimate the variances or covariances of IGF-I concentration with reproductive traits. Data were collected from a divergent selection experiment for serum IGF-I concentration at the Eastern Agricultural Research Station owned by The Ohio State University. The study included a total of 2,662 calves in the 1989 to 2005 calf crops. Variance or covariance components were estimated for direct and maternal genetic effects, maternal environment effects, environment effects, and phenotypic effects using an animal model in a multiple-trait, derivative-free, restricted maximum likelihood (MTDFREML, Boldman et al., 1995) computer program. Direct additive genetic correlations suggest that selection for greater IGF-I concentration (heritability = 0.50 ± 0.07) could lead to increased conception rate (heritability = 0.11 ± 0.06, r = 0.32, P < 0.001) and calving rate (heritability = 0.13 ± 0.06, r = 0.43, P < 0.001) and decreased age at first calving in heifers (heritability = 0.35 ± 0.20, r = -0.40, P < 0.001).

Sequence-length variation of mtDNA HVS-I C-stretch in Chinese ethnic groups.

PubMed

Chen, Feng; Dang, Yong-hui; Yan, Chun-xia; Liu, Yan-ling; Deng, Ya-jun; Fulton, David J R; Chen, Teng

2009-10-01

The purpose of this study was to investigate mitochondrial DNA (mtDNA) hypervariable segment-I (HVS-I) C-stretch variations and explore the significance of these variations in forensic and population genetics studies. The C-stretch sequence variation was studied in 919 unrelated individuals from 8 Chinese ethnic groups using both direct and clone sequencing approaches. Thirty eight C-stretch haplotypes were identified, and some novel and population specific haplotypes were also detected. The C-stretch genetic diversity (GD) values were relatively high, and probability (P) values were low. Additionally, C-stretch length heteroplasmy was observed in approximately 9% of individuals studied. There was a significant correlation (r=-0.961, P<0.01) between the expansion of the cytosine sequence length in the C-stretch of HVS-I and a reduction in the number of upstream adenines. These results indicate that the C-stretch could be a useful genetic maker in forensic identification of Chinese populations. The results from the Fst and dA genetic distance matrix, neighbor-joining tree, and principal component map also suggest that C-stretch could be used as a reliable genetic marker in population genetics.

Alternative life histories in the Atlantic salmon: genetic covariances within the sneaker sexual tactic in males.

PubMed

Páez, David James; Bernatchez, Louis; Dodson, Julian J

2011-07-22

Alternative reproductive tactics are ubiquitous in many species. Tactic expression often depends on whether an individual's condition surpasses thresholds that are responsible for activating particular developmental pathways. Two central goals in understanding the evolution of reproductive tactics are quantifying the extent to which thresholds are explained by additive genetic effects, and describing their covariation with condition-related traits. We monitored the development of early sexual maturation that leads to the sneaker reproductive tactic in Atlantic salmon (Salmo salar L.). We found evidence for additive genetic variance in the timing of sexual maturity (which is a measure of the surpassing of threshold values) and body-size traits. This suggests that selection can affect the patterns of sexual development by changing the timing of this event and/or body size. Significant levels of covariation between these traits also occurred, implying a potential for correlated responses to selection. Closer examination of genetic covariances suggests that the detected genetic variation is distributed along at least five directions of phenotypic variation. Our results show that the potential for evolution of the life-history traits constituting this reproductive phenotype is greatly influenced by their patterns of genetic covariance.

Alternative life histories in the Atlantic salmon: genetic covariances within the sneaker sexual tactic in males

PubMed Central

Páez, David James; Bernatchez, Louis; Dodson, Julian J.

2011-01-01

Alternative reproductive tactics are ubiquitous in many species. Tactic expression often depends on whether an individual's condition surpasses thresholds that are responsible for activating particular developmental pathways. Two central goals in understanding the evolution of reproductive tactics are quantifying the extent to which thresholds are explained by additive genetic effects, and describing their covariation with condition-related traits. We monitored the development of early sexual maturation that leads to the sneaker reproductive tactic in Atlantic salmon (Salmo salar L.). We found evidence for additive genetic variance in the timing of sexual maturity (which is a measure of the surpassing of threshold values) and body-size traits. This suggests that selection can affect the patterns of sexual development by changing the timing of this event and/or body size. Significant levels of covariation between these traits also occurred, implying a potential for correlated responses to selection. Closer examination of genetic covariances suggests that the detected genetic variation is distributed along at least five directions of phenotypic variation. Our results show that the potential for evolution of the life-history traits constituting this reproductive phenotype is greatly influenced by their patterns of genetic covariance. PMID:21177685

On the Genetic and Environmental Correlations between Trait Emotional Intelligence and Vocational Interest Factors.

PubMed

Schermer, Julie Aitken; Petrides, Konstantinos V; Vernon, Philip A

2015-04-01

The phenotypic (observed), genetic, and environmental correlations were examined in a sample of adult twins between the four factors and global score of the trait emotional intelligence questionnaire (TEIQue) and the seven vocational interest factors of the Jackson Career Explorer (JCE). Multiple significant correlations were found involving the work style vocational interest factor (consisting of job security, stamina, accountability, planfulness, and interpersonal confidence) and the social vocational interest factor (which included interests in the social sciences, personal services, teaching, social services, and elementary education), both of which correlated significantly with all of the TEIQue variables (well-being, self-control, emotionality, sociability, and global trait EI). Following bivariate genetic analyses, most of the significant phenotypic correlations were found to also have significant genetic correlations as well as significant non-shared (unique) environmental correlations.

Heritability of anti-predatory traits: vigilance and locomotor performance in marmots.

PubMed

Blumstein, D T; Lea, A J; Olson, L E; Martin, J G A

2010-05-01

Animals must allocate some proportion of their time to detecting predators. In birds and mammals, such anti-predator vigilance has been well studied, and we know that it may be influenced by a variety of intrinsic and extrinsic factors. Despite hundreds of studies focusing on vigilance and suggestions that there are individual differences in vigilance, there have been no prior studies examining its heritability in the field. Here, we present one of the first reports of (additive) genetic variation in vigilance. Using a restricted maximum likelihood procedure, we found that, in yellow-bellied marmots (Marmota flaviventris), the heritability of locomotor ability (h(2)=0.21), and especially vigilance (h(2) = 0.08), is low. These modest heritability estimates suggest great environmental variation or a history of directional selection eliminating genetic variation in these traits. We also found a significant phenotypic (r(P) = -0.09 +/- 0.04, P = 0.024) and a substantial, but not significant, genetic correlation (r(A) = -0.57 +/- 0.28, P = 0.082) between the two traits (slower animals are less vigilant while foraging). We found no evidence of differential survival or longevity associated with particular phenotypes of either trait. The genetic correlation may persist because of environmental heterogeneity and genotype-by-environment interactions maintaining the correlation, or because there are two ways to solve the problem of foraging in exposed areas: be very vigilant and rely on early detection coupled with speed to escape, or reduce vigilance to minimize time spent in an exposed location. Both strategies seem to be equally successful, and this 'locomotor ability-wariness' syndrome may therefore allow slow animals to compensate behaviourally for their impaired locomotor ability.

Estimating non-genetic and genetic parameters of pre-weaning growth traits in Raini Cashmere goat.

PubMed

Barazandeh, Arsalan; Moghbeli, Sadrollah Molaei; Vatankhah, Mahmood; Mohammadabadi, Mohammadreza

2012-04-01

Data and pedigree information used in the present study were 3,022 records of kids obtained from the breeding station of Raini goat. The studied traits were birth weight (BW), weaning weight (WW), average daily gain from birth to weaning (ADG) and Kleiber ratio at weaning (KR). The model included the fixed effects of sex of kid, type of birth, age of dam, year of birth, month of birth, and age of kid (days) as covariate that had significant effects, and random effects direct additive genetic, maternal additive genetic, maternal permanent environmental effects and residual. (Co) variance components were estimated using univariate and multivariate analysis by WOMBAT software applying four animal models including and ignoring maternal effects. Likelihood ratio test used to determine the most appropriate models. Heritability (h(a)(2)) estimates for BW, WW, ADG, and KR according to suitable model were 0.12 ± 0.05, 0.08 ± 0.06, 0.10 ± 0.06, and 0.06 ± 0.05, respectively. Estimates of the proportion of maternal permanent environmental effect to phenotypic variance (c(2)) were 0.17 ± 0.03, 0.07 ± 0.03, and 0.07 ± 0.03 for BW, WW, and ADG, respectively. Genetic correlations among traits were positive and ranged from 0.53 (BW-ADG) to 1.00 (WW-ADG, WW-KR, and ADG-KR). The maternal permanent environmental correlations between BW-WW, BW-ADG, and WW-ADG were 0.54, 0.48, and 0.99, respectively. Results indicated that maternal effects, especially maternal permanent environmental effects are an important source of variation in pre-weaning growth trait and ignoring those in the model redound incorrect genetic evaluation of kids.

Evaluation of body condition score measured throughout lactation as an indicator of fertility in dairy cattle.

PubMed

Banos, G; Brotherstone, S; Coffey, M P

2004-08-01

Body condition score (BCS) records of primiparous Holstein cows were analyzed both as a single measure per animal and as repeated measures per sire of cow. The former resulted in a single, average, genetic evaluation for each sire, and the latter resulted in separate genetic evaluations per day of lactation. Repeated measure analysis yielded genetic correlations of less than unity between days of lactation, suggesting that BCS may not be the same trait across lactation. Differences between daily genetic evaluations on d 10 or 30 and subsequent daily evaluations were used to assess BCS change at different stages of lactation. Genetic evaluations for BCS level or change were used to estimate genetic correlations between BCS measures and fertility traits in order to assess the capacity of BCS to predict fertility. Genetic correlation estimates with calving interval and non-return rate were consistently higher for daily BCS than single measure BCS evaluations, but results were not always statistically different. Genetic correlations between BCS change and fertility traits were not significantly different from zero. The product of the accuracy of BCS evaluations with their genetic correlation with the UK fertility index, comprising calving interval and non-return rate, was consistently higher for daily than for single BCS evaluations, by 28 to 53%. This product is associated with the conceptual correlated response in fertility from BCS selection and was highest for early (d 10 to 75) evaluations.

The intergenerational correlation in weight: How genetic resemblance reveals the social role of families*

PubMed Central

Martin, Molly A.

2009-01-01

According to behavioral genetics research, the intergenerational correlation in weight derives solely from shared genetic predispositions, but complete genetic determinism contradicts the scientific consensus that social and behavioral change underlies the modern obesity epidemic. To address this conundrum, this article utilizes sibling data from the National Longitudinal Study of Adolescent Health and extends structural equation sibling models to incorporate siblings’ genetic relationships to explore the role of families’ social characteristics for adolescent weight. The article is the first to demonstrate that the association between parents’ obesity and adolescent weight is both social and genetic. Furthermore, by incorporating genetic information, the shared and social origins of the correlation between inactivity and weight are better revealed. PMID:19569401

Longitudinal changes in telomere length and associated genetic parameters in dairy cattle analysed using random regression models.

PubMed

Seeker, Luise A; Ilska, Joanna J; Psifidi, Androniki; Wilbourn, Rachael V; Underwood, Sarah L; Fairlie, Jennifer; Holland, Rebecca; Froy, Hannah; Bagnall, Ainsley; Whitelaw, Bruce; Coffey, Mike; Nussey, Daniel H; Banos, Georgios

2018-01-01

Telomeres cap the ends of linear chromosomes and shorten with age in many organisms. In humans short telomeres have been linked to morbidity and mortality. With the accumulation of longitudinal datasets the focus shifts from investigating telomere length (TL) to exploring TL change within individuals over time. Some studies indicate that the speed of telomere attrition is predictive of future disease. The objectives of the present study were to 1) characterize the change in bovine relative leukocyte TL (RLTL) across the lifetime in Holstein Friesian dairy cattle, 2) estimate genetic parameters of RLTL over time and 3) investigate the association of differences in individual RLTL profiles with productive lifespan. RLTL measurements were analysed using Legendre polynomials in a random regression model to describe TL profiles and genetic variance over age. The analyses were based on 1,328 repeated RLTL measurements of 308 female Holstein Friesian dairy cattle. A quadratic Legendre polynomial was fitted to the fixed effect of age in months and to the random effect of the animal identity. Changes in RLTL, heritability and within-trait genetic correlation along the age trajectory were calculated and illustrated. At a population level, the relationship between RLTL and age was described by a positive quadratic function. Individuals varied significantly regarding the direction and amount of RLTL change over life. The heritability of RLTL ranged from 0.36 to 0.47 (SE = 0.05-0.08) and remained statistically unchanged over time. The genetic correlation of RLTL at birth with measurements later in life decreased with the time interval between samplings from near unity to 0.69, indicating that TL later in life might be regulated by different genes than TL early in life. Even though animals differed in their RLTL profiles significantly, those differences were not correlated with productive lifespan (p = 0.954).

Longitudinal changes in telomere length and associated genetic parameters in dairy cattle analysed using random regression models

PubMed Central

Ilska, Joanna J.; Psifidi, Androniki; Wilbourn, Rachael V.; Underwood, Sarah L.; Fairlie, Jennifer; Holland, Rebecca; Froy, Hannah; Bagnall, Ainsley; Whitelaw, Bruce; Coffey, Mike; Nussey, Daniel H.; Banos, Georgios

2018-01-01

Telomeres cap the ends of linear chromosomes and shorten with age in many organisms. In humans short telomeres have been linked to morbidity and mortality. With the accumulation of longitudinal datasets the focus shifts from investigating telomere length (TL) to exploring TL change within individuals over time. Some studies indicate that the speed of telomere attrition is predictive of future disease. The objectives of the present study were to 1) characterize the change in bovine relative leukocyte TL (RLTL) across the lifetime in Holstein Friesian dairy cattle, 2) estimate genetic parameters of RLTL over time and 3) investigate the association of differences in individual RLTL profiles with productive lifespan. RLTL measurements were analysed using Legendre polynomials in a random regression model to describe TL profiles and genetic variance over age. The analyses were based on 1,328 repeated RLTL measurements of 308 female Holstein Friesian dairy cattle. A quadratic Legendre polynomial was fitted to the fixed effect of age in months and to the random effect of the animal identity. Changes in RLTL, heritability and within-trait genetic correlation along the age trajectory were calculated and illustrated. At a population level, the relationship between RLTL and age was described by a positive quadratic function. Individuals varied significantly regarding the direction and amount of RLTL change over life. The heritability of RLTL ranged from 0.36 to 0.47 (SE = 0.05–0.08) and remained statistically unchanged over time. The genetic correlation of RLTL at birth with measurements later in life decreased with the time interval between samplings from near unity to 0.69, indicating that TL later in life might be regulated by different genes than TL early in life. Even though animals differed in their RLTL profiles significantly, those differences were not correlated with productive lifespan (p = 0.954). PMID:29438415

Heritability and genetic correlations of personality traits in a wild population of yellow-bellied marmots (Marmota flaviventris).

PubMed

Petelle, M B; Martin, J G A; Blumstein, D T

2015-10-01

Describing and quantifying animal personality is now an integral part of behavioural studies because individually distinctive behaviours have ecological and evolutionary consequences. Yet, to fully understand how personality traits may respond to selection, one must understand the underlying heritability and genetic correlations between traits. Previous studies have reported a moderate degree of heritability of personality traits, but few of these studies have either been conducted in the wild or estimated the genetic correlations between personality traits. Estimating the additive genetic variance and covariance in the wild is crucial to understand the evolutionary potential of behavioural traits. Enhanced environmental variation could reduce heritability and genetic correlations, thus leading to different evolutionary predictions. We estimated the additive genetic variance and covariance of docility in the trap, sociability (mirror image stimulation), and exploration and activity in two different contexts (open-field and mirror image simulation experiments) in a wild population of yellow-bellied marmots (Marmota flaviventris). We estimated both heritability of behaviours and of personality traits and found nonzero additive genetic variance in these traits. We also found nonzero maternal, permanent environment and year effects. Finally, we found four phenotypic correlations between traits, and one positive genetic correlation between activity in the open-field test and sociability. We also found permanent environment correlations between activity in both tests and docility and exploration in the MIS test. This is one of a handful of studies to adopt a quantitative genetic approach to explain variation in personality traits in the wild and, thus, provides important insights into the potential variance available for selection. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Oceanographic connectivity and environmental correlates of genetic structuring in Atlantic herring in the Baltic Sea

PubMed Central

Teacher, Amber GF; André, Carl; Jonsson, Per R; Merilä, Juha

2013-01-01

Marine fish often show little genetic structuring in neutral marker genes, and Atlantic herring (Clupea harengus) in the Baltic Sea are no exception; historically, very low levels of population differentiation (FST ≍ 0.002) have been found, despite a high degree of interpopulation environmental heterogeneity in salinity and temperature. Recent exome sequencing and SNP studies have however shown that many loci are under selection in this system. Here, we combined population genetic analyses of a large number of transcriptome-derived microsatellite markers with oceanographic modelling to investigate genetic differentiation and connectivity in Atlantic herring at a relatively fine scale within the Baltic Sea. We found evidence for weak but robust and significant genetic structuring (FST = 0.008) explainable by oceanographic connectivity. Genetic differentiation was also associated with site differences in temperature and salinity, with the result driven by the locus Her14 which appears to be under directional selection (FST = 0.08). The results show that Baltic herring are genetically structured within the Baltic Sea, and highlight the role of oceanography and environmental factors in explaining this structuring. The results also have implications for the management of herring fisheries, the most economically important fishery in the Baltic Sea, suggesting that the current fisheries management units may be in need of revision. PMID:23745145

Gene flow of common ash (Fraxinus excelsior L.) in a fragmented landscape.

PubMed

Semizer-Cuming, Devrim; Kjær, Erik Dahl; Finkeldey, Reiner

2017-01-01

Gene flow dynamics of common ash (Fraxinus excelsior L.) is affected by several human activities in Central Europe, including habitat fragmentation, agroforestry expansion, controlled and uncontrolled transfer of reproductive material, and a recently introduced emerging infectious disease, ash dieback, caused by Hymenoscyphus fraxineus. Habitat fragmentation may alter genetic connectivity and effective population size, leading to loss of genetic diversity and increased inbreeding in ash populations. Gene flow from cultivated trees in landscapes close to their native counterparts may also influence the adaptability of future generations. The devastating effects of ash dieback have already been observed in both natural and managed populations in continental Europe. However, potential long-term effects of genetic bottlenecks depend on gene flow across fragmented landscapes. For this reason, we studied the genetic connectivity of ash trees in an isolated forest patch of a fragmented landscape in Rösenbeck, Germany. We applied two approaches to parentage analysis to estimate gene flow patterns at the study site. We specifically investigated the presence of background pollination at the landscape level and the degree of genetic isolation between native and cultivated trees. Local meteorological data was utilized to understand the effect of wind on the pollen and seed dispersal patterns. Gender information of the adult trees was considered for calculating the dispersal distances. We found that the majority of the studied seeds (55-64%) and seedlings (75-98%) in the forest patch were fathered and mothered by the trees within the same patch. However, we determined a considerable amount of pollen flow (26-45%) from outside of the study site, representing background pollination at the landscape level. Limited pollen flow was observed from neighbouring cultivated trees (2%). Both pollen and seeds were dispersed in all directions in accordance with the local wind directions. Whereas there was no positive correlation between pollen dispersal distance and wind speed, the correlation between seed dispersal distance and wind speed was significant (0.71, p < 0.001), indicating that strong wind favours long-distance dispersal of ash seeds. Finally, we discussed the implications of establishing gene conservation stands and the use of enrichment planting in the face of ash dieback.

Gene flow of common ash (Fraxinus excelsior L.) in a fragmented landscape

PubMed Central

Kjær, Erik Dahl; Finkeldey, Reiner

2017-01-01

Gene flow dynamics of common ash (Fraxinus excelsior L.) is affected by several human activities in Central Europe, including habitat fragmentation, agroforestry expansion, controlled and uncontrolled transfer of reproductive material, and a recently introduced emerging infectious disease, ash dieback, caused by Hymenoscyphus fraxineus. Habitat fragmentation may alter genetic connectivity and effective population size, leading to loss of genetic diversity and increased inbreeding in ash populations. Gene flow from cultivated trees in landscapes close to their native counterparts may also influence the adaptability of future generations. The devastating effects of ash dieback have already been observed in both natural and managed populations in continental Europe. However, potential long-term effects of genetic bottlenecks depend on gene flow across fragmented landscapes. For this reason, we studied the genetic connectivity of ash trees in an isolated forest patch of a fragmented landscape in Rösenbeck, Germany. We applied two approaches to parentage analysis to estimate gene flow patterns at the study site. We specifically investigated the presence of background pollination at the landscape level and the degree of genetic isolation between native and cultivated trees. Local meteorological data was utilized to understand the effect of wind on the pollen and seed dispersal patterns. Gender information of the adult trees was considered for calculating the dispersal distances. We found that the majority of the studied seeds (55–64%) and seedlings (75–98%) in the forest patch were fathered and mothered by the trees within the same patch. However, we determined a considerable amount of pollen flow (26–45%) from outside of the study site, representing background pollination at the landscape level. Limited pollen flow was observed from neighbouring cultivated trees (2%). Both pollen and seeds were dispersed in all directions in accordance with the local wind directions. Whereas there was no positive correlation between pollen dispersal distance and wind speed, the correlation between seed dispersal distance and wind speed was significant (0.71, p < 0.001), indicating that strong wind favours long-distance dispersal of ash seeds. Finally, we discussed the implications of establishing gene conservation stands and the use of enrichment planting in the face of ash dieback. PMID:29053740

Genetic relationships between detailed reproductive traits and performance traits in Holstein-Friesian dairy cattle.

PubMed

Carthy, T R; Ryan, D P; Fitzgerald, A M; Evans, R D; Berry, D P

2016-02-01

The objective of the study was to estimate the genetic relationships between detailed reproductive traits derived from ultrasound examination of the reproductive tract and a range of performance traits in Holstein-Friesian dairy cows. The performance traits investigated included calving performance, milk production, somatic cell score (i.e., logarithm transformation of somatic cell count), carcass traits, and body-related linear type traits. Detailed reproductive traits included (1) resumed cyclicity at the time of examination, (2) multiple ovulations, (3) early ovulation, (4) heat detection, (5) ovarian cystic structures, (6) embryo loss, and (7) uterine score, measured on a 1 (little or no fluid with normal tone) to 4 (large quantity of fluid with a flaccid tone) scale, based on the tone of the uterine wall and the quantity of fluid present in the uterus. (Co)variance components were estimated using a repeatability animal linear mixed model. Genetic merit for greater milk, fat, and protein yield was associated with a reduced ability to resume cyclicity postpartum (genetic correlations ranged from -0.25 to -0.15). Higher genetic merit for milk yield was also associated with a greater genetic susceptibility to multiple ovulations. Genetic predisposition to elevated somatic cell score was associated with a decreased likelihood of cyclicity postpartum (genetic correlation of -0.32) and a greater risk of both multiple ovulations (genetic correlation of 0.25) and embryo loss (genetic correlation of 0.32). Greater body condition score was genetically associated with an increased likelihood of resumption of cyclicity postpartum (genetic correlation of 0.52). Genetically heavier, fatter carcasses with better conformation were also associated with an increased likelihood of resumed cyclicity by the time of examination (genetic correlations ranged from 0.24 to 0.41). Genetically heavier carcasses were associated with an inferior uterine score as well as a greater predisposition to embryo loss. Despite the overall antagonistic relationship between reproductive performance and both milk and carcass traits, not all detailed aspects of reproduction performance exhibited an antagonistic relationship. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

A Parallel Genetic Algorithm to Discover Patterns in Genetic Markers that Indicate Predisposition to Multifactorial Disease

PubMed Central

Rausch, Tobias; Thomas, Alun; Camp, Nicola J.; Cannon-Albright, Lisa A.; Facelli, Julio C.

2008-01-01

This paper describes a novel algorithm to analyze genetic linkage data using pattern recognition techniques and genetic algorithms (GA). The method allows a search for regions of the chromosome that may contain genetic variations that jointly predispose individuals for a particular disease. The method uses correlation analysis, filtering theory and genetic algorithms (GA) to achieve this goal. Because current genome scans use from hundreds to hundreds of thousands of markers, two versions of the method have been implemented. The first is an exhaustive analysis version that can be used to visualize, explore, and analyze small genetic data sets for two marker correlations; the second is a GA version, which uses a parallel implementation allowing searches of higher-order correlations in large data sets. Results on simulated data sets indicate that the method can be informative in the identification of major disease loci and gene-gene interactions in genome-wide linkage data and that further exploration of these techniques is justified. The results presented for both variants of the method show that it can help genetic epidemiologists to identify promising combinations of genetic factors that might predispose to complex disorders. In particular, the correlation analysis of IBD expression patterns might hint to possible gene-gene interactions and the filtering might be a fruitful approach to distinguish true correlation signals from noise. PMID:18547558

Neuronal boost to evolutionary dynamics

PubMed Central

de Vladar, Harold P.; Szathmáry, Eörs

2015-01-01

Standard evolutionary dynamics is limited by the constraints of the genetic system. A central message of evolutionary neurodynamics is that evolutionary dynamics in the brain can happen in a neuronal niche in real time, despite the fact that neurons do not reproduce. We show that Hebbian learning and structural synaptic plasticity broaden the capacity for informational replication and guided variability provided a neuronally plausible mechanism of replication is in place. The synergy between learning and selection is more efficient than the equivalent search by mutation selection. We also consider asymmetric landscapes and show that the learning weights become correlated with the fitness gradient. That is, the neuronal complexes learn the local properties of the fitness landscape, resulting in the generation of variability directed towards the direction of fitness increase, as if mutations in a genetic pool were drawn such that they would increase reproductive success. Evolution might thus be more efficient within evolved brains than among organisms out in the wild. PMID:26640653

Relationships between adaptive and neutral genetic diversity and ecological structure and functioning: a meta-analysis

PubMed Central

Whitlock, Raj

2014-01-01

Understanding the effects of intraspecific genetic diversity on the structure and functioning of ecological communities is a fundamentally important part of evolutionary ecology and may also have conservation relevance in identifying the situations in which genetic diversity coincides with species-level diversity.Early studies within this field documented positive relationships between genetic diversity and ecological structure, but recent studies have challenged these findings. Conceptual synthesis has been hampered because studies have used different measures of intraspecific variation (phenotypically adaptive vs. neutral) and have considered different measures of ecological structure in different ecological and spatial contexts. The aim of this study is to strengthen conceptual understanding by providing an empirical synthesis quantifying the relationship between genetic diversity and ecological structure.Here, I present a meta-analysis of the relationship between genetic diversity within plant populations and the structure and functioning of associated ecological communities (including 423 effect sizes from 70 studies). I used Bayesian meta-analyses to examine (i) the strength and direction of this relationship, (ii) the extent to which phenotypically adaptive and neutral (molecular) measures of diversity differ in their association with ecological structure and (iii) variation in outcomes among different measures of ecological structure and in different ecological contexts.Effect sizes measuring the relationship between adaptive diversity (genotypic richness) and both community- and ecosystem-level ecological responses were small, but significantly positive. These associations were supported by genetic effects on species richness and productivity, respectively.There was no overall association between neutral genetic diversity and measures of ecological structure, but a positive correlation was observed under a limited set of demographic conditions. These results suggest that adaptive and neutral genetic diversity should not be treated as ecologically equivalent measures of intraspecific variation.Synthesis. This study advances the debate over whether relationships between genetic diversity and ecological structure are either simply positive or negative, by showing how the strength and direction of these relationships changes with different measures of diversity and in different ecological contexts. The results provide a solid foundation for assessing when and where an expanded synthesis between ecology and genetics will be most fruitful. PMID:25210204

Genetic correlations between dressage, show jumping and studbook-entry inspection traits in a process of specialization in Dutch Warmblood horses.

PubMed

Rovere, G; Ducro, B J; van Arendonk, J A M; Norberg, E; Madsen, P

2017-04-01

Sport performance in dressage and show jumping are two important traits in the breeding goals of many studbooks. To determine the optimum selection scheme for jumping and dressage, knowledge is needed on the genetic correlation between both disciplines and between traits measured early in life and performance in competition in each discipline. This study aimed to estimate genetic parameters to support decision-making on specialization of breeding horses for dressage and show jumping in Dutch warmblood horses. Genetic correlations between performance of horses in dressage and show jumping were estimated as well as the genetic correlation between traits recorded during studbook-entry inspections and performance in dressage and show jumping competitions. The information on competition comprised the performance of 82 694 horses in dressage and 62 072 horses in show jumping, recorded in the period 1993-2012. For 26 056 horses, information was available for both disciplines. The information on traits recorded at studbook-entry inspections comprised 62 628 horses, recorded in the period 1992-2013. Genetic parameters were estimated from the whole dataset and from a subset without horses recorded in both disciplines. Additionally, the genetic parameters were estimated in three different time periods defined by horses' birth year. The genetic correlation between dressage and show jumping in the whole dataset was -0.23, and it was -0.03 when it was estimated from horses recorded in only one discipline. The genetic correlation between dressage and show jumping was more negative in the most recent time period in all the cases. The more negative correlation between disciplines in more recent time periods was not reflected in changes in the correlations between competitions traits and the traits recorded in the studbook-first inspection. These results suggest that a breeding programme under specialization might be most effective defining two separate aggregate breeding goals for each of the disciplines. © 2016 Blackwell Verlag GmbH.

Genetic variation in the functional ENG allele inherited from the non-affected parent associates with presence of pulmonary arteriovenous malformation in hereditary hemorrhagic telangiectasia 1 (HHT1) and may influence expression of PTPN14.

PubMed

Letteboer, Tom G W; Benzinou, Michael; Merrick, Christopher B; Quigley, David A; Zhau, Kechen; Kim, Il-Jin; To, Minh D; Jablons, David M; van Amstel, Johannes K P; Westermann, Cornelius J J; Giraud, Sophie; Dupuis-Girod, Sophie; Lesca, Gaetan; Berg, Jonathan H; Balmain, Allan; Akhurst, Rosemary J

2015-01-01

HHT shows clinical variability within and between families. Organ site and prevalence of arteriovenous malformations (AVMs) depend on the HHT causative gene and on environmental and genetic modifiers. We tested whether variation in the functional ENG allele, inherited from the unaffected parent, alters risk for pulmonary AVM in HHT1 mutation carriers who are ENG haploinsufficient. Genetic association was found between rs10987746 of the wild type ENG allele and presence of pulmonary AVM [relative risk = 1.3 (1.0018-1.7424)]. The rs10987746-C at-risk allele associated with lower expression of ENG RNA in a panel of human lymphoblastoid cell lines (P = 0.004). Moreover, in angiogenically active human lung adenocarcinoma tissue, but not in uninvolved quiescent lung, rs10987746-C was correlated with expression of PTPN14 (P = 0.004), another modifier of HHT. Quantitative TAQMAN expression analysis in a panel of normal lung tissues from 69 genetically heterogeneous inter-specific backcross mice, demonstrated strong correlation between expression levels of Eng, Acvrl1, and Ptpn14 (r2 = 0.75-0.9, P < 1 × 10(-12)), further suggesting a direct or indirect interaction between these three genes in lung in vivo. Our data indicate that genetic variation within the single functional ENG gene influences quantitative and/or qualitative differences in ENG expression that contribute to risk of pulmonary AVM in HHT1, and provide correlative support for PTPN14 involvement in endoglin/ALK1 lung biology in vivo. PTPN14 has been shown to be a negative regulator of Yap/Taz signaling, which is implicated in mechanotransduction, providing a possible molecular link between endoglin/ALK1 signaling and mechanical stress. EMILIN2, which showed suggestive genetic association with pulmonary AVM, is also reported to interact with Taz in angiogenesis. Elucidation of the molecular mechanisms regulating these interactions in endothelial cells may ultimately provide more rational choices for HHT therapy.

Effects of landscape features on population genetic variation of a tropical stream fish, Stone lapping minnow, Garra cambodgiensis, in the upper Nan River drainage basin, northern Thailand.

PubMed

Jaisuk, Chaowalee; Senanan, Wansuk

2018-01-01

Spatial genetic variation of river-dwelling freshwater fishes is typically affected by the historical and contemporary river landscape as well as life-history traits. Tropical river and stream landscapes have endured extended geological change, shaping the existing pattern of genetic diversity, but were not directly affected by glaciation. Thus, spatial genetic variation of tropical fish populations should look very different from the pattern observed in temperate fish populations. These data are becoming important for designing appropriate management and conservation plans, as these aquatic systems are undergoing intense development and exploitation. This study evaluated the effects of landscape features on population genetic diversity of Garra cambodgiensis, a stream cyprinid , in eight tributary streams in the upper Nan River drainage basin ( n  = 30-100 individuals/location), Nan Province, Thailand. These populations are under intense fishing pressure from local communities. Based on 11 microsatellite loci, we detected moderate genetic diversity within eight population samples (average number of alleles per locus = 10.99 ± 3.00; allelic richness = 10.12 ± 2.44). Allelic richness within samples and stream order of the sampling location were negatively correlated ( P  < 0.05). We did not detect recent bottleneck events in these populations, but we did detect genetic divergence among populations (Global F ST = 0.022, P  < 0.01). The Bayesian clustering algorithms (TESS and STRUCTURE) suggested that four to five genetic clusters roughly coincide with sub-basins: (1) headwater streams/main stem of the Nan River, (2) a middle tributary, (3) a southeastern tributary and (4) a southwestern tributary. We observed positive correlation between geographic distance and linearized F ST ( P  < 0.05), and the genetic differentiation pattern can be moderately explained by the contemporary stream network (STREAMTREE analysis, R 2 = 0.75). The MEMGENE analysis suggested genetic division between northern (genetic clusters 1 and 2) and southern (clusters 3 and 4) sub-basins. We observed a high degree of genetic admixture in each location, highlighting the importance of natural flooding patterns and possible genetic impacts of supplementary stocking. Insights obtained from this research advance our knowledge of the complexity of a tropical stream system, and guide current conservation and restoration efforts for this species in Thailand.

Phenotypic and genetic associations between the big five and trait emotional intelligence.

PubMed

Vernon, Philip A; Villani, Vanessa C; Schermer, Julie Aitken; Petrides, K V

2008-10-01

This study reports the first behavioral genetic investigation of the extent to which genetic and/or environmental factors contribute to the relationship between the Big Five personality factors and trait emotional intelligence. 213 pairs of adult monozygotic twins and 103 pairs of same-sex dizygotic twins completed the NEO-PI-R and the Trait Emotional Intelligence Questionnaire (TEIQue). Replicating previous non-twin studies, many significant phenotypic correlations were found between the Big Five factors - especially Neuroticism, Extraversion, and Conscientiousness - and the facets, factors, and global scores derived from the TEIQue. Bivariate behavioral genetic model-fitting analyses revealed that these phenotypic correlations were primarily attributable to correlated genetic factors and secondarily to correlated non-shared environmental factors. The results support the feasibility of incorporating EI as a trait within existing personality taxonomies.

Estimates of genetic parameters, genetic trends, and inbreeding in a crossbred dairy sheep research flock in the United States.

PubMed

Murphy, T W; Berger, Y M; Holman, P W; Baldin, M; Burgett, R L; Thomas, D L

2017-10-01

For the past 2 decades, the Spooner Agriculture Research Station (ARS) of the University of Wisconsin-Madison operated the only dairy sheep research flock in North America. The objectives of the present study were to 1) obtain estimates of genetic parameters for lactation and reproductive traits in dairy ewes, 2) estimate the amount of genetic change in these traits over time, and 3) quantify the level of inbreeding in this flock over the last 20 yr. Multiple-trait repeatability models (MTRM) were used to analyze ewe traits through their first 6 parities. The first MTRM jointly analyzed milk (180-d-adjusted milk yield [180d MY]), fat (180-d-adjusted fat yield [180d FY]), and protein (180-d-adjusted protein yield [180d PY]) yields adjusted to 180 d of lactation; number of lambs born per ewe lambing (NLB); and lactation average test-day somatic cell score (LSCS). A second MTRM analyzed 180d MY, NLB, LSCS, and percentage milk fat (%F) and percentage milk protein (%P). The 3 yield traits were moderately heritable (0.26 to 0.32) and strongly genetically correlated (0.91 to 0.96). Percentage milk fat and %P were highly heritable (0.53 and 0.61, respectively) and moderately genetically correlated (0.61). Milk yield adjusted to 180 d was negatively genetically correlated with %F and %P (-0.31 and -0.34, respectively). Ewe prolificacy was not significantly ( > 0.67) genetically correlated with yield traits, %P, or LSCS but lowly negatively correlated with %F (-0.26). Lactation somatic cell score was unfavorably genetically correlated with yield traits (0.28 to 0.39) but not significantly ( > 0.09) correlated with %F, %P, and NLB. Within-trait multiple-trait models through the first 4 parities revealed that 180d MY, 180d FY, 180d PY, %F, and %P were strongly genetically correlated across parity (0.67 to 1.00). However, the genetic correlations across parity for NLB and LSCS were somewhat lower (0.51 to 0.96). Regressing predicted breeding values for 180d MY, without and with the addition of breed effects, on ewe year of birth revealed a positive genetic gain of 2.30 and 6.24 kg/yr, respectively, over the past 20 yr in this flock. Inbreeding coefficients of ewes with an extended pedigree ranged from 0.0 to 0.29, with an average of 0.07. To optimize genetic gains and avoid excessive inbreeding, the development of a national genetic improvement program should be a top priority for the growing dairy sheep industry.

Genetic relationships among body condition score, body weight, milk yield, and fertility in dairy cows.

PubMed

Berry, D P; Buckley, F; Dillon, P; Evans, R D; Rath, M; Veerkamp, R F

2003-06-01

Genetic (co)variances between body condition score (BCS), body weight (BW), milk production, and fertility-related traits were estimated. The data analyzed included 8591 multiparous Holstein-Friesian cows with records for BCS, BW, milk production, and/or fertility from 78 seasonal calving grass-based farms throughout southern Ireland. Of the cows included in the analysis, 4402 had repeated records across the 2 yr of the study. Genetic correlations between level of BCS at different stages of lactation and total lactation milk production were negative (-0.51 to -0.14). Genetic correlations between BW at different stages of lactation and total lactation milk production were all close to zero but became positive (0.01 to 0.39) after adjusting BW for differences in BCS. Body condition score at different stages of lactation correlated favorably with improved fertility; genetic correlations between BCS and pregnant 63 d after the start of breeding season ranged from 0.29 to 0.42. Both BW at different stages of lactation and milk production tended to exhibit negative genetic correlations with pregnant to first service and pregnant 63 d after the start of the breeding season and positive genetic correlations with number of services and the interval from first service to conception. Selection indexes investigated illustrate the possibility of continued selection for increased milk production without any deleterious effects on fertility or average BCS, albeit, genetic merit for milk production would increase at a slower rate.

Genetic and environmental integration of the hawkmoth pollination syndrome in Ruellia humilis (Acanthaceae).

PubMed

Heywood, John S; Michalski, Joseph S; McCann, Braden K; Russo, Amber D; Andres, Kara J; Hall, Allison R; Middleton, Tessa C

2017-05-01

The serial homology of floral structures has made it difficult to assess the relative contributions of selection and constraint to floral integration. The interpretation of floral integration may also be clouded by the tacit, but largely untested, assumption that genetic and environmental perturbations affect trait correlations in similar ways. In this study, estimates of both the genetic and environmental correlations between components of the hawkmoth pollination syndrome are presented for chasmogamous flowers of Ruellia humilis , including two levels of control for serial homology. A greenhouse population for quantitative genetic analysis was generated by a partial diallel cross between field-collected plants. An average of 634 chasmogamous flowers were measured for each of eight floral traits that contribute to the hawkmoth syndrome. Genetic correlations (across parents) and environmental correlations (across replicate flowers) were estimated by restricted maximum likelihood. Stigma height, anther height and floral tube length were very tightly integrated in their responses to both genetic and environmental perturbations. The inclusion of floral disc width as a control for serial homology suggests this integration is an adaptive response to correlational selection imposed by pollinators. In contrast, integration of non-homologous traits was low. Furthermore, when comparisons between the dimensions of serially homologous structures were excluded, the genetic and environmental correlation matrices showed little congruence. The results suggest that hawkmoths have imposed strong correlational selection on floral traits involved in the deposition and removal of pollen, and that this is a consequence of stabilizing selection on the relative positions of stigmas and anthers in the face of substantial flower size variation. Low integration of other floral traits, and conflicting patterns of genetic and environmental correlations among these traits, suggest weak or no correlational selection within the range of variability expressed within a population. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Complex nature of SNP genotype effects on gene expression in primary human leucocytes.

PubMed

Heap, Graham A; Trynka, Gosia; Jansen, Ritsert C; Bruinenberg, Marcel; Swertz, Morris A; Dinesen, Lotte C; Hunt, Karen A; Wijmenga, Cisca; Vanheel, David A; Franke, Lude

2009-01-07

Genome wide association studies have been hugely successful in identifying disease risk variants, yet most variants do not lead to coding changes and how variants influence biological function is usually unknown. We correlated gene expression and genetic variation in untouched primary leucocytes (n = 110) from individuals with celiac disease - a common condition with multiple risk variants identified. We compared our observations with an EBV-transformed HapMap B cell line dataset (n = 90), and performed a meta-analysis to increase power to detect non-tissue specific effects. In celiac peripheral blood, 2,315 SNP variants influenced gene expression at 765 different transcripts (< 250 kb from SNP, at FDR = 0.05, cis expression quantitative trait loci, eQTLs). 135 of the detected SNP-probe effects (reflecting 51 unique probes) were also detected in a HapMap B cell line published dataset, all with effects in the same allelic direction. Overall gene expression differences within the two datasets predominantly explain the limited overlap in observed cis-eQTLs. Celiac associated risk variants from two regions, containing genes IL18RAP and CCR3, showed significant cis genotype-expression correlations in the peripheral blood but not in the B cell line datasets. We identified 14 genes where a SNP affected the expression of different probes within the same gene, but in opposite allelic directions. By incorporating genetic variation in co-expression analyses, functional relationships between genes can be more significantly detected. In conclusion, the complex nature of genotypic effects in human populations makes the use of a relevant tissue, large datasets, and analysis of different exons essential to enable the identification of the function for many genetic risk variants in common diseases.

Genetic analysis of litter size, parturition length, and birth assistance requirements in primiparous sows using a joint linear-threshold animal model.

PubMed

Holm, B; Bakken, M; Vangen, O; Rekaya, R

2004-09-01

The aim of this study was to investigate whether selection for number of live born piglets has led to prolonged parturition and increased requirement for birth assistance, resulting in increased numbers of stillborn piglets. Data were collected from 6,718 primiparous Norwegian Landrace sows farrowing between 2001 and 2003. The need for birth assistance was recorded as a binary response. Physical intervention in the birth of piglets and/or hormonal treatment by the farmer was recorded as birth assistance. The duration of the parturition was analyzed as a binary trait (<4 h and >4 h). The statistical model used for analysis included contemporary groups of herd-year, litter breed, season of farrowing, parity in which the sow was born, a regression on the age of sow at farrowing, an additive genetic effect, and a service sire effect. A full Bayesian approach via Gibbs sampling was adopted to estimate the genetic relationships between these four traits. A total chain length of 100,000 iterations was run. The first 10,000 samples were discarded as burn-in, and the remaining 90,000 iterations were retained without thinning for post-Gibbs analysis. The highest direct heritability was estimated for the number of live-born piglets (h2 = 0.07), followed by the duration of farrowing (h2 = 0.05), the need for birth assistance (h2 = 0.05), and the number of stillborn piglets (h2 = 0.04). The genetic correlations revealed that the number of live and stillborn piglets was uncorrelated; however, the number of live piglets born had a moderate genetic correlation to the need for birth assistance (rg = 0.24 +/- 0.01) and duration of farrowing (rg = -0.20 +/- 0.01), whereas the number of stillborn piglets was highly correlated to the need for birth assistance (rg = 0.74 +/- 0.01) and the duration of parturition (rg = 0.66 +/- 0.01). The duration of farrowing and the need for birth assistance were genetically highly correlated (rg = 0.89 +/- 0.00). For all traits, the service sire variance was approximately one quarter in magnitude compared with its respective genetic variance. The results showed that selection for the number of live born piglets is not expected to influence the number of stillborn piglets. Increasing the number of live piglets born through selection should have a slight negative effect on farrowing duration and a minor increase in the need for birth assistance. Sows with a high genetic potential for birth assistance and prolonged parturition were more likely to give birth to greater numbers of stillborn piglets.

Invited review: Genetics and claw health: Opportunities to enhance claw health by genetic selection.

PubMed

Heringstad, B; Egger-Danner, C; Charfeddine, N; Pryce, J E; Stock, K F; Kofler, J; Sogstad, A M; Holzhauer, M; Fiedler, A; Müller, K; Nielsen, P; Thomas, G; Gengler, N; de Jong, G; Ødegård, C; Malchiodi, F; Miglior, F; Alsaaod, M; Cole, J B

2018-06-01

Routine recording of claw health status at claw trimming of dairy cattle has been established in several countries, providing valuable data for genetic evaluation. In this review, we examine issues related to genetic evaluation of claw health; discuss data sources, trait definitions, and data validation procedures; and present a review of genetic parameters, possible indicator traits, and status of genetic and genomic evaluations for claw disorders. Different sources of data and traits can be used to describe claw health. Severe cases of claw disorders can be identified by veterinary diagnoses. Data from lameness and locomotion scoring, activity information from sensors, and feet and leg conformation traits are used as auxiliary traits. The most reliable and comprehensive information is data from regular hoof trimming. In genetic evaluation, claw disorders are usually defined as binary traits, based on whether or not the claw disorder was present (recorded) at least once during a defined time period. The traits can be specific disorders, composite traits, or overall claw health. Data validation and editing criteria are needed to ensure reliable data at the trimmer, herd, animal, and record levels. Different strategies have been chosen, reflecting differences in herd sizes, data structures, management practices, and recording systems among countries. Heritabilities of the most commonly analyzed claw disorders based on data from routine claw trimming were generally low, with ranges of linear model estimates from 0.01 to 0.14, and threshold model estimates from 0.06 to 0.39. Estimated genetic correlations among claw disorders varied from -0.40 to 0.98. The strongest genetic correlations were found among sole hemorrhage (SH), sole ulcer (SU), and white line disease (WL), and between digital/interdigital dermatitis (DD/ID) and heel horn erosion (HHE). Genetic correlations between DD/ID and HHE on the one hand and SH, SU, or WL on the other hand were, in most cases, low. Although some of the studies were based on relatively few records and the estimated genetic parameters had large standard errors, there was, with some exceptions, consistency among studies. Various studies evaluate the potential of various data soureces for use in breeding. The use of hoof trimming data is recommended for maximization of genetic gain, although auxiliary traits, such as locomotion score and some conformation traits, may be valuable for increasing the reliability of genetic evaluations. Routine genetic evaluation of direct claw health has been implemented in the Netherlands (2010); Denmark, Finland, and Sweden (joint Nordic evaluation; 2011); and Norway (2014), and other countries plan to implement evaluations in the near future. The Authors. Published by FASS Inc. and Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).

Genetic correlations and the evolution of photoperiodic time measurement within a local population of the pitcher-plant mosquito, Wyeomyia smithii

PubMed Central

Bradshaw, W E; Emerson, K J; Holzapfel, C M

2012-01-01

The genetic relationship between the daily circadian clock and the seasonal photoperiodic timer remains a subject of intense controversy. In Wyeomyia smithii, the critical photoperiod (an overt expression of the photoperiodic timer) evolves independently of the rhythmic response to the Nanda–Hamner protocol (an overt expression of the daily circadian clock) over a wide geographical range in North America. Herein, we focus on these two processes within a single local population in which there is a negative genetic correlation between them. We show that antagonistic selection against this genetic correlation rapidly breaks it down and, in fact, reverses its sign, showing that the genetic correlation is due primarily to linkage and not to pleiotropy. This rapid reversal of the genetic correlation within a small, single population means that it is difficult to argue that circadian rhythmicity forms the necessary, causal basis for the adaptive divergence of photoperiodic time measurement within populations or for the evolution of photoperiodic time measurement among populations over a broad geographical gradient of seasonal selection. PMID:22072069

Genetic versus census estimators of the opportunity for sexual selection in the wild.

PubMed

Dunn, Stacey J; Waits, Lisette P; Byers, John A

2012-04-01

Abstract The existence of a direct link between intensity of sexual selection and mating-system type is widely accepted. However, the quantification of sexual selection has proven problematic. Several measures of sexual selection have been proposed, including the operational sex ratio (OSR), the breeding sex ratio (BSR), and the opportunity for sexual selection (I(mates)). For a wild population of pronghorn (Antilocapra americana), we calculated OSR and BSR. We estimated I(mates) from census data on the spatial and temporal distribution of receptive females in rut and from a multigenerational genetic pedigree. OSR and BSR indicated weak sexual selection on males, but census and pedigree I(mates) suggested stronger sexual selection on males than on females. OSR and BSR correlated with census but not pedigree estimates of I(mates), and census I(mates) did not correlate with pedigree estimates. This suggests that the behavioral mating system, as deduced from the spatial and temporal distribution of females, does not predict the genetic mating system of pronghorn. The differences we observed between estimators were primarily due to female mate sampling and choice and to the sex ratio. For most species, behavioral data are not perfectly accurate and therefore will be an insufficient alternative to using multigenerational pedigrees to quantify sexual selection.

Environmental and genetic effects on weight and visual score traits at postweaning in Suffolk sheep.

PubMed

Nascimento, Bárbara Mazetti; Somavilla, Adriana Luiza; Dias, Laila Talarico; Teixeira, Rodrigo de Almeida

2014-10-01

This study aimed to investigate the following environmental effects in Suffolk lambing: contemporary groups, type of birth, and age of animal and age of dam at lambing on conformation (C), precocity (P), musculature (M), and body weight at postweaning (W), and the heritability coefficients and genetic correlations among these traits. Contemporary groups, type of birth, and age of animal and age of dam at lambing were significant for W. For C, all the effects studied were significant, except linear and quadratic effects of age of the animal. For P, all effects studied were significant, except the quadratic effect of age of the animal. For M, the effects of contemporary group, type of birth, and the linear effect of the age of the animal were significant. Heritability estimates were 0.07 ± 0.03, 0.14 ± 0.03, 0.09 ± 0.03, and 0.11 ± 0.03 for C, P, M, and W, respectively, indicating a positive low response for direct selection. Estimates of genetic correlations among the visual scores (C, P, and M) and W were moderate to highly favorable and positive, ranging from 0.48 to 0.90. These results indicate that selection for visual scores will increase body weight.

Evaluation of approaches for estimating the accuracy of genomic prediction in plant breeding

PubMed Central

2013-01-01

Background In genomic prediction, an important measure of accuracy is the correlation between the predicted and the true breeding values. Direct computation of this quantity for real datasets is not possible, because the true breeding value is unknown. Instead, the correlation between the predicted breeding values and the observed phenotypic values, called predictive ability, is often computed. In order to indirectly estimate predictive accuracy, this latter correlation is usually divided by an estimate of the square root of heritability. In this study we use simulation to evaluate estimates of predictive accuracy for seven methods, four (1 to 4) of which use an estimate of heritability to divide predictive ability computed by cross-validation. Between them the seven methods cover balanced and unbalanced datasets as well as correlated and uncorrelated genotypes. We propose one new indirect method (4) and two direct methods (5 and 6) for estimating predictive accuracy and compare their performances and those of four other existing approaches (three indirect (1 to 3) and one direct (7)) with simulated true predictive accuracy as the benchmark and with each other. Results The size of the estimated genetic variance and hence heritability exerted the strongest influence on the variation in the estimated predictive accuracy. Increasing the number of genotypes considerably increases the time required to compute predictive accuracy by all the seven methods, most notably for the five methods that require cross-validation (Methods 1, 2, 3, 4 and 6). A new method that we propose (Method 5) and an existing method (Method 7) used in animal breeding programs were the fastest and gave the least biased, most precise and stable estimates of predictive accuracy. Of the methods that use cross-validation Methods 4 and 6 were often the best. Conclusions The estimated genetic variance and the number of genotypes had the greatest influence on predictive accuracy. Methods 5 and 7 were the fastest and produced the least biased, the most precise, robust and stable estimates of predictive accuracy. These properties argue for routinely using Methods 5 and 7 to assess predictive accuracy in genomic selection studies. PMID:24314298

Evaluation of approaches for estimating the accuracy of genomic prediction in plant breeding.

PubMed

Ould Estaghvirou, Sidi Boubacar; Ogutu, Joseph O; Schulz-Streeck, Torben; Knaak, Carsten; Ouzunova, Milena; Gordillo, Andres; Piepho, Hans-Peter

2013-12-06

In genomic prediction, an important measure of accuracy is the correlation between the predicted and the true breeding values. Direct computation of this quantity for real datasets is not possible, because the true breeding value is unknown. Instead, the correlation between the predicted breeding values and the observed phenotypic values, called predictive ability, is often computed. In order to indirectly estimate predictive accuracy, this latter correlation is usually divided by an estimate of the square root of heritability. In this study we use simulation to evaluate estimates of predictive accuracy for seven methods, four (1 to 4) of which use an estimate of heritability to divide predictive ability computed by cross-validation. Between them the seven methods cover balanced and unbalanced datasets as well as correlated and uncorrelated genotypes. We propose one new indirect method (4) and two direct methods (5 and 6) for estimating predictive accuracy and compare their performances and those of four other existing approaches (three indirect (1 to 3) and one direct (7)) with simulated true predictive accuracy as the benchmark and with each other. The size of the estimated genetic variance and hence heritability exerted the strongest influence on the variation in the estimated predictive accuracy. Increasing the number of genotypes considerably increases the time required to compute predictive accuracy by all the seven methods, most notably for the five methods that require cross-validation (Methods 1, 2, 3, 4 and 6). A new method that we propose (Method 5) and an existing method (Method 7) used in animal breeding programs were the fastest and gave the least biased, most precise and stable estimates of predictive accuracy. Of the methods that use cross-validation Methods 4 and 6 were often the best. The estimated genetic variance and the number of genotypes had the greatest influence on predictive accuracy. Methods 5 and 7 were the fastest and produced the least biased, the most precise, robust and stable estimates of predictive accuracy. These properties argue for routinely using Methods 5 and 7 to assess predictive accuracy in genomic selection studies.

To grow or not to grow: hair morphogenesis and human genetic hair disorders.

PubMed

Duverger, Olivier; Morasso, Maria I

2014-01-01

Mouse models have greatly helped in elucidating the molecular mechanisms involved in hair formation and regeneration. Recent publications have reviewed the genes involved in mouse hair development based on the phenotype of transgenic, knockout and mutant animal models. While much of this information has been instrumental in determining molecular aspects of human hair development and cycling, mice exhibit a specific pattern of hair morphogenesis and hair distribution throughout the body that cannot be directly correlated to human hair. In this mini-review, we discuss specific aspects of human hair follicle development and present an up-to-date summary of human genetic disorders associated with abnormalities in hair follicle morphogenesis, structure or regeneration. Published by Elsevier Ltd.

Quantitative genetic properties of four measures of deformity in yellowtail kingfish Seriola lalandi Valenciennes, 1833.

PubMed

Nguyen, N H; Whatmore, P; Miller, A; Knibb, W

2016-02-01

The main aim of this study was to estimate the heritability for four measures of deformity and their genetic associations with growth (body weight and length), carcass (fillet weight and yield) and flesh-quality (fillet fat content) traits in yellowtail kingfish Seriola lalandi. The observed major deformities included lower jaw, nasal erosion, deformed operculum and skinny fish on 480 individuals from 22 families at Clean Seas Tuna Ltd. They were typically recorded as binary traits (presence or absence) and were analysed separately by both threshold generalized models and standard animal mixed models. Consistency of the models was evaluated by calculating simple Pearson correlation of breeding values of full-sib families for jaw deformity. Genetic and phenotypic correlations among traits were estimated using a multitrait linear mixed model in ASReml. Both threshold and linear mixed model analysis showed that there is additive genetic variation in the four measures of deformity, with the estimates of heritability obtained from the former (threshold) models on liability scale ranging from 0.14 to 0.66 (SE 0.32-0.56) and from the latter (linear animal and sire) models on original (observed) scale, 0.01-0.23 (SE 0.03-0.16). When the estimates on the underlying liability were transformed to the observed scale (0, 1), they were generally consistent between threshold and linear mixed models. Phenotypic correlations among deformity traits were weak (close to zero). The genetic correlations among deformity traits were not significantly different from zero. Body weight and fillet carcass showed significant positive genetic correlations with jaw deformity (0.75 and 0.95, respectively). Genetic correlation between body weight and operculum was negative (-0.51, P < 0.05). The genetic correlations' estimates of body and carcass traits with other deformity were not significant due to their relatively high standard errors. Our results showed that there are prospects for genetic selection to improve deformity in yellowtail kingfish and that measures of deformity should be included in the recording scheme, breeding objectives and selection index in practical selective breeding programmes due to the antagonistic genetic correlations of deformed jaws with body and carcass performance. © 2015 John Wiley & Sons Ltd.

Adoptive parent hostility and children's peer behavior problems: examining the role of genetically informed child attributes on adoptive parent behavior.

PubMed

Elam, Kit K; Harold, Gordon T; Neiderhiser, Jenae M; Reiss, David; Shaw, Daniel S; Natsuaki, Misaki N; Gaysina, Darya; Barrett, Doug; Leve, Leslie D

2014-05-01

Socially disruptive behavior during peer interactions in early childhood is detrimental to children's social, emotional, and academic development. Few studies have investigated the developmental underpinnings of children's socially disruptive behavior using genetically sensitive research designs that allow examination of parent-on-child and child-on-parent (evocative genotype-environment correlation [rGE]) effects when examining family process and child outcome associations. Using an adoption-at-birth design, the present study controlled for passive genotype-environment correlation and directly examined evocative rGE while examining the associations between family processes and children's peer behavior. Specifically, the present study examined the evocative effect of genetic influences underlying toddler low social motivation on mother-child and father-child hostility and the subsequent influence of parent hostility on disruptive peer behavior during the preschool period. Participants were 316 linked triads of birth mothers, adoptive parents, and adopted children. Path analysis showed that birth mother low behavioral motivation predicted toddler low social motivation, which predicted both adoptive mother-child and father-child hostility, suggesting the presence of an evocative genotype-environment association. In addition, both mother-child and father-child hostility predicted children's later disruptive peer behavior. Results highlight the importance of considering genetically influenced child attributes on parental hostility that in turn links to later child social behavior. Implications for intervention programs focusing on early family processes and the precursors of disrupted child social development are discussed. (PsycINFO Database Record (c) 2014 APA, all rights reserved).

[Analytic methods for seed models with genotype x environment interactions].

PubMed

Zhu, J

1996-01-01

Genetic models with genotype effect (G) and genotype x environment interaction effect (GE) are proposed for analyzing generation means of seed quantitative traits in crops. The total genetic effect (G) is partitioned into seed direct genetic effect (G0), cytoplasm genetic of effect (C), and maternal plant genetic effect (Gm). Seed direct genetic effect (G0) can be further partitioned into direct additive (A) and direct dominance (D) genetic components. Maternal genetic effect (Gm) can also be partitioned into maternal additive (Am) and maternal dominance (Dm) genetic components. The total genotype x environment interaction effect (GE) can also be partitioned into direct genetic by environment interaction effect (G0E), cytoplasm genetic by environment interaction effect (CE), and maternal genetic by environment interaction effect (GmE). G0E can be partitioned into direct additive by environment interaction (AE) and direct dominance by environment interaction (DE) genetic components. GmE can also be partitioned into maternal additive by environment interaction (AmE) and maternal dominance by environment interaction (DmE) genetic components. Partitions of genetic components are listed for parent, F1, F2 and backcrosses. A set of parents, their reciprocal F1 and F2 seeds is applicable for efficient analysis of seed quantitative traits. MINQUE(0/1) method can be used for estimating variance and covariance components. Unbiased estimation for covariance components between two traits can also be obtained by the MINQUE(0/1) method. Random genetic effects in seed models are predictable by the Adjusted Unbiased Prediction (AUP) approach with MINQUE(0/1) method. The jackknife procedure is suggested for estimation of sampling variances of estimated variance and covariance components and of predicted genetic effects, which can be further used in a t-test for parameter. Unbiasedness and efficiency for estimating variance components and predicting genetic effects are tested by Monte Carlo simulations.

Molecular genetic analysis of volatile-anesthetic action.

PubMed Central

Keil, R L; Wolfe, D; Reiner, T; Peterson, C J; Riley, J L

1996-01-01

The mechanism(s) and site(s) of action of volatile inhaled anesthetics are unknown in spite of the clinical use of these agents for more than 150 years. In the present study, the model eukaryote Saccharomyces cerevisiae was used to investigate the action of anesthetic agents because of its powerful molecular genetics. It was found that growth of yeast cells is inhibited by the five common volatile anesthetics tested (isoflurane, halothane, enflurane, sevoflurane, and methoxyflurane). Growth inhibition by the agents is relatively rapid and reversible. The potency of these compounds as yeast growth inhibitors directly correlates with their lipophilicity as is predicted by the Meyer-Overton relationship, which directly correlates anesthetic potency of agents and their lipophilicity. The effects of isoflurane on yeast cells were characterized in the most detail. Yeast cells survive at least 48 h in a concentration of isoflurane that inhibits colony formation. Mutants resistant to the growth-inhibitory effects of isoflurane are readily selected. The gene identified by one of these mutations, zzz4-1, has been cloned and characterized. The predicted ZZZ4 gene product has extensive homology to phospholipase A2-activating protein, a GO effector protein of mice. Both zzz4-1 and a deletion of ZZZ4 confer resistance to all five of the agents tested, suggesting that signal transduction may be involved in the response of these cells to volatile anesthetics. PMID:8668160

Genetic analysis of resistance to ticks, gastrointestinal nematodes and Eimeria spp. in Nellore cattle.

PubMed

Passafaro, Tiago Luciano; Carrera, Juan Pablo Botero; dos Santos, Livia Loiola; Raidan, Fernanda Santos Silva; dos Santos, Dalinne Chrystian Carvalho; Cardoso, Eduardo Penteado; Leite, Romário Cerqueira; Toral, Fabio Luiz Buranelo

2015-06-15

The aim of the present study was to obtain genetic parameters for resistance to ticks, gastrointestinal nematodes (worms) and Eimeria spp. in Nellore cattle, analyze the inclusion of resistance traits in Nellore breeding programs and evaluate genetic selection as a complementary tool in parasite control programs. Counting of ticks, gastrointestinal nematode eggs and Eimeria spp. oocysts per gram of feces totaling 4270; 3872 and 3872 records from 1188; 1142 and 1142 animals, respectively, aged 146 to 597 days were used. The animals were classified as resistant (counts equal to zero) or susceptible (counts above zero) to each parasite. The statistical models included systematics effects of contemporary groups and the mean trajectory. The random effects included additive genetic effects, direct permanent environmental effects and residual. The mean trajectory and random effects were modeled with linear Legendre polynomials for all traits except for the mean trajectory of resistance to Eimeria spp., which employed the cubic polynomial. Heritability estimates were of low to moderate magnitude and ranged from 0.06 to 0.30, 0.06 to 0.33 and 0.04 to 0.33 for resistance to ticks, gastrointestinal nematodes and Eimeria spp., respectively. The posterior mean of genetic and environmental correlations for the same trait at different ages (205, 365, 450 and 550 days) were favorable at adjacent ages and unfavorable at distant ages. In general, the posterior mean of the genetic and environmental correlations between traits of resistance were low and high-density intervals were large and included zero in many cases. The heritability estimates support the inclusion of resistance to ticks, gastrointestinal nematodes and Eimeria spp. in Nellore breeding programs. Genetic selection can increase the frequency of resistant animals and be used as a complementary tool in parasite control programs. Copyright © 2015 Elsevier B.V. All rights reserved.

Genetic variation and correlated changes in reproductive performance of a red tilapia line selected for improved growth over three generations.

PubMed

Thoa, Ngo Phu; Hamzah, Azhar; Nguyen, Nguyen Hong

2017-09-01

The present study examines genetic variation and correlated changes in reproductive performance traits in a red tilapia (Oreochromis spp.) population selected over three generations for improved growth. A total of 328 breeding females (offspring of 111 sires and 118 dams) had measurements of body weight prior to spawning (WBS), number of fry at hatching (NFH), total fry weight (TFW) and number of dead fry (NDF) or mortality of fry including unhatched eggs at hatching (MFH). Restricted maximum likelihood (REML) analysis in a multi-trait model showed that there are heritable genetic components for all traits studied. The heritability for WBS was very high (0.80). The estimates for traits related to fecundity (NFH, TFW) and survival (NDF) were low and they were associated with high standard errors. Genetic correlations of WBS with other reproductive performance traits (NFH, TFW and NDF) were generally positive. However, NFH was negatively correlated genetically with TFW. As expected, body measurements during growth stage exhibited strong positive genetic correlations with WBS. The genetic correlations between body traits and reproductive performance (NFH, TFW, NDF) were not significant. Correlated responses in reproductive traits were measured as changes in least squares means between generations or spawning years. Except for WBS that increased with the selection programs, the phenotypic changes in other reproductive traits observed were not statistically significant (P>0.05). It is concluded that the selection program for red tilapia has resulted in very little changes in reproductive performance of the animals after three generations. However, periodic monitoring of genetic changes in fecundity and fitness related traits such as NDF or MFH should be made in selective breeding programs for red tilapia. Copyright © 2017 Elsevier B.V. All rights reserved.

Parental criticism and externalizing behavior problems in adolescents: the role of environment and genotype-environment correlation.

PubMed

Narusyte, Jurgita; Neiderhiser, Jenae M; Andershed, Anna-Karin; D'Onofrio, Brian M; Reiss, David; Spotts, Erica; Ganiban, Jody; Lichtenstein, Paul

2011-05-01

Genetic factors are important for the association between parental negativity and child problem behavior, but it is not clear whether this is due to passive or evocative genotype-environment correlation (rGE). In this study, we applied the extended children-of-twins model to directly examine the presence of passive and evocative rGE as well as direct environmental effects in the association between parental criticism and adolescent externalizing problem behavior. The cross-sectional data come from the Twin and Offspring Study in Sweden (N = 909 pairs of adult twins) and from the Twin Study of Child and Adolescent Development (N = 915 pairs of twin children). The results revealed that maternal criticism was primarily due to evocative rGE emanating from their adolescent's externalizing behavior. On the other hand, fathers' critical remarks tended to affect adolescent problem behavior in a direct environmental way. This suggests that previously reported differences in caretaking between mothers and fathers also are reflected in differences in why parenting is associated with externalizing behavior in offspring.

Parental criticism and externalizing behavior problems in adolescents– the role of environment and genotype-environment correlation

PubMed Central

Narusyte, Jurgita; Neiderhiser, Jenae M.; Andershed, Anna-Karin; D’Onofrio, Brian M.; Reiss, David; Spotts, Erica; Ganiban, Jody; Lichtenstein, Paul

2011-01-01

Genetic factors are important for the association between parental negativity and child problem behavior, but it is not clear whether this is dueto passive or evocative genotype-environment correlation (rGE). In this study we applied the extended children-of-twins model to directly examine the presence of passive and evocative rGE as well as direct environmental effects in the association between parental criticism and adolescent externalizing problem behavior. The cross-sectional data come from the Twin and Offspring Study in Sweden (TOSS) (N=909 pairs of adult twins) and from the Twin study of CHild and Adolescent Development (TCHAD) (N=915 pairs of twin children). The results revealed that maternal criticism was primarily due to evocative rGE emanating from their adolescent’s externalizing behavior. On the other hand, fathers’ critical remarks tended to affect adolescent problem behavior in a direct environmental way. This suggests that previously reported differences in caretaking between mothers and fathers also are reflected in differences in why parenting is associated with externalizing behavior in offspring. PMID:21280930

Alcohol use disorder and divorce: Evidence for a genetic correlation in a population-based Swedish sample

PubMed Central

Salvatore, Jessica E.; Lönn, Sara Larsson; Sundquist, Jan; Lichtenstein, Paul; Sundquist, Kristina; Kendler, Kenneth S.

2016-01-01

Aims We tested the association between alcohol use disorder (AUD) and divorce; estimated the genetic and environmental influences on divorce; estimated how much genetic and environmental influences accounted for covariance between AUD and divorce; and estimated latent genetic and environmental correlations between AUD and divorce. We tested sex differences in these effects. Design We identified twin and sibling pairs with AUD and divorce information in Swedish national registers. We described the association between AUD and divorce using tetrachorics; and used twin and sibling models to estimate genetic and environmental influences on divorce, on the covariance between AUD and divorce, and the latent genetic and environmental correlations between AUD and divorce. Setting Sweden. Participants 670,836 individuals (53% male) born 1940–1965. Measurements Lifetime measures of AUD and divorce. Findings AUD and divorce were strongly related (estimates [95% CIs]: males: rtet = +0.44 [0.43, 0.45]; females rtet = +0.37 [0.36, 0.38]). Genetic factors accounted for a modest proportion of the variance in divorce (males: 21.3% [7.6, 28.5]; females: 31.0% [18.8, 37.1]). Genetic factors accounted for most of the covariance between AUD and divorce (males: 52.0% [48.8, 67.9]; females: 53.74% [17.6, 54.5]), followed by nonshared environmental factors (males: 45.0% [37.5, 54.9]; females: 41.6% [40.3, 60.2]). Shared environmental factors accounted for a negligible proportion of the covariance (males: 3.0% [−3.0, 13.5]; females: 4.75%, [0.0, 6.6].) The AUD-divorce genetic correlations were high (males: rA = +0.76 [0.53, 0.90]; females +0.52 [0.24, 0.67]). The nonshared environmental correlations were modest (males: rE = +0.32 [0.31, 0.40]; females: +0.27 [0.27, 0.36]). Conclusions Divorce and alcohol use disorder (AUD) are strongly correlated in the Swedish population, and the heritability of divorce is consistent with previous studies. Covariation between AUD and divorce results from overlapping genetic and nonshared environmental factors. Latent genetic and nonshared environmental correlations for AUD and divorce are high and moderate. PMID:27981669

Genetic parameters for carcass weight, conformation and fat in five beef cattle breeds.

PubMed

Kause, A; Mikkola, L; Strandén, I; Sirkko, K

2015-01-01

Profitability of beef production can be increased by genetically improving carcass traits. To construct breeding value evaluations for carcass traits, breed-specific genetic parameters were estimated for carcass weight, carcass conformation and carcass fat in five beef cattle breeds in Finland (Hereford, Aberdeen Angus, Simmental, Charolais and Limousin). Conformation and fat were visually scored using the EUROP carcass classification. Each breed was separately analyzed using a multitrait animal model. A total of 6879-19 539 animals per breed had phenotypes. For the five breeds, heritabilities were moderate for carcass weight (h 2=0.39 to 0.48, s.e.=0.02 to 0.04) and slightly lower for conformation (h 2=0.30 to 0.44, s.e.=0.02 to 0.04) and carcass fat (h 2=0.29 to 0.44, s.e.=0.02 to 0.04). The genetic correlation between carcass weight and conformation was favorable in all breeds (r G=0.37 to 0.53, s.e.=0.04 to 0.05), heavy carcasses being genetically more conformed. The phenotypic correlation between carcass weight and carcass fat was moderately positive in all breeds (r P=0.21 to 0.32), implying that increasing carcass weight was related to increasing fat levels. The respective genetic correlation was the strongest in Hereford (r G=0.28, s.e.=0.05) and Angus (r G=0.15, s.e.=0.05), the two small body-sized British breeds with the lowest conformation and the highest fat level. The correlation was weaker in the other breeds (r G=0.08 to 0.14). For Hereford, Angus and Simmental, more conformed carcasses were phenotypically fatter (r P=0.11 to 0.15), but the respective genetic correlations were close to zero (r G=-0.05 to 0.04). In contrast, in the two large body-sized and muscular French breeds, the genetic correlation between conformation and fat was negative and the phenotypic correlation was close to zero or negative (Charolais: r G=-0.18, s.e.=0.06, r P=0.02; Limousin: r G=-0.56, s.e.=0.04, r P=-0.13). The results indicate genetic variation for the genetic improvement of the carcass traits, favorable correlations for the simultaneous improvement of carcass weight and conformation in all breeds, and breed differences in the correlations of carcass fat.

Genetic correlations between body condition scores and fertility in dairy cattle using bivariate random regression models.

PubMed

De Haas, Y; Janss, L L G; Kadarmideen, H N

2007-10-01

Genetic correlations between body condition score (BCS) and fertility traits in dairy cattle were estimated using bivariate random regression models. BCS was recorded by the Swiss Holstein Association on 22,075 lactating heifers (primiparous cows) from 856 sires. Fertility data during first lactation were extracted for 40,736 cows. The fertility traits were days to first service (DFS), days between first and last insemination (DFLI), calving interval (CI), number of services per conception (NSPC) and conception rate to first insemination (CRFI). A bivariate model was used to estimate genetic correlations between BCS as a longitudinal trait by random regression components, and daughter's fertility at the sire level as a single lactation measurement. Heritability of BCS was 0.17, and heritabilities for fertility traits were low (0.01-0.08). Genetic correlations between BCS and fertility over the lactation varied from: -0.45 to -0.14 for DFS; -0.75 to 0.03 for DFLI; from -0.59 to -0.02 for CI; from -0.47 to 0.33 for NSPC and from 0.08 to 0.82 for CRFI. These results show (genetic) interactions between fat reserves and reproduction along the lactation trajectory of modern dairy cows, which can be useful in genetic selection as well as in management. Maximum genetic gain in fertility from indirect selection on BCS should be based on measurements taken in mid lactation when the genetic variance for BCS is largest, and the genetic correlations between BCS and fertility is strongest.

Common Psychiatric Disorders and Caffeine Use, Tolerance, and Withdrawal: An Examination of Shared Genetic and Environmental Effects

PubMed Central

Bergin, Jocilyn E.; Kendler, Kenneth S.

2012-01-01

Background Previous studies examined caffeine use and caffeine dependence and risk for the symptoms, or diagnosis, of psychiatric disorders. The current study aimed to determine if generalized anxiety disorder (GAD), panic disorder, phobias, major depressive disorder (MDD), anorexia nervosa (AN), or bulimia nervosa (BN) shared common genetic or environmental factors with caffeine use, caffeine tolerance, or caffeine withdrawal. Method Using 2,270 women from the Virginia Adult Twin Study of Psychiatric and Substance Use Disorders, bivariate Cholesky decomposition models were used to determine if any of the psychiatric disorders shared genetic or environmental factors with caffeine use phenotypes. Results GAD, phobias, and MDD shared genetic factors with caffeine use, with genetic correlations estimated to be 0.48, 0.25, and 0.38, respectively. Removal of the shared genetic and environmental parameter for phobias and caffeine use resulted in a significantly worse fitting model. MDD shared unique environmental factors (environmental correlation = 0.23) with caffeine tolerance; the genetic correlation between AN and caffeine tolerance and BN and caffeine tolerance were 0.64 and 0.49, respectively. Removal of the genetic and environmental correlation parameters resulted in significantly worse fitting models for GAD, phobias, MDD, AN, and BN, which suggested that there was significant shared liability between each of these phenotypes and caffeine tolerance. GAD had modest genetic correlations with caffeine tolerance, 0.24, and caffeine withdrawal, 0.35. Conclusions There was suggestive evidence of shared genetic and environmental liability between psychiatric disorders and caffeine phenotypes. This might inform us about the etiology of the comorbidity between these phenotypes. PMID:22854069

Common psychiatric disorders and caffeine use, tolerance, and withdrawal: an examination of shared genetic and environmental effects.

PubMed

Bergin, Jocilyn E; Kendler, Kenneth S

2012-08-01

Previous studies examined caffeine use and caffeine dependence and risk for the symptoms, or diagnosis, of psychiatric disorders. The current study aimed to determine if generalized anxiety disorder (GAD), panic disorder, phobias, major depressive disorder (MDD), anorexia nervosa (AN), or bulimia nervosa (BN) shared common genetic or environmental factors with caffeine use, caffeine tolerance, or caffeine withdrawal. Using 2,270 women from the Virginia Adult Twin Study of Psychiatric and Substance Use Disorders, bivariate Cholesky decomposition models were used to determine if any of the psychiatric disorders shared genetic or environmental factors with caffeine use phenotypes. GAD, phobias, and MDD shared genetic factors with caffeine use, with genetic correlations estimated to be 0.48, 0.25, and 0.38, respectively. Removal of the shared genetic and environmental parameter for phobias and caffeine use resulted in a significantly worse fitting model. MDD shared unique environmental factors (environmental correlation=0.23) with caffeine tolerance; the genetic correlation between AN and caffeine tolerance and BN and caffeine tolerance were 0.64 and 0.49, respectively. Removal of the genetic and environmental correlation parameters resulted in significantly worse fitting models for GAD, phobias, MDD, AN, and BN, which suggested that there was significant shared liability between each of these phenotypes and caffeine tolerance. GAD had modest genetic correlations with caffeine tolerance, 0.24, and caffeine withdrawal, 0.35. There was suggestive evidence of shared genetic and environmental liability between psychiatric disorders and caffeine phenotypes. This might inform us about the etiology of the comorbidity between these phenotypes.

Genetic parameters of body weight and ascites in broilers: effect of different incidence rates of ascites syndrome.

PubMed

Ahmadpanah, J; Ghavi Hossein-Zadeh, N; Shadparvar, A A; Pakdel, A

2017-02-01

1. The objectives of the current study were to investigate the effect of incidence rate (5%, 10%, 20%, 30% and 50%) of ascites syndrome on the expression of genetic characteristics for body weight at 5 weeks of age (BW5) and AS and to compare different methods of genetic parameter estimation for these traits. 2. Based on stochastic simulation, a population with discrete generations was created in which random mating was used for 10 generations. Two methods of restricted maximum likelihood and Bayesian approach via Gibbs sampling were used for the estimation of genetic parameters. A bivariate model including maternal effects was used. The root mean square error for direct heritabilities was also calculated. 3. The results showed that when incidence rates of ascites increased from 5% to 30%, the heritability of AS increased from 0.013 and 0.005 to 0.110 and 0.162 for linear and threshold models, respectively. 4. Maternal effects were significant for both BW5 and AS. Genetic correlations were decreased by increasing incidence rates of ascites in the population from 0.678 and 0.587 at 5% level of ascites to 0.393 and -0.260 at 50% occurrence for linear and threshold models, respectively. 5. The RMSE of direct heritability from true values for BW5 was greater based on a linear-threshold model compared with the linear model of analysis (0.0092 vs. 0.0015). The RMSE of direct heritability from true values for AS was greater based on a linear-linear model (1.21 vs. 1.14). 6. In order to rank birds for ascites incidence, it is recommended to use a threshold model because it resulted in higher heritability estimates compared with the linear model and that BW5 could be one of the main components of selection goals.

Direct-to-consumer sales of genetic services on the Internet.

PubMed

Gollust, Sarah E; Wilfond, Benjamin S; Hull, Sara Chandros

2003-01-01

PURPOSE The increasing use of the Internet to obtain genetics information and to order medical services without a prescription, combined with a rise in direct-to-consumer marketing for genetic testing, suggests the potential for the Internet to be used to sell genetic services. METHODS A systematic World Wide Web search was conducted in May 2002 to assess the availability of genetic services sold directly to consumers on the Internet. RESULTS Out of 105 sites that offered genetic services directly, most offered non-health-related services, including parentage confirmation testing (83%), identity testing (56%), and DNA banking (24%); however, health-related genetic tests were offered through 14 sites (13%). The health-related genetic tests available ranged from standard tests, such as hemochromatosis and cystic fibrosis, to more unconventional tests related to nutrition, behavior, and aging. Of these 14 sites, 5 described risks associated with the genetic services and 6 described the availability of counseling. CONCLUSIONS The availability of direct sales of health-related genetic tests creates the potential for inadequate pretest decision making, misunderstanding test results, and access to tests of questionable clinical value.

Direct-to-consumer sales of genetic services on the Internet

PubMed Central

Gollust, Sarah E.; Wilfond, Benjamin S.; Hull, Sara Chandros

2016-01-01

Purpose The increasing use of the Internet to obtain genetics information and to order medical services without a prescription, combined with a rise in direct-to-consumer marketing for genetic testing, suggests the potential for the Internet to be used to sell genetic services. Methods A systematic World Wide Web search was conducted in May 2002 to assess the availability of genetic services sold directly to consumers on the Internet. Results Out of 105 sites that offered genetic services directly, most offered non–health-related services, including parentage confirmation testing (83%), identity testing (56%), and DNA banking (24%); however, health-related genetic tests were offered through 14 sites (13%). The health-related genetic tests available ranged from standard tests, such as hemochromatosis and cystic fibrosis, to more unconventional tests related to nutrition, behavior, and aging. Of these 14 sites, 5 described risks associated with the genetic services and 6 described the availability of counseling. Conclusions The availability of direct sales of health-related genetic tests creates the potential for inadequate pretest decision making, misunderstanding test results, and access to tests of questionable clinical value. PMID:12865763

Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast

PubMed Central

Ye, Ping; Peyser, Brian D; Spencer, Forrest A; Bader, Joel S

2005-01-01

Background In a genetic interaction, the phenotype of a double mutant differs from the combined phenotypes of the underlying single mutants. When the single mutants have no growth defect, but the double mutant is lethal or exhibits slow growth, the interaction is termed synthetic lethality or synthetic fitness. These genetic interactions reveal gene redundancy and compensating pathways. Recently available large-scale data sets of genetic interactions and protein interactions in Saccharomyces cerevisiae provide a unique opportunity to elucidate the topological structure of biological pathways and how genes function in these pathways. Results We have defined congruent genes as pairs of genes with similar sets of genetic interaction partners and constructed a genetic congruence network by linking congruent genes. By comparing path lengths in three types of networks (genetic interaction, genetic congruence, and protein interaction), we discovered that high genetic congruence not only exhibits correlation with direct protein interaction linkage but also exhibits commensurate distance with the protein interaction network. However, consistent distances were not observed between genetic and protein interaction networks. We also demonstrated that congruence and protein networks are enriched with motifs that indicate network transitivity, while the genetic network has both transitive (triangle) and intransitive (square) types of motifs. These results suggest that robustness of yeast cells to gene deletions is due in part to two complementary pathways (square motif) or three complementary pathways, any two of which are required for viability (triangle motif). Conclusion Genetic congruence is superior to genetic interaction in prediction of protein interactions and function associations. Genetically interacting pairs usually belong to parallel compensatory pathways, which can generate transitive motifs (any two of three pathways needed) or intransitive motifs (either of two pathways needed). PMID:16283923

Genetic interrelationships among phosphorus, nitrogen, calcium, and energy bioavailability in a growing chicken population.

PubMed

Ankra-Badu, G A; Pesti, G M; Aggrey, S E

2010-11-01

A random-mating population was used to study the genetic interrelationship between phytate P (PPB), Ca (CaB), N (NB), and energy bioavailability (EB), BW at 4 wk of age, relative growth (RG), and feed conversion ratio (FCR). Heritability estimates for PPB, CaB, NB, and EB were 0.09, 0.13, 0.16, and 0.10, respectively, and those of BW, RG, and FCR were 0.66, 0.15, and 0.10, respectively. Genetic correlations between PPB and BW, and FCR were moderate and negative, suggesting that improvement in PPB will impair growth. The genetic correlations between PPB and CaB, and EB and RG were positive and moderate, indicating that improvement in PPB would also lead to improved CaB, EB, and RG. Energy bioavailability was positively correlated with CaB, NB, PPB, and BW. Even though the genetic correlation between EB and the other traits measured, except RG and FCR, ranged from low to moderate, improving the ability of birds to utilize caloric energy in the feed would consequently improve PPB as well as growth. Improving PPB would reduce the amount of P in excreta and provide an additional savings if exogenous phytase were not added to poultry feed. The genetic correlation between PPB and NB was low but positive, whereas NB had a positive genetic correlation with BW. Therefore, selecting on NB will result in positive correlated responses in BW and PPB. Improving PPB and NB will not only improve productivity, but also reduce the polluting effects of P and N on the environment.

Pleiotropy of cardiometabolic syndrome with obesity-related anthropometric traits determined using empirically derived kinships from the Busselton Health Study.

PubMed

Cadby, Gemma; Melton, Phillip E; McCarthy, Nina S; Almeida, Marcio; Williams-Blangero, Sarah; Curran, Joanne E; VandeBerg, John L; Hui, Jennie; Beilby, John; Musk, A W; James, Alan L; Hung, Joseph; Blangero, John; Moses, Eric K

2018-01-01

Over two billion adults are overweight or obese and therefore at an increased risk of cardiometabolic syndrome (CMS). Obesity-related anthropometric traits genetically correlated with CMS may provide insight into CMS aetiology. The aim of this study was to utilise an empirically derived genetic relatedness matrix to calculate heritabilities and genetic correlations between CMS and anthropometric traits to determine whether they share genetic risk factors (pleiotropy). We used genome-wide single nucleotide polymorphism (SNP) data on 4671 Busselton Health Study participants. Exploiting both known and unknown relatedness, empirical kinship probabilities were estimated using these SNP data. General linear mixed models implemented in SOLAR were used to estimate narrow-sense heritabilities (h 2 ) and genetic correlations (r g ) between 15 anthropometric and 9 CMS traits. Anthropometric traits were adjusted by body mass index (BMI) to determine whether the observed genetic correlation was independent of obesity. After adjustment for multiple testing, all CMS and anthropometric traits were significantly heritable (h 2 range 0.18-0.57). We identified 50 significant genetic correlations (r g range: - 0.37 to 0.75) between CMS and anthropometric traits. Five genetic correlations remained significant after adjustment for BMI [high density lipoprotein cholesterol (HDL-C) and waist-hip ratio; triglycerides and waist-hip ratio; triglycerides and waist-height ratio; non-HDL-C and waist-height ratio; insulin and iliac skinfold thickness]. This study provides evidence for the presence of potentially pleiotropic genes that affect both anthropometric and CMS traits, independently of obesity.

Experimental studies related to the origin of the genetic code and the process of protein synthesis - A review

NASA Technical Reports Server (NTRS)

Lacey, J. C., Jr.; Mullins, D. W., Jr.

1983-01-01

A survey is presented of the literature on the experimental evidence for the genetic code assignments and the chemical reactions involved in the process of protein synthesis. In view of the enormous number of theoretical models that have been advanced to explain the origin of the genetic code, attention is confined to experimental studies. Since genetic coding has significance only within the context of protein synthesis, it is believed that the problem of the origin of the code must be dealt with in terms of the origin of the process of protein synthesis. It is contended that the answers must lie in the nature of the molecules, amino acids and nucleotides, the affinities they might have for one another, and the effect that those affinities must have on the chemical reactions that are related to primitive protein synthesis. The survey establishes that for the bulk of amino acids, there is a direct and significant correlation between the hydrophobicity rank of the amino acids and the hydrophobicity rank of their anticodonic dinucleotides.

Mindfulness Among Genetic Counselors Is Associated with Increased Empathy and Work Engagement and Decreased Burnout and Compassion Fatigue.

PubMed

Silver, Julia; Caleshu, Colleen; Casson-Parkin, Sylvie; Ormond, Kelly

2018-03-04

Genetic counselors experience high rates of compassion fatigue and an elevated risk for burnout, both of which can negatively impact patient care and retention in the profession. In other healthcare professions, mindfulness training has been successfully used to address similar negative psychological sequelae and to bolster empathy, which is the foundation of our counseling work. We aimed to assess associations between mindfulness and key professional variables, including burnout, compassion fatigue, work engagement, and empathy. Data were collected via an anonymous, online survey that included validated measures of mindfulness and these key professional variables. The survey was completed by 441 genetic counselors involved in direct patient care. Half of the respondents (50.1%) reported engaging in yoga, meditation, and/or breathing exercises. Mindfulness was positively correlated with work engagement (r = 0.24, p < 0.001) and empathy (as measured through four subscales: perspective taking (r = 0.15, p = 0.002), empathic concern (r = 0.11, p = 0.03), fantasy (r = - 0.11, p = 0.03) and personal distress (r = - 0.15, p = 0.001)). Mindfulness was negatively correlated with compassion fatigue (r = - 0.48, p < 0.001) and burnout (r = - 0.50, p < 0.001). Given these findings, mindfulness training may be a valuable addition to graduate and continuing education for genetic counselors. The integration of mindfulness into the genetic counseling field will likely improve professional morale and well-being, while promoting workforce retention and bolstering the relational and counseling aspects of our clinical work.

Allele-Selective Transcriptome Recruitment to Polysomes Primed for Translation: Protein-Coding and Noncoding RNAs, and RNA Isoforms.

PubMed

Mascarenhas, Roshan; Pietrzak, Maciej; Smith, Ryan M; Webb, Amy; Wang, Danxin; Papp, Audrey C; Pinsonneault, Julia K; Seweryn, Michal; Rempala, Grzegorz; Sadee, Wolfgang

2015-01-01

mRNA translation into proteins is highly regulated, but the role of mRNA isoforms, noncoding RNAs (ncRNAs), and genetic variants remains poorly understood. mRNA levels on polysomes have been shown to correlate well with expressed protein levels, pointing to polysomal loading as a critical factor. To study regulation and genetic factors of protein translation we measured levels and allelic ratios of mRNAs and ncRNAs (including microRNAs) in lymphoblast cell lines (LCL) and in polysomal fractions. We first used targeted assays to measure polysomal loading of mRNA alleles, confirming reported genetic effects on translation of OPRM1 and NAT1, and detecting no effect of rs1045642 (3435C>T) in ABCB1 (MDR1) on polysomal loading while supporting previous results showing increased mRNA turnover of the 3435T allele. Use of high-throughput sequencing of complete transcript profiles (RNA-Seq) in three LCLs revealed significant differences in polysomal loading of individual RNA classes and isoforms. Correlated polysomal distribution between protein-coding and non-coding RNAs suggests interactions between them. Allele-selective polysome recruitment revealed strong genetic influence for multiple RNAs, attributable either to differential expression of RNA isoforms or to differential loading onto polysomes, the latter defining a direct genetic effect on translation. Genes identified by different allelic RNA ratios between cytosol and polysomes were enriched with published expression quantitative trait loci (eQTLs) affecting RNA functions, and associations with clinical phenotypes. Polysomal RNA-Seq combined with allelic ratio analysis provides a powerful approach to study polysomal RNA recruitment and regulatory variants affecting protein translation.

QTL analysis of root morphology, flowering time, and yield reveals trade-offs in response to drought in Brassica napus.

PubMed

Fletcher, Richard S; Mullen, Jack L; Heiliger, Annie; McKay, John K

2015-01-01

Drought escape and dehydration avoidance represent alternative strategies for drought adaptation in annual crops. The mechanisms underlying these two strategies are reported to have a negative correlation, suggesting a trade-off. We conducted a quantitative trait locus (QTL) analysis of flowering time and root mass, traits representing each strategy, in Brassica napus to understand if a trade-off exists and what the genetic basis might be. Our field experiment used a genotyped population of doubled haploid lines and included both irrigated and rainfed treatments, allowing analysis of plasticity in each trait. We found strong genetic correlations among all traits, suggesting a trade-off among traits may exist. Summing across traits and treatments we found 20 QTLs, but many of these co-localized to two major QTLs, providing evidence that the trade-off is genetically constrained. To understand the mechanistic relationship between root mass, flowering time, and QTLs, we analysed the data by conditioning upon correlated traits. Our results suggest a causal model where such QTLs affect root mass directly as well as through their impacts on flowering time. Additionally, we used draft Brassica genomes to identify orthologues of well characterized Arabidopsis thaliana flowering time genes as candidate genes. This research provides valuable clues to breeding for drought adaptation as it is the first to analyse the inheritance of the root system in B. napus in relation to drought. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Direct-to-consumer genetic testing: where and how does genetic counseling fit?

PubMed

Middleton, Anna; Mendes, Álvaro; Benjamin, Caroline M; Howard, Heidi Carmen

2017-05-01

Direct-to-consumer genetic testing for disease ranges from well-validated diagnostic and predictive tests to 'research' results conferring increased risks. While being targeted at public curious about their health, they are also marketed for use in reproductive decision-making or management of disease. By virtue of being 'direct-to-consumer' much of this testing bypasses traditional healthcare systems. We argue that direct-to-consumer genetic testing companies should make genetic counseling available, pre- as well as post-test. While we do not advocate that mandatory genetic counseling should gate-keep access to direct-to-consumer genetic testing, if the testing process has the potential to cause psychological distress, then companies have a responsibility to provide support and should not rely on traditional healthcare systems to pick up the pieces. A video abstract is available for this article via this link .

Effects of Genotype by Environment Interaction on Genetic Gain and Genetic Parameter Estimates in Red Tilapia (Oreochromis spp.)

PubMed Central

Nguyen, Nguyen H.; Hamzah, Azhar; Thoa, Ngo P.

2017-01-01

The extent to which genetic gain achieved from selection programs under strictly controlled environments in the nucleus that can be expressed in commercial production systems is not well-documented in aquaculture species. The main aim of this paper was to assess the effects of genotype by environment interaction on genetic response and genetic parameters for four body traits (harvest weight, standard length, body depth, body width) and survival in Red tilapia (Oreochromis spp.). The growth and survival data were recorded on 19,916 individual fish from a pedigreed population undergoing three generations of selection for increased harvest weight in earthen ponds from 2010 to 2012 at the Aquaculture Extension Center, Department of Fisheries, Jitra in Kedah, Malaysia. The pedigree comprised a total of 224 sires and 262 dams, tracing back to the base population in 2009. A multivariate animal model was used to measure genetic response and estimate variance and covariance components. When the homologous body traits in freshwater pond and cage were treated as genetically distinct traits, the genetic correlations between the two environments were high (0.85–0.90) for harvest weight and square root of harvest weight but the estimates were of lower magnitudes for length, width and depth (0.63–0.79). The heritabilities estimated for the five traits studied differed between pond (0.02 to 0.22) and cage (0.07 to 0.68). The common full-sib effects were large, ranging from 0.23 to 0.59 in pond and 0.11 to 0.31 in cage across all traits. The direct and correlated responses for four body traits were generally greater in pond than in cage environments (0.011–1.561 vs. −0.033–0.567 genetic standard deviation units, respectively). Selection for increased harvest body weight resulted in positive genetic changes in survival rate in both pond and cage culture. In conclusion, the reduced selection response and the magnitude of the genetic parameter estimates in the production environment (i.e., cage) relative to those achieved in the nucleus (pond) were a result of the genotype by environment interaction and this effect should be taken into consideration in the future breeding program for Red tilapia. PMID:28659970

Efficient Generation of Gene-Modified Pigs Harboring Precise Orthologous Human Mutation via CRISPR/Cas9-Induced Homology-Directed Repair in Zygotes.

PubMed

Zhou, Xiaoyang; Wang, Lulu; Du, Yinan; Xie, Fei; Li, Liang; Liu, Yu; Liu, Chuanhong; Wang, Shiqiang; Zhang, Shibing; Huang, Xingxu; Wang, Yong; Wei, Hong

2016-01-01

Precise genetic mutation of model animals is highly valuable for functional investigation of human mutations. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9)-induced homology-directed repair (HDR) is usually used for precise genetic mutation, being limited by the relatively low efficiency compared with that of non-homologous end joining (NHEJ). Although inhibition of NHEJ was shown to enhance HDR-derived mutation, in this work, without inhibition of NHEJ, we first generated gene-modified pigs harboring precise orthologous human mutation (Sox10 c.A325>T) via CRISPR/Cas9-induced HDR in zygotes using single-strand oligo DNA (ssODN) as template with an efficiency as high as 80%, indicating that pig zygotes exhibited high activities of HDR relative to NHEJ and were highly amendable to genetic mutation via CIRSPR/Cas9-induced HDR. Besides, we found a higher concentration of ssODN remarkably reduced HDR-derived mutation in pig zygotes, suggesting a possible balance for optimal HDR-derived mutation in zygotes between the excessive accessibility to HDR templates and the activities of HDR relative to NHEJ which appeared to be negatively correlated to ssODN concentration. In addition, the HDR-derived mutation, as well as those from NHEJ, extensively integrated into various tissues including gonad of founder pig without detected off-targeting, suggesting CRISPR/Cas9-induced HDR in zygotes is a reliable approach for precise genetic mutation in pigs. © 2015 WILEY PERIODICALS, INC.

Radial Domany-Kinzel models with mutation and selection

NASA Astrophysics Data System (ADS)

Lavrentovich, Maxim O.; Korolev, Kirill S.; Nelson, David R.

2013-01-01

We study the effect of spatial structure, genetic drift, mutation, and selective pressure on the evolutionary dynamics in a simplified model of asexual organisms colonizing a new territory. Under an appropriate coarse-graining, the evolutionary dynamics is related to the directed percolation processes that arise in voter models, the Domany-Kinzel (DK) model, contact process, and so on. We explore the differences between linear (flat front) expansions and the much less familiar radial (curved front) range expansions. For the radial expansion, we develop a generalized, off-lattice DK model that minimizes otherwise persistent lattice artifacts. With both simulations and analytical techniques, we study the survival probability of advantageous mutants, the spatial correlations between domains of neutral strains, and the dynamics of populations with deleterious mutations. “Inflation” at the frontier leads to striking differences between radial and linear expansions. For a colony with initial radius R0 expanding at velocity v, significant genetic demixing, caused by local genetic drift, occurs only up to a finite time t*=R0/v, after which portions of the colony become causally disconnected due to the inflating perimeter of the expanding front. As a result, the effect of a selective advantage is amplified relative to genetic drift, increasing the survival probability of advantageous mutants. Inflation also modifies the underlying directed percolation transition, introducing novel scaling functions and modifications similar to a finite-size effect. Finally, we consider radial range expansions with deflating perimeters, as might arise from colonization initiated along the shores of an island.

Consumers report lower confidence in their genetics knowledge following direct-to-consumer personal genomic testing

PubMed Central

Carere, Deanna Alexis; Kraft, Peter; Kaphingst, Kimberly A.; Roberts, J. Scott; Green, Robert C.

2015-01-01

Purpose To measure changes to genetics knowledge and self-efficacy following personal genomic testing (PGT). Methods New customers of 23andMe and Pathway Genomics completed a series of online surveys. Prior to receipt of results, and 6 months post-results, we measured genetics knowledge (9 true/false items) and genetics self-efficacy (5 Likert-scale items) and used paired methods to evaluate change over time. Correlates of change (e.g., decision regret) were identified using linear regression. Results 998 PGT customers (59.9% female; 85.8% White; mean age 46.9±15.5 years) were included in our analyses. Mean genetics knowledge score out of 9 was 8.15±0.95 at baseline and 8.25±0.92 at 6 months (p = .0024). Mean self-efficacy score out of 35 was 29.06±5.59 at baseline and 27.7±5.46 at 6 months (p < .0001); on each item, 30–45% of participants reported lower self-efficacy following PGT. Change in self-efficacy was positively associated with health care provider consultation (p = .0042), impact of PGT on perceived control over one’s health (p < .0001), and perceived value of PGT (p < .0001), and negatively associated with decision regret (p < .0001). Conclusion Lowered genetics self-efficacy following PGT may reflect an appropriate reevaluation by consumers in response to receiving complex genetic information. PMID:25812042

Investigating the Genetic Architecture of the PR Interval Using Clinical Phenotypes.

PubMed

Mosley, Jonathan D; Shoemaker, M Benjamin; Wells, Quinn S; Darbar, Dawood; Shaffer, Christian M; Edwards, Todd L; Bastarache, Lisa; McCarty, Catherine A; Thompson, Will; Chute, Christopher G; Jarvik, Gail P; Crosslin, David R; Larson, Eric B; Kullo, Iftikhar J; Pacheco, Jennifer A; Peissig, Peggy L; Brilliant, Murray H; Linneman, James G; Witte, John S; Denny, Josh C; Roden, Dan M

2017-04-01

One potential use for the PR interval is as a biomarker of disease risk. We hypothesized that quantifying the shared genetic architectures of the PR interval and a set of clinical phenotypes would identify genetic mechanisms contributing to PR variability and identify diseases associated with a genetic predictor of PR variability. We used ECG measurements from the ARIC study (Atherosclerosis Risk in Communities; n=6731 subjects) and 63 genetically modulated diseases from the eMERGE network (Electronic Medical Records and Genomics; n=12 978). We measured pairwise genetic correlations (rG) between PR phenotypes (PR interval, PR segment, P-wave duration) and each of the 63 phenotypes. The PR segment was genetically correlated with atrial fibrillation (rG=-0.88; P =0.0009). An analysis of metabolic phenotypes in ARIC also showed that the P wave was genetically correlated with waist circumference (rG=0.47; P =0.02). A genetically predicted PR interval phenotype based on 645 714 single-nucleotide polymorphisms was associated with atrial fibrillation (odds ratio=0.89 per SD change; 95% confidence interval, 0.83-0.95; P =0.0006). The differing pattern of associations among the PR phenotypes is consistent with analyses that show that the genetic correlation between the P wave and PR segment was not significantly different from 0 (rG=-0.03 [0.16]). The genetic architecture of the PR interval comprises modulators of atrial fibrillation risk and obesity. © 2017 American Heart Association, Inc.

Mosaic microecological differential stress causes adaptive microsatellite divergence in wild barley, Hordeum spontaneum, at Neve Yaar, Israel.

PubMed

Huang, Qingyang; Beharav, Alex; Li, Youchun; Kirzhner, Valery; Nevo, Eviatar

2002-12-01

Genetic diversity at 38 microsatellite (short sequence repeats (SSRs)) loci was studied in a sample of 54 plants representing a natural population of wild barley, Hordeum spontaneum, at the Neve Yaar microsite in Israel. Wild barley at the microsite was organized in a mosaic pattern over an area of 3180 m2 in the open Tabor oak forest, which was subdivided into four microniches: (i) sun-rock (11 genotypes), (ii) sun-soil (18 genotypes), (iii) shade-soil (11 genotypes), and (iv) shade-rock (14 genotypes). Fifty-four genotypes were tested for ecological-genetic microniche correlates. Analysis of 36 loci showed that allele distributions at SSR loci were nonrandom but structured by ecological stresses (climatic and edaphic). Sixteen (45.7%) of 35 polymorphic loci varied significantly (p < 0.05) in allele frequencies among the microniches. Significant genetic divergence and diversity were found among the four subpopulations. The soil and shade subpopulations showed higher genetic diversities at SSR loci than the rock and sun subpopulations, and the lowest genetic diversity was observed in the sun-rock subpopulation, in contrast with the previous allozyme and RAPD studies. On average, of 36 loci, 88.75% of the total genetic diversity exists within the four microniches, while 11.25% exists between the microniches. In a permutation test, G(ST) was lower for 4999 out of 5000 randomized data sets (p < 0.001) when compared with real data (0.1125). The highest genetic distance was between shade-soil and sun-rock (D = 0.222). Our results suggest that diversifying natural selection may act upon some regulatory regions, resulting in adaptive SSR divergence. Fixation of some loci (GMS61, GMS1, and EBMAC824) at a specific microniche seems to suggest directional selection. The pattern of other SSR loci suggests the operation of balancing selection. SSRs may be either direct targets of selection or markers of selected haplotypes (selective sweep).

Genetic parameters for cattle price and body weight from routinely collected data at livestock auctions and commercial farms.

PubMed

Mc Hugh, N; Evans, R D; Amer, P R; Fahey, A G; Berry, D P

2011-01-01

Beef outputs from dairy farms make an important contribution to overall profitability in Irish dairy herds and are the sole source of revenue in many beef herds. The aim of this study was to estimate genetic parameters for animal BW and price across different stages of maturity. Data originated from 2 main sources: price and BW from livestock auctions and BW from on-farm weighings between 2000 and 2008. The data were divided into 4 distinct maturity categories: calves (n = 24,513), weanlings (n = 27,877), postweanlings (n = 23,279), and cows (n = 4,894). A univariate animal model used to estimate variance components was progressively built up to include a maternal genetic effect and a permanent environmental maternal effect. Bivariate analyses were used to estimate genetic covariances between BW and price per animal within and across maturity category. Direct heritability estimates for price per animal were 0.34 ± 0.03, 0.31 ± 0.05, 0.19 ± 0.04, and 0.10 ± 0.04 for calves, weanling, postweanlings, and cows, respectively. Direct heritability estimates for BW were 0.26 ± 0.03 for weanlings, 0.25 ± 0.04 for postweanlings, and 0.24 ± 0.06 for cows; no BW data were available on calves. Significant maternal genetic and maternal permanent environmental effects were observed for weanling BW only. The genetic correlation between price per animal and BW within each maturity group varied from 0.55 ± 0.06 (postweanling price and BW) to 0.91 ± 0.04 (cow price and BW). The availability of routinely collected data, along with the existence of ample genetic variation for animal BW and price per animal, facilitates their inclusion in Irish dairy and beef breeding objectives to better reflect the profitability of both enterprises.

Temperature regulates limb length in homeotherms by directly modulating cartilage growth

PubMed Central

Serrat, Maria A.; King, Donna; Lovejoy, C. Owen

2008-01-01

Allen's Rule documents a century-old biological observation that strong positive correlations exist among latitude, ambient temperature, and limb length in mammals. Although genetic selection for thermoregulatory adaptation is frequently presumed to be the primary basis of this phenomenon, important but frequently overlooked research has shown that appendage outgrowth is also markedly influenced by environmental temperature. Alteration of limb blood flow via vasoconstriction/vasodilation is the current default hypothesis for this growth plasticity, but here we show that tissue perfusion does not fully account for differences in extremity elongation in mice. We show that peripheral tissue temperature closely reflects housing temperature in vivo, and we demonstrate that chondrocyte proliferation and extracellular matrix volume strongly correlate with tissue temperature in metatarsals cultured without vasculature in vitro. Taken together, these data suggest that vasomotor changes likely modulate extremity growth indirectly, via their effects on appendage temperature, rather than vascular nutrient delivery. When combined with classic evolutionary theory, especially genetic assimilation, these results provide a potentially comprehensive explanation of Allen's Rule, and may substantially impact our understanding of phenotypic variation in living and extinct mammals, including humans. PMID:19047632

Genetic Variance in the SES-IQ Correlation.

ERIC Educational Resources Information Center

Eckland, Bruce K.

1979-01-01

Discusses questions dealing with genetic aspects of the correlation between IQ and socioeconomic status (SES). Questions include: How does assortative mating affect the genetic variance of IQ? Is the relationship between an individual's IQ and adult SES a causal one? And how can IQ research improve schools and schooling? (Author/DB)

Genetic Stability of Cognitive Development from Childhood to Adulthood.

ERIC Educational Resources Information Center

DeFries, J. C.; And Others

1987-01-01

A path model of genetic and family environmental transmission was fitted to published twin correlations and to general cognitive ability data from adoptive and nonadoptive families in which children were tested yearly through the fourth year. Longitudinal genetic correlations from infancy to adulthood were modeled explicitly, as were effects of…

Correlated responses to clonal selection in populations of Daphnia pulicaria: mechanisms of genetic correlation and the creative power of sex.

PubMed

Dudycha, Jeffry L; Snoke-Smith, Margaret; Alía, Ricardo

2013-02-01

Genetic correlations among traits alter evolutionary trajectories due to indirect selection. Pleiotropy, chance linkage, and selection can all lead to genetic correlations, but have different consequences for phenotypic evolution. We sought to assess the mechanisms contributing to correlations with size at maturity in the cyclic parthenogen Daphnia pulicaria. We selected on size in each of four populations that differ in the frequency of sex, and evaluated correlated responses in a life table. Size at advanced adulthood, reproductive output, and adult growth rate clearly showed greater responses in high-sex populations, with a similar pattern in neonate size and r. This pattern is expected only when trait correlations are favored by selection and the frequency of sex favors the creation and demographic expansion of highly fit clones. Juvenile growth and age at maturity did not diverge consistently. The inter-clutch interval appeared to respond more strongly in low-sex populations, but this was not statistically significant. Our data support the hypothesis that correlated selection is the strongest driver of genetic correlations, and suggest that in organisms with both sexual and asexual reproduction, adaptation can be enhanced by recombination.

Genetic correlations among and between wool, growth and reproduction traits in Merino sheep.

PubMed

Safari, E; Fogarty, N M; Gilmour, A R; Atkins, K D; Mortimer, S I; Swan, A A; Brien, F D; Greeff, J C; van der Werf, J H J

2007-04-01

Data from seven research resource flocks across Australia were combined to provide accurate estimates of genetic correlations among production traits in Merino sheep. The flocks represented contemporary Australian Merino fine, medium and broad wool strains over the past 30 years. Over 110,000 records were available for analysis for each of the major wool traits, and 50,000 records for reproduction and growth traits with over 2700 sires and 25,000 dams. Individual models developed from the single trait analyses were extended to the various combinations of two-trait models to obtain genetic correlations among six wool traits [clean fleece weight (CFW), greasy fleece weight, fibre diameter (FD), yield, coefficient of variation of fibre diameter and standard deviation of fibre diameter], four growth traits [birth weight, weaning weight, yearling weight (YWT), and hogget weight] and four reproduction traits [fertility, litter size, lambs born per ewe joined, lambs weaned per ewe joined (LW/EJ)]. This study has provided for the first time a comprehensive matrix of genetic correlations among these 14 wool, growth and reproduction traits. The large size of the data set has also provided estimates with very low standard errors. A moderate positive genetic correlation was observed between CFW and FD (0.29 +/- 0.02). YWT was positively correlated with CFW (0.23 +/- 0.04), FD (0.17 +/- 0.04) and LWEJ (0.58 +/- 0.06), while LW/EJ was negatively correlated with CFW (-0.26 +/- 0.05) and positively correlated with FD (0.06 +/- 0.04) and LS (0.68 +/- 0.04). These genetic correlations, together with the estimates of heritability and other parameters provide the basis for more accurate prediction of outcomes in complex sheep-breeding programmes designed to improve several traits.

Evidence that pairing with genetically similar mates is maladaptive in a monogamous bird

USGS Publications Warehouse

Mulard, Hervé; Danchin, E.; Talbot, S.L.; Ramey, A.M.; Hatch, Shyla A.; White, J.F.; Helfenstein, F.; Wagner, R.H.

2009-01-01

Background. Evidence of multiple genetic criteria of mate choice is accumulating in numerous taxa. In many species, females have been shown to pair with genetically dissimilar mates or with extra-pair partners that are more genetically compatible than their social mates, thereby increasing their offsprings' heterozygosity which often correlates with offspring fitness. While most studies have focused on genetically promiscuous species, few studies have addressed genetically monogamous species, in which mate choice tends to be mutual. Results. Here, we used microsatellite markers to assess individual global heterozygosity and genetic similarity of pairs in a socially and genetically monogamous seabird, the black-legged kittiwake Rissa tridactyla. We found that pairs were more genetically dissimilar than expected by chance. We also identified fitness costs of breeding with genetically similar partners: (i) genetic similarity of pairs was negatively correlated with the number of chicks hatched, and (ii) offspring heterozygosity was positively correlated with growth rate and survival. Conclusion. These findings provide evidence that breeders in a genetically monogamous species may avoid the fitness costs of reproducing with a genetically similar mate. In such species that lack the opportunity to obtain extra-pair fertilizations, mate choice may therefore be under high selective pressure. ?? 2009 Mulard et al; licensee BioMed Central Ltd.

Genetic correlations between the cumulative pseudo-survival rate, milk yield, and somatic cell score during lactation in Holstein cattle in Japan using a random regression model.

PubMed

Sasaki, O; Aihara, M; Nishiura, A; Takeda, H

2017-09-01

Trends in genetic correlations between longevity, milk yield, and somatic cell score (SCS) during lactation in cows are difficult to trace. In this study, changes in the genetic correlations between milk yield, SCS, and cumulative pseudo-survival rate (PSR) during lactation were examined, and the effect of milk yield and SCS information on the reliability of estimated breeding value (EBV) of PSR were determined. Test day milk yield, SCS, and PSR records were obtained for Holstein cows in Japan from 2004 to 2013. A random subset of the data was used for the analysis (825 herds, 205,383 cows). This data set was randomly divided into 5 subsets (162-168 herds, 83,389-95,854 cows), and genetic parameters were estimated in each subset independently. Data were analyzed using multiple-trait random regression animal models including either the residual effect for the whole lactation period (H0), the residual effects for 5 lactation stages (H5), or both of these residual effects (HD). Milk yield heritability increased until 310 to 351 d in milk (DIM) and SCS heritability increased until 330 to 344 DIM. Heritability estimates for PSR increased with DIM from 0.00 to 0.05. The genetic correlation between milk yield and SCS increased negatively to under -0.60 at 455 DIM. The genetic correlation between milk yield and PSR increased until 342 to 355 DIM (0.53-0.57). The genetic correlation between the SCS and PSR was -0.82 to -0.83 at around 180 DIM, and decreased to -0.65 to -0.71 at 455 DIM. The reliability of EBV of PSR for sires with 30 or more recorded daughters was 0.17 to 0.45 when the effects of correlated traits were ignored. The maximum reliability of EBV was observed at 257 (H0) or 322 (HD) DIM. When the correlations of PSR with milk yield and SCS were considered, the reliabilities of PSR estimates increased to 0.31-0.76. The genetic parameter estimates of H5 were the same as those for HD. The rank correlation coefficients of the EBV of PSR between H0 and H5 or HD were greater than 0.9. Additionally, the reliabilities of EBV of PSR of H0 were similar to those for H5 and HD. Therefore, the genetic parameter estimates in H0 were not substantially different from those in H5 and HD. When milk yield and SCS, which were genetically correlated with PSR, were used, the reliability of PSR increased. Estimates of the genetic correlations between PSR and milk yield and between PSR and SCS are useful for management and breeding decisions to extend the herd life of cows. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Genetic correlations between endo-parasite phenotypes and economically important traits in dairy and beef cattle.

PubMed

Twomey, Alan J; Carroll, Rebecca I; Doherty, Michael L; Byrne, Noel; Graham, David A; Sayers, Riona G; Blom, Astrid; Berry, Donagh P

2018-03-06

Parasitic diseases have economic consequences in cattle production systems. Although breeding for parasite resistance can complement current control practices to reduce the prevalence globally, there is little knowledge of the implications of such a strategy on other performance traits. Records on individual animal antibody responses to Fasciola hepatica, Ostertagia ostertagi, and Neospora caninum were available from cows in 68 dairy herds (study herds); national abattoir data on F. hepatica-damaged livers were also available from dairy and beef cattle. After data edits, 9,271 dairy cows remained in the study herd dataset, whereas 19,542 dairy cows and 68,048 young dairy and beef animals had a record for the presence or absence of F. hepatica-damaged liver in the national dataset. Milk, reproductive, and carcass phenotypes were also available for a proportion of these animals as well as their contemporaries. Linear mixed models were used to estimate variance components of antibody responses to the three parasites; covariance components were estimated between the parasite phenotypes and economically important traits. Heritability of antibody responses to the different parasites, when treated as a continuous trait, ranged from 0.07 (O. ostertagi) to 0.13 (F. hepatica), whereas the coefficient of genetic variation ranged from 4% (O. ostertagi) to 20% (F. hepatica). The antibody response to N. caninum was genetically correlated with the antibody response to both F. hepatica (-0.29) and O. ostertagi (-0.67); a moderately positive genetic correlation existed between the antibody response to F. hepatica and O. ostertagi (0.66). Genetic correlations between the parasite phenotypes and the milk production traits were all close to zero (-0.14 to 0.10), as were the genetic correlations between F. hepatica-damaged livers and the carcass traits of carcass weight, conformation, and fat score evaluated in cows and young animals (0.00 to 0.16). The genetic correlation between F. hepatica-damaged livers in cows and milk somatic cell score was 0.32 (SE = 0.20). Antibody responses to F. hepatica and O. ostertagi had favorable genetic correlations with fertility traits, but conversely, antibody response to N. caninum and F. hepatica-damaged livers were unfavorably genetically correlated with fertility. This study provides the necessary information to undertake national multitrait genetic evaluations for parasite phenotypes.

Same genetic components underlie different measures of sweet taste preference.

PubMed

Keskitalo, Kaisu; Tuorila, Hely; Spector, Tim D; Cherkas, Lynn F; Knaapila, Antti; Silventoinen, Karri; Perola, Markus

2007-12-01

Sweet taste preferences are measured by several often correlated measures. We examined the relative proportions of genetic and environmental effects on sweet taste preference indicators and their mutual correlations. A total of 663 female twins (324 complete pairs, 149 monozygous and 175 dizygous pairs) aged 17-80 y rated the liking and intensity of a 20% (wt/vol) sucrose solution, reported the liking and the use-frequency of 6 sweet foods (sweet desserts, sweets, sweet pastry, ice cream, hard candy, and chocolate), and completed a questionnaire on cravings of sweet foods. The estimated contributions of genetic factors, environmental factors shared by a twin pair, and environmental factors unique to each twin individual to the variance and covariance of the traits were obtained with the use of linear structural equation modeling. Approximately half of the variation in liking for sweet solution and liking and use-frequency of sweet foods (49-53%) was explained by genetic factors, whereas the rest of the variation was due to environmental factors unique to each twin individual. Sweet taste preference-related traits were correlated. Tetravariate modeling showed that the correlation between liking for the sweet solution and liking for sweet foods was due to genetic factors (genetic r = 0.27). Correlations between liking, use-frequency, and craving for sweet foods were due to both genetic and unshared environmental factors. Detailed information on the associations between preference measures is an important intermediate goal in the determination of the genetic components affecting sweet taste preferences.

Low extraversion and high neuroticism as indices of genetic and environmental risk for social phobia, agoraphobia, and animal phobia.

PubMed

Bienvenu, O Joseph; Hettema, John M; Neale, Michael C; Prescott, Carol A; Kendler, Kenneth S

2007-11-01

The authors examined the extent to which two major personality dimensions (extraversion and neuroticism) index the genetic and environmental risk for three phobias (social phobia, agoraphobia, and animal phobia) in twins ascertained from a large, population-based registry. Lifetime phobias and personality traits were assessed through diagnostic interview and self-report questionnaire, respectively, in 7,800 twins from female-female, male-male, and opposite-sex pairs. Sex-limited trivariate Cholesky structural equation models were used to decompose the correlations among extraversion, neuroticism, and each phobia. In the best-fitting models, genetic correlations were moderate and negative between extraversion and both social phobia and agoraphobia, and that between extraversion and animal phobia was effectively zero. Genetic correlations were high and positive between neuroticism and both social phobia and agoraphobia, and that between neuroticism and animal phobia was moderate. All of the genetic risk factors for social phobia and agoraphobia were shared with those that influence extraversion and neuroticism; in contrast, only a small proportion of the genetic risk factors for animal phobia (16%) was shared with those that influence personality. Shared environmental experiences were not a source of correlations between personality traits and phobias, and unique environmental correlations were relatively modest. Genetic factors that influence individual variation in extraversion and neuroticism appear to account entirely for the genetic liability to social phobia and agoraphobia, but not animal phobia. These findings underline the importance of both introversion (low extraversion) and neuroticism in some psychiatric disorders.

Heritability of rectal temperature and genetic correlations with production and reproduction traits in dairy cattle.

PubMed

Dikmen, S; Cole, J B; Null, D J; Hansen, P J

2012-06-01

Genetic selection for body temperature during heat stress might be a useful approach to reduce the magnitude of heat stress effects on production and reproduction. Objectives of the study were to estimate the genetic parameters of rectal temperature (RT) in dairy cows in freestall barns under heat stress conditions and to determine the genetic and phenotypic correlations of rectal temperature with other traits. Afternoon RT were measured in a total of 1,695 lactating Holstein cows sired by 509 bulls during the summer in North Florida. Genetic parameters were estimated with Gibbs sampling, and best linear unbiased predictions of breeding values were predicted using an animal model. The heritability of RT was estimated to be 0.17 ± 0.13. Predicted transmitting abilities for rectal temperature changed 0.0068 ± 0.0020°C/yr from (birth year) 2002 to 2008. Approximate genetic correlations between RT and 305-d milk, fat, and protein yields, productive life, and net merit were significant and positive, whereas approximate genetic correlations between RT and somatic cell count score and daughter pregnancy rate were significant and negative. Rectal temperature during heat stress has moderate heritability, but genetic correlations with economically important traits mean that selection for RT could lead to lower productivity unless methods are used to identify genes affecting RT that do not adversely affect other traits of economic importance. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Predictors for reproductive isolation in a ring species complex following genetic and ecological divergence.

PubMed

Pereira, Ricardo J; Monahan, William B; Wake, David B

2011-07-06

Reproductive isolation (RI) is widely accepted as an important "check point" in the diversification process, since it defines irreversible evolutionary trajectories. Much less consensus exists about the processes that might drive RI. Here, we employ a formal quantitative analysis of genetic interactions at several stages of divergence within the ring species complex Ensatina eschscholtzii in order to assess the relative contribution of genetic and ecological divergence for the development of RI. By augmenting previous genetic datasets and adding new ecological data, we quantify levels of genetic and ecological divergence between populations and test how they correlate with a restriction of genetic admixture upon secondary contact. Our results indicate that the isolated effect of ecological divergence between parental populations does not result in reproductively isolated taxa, even when genetic transitions between parental taxa are narrow. Instead, processes associated with overall genetic divergence are the best predictors of reproductive isolation, and when parental taxa diverge in nuclear markers we observe a complete cessation of hybridization, even to sympatric occurrence of distinct evolutionary lineages. Although every parental population has diverged in mitochondrial DNA, its degree of divergence does not predict the extent of RI. These results show that in Ensatina, the evolutionary outcomes of ecological divergence differ from those of genetic divergence. While evident properties of taxa may emerge via ecological divergence, such as adaptation to local environment, RI is likely to be a byproduct of processes that contribute to overall genetic divergence, such as time in geographic isolation, rather than being a direct outcome of local adaptation.

Translation and validation of a Spanish-language genetic health literacy screening tool.

PubMed

Rodríguez, Sally Ann; Roter, Debra L; Castillo-Salgado, Carlos; Hooker, Gillian W; Erby, Lori H

2015-02-01

Literacy deficits and underutilization of medical services have been linked to health disparities among minorities, and this appears especially relevant for the Latino population. Given the increasing importance of genetics, assessment of genetic health literacy may direct future efforts to better serve this vulnerable population. The current study was designed to contribute to this area by translating and validating a Spanish-language genetic health literacy measure. This was a cross-sectional study involving an interviewer-administered questionnaire. Eligible individuals were Latinos between the ages of 18 and 75 residing in Maryland, who self-reported Spanish as their primary language, recruited through convenience sampling. The genetic health literacy measure components were adapted from existing English-language measures [Erby, Roter, Larson, & Cho's (2008) Rapid Estimate of Adult Literacy in Genetics (REAL-G) and Hooker et al.'s (2014) Genetic Literacy and Comprehension]. An existing Spanish-language general health literacy measure was used to establish preliminary concurrent validity [Lee, Bender, Ruiz, & Cho's (2006) SAHLSA]. 116 individuals completed the assessment. The Spanish-language REAL-G (REAL-G-Sp) was found to correlate well with the SAHLSA (Pearson's r = .77, p < .01). A cut-off score of 59 (out of 62) distinguished low versus high genetic health literacy with a sensitivity of 86% and specificity of 71%, identifying 28% of participants as having inadequate genetic health literacy. The REAL-G-Sp was found to have preliminary concurrent validity with an existing health literacy measure in the Latino population residing in Maryland. Significant proportions of this population are predicted to have limitations in genetic health literacy, even when information is provided in Spanish.

A comparison of direct and indirect analytical approaches to measuring total nicotine equivalents in urine.

PubMed

Taghavi, Taraneh; Novalen, Maria; Lerman, Caryn; George, Tony P; Tyndale, Rachel F

2018-05-31

Total nicotine equivalents (TNE), the sum of nicotine and metabolites in urine, is a valuable tool for evaluating nicotine exposure. Most methods for measuring TNE involve two-step enzymatic hydrolysis for indirect quantification of glucuronide metabolites. Here, we describe a rapid, low-cost direct liquid chromatography - tandem mass spectrometry (LCMS) assay. In 139 smokers' urine samples, Bland-Altman, correlation, and regression analyses were used to investigate differences in quantification of nicotine and metabolites, TNE, and nicotine metabolite ratio (NMR) between direct and indirect LCMS methods. DNA from a subset (n=97 smokers) was genotyped for UGT2B10*2 and UGT2B17*2 and the known impact of these variants was evaluated using urinary ratios determined by the direct versus indirect method. The direct method showed high accuracy (0-9% bias) and precision (3-14% coefficient of variation) with similar distribution of nicotine metabolites to literary estimates and good agreement between the direct and indirect methods for nicotine, cotinine, and 3-hydroxycotinine (ratios 0.99-1.07), but less agreement for their respective glucuronides (ratios 1.16-4.17). The direct method identified urinary 3HC+3HC-GLUC/COT as having the highest concordance with plasma NMR and provided substantially better estimations of the established genetic impact of glucuronidation variants compared to the indirect method. Direct quantification of nicotine and metabolites is less time-consuming and less costly, and provides accurate estimates of nicotine intake, metabolism rate and the impact of genetic variation in smokers. Lower cost and maintenance combined with high accuracy and reproducibility make the direct method ideal for smoking biomarker, NMR and pharmacogenomics studies. Copyright ©2018, American Association for Cancer Research.

Heritabilities of measured and mid-infrared predicted milk fat globule size, milk fat and protein percentages, and their genetic correlations.

PubMed

Fleming, A; Schenkel, F S; Koeck, A; Malchiodi, F; Ali, R A; Corredig, M; Mallard, B; Sargolzaei, M; Miglior, F

2017-05-01

The objective of this study was to estimate the heritability of milk fat globule (MFG) size and mid-infrared (MIR) predicted MFG size in Holstein cattle. The genetic correlations between measured and predicted MFG size with milk fat and protein percentage were also investigated. Average MFG size was measured in 1,583 milk samples taken from 254 Holstein cows from 29 herds across Canada. Size was expressed as volume moment mean (D[4,3]) and surface moment mean (D[3,2]). Analyzed milk samples also had average MFG size predicted from their MIR spectral records. Fat and protein percentages were obtained for all test-day milk samples in the cow's lactation. Univariate and bivariate repeatability animal models were used to estimate heritability and genetic correlations. Moderate heritabilities of 0.364 and 0.466 were found for D[4,3] and D[3,2], respectively, and a strong genetic correlation was found between the 2 traits (0.98). The heritabilities for the MIR-predicted MFG size were lower than those estimated for the measured MFG size at 0.300 for predicted D[4,3] and 0.239 for predicted D[3,2]. The genetic correlation between measured and predicted D[4,3] was 0.685; the correlation was slightly higher between measured and predicted D[3,2] at 0.764, likely due to the better prediction accuracy of D[3,2]. Milk fat percentage had moderate genetic correlations with both D[4,3] and D[3,2] (0.538 and 0.681, respectively). The genetic correlation between predicted MFG size and fat percentage was much stronger (greater than 0.97 for both predicted D[4,3] and D[3,2]). The stronger correlation suggests a limitation for the use of the predicted values of MFG size as indicator traits for true average MFG size in milk in selection programs. Larger samples sizes are required to provide better evidence of the estimated genetic parameters. A genetic component appears to exist for the average MFG size in bovine milk, and the variation could be exploited in selection programs. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Genome-wide analysis of genetic correlation in dementia with Lewy bodies, Parkinson's and Alzheimer's diseases

PubMed Central

Guerreiro, Rita; Escott-Price, Valentina; Darwent, Lee; Parkkinen, Laura; Ansorge, Olaf; Hernandez, Dena G.; Nalls, Michael A.; Clark, Lorraine; Honig, Lawrence; Marder, Karen; van der Flier, Wiesje; Holstege, Henne; Louwersheimer, Eva; Lemstra, Afina; Scheltens, Philip; Rogaeva, Ekaterina; St George-Hyslop, Peter; Londos, Elisabet; Zetterberg, Henrik; Ortega-Cubero, Sara; Pastor, Pau; Ferman, Tanis J.; Graff-Radford, Neill R.; Ross, Owen A.; Barber, Imelda; Braae, Anne; Brown, Kristelle; Morgan, Kevin; Maetzler, Walter; Berg, Daniela; Troakes, Claire; Al-Sarraj, Safa; Lashley, Tammaryn; Compta, Yaroslau; Revesz, Tamas; Lees, Andrew; Cairns, Nigel J.; Halliday, Glenda M.; Mann, David; Pickering-Brown, Stuart; Powell, John; Lunnon, Katie; Lupton, Michelle K.; Dickson, Dennis; Hardy, John; Singleton, Andrew; Bras, Jose

2016-01-01

The similarities between dementia with Lewy bodies (DLB) and both Parkinson's disease (PD) and Alzheimer's disease (AD) are many and range from clinical presentation, to neuropathological characteristics, to more recently identified, genetic determinants of risk. Because of these overlapping features, diagnosing DLB is challenging and has clinical implications since some therapeutic agents that are applicable in other diseases have adverse effects in DLB. Having shown that DLB shares some genetic risk with PD and AD, we have now quantified the amount of sharing through the application of genetic correlation estimates, and show that, from a purely genetic perspective, and excluding the strong association at the APOE locus, DLB is equally correlated to AD and PD. PMID:26643944

Blood pressure and cerebral white matter share common genetic factors in Mexican Americans.

PubMed

Kochunov, Peter; Glahn, David C; Lancaster, Jack; Winkler, Anderson; Karlsgodt, Kathrin; Olvera, Rene L; Curran, Joanna E; Carless, Melanie A; Dyer, Thomas D; Almasy, Laura; Duggirala, Ravi; Fox, Peter T; Blangero, John

2011-02-01

Elevated arterial pulse pressure and blood pressure (BP) can lead to atrophy of cerebral white matter (WM), potentially attributable to shared genetic factors. We calculated the magnitude of shared genetic variance between BP and fractional anisotropy of water diffusion, a sensitive measurement of WM integrity in a well-characterized population of Mexican Americans. The patterns of whole-brain and regional genetic overlap between BP and fractional anisotropy were interpreted in the context the pulse-wave encephalopathy theory. We also tested whether regional pattern in genetic pleiotropy is modulated by the phylogeny of WM development. BP and high-resolution (1.7 × 1.7 × 3 mm; 55 directions) diffusion tensor imaging data were analyzed for 332 (202 females; mean age 47.9 ± 13.3 years) members of the San Antonio Family Heart Study. Bivariate genetic correlation analysis was used to calculate the genetic overlap between several BP measurements (pulse pressure, systolic BP, and diastolic BP) and fractional anisotropy (whole-brain and regional values). Intersubject variance in pulse pressure and systolic BP exhibited a significant genetic overlap with variance in whole-brain fractional anisotropy values, sharing 36% and 22% of genetic variance, respectively. Regionally, shared genetic variance was significantly influenced by rates of WM development (r=-0.75; P=0.01). The pattern of genetic overlap between BP and WM integrity was generally in agreement with the pulse-wave encephalopathy theory. Our study provides evidence that a set of pleiotropically acting genetic factors jointly influence phenotypic variation in BP and WM integrity. The magnitude of this overlap appears to be influenced by phylogeny of WM development, suggesting a possible role for genotype-by-age interactions.

Blood Pressure and Cerebral White Matter Share Common Genetic Factors in Mexican-Americans

PubMed Central

Kochunov, Peter; Glahn, David C; Lancaster, Jack; Winkler, Anderson; Karlsgodt, Kathrin; Olvera, Rene L; Curran, Joanna E; Carless, Melanie A; Dyer, Thomas D; Almasy, Laura; Duggirala, Ravi; Fox, Peter T; Blangero, John

2010-01-01

Elevated arterial pulse pressure (PP) and blood pressure (BP) can lead to atrophy of cerebral white matter (WM), potentially due to shared genetic factors. We calculated the magnitude of shared genetic variance between BP and fractional anisotropy (FA) of water diffusion, a sensitive measurement of WM integrity in a well-characterized population of Mexican-Americans. The patterns of whole-brain and regional genetic overlap between BP and FA were interpreted in the context the pulse-wave encephalopathy (PWE) theory. We also tested whether regional pattern in genetic pleiotropy is modulated by the phylogeny of WM development. BP and high-resolution (1.7×1.7×3mm, 55 directions) diffusion tensor imaging (DTI) data were analyzed for 332 (202 females; mean age=47.9±13.3years) members of the San Antonio Family Heart Study. Bivariate genetic correlation analysis was used to calculate the genetic overlap between several BP measurements [PP, systolic (SBP) and diastolic (DBP)] and FA (whole-brain and regional values). Intersubject variance in PP and SBP exhibited a significant genetic overlap with variance in whole-brain FA values, sharing 36% and 22% of genetic variance, respectively. Regionally, shared genetic variance was significantly influenced by rates of WM development (r=−.75, p=0.01). The pattern of genetic overlap between BP and WM integrity was generally in-agreement with the PWE theory. Our study provides evidence that a set of pleiotropically acting genetic factors jointly influence phenotypic variation in BP and WM integrity. The magnitude of this overlap appears to be influenced by phylogeny of WM development suggesting a possible role for genotype-by-age interactions. PMID:21135356

Neural Correlates of the Y Chromosome in Autism: XYY Syndrome as a Genetic Model

DTIC Science & Technology

2017-09-01

AWARD NUMBER: W81XWH-15-1-0355 TITLE: Neural Correlates of the Y Chromosome in Autism: XYY Syndrome as a Genetic Model PRINCIPAL INVESTIGATOR...SUBJECT TERMS Autism spectrum disorder, ASD; 47,XYY syndrome (XYY); neuroimaging; MRI; MEG; Comorbid behaviors 15T 6. SECURITY CLASSIFICATION OF...by ANSI Std. Z39.18 Neural Correlates of the Y Chromosome in Autism: XYY Syndrome as a Genetic Model Table of Contents Page 1. Introduction

Genetic analysis of fat-to-protein ratio, milk yield and somatic cell score of Holstein cows in Japan in the first three lactations by using a random regression model.

PubMed

Nishiura, Akiko; Sasaki, Osamu; Aihara, Mitsuo; Takeda, Hisato; Satoh, Masahiro

2015-12-01

We estimated the genetic parameters of fat-to-protein ratio (FPR) and the genetic correlations between FPR and milk yield or somatic cell score in the first three lactations in dairy cows. Data included 3,079,517 test-day records of 201,138 Holstein cows in Japan from 2006 to 2011. Genetic parameters were estimated with a multiple-trait random regression model in which the records within and between parities were treated as separate traits. The phenotypic values of FPR increased soon after parturition and peaked at 10 to 20 days in milk, then decreased slowly in mid- and late lactation. Heritability estimates for FPR yielded moderate values. Genetic correlations of FPR among parities were low in early lactation. Genetic correlations between FPR and milk yield were positive and low in early lactation, but only in the first lactation. Genetic correlations between FPR and somatic cell score were positive in early lactation and decreased to become negative in mid- to late lactation. By using these results for genetic evaluation it should be possible to improve energy balance in dairy cows. © 2015 Japanese Society of Animal Science.

Environmental effects on the structure of the G-matrix.

PubMed

Wood, Corlett W; Brodie, Edmund D

2015-11-01

Genetic correlations between traits determine the multivariate response to selection in the short term, and thereby play a causal role in evolutionary change. Although individual studies have documented environmentally induced changes in genetic correlations, the nature and extent of environmental effects on multivariate genetic architecture across species and environments remain largely uncharacterized. We reviewed the literature for estimates of the genetic variance-covariance (G) matrix in multiple environments, and compared differences in G between environments to the divergence in G between conspecific populations (measured in a common garden). We found that the predicted evolutionary trajectory differed as strongly between environments as it did between populations. Between-environment differences in the underlying structure of G (total genetic variance and the relative magnitude and orientation of genetic correlations) were equal to or greater than between-population differences. Neither environmental novelty, nor the difference in mean phenotype predicted these differences in G. Our results suggest that environmental effects on multivariate genetic architecture may be comparable to the divergence that accumulates over dozens or hundreds of generations between populations. We outline avenues of future research to address the limitations of existing data and characterize the extent to which lability in genetic correlations shapes evolution in changing environments. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Role of introduction history and landscape in the range expansion of brown trout (Salmo trutta L.) in the Kerguelen Islands.

PubMed

Launey, Sophie; Brunet, Geraldine; Guyomard, René; Davaine, Patrick

2010-01-01

Human-mediated biological invasions constitute interesting case studies to understand evolutionary processes, including the role of founder effects. Population expansion of newly introduced species can be highly dependant on barriers caused by landscape features, but identifying these barriers and their impact on genetic structure is a relatively recent concern in population genetics and ecology. Salmonid populations of the Kerguelen Islands archipelago are a favorable model system to address these questions as these populations are characterized by a simple history of introduction, little or no anthropogenic influence, and demographic monitoring since the first introductions. We analyzed genetic variation at 10 microsatellite loci in 19 populations of brown trout (Salmo trutta L.) in the Courbet Peninsula (Kerguelen Islands), where the species, introduced in 3 rivers only, has colonized the whole water system in 40 years. Despite a limited numbers of introductions, trout populations have maintained a genetic diversity comparable with what is found in hatchery or wild populations in Europe, but they are genetically structured. The main factor explaining the observed patterns of genetic diversity is the history of introductions, with each introduced population acting as a source for colonization of nearby rivers. Correlations between environmental and genetic parameters show that within each "source population" group, landscape characteristics (type of coast, accessibility of river mouth, distances between rivers, river length ...) play a role in shaping directions and rates of migration, and thus the genetic structure of the colonizing populations.

Consumers report lower confidence in their genetics knowledge following direct-to-consumer personal genomic testing.

PubMed

Carere, Deanna Alexis; Kraft, Peter; Kaphingst, Kimberly A; Roberts, J Scott; Green, Robert C

2016-01-01

The aim of this study was to measure changes to genetics knowledge and self-efficacy following personal genomic testing (PGT). New customers of 23andMe and Pathway Genomics completed a series of online surveys. We measured genetics knowledge (nine true/false items) and genetics self-efficacy (five Likert-scale items) before receipt of results and 6 months after results and used paired methods to evaluate change over time. Correlates of change (e.g., decision regret) were identified using linear regression. 998 PGT customers (59.9% female; 85.8% White; mean age 46.9 ± 15.5 years) were included in our analyses. Mean genetics knowledge score was 8.15 ± 0.95 (out of 9) at baseline and 8.25 ± 0.92 at 6 months (P = 0.0024). Mean self-efficacy score was 29.06 ± 5.59 (out of 35) at baseline and 27.7 ± 5.46 at 6 months (P < 0.0001); on each item, 30-45% of participants reported lower self-efficacy following PGT. Change in self-efficacy was positively associated with health-care provider consultation (P = 0.0042), impact of PGT on perceived control over one's health (P < 0.0001), and perceived value of PGT (P < 0.0001) and was negatively associated with decision regret (P < 0.0001). Lowered genetics self-efficacy following PGT may reflect an appropriate reevaluation by consumers in response to receiving complex genetic information.Genet Med 18 1, 65-72.

Genetic correlations of mid-infrared-predicted milk fatty acid groups with milk production traits.

PubMed

Fleming, A; Schenkel, F S; Malchiodi, F; Ali, R A; Mallard, B; Sargolzaei, M; Jamrozik, J; Johnston, J; Miglior, F

2018-05-01

The objective of this research was to estimate the genetic correlations between milk mid-infrared-predicted fatty acid groups and production traits in first-parity Canadian Holsteins. Contents of short-chain, medium-chain, long-chain, saturated, and unsaturated fatty acid groupings in milk samples can be predicted using mid-infrared spectral data for cows enrolled in milk recording programs. Predicted fatty acid group contents were obtained for 49,127 test-day milk samples from 10,029 first-parity Holstein cows in 810 herds. Milk yield, fat and protein yield, fat and protein percentage, fat-to-protein ratio, and somatic cell score were also available for these test days. Genetic parameters were estimated for the fatty acid groups and production traits using multiple-trait random regression test day models by Bayesian methods via Gibbs sampling. Three separate 8- or 9-trait analyses were performed, including the 5 fatty acid groups with different combinations of the production traits. Posterior standard deviations ranged from <0.001 to 0.01. Average daily genetic correlations were negative and similar to each other for the fatty acid groups with milk yield (-0.62 to -0.59) and with protein yield (-0.32 to -0.25). Weak and positive average daily genetic correlations were found between somatic cell score and the fatty acid groups (from 0.25 to 0.36). Stronger genetic correlations with fat yield, fat and protein percentage, and fat-to-protein ratio were found with medium-chain and saturated fatty acid groups compared with those with long-chain and unsaturated fatty acid groups. Genetic correlations were very strong between the fatty acid groups and fat percentage, ranging between 0.88 for unsaturated and 0.99 for saturated fatty acids. Daily genetic correlations from 5 to 305 d in milk with milk, protein yield and percentage, and somatic cell score traits showed similar patterns for all fatty acid groups. The daily genetic correlations with fat yield at the beginning of lactation were decreasing for long-chain and unsaturated fatty acid groups and increasing for short-chain fatty acids. Genetic correlations between fat percentage and fatty acids were increasing at the beginning of lactation for short- and medium-chain and saturated fatty acids, but slightly decreasing for long-chain and unsaturated fatty acid groups. These results can be used in defining fatty acid traits and breeding objectives. Copyright © 2018 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Genome-wide variation in recombination rate in Eucalyptus.

PubMed

Gion, Jean-Marc; Hudson, Corey J; Lesur, Isabelle; Vaillancourt, René E; Potts, Brad M; Freeman, Jules S

2016-08-09

Meiotic recombination is a fundamental evolutionary process. It not only generates diversity, but influences the efficacy of natural selection and genome evolution. There can be significant heterogeneity in recombination rates within and between species, however this variation is not well understood outside of a few model taxa, particularly in forest trees. Eucalypts are forest trees of global economic importance, and dominate many Australian ecosystems. We studied recombination rate in Eucalyptus globulus using genetic linkage maps constructed in 10 unrelated individuals, and markers anchored to the Eucalyptus reference genome. This experimental design provided the replication to study whether recombination rate varied between individuals and chromosomes, and allowed us to study the genomic attributes and population genetic parameters correlated with this variation. Recombination rate varied significantly between individuals (range = 2.71 to 3.51 centimorgans/megabase [cM/Mb]), but was not significantly influenced by sex or cross type (F1 vs. F2). Significant differences in recombination rate between chromosomes were also evident (range = 1.98 to 3.81 cM/Mb), beyond those which were due to variation in chromosome size. Variation in chromosomal recombination rate was significantly correlated with gene density (r = 0.94), GC content (r = 0.90), and the number of tandem duplicated genes (r = -0.72) per chromosome. Notably, chromosome level recombination rate was also negatively correlated with the average genetic diversity across six species from an independent set of samples (r = -0.75). The correlations with genomic attributes are consistent with findings in other taxa, however, the direction of the correlation between diversity and recombination rate is opposite to that commonly observed. We argue this is likely to reflect the interaction of selection and specific genome architecture of Eucalyptus. Interestingly, the differences amongst chromosomes in recombination rates appear stable across Eucalyptus species. Together with the strong correlations between recombination rate and features of the Eucalyptus reference genome, we maintain these findings provide further evidence for a broad conservation of genome architecture across the globally significant lineages of Eucalyptus.

The Molecular Basis of Human Brain Evolution.

PubMed

Enard, Wolfgang

2016-10-24

Humans are a remarkable species, especially because of the remarkable properties of their brain. Since the split from the chimpanzee lineage, the human brain has increased three-fold in size and has acquired abilities for vocal learning, language and intense cooperation. To better understand the molecular basis of these changes is of great biological and biomedical interest. However, all the about 16 million fixed genetic changes that occurred during human evolution are fully correlated with all molecular, cellular, anatomical and behavioral changes that occurred during this time. Hence, as humans and chimpanzees cannot be crossed or genetically manipulated, no direct evidence for linking particular genetic and molecular changes to human brain evolution can be obtained. Here, I sketch a framework how indirect evidence can be obtained and review findings related to the molecular basis of human cognition, vocal learning and brain size. In particular, I discuss how a comprehensive comparative approach, leveraging cellular systems and genomic technologies, could inform the evolution of our brain in the future. Copyright © 2016 Elsevier Ltd. All rights reserved.

Shared influence of pathogen and host genetics on a trade-off between latent period and spore production capacity in the wheat pathogen, Puccinia triticina.

PubMed

Pariaud, Bénédicte; Berg, Femke; Bosch, Frank; Powers, Stephen J; Kaltz, Oliver; Lannou, Christian

2013-02-01

Crop pathogens are notorious for their rapid adaptation to their host. We still know little about the evolution of their life cycles and whether there might be trade-offs between fitness components, limiting the evolutionary potential of these pathogens. In this study, we explored a trade-off between spore production capacity and latent period in Puccinia triticina, a fungal pathogen causing leaf rust on wheat. Using a simple multivariate (manova) technique, we showed that the covariance between the two traits is under shared control of host and pathogen, with contributions from host genotype (57%), pathogen genotype (18.4%) and genotype × genotype interactions (12.5%). We also found variation in sign and strength of genetic correlations for the pathogen, when measured on different host varieties. Our results suggest that these important pathogen life-history traits do not freely respond to directional selection and that precise evolutionary trajectories are contingent on the genetic identity of the interacting host and pathogen.

Use of qualitative environmental and phenotypic variables in the context of allele distribution models: detecting signatures of selection in the genome of Lake Victoria cichlids.

PubMed

Joost, Stéphane; Kalbermatten, Michael; Bezault, Etienne; Seehausen, Ole

2012-01-01

When searching for loci possibly under selection in the genome, an alternative to population genetics theoretical models is to establish allele distribution models (ADM) for each locus to directly correlate allelic frequencies and environmental variables such as precipitation, temperature, or sun radiation. Such an approach implementing multiple logistic regression models in parallel was implemented within a computing program named MATSAM: . Recently, this application was improved in order to support qualitative environmental predictors as well as to permit the identification of associations between genomic variation and individual phenotypes, allowing the detection of loci involved in the genetic architecture of polymorphic characters. Here, we present the corresponding methodological developments and compare the results produced by software implementing population genetics theoretical models (DFDIST: and BAYESCAN: ) and ADM (MATSAM: ) in an empirical context to detect signatures of genomic divergence associated with speciation in Lake Victoria cichlid fishes.

Directional Asymmetry in the Limbs, Skull and Pelvis of the Silver Fox (V. vulpes)

PubMed Central

Kharlamova, Anastasia V.; Trut, Lyudmila N.; Chase, Kevin; Kukekova, Anna V.; Lark, Karl G.

2011-01-01

Directional asymmetry (DA) is a characteristic of most vertebrates, most strikingly exhibited by the placement of various organs (heart, lungs, liver, etc.) but also noted in small differences in the metrics of skeletal structures such as the pelvis of certain fish or sauropsids. We have analyzed DA in the skeleton of the fox (V. vulpes), using ~1,000 radiographs of foxes from populations used in the genetic analysis of behavior and morphology. Careful measurements from this robust data base demonstrate that: 1) DA occurs in the limb bones, the ileum, and ischium and in the mandible; 2) regardless of the direction of the length asymmetry vector of a particular skeletal unit, the vectorial direction of length is always opposite to that of width; 3) with the exception of the humerus and radius, there is no correlation or inverse correlation between vectorial amplitudes or magnitudes of bone asymmetries. 4) Postnatal measurements on foxes demonstrate that the asymmetry increases after birth and continues to change (increasing or decreasing) during postnatal growth. 5) A behavior test for preferential use of a specific forelimb exhibited fluctuating asymmetry but not DA. None of the skeletal asymmetries were significantly correlated with a preferential use of a specific forelimb. We suggest that for the majority of fox skeletal parameters, growth on the right and left side of the fox are differentially biased resulting in fixed differences between the two sides in either the rate of growth or the length of the period during which growth occurs. Random effects around these fixed differences perturb the magnitude of the effects such that the magnitudes of length and width asymmetries are not inversely correlated at the level of individual animals. PMID:20862692

Directional asymmetry in the limbs, skull and pelvis of the silver fox (V. vulpes).

PubMed

Kharlamova, Anastasia V; Trut, Lyudmila N; Chase, Kevin; Kukekova, Anna V; Lark, Karl G

2010-12-01

Directional asymmetry (DA) is a characteristic of most vertebrates, most strikingly exhibited by the placement of various organs (heart, lungs, liver, etc.) but also noted in small differences in the metrics of skeletal structures such as the pelvis of certain fish or sauropsids. We have analyzed DA in the skeleton of the fox (V. vulpes), using ∼1,000 radiographs of foxes from populations used in the genetic analysis of behavior and morphology. Careful measurements from this robust data base demonstrate that: 1) DA occurs in the limb bones, the ileum, and ischium and in the mandible; 2) regardless of the direction of the length asymmetry vector of a particular skeletal unit, the vectorial direction of length is always opposite to that of width; 3) with the exception of the humerus and radius, there is no correlation or inverse correlation between vectorial amplitudes or magnitudes of bone asymmetries. 4) Postnatal measurements on foxes demonstrate that the asymmetry increases after birth and continues to change (increasing or decreasing) during postnatal growth. 5) A behavior test for preferential use of a specific forelimb exhibited fluctuating asymmetry but not DA. None of the skeletal asymmetries were significantly correlated with a preferential use of a specific forelimb. We suggest that for the majority of fox skeletal parameters, growth on the right and left side of the fox are differentially biased resulting in fixed differences between the two sides in either the rate of growth or the length of the period during which growth occurs. Random effects around these fixed differences perturb the magnitude of the effects such that the magnitudes of length and width asymmetries are not inversely correlated at the level of individual animals. © 2010 Wiley-Liss, Inc.

A predictive assessment of genetic correlations between traits in chickens using markers.

PubMed

Momen, Mehdi; Mehrgardi, Ahmad Ayatollahi; Sheikhy, Ayoub; Esmailizadeh, Ali; Fozi, Masood Asadi; Kranis, Andreas; Valente, Bruno D; Rosa, Guilherme J M; Gianola, Daniel

2017-02-01

Genomic selection has been successfully implemented in plant and animal breeding programs to shorten generation intervals and accelerate genetic progress per unit of time. In practice, genomic selection can be used to improve several correlated traits simultaneously via multiple-trait prediction, which exploits correlations between traits. However, few studies have explored multiple-trait genomic selection. Our aim was to infer genetic correlations between three traits measured in broiler chickens by exploring kinship matrices based on a linear combination of measures of pedigree and marker-based relatedness. A predictive assessment was used to gauge genetic correlations. A multivariate genomic best linear unbiased prediction model was designed to combine information from pedigree and genome-wide markers in order to assess genetic correlations between three complex traits in chickens, i.e. body weight at 35 days of age (BW), ultrasound area of breast meat (BM) and hen-house egg production (HHP). A dataset with 1351 birds that were genotyped with the 600 K Affymetrix platform was used. A kinship kernel (K) was constructed as K = λ G + (1 - λ)A, where A is the numerator relationship matrix, measuring pedigree-based relatedness, and G is a genomic relationship matrix. The weight (λ) assigned to each source of information varied over the grid λ = (0, 0.2, 0.4, 0.6, 0.8, 1). Maximum likelihood estimates of heritability and genetic correlations were obtained at each λ, and the "optimum" λ was determined using cross-validation. Estimates of genetic correlations were affected by the weight placed on the source of information used to build K. For example, the genetic correlation between BW-HHP and BM-HHP changed markedly when λ varied from 0 (only A used for measuring relatedness) to 1 (only genomic information used). As λ increased, predictive correlations (correlation between observed phenotypes and predicted breeding values) increased and mean-squared predictive error decreased. However, the improvement in predictive ability was not monotonic, with an optimum found at some 0 < λ < 1, i.e., when both sources of information were used together. Our findings indicate that multiple-trait prediction may benefit from combining pedigree and marker information. Also, it appeared that expected correlated responses to selection computed from standard theory may differ from realized responses. The predictive assessment provided a metric for performance evaluation as well as a means for expressing uncertainty of outcomes of multiple-trait selection.

Muscle MRI in Duchenne muscular dystrophy: Evidence of a distinctive pattern.

PubMed

Polavarapu, Kiran; Manjunath, Mahadevappa; Preethish-Kumar, Veeramani; Sekar, Deepha; Vengalil, Seena; Thomas, PriyaTreesa; Sathyaprabha, Talakad N; Bharath, Rose Dawn; Nalini, Atchayaram

2016-11-01

The purpose of this study was to describe the pattern of muscle involvement using MRI findings and correlate with functional as well as muscle strength measurements. Fifty genetically confirmed DMD children with a mean age of 7.6 ± 2.8 (4-15 years) underwent muscle MRI and qualitative assessment was done for muscle changes using Mercuri staging for fibro-fatty replacement on T1 sequence and Borsato score for myoedema on STIR sequence. Detailed phenotypic characterisation was done with Manual muscle testing (modified MRC grading) and Muscular Dystrophy Functional Rating Scale (MDFRS). Mercuri scoring showed severe fibro-fatty changes in Gluteus medius, minimus and Adductor magnus followed by moderate to severe changes in Gluteus maximus and Quadriceps muscles. Total sparing of Gracilis, Sartorius and Semimembranosus muscles was observed. Superficial posterior and lateral leg muscles were preferentially involved with sparing of deep posterior and anterior leg muscles. Myoedema showed significant inverse correlation with fatty infiltration in thigh muscles. Similarly, significant inverse correlation was observed between Mercuri scores and MRC grading as well as MDFRS scores. A direct linear correlation was observed between duration of illness and fibro-fatty changes in piriformis, quadriceps and superficial posterior leg muscles. There was no correlation between MRI findings and genotypic characteristics. However, this specific pattern of muscle involvement in MRI could aid in proceeding for genetic testing when clinical suspicion is high, thus reducing the need for muscle biopsy. Fibro fatty infiltration as measured by Mercuri scoring can be a useful marker for assessing the disease severity and progression. Copyright © 2016 Elsevier B.V. All rights reserved.

Population genetic differentiation of height and body mass index across Europe

PubMed Central

Robinson, Matthew R.; Hemani, Gibran; Medina-Gomez, Carolina; Mezzavilla, Massimo; Esko, Tonu; Shakhbazov, Konstantin; Powell, Joseph E.; Vinkhuyzen, Anna; Berndt, Sonja I.; Gustafsson, Stefan; Justice, Anne E.; Kahali, Bratati; Locke, Adam E.; Pers, Tune H.; Vedantam, Sailaja; Wood, Andrew R.; van Rheenen, Wouter; Andreassen, Ole A.; Gasparini, Paolo; Metspalu, Andres; van den Berg, Leonard H.; Veldink, Jan H.; Rivadeneira, Fernando; Werge, Thomas M.; Abecasis, Goncalo R.; Boomsma, Dorret I.; Chasman, Daniel I.; de Geus, Eco J.C.; Frayling, Timothy M.; Hirschhorn, Joel N.; Hottenga, Jouke Jan; Ingelsson, Erik; Loos, Ruth J.F.; Magnusson, Patrik K. E.; Martin, Nicholas G.; Montgomery, Grant W.; North, Kari E.; Pedersen, Nancy L.; Spector, Timothy D.; Speliotes, Elizabeth K.; Goddard, Michael E.; Yang, Jian; Visscher, Peter M.

2016-01-01

Across-nation differences in the mean of complex traits such as obesity and stature are common1–8, but the reasons for these differences are not known. Here, we find evidence that many independent loci of small effect combine to create population genetic differences in height and body mass index (BMI) in a sample of 9,416 individuals across 14 European countries. Using discovery data on over 250,000 individuals and unbiased estimates of effect sizes from 17,500 sib pairs, we estimate that 24% (95% CI: 9%, 41%) and 8% (95% CI: 4%, 16%) of the captured additive genetic variance for height and BMI across Europe are attributed to among-population genetic differences. Population genetic divergence differed significantly from that expected under a null model (P <3.94e−08 for height and P<5.95e−04 for BMI), and we find an among-population genetic correlation for tall and slender nations (r = −0.80 (95% CI: −0.95, −0.60), contrasting no genetic correlation between height and BMI within populations (r = −0.016, 95% CI: −0.041, 0.001), consistent with selection on height genes that also act to reduce BMI. Observations of mean height across nations correlated with the predicted genetic means for height (r = 0.51, P<0.001), so that a proportion of observed differences in height within Europe reflect genetic factors. In contrast, observed mean BMI did not correlate with the genetic estimates (P<0.58), implying that genetic differentiation in BMI is masked by environmental differences across Europe. PMID:26366552

[Genetic characteristics associated with drought tolerance of plant height and thousand-grain mass of recombinant inbred lines of wheat].

PubMed

Yang, De-Long; Zhang, Guo-Hong; Li, Xing-Mao; Xing, Hua; Cheng, Hong-Bo; Ni, Sheng-Li; Chen, Xiao-Ping

2012-06-01

A total of 120 recombinant inbred lines (RIL) derived from Chinese winter wheat cultivars Longjian 19xQ9086 and the two parents were taken as test materials to study the quantitative genetics characteristics of their plant height at different development stages, thousand-grain mass, as well as the correlations between the two traits under rainfed (drought stress) and well-watered conditions, and evaluate the genetic variation of the RIL. Under the two water conditions, the target traits of the RIL showed substantial transgressive segregation and great sensitivity to water condition. The drought stress coefficient of the plant height was higher at jointing stage, being up to 0.851. There was a significant positive correlation between the plant height at different development stages and the thousand-grain mass, and comparing with that at other growth stages, the plant height at jointing stage had a higher correlation coefficient with the thousand-grain mass (R2DS = 0.32, R2WW = 0.28). The plant height at both jointing and flowering stages had significant positive and direct effect but negative and indirect gross effect on the thousand-grain mass, while the plant height at heading and maturing stages was in adverse. The target traits showed a lower heritability ranged from 0.27 to 0.60. The numbers of the gene pairs controlling the thousand-grain mass were 10 under rainfed and 13 under well-watered conditions, while those of the gene pairs controlling the plant height at different development stages were 3-7 under rainfed and 4-14 under well-watered conditions, respectively. According to the clustering of the drought stress coefficient of plant height, the RIL could be classified into five subgroups, showing the abundant variation of the RIL in their phe- notypes and in the sensitivity to water condition. It was considered that the test RIL were appropriate for the study of the quantitative genetics of wheat drought resistance.

Social Communication and Theory of Mind in Boys with Autism and Fragile X Syndrome

PubMed Central

Losh, Molly; Martin, Gary E.; Klusek, Jessica; Hogan-Brown, Abigail L.; Sideris, John

2012-01-01

Impairments in the social use of language, or pragmatics, constitute a core characteristic of autism. Problems with pragmatic language have also been documented in fragile X syndrome (FXS), a monogenic condition that is the most common known genetic cause of autism. Evidence suggests that social cognitive ability, or theory of mind, may also be impaired in both conditions, and in autism, may importantly relate to pragmatic language ability. Given the substantial overlap observed in autism and FXS, this study aimed to better define those social-communicative phenotypes that overlap in these two conditions by comparing pragmatic language ability and theory of mind in children with idiopathic autism and children with FXS, with and without autism, as well as children with Down syndrome and typically developing controls. We further examined correlations between these cognitive-behavioral phenotypes and molecular genetic variation related to the Fragile X Mental Retardation-1 gene (FMR1) in the FXS group. Results indicated that children with idiopathic autism and those with FXS and autism performed comparably on direct-assessment measures of pragmatic language and theory of mind, whereas those with FXS only did not differ from controls. Theory of mind was related to pragmatic language ability in all groups. Pragmatic language and theory of mind also correlated with genetic variation at the FMR1 locus (Cytosine-Guanine-Guanine repeats and percent methylation). These results point toward substantial overlap in the social and language phenotypes in autism and FXS and suggest a molecular genetic basis to these phenotypic profiles. PMID:22934085

Social communication and theory of mind in boys with autism and fragile x syndrome.

PubMed

Losh, Molly; Martin, Gary E; Klusek, Jessica; Hogan-Brown, Abigail L; Sideris, John

2012-01-01

Impairments in the social use of language, or pragmatics, constitute a core characteristic of autism. Problems with pragmatic language have also been documented in fragile X syndrome (FXS), a monogenic condition that is the most common known genetic cause of autism. Evidence suggests that social cognitive ability, or theory of mind, may also be impaired in both conditions, and in autism, may importantly relate to pragmatic language ability. Given the substantial overlap observed in autism and FXS, this study aimed to better define those social-communicative phenotypes that overlap in these two conditions by comparing pragmatic language ability and theory of mind in children with idiopathic autism and children with FXS, with and without autism, as well as children with Down syndrome and typically developing controls. We further examined correlations between these cognitive-behavioral phenotypes and molecular genetic variation related to the Fragile X Mental Retardation-1 gene (FMR1) in the FXS group. Results indicated that children with idiopathic autism and those with FXS and autism performed comparably on direct-assessment measures of pragmatic language and theory of mind, whereas those with FXS only did not differ from controls. Theory of mind was related to pragmatic language ability in all groups. Pragmatic language and theory of mind also correlated with genetic variation at the FMR1 locus (Cytosine-Guanine-Guanine repeats and percent methylation). These results point toward substantial overlap in the social and language phenotypes in autism and FXS and suggest a molecular genetic basis to these phenotypic profiles.

Neural Correlates of the Y Chromosome in Autism: XYY Syndrome as a Genetic Model

DTIC Science & Technology

2016-09-01

AWARD NUMBER: W81XWH-15-1-0355 TITLE: Neural Correlates of the Y Chromosome in Autism: XYY Syndrome as a Genetic Model PRINCIPAL INVESTIGATOR...14 Aug 2016 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER 15T 15T Neural Correlates of the Y Chromosome in Autism: XYY Syndrome as a Genetic Model 5b...this award. 15T 5. SUBJECT TERMS Autism spectrum disorder, ASD; 47,XYY syndrome (XYY); neuroimaging; MRI; MEG; Comorbid behaviors 15T 6. SECURITY

Novel applications of multitask learning and multiple output regression to multiple genetic trait prediction.

PubMed

He, Dan; Kuhn, David; Parida, Laxmi

2016-06-15

Given a set of biallelic molecular markers, such as SNPs, with genotype values encoded numerically on a collection of plant, animal or human samples, the goal of genetic trait prediction is to predict the quantitative trait values by simultaneously modeling all marker effects. Genetic trait prediction is usually represented as linear regression models. In many cases, for the same set of samples and markers, multiple traits are observed. Some of these traits might be correlated with each other. Therefore, modeling all the multiple traits together may improve the prediction accuracy. In this work, we view the multitrait prediction problem from a machine learning angle: as either a multitask learning problem or a multiple output regression problem, depending on whether different traits share the same genotype matrix or not. We then adapted multitask learning algorithms and multiple output regression algorithms to solve the multitrait prediction problem. We proposed a few strategies to improve the least square error of the prediction from these algorithms. Our experiments show that modeling multiple traits together could improve the prediction accuracy for correlated traits. The programs we used are either public or directly from the referred authors, such as MALSAR (http://www.public.asu.edu/~jye02/Software/MALSAR/) package. The Avocado data set has not been published yet and is available upon request. dhe@us.ibm.com. © The Author 2016. Published by Oxford University Press.

Evidence of Phenotypic and Genetic Relationships between Sociality, Emotional Reactivity and Production Traits in Japanese Quail

PubMed Central

Recoquillay, Julien; Leterrier, Christine; Calandreau, Ludovic; Bertin, Aline; Pitel, Frédérique; Gourichon, David; Vignal, Alain; Beaumont, Catherine; Le Bihan-Duval, Elisabeth; Arnould, Cécile

2013-01-01

The social behavior of animals, which is partially controlled by genetics, is one of the factors involved in their adaptation to large breeding groups. To understand better the relationships between different social behaviors, fear behaviors and production traits, we analyzed the phenotypic and genetic correlations of these traits in Japanese quail by a second generation crossing of two lines divergently selected for their social reinstatement behavior. Analyses of results for 900 individuals showed that the phenotypic correlations between behavioral traits were low with the exception of significant correlations between sexual behavior and aggressive pecks both at phenotypic (0.51) and genetic (0.90) levels. Significant positive genetic correlations were observed between emotional reactivity toward a novel object and sexual (0.89) or aggressive (0.63) behaviors. The other genetic correlations were observed mainly between behavioral and production traits. Thus, the level of emotional reactivity, estimated by the duration of tonic immobility, was positively correlated with weight at 17 and 65 days of age (0.76 and 0.79, respectively) and with delayed egg laying onset (0.74). In contrast, a higher level of social reinstatement behavior was associated with an earlier egg laying onset (-0.71). In addition, a strong sexual motivation was correlated with an earlier laying onset (-0.68) and a higher number of eggs laid (0.82). A low level of emotional reactivity toward a novel object and also a higher aggressive behavior were genetically correlated with a higher number of eggs laid (0.61 and 0.58, respectively). These results bring new insights into the complex determinism of social and emotional reactivity behaviors in birds and their relationships with production traits. Furthermore, they highlight the need to combine animal welfare and production traits in selection programs by taking into account traits of sociability and emotional reactivity. PMID:24324761

Genetic correlations among body condition score, yield, and fertility in first-parity cows estimated by random regression models.

PubMed

Veerkamp, R F; Koenen, E P; De Jong, G

2001-10-01

Twenty type classifiers scored body condition (BCS) of 91,738 first-parity cows from 601 sires and 5518 maternal grandsires. Fertility data during first lactation were extracted for 177,220 cows, of which 67,278 also had a BCS observation, and first-lactation 305-d milk, fat, and protein yields were added for 180,631 cows. Heritabilities and genetic correlations were estimated using a sire-maternal grandsire model. Heritability of BCS was 0.38. Heritabilities for fertility traits were low (0.01 to 0.07), but genetic standard deviations were substantial, 9 d for days to first service and calving interval, 0.25 for number of services, and 5% for first-service conception. Phenotypic correlations between fertility and yield or BCS were small (-0.15 to 0.20). Genetic correlations between yield and all fertility traits were unfavorable (0.37 to 0.74). Genetic correlations with BCS were between -0.4 and -0.6 for calving interval and days to first service. Random regression analysis (RR) showed that correlations changed with days in milk for BCS. Little agreement was found between variances and correlations from RR, and analysis including a single month (mo 1 to 10) of data for BCS, especially during early and late lactation. However, this was due to excluding data from the conventional analysis, rather than due to the polynomials used. RR and a conventional five-traits model where BCS in mo 1, 4, 7, and 10 was treated as a separate traits (plus yield or fertility) gave similar results. Thus a parsimonious random regression model gave more realistic estimates for the (co)variances than a series of bivariate analysis on subsets of the data for BCS. A higher genetic merit for yield has unfavorable effects on fertility, but the genetic correlation suggests that BCS (at some stages of lactation) might help to alleviate the unfavorable effect of selection for higher yield on fertility.

Divergent selection on, but no genetic conflict over, female and male timing and rate of reproduction in a human population

PubMed Central

Bolund, Elisabeth; Bouwhuis, Sandra; Pettay, Jenni E.; Lummaa, Virpi

2013-01-01

The sexes often have different phenotypic optima for important life-history traits, and because of a largely shared genome this can lead to a conflict over trait expression. In mammals, the obligate costs of reproduction are higher for females, making reproductive timing and rate especially liable to conflict between the sexes. While studies from wild vertebrates support such sexual conflict, it remains unexplored in humans. We used a pedigreed human population from preindustrial Finland to estimate sexual conflict over age at first and last reproduction, reproductive lifespan and reproductive rate. We found that the phenotypic selection gradients differed between the sexes. We next established significant heritabilities in both sexes for all traits. All traits, except reproductive rate, showed strongly positive intersexual genetic correlations and were strongly genetically correlated with fitness in both sexes. Moreover, the genetic correlations with fitness were almost identical in men and women. For reproductive rate, the intersexual correlation and the correlation with fitness were weaker but again similar between the sexes. Thus, in this population, an apparent sexual conflict at the phenotypic level did not reflect an underlying genetic conflict over the studied reproductive traits. These findings emphasize the need for incorporating genetic perspectives into studies of human life-history evolution. PMID:24107531

Divergent selection on, but no genetic conflict over, female and male timing and rate of reproduction in a human population.

PubMed

Bolund, Elisabeth; Bouwhuis, Sandra; Pettay, Jenni E; Lummaa, Virpi

2013-12-07

The sexes often have different phenotypic optima for important life-history traits, and because of a largely shared genome this can lead to a conflict over trait expression. In mammals, the obligate costs of reproduction are higher for females, making reproductive timing and rate especially liable to conflict between the sexes. While studies from wild vertebrates support such sexual conflict, it remains unexplored in humans. We used a pedigreed human population from preindustrial Finland to estimate sexual conflict over age at first and last reproduction, reproductive lifespan and reproductive rate. We found that the phenotypic selection gradients differed between the sexes. We next established significant heritabilities in both sexes for all traits. All traits, except reproductive rate, showed strongly positive intersexual genetic correlations and were strongly genetically correlated with fitness in both sexes. Moreover, the genetic correlations with fitness were almost identical in men and women. For reproductive rate, the intersexual correlation and the correlation with fitness were weaker but again similar between the sexes. Thus, in this population, an apparent sexual conflict at the phenotypic level did not reflect an underlying genetic conflict over the studied reproductive traits. These findings emphasize the need for incorporating genetic perspectives into studies of human life-history evolution.

Genetic parameters of eventing horse competition in France

PubMed Central

Ricard, Anne; Chanu, Isabelle

2001-01-01

Genetic parameters of eventing horse competitions were estimated. About 13 000 horses, 30 000 annual results during 17 years and 110 000 starts in eventing competitions during 8 years were recorded. The measures of performance were logarithmic transformations of annual earnings, annual earnings per start, and annual earnings per place, and underlying variables responsible for ranks in each competition. Heritabilities were low (0.11/0.17 for annual results, 0.07 for ranks). Genetic correlations between criteria were high (greater than 0.90) except between ranks and earnings per place (0.58) or per start (0.67). Genetic correlations between ages (from 5 to 10 years old) were also high (more than 0.85) and allow selection on early performances. The genetic correlation between the results in different levels of competition (high/international and low/amateur) was near 1. Genetic correlations of eventing with other disciplines, which included partial aptitude needed for eventing, were very low for steeplechase races (0.18) and moderate with sport: jumping (0.45), dressage (0.58). The results suggest that selection on jumping performance will lead to some positive correlated response for eventing performance, but much more response could be obtained if a specific breeding objective and selection criteria were developed for eventing. PMID:11333833

Marital assortment for genetic similarity.

PubMed

Eckman, Ronael E; Williams, Robert; Nagoshi, Craig

2002-10-01

The present study involved analyses of a Caucasian American sample (n=949) and a Japanese American sample (n=400) for factors supporting Genetic Similarity Theory (GST). The analyses found no evidence for the presence of genetic similarity between spouses in either sample for the blood group analyses of nine loci. All results indicated random mating for blood group genes. The results did not provide consistent substantial support to show that spousal similarity is correlated with the degree of genetic component of a trait for a set of seventeen individual differences variables, with only the Caucasian sample yielding significant correlations for this analysis. A third analysis examining the correlation between presence of spousal genetic similarity and spousal similarity on observable traits was not performed because spousal genetic similarity was not observed in either sample. The overall implication of the study is that GST is not supported as an explanation for spousal similarity in humans.

Defining a Contemporary Ischemic Heart Disease Genetic Risk Profile Using Historical Data.

PubMed

Mosley, Jonathan D; van Driest, Sara L; Wells, Quinn S; Shaffer, Christian M; Edwards, Todd L; Bastarache, Lisa; McCarty, Catherine A; Thompson, Will; Chute, Christopher G; Jarvik, Gail P; Crosslin, David R; Larson, Eric B; Kullo, Iftikhar J; Pacheco, Jennifer A; Peissig, Peggy L; Brilliant, Murray H; Linneman, James G; Denny, Josh C; Roden, Dan M

2016-12-01

Continued reductions in morbidity and mortality attributable to ischemic heart disease (IHD) require an understanding of the changing epidemiology of this disease. We hypothesized that we could use genetic correlations, which quantify the shared genetic architectures of phenotype pairs and extant risk factors from a historical prospective study to define the risk profile of a contemporary IHD phenotype. We used 37 phenotypes measured in the ARIC study (Atherosclerosis Risk in Communities; n=7716, European ancestry subjects) and clinical diagnoses from an electronic health record (EHR) data set (n=19 093). All subjects had genome-wide single-nucleotide polymorphism genotyping. We measured pairwise genetic correlations (rG) between the ARIC and EHR phenotypes using linear mixed models. The genetic correlation estimates between the ARIC risk factors and the EHR IHD were modestly linearly correlated with hazards ratio estimates for incident IHD in ARIC (Pearson correlation [r]=0.62), indicating that the 2 IHD phenotypes had differing risk profiles. For comparison, this correlation was 0.80 when comparing EHR and ARIC type 2 diabetes mellitus phenotypes. The EHR IHD phenotype was most strongly correlated with ARIC metabolic phenotypes, including total:high-density lipoprotein cholesterol ratio (rG=-0.44, P=0.005), high-density lipoprotein (rG=-0.48, P=0.005), systolic blood pressure (rG=0.44, P=0.02), and triglycerides (rG=0.38, P=0.02). EHR phenotypes related to type 2 diabetes mellitus, atherosclerotic, and hypertensive diseases were also genetically correlated with these ARIC risk factors. The EHR IHD risk profile differed from ARIC and indicates that treatment and prevention efforts in this population should target hypertensive and metabolic disease. © 2016 American Heart Association, Inc.

Genetics and intelligence differences: five special findings.

PubMed

Plomin, R; Deary, I J

2015-02-01

Intelligence is a core construct in differential psychology and behavioural genetics, and should be so in cognitive neuroscience. It is one of the best predictors of important life outcomes such as education, occupation, mental and physical health and illness, and mortality. Intelligence is one of the most heritable behavioural traits. Here, we highlight five genetic findings that are special to intelligence differences and that have important implications for its genetic architecture and for gene-hunting expeditions. (i) The heritability of intelligence increases from about 20% in infancy to perhaps 80% in later adulthood. (ii) Intelligence captures genetic effects on diverse cognitive and learning abilities, which correlate phenotypically about 0.30 on average but correlate genetically about 0.60 or higher. (iii) Assortative mating is greater for intelligence (spouse correlations ~0.40) than for other behavioural traits such as personality and psychopathology (~0.10) or physical traits such as height and weight (~0.20). Assortative mating pumps additive genetic variance into the population every generation, contributing to the high narrow heritability (additive genetic variance) of intelligence. (iv) Unlike psychiatric disorders, intelligence is normally distributed with a positive end of exceptional performance that is a model for 'positive genetics'. (v) Intelligence is associated with education and social class and broadens the causal perspectives on how these three inter-correlated variables contribute to social mobility, and health, illness and mortality differences. These five findings arose primarily from twin studies. They are being confirmed by the first new quantitative genetic technique in a century-Genome-wide Complex Trait Analysis (GCTA)-which estimates genetic influence using genome-wide genotypes in large samples of unrelated individuals. Comparing GCTA results to the results of twin studies reveals important insights into the genetic architecture of intelligence that are relevant to attempts to narrow the 'missing heritability' gap.

Genetics and intelligence differences: five special findings

PubMed Central

Plomin, R; Deary, I J

2015-01-01

Intelligence is a core construct in differential psychology and behavioural genetics, and should be so in cognitive neuroscience. It is one of the best predictors of important life outcomes such as education, occupation, mental and physical health and illness, and mortality. Intelligence is one of the most heritable behavioural traits. Here, we highlight five genetic findings that are special to intelligence differences and that have important implications for its genetic architecture and for gene-hunting expeditions. (i) The heritability of intelligence increases from about 20% in infancy to perhaps 80% in later adulthood. (ii) Intelligence captures genetic effects on diverse cognitive and learning abilities, which correlate phenotypically about 0.30 on average but correlate genetically about 0.60 or higher. (iii) Assortative mating is greater for intelligence (spouse correlations ~0.40) than for other behavioural traits such as personality and psychopathology (~0.10) or physical traits such as height and weight (~0.20). Assortative mating pumps additive genetic variance into the population every generation, contributing to the high narrow heritability (additive genetic variance) of intelligence. (iv) Unlike psychiatric disorders, intelligence is normally distributed with a positive end of exceptional performance that is a model for ‘positive genetics'. (v) Intelligence is associated with education and social class and broadens the causal perspectives on how these three inter-correlated variables contribute to social mobility, and health, illness and mortality differences. These five findings arose primarily from twin studies. They are being confirmed by the first new quantitative genetic technique in a century—Genome-wide Complex Trait Analysis (GCTA)—which estimates genetic influence using genome-wide genotypes in large samples of unrelated individuals. Comparing GCTA results to the results of twin studies reveals important insights into the genetic architecture of intelligence that are relevant to attempts to narrow the ‘missing heritability' gap. PMID:25224258

Genome-wide analysis of genetic correlation in dementia with Lewy bodies, Parkinson's and Alzheimer's diseases.

PubMed

Guerreiro, Rita; Escott-Price, Valentina; Darwent, Lee; Parkkinen, Laura; Ansorge, Olaf; Hernandez, Dena G; Nalls, Michael A; Clark, Lorraine; Honig, Lawrence; Marder, Karen; van der Flier, Wiesje; Holstege, Henne; Louwersheimer, Eva; Lemstra, Afina; Scheltens, Philip; Rogaeva, Ekaterina; St George-Hyslop, Peter; Londos, Elisabet; Zetterberg, Henrik; Ortega-Cubero, Sara; Pastor, Pau; Ferman, Tanis J; Graff-Radford, Neill R; Ross, Owen A; Barber, Imelda; Braae, Anne; Brown, Kristelle; Morgan, Kevin; Maetzler, Walter; Berg, Daniela; Troakes, Claire; Al-Sarraj, Safa; Lashley, Tammaryn; Compta, Yaroslau; Revesz, Tamas; Lees, Andrew; Cairns, Nigel J; Halliday, Glenda M; Mann, David; Pickering-Brown, Stuart; Powell, John; Lunnon, Katie; Lupton, Michelle K; Dickson, Dennis; Hardy, John; Singleton, Andrew; Bras, Jose

2016-02-01

The similarities between dementia with Lewy bodies (DLB) and both Parkinson's disease (PD) and Alzheimer's disease (AD) are many and range from clinical presentation, to neuropathological characteristics, to more recently identified, genetic determinants of risk. Because of these overlapping features, diagnosing DLB is challenging and has clinical implications since some therapeutic agents that are applicable in other diseases have adverse effects in DLB. Having shown that DLB shares some genetic risk with PD and AD, we have now quantified the amount of sharing through the application of genetic correlation estimates, and show that, from a purely genetic perspective, and excluding the strong association at the APOE locus, DLB is equally correlated to AD and PD. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Genetic Alterations and Their Clinical Implications in High-Recurrence Risk Papillary Thyroid Cancer.

PubMed

Lee, Min-Young; Ku, Bo Mi; Kim, Hae Su; Lee, Ji Yun; Lim, Sung Hee; Sun, Jong-Mu; Lee, Se-Hoon; Park, Keunchil; Oh, Young Lyun; Hong, Mineui; Jeong, Han-Sin; Son, Young-Ik; Baek, Chung-Hwan; Ahn, Myung-Ju

2017-10-01

Papillary thyroid carcinomas (PTCs) frequently involve genetic alterations. The objective of this study was to investigate genetic alterations and further explore the relationships between these genetic alterations and clinicopathological characteristics in a high-recurrence risk (node positive, N1) PTC group. Tumor tissue blocks were obtained from 240 surgically resected patients with histologically confirmed stage III/IV (pT3/4 or N1) PTCs. We screened gene fusions using NanoString's nCounter technology and mutational analysis was performed by direct DNA sequencing. Data describing the clinicopathological characteristics and clinical courses were retrospectively collected. Of the 240 PTC patients, 207 (86.3%) had at least one genetic alteration, including BRAF mutation in 190 patients (79.2%), PIK3CA mutation in 25 patients (10.4%), NTRK1/3 fusion in six patients (2.5%), and RET fusion in 24 patients (10.0%). Concomitant presence of more than two genetic alterations was seen in 36 patients (15%). PTCs harboring BRAF mutation were associated with RET wild-type expression (p=0.001). RET fusion genes have been found to occur with significantly higher frequency in N1b stage patients (p=0.003) or groups of patients aged 45 years or older (p=0.031); however, no significant correlation was found between other genetic alterations. There was no trend toward favorable recurrence-free survival or overall survival among patients lacking genetic alterations. In the selected high-recurrence risk PTC group, most patients had more than one genetic alteration. However, these known alterations could not entirely account for clinicopathological features of high-recurrence risk PTC.

Age at First Use and Later Substance Use Disorder: Shared Genetic and Environmental Pathways for Nicotine, Alcohol, and Cannabis

PubMed Central

Richmond-Rakerd, Leah S.; Slutske, Wendy S.; Lynskey, Michael T.; Agrawal, Arpana; Madden, Pamela A.F.; Bucholz, Kathleen K.; Heath, Andrew C.; Statham, Dixie J.; Martin, Nicholas G.

2016-01-01

Behavioral genetic studies have provided insights into why early substance use initiation is associated with increased risk for disorder. Few genetically-informative studies, however, have operationalized initiation as the timing of first use and simultaneously modeled the timing of initiation and problematic use of multiple substances. Such research can help capture the risk associated with early initiation and determine the extent to which genetic and environmental risk generalizes across substances. This study utilized a behavior genetic approach to examine the relation between the age of substance use initiation and symptoms of substance use disorder. Participants were 7,285 monozygotic and dizygotic twins (40% male, mean age at interview=30.6) from the Australian Twin Registry who reported on their ages of tobacco, alcohol, and cannabis initiation and symptoms of DSM-IV nicotine dependence, alcohol use disorder, and cannabis use disorder. Biometric modeling was conducted to (a) determine the structure of genetic and environmental influences on initiation and disorder and (b) examine their genetic and environmental overlap. The latent structure of initiation differed across men and women. The familial covariance between initiation and disorder was genetic among men and genetic and environmental among women, suggesting that the relation between first substance use and disorder is partly explained by a shared liability. After accounting for familial overlap, significant unique environmental correlations were observed, indicating that the age of initiation of multiple drugs may directly increase risk for substance-related problems. Results support the utility of conceptualizing initiation in terms of age and of adopting a multivariate approach. PMID:27537477

Molecular Docking and Prediction of Pharmacokinetic Properties of Dual Mechanism Drugs that Block MAO-B and Adenosine A2A Receptors for the Treatment of Parkinson's Disease

PubMed Central

Azam, Faizul; Madi, Arwa M.; Ali, Hamed I.

2012-01-01

Monoamine oxidase B (MAO-B) inhibitory potential of adenosine A2A receptor (AA2AR) antagonists has raised the possibility of designing dual-target–directed drugs that may provide enhanced symptomatic relief and that may also slow the progression of Parkinson's disease (PD) by protecting against further neurodegeneration. To explain the dual inhibition of MAO-B and AA2AR at the molecular level, molecular docking technique was employed. Lamarckian genetic algorithm methodology was used for flexible ligand docking studies. A good correlation (R2= 0.524 and 0.627 for MAO-B and AA2AR, respectively) was established between docking predicted and experimental Ki values, which confirms that the molecular docking approach is reliable to study the mechanism of dual interaction of caffeinyl analogs with MAO-B and AA2AR. Parameters for Lipinski's “Rule-of-Five” were also calculated to estimate the pharmacokinetic properties of dual-target–directed drugs where both MAO-B inhibition and AA2AR antagonism exhibited a positive correlation with calculated LogP having a correlation coefficient R2 of 0.535 and 0.607, respectively. These results provide some beneficial clues in structural modification for designing new inhibitors as dual-target–directed drugs with desired pharmacokinetic properties for the treatment of PD. PMID:23112538

The association between conduct problems and maltreatment: testing genetic and environmental mediation.

PubMed

Schulz-Heik, R Jay; Rhee, Soo Hyun; Silvern, Louise E; Haberstick, Brett C; Hopfer, Christian; Lessem, Jeffrey M; Hewitt, John K

2010-05-01

It is often assumed that childhood maltreatment causes conduct problems via an environmentally mediated process. However, the association may be due alternatively to either a nonpassive gene-environment correlation, in which parents react to children's genetically-influenced conduct problems by maltreating them, or a passive gene-environment correlation, in which parents' tendency to engage in maltreatment and children's conduct problems are both influenced by a hereditary vulnerability to antisocial behavior (i.e. genetic mediation). The present study estimated the contribution of these processes to the association between maltreatment and conduct problems. Bivariate behavior genetic analyses were conducted on approximately 1,650 twin and sibling pairs drawn from a large longitudinal study of adolescent health (Add Health). The correlation between maltreatment and conduct problems was small; much of the association between maltreatment and conduct problems was due to a nonpassive gene-environment correlation. Results were more consistent with the hypothesis that parents respond to children's genetically-influenced conduct problems by maltreating them than the hypothesis that maltreatment causes conduct problems.

Perceived knowledge and clinical comfort with genetics among Taiwanese nurses enrolled in a RN-to-BSN program.

PubMed

Hsiao, Chiu-Yueh; Lee, Shu-Hsin; Chen, Suh-Jen; Lin, Shu-Chin

2013-08-01

Advances in genetics have had a profound impact on health care. Yet, many nurses, as well as other health care providers, have limited genetic knowledge and feel uncomfortable integrating genetics into their practice. Very little is known about perceived genetic knowledge and clinical comfort among Taiwanese nurses enrolled in a Registered Nurse to Bachelor of Science in Nursing program. To examine perceived knowledge and clinical comfort with genetics among Taiwanese nurses enrolled in a Registered Nurse to Bachelor of Science in Nursing program and to assess how genetics has been integrated into their past and current nursing programs. The study also sought to examine correlations among perceived knowledge, integration of genetics into the nursing curriculum, and clinical comfort with genetics. A descriptive, cross-sectional study. Taiwanese nurses enrolled in a Registered Nurse to Bachelor of Science in Nursing program were recruited. A total of 190 of 220 nurses returned the completed survey (86.36% response rate). Descriptive statistics and the Pearson product-moment correlation were used for data analysis. Most nurses indicated limited perceived knowledge and clinical comfort with genetics. Curricular hours focused on genetics in a current nursing program were greater than those in past nursing programs. The use of genetic materials, attendance at genetic workshops and conferences, and clinically relevant genetics in nursing practice significantly related with perceived knowledge and clinical comfort with genetics. However, there were no correlations between prior genetic-based health care, perceived knowledge, and clinical comfort with genetics. This study demonstrated the need for emphasizing genetic education and practice to ensure health-related professionals become knowledgeable about genetic information. Given the rapidly developing genetic revolution, nurses and other health care providers need to utilize genetic discoveries to optimize health outcomes. Copyright © 2012 Elsevier Ltd. All rights reserved.

Genetic associations between scrotal circumference and female reproductive traits in Nelore cattle.

PubMed

Terakado, A P N; Boligon, A A; Baldi, F; Silva, J A I I V; Albuquerque, L G

2015-06-01

The objective of this study was to estimate genetic associations between scrotal circumference obtained at 12 (SC12; mean of 21.46 ± 2.74 cm), 15 (SC15; mean of 25.31 ± 3.19 cm), and 18 mo of age (SC18; mean of 26.77 ± 2.95 cm) and reproductive traits measured directly in heifers (age at first calving [AFC]: mean of 1,062.06 ± 114.79 d; heifer pregnancy at 16 mo of age [HP]: mean of 15.4 ± 0.36%; and subsequent rebreeding of primiparous heifers [HR]: mean of 27.1 ± 0.44%) using Bayesian inference to evaluate the possible inclusion of these traits as selection criteria in beef cattle breeding programs. Genetic gains comparisons were also estimated. A total of 53,683 data of Nelore animals born between 1990 and 2006, obtained from the livestock archive of Agropecuária Jacarezinho Ltda. (Valparaíso, São Paulo, Brazil), were analyzed. Two-trait analysis provided heritability estimates of 0.35 ± 0.08, 0.40 ± 0.04, 0.37 ± 0.03, 0.21 ± 0.01, 0.55 ± 0.03, and 0.17 ± 0.03 for SC12, SC15, SC18, AFC, HP, and HR, respectively. The genetic correlations between scrotal circumference and AFC, HP, and HR were -0.42 ± 0.12, 0.43 ± 0.13, and -0.13 ± 0.17, respectively, for SC12; -0.25 ± 0.07, 0.26 ± 0.07, and -0.11 ± 0.10, respectively, for SC15; and -0.22 ± 0.06, 0.39 ± 0.06, and 0.11 ± 0.09, respectively, for SC18. The direct selection response for HP was 0.12%, but when HP is indirectly selected based on the scrotal circumferences, the gains on these correlated responses were higher (0.16, 0.16, and 0.22%) for selection based on SC12, SC15, and SC18, respectively. These findings suggest that the selection of animals for larger scrotal circumference, particularly at 12 mo of age, should result in higher rates of HP and younger AFC of Nelore females.

Correlation and path analysis of biomass sorghum production.

PubMed

Vendruscolo, T P S; Barelli, M A A; Castrillon, M A S; da Silva, R S; de Oliveira, F T; Corrêa, C L; Zago, B W; Tardin, F D

2016-12-23

Sorghum biomass is an interesting raw material for bioenergy production due to its versatility, potential of being a renewable energy source, and low-cost of production. The objective of this study was to evaluate the genetic variability of biomass sorghum genotypes and to estimate genotypic, phenotypic, and environmental correlations, and direct and indirect effects of seven agronomic traits through path analysis. Thirty-four biomass sorghum genotypes and two forage sorghum genotypes were cultivated in a randomized block design with three replicates. The following morpho-agronomic traits were evaluated: flowering date, stem diameter, number of stems, plant height, number of leaves, green mass production, and dry matter production. There were significant differences at the 1% level for all traits. The highest genotypic correlation was found between the traits green mass production and dry matter production. The path analysis demonstrated that green mass production and number of leaves can assist in the selection of dry matter production.

Application of bacterial artificial chromosome array-based comparative genomic hybridization and spectral karyotyping to the analysis of glioblastoma multiforme.

PubMed

Cowell, John K; Matsui, Sei-Ichi; Wang, Yong D; LaDuca, Jeffrey; Conroy, Jeffrey; McQuaid, Devin; Nowak, Norma J

2004-05-01

Identification of genetic losses and gains is valuable in analysis of brain tumors. Locus-by-locus analyses have revealed correlations between prognosis and response to chemotherapy and loss or gain of specific genes and loci. These approaches are labor intensive and do not provide a global view of the genetic changes within the tumor cells. Bacterial artificial chromosome (BAC) arrays, which cover the genome with an average resolution of less than 1 MbP, allow defining the sum total of these genetic changes in a single comparative genomic hybridization (CGH) experiment. These changes are directly overlaid on the human genome sequence, thus providing the extent of the amplification or deletion, reflected by a megabase position, and gene content of the abnormal region. Although this array-based CGH approach (CGHa) seems to detect the extent of the genetic changes in tumors reliably, it has not been robustly tested. We compared genetic changes in four newly derived, early-passage glioma cell lines, using spectral karyotyping (SKY) and CGHa. Chromosome changes seen in cell lines under SKY analysis were also detected with CGHa. In addition, CGHa detected cryptic genetic gains and losses and resolved the nature of subtle marker chromosomes that could not be resolved with SKY, thus providing distinct advantages over previous technologies. There was remarkable general concordance between the CGHa results comparing the cell lines to the original tumor, except that the magnitude of the changes seen in the tumor sample was generally suppressed compared with the cell lines, a consequence of normal cells contaminating the tumor sample. CGHa revealed changes in cell lines that were not present in the original tumors and vice versa, even when analyzed at the earliest passage possible, which highlights the adaptation of the cells to in vitro culture. CGHa proved to be highly accurate and efficient for identifying genetic changes in tumor cells. This approach can accurately identify subtle, novel genetic abnormalities in tumors directly linked to the human genome sequence. CGHa far surpasses the resolution and information provided by conventional metaphase CGH, without relying on in vitro culture of tumors for metaphase spreads.

Clinal patterns in genetic variation for northern leopard frog (Rana pipiens): Conservation status and population histories

USGS Publications Warehouse

Stockwell, Craig A.; Fisher, Justin D.L.; McLean, Kyle I.

2016-01-01

The security of the northern leopard frog (Rana pipiens) varies spatially with populations east and west of North Dakota considered as secure and at risk, respectively. We used genetic markers to characterize the conservation status of northern leopard frog populations across North Dakota. We used multiple regression analyses and model selection to evaluate correlations of expected heterozygosity (HE) with the direct and additive effects of: i) geographic location,ii) wetland density and iii) average annual precipitation. There was lower genetic diversity in the western portion of the state due to lower levels of diversity for populations southwest of the Missouri River. This may reflect a refugial/colonization signature for the only non-glaciated area of North Dakota. Genetic diversity was also positively associated with wetland densities which is consistent with the reliance of this species on a mosaic of wetlands. Our findings suggest that populations in the southwestern part of North Dakota are of higher conservation concern, a finding consistent with the higher risk noted for northern leopard frog populations in most states west of North Dakota. Our findings also pose the hypothesis that climate change induced changes in wetland densities will reduce genetic diversity of northern leopard frog populations.

Gene-dietary fat interaction, bone mineral density and bone speed of sound in Children: a twin study in China

PubMed Central

Huang, Tao; Liu, Huijuan; Zhao, Wei; Li, Ji; Wang, Youfa

2015-01-01

Scope Dietary fat correlates with bone mineral density (BMD). We tested the association between fat intake and BMD, and tested if fat intake modified the degree of genetic influence on BMD and bone speed of sound (SOS). Methods and results We included 622 twins aged 7–15 y from South China. Data on anthropometry, dietary intake, BMD, and SOS were collected. Quantitative genetic analyses of structural equation models were fit using the Mx statistical package. The within-pair intra-class correlations (ICC) for BMD in DZ twins were nearly half of that for MZ twins (ICC=0.39 vs 0.70). The heritability of BMD and SOS were 71% and 79%. Phenotypic correlation between fat intake and SOS was significant (r=−0.19, p=0.04). SOS was negatively correlated with fat intake in boys (r=−0.11, p=0.05), but not in girls. Full Cholesky decomposition models showed SOS has a strong genetic correlation with fat intake (rA =−0.88, 95% CI=−0.94, 0.01); the environmental correlation between fat intake and SOS was weak (rE =−0.04, 95% CI=−0.20, 0.13). Fat intake modified the additive genetic effects on BMD. Conclusion Genetic factors explained 71% and 79% of individual variance in BMD and SOS, respectively. Low fat intake counteracts genetic predisposition to low BMD. PMID:25546604

Directional selection effects on patterns of phenotypic (co)variation in wild populations

PubMed Central

Patton, J. L.; Hubbe, A.; Marroig, G.

2016-01-01

Phenotypic (co)variation is a prerequisite for evolutionary change, and understanding how (co)variation evolves is of crucial importance to the biological sciences. Theoretical models predict that under directional selection, phenotypic (co)variation should evolve in step with the underlying adaptive landscape, increasing the degree of correlation among co-selected traits as well as the amount of genetic variance in the direction of selection. Whether either of these outcomes occurs in natural populations is an open question and thus an important gap in evolutionary theory. Here, we documented changes in the phenotypic (co)variation structure in two separate natural populations in each of two chipmunk species (Tamias alpinus and T. speciosus) undergoing directional selection. In populations where selection was strongest (those of T. alpinus), we observed changes, at least for one population, in phenotypic (co)variation that matched theoretical expectations, namely an increase of both phenotypic integration and (co)variance in the direction of selection and a re-alignment of the major axis of variation with the selection gradient. PMID:27881744

Determinants of echolocation call frequency variation in the Formosan lesser horseshoe bat (Rhinolophus monoceros)

PubMed Central

Chen, Shiang-Fan; Jones, Gareth; Rossiter, Stephen J.

2009-01-01

The origin and maintenance of intraspecific variation in vocal signals is important for population divergence and speciation. Where vocalizations are transmitted by vertical cultural inheritance, similarity will reflect co-ancestry, and thus vocal divergence should reflect genetic structure. Horseshoe bats are characterized by echolocation calls dominated by a constant frequency component that is partly determined by maternal imprinting. Although previous studies showed that constant frequency calls are also influenced by some non-genetic factors, it is not known how frequency relates to genetic structure. To test this, we related constant frequency variation to genetic and non-genetic variables in the Formosan lesser horseshoe bat (Rhinolophus monoceros). Recordings of bats from across Taiwan revealed that females called at higher frequencies than males; however, we found no effect of environmental or morphological factors on call frequency. By comparison, variation showed clear population structure, with frequencies lower in the centre and east, and higher in the north and south. Within these regions, frequency divergence was directional and correlated with geographical distance, suggesting that call frequencies are subject to cultural drift. However, microsatellite clustering analysis showed that broad differences in constant frequency among populations corresponded to discontinuities in allele frequencies resulting from vicariant events. Our results provide evidence that the processes shaping genetic subdivision have concomitant consequences for divergence in echolocation call frequency. PMID:19692399

How Well Do Customers of Direct-to-Consumer Personal Genomic Testing Services Comprehend Genetic Test Results? Findings from the Impact of Personal Genomics Study.

PubMed

Ostergren, Jenny E; Gornick, Michele C; Carere, Deanna Alexis; Kalia, Sarah S; Uhlmann, Wendy R; Ruffin, Mack T; Mountain, Joanna L; Green, Robert C; Roberts, J Scott

2015-01-01

To assess customer comprehension of health-related personal genomic testing (PGT) results. We presented sample reports of genetic results and examined responses to comprehension questions in 1,030 PGT customers (mean age: 46.7 years; 59.9% female; 79.0% college graduates; 14.9% non-White; 4.7% of Hispanic/Latino ethnicity). Sample reports presented a genetic risk for Alzheimer's disease and type 2 diabetes, carrier screening summary results for >30 conditions, results for phenylketonuria and cystic fibrosis, and drug response results for a statin drug. Logistic regression was used to identify correlates of participant comprehension. Participants exhibited high overall comprehension (mean score: 79.1% correct). The highest comprehension (range: 81.1-97.4% correct) was observed in the statin drug response and carrier screening summary results, and lower comprehension (range: 63.6-74.8% correct) on specific carrier screening results. Higher levels of numeracy, genetic knowledge, and education were significantly associated with greater comprehension. Older age (≥ 60 years) was associated with lower comprehension scores. Most customers accurately interpreted the health implications of PGT results; however, comprehension varied by demographic characteristics, numeracy and genetic knowledge, and types and format of the genetic information presented. Results suggest a need to tailor the presentation of PGT results by test type and customer characteristics. © 2015 S. Karger AG, Basel.

How Well Do Customers of Direct-to-Consumer Personal Genomic Testing Services Comprehend Genetic Test Results? Findings from the Impact of Personal Genomics Study

PubMed Central

Ostergren, Jenny E.; Gornick, Michele C.; Carere, Deanna Alexis; Kalia, Sarah S.; Uhlmann, Wendy R.; Ruffin, Mack T.; Mountain, Joanna L.; Green, Robert C.; Roberts, J. Scott

2016-01-01

Aim To assess customer comprehension of health-related personal genomic testing (PGT) results. Methods We presented sample reports of genetic results and examined responses to comprehension questions in 1,030 PGT customers (mean age: 46.7 years; 59.9% female; 79.0% college graduates; 14.9% non-White; 4.7% of Hispanic/Latino ethnicity). Sample reports presented a genetic risk for Alzheimer’s disease and type 2 diabetes, carrier screening summary results for >30 conditions, results for phenylketonuria and cystic fibrosis, and drug response results for a statin drug. Logistic regression was used to identify correlates of participant comprehension. Results Participants exhibited high overall comprehension (mean score: 79.1% correct). The highest comprehension (range: 81.1–97.4% correct) was observed in the statin drug response and carrier screening summary results, and lower comprehension (range: 63.6–74.8% correct) on specific carrier screening results. Higher levels of numeracy, genetic knowledge, and education were significantly associated with greater comprehension. Older age (≥ 60 years) was associated with lower comprehension scores. Conclusions Most customers accurately interpreted the health implications of PGT results; however, comprehension varied by demographic characteristics, numeracy and genetic knowledge, and types and format of the genetic information presented. Results suggest a need to tailor the presentation of PGT results by test type and customer characteristics. PMID:26087778

Etiologies of the Relationships Among Body Mass Index and Cold-Heat Patterns: A Twin Study.

PubMed

Hur, Yoon-Mi; Jin, Hee-Jeong; Lee, Siwoo

2018-06-01

The phenotypic relationships between body mass index (BMI) and cold-heat patterns have been frequently reported, but the etiology of these relationships remains unknown. We previously demonstrated that the cold pattern (CP) and the heat pattern (HP) were heritable traits. In the present study, we explored underlying genetic and environmental structures of the relationships among BMI and the CP and the HP. Twins (N = 1,752) drawn from the South Korean twin registry completed a cold-heat pattern questionnaire via a telephone interview. The phenotypic correlations among the three phenotypes were moderate but significant. Cross-twin, cross-trait correlations among BMI and the CP and the HP were consistently greater in monozygotic than in dizygotic twins, suggesting the presence of genetic effects on the relationships between BMI and the two patterns. A trivariate Cholesky model was applied to the raw data. The results indicated that the phenotypic relationship between the HP and BMI was completely determined by common genetic influences, while the relationship between the CP and BMI was explained by both common genetic and common individual-specific environmental influences. The genetic correlation between the HP and the CP was not significant, suggesting that the two patterns may be genetically independent from each other. Genetic correlations were 0.31 between the HP and BMI, and -0.22 between the CP and BMI. The individual-specific environmental correlation was -0.22 between HP and CP, and between CP and BMI.

Prioritization based on neutral genetic diversity may fail to conserve important characteristics in cattle breeds.

PubMed

Hall, S J G; Lenstra, J A; Deeming, D C

2012-06-01

Conservation of the intraspecific genetic diversity of livestock species requires protocols that assess between-breed genetic variability and also take into account differences among individuals within breeds. Here, we focus on variation between breeds. Conservation of neutral genetic variation has been seen as promoting, through linkage processes, the retention of useful and potentially useful variation. Using public information on beef cattle breeds, with a total of 165 data sets each relating to a breed comparison of a performance variable, we have tested this paradigm by calculating the correlations between pairwise breed differences in performance and pairwise genetic distances deduced from biochemical and immunological polymorphisms, microsatellites and single-nucleotide polymorphisms. As already observed in floral and faunal biodiversity, significant positive correlations (n=54) were found, but many correlations were non-significant (n=100) or significantly negative (n=11). This implies that maximizing conserved neutral genetic variation with current techniques may conserve breed-level genetic variation in some traits but not in others and supports the view that genetic distance measurements based on neutral genetic variation are not sufficient as a determinant of conservation priority among breeds. © 2011 Blackwell Verlag GmbH.

Sex-specific genetic variances in life-history and morphological traits of the seed beetle Callosobruchus maculatus.

PubMed

Hallsson, Lára R; Björklund, Mats

2012-01-01

Knowledge of heritability and genetic correlations are of central importance in the study of adaptive trait evolution and genetic constraints. We use a paternal half-sib-full-sib breeding design to investigate the genetic architecture of three life-history and morphological traits in the seed beetle, Callosobruchus maculatus. Heritability was significant for all traits under observation and genetic correlations between traits (r(A)) were low. Interestingly, we found substantial sex-specific genetic effects and low genetic correlations between sexes (r(MF)) in traits that are only moderately (weight at emergence) to slightly (longevity) sexually dimorphic. Furthermore, we found an increased sire ([Formula: see text]) compared to dam ([Formula: see text]) variance component within trait and sex. Our results highlight that the genetic architecture even of the same trait should not be assumed to be the same for males and females. Furthermore, it raises the issue of the presence of unnoticed environmental effects that may inflate estimates of heritability. Overall, our study stresses the fact that estimates of quantitative genetic parameters are not only population, time, environment, but also sex specific. Thus, extrapolation between sexes and studies should be treated with caution.

Sex-specific genetic variances in life-history and morphological traits of the seed beetle Callosobruchus maculatus

PubMed Central

Hallsson, Lára R; Björklund, Mats

2012-01-01

Knowledge of heritability and genetic correlations are of central importance in the study of adaptive trait evolution and genetic constraints. We use a paternal half-sib-full-sib breeding design to investigate the genetic architecture of three life-history and morphological traits in the seed beetle, Callosobruchus maculatus. Heritability was significant for all traits under observation and genetic correlations between traits (rA) were low. Interestingly, we found substantial sex-specific genetic effects and low genetic correlations between sexes (rMF) in traits that are only moderately (weight at emergence) to slightly (longevity) sexually dimorphic. Furthermore, we found an increased sire () compared to dam () variance component within trait and sex. Our results highlight that the genetic architecture even of the same trait should not be assumed to be the same for males and females. Furthermore, it raises the issue of the presence of unnoticed environmental effects that may inflate estimates of heritability. Overall, our study stresses the fact that estimates of quantitative genetic parameters are not only population, time, environment, but also sex specific. Thus, extrapolation between sexes and studies should be treated with caution. PMID:22408731

Dual gene activation and knockout screen reveals directional dependencies in genetic networks. | Office of Cancer Genomics

Cancer.gov

Understanding the direction of information flow is essential for characterizing how genetic networks affect phenotypes. However, methods to find genetic interactions largely fail to reveal directional dependencies. We combine two orthogonal Cas9 proteins from Streptococcus pyogenes and Staphylococcus aureus to carry out a dual screen in which one gene is activated while a second gene is deleted in the same cell. We analyze the quantitative effects of activation and knockout to calculate genetic interaction and directionality scores for each gene pair.

Significant Locus and Metabolic Genetic Correlations Revealed in Genome-Wide Association Study of Anorexia Nervosa.

PubMed

Duncan, Laramie; Yilmaz, Zeynep; Gaspar, Helena; Walters, Raymond; Goldstein, Jackie; Anttila, Verneri; Bulik-Sullivan, Brendan; Ripke, Stephan; Thornton, Laura; Hinney, Anke; Daly, Mark; Sullivan, Patrick F; Zeggini, Eleftheria; Breen, Gerome; Bulik, Cynthia M

2017-09-01

The authors conducted a genome-wide association study of anorexia nervosa and calculated genetic correlations with a series of psychiatric, educational, and metabolic phenotypes. Following uniform quality control and imputation procedures using the 1000 Genomes Project (phase 3) in 12 case-control cohorts comprising 3,495 anorexia nervosa cases and 10,982 controls, the authors performed standard association analysis followed by a meta-analysis across cohorts. Linkage disequilibrium score regression was used to calculate genome-wide common variant heritability (single-nucleotide polymorphism [SNP]-based heritability [h 2 SNP ]), partitioned heritability, and genetic correlations (r g ) between anorexia nervosa and 159 other phenotypes. Results were obtained for 10,641,224 SNPs and insertion-deletion variants with minor allele frequencies >1% and imputation quality scores >0.6. The h 2 SNP of anorexia nervosa was 0.20 (SE=0.02), suggesting that a substantial fraction of the twin-based heritability arises from common genetic variation. The authors identified one genome-wide significant locus on chromosome 12 (rs4622308) in a region harboring a previously reported type 1 diabetes and autoimmune disorder locus. Significant positive genetic correlations were observed between anorexia nervosa and schizophrenia, neuroticism, educational attainment, and high-density lipoprotein cholesterol, and significant negative genetic correlations were observed between anorexia nervosa and body mass index, insulin, glucose, and lipid phenotypes. Anorexia nervosa is a complex heritable phenotype for which this study has uncovered the first genome-wide significant locus. Anorexia nervosa also has large and significant genetic correlations with both psychiatric phenotypes and metabolic traits. The study results encourage a reconceptualization of this frequently lethal disorder as one with both psychiatric and metabolic etiology.

Concerted evolution of life stage performances signals recent selection on yeast nitrogen use.

PubMed

Ibstedt, Sebastian; Stenberg, Simon; Bagés, Sara; Gjuvsland, Arne B; Salinas, Francisco; Kourtchenko, Olga; Samy, Jeevan K A; Blomberg, Anders; Omholt, Stig W; Liti, Gianni; Beltran, Gemma; Warringer, Jonas

2015-01-01

Exposing natural selection driving phenotypic and genotypic adaptive differentiation is an extraordinary challenge. Given that an organism's life stages are exposed to the same environmental variations, we reasoned that fitness components, such as the lag, rate, and efficiency of growth, directly reflecting performance in these life stages, should often be selected in concert. We therefore conjectured that correlations between fitness components over natural isolates, in a particular environmental context, would constitute a robust signal of recent selection. Critically, this test for selection requires fitness components to be determined by different genetic loci. To explore our conjecture, we exhaustively evaluated the lag, rate, and efficiency of asexual population growth of natural isolates of the model yeast Saccharomyces cerevisiae in a large variety of nitrogen-limited environments. Overall, fitness components were well correlated under nitrogen restriction. Yeast isolates were further crossed in all pairwise combinations and coinheritance of each fitness component and genetic markers were traced. Trait variations tended to map to quantitative trait loci (QTL) that were private to a single fitness component. We further traced QTLs down to single-nucleotide resolution and uncovered loss-of-function mutations in RIM15, PUT4, DAL1, and DAL4 as the genetic basis for nitrogen source use variations. Effects of SNPs were unique for a single fitness component, strongly arguing against pleiotropy between lag, rate, and efficiency of reproduction under nitrogen restriction. The strong correlations between life stage performances that cannot be explained by pleiotropy compellingly support adaptive differentiation of yeast nitrogen source use and suggest a generic approach for detecting selection. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Selection Indices and Multivariate Analysis Show Similar Results in the Evaluation of Growth and Carcass Traits in Beef Cattle

PubMed Central

Brito Lopes, Fernando; da Silva, Marcelo Corrêa; Magnabosco, Cláudio Ulhôa; Goncalves Narciso, Marcelo; Sainz, Roberto Daniel

2016-01-01

This research evaluated a multivariate approach as an alternative tool for the purpose of selection regarding expected progeny differences (EPDs). Data were fitted using a multi-trait model and consisted of growth traits (birth weight and weights at 120, 210, 365 and 450 days of age) and carcass traits (longissimus muscle area (LMA), back-fat thickness (BF), and rump fat thickness (RF)), registered over 21 years in extensive breeding systems of Polled Nellore cattle in Brazil. Multivariate analyses were performed using standardized (zero mean and unit variance) EPDs. The k mean method revealed that the best fit of data occurred using three clusters (k = 3) (P < 0.001). Estimates of genetic correlation among growth and carcass traits and the estimates of heritability were moderate to high, suggesting that a correlated response approach is suitable for practical decision making. Estimates of correlation between selection indices and the multivariate index (LD1) were moderate to high, ranging from 0.48 to 0.97. This reveals that both types of indices give similar results and that the multivariate approach is reliable for the purpose of selection. The alternative tool seems very handy when economic weights are not available or in cases where more rapid identification of the best animals is desired. Interestingly, multivariate analysis allowed forecasting information based on the relationships among breeding values (EPDs). Also, it enabled fine discrimination, rapid data summarization after genetic evaluation, and permitted accounting for maternal ability and the genetic direct potential of the animals. In addition, we recommend the use of longissimus muscle area and subcutaneous fat thickness as selection criteria, to allow estimation of breeding values before the first mating season in order to accelerate the response to individual selection. PMID:26789008

Selection Indices and Multivariate Analysis Show Similar Results in the Evaluation of Growth and Carcass Traits in Beef Cattle.

PubMed

Brito Lopes, Fernando; da Silva, Marcelo Corrêa; Magnabosco, Cláudio Ulhôa; Goncalves Narciso, Marcelo; Sainz, Roberto Daniel

2016-01-01

This research evaluated a multivariate approach as an alternative tool for the purpose of selection regarding expected progeny differences (EPDs). Data were fitted using a multi-trait model and consisted of growth traits (birth weight and weights at 120, 210, 365 and 450 days of age) and carcass traits (longissimus muscle area (LMA), back-fat thickness (BF), and rump fat thickness (RF)), registered over 21 years in extensive breeding systems of Polled Nellore cattle in Brazil. Multivariate analyses were performed using standardized (zero mean and unit variance) EPDs. The k mean method revealed that the best fit of data occurred using three clusters (k = 3) (P < 0.001). Estimates of genetic correlation among growth and carcass traits and the estimates of heritability were moderate to high, suggesting that a correlated response approach is suitable for practical decision making. Estimates of correlation between selection indices and the multivariate index (LD1) were moderate to high, ranging from 0.48 to 0.97. This reveals that both types of indices give similar results and that the multivariate approach is reliable for the purpose of selection. The alternative tool seems very handy when economic weights are not available or in cases where more rapid identification of the best animals is desired. Interestingly, multivariate analysis allowed forecasting information based on the relationships among breeding values (EPDs). Also, it enabled fine discrimination, rapid data summarization after genetic evaluation, and permitted accounting for maternal ability and the genetic direct potential of the animals. In addition, we recommend the use of longissimus muscle area and subcutaneous fat thickness as selection criteria, to allow estimation of breeding values before the first mating season in order to accelerate the response to individual selection.

Genetic diversity in three invasive clonal aquatic species in New Zealand

PubMed Central

2010-01-01

Background Elodea canadensis, Egeria densa and Lagarosiphon major are dioecious clonal species which are invasive in New Zealand and other regions. Unlike many other invasive species, the genetic variation in New Zealand is very limited. Clonal reproduction is often considered an evolutionary dead end, even though a certain amount of genetic divergence may arise due to somatic mutations. The successful growth and establishment of invasive clonal species may be explained not by adaptability but by pre-existing ecological traits that prove advantageous in the new environment. We studied the genetic diversity and population structure in the North Island of New Zealand using AFLPs and related the findings to the number of introductions and the evolution that has occurred in the introduced area. Results Low levels of genetic diversity were found in all three species and appeared to be due to highly homogeneous founding gene pools. Elodea canadensis was introduced in 1868, and its populations showed more genetic structure than those of the more recently introduced of E. densa (1946) and L. major (1950). Elodea canadensis and L. major, however, had similar phylogeographic patterns, in spite of the difference in time since introduction. Conclusions The presence of a certain level of geographically correlated genetic structure in the absence of sexual reproduction, and in spite of random human dispersal of vegetative propagules, can be reasonably attributed to post-dispersal somatic mutations. Direct evidence of such evolutionary events is, however, still insufficient. PMID:20565861

Determinants of genetic structure in a nonequilibrium metapopulation of the plant Silene latifolia.

PubMed

Fields, Peter D; Taylor, Douglas R

2014-01-01

Population genetic differentiation will be influenced by the demographic history of populations, opportunities for migration among neighboring demes and founder effects associated with repeated extinction and recolonization. In natural populations, these factors are expected to interact with each other and their magnitudes will vary depending on the spatial distribution and age structure of local demes. Although each of these effects has been individually identified as important in structuring genetic variance, their relative magnitude is seldom estimated in nature. We conducted a population genetic analysis in a metapopulation of the angiosperm, Silene latifolia, from which we had more than 20 years of data on the spatial distribution, demographic history, and extinction and colonization of demes. We used hierarchical Bayesian methods to disentangle which features of the populations contributed to among population variation in allele frequencies, including the magnitude and direction of their effects. We show that population age, long-term size and degree of connectivity all combine to affect the distribution of genetic variance; small, recently-founded, isolated populations contributed most to increase FST in the metapopulation. However, the effects of population size and population age are best understood as being modulated through the effects of connectivity to other extant populations, i.e. FST diminishes as populations age, but at a rate that depends how isolated the population is. These spatial and temporal correlates of population structure give insight into how migration, founder effect and within-deme genetic drift have combined to enhance and restrict genetic divergence in a natural metapopulation.

Population Genetic Structure of a Widespread Bat-Pollinated Columnar Cactus

PubMed Central

Bustamante, Enriquena; Búrquez, Alberto; Scheinvar, Enrique; Eguiarte, Luis Enrique

2016-01-01

Bats are the main pollinators and seed dispersers of Stenocereus thurberi, a xenogamous columnar cactus of northwestern Mexico and a good model to illustrate spatial dynamics of gene flow in long-lived species. Previous studies in this cactus showed differences among populations in the type and abundance of pollinators, and in the timing of flowering and fruiting. In this study we analyzed genetic variability and population differentiation among populations. We used three primers of ISSR to analyze within and among populations genetic variation from eight widely separated populations of S. thurberi in Sonora, Mexico. Sixty-six out of 99 of the ISSR bands (P = 66.7%) were polymorphic. Total heterozygosity for all populations sampled revealed high genetic diversity (Hsp = 0.207, HBT = 0.224). The AMOVA showed that most of the genetic variation was within populations (80.5%). At the species level, estimates of population differentiation, θ = 0.175 and θB = 0.194, indicated moderate gene flow among populations. The absence of a significant correlation between genetic and geographic distances indicated little isolation by geographic distance. The large genetic variation and diversity found in S. thurberi is consistent with its open reproductive system and the high mobility of bats, a major pollinator. However, small changes in number or kind of pollinators and seed dispersal agents, in the directionality of migratory routes, and/or in the timing of flowering and fruiting among populations, can critically affect gene flow dynamics. PMID:27015281

Population Genetic Structure of a Widespread Bat-Pollinated Columnar Cactus.

PubMed

Bustamante, Enriquena; Búrquez, Alberto; Scheinvar, Enrique; Eguiarte, Luis Enrique

2016-01-01

Bats are the main pollinators and seed dispersers of Stenocereus thurberi, a xenogamous columnar cactus of northwestern Mexico and a good model to illustrate spatial dynamics of gene flow in long-lived species. Previous studies in this cactus showed differences among populations in the type and abundance of pollinators, and in the timing of flowering and fruiting. In this study we analyzed genetic variability and population differentiation among populations. We used three primers of ISSR to analyze within and among populations genetic variation from eight widely separated populations of S. thurberi in Sonora, Mexico. Sixty-six out of 99 of the ISSR bands (P = 66.7%) were polymorphic. Total heterozygosity for all populations sampled revealed high genetic diversity (Hsp = 0.207, HBT = 0.224). The AMOVA showed that most of the genetic variation was within populations (80.5%). At the species level, estimates of population differentiation, θ = 0.175 and θB = 0.194, indicated moderate gene flow among populations. The absence of a significant correlation between genetic and geographic distances indicated little isolation by geographic distance. The large genetic variation and diversity found in S. thurberi is consistent with its open reproductive system and the high mobility of bats, a major pollinator. However, small changes in number or kind of pollinators and seed dispersal agents, in the directionality of migratory routes, and/or in the timing of flowering and fruiting among populations, can critically affect gene flow dynamics.

Facial averageness and genetic quality: Testing heritability, genetic correlation with attractiveness, and the paternal age effect.

PubMed

Lee, Anthony J; Mitchem, Dorian G; Wright, Margaret J; Martin, Nicholas G; Keller, Matthew C; Zietsch, Brendan P

2016-01-01

Popular theory suggests that facial averageness is preferred in a partner for genetic benefits to offspring. However, whether facial averageness is associated with genetic quality is yet to be established. Here, we computed an objective measure of facial averageness for a large sample ( N = 1,823) of identical and nonidentical twins and their siblings to test two predictions from the theory that facial averageness reflects genetic quality. First, we use biometrical modelling to estimate the heritability of facial averageness, which is necessary if it reflects genetic quality. We also test for a genetic association between facial averageness and facial attractiveness. Second, we assess whether paternal age at conception (a proxy of mutation load) is associated with facial averageness and facial attractiveness. Our findings are mixed with respect to our hypotheses. While we found that facial averageness does have a genetic component, and a significant phenotypic correlation exists between facial averageness and attractiveness, we did not find a genetic correlation between facial averageness and attractiveness (therefore, we cannot say that the genes that affect facial averageness also affect facial attractiveness) and paternal age at conception was not negatively associated with facial averageness. These findings support some of the previously untested assumptions of the 'genetic benefits' account of facial averageness, but cast doubt on others.

Alcohol use disorder and divorce: evidence for a genetic correlation in a population-based Swedish sample.

PubMed

Salvatore, Jessica E; Larsson Lönn, Sara; Sundquist, Jan; Lichtenstein, Paul; Sundquist, Kristina; Kendler, Kenneth S

2017-04-01

We tested the association between alcohol use disorder (AUD) and divorce; estimated the genetic and environmental influences on divorce; estimated how much genetic and environmental influences accounted for covariance between AUD and divorce; and estimated latent genetic and environmental correlations between AUD and divorce. We tested sex differences in these effects. We identified twin and sibling pairs with AUD and divorce information in Swedish national registers. We described the association between AUD and divorce using tetrachorics and used twin and sibling models to estimate genetic and environmental influences on divorce, on the covariance between AUD and divorce and the latent genetic and environmental correlations between AUD and divorce. Sweden. A total of 670 836 individuals (53% male) born 1940-1965. Life-time measures of AUD and divorce. AUD and divorce were related strongly (males: r tet  = +0.44, 95% CI = 0.43, 0.45; females r tet  = +0.37, 95% CI = 0.36, 0.38). Genetic factors accounted for a modest proportion of the variance in divorce (males: 21.3%, 95% CI = 7.6, 28.5; females: 31.0%, 95% CI = 18.8, 37.1). Genetic factors accounted for most of the covariance between AUD and divorce (males: 52.0%, 95% CI = 48.8, 67.9; females: 53.74%, 95% CI = 17.6, 54.5), followed by non-shared environmental factors (males: 45.0%, 95% CI = 37.5, 54.9; females: 41.6%, 95% CI = 40.3, 60.2). Shared environmental factors accounted for a negligible proportion of the covariance (males: 3.0%, 95% CI = -3.0, 13.5; females: 4.75%, 95% CI = 0.0, 6.6). The AUD-divorce genetic correlations were high (males: rA = +0.76, 95% CI = 0.53, 0.90; females +0.52, 95% CI = 0.24, 0.67). The non-shared environmental correlations were modest (males: rE = +0.32, 95% CI = 0.31, 0.40; females: +0.27, 95% CI = 0.27, 0.36). Divorce and alcohol use disorder are correlated strongly in the Swedish population, and the heritability of divorce is consistent with previous studies. Covariation between AUD and divorce results from overlapping genetic and non-shared environmental factors. Latent genetic and non-shared environmental correlations for alcohol use disorder and divorce are high and moderate. © 2016 Society for the Study of Addiction.

Fungal Genetics and Functional Diversity of Microbial Communities in the Soil under Long-Term Monoculture of Maize Using Different Cultivation Techniques

PubMed Central

Gałązka, Anna; Grządziel, Jarosław

2018-01-01

Fungal diversity in the soil may be limited under natural conditions by inappropriate environmental factors such as: nutrient resources, biotic and abiotic factors, tillage system and microbial interactions that prevent the occurrence or survival of the species in the environment. The aim of this paper was to determine fungal genetic diversity and community level physiological profiling of microbial communities in the soil under long-term maize monoculture. The experimental scheme involved four cultivation techniques: direct sowing (DS), reduced tillage (RT), full tillage (FT), and crop rotation (CR). Soil samples were taken in two stages: before sowing of maize (DSBS-direct sowing, RTBS-reduced tillage, FTBS-full tillage, CRBS-crop rotation) and the flowering stage of maize growth (DSF-direct sowing, RTF-reduced tillage, FTF-full tillage, CRF-crop rotation). The following plants were used in the crop rotation: spring barley, winter wheat and maize. The study included fungal genetic diversity assessment by ITS-1 next generation sequencing (NGS) analyses as well as the characterization of the catabolic potential of microbial communities (Biolog EcoPlates) in the soil under long-term monoculture of maize using different cultivation techniques. The results obtained from the ITS-1 NGS technique enabled to classify and correlate the fungi species or genus to the soil metabolome. The research methods used in this paper have contributed to a better understanding of genetic diversity and composition of the population of fungi in the soil under the influence of the changes that have occurred in the soil under long-term maize cultivation. In all cultivation techniques, the season had a great influence on the fungal genetic structure in the soil. Significant differences were found on the family level (P = 0.032, F = 3.895), genus level (P = 0.026, F = 3.313) and on the species level (P = 0.033, F = 2.718). This study has shown that: (1) fungal diversity was changed under the influence different cultivation techniques; (2) techniques of maize cultivation and season were an important factors that can influence the biochemical activity of soil. Maize cultivated in direct sowing did not cause negative changes in the fungal structure, even making it more stable during seasonal changes; (3) full tillage and crop rotation may change fungal community and soil function. PMID:29441054

Genome-wide association studies dissect the genetic networks underlying agronomical traits in soybean.

PubMed

Fang, Chao; Ma, Yanming; Wu, Shiwen; Liu, Zhi; Wang, Zheng; Yang, Rui; Hu, Guanghui; Zhou, Zhengkui; Yu, Hong; Zhang, Min; Pan, Yi; Zhou, Guoan; Ren, Haixiang; Du, Weiguang; Yan, Hongrui; Wang, Yanping; Han, Dezhi; Shen, Yanting; Liu, Shulin; Liu, Tengfei; Zhang, Jixiang; Qin, Hao; Yuan, Jia; Yuan, Xiaohui; Kong, Fanjiang; Liu, Baohui; Li, Jiayang; Zhang, Zhiwu; Wang, Guodong; Zhu, Baoge; Tian, Zhixi

2017-08-24

Soybean (Glycine max [L.] Merr.) is one of the most important oil and protein crops. Ever-increasing soybean consumption necessitates the improvement of varieties for more efficient production. However, both correlations among different traits and genetic interactions among genes that affect a single trait pose a challenge to soybean breeding. To understand the genetic networks underlying phenotypic correlations, we collected 809 soybean accessions worldwide and phenotyped them for two years at three locations for 84 agronomic traits. Genome-wide association studies identified 245 significant genetic loci, among which 95 genetically interacted with other loci. We determined that 14 oil synthesis-related genes are responsible for fatty acid accumulation in soybean and function in line with an additive model. Network analyses demonstrated that 51 traits could be linked through the linkage disequilibrium of 115 associated loci and these links reflect phenotypic correlations. We revealed that 23 loci, including the known Dt1, E2, E1, Ln, Dt2, Fan, and Fap loci, as well as 16 undefined associated loci, have pleiotropic effects on different traits. This study provides insights into the genetic correlation among complex traits and will facilitate future soybean functional studies and breeding through molecular design.

Genetic parameters of ovarian and uterine reproductive traits in dairy cows.

PubMed

Carthy, T R; Ryan, D P; Fitzgerald, A M; Evans, R D; Berry, D P

2015-06-01

The objective of the study was to estimate genetic parameters of detailed reproductive traits derived from ultrasound examination of the reproductive tract as well as their genetic correlations with traditional reproductive traits. A total of 226,141 calving and insemination records as well as 74,134 ultrasound records from Irish dairy cows were used. Traditional reproductive traits included postpartum interval to first service, conception, and next calving, as well as the interval from first to last service; number of inseminations, pregnancy rate to first service, pregnant within 42 d of the herd breeding season, and submission in the first 21 d of the herd breeding season were also available. Detailed reproductive traits included resumed cyclicity at the time of ultrasound examination, incidence of multiple ovulations, incidence of early postpartum ovulation, heat detection, ovarian cystic structures, embryo loss, and uterine score; the latter was a subjectively assessed on a scale of 1 (little fluid with normal uterine tone) to 4 (large quantity of fluid with a flaccid uterine tone). Variance (and covariance) components were estimated using repeatability animal linear mixed models. Heritability for all reproductive traits were generally low (0.001-0.05), with the exception of traits related to cyclicity postpartum, regardless if defined traditionally (0.07; calving to first service) or from ultrasound examination [resumed cyclicity at the time of examination (0.07) or early postpartum ovulation (0.10)]. The genetic correlations among the detailed reproductive traits were generally favorable. The exception was the genetic correlation (0.29) between resumed cyclicity and uterine score; superior genetic merit for cyclicity postpartum was associated with inferior uterine score. Superior genetic merit for most traditional reproductive traits was associated with superior genetic merit for resumed cyclicity (genetic correlations ranged from -0.59 to -0.36 and from 0.56 to 0.70) and uterine score (genetic correlations ranged from -0.47 to 0.32 and from 0.25 to 0.52). Genetic predisposition to an increased incidence of embryo loss was associated with both an inferior uterine score (0.24) and inferior genetic merit for traditional reproductive traits (genetic correlations ranged from -0.52 to -0.42 and from 0.33 to 0.80). The results from the present study indicate that selection based on traditional reproductive traits, such as calving interval or days open, resulted in improved genetic merit of all the detailed reproductive traits evaluated in this study. Additionally, greater accuracy of selection for calving interval is expected for a relatively small progeny group size when detailed reproductive traits are included in a multitrait genetic evaluation. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Epigenetic regulation of immune checkpoints: another target for cancer immunotherapy?

PubMed

Ali, Mahmoud A; Matboli, Marwa; Tarek, Marwa; Reda, Maged; Kamal, Kamal M; Nouh, Mahmoud; Ashry, Ahmed M; El-Bab, Ahmed Fath; Mesalam, Hend A; Shafei, Ayman El-Sayed; Abdel-Rahman, Omar

2017-01-01

Epigenetic changes in oncogenes and tumor-suppressor genes contribute to carcinogenesis. Understanding the epigenetic and genetic components of tumor immune evasion is crucial. Few cancer genetic mutations have been linked to direct correlations with immune evasion. Studies on the epigenetic modulation of the immune checkpoints have revealed a critical interaction between epigenetic and immune modulation. Epigenetic modifiers can activate many silenced genes. Some of them are immune checkpoints regulators that turn on immune responses and others turn them off resulting in immune evasion. Many forms of epigenetic inheritance mechanisms may play a role in regulation of immune checkpoints including: covalent modifications, noncoding RNA and histone modifications. In this review, we will show how the potential interaction between epigenetic and immune modulation may lead to new approaches for specific epigenome/immunome-targeted therapies for cancer.

Genetic and phenotypic relationships between and within support and demand tissues in a single line of broiler chicken.

PubMed

Rance, K A; McEntee, G M; McDevitt, R M

2002-09-01

1. With commercial selection for increased broiler performance there has been a correlated increase in the incidence of several metabolic disorders. A study was undertaken to investigate the balance between the unselected support tissues (including the heart, liver, spleen and the components of the gastrointestinal tract (GIT)) which drive growth in the selected demand tissues (eviscerated body mass) by assessing the genetic correlations between these traits. 2. Data were collected on 483 broiler birds taken from a commercial male broiler line with pedigree information. 3. Genetic parameters were estimated by restricted maximum likelihood with an individual animal model. Heritability estimates for the production traits ranged between h2 = 0.48 and 0.59 for leg and breast mass, respectively. The support tissues were generally associated with low to moderate heritabilities ranging between h2 = 0.19 for proventriculus to h2 = 0.38 for duodenum mass, although moderately high heritability estimates (h2 = 0.51 to 0.54) were associated with the spleen and gizzard. 4. The genetic correlations between production traits and support organs were generally low, however, heart mass was positively correlated with all carcase components of the lean tissue mass; the genetic correlations ranged between r(g) = 0.55 with breast mass to r(g) = 0.64 with eviscerated body mass. 5. In general, there were strong positive genetic correlations between the different components of the GIT. Organs that have been implicated in the development of metabolic disorders such as ascites (for example, the heart) could theoretically be used in commercial selection indices due to moderate heritabilities (heart: h2 = 0.30) and favourable correlations with commercially important traits.

Association between dietary fat intake and insulin resistance in Chinese child twins.

PubMed

Huang, Tao; Beaty, Terri; Li, Ji; Liu, Huijuan; Zhao, Wei; Wang, Youfa

2017-01-01

Dietary fat intake is correlated with increased insulin resistance (IR). However, it is unknown whether gene-diet interaction modulates the association. This study estimated heritability of IR measures and the related genetic correlations with fat intake, and tested whether dietary fat intake modifies the genetic influence on type 2 diabetes (T2D)-related traits in Chinese child twins. We included 622 twins aged 7-15 years (n 311 pairs, 162 monozygotic (MZ), 149 dizygotic (DZ)) from south-eastern China. Dietary factors were measured using FFQ. Structural equation models were fit using Mx statistical package. The intra-class correlation coefficients for all traits related to T2D were higher for MZ twins than for DZ twins. Dietary fat and fasting serum insulin (additive genetic correlation (r A) 0·20; 95 % CI 0·08, 0·43), glucose (r A 0·12; 95 % CI 0·01, 0·40), homoeostasis model of assessment-insulin resistance (Homa-IR) (r A 0·22; 95 % CI 0·10, 0·50) and the quantitative insulin sensitivity check index (Quicki) (r A -0·22; 95 % CI -0·40, 0·04) showed strong genetic correlations. Heritabilities of dietary fat intake, fasting glucose and insulin were estimated to be 52, 70 and 70 %, respectively. More than 70 % of the phenotypic correlations between dietary fat and insulin, glucose, Homa-IR and the Quicki index appeared to be mediated by shared genetic influence. Dietary fat significantly modified additive genetic effects on these quantitative traits associated with T2D. Analysis of Chinese twins yielded high estimates of heritability of dietary fat intake and IR. Genetic factors appear to contribute to a high proportion of the variance for both insulin sensitivity and IR. Dietary fat intake modifies the genetic influence on blood levels of insulin and glucose, Homa-IR and the Quicki index.

Impact of presymptomatic genetic testing on young adults: a systematic review.

PubMed

Godino, Lea; Turchetti, Daniela; Jackson, Leigh; Hennessy, Catherine; Skirton, Heather

2016-04-01

Presymptomatic and predictive genetic testing should involve a considered choice, which is particularly true when testing is undertaken in early adulthood. Young adults are at a key life stage as they may be developing a career, forming partnerships and potentially becoming parents: presymptomatic testing may affect many facets of their future lives. The aim of this integrative systematic review was to assess factors that influence young adults' or adolescents' choices to have a presymptomatic genetic test and the emotional impact of those choices. Peer-reviewed papers published between January 1993 and December 2014 were searched using eight databases. Of 3373 studies identified, 29 were reviewed in full text: 11 met the inclusion criteria. Thematic analysis was used to identify five major themes: period before testing, experience of genetic counselling, parental involvement in decision-making, impact of test result communication, and living with genetic risk. Many participants grew up with little or no information concerning their genetic risk. The experience of genetic counselling was either reported as an opportunity for discussing problems or associated with feelings of disempowerment. Emotional outcomes of disclosure did not directly correlate with test results: some mutation carriers were relieved to know their status, however, the knowledge they may have passed on the mutation to their children was a common concern. Parents appeared to have exerted pressure on their children during the decision-making process about testing and risk reduction surgery. Health professionals should take into account all these issues to effectively assist young adults in making decisions about presymptomatic genetic testing.

Genetic parameters for sensory traits in longissimus muscle and their associations with tenderness, marbling score, and intramuscular fat in Angus cattle.

PubMed

Mateescu, R G; Garrick, D J; Garmyn, A J; VanOverbeke, D L; Mafi, G G; Reecy, J M

2015-01-01

The objective of this study was to estimate heritabilities for sensory traits and genetic correlations among sensory traits and with marbling score (MS), Warner-Bratzler shear force (WBSF), and intramuscular fat content (IMFC). Samples of LM from 2,285 Angus cattle were obtained and fabricated into steaks for laboratory analysis and 1,720 steaks were analyzed by a trained sensory panel. Restricted maximum likelihood procedures were used to obtain estimates of variance and covariance components under a multitrait animal model. Estimates of heritability for MS, IMFC, WBSF, tenderness, juiciness, and connective tissue traits were 0.67, 0.38, 0.19, 0.18, 0.06, and 0.25, respectively. The genetic correlations of MS with tenderness, juiciness, and connective tissue were estimated to be 0.57 ± 0.14, 1.00 ± 0.17, and 0.49 ± 0.13, all positive and strong. Estimated genetic correlations of IMFC with tenderness, juiciness, and connective tissue were 0.56 ± 0.16, 1.00 ± 0.21, and 0.50 ± 0.15, respectively. The genetic correlations of WBSF with tenderness, juiciness, and connective tissue were all favorable and estimated to be -0.99 ± 0.08, -0.33 ± 0.30 and -0.99 ± 0.07, respectively. Strong and positive genetic correlations were estimated between tenderness and juiciness (0.54 ± 0.28) and between connective tissue and juiciness (0.58 ± 0.26). In general, genetic correlations were large and favorable, which indicated that strong relationships exist and similar gene and gene networks may control MS, IMFC, and juiciness or WBSF, panel tenderness, and connective tissue. The results from this study confirm that MS currently used in selection breeding programs has positive genetic correlations with tenderness and juiciness and, therefore, is an effective indicator trait for the improvement of tenderness and juiciness in beef. This study also indicated that a more objective measure, particularly WBSF, a trait not easy to improve through phenotypic selection, is an excellent candidate trait for genomic selection aimed at improving eating satisfaction.

The genotype-phenotype landscape of familial amyotrophic lateral sclerosis in Australia.

PubMed

McCann, E P; Williams, K L; Fifita, J A; Tarr, I S; O'Connor, J; Rowe, D B; Nicholson, G A; Blair, I P

2017-09-01

Amyotrophic lateral sclerosis (ALS) is a clinically and genetically heterogeneous fatal neurodegenerative disease. Around 10% of ALS cases are hereditary. ALS gene discoveries have provided most of our understanding of disease pathogenesis. We aimed to describe the genetic landscape of ALS in Australia by assessing 1013 Australian ALS patients for known ALS mutations by direct sequencing, whole exome sequencing or repeat primed polymerase chain reaction. Age of disease onset and disease duration were used for genotype-phenotype correlations. We report 60.8% of Australian ALS families in this cohort harbour a known ALS mutation. Hexanucleotide repeat expansions in C9orf72 accounted for 40.6% of families and 2.9% of sporadic patients. We also report ALS families with mutations in SOD1 (13.7%), FUS (2.4%), TARDBP (1.9%), UBQLN2 (.9%), OPTN (.5%), TBK1 (.5%) and CCNF (.5%). We present genotype-phenotype correlations between these genes as well as between gene mutations. Notably, C9orf72 hexanucleotide repeat expansion positive patients experienced significantly later disease onset than ALS mutation patients. Among SOD1 families, p.I114T positive patients had significantly later onset and longer survival. Our report highlights a unique spectrum of ALS gene frequencies among patients from the Australian population, and further, provides correlations between specific ALS mutations with disease onset and/or duration. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Identification, Replication, and Functional Fine-Mapping of Expression Quantitative Trait Loci in Primary Human Liver Tissue

PubMed Central

Stanaway, Ian B.; Gamazon, Eric R.; Smith, Joshua D.; Mirkov, Snezana; Ramirez, Jacqueline; Liu, Wanqing; Lin, Yvonne S.; Moloney, Cliona; Aldred, Shelly Force; Trinklein, Nathan D.; Schuetz, Erin; Nickerson, Deborah A.; Thummel, Ken E.; Rieder, Mark J.; Rettie, Allan E.; Ratain, Mark J.; Cox, Nancy J.; Brown, Christopher D.

2011-01-01

The discovery of expression quantitative trait loci (“eQTLs”) can help to unravel genetic contributions to complex traits. We identified genetic determinants of human liver gene expression variation using two independent collections of primary tissue profiled with Agilent (n = 206) and Illumina (n = 60) expression arrays and Illumina SNP genotyping (550K), and we also incorporated data from a published study (n = 266). We found that ∼30% of SNP-expression correlations in one study failed to replicate in either of the others, even at thresholds yielding high reproducibility in simulations, and we quantified numerous factors affecting reproducibility. Our data suggest that drug exposure, clinical descriptors, and unknown factors associated with tissue ascertainment and analysis have substantial effects on gene expression and that controlling for hidden confounding variables significantly increases replication rate. Furthermore, we found that reproducible eQTL SNPs were heavily enriched near gene starts and ends, and subsequently resequenced the promoters and 3′UTRs for 14 genes and tested the identified haplotypes using luciferase assays. For three genes, significant haplotype-specific in vitro functional differences correlated directly with expression levels, suggesting that many bona fide eQTLs result from functional variants that can be mechanistically isolated in a high-throughput fashion. Finally, given our study design, we were able to discover and validate hundreds of liver eQTLs. Many of these relate directly to complex traits for which liver-specific analyses are likely to be relevant, and we identified dozens of potential connections with disease-associated loci. These included previously characterized eQTL contributors to diabetes, drug response, and lipid levels, and they suggest novel candidates such as a role for NOD2 expression in leprosy risk and C2orf43 in prostate cancer. In general, the work presented here will be valuable for future efforts to precisely identify and functionally characterize genetic contributions to a variety of complex traits. PMID:21637794

Contrasting Patterns of Genomic Diversity Reveal Accelerated Genetic Drift but Reduced Directional Selection on X-Chromosome in Wild and Domestic Sheep Species.

PubMed

Chen, Ze-Hui; Zhang, Min; Lv, Feng-Hua; Ren, Xue; Li, Wen-Rong; Liu, Ming-Jun; Nam, Kiwoong; Bruford, Michael W; Li, Meng-Hua

2018-04-01

Analyses of genomic diversity along the X chromosome and of its correlation with autosomal diversity can facilitate understanding of evolutionary forces in shaping sex-linked genomic architecture. Strong selective sweeps and accelerated genetic drift on the X-chromosome have been inferred in primates and other model species, but no such insight has yet been gained in domestic animals compared with their wild relatives. Here, we analyzed X-chromosome variability in a large ovine data set, including a BeadChip array for 943 ewes from the world's sheep populations and 110 whole genomes of wild and domestic sheep. Analyzing whole-genome sequences, we observed a substantially reduced X-to-autosome diversity ratio (∼0.6) compared with the value expected under a neutral model (0.75). In particular, one large X-linked segment (43.05-79.25 Mb) was found to show extremely low diversity, most likely due to a high density of coding genes, featuring highly conserved regions. In general, we observed higher nucleotide diversity on the autosomes, but a flat diversity gradient in X-linked segments, as a function of increasing distance from the nearest genes, leading to a decreased X: autosome (X/A) diversity ratio and contrasting to the positive correlation detected in primates and other model animals. Our evidence suggests that accelerated genetic drift but reduced directional selection on X chromosome, as well as sex-biased demographic events, explain low X-chromosome diversity in sheep species. The distinct patterns of X-linked and X/A diversity we observed between Middle Eastern and non-Middle Eastern sheep populations can be explained by multiple migrations, selection, and admixture during the domestic sheep's recent postdomestication demographic expansion, coupled with natural selection for adaptation to new environments. In addition, we identify important novel genes involved in abnormal behavioral phenotypes, metabolism, and immunity, under selection on the sheep X-chromosome.

Contrasting Patterns of Genomic Diversity Reveal Accelerated Genetic Drift but Reduced Directional Selection on X-Chromosome in Wild and Domestic Sheep Species

PubMed Central

Chen, Ze-Hui; Zhang, Min; Lv, Feng-Hua; Ren, Xue; Li, Wen-Rong; Liu, Ming-Jun; Nam, Kiwoong; Bruford, Michael W; Li, Meng-Hua

2018-01-01

Abstract Analyses of genomic diversity along the X chromosome and of its correlation with autosomal diversity can facilitate understanding of evolutionary forces in shaping sex-linked genomic architecture. Strong selective sweeps and accelerated genetic drift on the X-chromosome have been inferred in primates and other model species, but no such insight has yet been gained in domestic animals compared with their wild relatives. Here, we analyzed X-chromosome variability in a large ovine data set, including a BeadChip array for 943 ewes from the world’s sheep populations and 110 whole genomes of wild and domestic sheep. Analyzing whole-genome sequences, we observed a substantially reduced X-to-autosome diversity ratio (∼0.6) compared with the value expected under a neutral model (0.75). In particular, one large X-linked segment (43.05–79.25 Mb) was found to show extremely low diversity, most likely due to a high density of coding genes, featuring highly conserved regions. In general, we observed higher nucleotide diversity on the autosomes, but a flat diversity gradient in X-linked segments, as a function of increasing distance from the nearest genes, leading to a decreased X: autosome (X/A) diversity ratio and contrasting to the positive correlation detected in primates and other model animals. Our evidence suggests that accelerated genetic drift but reduced directional selection on X chromosome, as well as sex-biased demographic events, explain low X-chromosome diversity in sheep species. The distinct patterns of X-linked and X/A diversity we observed between Middle Eastern and non-Middle Eastern sheep populations can be explained by multiple migrations, selection, and admixture during the domestic sheep’s recent postdomestication demographic expansion, coupled with natural selection for adaptation to new environments. In addition, we identify important novel genes involved in abnormal behavioral phenotypes, metabolism, and immunity, under selection on the sheep X-chromosome. PMID:29790980

Genetic pleiotropy explains associations between musical auditory discrimination and intelligence.

PubMed

Mosing, Miriam A; Pedersen, Nancy L; Madison, Guy; Ullén, Fredrik

2014-01-01

Musical aptitude is commonly measured using tasks that involve discrimination of different types of musical auditory stimuli. Performance on such different discrimination tasks correlates positively with each other and with intelligence. However, no study to date has explored these associations using a genetically informative sample to estimate underlying genetic and environmental influences. In the present study, a large sample of Swedish twins (N = 10,500) was used to investigate the genetic architecture of the associations between intelligence and performance on three musical auditory discrimination tasks (rhythm, melody and pitch). Phenotypic correlations between the tasks ranged between 0.23 and 0.42 (Pearson r values). Genetic modelling showed that the covariation between the variables could be explained by shared genetic influences. Neither shared, nor non-shared environment had a significant effect on the associations. Good fit was obtained with a two-factor model where one underlying shared genetic factor explained all the covariation between the musical discrimination tasks and IQ, and a second genetic factor explained variance exclusively shared among the discrimination tasks. The results suggest that positive correlations among musical aptitudes result from both genes with broad effects on cognition, and genes with potentially more specific influences on auditory functions.

Genetic Pleiotropy Explains Associations between Musical Auditory Discrimination and Intelligence

PubMed Central

Mosing, Miriam A.; Pedersen, Nancy L.; Madison, Guy; Ullén, Fredrik

2014-01-01

Musical aptitude is commonly measured using tasks that involve discrimination of different types of musical auditory stimuli. Performance on such different discrimination tasks correlates positively with each other and with intelligence. However, no study to date has explored these associations using a genetically informative sample to estimate underlying genetic and environmental influences. In the present study, a large sample of Swedish twins (N = 10,500) was used to investigate the genetic architecture of the associations between intelligence and performance on three musical auditory discrimination tasks (rhythm, melody and pitch). Phenotypic correlations between the tasks ranged between 0.23 and 0.42 (Pearson r values). Genetic modelling showed that the covariation between the variables could be explained by shared genetic influences. Neither shared, nor non-shared environment had a significant effect on the associations. Good fit was obtained with a two-factor model where one underlying shared genetic factor explained all the covariation between the musical discrimination tasks and IQ, and a second genetic factor explained variance exclusively shared among the discrimination tasks. The results suggest that positive correlations among musical aptitudes result from both genes with broad effects on cognition, and genes with potentially more specific influences on auditory functions. PMID:25419664

The genetic basis for the selection of dairy goats with enhanced resistance to gastrointestinal nematodes

PubMed Central

Heckendorn, Felix; Bieber, Anna; Werne, Steffen; Saratsis, Anastasios; Maurer, Veronika; Stricker, Chris

2017-01-01

Gastrointestinal nematodes (GIN) severely affect small ruminant production worldwide. Increasing problems of anthelmintic resistance have given strong impetus to the search for alternative strategies to control GIN. Selection of animals with an enhanced resistance to GIN has been shown to be successful in sheep. In goats, the corresponding information is comparatively poor. Therefore, the present study was designed to provide reliable data on heritabilities of and genetic correlations between phenotypic traits linked to GIN and milk yield in two major dairy goat breeds (Alpine and Saanen). In all, 20 herds totalling 1303 goats were enrolled in the study. All herds had (i) a history of gastrointestinal nematode infection, (ii) uniform GIN exposure on pasture and (iii) regular milk recordings. For all goats, individual recordings of faecal egg counts (FEC), FAMACHA© eye score, packed cell volume (PCV) and milk yield were performed twice a year with an anthelmintic treatment in between. The collected phenotypic data were multivariately modelled using animal as a random effect with its covariance structure inferred from the pedigree, enabling estimation of the heritabilities of the respective traits and the genetic correlation between them. The heritabilities of FEC, FAMACHA© and PCV were 0.07, 0.22 and 0.22, respectively. The genetic correlation between FEC and FAMACHA© was close to zero and −0.41 between FEC and PCV. The phenotypic correlation between FEC and milk yield was close to zero, whereas the genetic correlation was 0.49. Our data suggest low heritability of FEC in Saanen and Alpine goats and an unfavourable genetic correlation of FEC with milk yield. PMID:28792887

Genomic validation of the differential preservation of population history in modern human cranial anatomy.

PubMed

Reyes-Centeno, Hugo; Ghirotto, Silvia; Harvati, Katerina

2017-01-01

In modern humans, the significant correlation between neutral genetic loci and cranial anatomy suggests that the cranium preserves a population history signature. However, there is disagreement on whether certain parts of the cranium preserve this signature to a greater degree than other parts. It is also unclear how different quantitative measures of phenotype affect the association of genetic variation and anatomy. Here, we revisit these matters by testing the correlation of genetic distances and various phenotypic distances for ten modern human populations. Geometric morphometric shape data from the crania of adult individuals (n = 224) are used to calculate phenotypic P ST , Procrustes, and Mahalanobis distances. We calculate their correlation to neutral genetic distances, F ST , derived from single nucleotide polymorphisms (SNPs). We subset the cranial data into landmark configurations that include the neurocranium, the face, and the temporal bone in order to evaluate whether these cranial regions are differentially correlated to neutral genetic variation. Our results show that P ST , Mahalanobis, and Procrustes distances are correlated with F ST distances to varying degrees. They indicate that overall cranial shape is significantly correlated with neutral genetic variation. Of the component parts examined, P ST distances for both the temporal bone and the face have a stronger association with F ST distances than the neurocranium. When controlling for population divergence time, only the whole cranium and the temporal bone have a statistically significant association with F ST distances. Our results confirm that the cranium, as a whole, and the temporal bone can be used to reconstruct modern human population history. © 2016 Wiley Periodicals, Inc.

Genetic integration of molar cusp size variation in baboons

PubMed Central

Koh, Christina; Bates, Elizabeth; Broughton, Elizabeth; Do, Nicholas T.; Fletcher, Zachary; Mahaney, Michael C.; Hlusko, Leslea J.

2010-01-01

Many studies of primate diversity and evolution rely on dental morphology for insight into diet, behavior, and phylogenetic relationships. Consequently, variation in molar cusp size has increasingly become a phenotype of interest. In 2007 we published a quantitative genetic analysis of mandibular molar cusp size variation in baboons. Those results provided more questions than answers, as the pattern of genetic integration did not fit predictions from odontogenesis. To follow up, we expanded our study to include data from the maxillary molar cusps. Here we report on these later analyses, as well as inter-arch comparisons with the mandibular data. We analyzed variation in two-dimensional maxillary molar cusp size using data collected from a captive pedigreed breeding colony of baboons, Papio hamadryas, housed at the Southwest National Primate Research Center. These analyses show that variation in maxillary molar cusp size is heritable and sexually dimorphic. We also estimated additive genetic correlations between cusps on the same crown, homologous cusps along the tooth row, and maxillary and mandibular cusps. The pattern for maxillary molars yields genetic correlations of one between the paracone-metacone and protocone-hypocone. Bivariate analyses of cuspal homologues on adjacent teeth yield correlations that are high or not significantly different from one. Between dental arcades, the non-occluding cusps consistently yield high genetic correlations, especially the metaconid-paracone and metaconid-metacone. This pattern of genetic correlation does not immediately accord with the pattern of development and/or calcification, however these results do follow predictions that can be made from the evolutionary history of the tribosphenic molar. PMID:20034010

Genetic integration of molar cusp size variation in baboons.

PubMed

Koh, Christina; Bates, Elizabeth; Broughton, Elizabeth; Do, Nicholas T; Fletcher, Zachary; Mahaney, Michael C; Hlusko, Leslea J

2010-06-01

Many studies of primate diversity and evolution rely on dental morphology for insight into diet, behavior, and phylogenetic relationships. Consequently, variation in molar cusp size has increasingly become a phenotype of interest. In 2007 we published a quantitative genetic analysis of mandibular molar cusp size variation in baboons. Those results provided more questions than answers, as the pattern of genetic integration did not fit predictions from odontogenesis. To follow up, we expanded our study to include data from the maxillary molar cusps. Here we report on these later analyses, as well as inter-arch comparisons with the mandibular data. We analyzed variation in two-dimensional maxillary molar cusp size using data collected from a captive pedigreed breeding colony of baboons, Papio hamadryas, housed at the Southwest National Primate Research Center. These analyses show that variation in maxillary molar cusp size is heritable and sexually dimorphic. We also estimated additive genetic correlations between cusps on the same crown, homologous cusps along the tooth row, and maxillary and mandibular cusps. The pattern for maxillary molars yields genetic correlations of one between the paracone-metacone and protocone-hypocone. Bivariate analyses of cuspal homologues on adjacent teeth yield correlations that are high or not significantly different from one. Between dental arcades, the nonoccluding cusps consistently yield high genetic correlations, especially the metaconid-paracone and metaconid-metacone. This pattern of genetic correlation does not immediately accord with the pattern of development and/or calcification, however these results do follow predictions that can be made from the evolutionary history of the tribosphenic molar. Copyright 2009 Wiley-Liss, Inc.

Pantoea ananatis Genetic Diversity Analysis Reveals Limited Genomic Diversity as Well as Accessory Genes Correlated with Onion Pathogenicity.

PubMed

Stice, Shaun P; Stumpf, Spencer D; Gitaitis, Ron D; Kvitko, Brian H; Dutta, Bhabesh

2018-01-01

Pantoea ananatis is a member of the family Enterobacteriaceae and an enigmatic plant pathogen with a broad host range. Although P. ananatis strains can be aggressive on onion causing foliar necrosis and onion center rot, previous genomic analysis has shown that P. ananatis lacks the primary virulence secretion systems associated with other plant pathogens. We assessed a collection of fifty P. ananatis strains collected from Georgia over three decades to determine genetic factors that correlated with onion pathogenic potential. Previous genetic analysis studies have compared strains isolated from different hosts with varying diseases potential and isolation sources. Strains varied greatly in their pathogenic potential and aggressiveness on different cultivated Allium species like onion, leek, shallot, and chive. Using multi-locus sequence analysis (MLSA) and repetitive extragenic palindrome repeat (rep)-PCR techniques, we did not observe any correlation between onion pathogenic potential and genetic diversity among strains. Whole genome sequencing and pan-genomic analysis of a sub-set of 10 strains aided in the identification of a novel series of genetic regions, likely plasmid borne, and correlating with onion pathogenicity observed on single contigs of the genetic assemblies. We named these loci Onion Virulence Regions (OVR) A-D. The OVR loci contain genes involved in redox regulation as well as pectate lyase and rhamnogalacturonase genes. Previous studies have not identified distinct genetic loci or plasmids correlating with onion foliar pathogenicity or pathogenicity on a single host pathosystem. The lack of focus on a single host system for this phytopathgenic disease necessitates the pan-genomic analysis performed in this study.

Pantoea ananatis Genetic Diversity Analysis Reveals Limited Genomic Diversity as Well as Accessory Genes Correlated with Onion Pathogenicity

PubMed Central

Stice, Shaun P.; Stumpf, Spencer D.; Gitaitis, Ron D.; Kvitko, Brian H.; Dutta, Bhabesh

2018-01-01

Pantoea ananatis is a member of the family Enterobacteriaceae and an enigmatic plant pathogen with a broad host range. Although P. ananatis strains can be aggressive on onion causing foliar necrosis and onion center rot, previous genomic analysis has shown that P. ananatis lacks the primary virulence secretion systems associated with other plant pathogens. We assessed a collection of fifty P. ananatis strains collected from Georgia over three decades to determine genetic factors that correlated with onion pathogenic potential. Previous genetic analysis studies have compared strains isolated from different hosts with varying diseases potential and isolation sources. Strains varied greatly in their pathogenic potential and aggressiveness on different cultivated Allium species like onion, leek, shallot, and chive. Using multi-locus sequence analysis (MLSA) and repetitive extragenic palindrome repeat (rep)-PCR techniques, we did not observe any correlation between onion pathogenic potential and genetic diversity among strains. Whole genome sequencing and pan-genomic analysis of a sub-set of 10 strains aided in the identification of a novel series of genetic regions, likely plasmid borne, and correlating with onion pathogenicity observed on single contigs of the genetic assemblies. We named these loci Onion Virulence Regions (OVR) A-D. The OVR loci contain genes involved in redox regulation as well as pectate lyase and rhamnogalacturonase genes. Previous studies have not identified distinct genetic loci or plasmids correlating with onion foliar pathogenicity or pathogenicity on a single host pathosystem. The lack of focus on a single host system for this phytopathgenic disease necessitates the pan-genomic analysis performed in this study. PMID:29491851

A combined analysis of genetically correlated traits identifies 187 loci and a role for neurogenesis and myelination in intelligence.

PubMed

Hill, W D; Marioni, R E; Maghzian, O; Ritchie, S J; Hagenaars, S P; McIntosh, A M; Gale, C R; Davies, G; Deary, I J

2018-01-11

Intelligence, or general cognitive function, is phenotypically and genetically correlated with many traits, including a wide range of physical, and mental health variables. Education is strongly genetically correlated with intelligence (r g  = 0.70). We used these findings as foundations for our use of a novel approach-multi-trait analysis of genome-wide association studies (MTAG; Turley et al. 2017)-to combine two large genome-wide association studies (GWASs) of education and intelligence, increasing statistical power and resulting in the largest GWAS of intelligence yet reported. Our study had four goals: first, to facilitate the discovery of new genetic loci associated with intelligence; second, to add to our understanding of the biology of intelligence differences; third, to examine whether combining genetically correlated traits in this way produces results consistent with the primary phenotype of intelligence; and, finally, to test how well this new meta-analytic data sample on intelligence predicts phenotypic intelligence in an independent sample. By combining datasets using MTAG, our functional sample size increased from 199,242 participants to 248,482. We found 187 independent loci associated with intelligence, implicating 538 genes, using both SNP-based and gene-based GWAS. We found evidence that neurogenesis and myelination-as well as genes expressed in the synapse, and those involved in the regulation of the nervous system-may explain some of the biological differences in intelligence. The results of our combined analysis demonstrated the same pattern of genetic correlations as those from previous GWASs of intelligence, providing support for the meta-analysis of these genetically-related phenotypes.

How do emotional restrictions affect the use of humor? A behavior genetic analysis of alexithymia and humor styles.

PubMed

Atkinson, Breanna E; Lipton, Debra; Baughman, Holly M; Schermer, Julie A; Harris, Juliette; Vernon, Philip A

2015-04-01

This article reports the first behavioral genetic study of relationships between alexithymia and four styles of humor: affiliative, self-enhancing, self-defeating, and aggressive. A total of 509 MZ pairs and 264 DZ pairs of twins completed the Toronto Alexithymia Scale-20 (TAS-20) and the Humor Styles Questionnaire (HSQ). Consistent with our predictions, alexithymia correlated negatively with affiliative and self-enhancing humor and positively with self-defeating and aggressive humor. All but one of the 16 phenotypic correlations that we report are significant at the 0.01 level. Also consistent with our predictions, the phenotypic correlations between alexithymia and humor styles were primarily attributable to correlated genetic factors and to a lesser extent to correlated non-shared environmental factors. Correlated shared environmental factors had no significant effect. Implications and limitations of this study are discussed.

Predictive accuracy of combined genetic and environmental risk scores.

PubMed

Dudbridge, Frank; Pashayan, Nora; Yang, Jian

2018-02-01

The substantial heritability of most complex diseases suggests that genetic data could provide useful risk prediction. To date the performance of genetic risk scores has fallen short of the potential implied by heritability, but this can be explained by insufficient sample sizes for estimating highly polygenic models. When risk predictors already exist based on environment or lifestyle, two key questions are to what extent can they be improved by adding genetic information, and what is the ultimate potential of combined genetic and environmental risk scores? Here, we extend previous work on the predictive accuracy of polygenic scores to allow for an environmental score that may be correlated with the polygenic score, for example when the environmental factors mediate the genetic risk. We derive common measures of predictive accuracy and improvement as functions of the training sample size, chip heritabilities of disease and environmental score, and genetic correlation between disease and environmental risk factors. We consider simple addition of the two scores and a weighted sum that accounts for their correlation. Using examples from studies of cardiovascular disease and breast cancer, we show that improvements in discrimination are generally small but reasonable degrees of reclassification could be obtained with current sample sizes. Correlation between genetic and environmental scores has only minor effects on numerical results in realistic scenarios. In the longer term, as the accuracy of polygenic scores improves they will come to dominate the predictive accuracy compared to environmental scores. © 2017 WILEY PERIODICALS, INC.

Predictive accuracy of combined genetic and environmental risk scores

PubMed Central

Pashayan, Nora; Yang, Jian

2017-01-01

ABSTRACT The substantial heritability of most complex diseases suggests that genetic data could provide useful risk prediction. To date the performance of genetic risk scores has fallen short of the potential implied by heritability, but this can be explained by insufficient sample sizes for estimating highly polygenic models. When risk predictors already exist based on environment or lifestyle, two key questions are to what extent can they be improved by adding genetic information, and what is the ultimate potential of combined genetic and environmental risk scores? Here, we extend previous work on the predictive accuracy of polygenic scores to allow for an environmental score that may be correlated with the polygenic score, for example when the environmental factors mediate the genetic risk. We derive common measures of predictive accuracy and improvement as functions of the training sample size, chip heritabilities of disease and environmental score, and genetic correlation between disease and environmental risk factors. We consider simple addition of the two scores and a weighted sum that accounts for their correlation. Using examples from studies of cardiovascular disease and breast cancer, we show that improvements in discrimination are generally small but reasonable degrees of reclassification could be obtained with current sample sizes. Correlation between genetic and environmental scores has only minor effects on numerical results in realistic scenarios. In the longer term, as the accuracy of polygenic scores improves they will come to dominate the predictive accuracy compared to environmental scores. PMID:29178508

Prevalence, heritability and genetic correlations of congenital sensorineural deafness and pigmentation phenotypes in the Border Collie.

PubMed

De Risio, Luisa; Lewis, Tom; Freeman, Julia; de Stefani, Alberta; Matiasek, Lara; Blott, Sarah

2011-06-01

The objectives of this study were to estimate prevalence, heritability and genetic correlations of congenital sensorineural deafness (CSD) and pigmentation phenotypes in the Border Collie. Entire litters of Border Collies that presented to the Animal Health Trust (1994-2008) for assessment of hearing status by brain stem auditory evoked response (BAER) at 4-10 weeks of age were included. Heritability and genetic correlations were estimated using residual maximum likelihood (REML). Of 4143 puppies that met the inclusion criteria, 97.6% had normal hearing status, 2.0% were unilaterally deaf and 0.4% were bilaterally deaf. Heritability of deafness as a trichotomous trait (normal/unilaterally deaf/bilaterally deaf) was estimated at 0.42 using multivariate analysis. Genetic correlations of deafness with iris colour and merle coat colour were 0.58 and 0.26, respectively. These results indicate that there is a significant genetic effect on CSD in Border Collies and that some of the genes determining deafness also influence pigmentation phenotypes. Copyright © 2010 Elsevier Ltd. All rights reserved.

Genetic parameters for wool traits, live weight, and ultrasound carcass traits in Merino sheep.

PubMed

Mortimer, S I; Hatcher, S; Fogarty, N M; van der Werf, J H J; Brown, D J; Swan, A A; Greeff, J C; Refshauge, G; Edwards, J E Hocking; Gaunt, G M

2017-05-01

Genetic correlations between 29 wool production and quality traits and live weight and ultrasound fat depth (FAT) and eye muscle depth (EMD) traits were estimated from the Information Nucleus (IN). The IN comprised 8 genetically linked flocks managed across a range of Australian sheep production environments. The data were from a maximum of 9,135 progeny born over 5 yr from 184 Merino sires and 4,614 Merino dams. The wool traits included records for yearling and adult fleece weight, fiber diameter (FD), staple length (SL), fiber diameter CV (FDCV), scoured color, and visual scores for breech and body wrinkle. We found high heritability for the major yearling wool production traits and some wool quality traits, whereas other wool quality traits, wool color, and visual traits were moderately heritable. The estimates of heritability for live weight generally increased with age as maternal effects declined. Estimates of heritability for the ultrasound traits were also higher when measured at yearling age rather than at postweaning age. The genetic correlations for fleece weight with live weights were positive (favorable) and moderate (approximately 0.5 ± 0.1), whereas those with FD were approximately 0.3 (unfavorable). The other wool traits had lower genetic correlations with the live weights. The genetic correlations for FAT and EMD with FD and SL were positive and low, with FDCV low to moderate negative, but variable with wool weight and negligible for the other wool traits. The genetic correlations for FAT and EMD with postweaning weight were positive and high (0.61 ± 0.18 to 0.75 ± 0.14) but were generally moderate with weights at other ages. Selection for increased live weight will result in a moderate correlated increase in wool weight as well as favorable reductions in breech cover and wrinkle, along with some unfavorable increases in FD and wool yellowness but little impact on other wool traits. The ultrasound meat traits, FAT and EMD, were highly positively genetically correlated (0.8), and selection to increase them would result in a small unfavorable correlated increase in FD, moderately favorable reductions in breech cover and wrinkle, but equivocal or negligible changes in other wool traits. The estimated parameters provide the basis for calculation of more accurate Australian Sheep Breeding Values and selection indexes that combine wool and meat objectives in Merino breeding programs.

Land, language, and loci: mtDNA in Native Americans and the genetic history of Peru.

PubMed

Lewis, Cecil M; Tito, Raúl Y; Lizárraga, Beatriz; Stone, Anne C

2005-07-01

Despite a long history of complex societies and despite extensive present-day linguistic and ethnic diversity, relatively few populations in Peru have been sampled for population genetic investigations. In order to address questions about the relationships between South American populations and about the extent of correlation between genetic distance, language, and geography in the region, mitochondrial DNA (mtDNA) hypervariable region I sequences and mtDNA haplogroup markers were examined in 33 individuals from the state of Ancash, Peru. These sequences were compared to those from 19 American Indian populations using diversity estimates, AMOVA tests, mismatch distributions, a multidimensional scaling plot, and regressions. The results show correlations between genetics, linguistics, and geographical affinities, with stronger correlations between genetics and language. Additionally, the results suggest a pattern of differential gene flow and drift in western vs. eastern South America, supporting previous mtDNA and Y chromosome investigations. (c) 2004 Wiley-Liss, Inc

Working Memory and Parent-Rated Components of Attention in Middle Childhood: A Behavioral Genetic Study

PubMed Central

Deater-Deckard, Kirby; Cutting, Laurie; Thompson, Lee A.; Petrill, Stephen A.

2012-01-01

The purpose of the current study was to investigate potential genetic and environmental correlations between working memory and three behavioral aspects of the attention network (i.e., executive, alerting, and orienting) using a twin design. Data were from 90 monozygotic (39% male) and 112 same-sex dizygotic (41% male) twins. Individual differences in working memory performance (digit span) and parent-rated measures of executive, alerting, and orienting attention included modest to moderate genetic variance, modest shared environmental variance, and modest to moderate nonshared environmental variance. As hypothesized, working memory performance was correlated with executive and alerting attention, but not orienting attention. The correlation between working memory, executive attention, and alerting attention was completely accounted for by overlapping genetic covariance, suggesting a common genetic mechanism or mechanisms underlying the links between working memory and certain parent-rated indicators of attentive behavior. PMID:21948215

Environmental heterogeneity explains the genetic structure of Continental and Mediterranean populations of Fraxinus angustifolia Vahl.

PubMed

Temunović, Martina; Franjić, Jozo; Satovic, Zlatko; Grgurev, Marin; Frascaria-Lacoste, Nathalie; Fernández-Manjarrés, Juan F

2012-01-01

Tree species with wide distributions often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in a wind-pollinated Mediterranean tree species, Fraxinus angustifolia Vahl, within a recognised glacial refugium in Croatia. We sampled 11 populations from environmentally divergent habitats within the Continental and Mediterranean biogeographical regions. We combined genetic data analyses based on nuclear microsatellite loci, multivariate statistics on environmental data and ecological niche modelling (ENM). We identified a geographic structure with a high genetic diversity and low differentiation in the Continental region, which contrasted with the significantly lower genetic diversity and higher population divergence in the Mediterranean region. The positive and significant correlation between environmental and genetic distances after controlling for geographic distance suggests an important influence of ecological divergence of the sites in shaping genetic variation. The ENM provided support for niche differentiation between the populations from the Continental and Mediterranean regions, suggesting that contemporary populations may represent two divergent ecotypes. Ecotype differentiation was also supported by multivariate environmental and genetic distance analyses. Our results suggest that despite extensive gene flow in continental areas, long-term stability of heterogeneous environments have likely promoted genetic divergence of ashes in this region and can explain the present-day genetic variation patterns of these ancient populations.

Environmental Heterogeneity Explains the Genetic Structure of Continental and Mediterranean Populations of Fraxinus angustifolia Vahl

PubMed Central

Temunović, Martina; Franjić, Jozo; Satovic, Zlatko; Grgurev, Marin; Frascaria-Lacoste, Nathalie; Fernández-Manjarrés, Juan F.

2012-01-01

Tree species with wide distributions often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in a wind-pollinated Mediterranean tree species, Fraxinus angustifolia Vahl, within a recognised glacial refugium in Croatia. We sampled 11 populations from environmentally divergent habitats within the Continental and Mediterranean biogeographical regions. We combined genetic data analyses based on nuclear microsatellite loci, multivariate statistics on environmental data and ecological niche modelling (ENM). We identified a geographic structure with a high genetic diversity and low differentiation in the Continental region, which contrasted with the significantly lower genetic diversity and higher population divergence in the Mediterranean region. The positive and significant correlation between environmental and genetic distances after controlling for geographic distance suggests an important influence of ecological divergence of the sites in shaping genetic variation. The ENM provided support for niche differentiation between the populations from the Continental and Mediterranean regions, suggesting that contemporary populations may represent two divergent ecotypes. Ecotype differentiation was also supported by multivariate environmental and genetic distance analyses. Our results suggest that despite extensive gene flow in continental areas, long-term stability of heterogeneous environments have likely promoted genetic divergence of ashes in this region and can explain the present-day genetic variation patterns of these ancient populations. PMID:22905171

Searching for an environmental effect of parental alcoholism on offspring alcohol use disorder: A genetically-informed study of children of alcoholics

PubMed Central

Slutske, Wendy S.; D’Onofrio, Brian M.; Turkheimer, Eric; Emery, Robert E.; Harden, K. Paige; Heath, Andrew C.; Martin, Nicholas G.

2009-01-01

The children-of-twins design was used to isolate a potentially causal environmental impact of having an alcoholic parent on offspring alcohol use disorder by examining whether the children of alcoholics were at a higher risk for alcohol use disorders than the children of non-alcoholic parents even after correlated familial factors were controlled. Participants were 1,224 male and female twins from 836 twin pairs selected from the Australian Twin Registry, 2,334 of their 18–39 year-old offspring, and 983 spouses of the twins. Lifetime histories of DSM-IV alcohol use disorders were obtained by structured psychiatric telephone interviews conducted individually with each of the family members. Comparisons of the offspring of twins discordant for alcoholism indicated that there was no longer a statistically significant difference between the children of alcoholics and the children of non-alcoholics after genetic and family environmental factors correlated with having an alcoholic parent were controlled. The results of this study suggest that the direct causal effect of being exposed to an alcoholic parent on offspring alcohol use disorder is modest at best. PMID:18729607

Stress-related hormones and genetic diversity in sea otters (Enhydra lutris)

USGS Publications Warehouse

Larson, Shawn E.; Monson, Daniel H.; Ballachey, Brenda E.; Jameson, Ronald J.; Wasser, S.K.

2009-01-01

Sea otters (Enhydra lutris) once ranged throughout the coastal regions of the north Pacific, but were extirpated throughout their range during the fur trade of the 18th and 19th centuries, leaving only small, widely scattered, remnant populations. All extant sea otter populations are believed to have experienced a population bottleneck and thus have lost genetic variation. Populations that undergo severe population reduction and associated inbreeding may suffer from a general reduction in fitness termed inbreeding depression. Inbreeding depression may result in decreased testosterone levels in males, and reduced ability to respond to stressful stimuli associated with an increase in the stress-related adrenal glucocorticoid hormones, cortisol and corticosterone. We investigated correlations of testosterone, cortisol, and corticosterone with genetic diversity in sea otters from five populations. We found a significant negative correlation between genetic diversity and both mean population-level (r2= 0.27, P < 0.001) and individual-level (r2= 0.54, P < 0.001) corticosterone values, as well as a negative correlation between genetic diversity and cortisol at the individual level (r2= 0.17, P= 0.04). No relationship was found between genetic diversity and testosterone (P= 0.57). The strength of the correlations, especially with corticosterone, suggests potential negative consequences for overall population health, particularly for populations with the lowest genetic diversity.

Age at first use and later substance use disorder: Shared genetic and environmental pathways for nicotine, alcohol, and cannabis.

PubMed

Richmond-Rakerd, Leah S; Slutske, Wendy S; Lynskey, Michael T; Agrawal, Arpana; Madden, Pamela A F; Bucholz, Kathleen K; Heath, Andrew C; Statham, Dixie J; Martin, Nicholas G

2016-10-01

Behavioral genetic studies have provided insights into why early substance use initiation is associated with increased risk for disorder. Few genetically informative studies, however, have operationalized initiation as the timing of first use and simultaneously modeled the timing of initiation and problematic use of multiple substances. Such research can help capture the risk associated with early initiation and determine the extent to which genetic and environmental risk generalizes across substances. This study utilized a behavior genetic approach to examine the relation between the age of substance use initiation and symptoms of substance use disorder. Participants were 7,285 monozygotic and dizygotic twins (40% male, mean age at interview = 30.6 years) from the Australian Twin Registry who reported on their ages of tobacco, alcohol, and cannabis initiation and symptoms of Diagnostic and Statistical Manual of Mental Disorders (4th ed., DSM-IV) nicotine dependence, alcohol use disorder, and cannabis use disorder. Biometric modeling was conducted to (a) determine the structure of genetic and environmental influences on initiation and disorder and (b) examine their genetic and environmental overlap. The latent structure of initiation differed across men and women. The familial covariance between initiation and disorder was genetic among men and genetic and environmental among women, suggesting that the relation between first substance use and disorder is partly explained by a shared liability. After accounting for familial overlap, significant unique environmental correlations were observed, indicating that the age of initiation of multiple drugs may directly increase risk for substance-related problems. Results support the utility of conceptualizing initiation in terms of age and of adopting a multivariate approach. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Compensatory T-Cell Regulation in Unaffected Relatives of SLE Patients, and Opposite IL-2/CD25-Mediated Effects Suggested by Coreferentiality Modeling

PubMed Central

Fesel, Constantin; Barreto, Marta; Ferreira, Ricardo C.; Costa, Nuno; Venda, Lara L.; Pereira, Clara; Carvalho, Claudia; Morães-Fontes, Maria Francisca; Ferreira, Carlos M.; Vasconcelos, Carlos; Viana, João F.; Santos, Eugenia; Martins, Berta; Demengeot, Jocelyne; Vicente, Astrid M.

2012-01-01

In human systemic lupus erythematosus (SLE), diverse autoantibodies accumulate over years before disease manifestation. Unaffected relatives of SLE patients frequently share a sustained production of autoantibodies with indiscriminable specificity, usually without ever acquiring the disease. We studied relations of IgG autoantibody profiles and peripheral blood activated regulatory T-cells (aTregs), represented by CD4+CD25bright T-cells that were regularly 70–90% Foxp3+. We found consistent positive correlations of broad-range as well as specific SLE-associated IgG with aTreg frequencies within unaffected relatives, but not patients or unrelated controls. Our interpretation: unaffected relatives with shared genetic factors compensated pathogenic effects by aTregs engaged in parallel with the individual autoantibody production. To study this further, we applied a novel analytic approach named coreferentiality that tests the indirect relatedness of parameters in respect to multivariate phenotype data. Results show that independently of their direct correlation, aTreg frequencies and specific SLE-associated IgG were likely functionally related in unaffected relatives: they significantly parallelled each other in their relations to broad-range immunoblot autoantibody profiles. In unaffected relatives, we also found coreferential effects of genetic variation in the loci encoding IL-2 and CD25. A model of CD25 functional genetic effects constructed by coreferentiality maximization suggests that IL-2-CD25 interaction, likely stimulating aTregs in unaffected relatives, had an opposed effect in SLE patients, presumably triggering primarily T-effector cells in this group. Coreferentiality modeling as we do it here could also be useful in other contexts, particularly to explore combined functional genetic effects. PMID:22479496

Correlates of male fitness in captive zebra finches--a comparison of methods to disentangle genetic and environmental effects.

PubMed

Bolund, Elisabeth; Schielzeth, Holger; Forstmeier, Wolfgang

2011-11-08

It is a common observation in evolutionary studies that larger, more ornamented or earlier breeding individuals have higher fitness, but that body size, ornamentation or breeding time does not change despite of sometimes substantial heritability for these traits. A possible explanation for this is that these traits do not causally affect fitness, but rather happen to be indirectly correlated with fitness via unmeasured non-heritable aspects of condition (e.g. undernourished offspring grow small and have low fitness as adults due to poor health). Whether this explanation applies to a specific case can be examined by decomposing the covariance between trait and fitness into its genetic and environmental components using pedigree-based animal models. We here examine different methods of doing this for a captive zebra finch population where male fitness was measured in communal aviaries in relation to three phenotypic traits (tarsus length, beak colour and song rate). Our case study illustrates how methods that regress fitness over breeding values for phenotypic traits yield biased estimates as well as anti-conservative standard errors. Hence, it is necessary to estimate the genetic and environmental covariances between trait and fitness directly from a bivariate model. This method, however, is very demanding in terms of sample sizes. In our study parameter estimates of selection gradients for tarsus were consistent with the hypothesis of environmentally induced bias (βA=0.035±0.25 (SE), βE=0.57±0.28 (SE)), yet this differences between genetic and environmental selection gradients falls short of statistical significance. To examine the generality of the idea that phenotypic selection gradients for certain traits (like size) are consistently upwardly biased by environmental covariance a meta-analysis across study systems will be needed.

Correlates of male fitness in captive zebra finches - a comparison of methods to disentangle genetic and environmental effects

PubMed Central

2011-01-01

Backgound It is a common observation in evolutionary studies that larger, more ornamented or earlier breeding individuals have higher fitness, but that body size, ornamentation or breeding time does not change despite of sometimes substantial heritability for these traits. A possible explanation for this is that these traits do not causally affect fitness, but rather happen to be indirectly correlated with fitness via unmeasured non-heritable aspects of condition (e.g. undernourished offspring grow small and have low fitness as adults due to poor health). Whether this explanation applies to a specific case can be examined by decomposing the covariance between trait and fitness into its genetic and environmental components using pedigree-based animal models. We here examine different methods of doing this for a captive zebra finch population where male fitness was measured in communal aviaries in relation to three phenotypic traits (tarsus length, beak colour and song rate). Results Our case study illustrates how methods that regress fitness over breeding values for phenotypic traits yield biased estimates as well as anti-conservative standard errors. Hence, it is necessary to estimate the genetic and environmental covariances between trait and fitness directly from a bivariate model. This method, however, is very demanding in terms of sample sizes. In our study parameter estimates of selection gradients for tarsus were consistent with the hypothesis of environmentally induced bias (βA = 0.035 ± 0.25 (SE), βE = 0.57 ± 0.28 (SE)), yet this differences between genetic and environmental selection gradients falls short of statistical significance. Conclusions To examine the generality of the idea that phenotypic selection gradients for certain traits (like size) are consistently upwardly biased by environmental covariance a meta-analysis across study systems will be needed. PMID:22067225

QSAR modeling for anti-human African trypanosomiasis activity of substituted 2-Phenylimidazopyridines

NASA Astrophysics Data System (ADS)

Masand, Vijay H.; El-Sayed, Nahed N. E.; Mahajan, Devidas T.; Mercader, Andrew G.; Alafeefy, Ahmed M.; Shibi, I. G.

2017-02-01

In the present work, sixty substituted 2-Phenylimidazopyridines previously reported with potent anti-human African trypanosomiasis (HAT) activity were selected to build genetic algorithm (GA) based QSAR models to determine the structural features that have significant correlation with the activity. Multiple QSAR models were built using easily interpretable descriptors that are directly associated with the presence or the absence of a structural scaffold, or a specific atom. All the QSAR models have been thoroughly validated according to the OECD principles. All the QSAR models are statistically very robust (R2 = 0.80-0.87) with high external predictive ability (CCCex = 0.81-0.92). The QSAR analysis reveals that the HAT activity has good correlation with the presence of five membered rings in the molecule.

Lessons from Digestive-Tract Symbioses Between Bacteria and Invertebrates.

PubMed

Graf, Joerg

2016-09-08

In most animals, digestive tracts harbor the greatest number of bacteria in the animal that contribute to its health: by aiding in the digestion of nutrients, provisioning essential nutrients and protecting against colonization by pathogens. Invertebrates have been used to enhance our understanding of metabolic processes and microbe-host interactions owing to experimental advantages. This review describes how advances in DNA sequencing technologies have dramatically altered how researchers investigate microbe-host interactions, including 16S rRNA gene surveys, metagenome experiments, and metatranscriptome studies. Advantages and challenges of each of these approaches are described herein. Hypotheses generated through omics studies can be directly tested using site-directed mutagenesis, and findings from transposon studies and site-directed experiments are presented. Finally, unique structural aspects of invertebrate digestive tracts that contribute to symbiont specificity are presented. The combination of omics approaches with genetics and microscopy allows researchers to move beyond correlations to identify conserved mechanisms of microbe-host interactions.

Genetic parameters across lactation for feed intake, fat- and protein-corrected milk, and liveweight in first-parity Holstein cattle.

PubMed

Manzanilla Pech, C I V; Veerkamp, R F; Calus, M P L; Zom, R; van Knegsel, A; Pryce, J E; De Haas, Y

2014-09-01

Breeding values for dry matter intake (DMI) are important to optimize dairy cattle breeding goals for feed efficiency. However, generally, only small data sets are available for feed intake, due to the cost and difficulty of measuring DMI, which makes understanding the genetic associations between traits across lactation difficult, let alone the possibility for selection of breeding animals. However, estimating national breeding values through cheaper and more easily measured correlated traits, such as milk yield and liveweight (LW), could be a first step to predict DMI. Combining DMI data across historical nutritional experiments might help to expand the data sets. Therefore, the objective was to estimate genetic parameters for DMI, fat- and protein-corrected milk (FPCM) yield, and LW across the entire first lactation using a relatively large data set combining experimental data across the Netherlands. A total of 30,483 weekly records for DMI, 49,977 for FPCM yield, and 31,956 for LW were available from 2,283 Dutch Holstein-Friesian first-parity cows between 1990 and 2011. Heritabilities, covariance components, and genetic correlations were estimated using a multivariate random regression model. The model included an effect for year-season of calving, and polynomials for age of cow at calving and days in milk (DIM). The random effects were experimental treatment, year-month of measurement, and the additive genetic, permanent environmental, and residual term. Additive genetic and permanent environmental effects were modeled using a third-order orthogonal polynomial. Estimated heritabilities ranged from 0.21 to 0.40 for DMI, from 0.20 to 0.43 for FPCM yield, and from 0.25 to 0.48 for LW across DIM. Genetic correlations between DMI at different DIM were relatively low during early and late lactation, compared with mid lactation. The genetic correlations between DMI and FPCM yield varied across DIM. This correlation was negative (up to -0.5) between FPCM yield in early lactation and DMI across the entire lactation, but highly positive (above 0.8) when both traits were in mid lactation. The correlation between DMI and LW was 0.6 during early lactation, but decreased to 0.4 during mid lactation. The highest correlations between FPCM yield and LW (0.3-0.5) were estimated during mid lactation. However, the genetic correlations between DMI and either FPCM yield or LW were not symmetric across DIM, and differed depending on which trait was measured first. The results of our study are useful to understand the genetic relationship of DMI, FPCM yield, and LW on specific days across lactation. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

[A Study of the Relationship Among Genetic Distances, NIR Spectra Distances, and NIR-Based Identification Model Performance of the Seeds of Maize Iinbred Lines].

PubMed

Liu, Xu; Jia, Shi-qiang; Wang, Chun-ying; Liu, Zhe; Gu, Jian-cheng; Zhai, Wei; Li, Shao-ming; Zhang, Xiao-dong; Zhu, De-hai; Huang, Hua-jun; An, Dong

2015-09-01

This paper explored the relationship among genetic distances, NIR spectra distances and NIR-based identification model performance of the seeds of maize inbred lines. Using 3 groups (total 15 pairs) of maize inbred lines whose genetic distaches are different as experimental materials, we calculates the genetic distance between these seeds with SSR markers and uses Euclidean distance between distributed center points of maize NIR spectrum in the PCA space as the distances of NIR spectrum. BPR method is used to build identification model of inbred lines and the identification accuracy is used as a measure of model identification performance. The results showed that, the correlation of genetic distance and spectra distancesis 0.9868, and it has a correlation of 0.9110 with the identification accuracy, which is highly correlated. This means near-Infrared spectrum of seedscan reflect genetic relationship of maize inbred lines. The smaller the genetic distance, the smaller the distance of spectrum, the poorer ability of model to identify. In practical application, near infrared spectrum analysis technology has the potential to be used to analyze maize inbred genetic relations, contributing much to genetic breeding, identification of species, purity sorting and so on. What's more, when creating a NIR-based identification model, the impact of the maize inbred lines which have closer genetic relationship should be fully considered.

Genetic parameters for body condition score, body weight, milk yield, and fertility estimated using random regression models.

PubMed

Berry, D P; Buckley, F; Dillon, P; Evans, R D; Rath, M; Veerkamp, R F

2003-11-01

Genetic (co)variances between body condition score (BCS), body weight (BW), milk yield, and fertility were estimated using a random regression animal model extended to multivariate analysis. The data analyzed included 81,313 BCS observations, 91,937 BW observations, and 100,458 milk test-day yields from 8725 multiparous Holstein-Friesian cows. A cubic random regression was sufficient to model the changing genetic variances for BCS, BW, and milk across different days in milk. The genetic correlations between BCS and fertility changed little over the lactation; genetic correlations between BCS and interval to first service and between BCS and pregnancy rate to first service varied from -0.47 to -0.31, and from 0.15 to 0.38, respectively. This suggests that maximum genetic gain in fertility from indirect selection on BCS should be based on measurements taken in midlactation when the genetic variance for BCS is largest. Selection for increased BW resulted in shorter intervals to first service, but more services and poorer pregnancy rates; genetic correlations between BW and pregnancy rate to first service varied from -0.52 to -0.45. Genetic selection for higher lactation milk yield alone through selection on increased milk yield in early lactation is likely to have a more deleterious effect on genetic merit for fertility than selection on higher milk yield in late lactation.

Evolutionary response when selection and genetic variation covary across environments.

PubMed

Wood, Corlett W; Brodie, Edmund D

2016-10-01

Although models of evolution usually assume that the strength of selection on a trait and the expression of genetic variation in that trait are independent, whenever the same ecological factor impacts both parameters, a correlation between the two may arise that accelerates trait evolution in some environments and slows it in others. Here, we address the evolutionary consequences and ecological causes of a correlation between selection and expressed genetic variation. Using a simple analytical model, we show that the correlation has a modest effect on the mean evolutionary response and a large effect on its variance, increasing among-population or among-generation variation in the response when positive, and diminishing variation when negative. We performed a literature review to identify the ecological factors that influence selection and expressed genetic variation across traits. We found that some factors - temperature and competition - are unlikely to generate the correlation because they affected one parameter more than the other, and identified others - most notably, environmental novelty - that merit further investigation because little is known about their impact on one of the two parameters. We argue that the correlation between selection and genetic variation deserves attention alongside other factors that promote or constrain evolution in heterogeneous landscapes. © 2016 John Wiley & Sons Ltd/CNRS.

The correlation between reading and mathematics ability at age twelve has a substantial genetic component.

PubMed

Davis, Oliver S P; Band, Gavin; Pirinen, Matti; Haworth, Claire M A; Meaburn, Emma L; Kovas, Yulia; Harlaar, Nicole; Docherty, Sophia J; Hanscombe, Ken B; Trzaskowski, Maciej; Curtis, Charles J C; Strange, Amy; Freeman, Colin; Bellenguez, Céline; Su, Zhan; Pearson, Richard; Vukcevic, Damjan; Langford, Cordelia; Deloukas, Panos; Hunt, Sarah; Gray, Emma; Dronov, Serge; Potter, Simon C; Tashakkori-Ghanbaria, Avazeh; Edkins, Sarah; Bumpstead, Suzannah J; Blackwell, Jenefer M; Bramon, Elvira; Brown, Matthew A; Casas, Juan P; Corvin, Aiden; Duncanson, Audrey; Jankowski, Janusz A Z; Markus, Hugh S; Mathew, Christopher G; Palmer, Colin N A; Rautanen, Anna; Sawcer, Stephen J; Trembath, Richard C; Viswanathan, Ananth C; Wood, Nicholas W; Barroso, Ines; Peltonen, Leena; Dale, Philip S; Petrill, Stephen A; Schalkwyk, Leonard S; Craig, Ian W; Lewis, Cathryn M; Price, Thomas S; Donnelly, Peter; Plomin, Robert; Spencer, Chris C A

2014-07-08

Dissecting how genetic and environmental influences impact on learning is helpful for maximizing numeracy and literacy. Here we show, using twin and genome-wide analysis, that there is a substantial genetic component to children's ability in reading and mathematics, and estimate that around one half of the observed correlation in these traits is due to shared genetic effects (so-called Generalist Genes). Thus, our results highlight the potential role of the learning environment in contributing to differences in a child's cognitive abilities at age twelve.

Health care providers and direct-to-consumer access and advertising of genetic testing in the United States

PubMed Central

2011-01-01

Marketing pressures, regulatory policies, clinical guidelines, and consumer demand all affect health care providers' knowledge and use of health-related genetic tests that are sold and/or advertised to consumers. In addition, clinical guidelines, regulatory policies, and educational efforts are needed to promote the informed use of genetic tests that are sold and advertised to consumers and health care providers. A shift in culture regarding the regulation of genetic tests that are sold directly to consumers is suggested: by recent actions taken by the US Food and Drug Administration (FDA), including letters sent to direct-to-consumer (DTC) genetic testing companies stating that their tests meet the definition of medical devices; by public meetings held by the FDA to discuss laboratory developed tests; and by the convening of the Molecular and Clinical Genetics Panel to gather input on scientific issues concerning DTC genetic tests that make medical claims. This review provides a brief overview of DTC advertising and the regulation of pharmaceuticals and genetic tests in the United States. It highlights recent changes in the regulatory culture regarding genetic tests that are sold to consumers, and discusses the impact on health care providers of selling and advertising genetic tests directly to consumers. PMID:22204616

Health care providers and direct-to-consumer access and advertising of genetic testing in the United States.

PubMed

Myers, Melanie F

2011-12-28

Marketing pressures, regulatory policies, clinical guidelines, and consumer demand all affect health care providers' knowledge and use of health-related genetic tests that are sold and/or advertised to consumers. In addition, clinical guidelines, regulatory policies, and educational efforts are needed to promote the informed use of genetic tests that are sold and advertised to consumers and health care providers. A shift in culture regarding the regulation of genetic tests that are sold directly to consumers is suggested: by recent actions taken by the US Food and Drug Administration (FDA), including letters sent to direct-to-consumer (DTC) genetic testing companies stating that their tests meet the definition of medical devices; by public meetings held by the FDA to discuss laboratory developed tests; and by the convening of the Molecular and Clinical Genetics Panel to gather input on scientific issues concerning DTC genetic tests that make medical claims. This review provides a brief overview of DTC advertising and the regulation of pharmaceuticals and genetic tests in the United States. It highlights recent changes in the regulatory culture regarding genetic tests that are sold to consumers, and discusses the impact on health care providers of selling and advertising genetic tests directly to consumers.

Consumers' views of direct-to-consumer genetic information.

PubMed

McBride, Colleen M; Wade, Christopher H; Kaphingst, Kimberly A

2010-01-01

In this report, we describe the evolution and types of genetic information provided directly to consumers, discuss potential advantages and disadvantages of these products, and review research evaluating consumer responses to direct-to-consumer (DTC) genetic testing. The available evidence to date has focused on predictive tests and does not suggest that individuals, health care providers, or health care systems have been harmed by a DTC provision of genetic information. An understanding of consumer responses to susceptibility tests has lagged behind. The Multiplex Initiative is presented as a case study of research to understand consumers' responses to DTC susceptibility tests. Three priority areas are recommended for accelerated research activities to inform public policy regarding DTC genetic information: (a) exploring consumer's long-term responses to DTC genetic testing on a comprehensive set of outcomes, (b) evaluating optimal services to support decision making about genetic testing, and (c) evaluating best practices in promoting genetic competencies among health providers.

Genetic architecture of the Delis-Kaplan Executive Function System Trail Making Test: evidence for distinct genetic influences on executive function.

PubMed

Vasilopoulos, Terrie; Franz, Carol E; Panizzon, Matthew S; Xian, Hong; Grant, Michael D; Lyons, Michael J; Toomey, Rosemary; Jacobson, Kristen C; Kremen, William S

2012-03-01

To examine how genes and environments contribute to relationships among Trail Making Test (TMT) conditions and the extent to which these conditions have unique genetic and environmental influences. Participants included 1,237 middle-aged male twins from the Vietnam Era Twin Study of Aging. The Delis-Kaplan Executive Function System TMT included visual searching, number and letter sequencing, and set-shifting components. Phenotypic correlations among TMT conditions ranged from 0.29 to 0.60, and genes accounted for the majority (58-84%) of each correlation. Overall heritability ranged from 0.34 to 0.62 across conditions. Phenotypic factor analysis suggested a single factor. In contrast, genetic models revealed a single common genetic factor but also unique genetic influences separate from the common factor. Genetic variance (i.e., heritability) of number and letter sequencing was completely explained by the common genetic factor while unique genetic influences separate from the common factor accounted for 57% and 21% of the heritabilities of visual search and set shifting, respectively. After accounting for general cognitive ability, unique genetic influences accounted for 64% and 31% of those heritabilities. A common genetic factor, most likely representing a combination of speed and sequencing, accounted for most of the correlation among TMT 1-4. Distinct genetic factors, however, accounted for a portion of variance in visual scanning and set shifting. Thus, although traditional phenotypic shared variance analysis techniques suggest only one general factor underlying different neuropsychological functions in nonpatient populations, examining the genetic underpinnings of cognitive processes with twin analysis can uncover more complex etiological processes.

Childhood temperament: passive gene-environment correlation, gene-environment interaction, and the hidden importance of the family environment.

PubMed

Lemery-Chalfant, Kathryn; Kao, Karen; Swann, Gregory; Goldsmith, H Hill

2013-02-01

Biological parents pass on genotypes to their children, as well as provide home environments that correlate with their genotypes; thus, the association between the home environment and children's temperament can be genetically (i.e., passive gene-environment correlation) or environmentally mediated. Furthermore, family environments may suppress or facilitate the heritability of children's temperament (i.e., gene-environment interaction). The sample comprised 807 twin pairs (mean age = 7.93 years) from the longitudinal Wisconsin Twin Project. Important passive gene-environment correlations emerged, such that home environments were less chaotic for children with high effortful control, and this association was genetically mediated. Children with high extraversion/surgency experienced more chaotic home environments, and this correlation was also genetically mediated. In addition, heritability of children's temperament was moderated by home environments, such that effortful control and extraversion/surgency were more heritable in chaotic homes, and negative affectivity was more heritable under crowded or unsafe home conditions. Modeling multiple types of gene-environment interplay uncovered the complex role of genetic factors and the hidden importance of the family environment for children's temperament and development more generally.

What affects the predictability of evolutionary constraints using a G-matrix? The relative effects of modular pleiotropy and mutational correlation.

PubMed

Chebib, Jobran; Guillaume, Frédéric

2017-10-01

Phenotypic traits do not always respond to selection independently from each other and often show correlated responses to selection. The structure of a genotype-phenotype map (GP map) determines trait covariation, which involves variation in the degree and strength of the pleiotropic effects of the underlying genes. It is still unclear, and debated, how much of that structure can be deduced from variational properties of quantitative traits that are inferred from their genetic (co) variance matrix (G-matrix). Here we aim to clarify how the extent of pleiotropy and the correlation among the pleiotropic effects of mutations differentially affect the structure of a G-matrix and our ability to detect genetic constraints from its eigen decomposition. We show that the eigenvectors of a G-matrix can be predictive of evolutionary constraints when they map to underlying pleiotropic modules with correlated mutational effects. Without mutational correlation, evolutionary constraints caused by the fitness costs associated with increased pleiotropy are harder to infer from evolutionary metrics based on a G-matrix's geometric properties because uncorrelated pleiotropic effects do not affect traits' genetic correlations. Correlational selection induces much weaker modular partitioning of traits' genetic correlations in absence then in presence of underlying modular pleiotropy. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

The GABRB1 gene is associated with thalamus volume and modulates the association between thalamus volume and intelligence.

PubMed

Zhu, Bi; Chen, Chuansheng; Xue, Gui; Lei, Xuemei; Li, Jin; Moyzis, Robert K; Dong, Qi; Lin, Chongde

2014-11-15

The GABRB1 gene encodes the beta 1 subunit of the gamma-aminobutyric acid A receptor (GABA A receptor), which is responsible for mediating inhibitory neurotransmission in the thalamus. Potential relationships between the GABRB1 gene, thalamus volume, and intelligence have been suggested by previous clinical studies, but have not been directly examined among nonclinical samples. The current study collected structural MRI, genetic, and behavioral data from 316 healthy Chinese adults (including 187 females and 129 males), and examined associations between GABRB1 variants, thalamus volume, and intelligence (measured by the Wechsler Adult Intelligence Scale Revised). After controlling for intracranial volume, sex, and age, GABRB1 genetic polymorphism at the SNP rs7435958 had the strongest association with thalamus volume (p = 0.002 and 0.00008 for left and right thalamus volumes, respectively), with GG homozygotes having smaller bilateral thalamus volumes than the other genotypes. Furthermore, there were positive correlations between bilateral thalamus volumes and intelligence, especially for GABRB1 rs7435958 GG female homozygotes (r's = 0.31 and 0.29, p < 0.01, for the correlations of intelligence with left and right thalamus volumes, respectively). This study provides the first evidence for the involvement of the GABRB1 gene in the thalamus structure and their interactive effects on intelligence. Future studies of the thalamus-intelligence associations should consider genetic factors as potential moderators. Copyright © 2014 Elsevier Inc. All rights reserved.

Aibika (Abelmoschus manihot L.): Genetic variation, morphology and relationships to micronutrient composition.

PubMed

Rubiang-Yalambing, Lydia; Arcot, Jayashree; Greenfield, Heather; Holford, Paul

2016-02-15

Aibika (Abelmoschus manihot L.) is believed to be a good source of micronutrients. However, although many varieties of aibika are commonly consumed in Papua New Guinea, their micronutrient content is unknown. Therefore, the mineral (Ca, Fe, K, Mg, Mn, Na, Zn & Cu), folate composition and the genetic variation of 23 aibika accessions from the collection at the National Agricultural Research Institute were studied over a 3year period to provide data for nutritional studies and to inform breeding programs. The data showed that aibika is, potentially, a crop of high nutritional value with the potential to boost the micronutrient status of local PNG communities. However, there were substantial differences in the micronutrient concentrations of the accessions from year to year and accessions that had the highest concentration of a particular mineral in 1year did not have the high concentrations in other years. Clusters determined using unweighted pair group method with arithmetic mean analysis (UPGMA) of the micronutrient contents differed in each of the 3years. Genetic analysis made using random amplification of polymorphic DNA and directed amplification of mini satellite region DNA placed the accessions into five groups. There was no correlation between these groups and leaf morphology, nor were there correlations with the clusters determined from the UPGMA analyses. There appears to be considerable interaction between genotype and environmental factors determining micronutrient composition and environmental factors may play a greater role than genotype in influencing micronutrient composition. Copyright © 2014 Elsevier Ltd. All rights reserved.

Does selection in a challenging environment produce Nile tilapia genotypes that can thrive in a range of production systems?

PubMed

Thoa, Ngo Phu; Ninh, Nguyen Huu; Knibb, Wayne; Nguyen, Nguyen Hong

2016-02-19

This study assessed whether selection for high growth in a challenging environment of medium salinity produces tilapia genotypes that perform well across different production environments. We estimated the genetic correlations between trait expressions in saline and freshwater using a strain of Nile tilapia selected for fast growth under salinity water of 15-20 ppt. We also estimated the heritability and genetic correlations for new traits of commercial importance (sexual maturity, feed conversion ratio, deformity and gill condition) in a full pedigree comprising 36,145 fish. The genetic correlations for the novel characters between the two environments were 0.78-0.99, suggesting that the effect of genotype by environment interaction was not biologically important. Across the environments, the heritability for body weight was moderate to high (0.32-0.62), indicating that this population will continue responding to future selection. The estimates of heritability for sexual maturity and survival were low but significant. The additive genetic components also exist for FCR, gill condition and deformity. Genetic correlations of harvest body weight with sexual maturity were positive and those between harvest body weight with FCR were negative. Our results indicate that the genetic line selected under a moderate saline water environment can be cultured successfully in freshwater systems.

Heritability of Problem Drinking and the Genetic Overlap with Personality in a General Population Sample

PubMed Central

de Moor, Marleen H. M.; Vink, Jacqueline M.; van Beek, Jenny H. D. A.; Geels, Lot M.; Bartels, Meike; de Geus, Eco J. C.; Willemsen, Gonneke; Boomsma, Dorret I.

2011-01-01

This study examined the heritability of problem drinking and investigated the phenotypic and genetic relationships between problem drinking and personality. In a sample of 5,870 twins and siblings and 4,420 additional family members from the Netherlands Twin Register. Data on problem drinking (assessed with the AUDIT and CAGE; 12 items) and personality [NEO Five-Factor Inventory (FFI); 60 items] were collected in 2009/2010 by surveys. Confirmatory factor analysis on the AUDIT and CAGE items showed that the items clustered on two separate but highly correlated (r = 0.74) underlying factors. A higher-order factor was extracted that reflected those aspects of problem drinking that are common to the AUDIT and CAGE, which showed a heritability of 40%. The correlations between problem drinking and the five dimensions of personality were small but significant, ranging from 0.06 for Extraversion to −0.12 for Conscientiousness. All personality dimensions (with broad-sense heritabilities between 32 and 55%, and some evidence for non-additive genetic influences) were genetically correlated with problem drinking. The genetic correlations were small to modest (between |0.12| and |0.41|). Future studies with longitudinal data and DNA polymorphisms are needed to determine the biological mechanisms that underlie the genetic link between problem drinking and personality. PMID:22303371

Maternal serum alpha-fetoprotein and human chorionic gonadotropin levels in women with human immunodeficiency virus.

PubMed

Gross, Susan; Castillo, Wilfrido; Crane, Marilyn; Espinosa, Bialines; Carter, Suzanne; DeVeaux, Richard; Salafia, Carolyn

2003-04-01

The purpose of this study was to establish whether there is a correlation between maternal serum genetic screen analyte results in pregnant women with human immunodeficiency virus and corresponding human immunodeficiency virus index values. Medical records of all pregnant women with human immunodeficiency virus who were delivered at Bronx Lebanon Hospital Center from January 2000 through December 2001 were reviewed for maternal serum screen results, viral load, CD4 counts and percent, antiretroviral therapy, opportunistic infections, substance abuse, and other demographic data. Statistical analysis was accomplished with the chi(2) test, Mann-Whitney U test, and Spearman rank correlation test, with a probability value of <.05 considered significant. Of the 98 women with human immunodeficiency virus who were delivered, 49 women (50%) had a maternal serum genetic screen available. Screened and unscreened women had similar severity of human immunodeficiency virus disease, CD4 count and percentage, and viral loads. Serum screen results showed elevations in maternal serum human chorionic gonadotropin (1.43 +/- 1.04 multiples of the median [MoM]; range, 0.2-5.2 MoM) and maternal serum alpha-fetoprotein (1.29 +/- 0.9 MoM; range, 0.5-3.3 MoM) compared with expected values in the general obstetric population. Maternal serum human chorionic gonadotropin was correlated inversely with CD4 count (P =.002) and CD4 percent (P <.0001). Maternal serum alpha-fetoprotein varied directly with viral load (P <.0001). Increasing maternal serum human chorionic gonadotropin and maternal serum alpha-fetoprotein levels in patients with human immunodeficiency virus are correlated with increasing viral load and decreasing CD4 counts.

The efficiency of genome-wide selection for genetic improvement of net merit.

PubMed

Togashi, K; Lin, C Y; Yamazaki, T

2011-10-01

Four methods of selection for net merit comprising 2 correlated traits were compared in this study: 1) EBV-only index (I₁), which consists of the EBV of both traits (i.e., traditional 2-trait BLUP selection); 2) GEBV-only index (I₂), which comprises the genomic EBV (GEBV) of both traits; 3) GEBV-assisted index (I₃), which combines both the EBV and the GEBV of both traits; and 4) GBV-assisted index (I₄), which combines both the EBV and the true genomic breeding value (GBV) of both traits. Comparisons of these indices were based on 3 evaluation criteria [selection accuracy, genetic response (ΔH), and relative efficiency] under 64 scenarios that arise from combining 2 levels of genetic correlation (r(G)), 2 ratios of genetic variances between traits, 2 ratios of the genomic variance to total genetic variances for trait 1, 4 accuracies of EBV, and 2 proportions of r(G) explained by the GBV. Both selection accuracy and genetic responses of the indices I₁, I₃, and I₄ increased as the accuracy of EBV increased, but the efficiency of the indices I₃ and I₄ relative to I₁ decreased as the accuracy of EBV increased. The relative efficiency of both I₃ and I₄ was generally greater when the accuracy of EBV was 0.6 than when it was 0.9, suggesting that the genomic markers are most useful to assist selection when the accuracy of EBV is low. The GBV-assisted index I₄ was superior to the GEBV-assisted I₃ in all 64 cases examined, indicating the importance of improving the accuracy of prediction of genomic breeding values. Other parameters being identical, increasing the genetic variance of a high heritability trait would increase the genetic response of the genomic indices (I₂, I₃, and I₄). The genetic responses to I₂, I₃, and I(4) was greater when the genetic correlation between traits was positive (r(G) = 0.5) than when it was negative (r(G) = -0.5). The results of this study indicate that the effectiveness of the GEBV-assisted index I₃ is affected by heritability of and genetic correlation between traits, the ratio of genetic variances between traits, the genomic-genetic variance ratio of each index trait, the proportion of genetic correlation accounted for by the genomic markers, and the accuracy of predictions of both EBV and GBV. However, most of these affecting factors are genetic characteristics of a population that is beyond the control of the breeders. The key factor subject to manipulation is to maximize both the proportion of the genetic variance explained by GEBV and the accuracy of both GEBV and EBV. The developed procedures provide means to investigate the efficiency of various genomic indices for any given combination of the genetic factors studied.

Environmental stress alters genetic regulation of novelty seeking in vervet monkeys.

PubMed

Fairbanks, L A; Bailey, J N; Breidenthal, S E; Laudenslager, M L; Kaplan, J R; Jorgensen, M J

2011-08-01

Considerable attention has been paid to identifying genetic influences and gene-environment interactions that increase vulnerability to environmental stressors, with promising but inconsistent results. A nonhuman primate model is presented here that allows assessment of genetic influences in response to a stressful life event for a behavioural trait with relevance for psychopathology. Genetic and environmental influences on free-choice novelty seeking behaviour were assessed in a pedigreed colony of vervet monkeys before and after relocation from a low stress to a higher stress environment. Heritability of novelty seeking scores, and genetic correlations within and between environments were conducted using variance components analysis. The results showed that novelty seeking was markedly inhibited in the higher stress environment, with effects persisting across a 2-year period for adults but not for juveniles. There were significant genetic contributions to novelty seeking scores in each year (h(2) = 0.35-0.43), with high genetic correlations within each environment (rhoG > 0.80) and a lower genetic correlation (rhoG = 0.35, non-significant) between environments. There were also significant genetic contributions to individual change scores from before to after the move (h(2) = 0.48). These results indicate that genetic regulation of novelty seeking was modified by the level of environmental stress, and they support a role for gene-environment interactions in a behavioural trait with relevance for mental health. © 2011 The Authors. Genes, Brain and Behavior © 2011 Blackwell Publishing Ltd and International Behavioural and Neural Genetics Society.

Semiochemical compounds of preen secretion reflect genetic make-up in a seabird species

USGS Publications Warehouse

Leclaire, S.; Merkling, T.; Raynaud, C.; Mulard, Hervé; Bessiere, J.-M.; Lhuillier, E.M.; Hatch, Shyla A.; Danchin, E.

2012-01-01

Several vertebrates choose their mate according to genetic heterozygosity and relatedness, and use odour cues to assess their conspecifics' genetic make-up. In birds, although several species (including the blacklegged kittiwake) exhibit non-random mating according to genetic traits, the cues used to assess genetic characteristics remain unknown. The importance of olfaction in birds' social behaviour is gaining attention among researchers, and it has been suggested that, as in other vertebrates, bird body scent may convey information about genetic traits. Here, we combined gas chromatography data and genetic analyses at microsatellite loci to test whether semiochemical messages in preen secretion of kittiwakes carried information about genetic heterozygosity and relatedness. Semiochemical profile was correlated with heterozygosity in males and females, while semiochemical distance was correlated with genetic distance only in male-male dyads. Our study is the first to demonstrate a link between odour and genetics in birds, which sets the stage for the existence of sophisticated odour-based mechanisms of mate choice also in birds. ?? 2011 The Royal Society.

Germline and somatic genetic predictors of pathological response in neoadjuvant settings of rectal and esophageal cancers: systematic review and meta-analysis.

PubMed

Salnikova, L E; Kolobkov, D S

2016-06-01

Oncologists have pointed out an urgent need for biomarkers that can be useful for clinical application to predict the susceptibility of patients to preoperative therapy. This review collects, evaluates and combines data on the influence of reported somatic and germline genetic variations on histological tumor regression in neoadjuvant settings of rectal and esophageal cancers. Five hundred and twenty-seven articles were identified, 204 retrieved and 61 studies included. Among 24 and 14 genetic markers reported for rectal and esophageal cancers, respectively, significant associations in meta-analyses were demonstrated for the following markers. In rectal cancer, major response was more frequent in carriers of the TYMS genotype 2 R/2 R-2 R/3 R (rs34743033), MTHFR genotype 677C/C (rs1801133), wild-type TP53 and KRAS genes. In esophageal cancer, successful therapy appeared to correlate with wild-type TP53. These results may be useful for future research directions to translate reported data into practical clinical use.

Fitness change in relation to mutation number in spontaneous mutation accumulation lines of Chlamydomonas reinhardtii

PubMed Central

Kraemer, Susanne A.; Böndel, Katharina B.; Ness, Robert W.; Keightley, Peter D.; Colegrave, Nick

2017-01-01

Abstract Although all genetic variation ultimately stems from mutations, their properties are difficult to study directly. Here, we used multiple mutation accumulation (MA) lines derived from five genetic backgrounds of the green algae Chlamydomonas reinhardtii that have been previously subjected to whole genome sequencing to investigate the relationship between the number of spontaneous mutations and change in fitness from a nonevolved ancestor. MA lines were on average less fit than their ancestors and we detected a significantly negative correlation between the change in fitness and the total number of accumulated mutations in the genome. Likewise, the number of mutations located within coding regions significantly and negatively impacted MA line fitness. We used the fitness data to parameterize a maximum likelihood model to estimate discrete categories of mutational effects, and found that models containing one to two mutational effect categories (one neutral and one deleterious category) fitted the data best. However, the best‐fitting mutational effects models were highly dependent on the genetic background of the ancestral strain. PMID:28884790

The genetics of music accomplishment: evidence for gene-environment correlation and interaction.

PubMed

Hambrick, David Z; Tucker-Drob, Elliot M

2015-02-01

Theories of skilled performance that emphasize training history, such as K. Anders Ericsson and colleagues' deliberate-practice theory, have received a great deal of recent attention in both the scientific literature and the popular press. Twin studies, however, have demonstrated evidence for moderate-to-strong genetic influences on skilled performance. Focusing on musical accomplishment in a sample of over 800 pairs of twins, we found evidence for gene-environment correlation, in the form of a genetic effect on music practice. However, only about one quarter of the genetic effect on music accomplishment was explained by this genetic effect on music practice, suggesting that genetically influenced factors other than practice contribute to individual differences in music accomplishment. We also found evidence for gene-environment interaction, such that genetic effects on music accomplishment were most pronounced among those engaging in music practice, suggesting that genetic potentials for skilled performance are most fully expressed and fostered by practice.

Potential use of random amplified polymorphic DNA (RAPD) technique to study the genetic diversity in Indian mustard (Brassica juncea) and its relationship to heterosis.

PubMed

Jain, A; Bhatia, S; Banga, S S; Prakash, S; Lakshmikumaran, M

1994-04-01

RAPD assays were performed, using 34 arbitrary decamer oligonucleotide primers and six combinations of two primers, to detect inherent variations and genetic relationships among 12 Indian and 11 exotic B. juncea genotypes. Of 595 amplification products identified, 500 of them were polymorphic across all genotypes. A low level of genetic variability was detected among the Indian genotypes, while considerable polymorphism was present among the exotic ones. Based on the pair-wise comparisons of amplification products the genetic similarity was calculated using Jaccard's similarity coefficients and a dendrogram was constructed using an unweighted pair group method was arithmetical averages (UPGMA). On the basis of this analysis the genotypes were clustered into two groups, A and B. Group A comprised only exotic genotypes, whereas all the Indian genotypes and four of the exotic genotypes were clustered in group B. Almost similar genotypic rankings could also be established by computing as few as 200 amplification products. In general, a high per cent of heterosis was recorded in crosses involving Indian x exotic genotypes. On the other hand, when crosses were made amongst Indian or exotic genotypes, about 80% of them exhibited negative heterosis. Results from this study indicate that, despite the lack of direct correlation between the genetic distance and the degree of heterosis, genetic diversity forms a very useful guide not only for investigating the relationships among Brassica genotypes but also in the selection of parents for heterotic hybrid combinations.

Prediction of industrial tomato hybrids from agronomic traits and ISSR molecular markers.

PubMed

Figueiredo, A S T; Resende, J T V; Faria, M V; Da-Silva, P R; Fagundes, B S; Morales, R G F

2016-05-13

Heterosis is a highly relevant phenomenon in plant breeding. This condition is usually established in hybrids derived from crosses of highly divergent parents. The success of a breeder in obtaining heterosis is directly related to the correct identification of genetically contrasting parents. Currently, the diallel cross is the most commonly used methodology to detect contrasting parents; however, it is a time- and cost-consuming procedure. Therefore, new tools capable of performing this task quickly and accurately are required. Thus, the purpose of this study was to estimate the genetic divergence in industrial tomato lines, based on agronomic traits, and to compare with estimates obtained using inter-simple sequence repeat (ISSR) molecular markers. The genetic divergence among 10 industrial tomato lines, based on nine morphological characters and 12 ISSR primers was analyzed. For data analysis, Pearson and Spearman correlation coefficients were calculated between the genetic dissimilarity measures estimated by Mahalanobis distance and Jaccard's coefficient of genetic dissimilarity from the heterosis estimates, combining ability, and means of important traits of industrial tomato. The ISSR markers efficiently detected contrasting parents for hybrid production in tomato. Parent RVTD-08 was indicated as the most divergent, both by molecular and morphological markers, that positively contributed to increased heterosis and by the specific combining ability in the crosses in which it participated. The genetic dissimilarity estimated by ISSR molecular markers aided the identification of the best hybrids of the experiment in terms of total fruit yield, pulp yield, and soluble solids content.

AFLPs and Mitochondrial Haplotypes Reveal Local Adaptation to Extreme Thermal Environments in a Freshwater Gastropod

PubMed Central

Quintela, María; Johansson, Magnus P.; Kristjánsson, Bjarni K.; Barreiro, Rodolfo; Laurila, Anssi

2014-01-01

The way environmental variation shapes neutral and adaptive genetic variation in natural populations is a key issue in evolutionary biology. Genome scans allow the identification of the genetic basis of local adaptation without previous knowledge of genetic variation or traits under selection. Candidate loci for divergent adaptation are expected to show higher FST than neutral loci influenced solely by random genetic drift, migration and mutation. The comparison of spatial patterns of neutral markers and loci under selection may help disentangle the effects of gene flow, genetic drift and selection among populations living in contrasting environments. Using the gastropod Radix balthica as a system, we analyzed 376 AFLP markers and 25 mtDNA COI haplotypes for candidate loci and associations with local adaptation among contrasting thermal environments in Lake Mývatn, a volcanic lake in northern Iceland. We found that 2% of the analysed AFLP markers were under directional selection and 12% of the mitochondrial haplotypes correlated with differing thermal habitats. The genetic networks were concordant for AFLP markers and mitochondrial haplotypes, depicting distinct topologies at neutral and candidate loci. Neutral topologies were characterized by intense gene flow revealed by dense nets with edges connecting contrasting thermal habitats, whereas the connections at candidate loci were mostly restricted to populations within each thermal habitat and the number of edges decreased with temperature. Our results suggest microgeographic adaptation within Lake Mývatn and highlight the utility of genome scans in detecting adaptive divergence. PMID:25007329

Genetic line comparisons and genetic parameters for endoparasite infections and test-day milk production traits.

PubMed

May, Katharina; Brügemann, Kerstin; Yin, Tong; Scheper, Carsten; Strube, Christina; König, Sven

2017-09-01

Keeping dairy cows in grassland systems relies on detailed analyses of genetic resistance against endoparasite infections, including between- and within-breed genetic evaluations. The objectives of this study were (1) to compare different Black and White dairy cattle selection lines for endoparasite infections and (2) the estimation of genetic (co)variance components for endoparasite and test-day milk production traits within the Black and White cattle population. A total of 2,006 fecal samples were taken during 2 farm visits in summer and autumn 2015 from 1,166 cows kept in 17 small- and medium-scale organic and conventional German grassland farms. Fecal egg counts were determined for gastrointestinal nematodes (FEC-GIN) and flukes (FEC-FLU), and fecal larvae counts for the bovine lungworm Dictyocaulus viviparus (FLC-DV). The lowest values for gastrointestinal nematode infections were identified for genetic lines adopted to pasture-based production systems, especially selection lines from New Zealand. Heritabilities were low for FEC-GIN (0.05-0.06 ± 0.04) and FLC-DV (0.05 ± 0.04), but moderate for FEC-FLU (0.33 ± 0.06). Almost identical heritabilities were estimated for different endoparasite trait transformations (log-transformation, square root). The genetic correlation between FEC-GIN and FLC-DV was 1.00 ± 0.60, slightly negative between FEC-GIN and FEC-FLU (-0.10 ± 0.27), and close to zero between FLC-DV and FEC-FLU (0.03 ± 0.30). Random regression test-day models on a continuous time scale [days in milk (DIM)] were applied to estimate genetic relationships between endoparasite and longitudinal test-day production traits. Genetic correlations were negative between FEC-GIN and milk yield (MY) until DIM 85, and between FEC-FLU and MY until DIM 215. Genetic correlations between FLC-DV and MY were negative throughout lactation, indicating improved disease resistance for high-productivity cows. Genetic relationships between FEC-GIN and FEC-FLU with milk protein content were negative for all DIM. Apart from the very early and very late lactation stage, genetic correlations between FEC-GIN and milk fat content were negative, whereas they were positive for FEC-FLU. Genetic correlations between FEC-GIN and somatic cell score were positive, indicating similar genetic mechanisms for susceptibility to udder and endoparasite infections. The moderate heritabilities for FEC-FLU suggest inclusion of FEC-FLU into overall organic dairy cattle breeding goals to achieve long-term selection response for disease resistance. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Heritability and genetic correlation between GERD symptoms severity, metabolic syndrome, and inflammation markers in families living in Mexico City.

PubMed

Reding-Bernal, Arturo; Sánchez-Pedraza, Valentin; Moreno-Macías, Hortensia; Sobrino-Cossio, Sergio; Tejero-Barrera, María Elizabeth; Burguete-García, Ana Isabel; León-Hernández, Mireya; Serratos-Canales, María Fabiola; Duggirala, Ravindranath; López-Alvarenga, Juan Carlos

2017-01-01

The aim of this study was to estimate the heritability (h2) and genetic correlation (ρG) between GERD symptoms severity, metabolic syndrome components, and inflammation markers in Mexican families. Cross-sectional study which included 32 extended families resident in Mexico City. GERD symptoms severity was assessed by the ReQuest in Practice questionnaire. Heritability and genetic correlation were determined using the Sequential Oligogenic Linkage Analysis Routines software. 585 subjects were included, the mean age was 42 (±16.7) years, 57% were women. The heritability of the severity of some GERD symptoms was h2 = 0.27, 0.27, 0.37, and 0.34 (p-value <1.0x10-5) for acidity complaints, lower abdominal complaints, sleep disturbances, and total ReQuest score, respectively. Heritability of metabolic syndrome components ranged from 0.40 for fasting plasma glucose to 0.61 for body mass index and diabetes mellitus. The heritability for fibrinogen and C-reactive protein was 0.64 and 0.38, respectively. Statistically significant genetic correlations were found between acidity complaints and fasting plasma glucose (ρG = 0.40); sleep disturbances and fasting plasma glucose (ρG = 0.36); acidity complaints and diabetes mellitus (ρG = 0.49) and between total ReQuest score and fasting plasma glucose (ρG = 0.43). The rest of metabolic syndrome components did not correlate with GERD symptoms. Genetic factors substantially explain the phenotypic variance of the severity of some GERD symptoms, metabolic syndrome components and inflammation markers. Observed genetic correlations suggest that these phenotypes share common genes. These findings suggest conducting further investigation, as the determination of a linkage analysis in order to identify regions of susceptibility for developing of GERD and metabolic syndrome.

Heritability and genetic correlation between GERD symptoms severity, metabolic syndrome, and inflammation markers in families living in Mexico City

PubMed Central

Reding-Bernal, Arturo; Sánchez-Pedraza, Valentin; Moreno-Macías, Hortensia; Sobrino-Cossio, Sergio; Tejero-Barrera, María Elizabeth; Burguete-García, Ana Isabel; León-Hernández, Mireya; Serratos-Canales, María Fabiola; Duggirala, Ravindranath; López-Alvarenga, Juan Carlos

2017-01-01

Objective The aim of this study was to estimate the heritability (h2) and genetic correlation (ρG) between GERD symptoms severity, metabolic syndrome components, and inflammation markers in Mexican families. Methods Cross-sectional study which included 32 extended families resident in Mexico City. GERD symptoms severity was assessed by the ReQuest in Practice questionnaire. Heritability and genetic correlation were determined using the Sequential Oligogenic Linkage Analysis Routines software. Results 585 subjects were included, the mean age was 42 (±16.7) years, 57% were women. The heritability of the severity of some GERD symptoms was h2 = 0.27, 0.27, 0.37, and 0.34 (p-value <1.0x10-5) for acidity complaints, lower abdominal complaints, sleep disturbances, and total ReQuest score, respectively. Heritability of metabolic syndrome components ranged from 0.40 for fasting plasma glucose to 0.61 for body mass index and diabetes mellitus. The heritability for fibrinogen and C-reactive protein was 0.64 and 0.38, respectively. Statistically significant genetic correlations were found between acidity complaints and fasting plasma glucose (ρG = 0.40); sleep disturbances and fasting plasma glucose (ρG = 0.36); acidity complaints and diabetes mellitus (ρG = 0.49) and between total ReQuest score and fasting plasma glucose (ρG = 0.43). The rest of metabolic syndrome components did not correlate with GERD symptoms. Conclusion Genetic factors substantially explain the phenotypic variance of the severity of some GERD symptoms, metabolic syndrome components and inflammation markers. Observed genetic correlations suggest that these phenotypes share common genes. These findings suggest conducting further investigation, as the determination of a linkage analysis in order to identify regions of susceptibility for developing of GERD and metabolic syndrome. PMID:28582452

Heritability of body surface temperature in hens estimated by infrared thermography at normal or hot temperatures and genetic correlations with egg and feather quality.

PubMed

Loyau, T; Zerjal, T; Rodenburg, T B; Fablet, J; Tixier-Boichard, M; Pinard-van der Laan, M H; Mignon-Grasteau, S

2016-10-01

Exposure of laying hens to chronic heat stress results in loss of egg production. It should be possible to improve hen resilience to chronic heat stress by genetic selection but measuring their sensitivity through internal temperature is time consuming and is not very precise. In this study we used infrared thermography to measure the hen's capacity to dissipate heat, in a commercial line of laying hens subjected to cycles of neutral (N, 19.6°C) or high (H, 28.4°C) ambient temperatures. Mean body temperatures (BT) were estimated from 9355 infrared images of wing, comb and shank taken from 1200 hens. Genetic parameters were estimated separately for N and H temperatures. Correlations between BT and plumage condition were also investigated. Wing temperature had low heritability (0.00 to 0.09), consistent with the fact that wing temperature mainly reflects the environmental temperature and is not a zone of heat dissipation. The heritability of comb temperature was higher, from 0.15 to 0.19 in N and H conditions, respectively. Finally, the shank temperature provided the highest heritability estimates, with values of 0.20 to 0.22 in H and N conditions, respectively. Taken together, these results show that heat dissipation is partly under genetic control. Interestingly, the genetic correlation between plumage condition and shank and comb temperatures indicated that birds with poor condition plumage also had the possibility to dissipate heat through featherless areas. Genetic correlations of temperature measurements with egg quality showed that temperatures were correlated with egg width and weight, yolk brightness and yellowness and Haugh units only under H conditions. In contrast, shell colour was correlated with leg temperature only at thermo-neutrality.

Constraint, natural selection, and the evolution of human body form

PubMed Central

Savell, Kristen R. R.; Auerbach, Benjamin M.; Roseman, Charles C.

2016-01-01

Variation in body form among human groups is structured by a blend of natural selection driven by local climatic conditions and random genetic drift. However, attempts to test ecogeographic hypotheses have not distinguished between adaptive traits (i.e., those that evolved as a result of selection) and those that evolved as a correlated response to selection on other traits (i.e., nonadaptive traits), complicating our understanding of the relationship between climate and morphological distinctions among populations. Here, we use evolutionary quantitative methods to test if traits previously identified as supporting ecogeographic hypotheses were actually adaptive by estimating the force of selection on individual traits needed to drive among-group differentiation. Our results show that not all associations between trait means and latitude were caused by selection acting directly on each individual trait. Although radial and tibial length and biiliac and femoral head breadth show signs of responses to directional selection matching ecogeographic hypotheses, the femur was subject to little or no directional selection despite having shorter values by latitude. Additionally, in contradiction to ecogeographic hypotheses, the humerus was under directional selection for longer values by latitude. Responses to directional selection in the tibia and radius induced a nonadaptive correlated response in the humerus that overwhelmed its own trait-specific response to selection. This result emphasizes that mean differences between groups are not good indicators of which traits are adaptations in the absence of information about covariation among characteristics. PMID:27482101

Constraint, natural selection, and the evolution of human body form.

PubMed

Savell, Kristen R R; Auerbach, Benjamin M; Roseman, Charles C

2016-08-23

Variation in body form among human groups is structured by a blend of natural selection driven by local climatic conditions and random genetic drift. However, attempts to test ecogeographic hypotheses have not distinguished between adaptive traits (i.e., those that evolved as a result of selection) and those that evolved as a correlated response to selection on other traits (i.e., nonadaptive traits), complicating our understanding of the relationship between climate and morphological distinctions among populations. Here, we use evolutionary quantitative methods to test if traits previously identified as supporting ecogeographic hypotheses were actually adaptive by estimating the force of selection on individual traits needed to drive among-group differentiation. Our results show that not all associations between trait means and latitude were caused by selection acting directly on each individual trait. Although radial and tibial length and biiliac and femoral head breadth show signs of responses to directional selection matching ecogeographic hypotheses, the femur was subject to little or no directional selection despite having shorter values by latitude. Additionally, in contradiction to ecogeographic hypotheses, the humerus was under directional selection for longer values by latitude. Responses to directional selection in the tibia and radius induced a nonadaptive correlated response in the humerus that overwhelmed its own trait-specific response to selection. This result emphasizes that mean differences between groups are not good indicators of which traits are adaptations in the absence of information about covariation among characteristics.

Genetic parameters for uniformity of harvest weight and body size traits in the GIFT strain of Nile tilapia.

PubMed

Marjanovic, Jovana; Mulder, Han A; Khaw, Hooi L; Bijma, Piter

2016-06-10

Animal breeding programs have been very successful in improving the mean levels of traits through selection. However, in recent decades, reducing the variability of trait levels between individuals has become a highly desirable objective. Reaching this objective through genetic selection requires that there is genetic variation in the variability of trait levels, a phenomenon known as genetic heterogeneity of environmental (residual) variance. The aim of our study was to investigate the potential for genetic improvement of uniformity of harvest weight and body size traits (length, depth, and width) in the genetically improved farmed tilapia (GIFT) strain. In order to quantify the genetic variation in uniformity of traits and estimate the genetic correlations between level and variance of the traits, double hierarchical generalized linear models were applied to individual trait values. Our results showed substantial genetic variation in uniformity of all analyzed traits, with genetic coefficients of variation for residual variance ranging from 39 to 58 %. Genetic correlation between trait level and variance was strongly positive for harvest weight (0.60 ± 0.09), moderate and positive for body depth (0.37 ± 0.13), but not significantly different from 0 for body length and width. Our results on the genetic variation in uniformity of harvest weight and body size traits show good prospects for the genetic improvement of uniformity in the GIFT strain. A high and positive genetic correlation was estimated between level and variance of harvest weight, which suggests that selection for heavier fish will also result in more variation in harvest weight. Simultaneous improvement of harvest weight and its uniformity will thus require index selection.

Genetic parameters for milk urea concentration and milk traits in Polish Holstein-Friesian cows.

PubMed

Rzewuska, Katarzyna; Strabel, Tomasz

2013-11-01

Milk urea concentration (MU) used by dairy producers for management purposes can be affected by selection for milk traits. To assess this problem, genetic parameters for MU in Polish Holstein-Friesian cattle were estimated for the first three lactations. The genetic correlation of MU with milk production traits, lactose percentage, fat to protein ratio (FPR) and somatic cell score (SCS) were computed with two 5-trait random regression test-day models, separately for each lactation. Data used for estimation (159,044 daily observations) came from 50 randomly sampled herds. (Co)variance components were estimated with the Bayesian Gibbs sampling method. The coefficient of variation for MU in all three parities was high (40-41 %). Average daily heritabilities of MU were 0.22 for the first parity and 0.21 for the second and third lactations. Average genetic correlations for different days in milk in the first three lactations between MU and other traits varied. They were small and negative for protein percentage (from -0.24 to -0.11) and for SCS (from -0.14 to -0.09). The weakest genetic correlation between MU and fat percentage, and between MU and lactose percentage were observed (from -0.10 to 0.10). Negative average genetic correlation with the fat to protein ratio was observed only in the first lactation (-0.14). Genetic correlations with yield traits were positive and ranged from low to moderate for protein (from 0.09 to 0.33), fat (from 0.16 to 0.35) and milk yield (from 0.20 to 0.42). These results suggest that the selection on yield traits and SCS tends to increase MU slightly.

Relationship between the IQ of people with Prader-Willi syndrome and that of their siblings: evidence for imprinted gene effects.

PubMed

Whittington, J; Holland, A; Webb, T

2009-05-01

Genetic disorders occasionally provide the means to uncover potential mechanisms linking gene expression and physical or cognitive characteristics or behaviour. Prader-Willi syndrome (PWS) is one such genetic disorder in which differences between the two main genetic subtypes have been documented (e.g. higher verbal IQ in one vs. higher performance IQ in the other; slower than normal reaction time in one vs. normal in the other). In a population study of PWS, the IQ distribution of people with PWS was approximately normal. This raises the question of whether this distribution arose from a systematic effect of PWS on IQ (hypothesis 1) or whether it was the fortuitous result of random effects (hypothesis 2). The correlation between PWS and sibling IQ was determined in order to discriminate between the two hypotheses. In the first case we would expect the correlation to be similar to that found in the general population (0.5); in the second case it would be zero. It was found that the overall PWS-sibling IQ correlation was 0.3 but that the two main genetic subtypes of PWS differed in their familial IQ relationships. As expected, the IQs of normal siblings correlated 0.5, and this was also the case with one genetic subtype of PWS (uniparental disomy) and their siblings, while the other subtype IQ correlated -0.07 with sibling IQ. This is a potentially powerful result that gives another clue to the role of genes on chromosome 15 in the determination of IQ. It is another systematic difference between the genetic subtypes of PWS, which needs an explanation in terms of the very small genetic differences between them.

Cross-Disorder Genetic Analysis of Tic Disorders, Obsessive-Compulsive, and Hoarding Symptoms.

PubMed

Zilhão, Nuno R; Smit, Dirk J; Boomsma, Dorret I; Cath, Danielle C

2016-01-01

Hoarding, obsessive-compulsive disorder (OCD), and Tourette's disorder (TD) are psychiatric disorders that share symptom overlap, which might partly be the result of shared genetic variation. Population-based twin studies have found significant genetic correlations between hoarding and OCD symptoms, with genetic correlations varying between 0.1 and 0.45. For tic disorders, studies examining these correlations are lacking. Other lines of research, including clinical samples and GWAS or CNV data to explore genetic relationships between tic disorders and OCD, have only found very modest if any shared genetic variation. Our aim was to extend current knowledge on the genetic structure underlying hoarding, OC symptoms (OCS), and lifetime tic symptoms and, in a trivariate analysis, assess the degree of common and unique genetic factors contributing to the etiology of these disorders. Data have been gathered from participants in the Netherlands Twin Register comprising a total of 5293 individuals from a sample of adult monozygotic (n = 2460) and dizygotic (n = 2833) twin pairs (mean age 33.61 years). The data on Hoarding, OCS, and tic symptoms were simultaneously analyzed in Mplus. A liability threshold model was fitted to the twin data, analyzing heritability of phenotypes and of their comorbidity. Following the criteria for a probable clinical diagnosis in all phenotypes, 6.8% of participants had a diagnosis of probable hoarding disorder (HD), 6.3% of OCS, and 12.8% of any probable lifetime tic disorder. Genetic factors explained 50.4, 70.1, and 61.1% of the phenotypic covariance between hoarding-OCS, hoarding-tics, and OCS-tics, respectively. Substantial genetic correlations were observed between hoarding and OCS (0.41), hoarding and tics (0.35), and between OCS and tics (0.37). These results support the contribution of genetic factors in the development of these disorders and their comorbidity. Furthermore, tics were mostly influenced by specific environmental factors unshared with OCS and HD.

Culture modifies expectations of kinship and sex-biased dispersal patterns: a case study of patrilineality and patrilocality in tribal Yemen.

PubMed

Raaum, Ryan L; Al-Meeri, Ali; Mulligan, Connie J

2013-04-01

Studies of the impact of post-marital residence patterns on the distribution of genetic variation within populations have returned conflicting results. These studies have generally examined genetic diversity within and between groups with different post-marriage residence patterns. Here, we directly examine Y chromosome microsatellite variation in individuals carrying a chromosome in the same Y haplogroup. We analyze Y chromosome data from two samples of Yemeni males: a sample representing the entire country and a sample from a large highland village. Our results support a normative patrilocality in highland Yemeni tribal populations, but also suggest that patrilocality is violated often enough to break down the expected correlation of genetic and geographic distance. We propose that a great deal of variation in male dispersal distance distributions is subsumed under the "patrilocal" label and that few human societies are likely to realize the idealized male dispersal distribution expected under strict patrilocality. In addition, we found almost no specific correspondence between social kinship and genetic patriline at the level of the clan (large, extended patrilineal kinship group) within a large, highland Yemeni village. We discuss ethnographic accounts that offer several cultural practices that explain exceptions to patrilocality and means by which social kinship and genetic patriline may become disentangled. Copyright © 2013 Wiley Periodicals, Inc.

Local adaptation and oceanographic connectivity patterns explain genetic differentiation of a marine diatom across the North Sea–Baltic Sea salinity gradient

PubMed Central

Sjöqvist, C; Godhe, A; Jonsson, P R; Sundqvist, L; Kremp, A

2015-01-01

Drivers of population genetic structure are still poorly understood in marine micro-organisms. We exploited the North Sea–Baltic Sea transition for investigating the seascape genetics of a marine diatom, Skeletonema marinoi. Eight polymorphic microsatellite loci were analysed in 354 individuals from ten locations to analyse population structure of the species along a 1500-km-long salinity gradient ranging from 3 to 30 psu. To test for salinity adaptation, salinity reaction norms were determined for sets of strains originating from three different salinity regimes of the gradient. Modelled oceanographic connectivity was compared to directional relative migration by correlation analyses to examine oceanographic drivers. Population genetic analyses showed distinct genetic divergence of a low-salinity Baltic Sea population and a high-salinity North Sea population, coinciding with the most evident physical dispersal barrier in the area, the Danish Straits. Baltic Sea populations displayed reduced genetic diversity compared to North Sea populations. Growth optima of low salinity isolates were significantly lower than those of strains from higher native salinities, indicating local salinity adaptation. Although the North Sea–Baltic Sea transition was identified as a barrier to gene flow, migration between Baltic Sea and North Sea populations occurred. However, the presence of differentiated neutral markers on each side of the transition zone suggests that migrants are maladapted. It is concluded that local salinity adaptation, supported by oceanographic connectivity patterns creating an asymmetric migration pattern between the Baltic Sea and the North Sea, determines genetic differentiation patterns in the transition zone. PMID:25892181

The relationship between different measures of feed efficiency and feeding behavior traits in Duroc pigs.

PubMed

Lu, D; Jiao, S; Tiezzi, F; Knauer, M; Huang, Y; Gray, K A; Maltecca, C

2017-08-01

Utilization of feed in livestock species consists of a wide range of biological processes, and therefore, its efficiency can be expressed in various ways, including direct measurement, such as daily feed intake, as well as indicator measures, such as feeding behavior. Measuring feed efficiency is important to the swine industry, and its accuracy can be enhanced by using automated feeding systems, which record feed intake and associated feeding behavior of individual animals. Each automated feeder space is often shared among several pigs and therefore raises concerns about social interactions among pen mates with regard to feeding behavior. The study herein used a data set of 14,901 Duroc boars with individual records on feed intake, feeding behavior, and other off-test traits. These traits were modeled with and without the random spatial effect of Pen_Room, a concatenation of room and pen, or random social interaction among pen mates. The nonheritable spatial effect of common Pen-Room was observed for traits directly measuring feed intake and accounted for up to 13% of the total phenotypic variance in the average daily feeding rate. The social interaction effect explained larger proportions of phenotypic variation in all the traits studied, with the highest being 59% for ADFI in the group of feeding behaviors, 73% for residual feed intake (RFI; RFI4 and RFI6) in the feed efficiency traits, and 69% for intramuscular fat percentage in the off-test traits. After accounting for the social interaction effect, residual BW gain and RFI and BW gain (RIG) were found to have the heritability of 0.38 and 0.18, respectively, and had strong genetic correlations with growth and off-test traits. Feeding behavior traits were found to be moderately heritable, ranging from 0.14 (ADFI) to 0.52 (average daily occupation time), and some of them were strongly correlated with feed efficiency measures; for example, there was a genetic correlation of 0.88 between ADFI and RFI6. Our work suggested that accounting for the social common pen effect was important for estimating genetic parameters of traits recorded by the automated feeding system. Residual BW gain and RIG appeared to be two robust measures of feed efficiency. Feeding behavior measures are worth further investigation as indicators of feed efficiency.

Generalist genes and learning disabilities: a multivariate genetic analysis of low performance in reading, mathematics, language and general cognitive ability in a sample of 8000 12-year-old twins.

PubMed

Haworth, Claire M A; Kovas, Yulia; Harlaar, Nicole; Hayiou-Thomas, Marianna E; Petrill, Stephen A; Dale, Philip S; Plomin, Robert

2009-10-01

Our previous investigation found that the same genes influence poor reading and mathematics performance in 10-year-olds. Here we assess whether this finding extends to language and general cognitive disabilities, as well as replicating the earlier finding for reading and mathematics in an older and larger sample. Using a representative sample of 4000 pairs of 12-year-old twins from the UK Twins Early Development Study, we investigated the genetic and environmental overlap between internet-based batteries of language and general cognitive ability tests in addition to tests of reading and mathematics for the bottom 15% of the distribution using DeFries-Fulker extremes analysis. We compared these results to those for the entire distribution. All four traits were highly correlated at the low extreme (average group phenotypic correlation = .58). and in the entire distribution (average phenotypic correlation = .59). Genetic correlations for the low extreme were consistently high (average = .67), and non-shared environmental correlations were modest (average = .23). These results are similar to those seen across the entire distribution (.68 and .23, respectively). The 'Generalist Genes Hypothesis' holds for language and general cognitive disabilities, as well as reading and mathematics disabilities. Genetic correlations were high, indicating a strong degree of overlap in genetic influences on these diverse traits. In contrast, non-shared environmental influences were largely specific to each trait, causing phenotypic differentiation of traits.

Marker-based quantitative genetics in the wild?: the heritability and genetic correlation of chemical defenses in eucalyptus.

PubMed

Andrew, R L; Peakall, R; Wallis, I R; Wood, J T; Knight, E J; Foley, W J

2005-12-01

Marker-based methods for estimating heritability and genetic correlation in the wild have attracted interest because traditional methods may be impractical or introduce bias via G x E effects, mating system variation, and sampling effects. However, they have not been widely used, especially in plants. A regression-based approach, which uses a continuous measure of genetic relatedness, promises to be particularly appropriate for use in plants with mixed-mating systems and overlapping generations. Using this method, we found significant narrow-sense heritability of foliar defense chemicals in a natural population of Eucalyptus melliodora. We also demonstrated a genetic basis for the phenotypic correlation underlying an ecological example of conditioned flavor aversion involving different biosynthetic pathways. Our results revealed that heritability estimates depend on the spatial scale of the analysis in a way that offers insight into the distribution of genetic and environmental variance. This study is the first to successfully use a marker-based method to measure quantitative genetic parameters in a tree. We suggest that this method will prove to be a useful tool in other studies and offer some recommendations for future applications of the method.

Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles.

PubMed

Fujisawa, Tomochika; Vogler, Alfried P; Barraclough, Timothy G

2015-01-22

Comparative analysis is a potentially powerful approach to study the effects of ecological traits on genetic variation and rate of evolution across species. However, the lack of suitable datasets means that comparative studies of correlates of genetic traits across an entire clade have been rare. Here, we use a large DNA-barcode dataset (5062 sequences) of water beetles to test the effects of species ecology and geographical distribution on genetic variation within species and rates of molecular evolution across species. We investigated species traits predicted to influence their genetic characteristics, such as surrogate measures of species population size, latitudinal distribution and habitat types, taking phylogeny into account. Genetic variation of cytochrome oxidase I in water beetles was positively correlated with occupancy (numbers of sites of species presence) and negatively with latitude, whereas substitution rates across species depended mainly on habitat types, and running water specialists had the highest rate. These results are consistent with theoretical predictions from nearly-neutral theories of evolution, and suggest that the comparative analysis using large databases can give insights into correlates of genetic variation and molecular evolution.

Ecological correlates of population genetic structure: a comparative approach using a vertebrate metacommunity.

PubMed

Manier, Mollie K; Arnold, Stevan J

2006-12-07

Identifying ecological factors associated with population genetic differentiation is important for understanding microevolutionary processes and guiding the management of threatened populations. We identified ecological correlates of several population genetic parameters for three interacting species (two garter snakes and an anuran) that occupy a common landscape. Using multiple regression analysis, we found that species interactions were more important in explaining variation in population genetic parameters than habitat and nearest-neighbour characteristics. Effective population size was best explained by census size, while migration was associated with differences in species abundance. In contrast, genetic distance was poorly explained by the ecological correlates that we tested, but geographical distance was prominent in models for all species. We found substantially different population dynamics for the prey species relative to the two predators, characterized by larger effective sizes, lower gene flow and a state of migration-drift equilibrium. We also identified an escarpment formed by a series of block faults that serves as a barrier to dispersal for the predators. Our results suggest that successful landscape-level management should incorporate genetic and ecological data for all relevant species, because even closely associated species can exhibit very different population genetic dynamics on the same landscape.

Mendelian randomization with fine-mapped genetic data: Choosing from large numbers of correlated instrumental variables.

PubMed

Burgess, Stephen; Zuber, Verena; Valdes-Marquez, Elsa; Sun, Benjamin B; Hopewell, Jemma C

2017-12-01

Mendelian randomization uses genetic variants to make causal inferences about the effect of a risk factor on an outcome. With fine-mapped genetic data, there may be hundreds of genetic variants in a single gene region any of which could be used to assess this causal relationship. However, using too many genetic variants in the analysis can lead to spurious estimates and inflated Type 1 error rates. But if only a few genetic variants are used, then the majority of the data is ignored and estimates are highly sensitive to the particular choice of variants. We propose an approach based on summarized data only (genetic association and correlation estimates) that uses principal components analysis to form instruments. This approach has desirable theoretical properties: it takes the totality of data into account and does not suffer from numerical instabilities. It also has good properties in simulation studies: it is not particularly sensitive to varying the genetic variants included in the analysis or the genetic correlation matrix, and it does not have greatly inflated Type 1 error rates. Overall, the method gives estimates that are less precise than those from variable selection approaches (such as using a conditional analysis or pruning approach to select variants), but are more robust to seemingly arbitrary choices in the variable selection step. Methods are illustrated by an example using genetic associations with testosterone for 320 genetic variants to assess the effect of sex hormone related pathways on coronary artery disease risk, in which variable selection approaches give inconsistent inferences. © 2017 The Authors Genetic Epidemiology Published by Wiley Periodicals, Inc.

Sex-specific genetic variance and the evolution of sexual dimorphism: a systematic review of cross-sex genetic correlations.

PubMed

Poissant, Jocelyn; Wilson, Alastair J; Coltman, David W

2010-01-01

The independent evolution of the sexes may often be constrained if male and female homologous traits share a similar genetic architecture. Thus, cross-sex genetic covariance is assumed to play a key role in the evolution of sexual dimorphism (SD) with consequent impacts on sexual selection, population dynamics, and speciation processes. We compiled cross-sex genetic correlations (r(MF)) estimates from 114 sources to assess the extent to which the evolution of SD is typically constrained and test several specific hypotheses. First, we tested if r(MF) differed among trait types and especially between fitness components and other traits. We also tested the theoretical prediction of a negative relationship between r(MF) and SD based on the expectation that increases in SD should be facilitated by sex-specific genetic variance. We show that r(MF) is usually large and positive but that it is typically smaller for fitness components. This demonstrates that the evolution of SD is typically genetically constrained and that sex-specific selection coefficients may often be opposite in sign due to sub-optimal levels of SD. Most importantly, we confirm that sex-specific genetic variance is an important contributor to the evolution of SD by validating the prediction of a negative correlation between r(MF) and SD.

Genetic and environmental bases of the interplay between magical ideation and personality.

PubMed

Brambilla, Paolo; Fagnani, Corrado; Cecchetto, Filippo; Medda, Emanuela; Bellani, Marcella; Salemi, Miriam; Picardi, Angelo; Stazi, Maria Antonietta

2014-02-28

Sub-threshold psychotic symptoms are quite commonly present in general population. Among these, Magical Ideation (MI) has been proved to be a valid predictor of psychosis. However, the genetic and environmental influences on the interplay between MI and personality have not fully been explored. A total of 534 adult twins from the population-based Italian Twin Register were assessed for MI using the MI Scale (MIS) and for personality with the temperament and character inventory (TCI). A Multivariate Cholesky model was applied with Mx statistical program. The best-fitting model showed that additive genetic and unshared environmental factors explain approximately the same proportion of variance in MI, whereas a less strong genetic influence on personality traits emerged. Relevant correlations between MI and specific personality traits (novelty seeking, cooperativeness, self-directedness, self-transcendence) were found, suggesting shared influences for MI and these traits. Both genetic and environmental factors explained these correlations, with genetic factors playing a predominant role. Moderate-to-substantial genetic effects on MI and personality were found. Shared genetic and environmental effects underlie the phenotypic correlation between MI (psychosis-proneness) and personality traits, i.e. self-directedness (negative association) and self-transcendence (positive association), potentially representing predictive markers of psychosis liability related to schizotypy and personality. © 2013 Published by Elsevier Ireland Ltd.

Pleiotropy across academic subjects at the end of compulsory education

PubMed Central

Rimfeld, Kaili; Kovas, Yulia; Dale, Philip S.; Plomin, Robert

2015-01-01

Research has shown that genes play an important role in educational achievement. A key question is the extent to which the same genes affect different academic subjects before and after controlling for general intelligence. The present study investigated genetic and environmental influences on, and links between, the various subjects of the age-16 UK-wide standardized GCSE (General Certificate of Secondary Education) examination results for 12,632 twins. Using the twin method that compares identical and non-identical twins, we found that all GCSE subjects were substantially heritable, and that various academic subjects correlated substantially both phenotypically and genetically, even after controlling for intelligence. Further evidence for pleiotropy in academic achievement was found using a method based directly on DNA from unrelated individuals. We conclude that performance differences for all subjects are highly heritable at the end of compulsory education and that many of the same genes affect different subjects independent of intelligence. PMID:26203819

Comparison of dimensionality reduction methods to predict genomic breeding values for carcass traits in pigs.

PubMed

Azevedo, C F; Nascimento, M; Silva, F F; Resende, M D V; Lopes, P S; Guimarães, S E F; Glória, L S

2015-10-09

A significant contribution of molecular genetics is the direct use of DNA information to identify genetically superior individuals. With this approach, genome-wide selection (GWS) can be used for this purpose. GWS consists of analyzing a large number of single nucleotide polymorphism markers widely distributed in the genome; however, because the number of markers is much larger than the number of genotyped individuals, and such markers are highly correlated, special statistical methods are widely required. Among these methods, independent component regression, principal component regression, partial least squares, and partial principal components stand out. Thus, the aim of this study was to propose an application of the methods of dimensionality reduction to GWS of carcass traits in an F2 (Piau x commercial line) pig population. The results show similarities between the principal and the independent component methods and provided the most accurate genomic breeding estimates for most carcass traits in pigs.

Social and genetic structure of paper wasp cofoundress associations: tests of reproductive skew models.

PubMed

Field, J; Solís, C R; Queller, D C; Strassmann, J E

1998-06-01

Recent models postulate that the members of a social group assess their ecological and social environments and agree a "social contract" of reproductive partitioning (skew). We tested social contracts theory by using DNA microsatellites to measure skew in 24 cofoundress associations of paper wasps, Polistes bellicosus. In contrast to theoretical predictions, there was little variation in cofoundress relatedness, and relatedness either did not predict skew or was negatively correlated with it; the dominant/subordinate size ratio, assumed to reflect relative fighting ability, did not predict skew; and high skew was associated with decreased aggression by the rank 2 subordinate toward the dominant. High skew was associated with increased group size. A difficulty with measuring skew in real systems is the frequent changes in group composition that commonly occur in social animals. In P. bellicosus, 61% of egg layers and an unknown number of non-egg layers were absent by the time nests were collected. The social contracts models provide an attractive general framework linking genetics, ecology, and behavior, but there have been few direct tests of their predictions. We question assumptions underlying the models and suggest directions for future research.

Innate factors causing differences in gene flow frequency from transgenic rice to different weedy rice biotypes.

PubMed

Zuo, Jiao; Zhang, Lianju; Song, Xiaoling; Dai, Weimin; Qiang, Sheng

2011-06-01

The compatibility and outcrossing rates between transgenic rice and weedy rice biotypes have been studied in some previous cases. However, few studies have addressed the reasons for these differences. The present study compared the compatibility and outcrossing rates between transgenic rice and selected weedy rice biotypes using manual and natural crossing experiments to elucidate the key innate factors causing the different outcrossing rates. Hybrid seed sets from manual crossing between transgenic rice and weedy rice varied from 31.8 to 82.7%, which correlated directly with genetic compatibility. Moreover, the significant differences in the quantity of germinated donor pollens and pollen tubes entering the weedy rice ovule directly contributed to the different seed sets. The natural outcrossing rates varied from 0 to 6.66‰. The duration of flowering overlap was the key factor influencing natural outcrossing. Plant and panicle height also affected outcrossing success. From this study, it is concluded that the likelihood of gene flow between transgenic rice and weedy rice biotypes is primarily determined by floral synchronisation and secondarily influenced by genetic compatibility and some morphological characteristics. Copyright © 2011 Society of Chemical Industry.

Curcumin Treatment Improves Motor Behavior in α-Synuclein Transgenic Mice

PubMed Central

Spinelli, Kateri J.; Osterberg, Valerie R.; Meshul, Charles K.; Soumyanath, Amala; Unni, Vivek K.

2015-01-01

The curry spice curcumin plays a protective role in mouse models of neurodegenerative diseases, and can also directly modulate aggregation of α-synuclein protein in vitro, yet no studies have described the interaction of curcumin and α-synuclein in genetic synucleinopathy mouse models. Here we examined the effect of chronic and acute curcumin treatment in the Syn-GFP mouse line, which overexpresses wild-type human α-synuclein protein. We discovered that curcumin diet intervention significantly improved gait impairments and resulted in an increase in phosphorylated forms of α-synuclein at cortical presynaptic terminals. Acute curcumin treatment also caused an increase in phosphorylated α-synuclein in terminals, but had no direct effect on α-synuclein aggregation, as measured by in vivo multiphoton imaging and Proteinase-K digestion. Using LC-MS/MS, we detected ~5 ng/mL and ~12 ng/mL free curcumin in the plasma of chronic or acutely treated mice, with a glucuronidation rate of 94% and 97%, respectively. Despite the low plasma levels and extensive metabolism of curcumin, these results show that dietary curcumin intervention correlates with significant behavioral and molecular changes in a genetic synucleinopathy mouse model that mimics human disease. PMID:26035833

Freezability genetics in rabbit semen.

PubMed

Lavara, R; Mocé, E; Baselga, M; Vicente, J S

2017-10-15

The aim of this study was to estimate the heritability of semen freezability and to estimate the genetic correlation between frozen-thawed sperm traits and the growth rate in a paternal rabbit line. Estimated heritabilities showed that frozen-thawed semen traits are heritable (ranged between 0.08 and 0.15). In the case of Live-FT (percentage of viable sperm after freezing), the estimated heritability is the highest one, and suggests the possibility of effective selection. After the study of genetic correlations it seems that daily weight gain (DG) was negatively correlated with sperm freezability, but no further conclusions could be drawn due to the high HPD95%. More data should be included in order to obtain better accuracy for the estimates of these genetic correlations. If the results obtained at present study were confirmed, it would imply that selection for DG could alter sperm cell membranes or seminal plasma composition, both components related to sperm cryoresistance. Copyright © 2017 Elsevier Inc. All rights reserved.

Correlated responses of respiratory disease and immune capacity traits of Landrace pigs selected for Mycoplasmal pneumonia of swine (MPS) lesion.

PubMed

Okamura, Toshihiro; Maeda, Kouki; Onodera, Wataru; Kadowaki, Hiroshi; Kojima-Shibata, Chihiro; Suzuki, Eisaku; Uenishi, Hirohide; Satoh, Masahiro; Suzuki, Keiichi

2016-09-01

Five generations of Landrace pigs selected for average daily gain, backfat thickness, Mycoplasmal pneumonia of swine (MPS) lesion score, and plasma cortisol levels, was executed to decrease the MPS lesion score. Genetic parameters and correlated genetic responses for respiratory disease and peripheral blood immune traits were estimated in 1395 Landrace pigs. We estimated the negative genetic correlation of MPS lesion score with phagocytic activity (PA) at 7 weeks of age (-0.67). The breeding values of PA at 7 weeks of age and 105 kg body weight and the correlated selection response of the ratio of granular leukocytes to lymphocytes at 105 kg body weight were significantly increased, and sheep red blood cell-specific antibody production (AP) was significantly decreased in a selection-dependent manner. Increasing of natural immunological indicators (e.g. PA) and decreasing of humoral immunological indicator (e.g. AP) were observed due to genetically decreasing MPS lesion score. © 2015 Japanese Society of Animal Science.

Estimating the actual subject-specific genetic correlations in behavior genetics.

PubMed

Molenaar, Peter C M

2012-10-01

Generalization of the standard behavior longitudinal genetic factor model for the analysis of interindividual phenotypic variation to a genetic state space model for the analysis of intraindividual variation enables the possibility to estimate subject-specific heritabilities.

Genetic parameter estimation for long endurance trials in the Uruguayan Criollo horse.

PubMed

López-Correa, R D; Peñagaricano, F; Rovere, G; Urioste, J I

2018-06-01

The aim of this study was to estimate the genetic parameters of performance in a 750-km, 15-day ride in Criollo horses. Heritability (h 2 ) and maternal lineage effects (mt 2 ) were obtained for rank, a relative placing measure of performance. Additive genetic and maternal lineage (rmt) correlations among five medium-to-high intensity phase ranks (pRK) and final rank (RK) were also estimated. Individual records from 1,236 Criollo horses from 1979 to 2012 were used. A multivariate threshold animal model was applied to the pRK and RK. Heritability was moderate to low (0.156-0.275). Estimates of mt 2 were consistently low (0.04-0.06). Additive genetic correlations between individual pRK and RK were high (0.801-0.924), and the genetic correlations between individual pRKs ranged from 0.763 to 0.847. The pRK heritabilities revealed that some phases were explained by a greater additive component, whereas others showed stronger genetic relationships with RK. Thus, not all pRK may be considered as similar measures of performance in competition. © 2018 Blackwell Verlag GmbH.

A novel heat shock protein alpha 8 (Hspa8) molecular network mediating responses to stress- and ethanol-related behaviors.

PubMed

Urquhart, Kyle R; Zhao, Yinghong; Baker, Jessica A; Lu, Ye; Yan, Lei; Cook, Melloni N; Jones, Byron C; Hamre, Kristin M; Lu, Lu

2016-04-01

Genetic differences mediate individual differences in susceptibility and responses to stress and ethanol, although, the specific molecular pathways that control these responses are not fully understood. Heat shock protein alpha 8 (Hspa8) is a molecular chaperone and member of the heat shock protein family that plays an integral role in the stress response and that has been implicated as an ethanol-responsive gene. Therefore, we assessed its role in mediating responses to stress and ethanol across varying genetic backgrounds. The hippocampus is an important mediator of these responses, and thus, was examined in the BXD family of mice in this study. We conducted bioinformatic analyses to dissect genetic factors modulating Hspa8 expression, identify downstream targets of Hspa8, and examined its role. Hspa8 is trans-regulated by a gene or genes on chromosome 14 and is part of a molecular network that regulates stress- and ethanol-related behaviors. To determine additional components of this network, we identified direct or indirect targets of Hspa8 and show that these genes, as predicted, participate in processes such as protein folding and organic substance metabolic processes. Two phenotypes that map to the Hspa8 locus are anxiety-related and numerous other anxiety- and/or ethanol-related behaviors significantly correlate with Hspa8 expression. To more directly assay this relationship, we examined differences in gene expression following exposure to stress or alcohol and showed treatment-related differential expression of Hspa8 and a subset of the members of its network. Our findings suggest that Hspa8 plays a vital role in genetic differences in responses to stress and ethanol and their interactions.

Genetic parameters for growth performance, fillet traits, and fat percentage of male Nile tilapia (Oreochromis niloticus).

PubMed

Garcia, André Luiz Seccatto; de Oliveira, Carlos Antonio Lopes; Karim, Hanner Mahmud; Sary, César; Todesco, Humberto; Ribeiro, Ricardo Pereira

2017-11-01

Improvement of fillet traits and flesh quality attributes are of great interest in farmed tilapia and other aquaculture species. The main objective of this study was to estimate genetic parameters for fillet traits (fillet weight and fillet yield) and the fat content of fillets from 1136 males combined with 2585 data records on growth traits (body weight at 290 days, weight at slaughter, and daily weight gain) of 1485 males and 1100 females from a third generation of the Aquaamerica tilapia strain. Different models were tested for each trait, and the best models were used to estimate genetic parameters for the fat content, fillet, and growth traits. Genetic and phenotypic correlations were estimated using two-trait animal models. The heritability estimates were moderate for the fat content of fillets and fillet yield (0.2-0.32) and slightly higher for body weight at slaughter (0.41). The genetic correlation between fillet yield and fat was significant (0.6), but the genetic correlations were not significant between body weight and fillet yield, body weight and fat content, daily weight gain and fillet yield, and daily weight gain and fat content (- 0.032, - 0.1, - 0.09, and - 0.4, respectively). Based on the genetic correlation estimates, it is unlikely that changes in fillet yield and fat content will occur when using growth performance as a selection criterion, but indirect changes may be expected in fat content if selecting for higher fillet yield.

Genetics of serum carotenoid concentrations and their correlation with obesity-related traits in Mexican American children.

PubMed

Farook, Vidya S; Reddivari, Lavanya; Mummidi, Srinivas; Puppala, Sobha; Arya, Rector; Lopez-Alvarenga, Juan Carlos; Fowler, Sharon P; Chittoor, Geetha; Resendez, Roy G; Kumar, Birunda Mohan; Comuzzie, Anthony G; Curran, Joanne E; Lehman, Donna M; Jenkinson, Christopher P; Lynch, Jane L; DeFronzo, Ralph A; Blangero, John; Hale, Daniel E; Duggirala, Ravindranath; Vanamala, Jairam Kp

2017-07-01

Background: Dietary intake of phytonutrients present in fruits and vegetables, such as carotenoids, is associated with a lower risk of obesity and related traits, but the impact of genetic variation on these associations is poorly understood, especially in children. Objective: We estimated common genetic influences on serum carotenoid concentrations and obesity-related traits in Mexican American (MA) children. Design: Obesity-related data were obtained from 670 nondiabetic MA children, aged 6-17 y. Serum α- and β-carotenoid concentrations were measured in ∼570 (α-carotene in 565 and β-carotene in 572) of these children with the use of an ultraperformance liquid chromatography-photodiode array. We determined heritabilities for both carotenoids and examined their genetic relation with 10 obesity-related traits [body mass index (BMI), waist circumference (WC), high-density lipoprotein (HDL) cholesterol, triglycerides, fat mass (FM), systolic and diastolic blood pressure, fasting insulin and glucose, and homeostasis model assessment of insulin resistance] by using family data and a variance components approach. For these analyses, carotenoid values were inverse normalized, and all traits were adjusted for significant covariate effects of age and sex. Results: Carotenoid concentrations were highly heritable and significant [α-carotene: heritability ( h 2 ) = 0.81, P = 6.7 × 10 -11 ; β-carotene: h 2 = 0.90, P = 3.5 × 10 -15 ]. After adjusting for multiple comparisons, we found significant ( P ≤ 0.05) negative phenotypic correlations between carotenoid concentrations and the following traits: BMI, WC, FM, and triglycerides (range: α-carotene = -0.19 to -0.12; β-carotene = -0.24 to -0.13) and positive correlations with HDL cholesterol (α-carotene = 0.17; β-carotene = 0.24). However, when the phenotypic correlations were partitioned into genetic and environmental correlations, we found marginally significant ( P = 0.051) genetic correlations only between β-carotene and BMI (-0.27), WC (-0.30), and HDL cholesterol (0.31) after accounting for multiple comparisons. None of the environmental correlations were significant. Conclusions: The findings from this study suggest that the serum carotenoid concentrations were under strong additive genetic influences based on variance components analyses, and that the common genetic factors may influence β-carotene and obesity and lipid traits in MA children. © 2017 American Society for Nutrition.

Living with strangers: direct benefits favour non-kin cooperation in a communally nesting bird.

PubMed

Riehl, Christina

2011-06-07

The greater ani (Crotophaga major), a Neotropical cuckoo, exhibits an unusual breeding system in which several socially monogamous pairs lay eggs in a single nest and contribute care to the communal clutch. Cooperative nesting is costly-females compete for reproduction by ejecting each other's eggs-but the potential direct or indirect fitness benefits that might accrue to group members have not been identified. In this study, I used molecular genotyping to quantify patterns of genetic relatedness and individual reproductive success within social groups in a single colour-banded population. Microsatellite analysis of 122 individuals in 49 groups revealed that group members are not genetic relatives. Group size was strongly correlated with individual reproductive success: solitary pairs were extremely rare and never successful, and nests attended by two pairs were significantly more likely to be depredated than were nests attended by three pairs. Egg loss, a consequence of reproductive competition, was greater in large groups and disproportionately affected females that initiated laying. However, early-laying females compensated for egg losses by laying larger clutches, and female group members switched positions in the laying order across nesting attempts. The greater ani, therefore, appears to be one of the few species in which cooperative breeding among unrelated individuals is favoured by direct, shared benefits that outweigh the substantial costs of reproductive competition.

Drop or fly? Negative genetic correlation between death-feigning intensity and flying ability as alternative anti-predator strategies

PubMed Central

Ohno, Tatsunori; Miyatake, Takahisa

2006-01-01

A prey animal may have the alternative of flying away or feigning death when it encounters predators. These alternatives have a genetic base as anti-predator strategies in the adzuki bean beetle, Callosobruchus chinensis. A negative genetic correlation between death-feigning intensity and flying ability was found in C. chinensis, i.e. lower flying ability is genetically connected to escaping by dropping from a perch and then feigning death, whereas higher flying ability does not correspond to death-feigning behaviour. Two bidirectional artificial selections for death-feigning duration and flying ability were conducted independently in C. chinensis. The strains selected for shorter (longer) duration of death-feigning had higher (lower) flying ability, while the strains selected for lower (higher) flying ability showed longer (shorter) duration of death-feigning. When the two traits were compared in 21 populations of C. chinensis derived from different geographical regions, a significant negative correlation was found between death-feigning intensity and flying ability. Based on these results, the choice between alternative escaping behaviours in animals is discussed from two points of view: phenotypic plasticity, an individual with two tactics; and pleiotropic genetic correlation, different individuals with opposite strategies. PMID:17476776

Multiple Phenotype Association Tests Using Summary Statistics in Genome-Wide Association Studies

PubMed Central

Liu, Zhonghua; Lin, Xihong

2017-01-01

Summary We study in this paper jointly testing the associations of a genetic variant with correlated multiple phenotypes using the summary statistics of individual phenotype analysis from Genome-Wide Association Studies (GWASs). We estimated the between-phenotype correlation matrix using the summary statistics of individual phenotype GWAS analyses, and developed genetic association tests for multiple phenotypes by accounting for between-phenotype correlation without the need to access individual-level data. Since genetic variants often affect multiple phenotypes differently across the genome and the between-phenotype correlation can be arbitrary, we proposed robust and powerful multiple phenotype testing procedures by jointly testing a common mean and a variance component in linear mixed models for summary statistics. We computed the p-values of the proposed tests analytically. This computational advantage makes our methods practically appealing in large-scale GWASs. We performed simulation studies to show that the proposed tests maintained correct type I error rates, and to compare their powers in various settings with the existing methods. We applied the proposed tests to a GWAS Global Lipids Genetics Consortium summary statistics data set and identified additional genetic variants that were missed by the original single-trait analysis. PMID:28653391

Multiple phenotype association tests using summary statistics in genome-wide association studies.

PubMed

Liu, Zhonghua; Lin, Xihong

2018-03-01

We study in this article jointly testing the associations of a genetic variant with correlated multiple phenotypes using the summary statistics of individual phenotype analysis from Genome-Wide Association Studies (GWASs). We estimated the between-phenotype correlation matrix using the summary statistics of individual phenotype GWAS analyses, and developed genetic association tests for multiple phenotypes by accounting for between-phenotype correlation without the need to access individual-level data. Since genetic variants often affect multiple phenotypes differently across the genome and the between-phenotype correlation can be arbitrary, we proposed robust and powerful multiple phenotype testing procedures by jointly testing a common mean and a variance component in linear mixed models for summary statistics. We computed the p-values of the proposed tests analytically. This computational advantage makes our methods practically appealing in large-scale GWASs. We performed simulation studies to show that the proposed tests maintained correct type I error rates, and to compare their powers in various settings with the existing methods. We applied the proposed tests to a GWAS Global Lipids Genetics Consortium summary statistics data set and identified additional genetic variants that were missed by the original single-trait analysis. © 2017, The International Biometric Society.

The role of ecology, neutral processes and antagonistic coevolution in an apparent sexual arms race.

PubMed

Perry, Jennifer C; Garroway, Colin J; Rowe, Locke

2017-09-01

Some of the strongest examples of a sexual 'arms race' come from observations of correlated evolution in sexually antagonistic traits among populations. However, it remains unclear whether these cases truly represent sexually antagonistic coevolution; alternatively, ecological or neutral processes might also drive correlated evolution. To investigate these alternatives, we evaluated the contributions of intersex genetic correlations, ecological context, neutral genetic divergence and sexual coevolution in the correlated evolution of antagonistic traits among populations of Gerris incognitus water striders. We could not detect intersex genetic correlations for these sexually antagonistic traits. Ecological variation was related to population variation in the key female antagonistic trait (spine length, a defence against males), as well as body size. Nevertheless, population covariation between sexually antagonistic traits remained substantial and significant even after accounting for all of these processes. Our results therefore provide strong evidence for a contemporary sexual arms race. © 2017 John Wiley & Sons Ltd/CNRS.

Genetic diversity in natural populations of a soil bacterium across a landscape gradient

PubMed Central

McArthur, J. Vaun; Kovacic, David A.; Smith, Michael H.

1988-01-01

Genetic diversity in natural populations of the bacterium Pseudomonas cepacia was surveyed in 10 enzymes from 70 clones isolated along a landscape gradient. Estimates of genetic diversity, ranging from 0.54 to 0.70, were higher than any previously reported values of which we are aware and were positively correlated with habitat variability. Patterns of bacterial genetic diversity were correlated with habitat variability. Findings indicate that the source of strains used in genetic engineering will greatly affect the outcome of planned releases in variable environments. Selection of generalist strains may confer a large advantage to engineered populations, while selection of laboratory strains may result in quick elimination of the engineered strains. PMID:16594009