The heritable basis of gene-environment interactions in cardiometabolic traits.

PubMed

Poveda, Alaitz; Chen, Yan; Brändström, Anders; Engberg, Elisabeth; Hallmans, Göran; Johansson, Ingegerd; Renström, Frida; Kurbasic, Azra; Franks, Paul W

2017-03-01

Little is known about the heritable basis of gene-environment interactions in humans. We therefore screened multiple cardiometabolic traits to assess the probability that they are influenced by genotype-environment interactions. Fourteen established environmental risk exposures and 11 cardiometabolic traits were analysed in the VIKING study, a cohort of 16,430 Swedish adults from 1682 extended pedigrees with available detailed genealogical, phenotypic and demographic information, using a maximum likelihood variance decomposition method in Sequential Oligogenic Linkage Analysis Routines software. All cardiometabolic traits had statistically significant heritability estimates, with narrow-sense heritabilities (h 2 ) ranging from 24% to 47%. Genotype-environment interactions were detected for age and sex (for the majority of traits), physical activity (for triacylglycerols, 2 h glucose and diastolic BP), smoking (for weight), alcohol intake (for weight, BMI and 2 h glucose) and diet pattern (for weight, BMI, glycaemic traits and systolic BP). Genotype-age interactions for weight and systolic BP, genotype-sex interactions for BMI and triacylglycerols and genotype-alcohol intake interactions for weight remained significant after multiple test correction. Age, sex and alcohol intake are likely to be major modifiers of genetic effects for a range of cardiometabolic traits. This information may prove valuable for studies that seek to identify specific loci that modify the effects of lifestyle in cardiometabolic disease.

The statistical analysis of multi-environment data: modeling genotype-by-environment interaction and its genetic basis

PubMed Central

Malosetti, Marcos; Ribaut, Jean-Marcel; van Eeuwijk, Fred A.

2013-01-01

Genotype-by-environment interaction (GEI) is an important phenomenon in plant breeding. This paper presents a series of models for describing, exploring, understanding, and predicting GEI. All models depart from a two-way table of genotype by environment means. First, a series of descriptive and explorative models/approaches are presented: Finlay–Wilkinson model, AMMI model, GGE biplot. All of these approaches have in common that they merely try to group genotypes and environments and do not use other information than the two-way table of means. Next, factorial regression is introduced as an approach to explicitly introduce genotypic and environmental covariates for describing and explaining GEI. Finally, QTL modeling is presented as a natural extension of factorial regression, where marker information is translated into genetic predictors. Tests for regression coefficients corresponding to these genetic predictors are tests for main effect QTL expression and QTL by environment interaction (QEI). QTL models for which QEI depends on environmental covariables form an interesting model class for predicting GEI for new genotypes and new environments. For realistic modeling of genotypic differences across multiple environments, sophisticated mixed models are necessary to allow for heterogeneity of genetic variances and correlations across environments. The use and interpretation of all models is illustrated by an example data set from the CIMMYT maize breeding program, containing environments differing in drought and nitrogen stress. To help readers to carry out the statistical analyses, GenStat® programs, 15th Edition and Discovery® version, are presented as “Appendix.” PMID:23487515

[Association between MAOA-u VNTR polymorphism and its interaction with stressful life events and major depressive disorder in adolescents].

PubMed

Ma, Jing; Yu, Shun-Ying; Liang, Shan; Ding, Jun; Feng, Zhe; Yang, Fan; Gao, Wei-Jia; Lin, Jia-Ni; Huang, Chun-Xiang; Liu, Xue-Jun; Su, Lin-Yan

2013-07-01

To investigate whether the genetic polymorphism, upstream variable number of tandem repeats (uVNTR), in the monoamine oxidase A (MAOA) gene, is associated with major depressive disorder (MDD) in adolescents and to test whether there is gene-environment interaction between MAOA-uVNTR polymorphism and stressful life events (SLEs). A total of 394 Chinese Han subjects, including 187 adolescent patients with MDD and 207 normal students as a control group, were included in the study. Genotyping was performed by SNaP-shot assay. SLEs in the previous 12 months were evaluated. The groups were compared in terms of the frequency distributions of MAOA-uVNTR genotypes and alleles using statistical software. The binary logistic regression model of gene-environment interaction was established to analyze the association of the gene-environment interaction between MAOA-u VNTR genotypes and SLEs with adolescent MDD. The distribution profiles of MAOA-u VNTR genotypes and alleles were not related to the onset of MDD, severity of depression, comorbid anxiety and suicidal ideation/behavior/attempt in adolescents. The gene-environment interaction between MAOA-u VNTR genotypes and SLEs was not associated with MDD in male or female adolescents. It is not proven that MAOA-u VNTR polymorphism is associated with adolescent MDD. There is also no gene-environment interaction between MAOA-u VNTR polymorphism and SLEs that is associated with adolescent MDD.

Identification of sorghum hybrids with high phenotypic stability using GGE biplot methodology.

PubMed

Teodoro, P E; Almeida Filho, J E; Daher, R F; Menezes, C B; Cardoso, M J; Godinho, V P C; Torres, F E; Tardin, F D

2016-06-10

The aim of this study was to identify sorghum hybrids that have both high yield and phenotypic stability in Brazilian environments. Seven trials were conducted between February and March 2011. The experimental design was a randomized complete block with 25 treatments and three replicates. The treatments consisted of 20 simple pre-commercial hybrids and five witnesses of grain sorghum. Sorghum genotypes were analyzed by the genotype main effects + genotype environment interaction (GGE) biplot method if significant genotype x environment interaction, adaptability, and phenotypic stability were detected. GGE biplot methodology identified two groups of environments, the first composed of Água Comprida-MG, Montividiu-GO, and Vilhena- RO and the second of Guaíra-SP and Sete Lagoas-MG. The BRS 308 and 1G282 genotypes were found to have high grain yield, adaptability, and phenotypic stability and are thus indicated for cultivation in the first and second groups of environments, respectively.

Biplot analysis of strawberry genotypes recommended for the State of Espírito Santo.

PubMed

Costa, A F; Teodoro, P E; Bhering, L L; Leal, N R; Tardin, F D; Daher, R F

2016-08-26

Most strawberry genotypes grown commercially in Brazil originate from breeding programs in the United States, and are therefore not adapted to the various soil and climatic conditions found in Brazil. Thus, quantifying the magnitude of genotype x environment (GE) interactions serves as a primary means for increasing average Brazilian strawberry yields, and helps provide specific recommendations for farmers on which genotypes meet high yield and phenotypic stability thresholds. The aim of this study was to use AMMI (additive main effects and multiplicative interaction) and GGE biplot (genotype main effects + genotype x environment interaction) analyses to identify high-yield, stable strawberry genotypes grown at three locations in Espírito Santo for two agricultural years. We evaluated seven strawberry genotypes (Dover, Camino Real, Ventana, Camarosa, Seascape, Diamante, and Aromas) at three locations (Domingos Martins, Iúna, and Muniz Freire) in agricultural years 2006 and 2007, totaling six study environments. Joint analysis of variance was calculated using yield data (t/ha), and AMMI and GGE biplot analysis was conducted following the detection of a significant genotypes x agricultural years x locations (G x A x L) interaction. During the two agricultural years, evaluated locations were allocated to different regions on biplot graphics using both methods, indicating distinctions among them. Based on the results obtained from the two methods used in this study to investigate the G x A x L interaction, we recommend growing the Camarosa genotype for production at the three locations assessed due to the high frequency of favorable alleles, which were expressed in all localities evaluated regardless of the agricultural year.

Biomass and genotype × environment interactions of Populus energy crops in the midwestern United States

Treesearch

Ronald S., Jr. Zalesny; Richard B. Hall; Jill A. Zalesny; Bernard G. McMahon; William E. Berguson; Glen R. Stanosz

2009-01-01

Using Populus feedstocks for biofuels, bioenergy, and bioproducts is becoming economically feasible as global fossil fuel prices increase. Maximizing Populus biomass production across regional landscapes largely depends on understanding genotype × environment interactions, given broad genetic variation at strategic (...

Environment and genotype effects on the content of dietary fiber and its components in wheat in the HEALTHGRAIN diversity screen.

PubMed

Gebruers, Kurt; Dornez, Emmie; Bedõ, Zoltan; Rakszegi, Mariann; Frás, Anna; Boros, Danuta; Courtin, Christophe M; Delcour, Jan A

2010-09-08

Within the HEALTHGRAIN diversity screen, the variability of the contents of dietary fiber (DF) and components thereof was studied in wheat. Furthermore, the contribution of genotype and environment to this variability was estimated. The levels of total DF (TDF), total nonstarch polysaccharide (TOTNSP), water-extractable nonstarch polysaccharide (WENSP), total arabinoxylan (TOTAX), lignin, and beta-glucan in whole meal, flour, and/or bran varied approximately 1.8-fold. The highest variability was observed for the water-extractable arabinoxylan (WEAX) level in flour and bran (approximately 3.7-fold). Genotype and environment contributed to a similar extent to the variability in TDF, TOTNSP, and TOTAX content in wheat. The observed relatively high impact of genotype-environment interaction suggests that the levels of these constituents are weak breeding parameters. The WENSP level is a more stable parameter as the effect of the interaction term was much less than the impact of genotype. For TOTAX and WEAX in flour, WEAX in bran, beta-glucan in whole meal, and extract viscosity, wheat genotype determined approximately 50% or higher of the variation observed, whereas the impact of the genotype-environment interaction was relatively low. These findings suggest that the health-related and technological functionality of wheat can be directed to a certain extent by selection of appropriate wheat varieties.

Genotype x environment interaction, environmental heterogeneity, and the lek paradox

USDA-ARS?s Scientific Manuscript database

Substantial additive genetic variance (VA) often exists for male signaling traits in spite of the directional selection that female choice imposes. One solution to this problem, generally termed the ‘lek paradox’, is that genotype x environment interaction (GEI) occurs and generates a ‘crossover’ of...

Host Genotype and Nitrogen Form Shape the Root Microbiome of Pinus radiata.

PubMed

Gallart, Marta; Adair, Karen L; Love, Jonathan; Meason, Dean F; Clinton, Peter W; Xue, Jianming; Turnbull, Matthew H

2018-02-01

A central challenge in community ecology is understanding the role that phenotypic variation among genotypes plays in structuring host-associated communities. While recent studies have investigated the relationship between plant genotype and the composition of soil microbial communities, the effect of genotype-by-environment interactions on the plant microbiome remains unclear. In this study, we assessed the influence of tree genetics (G), nitrogen (N) form and genotype-by-environment interaction (G x N) on the composition of the root microbiome. Rhizosphere communities (bacteria and fungi) and root-associated fungi (including ectomycorrhizal and saprotrophic guilds) were characterised in two genotypes of Pinus radiata with contrasting physiological responses to exogenous organic or inorganic N supply. Genotype-specific responses to N form influenced the composition of the root microbiome. Specifically, (1) diversity and composition of rhizosphere bacterial and root-associated fungal communities differed between genotypes that had distinct responses to N form, (2) shifts in the relative abundance of individual taxa were driven by the main effects of N form or host genotype and (3) the root microbiome of the P. radiata genotype with the most divergent growth responses to organic and inorganic N was most sensitive to differences in N form. Our results show that intraspecific variation in tree response to N form has significant consequences for the root microbiome of P. radiata, demonstrating the importance of genotype-by-environment interactions in shaping host-associated communities.

[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.

Genotypic diversity and environmental stability of starch physicochemical properties in the USDA rice mini-core collection.

PubMed

Li, Kehu; Bao, Jinsong; Corke, Harold; Sun, Mei

2017-04-15

The USDA rice mini-core collection consists of 217 accessions representative of a world-wide germplam bank. We investigated its genotypic diversity in starch physicochemical properties and the effects of genotype, environment and G×E interaction in this study. High genotypic diversity was found in all 18 measured starch quality traits in the mini-core rice in two location-years in China. Genotype, environment and G×E effects on these traits were analysed using 115 common accessions successfully produced in both environments. Thermal properties (T o , T p and T c ) were very stable whereas most other traits differed significantly between environments. However, when these accessions were divided into five subgroups based on amylose content, environment was found to have differential effects. G×E interaction also played a significant role in determining the starch traits. These findings will provide guidance for selection from the diverse genotypes in the USDA mini-core collection for cultivation and for developing cultivars with desired cooking and eating quality. Copyright © 2016 Elsevier Ltd. All rights reserved.

[The nature of personality: a co-evolutionary perspective].

PubMed

Asendorpf, J B

1996-01-01

Personality psychologists' attempts to explain human diversity have traditionally focused upon processes of person-situation interaction, and genotype-environment interaction. The great variability of genotypes and environments within cultures has remained unexplained in these efforts. Which processes may be responsible for the genetic and environmental variability within cultures? Answers to this question are sought in processes of genetic-cultural coevolution: mutation and sexual recombination of genes, innovation and synthesis of memes (units of cultural transmission), genotype-->environment and meme-->environment effects, and frequency-dependent natural and cultural selection. This twofold evolutionary explanation of personality differences within cultures suggests that a solid foundation of personality psychology requires bridging biology and cultural science.

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

USDA-ARS?s Scientific Manuscript database

That genotype by environment interaction potentially influences genetic evaluation of beef cattle has long been recognized. 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 geneti...

Dissecting genotype × environment interactions and trait correlations present in the Pee Dee cotton germplasm collection following seventy years of plant breeding

USDA-ARS?s Scientific Manuscript database

Genotype × environment interactions and trait correlations significantly impact efforts to develop high yield, high quality, and environmentally stable Upland cotton (Gossypium hirsutum L.) cultivars. Knowledge of both can and should be used to design optimal breeding programs and effective selectio...

Estimates of genetics and phenotypics parameters for the yield and quality of soybean seeds.

PubMed

Zambiazzi, E V; Bruzi, A T; Guilherme, S R; Pereira, D R; Lima, J G; Zuffo, A M; Ribeiro, F O; Mendes, A E S; Godinho, S H M; Carvalho, M L M

2017-09-27

Estimating genotype x environment (GxE) parameters for quality and yield in soybean seed grown in different environments in Minas Gerais State was the goal of this study, as well as to evaluate interaction effects of GxE for soybean seeds yield and quality. Seeds were produced in three locations in Minas Gerais State (Lavras, Inconfidentes, and Patos de Minas) in 2013/14 and 2014/15 seasons. Field experiments were conducted in randomized blocks in a factorial 17 x 6 (GxE), and three replications. Seed yield and quality were evaluated for germination in substrates paper and sand, seedling emergence, speed emergency index, mechanical damage by sodium hypochlorite, electrical conductivity, speed aging, vigor and viability of seeds by tetrazolium test in laboratory using completely randomized design. Quadratic component genotypic, GXE variance component, genotype determination coefficient, genetic variation coefficient and environmental variation coefficient were estimated using the Genes software. Percentage analysis of genotypes contribution, environments and genotype x environment interaction were conducted by sites combination two by two and three sites combination, using the R software. Considering genotypes selection of broad adaptation, TMG 1179 RR, CD 2737 RR, and CD 237 RR associated better yield performance at high physical and physiological potential of seed. Environmental effect was more expressive for most of the characters related to soybean seed quality. GxE interaction effects were expressive though genotypes did not present coincidental behavior in different environments.

Additive-Multiplicative Approximation of Genotype-Environment Interaction

PubMed Central

Gimelfarb, A.

1994-01-01

A model of genotype-environment interaction in quantitative traits is considered. The model represents an expansion of the traditional additive (first degree polynomial) approximation of genotypic and environmental effects to a second degree polynomial incorporating a multiplicative term besides the additive terms. An experimental evaluation of the model is suggested and applied to a trait in Drosophila melanogaster. The environmental variance of a genotype in the model is shown to be a function of the genotypic value: it is a convex parabola. The broad sense heritability in a population depends not only on the genotypic and environmental variances, but also on the position of the genotypic mean in the population relative to the minimum of the parabola. It is demonstrated, using the model, that GXE interaction rectional may cause a substantial non-linearity in offspring-parent regression and a reversed response to directional selection. It is also shown that directional selection may be accompanied by an increase in the heritability. PMID:7896113

Genetic by environment interactions affect plant–soil linkages

PubMed Central

Pregitzer, Clara C; Bailey, Joseph K; Schweitzer, Jennifer A

2013-01-01

The role of plant intraspecific variation in plant–soil linkages is poorly understood, especially in the context of natural environmental variation, but has important implications in evolutionary ecology. We utilized three 18- to 21-year-old common gardens across an elevational gradient, planted with replicates of five Populus angustifolia genotypes each, to address the hypothesis that tree genotype (G), environment (E), and G × E interactions would affect soil carbon and nitrogen dynamics beneath individual trees. We found that soil nitrogen and carbon varied by over 50% and 62%, respectively, across all common garden environments. We found that plant leaf litter (but not root) traits vary by genotype and environment while soil nutrient pools demonstrated genotype, environment, and sometimes G × E interactions, while process rates (net N mineralization and net nitrification) demonstrated G × E interactions. Plasticity in tree growth and litter chemistry was significantly related to the variation in soil nutrient pools and processes across environments, reflecting tight plant–soil linkages. These data overall suggest that plant genetic variation can have differential affects on carbon storage and nitrogen cycling, with implications for understanding the role of genetic variation in plant–soil feedback as well as management plans for conservation and restoration of forest habitats with a changing climate. PMID:23919173

Detecting small-scale genotype-environment interactions in apomictic dandelion (Taraxacum officinale) populations.

PubMed

McLeod, K A; Scascitelli, M; Vellend, M

2012-08-01

Studies of genotype × environment interactions (G × E) and local adaptation provide critical tests of natural selection's ability to counter opposing forces such as gene flow. Such studies may be greatly facilitated in asexual species, given the possibility for experimental replication at the level of true genotypes (rather than populations) and the possibility of using molecular markers to assess genotype-environment associations in the field (neither of which is possible for most sexual species). Here, we tested for G × E in asexual dandelions (Taraxacum officinale) by subjecting six genotypes to experimental drought, mown and benign (control) conditions and subsequently using microsatellites to assess genotype-environment associations in the field. We found strong G × E, with genotypes that performed poorly under benign conditions showing the highest performance under stressful conditions (drought or mown). Our six focal genotypes comprise > 80% of plants in local populations. The most common genotype in the field showed its highest relative performance under mown conditions (the most common habitat in our study area), and almost all plants of this genotype in the field were found growing in mowed lawns. Genotypes performing best under benign experimental conditions were found most frequently in unmown conditions in the field. These results are strongly indicative of local adaptation at a very small scale, with unmown microsites of only a few square metres typically embedded within larger mown lawns. By studying an asexual species, we were able to map genotypes with known ecological characteristics to environments with high spatial precision. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Effects of genetics and environment on fatty acid stability in soybean seed

USDA-ARS?s Scientific Manuscript database

Although seed oil production and composition are genetically controlled, changes of oil level and oil composition across genotypes and environments such as drought and temperature were observed. The mechanisms of how genotypes interact with environment, affecting oil production and composition, are ...

Physical and verbal aggressive behavior and COMT genotype: Sensitivity to the environment.

PubMed

Tuvblad, Catherine; Narusyte, Jurgita; Comasco, Erika; Andershed, Henrik; Andershed, Anna-Karin; Colins, Olivier F; Fanti, Kostas A; Nilsson, Kent W

2016-07-01

Catechol-O-methyltransferase (COMT) genotype has been implicated as a vulnerability factor for several psychiatric diseases as well as aggressive behavior, either directly, or in interaction with an adverse environment. The present study aimed at investigating the susceptibility properties of COMT genotype to adverse and favorable environment in relation to physical and verbal aggressive behavior. The COMT Val158Met polymorphism was genotyped in a Swedish population-based cohort including 1,783 individuals, ages 20-24 years (47% males). A significant three-way interaction was found, after correction for multiple testing, between COMT genotype, exposure to violence, and parent-child relationship in association with physical but not verbal aggressive behavior. Homozygous for the Val allele reported lower levels of physical aggressive behavior when they were exposed to violence and at the same time experienced a positive parent-child relationship compared to Met carriers. Thus, susceptibility properties of COMT genotype were observed in relation to physical aggressive behavior supporting the hypothesis that COMT genotypes are modifying the sensitivity to environment that confers either risk or protection for aggressive behavior. As these are novel findings, they warrant further investigation and replication in independent samples. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Evaluating hybrid poplar rooting. I. genotype x environment interactions in three contrasting sites

Treesearch

Ronald S., Jr. Zalesny; Don E. Riemenschneider; Richard B. Hall

2002-01-01

We need to learn more about environmental conditions that promote or hinder rooting of unrooted dormant hybrid poplar cuttings. Planting cuttings and recording survival after the growing season is not suitable to keep up with industrial demands for improved stock. This method does not provide information about specific genotype x environment interactions. We know very...

Genotype * environment interaction: a case study for Douglas-fir in western Oregon.

Treesearch

Robert K. Campbell

1992-01-01

Unrecognized genotype x environment interactions (g,e) can bias genetic-gain predictions and models for predicting growth dynamics or species perturbations by global climate change. This study tested six sets of families in 10 plantation sites in a 78-thousand-hectare breeding zone. Plantation differences accounted for 71 percent of sums of squares (15-year heights),...

Culture, distress, and oxytocin receptor polymorphism (OXTR) interact to influence emotional support seeking.

PubMed

Kim, Heejung S; Sherman, David K; Sasaki, Joni Y; Xu, Jun; Chu, Thai Q; Ryu, Chorong; Suh, Eunkook M; Graham, Kelsey; Taylor, Shelley E

2010-09-07

Research has demonstrated that certain genotypes are expressed in different forms, depending on input from the social environment. To examine sensitivity to cultural norms regarding emotional support seeking as a type of social environment, we explored the behavioral expression of oxytocin receptor polymorphism (OXTR) rs53576, a gene previously related to socio-emotional sensitivity. Seeking emotional support in times of distress is normative in American culture but not in Korean culture. Consequently, we predicted a three-way interaction of culture, distress, and OXTR genotype on emotional support seeking. Korean and American participants (n = 274) completed assessments of psychological distress and emotional support seeking and were genotyped for OXTR. We found the predicted three-way interaction: among distressed American participants, those with the GG/AG genotypes reported seeking more emotional social support, compared with those with the AA genotype, whereas Korean participants did not differ significantly by genotype; under conditions of low distress, OXTR groups did not differ significantly in either cultural group. These findings suggest that OXTR rs53576 is sensitive to input from the social environment, specifically cultural norms regarding emotional social support seeking. These findings also indicate that psychological distress and culture are important moderators that shape behavioral outcomes associated with OXTR genotypes.

AMMI adjustment for statistical analysis of an international wheat yield trial.

PubMed

Crossa, J; Fox, P N; Pfeiffer, W H; Rajaram, S; Gauch, H G

1991-01-01

Multilocation trials are important for the CIMMYT Bread Wheat Program in producing high-yielding, adapted lines for a wide range of environments. This study investigated procedures for improving predictive success of a yield trial, grouping environments and genotypes into homogeneous subsets, and determining the yield stability of 18 CIMMYT bread wheats evaluated at 25 locations. Additive Main effects and Multiplicative Interaction (AMMI) analysis gave more precise estimates of genotypic yields within locations than means across replicates. This precision facilitated formation by cluster analysis of more cohesive groups of genotypes and locations for biological interpretation of interactions than occurred with unadjusted means. Locations were clustered into two subsets for which genotypes with positive interactions manifested in high, stable yields were identified. The analyses highlighted superior selections with both broad and specific adaptation.

Shape and size variation on the wing of Drosophila mediopunctata: influence of chromosome inversions and genotype-environment interaction.

PubMed

Hatadani, Luciane Mendes; Klaczko, Louis Bernard

2008-07-01

The second chromosome of Drosophila mediopunctata is highly polymorphic for inversions. Previous work reported a significant interaction between these inversions and collecting date on wing size, suggesting the presence of genotype-environment interaction. We performed experiments in the laboratory to test for the joint effects of temperature and chromosome inversions on size and shape of the wing in D. mediopunctata. Size was measured as the centroid size, and shape was analyzed using the generalized least squares Procrustes superimposition followed by discriminant analysis and canonical variates analysis of partial warps and uniform components scores. Our findings show that wing size and shape are influenced by temperature, sex, and karyotype. We also found evidence suggestive of an interaction between the effects of karyotype and temperature on wing shape, indicating the existence of genotype-environment interaction for this trait in D. mediopunctata. In addition, the association between wing size and chromosome inversions is in agreement with previous results indicating that these inversions might be accumulating alleles adapted to different temperatures. However, no significant interaction between temperature and karyotype for size was found--in spite of the significant presence of temperature-genotype (cross) interaction. We suggest that other ecological factors--such as larval crowding--or seasonal variation of genetic content within inversions may explain the previous results.

Using probe genotypes to dissect QTL × environment interactions for grain yield components in winter wheat.

PubMed

Zheng, Bing Song; Le Gouis, Jacques; Leflon, Martine; Rong, Wen Ying; Laperche, Anne; Brancourt-Hulmel, Maryse

2010-11-01

Yield is known to be a complex trait, the expression of which interacts strongly with environmental conditions. Understanding the genetic basis of these genotype × environment interactions, particularly under limited input levels, is a key objective when selecting wheat genotypes adapted to specific environments. Our principal objectives were thus: (1) to identify genomic regions [quantitative trait loci (QTL)] involving QTL × environment interactions (QEI) and (2) to develop a strategy to understand the specificity of these regions to certain environments. The two main components of yield were studied: kernel number (KN) and thousand-kernel weight (TKW). The Arche × Récital doubled-haploid population of 222 lines was grown in replicated field trials during 2000 and 2001 at three locations in France, under two nitrogen levels. The 12 environments were characterized in terms of water deficit, radiation, temperature and nitrogen stress based on measurements conducted on the four-probe genotypes: Arche, Récital, Ritmo and Soissons. A four-step strategy was developed to explain QTL specificity to some environments: (1) the detection of QTL for KN and TKW in each environment; (2) the estimation of genotypic sensitivities as the factorial regression slope of KN and TKW to environmental covariates and the detection of QTL for these genotypic sensitivities; (3) study of the co-locations of QTL for KN and TKW and of the QTL for sensitivities; in the event of a co-location partitioning the QEI, appropriate covariates were employed; (4) a description of the environments where QTL were detected for KN and TKW using the environmental covariates. A total of 131 QTL were found to be associated with KN, TKW and their sensitivity to environmental covariates across the 12 environments. Four of these QTL, for both KN and TKW, were located on linkage groups 1B, 2D1, 4B and 5A1, and displayed pleiotropic effects. Factorial regression explained from 15.1 to 83.2% of the QEI for KN and involved three major environmental covariates: cumulative radiation-days ±3 days at meiosis, cumulative degree-days >25°C ±3 days at meiosis and nitrogen stress at flowering. For TKW, 13.5-81.8% of the effect of the QEI was partitioned and involved three major environmental covariates: water deficit from flowering to the milk stage, cumulative degree-days >0°C from the milk stage to maturity and soil water deficit at maturity. A comparative analysis was then performed on the QTL detected during this and previous studies published on QEI and some interacting QTL may be common to different genetic backgrounds. Focusing on these QTL common to different genetic backgrounds would give some guidance to understand genotype × environment interaction.

MAOA, childhood maltreatment and antisocial behavior: Meta-analysis of a gene-environment interaction

PubMed Central

Byrd, Amy L.; Manuck, Stephen B.

2013-01-01

Background In a seminal study of gene-environment interaction, childhood maltreatment predicted antisocial behavior more strongly in males carrying an MAOA promoter variant of lesser, compared to higher, transcriptional efficiency. Many further investigations have been reported, including studies of other early environmental exposures and females. Here we report a meta-analysis of studies testing the interaction of MAOA genotype and childhood adversities on antisocial outcomes in predominantly non-clinical samples. Method Included were 27 peer-reviewed, English-language studies published through August, 2012, that contained indicators of maltreatment or “other” family (e.g., parenting, sociodemographic) hardships; MAOA genotype; indices of aggressive and antisocial behavior; and statistical test of genotype-environment interaction. Studies of forensic and exclusively clinical samples, clinical cohorts lacking proportionally matched controls, or outcomes non-specific for antisocial behavior were excluded. The Liptak-Stouffer weighted Z-test for meta-analysis was implemented to maximize study inclusion and calculated separately for male and female cohorts. Results Across 20 male cohorts, early adversity presaged antisocial outcomes more strongly for low, relative to high, activity MAOA genotype (P=.0044). Stratified analyses showed the interaction specific to maltreatment (P=.0000008) and robust to several sensitivity analyses. Across 11 female cohorts, MAOA did not interact with combined early life adversities, whereas maltreatment alone predicted antisocial behaviors preferentially, but weakly, in females of high activity MAOA genotype (P=.02). Conclusions We found common regulatory variation in MAOA to moderate effects of childhood maltreatment on male antisocial behaviors, confirming a sentinel finding in research on gene-environment interaction. An analogous, but less consistent, finding in females warrants further investigation. PMID:23786983

MAOA, childhood maltreatment, and antisocial behavior: meta-analysis of a gene-environment interaction.

PubMed

Byrd, Amy L; Manuck, Stephen B

2014-01-01

In a seminal study of gene-environment interaction, childhood maltreatment predicted antisocial behavior more strongly in male subjects carrying an MAOA promoter variant of lesser, compared with higher, transcriptional efficiency. Many further investigations have been reported, including studies of other early environmental exposures and female subjects. Here, we report a meta-analysis of studies testing the interaction of MAOA genotype and childhood adversities on antisocial outcomes in predominantly nonclinical samples. Included were 27 peer-reviewed, English-language studies published through August, 2012, that contained indicators of maltreatment or other family (e.g., parenting, sociodemographic) hardships; MAOA genotype; indices of aggressive and antisocial behavior; and statistical test of genotype-environment interaction. Studies of forensic and exclusively clinical samples, clinical cohorts lacking proportionally matched control subjects, or outcomes nonspecific for antisocial behavior were excluded. The Liptak-Stouffer weighted Z-test for meta-analysis was implemented to maximize study inclusion and calculated separately for male and female cohorts. Across 20 male cohorts, early adversity presaged antisocial outcomes more strongly for low-activity, relative to high- activity, MAOA genotype (p = .0044). Stratified analyses showed the interaction specific to maltreatment (p = .00000082) and robust to several sensitivity analyses. Across 11 female cohorts, MAOA did not interact with combined early life adversities, whereas maltreatment alone predicted antisocial behaviors preferentially, but weakly, in female subjects of high-activity MAOA genotype (p = .02). We found common regulatory variation in MAOA to moderate effects of childhood maltreatment on male antisocial behaviors, confirming a sentinel finding in research on gene-environment interaction. An analogous, but less consistent, finding in female subjects warrants further investigation. Copyright © 2014 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Biplot evaluation of test environments and identification of mega-environment for sugarcane cultivars in China

PubMed Central

Luo, Jun; Pan, Yong-Bao; Que, Youxiong; Zhang, Hua; Grisham, Michael Paul; Xu, Liping

2015-01-01

Test environments and classification of regional ecological zones into mega environments are the two key components in regional testing of sugarcane cultivars. This study aims to provide the theoretical basis for test environment evaluation and ecological zone division for sugarcane cultivars. In the present study, sugarcane yield data from a three-year nationwide field trial involving 21 cultivars and 14 pilot test locations were analysed using both analysis of variance (ANOVA) and heritability adjusted-genotype main effect plus genotype-environment interaction (HA-GGE) biplot. The results showed that among the interactive factors, the GE interaction had the greatest impact, while the genotype and year interaction showed the lowest impact. Kaiyuan, Lincang and Baoshan of Yunnan, Zhangzhou and Fuzhou of Fujian, and Hechi, Liuzhou and Chongzuo of Guangxi, and Lingao of Hainan were ideal test environments with a demonstrated high efficiency in selecting new cultivars with a wide adaptability, whereas Baise of Guangxi was not. Based on HA-GGE biplot analysis, there are three ecological sugarcane production zones in China, the Southern China Inland Zone, the Southwestern Plateau Zone, and the Southern Coastal Zone. The HA-GGE biplot analysis here presents the ideal test environments and also identifies the mega-environment for sugarcane cultivars in China. PMID:26489689

Biplot evaluation of test environments and identification of mega-environment for sugarcane cultivars in China.

PubMed

Luo, Jun; Pan, Yong-Bao; Que, Youxiong; Zhang, Hua; Grisham, Michael Paul; Xu, Liping

2015-10-22

Test environments and classification of regional ecological zones into mega environments are the two key components in regional testing of sugarcane cultivars. This study aims to provide the theoretical basis for test environment evaluation and ecological zone division for sugarcane cultivars. In the present study, sugarcane yield data from a three-year nationwide field trial involving 21 cultivars and 14 pilot test locations were analysed using both analysis of variance (ANOVA) and heritability adjusted-genotype main effect plus genotype-environment interaction (HA-GGE) biplot. The results showed that among the interactive factors, the GE interaction had the greatest impact, while the genotype and year interaction showed the lowest impact. Kaiyuan, Lincang and Baoshan of Yunnan, Zhangzhou and Fuzhou of Fujian, and Hechi, Liuzhou and Chongzuo of Guangxi, and Lingao of Hainan were ideal test environments with a demonstrated high efficiency in selecting new cultivars with a wide adaptability, whereas Baise of Guangxi was not. Based on HA-GGE biplot analysis, there are three ecological sugarcane production zones in China, the Southern China Inland Zone, the Southwestern Plateau Zone, and the Southern Coastal Zone. The HA-GGE biplot analysis here presents the ideal test environments and also identifies the mega-environment for sugarcane cultivars in China.

Genome-Wide Analysis of Grain Yield Stability and Environmental Interactions in a Multiparental Soybean Population.

PubMed

Xavier, Alencar; Jarquin, Diego; Howard, Reka; Ramasubramanian, Vishnu; Specht, James E; Graef, George L; Beavis, William D; Diers, Brian W; Song, Qijian; Cregan, Perry B; Nelson, Randall; Mian, Rouf; Shannon, J Grover; McHale, Leah; Wang, Dechun; Schapaugh, William; Lorenz, Aaron J; Xu, Shizhong; Muir, William M; Rainey, Katy M

2018-02-02

Genetic improvement toward optimized and stable agronomic performance of soybean genotypes is desirable for food security. Understanding how genotypes perform in different environmental conditions helps breeders develop sustainable cultivars adapted to target regions. Complex traits of importance are known to be controlled by a large number of genomic regions with small effects whose magnitude and direction are modulated by environmental factors. Knowledge of the constraints and undesirable effects resulting from genotype by environmental interactions is a key objective in improving selection procedures in soybean breeding programs. In this study, the genetic basis of soybean grain yield responsiveness to environmental factors was examined in a large soybean nested association population. For this, a genome-wide association to performance stability estimates generated from a Finlay-Wilkinson analysis and the inclusion of the interaction between marker genotypes and environmental factors was implemented. Genomic footprints were investigated by analysis and meta-analysis using a recently published multiparent model. Results indicated that specific soybean genomic regions were associated with stability, and that multiplicative interactions were present between environments and genetic background. Seven genomic regions in six chromosomes were identified as being associated with genotype-by-environment interactions. This study provides insight into genomic assisted breeding aimed at achieving a more stable agronomic performance of soybean, and documented opportunities to exploit genomic regions that were specifically associated with interactions involving environments and subpopulations. Copyright © 2018 Xavier et al.

Genotype-environment interaction and sociology: contributions and complexities.

PubMed

Seabrook, Jamie A; Avison, William R

2010-05-01

Genotype-environment interaction (G x E) refers to situations in which genetic effects connected to a phenotype are dependent upon variability in the environment, or when genes modify an organism's sensitivity to particular environmental features. Using a typology suggested in the G x E literature, we provide an overview of recent papers that show how social context can trigger a genetic vulnerability, compensate for a genetic vulnerability, control behaviors for which a genetic vulnerability exists, and improve adaptation via proximal causes. We argue that to improve their understanding of social structure, sociologists can take advantage of research in behavior genetics by assessing the impact of within-group variance of various health outcomes and complex human behaviors that are explainable by genotype, environment and their interaction. Insights from life course sociology can aid in ensuring that the dynamic nature of the environment in G x E has been accounted for. Identification of an appropriate entry point for sociologists interested in G x E research could begin with the choice of an environmental feature of interest, a genetic factor of interest, and/or behavior of interest. Optimizing measurement in order to capture the complexity of G x E is critical. Examining the interaction between poorly measured environmental factors and well measured genetic variables will overestimate the effects of genetic variables while underestimating the effect of environmental influences, thereby distorting the interaction between genotype and environment. Although the expense of collecting environmental data is very high, reliable and precise measurement of an environmental pathogen enhances a study's statistical power. Copyright 2010 Elsevier Ltd. All rights reserved.

Interactive effects of 5-HTTLPR genotype and rearing environment on affective attitude towards own infant in Japanese mothers.

PubMed

Sawano, Erika; Doi, Hirokazu; Nagai, Tomoko; Ikeda, Satoko; Shinohara, Kauyuki

2017-05-15

Maternal positive attitude towards one's own infant is the cornerstone of effective parenting. Previous research has revealed an influence of both genetic and environmental factors on maternal parenting behavior, but little is known of the potential gene-environment interaction in shaping a mother's affective attitude. To address this gap, we investigated the effect of a mother's childhood rearing environment and a serotonin transporter gene polymorphism (5-HTTLPR) on affective attitude towards her infant. Our analyses found an interactive effect between rearing environment and 5-HTTLPR genotype on maternal attitude. Specifically, a poor rearing environment (characterized by low maternal care and high paternal overprotection) decreased positive attitude towards one's own infant in mothers with homozygous short allele genotype. In contrast, this detrimental effect was almost eliminated in long allele carriers. Altogether, our results indicate that the 5-HTTLPR gene moderates the influence of experienced rearing environment on maternal parental behavior in a manner consistent with the notion that the short 5-HTTLPR allele amplifies environmental influence. Copyright © 2016 Elsevier B.V. All rights reserved.

Analysis of Behavioral and Emotional Problems in Children Highlights the Role of Genotype × Environment Interaction.

PubMed

Molenaar, Dylan; Middeldorp, Christel; van Beijsterveldt, Toos; Boomsma, Dorret I

2015-01-01

This study tested for Genotype × Environment (G × E) interaction on behavioral and emotional problems in children using new methods that do not require identification of candidate genes or environments, can distinguish between interaction with shared and unique environment, and are insensitive to scale effects. Parental ratings of problem behavior from 14,755 twin pairs (5.3 years, SD = 0.22) indicated G × E interaction on emotional liability, social isolation, aggression, attention problems, dependency, anxiety, and physical coordination. Environmental influences increased in children who were genetically more predisposed to problem behavior, with ~20% of the variance due to G × E interaction (8% for anxiety to 37% for attention problems). Ignoring G × E interaction does not greatly bias heritability estimates, but it does offer a comprehensive model of the etiology for childhood problems. © 2015 The Authors. Child Development © 2015 Society for Research in Child Development, Inc.

Simultaneous selection for cowpea (Vigna unguiculata L.) genotypes with adaptability and yield stability using mixed models.

PubMed

Torres, F E; Teodoro, P E; Rodrigues, E V; Santos, A; Corrêa, A M; Ceccon, G

2016-04-29

The aim of this study was to select erect cowpea (Vigna unguiculata L.) genotypes simultaneously for high adaptability, stability, and yield grain in Mato Grosso do Sul, Brazil using mixed models. We conducted six trials of different cowpea genotypes in 2005 and 2006 in Aquidauana, Chapadão do Sul, Dourados, and Primavera do Leste. The experimental design was randomized complete blocks with four replications and 20 genotypes. Genetic parameters were estimated by restricted maximum likelihood/best linear unbiased prediction, and selection was based on the harmonic mean of the relative performance of genetic values method using three strategies: selection based on the predicted breeding value, having considered the performance mean of the genotypes in all environments (no interaction effect); the performance in each environment (with an interaction effect); and the simultaneous selection for grain yield, stability, and adaptability. The MNC99542F-5 and MNC99-537F-4 genotypes could be grown in various environments, as they exhibited high grain yield, adaptability, and stability. The average heritability of the genotypes was moderate to high and the selective accuracy was 82%, indicating an excellent potential for selection.

Maternal environment affects the genetic basis of seed dormancy in Arabidopsis thaliana.

PubMed

Postma, Froukje M; Ågren, Jon

2015-02-01

The genetic basis of seed dormancy, a key life history trait important for adaptive evolution in plant populations, has yet been studied only using seeds produced under controlled conditions in greenhouse environments. However, dormancy is strongly affected by maternal environmental conditions, and interactions between seed genotype and maternal environment have been reported. Consequently, the genetic basis of dormancy of seeds produced under natural field conditions remains unclear. We examined the effect of maternal environment on the genetic architecture of seed dormancy using a recombinant inbred line (RIL) population derived from a cross between two locally adapted populations of Arabidopsis thaliana from Italy and Sweden. We mapped quantitative trait loci (QTL) for dormancy of seeds produced in the greenhouse and at the native field sites of the parental genotypes. The Italian genotype produced seeds with stronger dormancy at fruit maturation than did the Swedish genotype in all three environments, and the maternal field environments induced higher dormancy levels compared to the greenhouse environment in both genotypes. Across the three maternal environments, a total of nine dormancy QTL were detected, three of which were only detected among seeds matured in the field, and six of which showed significant QTL × maternal environment interactions. One QTL had a large effect on dormancy across all three environments and colocalized with the candidate gene DOG1. Our results demonstrate the importance of studying the genetic basis of putatively adaptive traits under relevant conditions. © 2015 John Wiley & Sons Ltd.

QTL and QTL x environment effects on agronomic and nitrogen acquisition traits in rice.

PubMed

Senthilvel, Senapathy; Vinod, Kunnummal Kurungara; Malarvizhi, Palaniappan; Maheswaran, Marappa

2008-09-01

Agricultural environments deteriorate due to excess nitrogen application. Breeding for low nitrogen responsive genotypes can reduce soil nitrogen input. Rice genotypes respond variably to soil available nitrogen. The present study attempted quantification of genotype x nitrogen level interaction and mapping of quantitative trait loci (QTLs) associated with nitrogen use efficiency (NUE) and other associated agronomic traits. Twelve parameters were observed across a set of 82 double haploid (DH) lines derived from IR64/Azucena. Three nitrogen regimes namely, native (0 kg/ha; no nitrogen applied), optimum (100 kg/ha) and high (200 kg/ha) replicated thrice were the environments. The parents and DH lines were significantly varying for all traits under different nitrogen regimes. All traits except plant height recorded significant genotype x environment interaction. Individual plant yield was positively correlated with nitrogen use efficiency and nitrogen uptake. Sixteen QTLs were detected by composite interval mapping. Eleven QTLs showed significant QTL x environment interactions. On chromosome 3, seven QTLs were detected associated with nitrogen use, plant yield and associated traits. A QTL region between markers RZ678, RZ574 and RZ284 was associated with nitrogen use and yield. This chromosomal region was enriched with expressed gene sequences of known key nitrogen assimilation genes.

Association of Positive and Negative Parenting Behavior with Childhood ADHD: Interactions with Offspring Monoamine Oxidase A (MAO-A) Genotype

ERIC Educational Resources Information Center

Li, James J.; Lee, Steve S.

2012-01-01

Relatively little is known about the potential interplay between genetic and environmental influences on attention-deficit/hyperactivity disorder (ADHD), including gene-environment interaction (GxE). There is evidence that parenting behavior interacts with offspring genotype in the development of externalizing problems, but studies have largely…

Environment characterization as an aid to wheat improvement: interpreting genotype-environment interactions by modelling water-deficit patterns in North-Eastern Australia.

PubMed

Chenu, K; Cooper, M; Hammer, G L; Mathews, K L; Dreccer, M F; Chapman, S C

2011-03-01

Genotype-environment interactions (GEI) limit genetic gain for complex traits such as tolerance to drought. Characterization of the crop environment is an important step in understanding GEI. A modelling approach is proposed here to characterize broadly (large geographic area, long-term period) and locally (field experiment) drought-related environmental stresses, which enables breeders to analyse their experimental trials with regard to the broad population of environments that they target. Water-deficit patterns experienced by wheat crops were determined for drought-prone north-eastern Australia, using the APSIM crop model to account for the interactions of crops with their environment (e.g. feedback of plant growth on water depletion). Simulations based on more than 100 years of historical climate data were conducted for representative locations, soils, and management systems, for a check cultivar, Hartog. The three main environment types identified differed in their patterns of simulated water stress around flowering and during grain-filling. Over the entire region, the terminal drought-stress pattern was most common (50% of production environments) followed by a flowering stress (24%), although the frequencies of occurrence of the three types varied greatly across regions, years, and management. This environment classification was applied to 16 trials relevant to late stages testing of a breeding programme. The incorporation of the independently-determined environment types in a statistical analysis assisted interpretation of the GEI for yield among the 18 representative genotypes by reducing the relative effect of GEI compared with genotypic variance, and helped to identify opportunities to improve breeding and germplasm-testing strategies for this region.

Cerebellum Transcriptome of Mice Bred for High Voluntary Activity Offers Insights into Locomotor Control and Reward-Dependent Behaviors.

PubMed

Caetano-Anollés, Kelsey; Rhodes, Justin S; Garland, Theodore; Perez, Sam D; Hernandez, Alvaro G; Southey, Bruce R; Rodriguez-Zas, Sandra L

2016-01-01

The role of the cerebellum in motivation and addictive behaviors is less understood than that in control and coordination of movements. High running can be a self-rewarding behavior exhibiting addictive properties. Changes in the cerebellum transcriptional networks of mice from a line selectively bred for High voluntary running (H) were profiled relative to an unselected Control (C) line. The environmental modulation of these changes was assessed both in activity environments corresponding to 7 days of Free (F) access to running wheel and to Blocked (B) access on day 7. Overall, 457 genes exhibited a significant (FDR-adjusted P-value < 0.05) genotype-by-environment interaction effect, indicating that activity genotype differences in gene expression depend on environmental access to running. Among these genes, network analysis highlighted 6 genes (Nrgn, Drd2, Rxrg, Gda, Adora2a, and Rab40b) connected by their products that displayed opposite expression patterns in the activity genotype contrast within the B and F environments. The comparison of network expression topologies suggests that selection for high voluntary running is linked to a predominant dysregulation of hub genes in the F environment that enables running whereas a dysregulation of ancillary genes is favored in the B environment that blocks running. Genes associated with locomotor regulation, signaling pathways, reward-processing, goal-focused, and reward-dependent behaviors exhibited significant genotype-by-environment interaction (e.g. Pak6, Adora2a, Drd2, and Arhgap8). Neuropeptide genes including Adcyap1, Cck, Sst, Vgf, Npy, Nts, Penk, and Tac2 and related receptor genes also exhibited significant genotype-by-environment interaction. The majority of the 183 differentially expressed genes between activity genotypes (e.g. Drd1) were under-expressed in C relative to H genotypes and were also under-expressed in B relative to F environments. Our findings indicate that the high voluntary running mouse line studied is a helpful model for understanding the molecular mechanisms in the cerebellum that influence locomotor control and reward-dependent behaviors.

Cerebellum Transcriptome of Mice Bred for High Voluntary Activity Offers Insights into Locomotor Control and Reward-Dependent Behaviors

PubMed Central

Caetano-Anollés, Kelsey; Rhodes, Justin S.; Garland, Theodore; Perez, Sam D.; Hernandez, Alvaro G.; Southey, Bruce R.; Rodriguez-Zas, Sandra L.

2016-01-01

The role of the cerebellum in motivation and addictive behaviors is less understood than that in control and coordination of movements. High running can be a self-rewarding behavior exhibiting addictive properties. Changes in the cerebellum transcriptional networks of mice from a line selectively bred for High voluntary running (H) were profiled relative to an unselected Control (C) line. The environmental modulation of these changes was assessed both in activity environments corresponding to 7 days of Free (F) access to running wheel and to Blocked (B) access on day 7. Overall, 457 genes exhibited a significant (FDR-adjusted P-value < 0.05) genotype-by-environment interaction effect, indicating that activity genotype differences in gene expression depend on environmental access to running. Among these genes, network analysis highlighted 6 genes (Nrgn, Drd2, Rxrg, Gda, Adora2a, and Rab40b) connected by their products that displayed opposite expression patterns in the activity genotype contrast within the B and F environments. The comparison of network expression topologies suggests that selection for high voluntary running is linked to a predominant dysregulation of hub genes in the F environment that enables running whereas a dysregulation of ancillary genes is favored in the B environment that blocks running. Genes associated with locomotor regulation, signaling pathways, reward-processing, goal-focused, and reward-dependent behaviors exhibited significant genotype-by-environment interaction (e.g. Pak6, Adora2a, Drd2, and Arhgap8). Neuropeptide genes including Adcyap1, Cck, Sst, Vgf, Npy, Nts, Penk, and Tac2 and related receptor genes also exhibited significant genotype-by-environment interaction. The majority of the 183 differentially expressed genes between activity genotypes (e.g. Drd1) were under-expressed in C relative to H genotypes and were also under-expressed in B relative to F environments. Our findings indicate that the high voluntary running mouse line studied is a helpful model for understanding the molecular mechanisms in the cerebellum that influence locomotor control and reward-dependent behaviors. PMID:27893846

Mental and physical distress is modulated by a polymorphism in the 5-HT transporter gene interacting with social stressors and chronic disease burden.

PubMed

Grabe, H J; Lange, M; Wolff, B; Völzke, H; Lucht, M; Freyberger, H J; John, U; Cascorbi, I

2005-02-01

Previous studies have yielded conflicting results as to the putative role of the functional polymorphism of the promoter region of the serotonin transporter gene (SLC6A4) in the etiology of anxiety-related traits and depressive disorders. Recently, a significant gene-environment interaction was found between life stressors, the short allele of the SLC6A4 polymorphism and depression. The aim of the present study was to investigate if such a gene-environment interaction could be replicated within a different population with a different risk structure. A total of 1005 subjects from a general population sample (Study of Health in Pomerania) were genotyped. Mental and physical distress were assessed on 38 items of the modified complaint scale (BL-38). The interaction between the SLC6A4 genotype, social stressors and chronic diseases with regard to the BL-38 score was evaluated by ANOVA. There was no independent association of genotype with mental and physical distress. However, significant interactions between genotype, unemployment and chronic diseases (F = 6.6; df = 3, 671; P < 0.001) were found in females but not in males. The genotype explained 2% of the total variance of the BL-38 score and 9.1% of the explained variance. The results partly confirm previous findings of a significant gene-environment interaction of the short allele, indicating a higher mental vulnerability to social stressors and chronic diseases. The relevance of this finding is sustained by the fact that the sample characteristics and the risk structure were highly different from previous studies.

Detecting regulatory gene-environment interactions with unmeasured environmental factors.

PubMed

Fusi, Nicoló; Lippert, Christoph; Borgwardt, Karsten; Lawrence, Neil D; Stegle, Oliver

2013-06-01

Genomic studies have revealed a substantial heritable component of the transcriptional state of the cell. To fully understand the genetic regulation of gene expression variability, it is important to study the effect of genotype in the context of external factors such as alternative environmental conditions. In model systems, explicit environmental perturbations have been considered for this purpose, allowing to directly test for environment-specific genetic effects. However, such experiments are limited to species that can be profiled in controlled environments, hampering their use in important systems such as human. Moreover, even in seemingly tightly regulated experimental conditions, subtle environmental perturbations cannot be ruled out, and hence unknown environmental influences are frequent. Here, we propose a model-based approach to simultaneously infer unmeasured environmental factors from gene expression profiles and use them in genetic analyses, identifying environment-specific associations between polymorphic loci and individual gene expression traits. In extensive simulation studies, we show that our method is able to accurately reconstruct environmental factors and their interactions with genotype in a variety of settings. We further illustrate the use of our model in a real-world dataset in which one environmental factor has been explicitly experimentally controlled. Our method is able to accurately reconstruct the true underlying environmental factor even if it is not given as an input, allowing to detect genuine genotype-environment interactions. In addition to the known environmental factor, we find unmeasured factors involved in novel genotype-environment interactions. Our results suggest that interactions with both known and unknown environmental factors significantly contribute to gene expression variability. and implementation: Software available at http://pmbio.github.io/envGPLVM/. Supplementary data are available at Bioinformatics online.

Genotype by environment interactions and combining ability for strawberry families grown in diverse environments

USDA-ARS?s Scientific Manuscript database

Ten seedlings from 36 crosses representing eastern and western North American short day and remontant genotypes were evaluated in 2011 and 2012 in California, Michigan, New Hampshire and Oregon, for phenology, flower related traits, plant characteristics, fruit characteristics and fruit chemistry tr...

Mathematical Ability and Socio-Economic Background: IRT Modeling to Estimate Genotype by Environment Interaction.

PubMed

Schwabe, Inga; Boomsma, Dorret I; van den Berg, Stéphanie M

2017-12-01

Genotype by environment interaction in behavioral traits may be assessed by estimating the proportion of variance that is explained by genetic and environmental influences conditional on a measured moderating variable, such as a known environmental exposure. Behavioral traits of interest are often measured by questionnaires and analyzed as sum scores on the items. However, statistical results on genotype by environment interaction based on sum scores can be biased due to the properties of a scale. This article presents a method that makes it possible to analyze the actually observed (phenotypic) item data rather than a sum score by simultaneously estimating the genetic model and an item response theory (IRT) model. In the proposed model, the estimation of genotype by environment interaction is based on an alternative parametrization that is uniquely identified and therefore to be preferred over standard parametrizations. A simulation study shows good performance of our method compared to analyzing sum scores in terms of bias. Next, we analyzed data of 2,110 12-year-old Dutch twin pairs on mathematical ability. Genetic models were evaluated and genetic and environmental variance components estimated as a function of a family's socio-economic status (SES). Results suggested that common environmental influences are less important in creating individual differences in mathematical ability in families with a high SES than in creating individual differences in mathematical ability in twin pairs with a low or average SES.

Genotype × Environment Interactions of Yield Traits in Backcross Introgression Lines Derived from Oryza sativa cv. Swarna/Oryza nivara

PubMed Central

Balakrishnan, Divya; Subrahmanyam, Desiraju; Badri, Jyothi; Raju, Addanki Krishnam; Rao, Yadavalli Venkateswara; Beerelli, Kavitha; Mesapogu, Sukumar; Surapaneni, Malathi; Ponnuswamy, Revathi; Padmavathi, G.; Babu, V. Ravindra; Neelamraju, Sarla

2016-01-01

Advanced backcross introgression lines (BILs) developed from crosses of Oryza sativa var. Swarna/O. nivara accessions were grown and evaluated for yield and related traits. Trials were conducted for consecutive three seasons in field conditions in a randomized complete block design with three replications. Data on yield traits under irrigated conditions were analyzed using the Additive Main Effect and Multiplicative Interaction (AMMI), Genotype and Genotype × Environment Interaction (GGE) and modified rank-sum statistic (YSi) for yield stability. BILs viz., G3 (14S) and G6 (166S) showed yield stability across the seasons along with high mean yield performance. G3 is early in flowering with high yield and has good grain quality and medium height, hence could be recommended for most of the irrigated locations. G6 is a late duration genotype, with strong culm strength, high grain number and panicle weight. G6 has higher yield and stability than Swarna but has Swarna grain type. Among the varieties tested DRRDhan 40 and recurrent parent Swarna showed stability for yield traits across the seasons. The component traits thousand grain weight, panicle weight, panicle length, grain number and plant height explained highest genotypic percentage over environment and interaction factors and can be prioritized to dissect stable QTLs/ genes. These lines were genotyped using microsatellite markers covering the entire rice genome and also using a set of markers linked to previously reported yield QTLs. It was observed that wild derived lines with more than 70% of recurrent parent genome were stable and showed enhanced yield levels compared to genotypes with higher donor genome introgressions. PMID:27807437

Use of AMMI and linear regression models to analyze genotype-environment interaction in durum wheat.

PubMed

Nachit, M M; Nachit, G; Ketata, H; Gauch, H G; Zobel, R W

1992-03-01

The joint durum wheat (Triticum turgidum L var 'durum') breeding program of the International Maize and Wheat Improvement Center (CIMMYT) and the International Center for Agricultural Research in the Dry Areas (ICARDA) for the Mediterranean region employs extensive multilocation testing. Multilocation testing produces significant genotype-environment (GE) interaction that reduces the accuracy for estimating yield and selecting appropriate germ plasm. The sum of squares (SS) of GE interaction was partitioned by linear regression techniques into joint, genotypic, and environmental regressions, and by Additive Main effects and the Multiplicative Interactions (AMMI) model into five significant Interaction Principal Component Axes (IPCA). The AMMI model was more effective in partitioning the interaction SS than the linear regression technique. The SS contained in the AMMI model was 6 times higher than the SS for all three regressions. Postdictive assessment recommended the use of the first five IPCA axes, while predictive assessment AMMI1 (main effects plus IPCA1). After elimination of random variation, AMMI1 estimates for genotypic yields within sites were more precise than unadjusted means. This increased precision was equivalent to increasing the number of replications by a factor of 3.7.

Genotype-environment interaction in passive avoidance learning of the paradise fish (Macropodus opercularis).

PubMed

Csányi, V; Gervai, J

1985-01-01

Passive dark avoidance conditioning and effects of the presence and absence of a fish-like dummy on the training process were studied in four inbred strains of paradise fish. Strain differences were found in the shuttle activity during habituation trials, and in the sensitivity to the mild electric shock punishment. The presence or absence of the dummy in the punished dark side of the shuttle box had a genotype-dependent effect on the measures taken during the conditioning process. The statistical analysis of the learning curves revealed differences in the way the strains varied in the different environments, i.e. genotype--environment interaction components of variances were identified. The results are discussed in the light of previous investigations and their implication in further genetic analysis.

The effect of genotype and in utero environment on interindividual variation in neonate DNA methylomes.

PubMed

Teh, Ai Ling; Pan, Hong; Chen, Li; Ong, Mei-Lyn; Dogra, Shaillay; Wong, Johnny; MacIsaac, Julia L; Mah, Sarah M; McEwen, Lisa M; Saw, Seang-Mei; Godfrey, Keith M; Chong, Yap-Seng; Kwek, Kenneth; Kwoh, Chee-Keong; Soh, Shu-E; Chong, Mary F F; Barton, Sheila; Karnani, Neerja; Cheong, Clara Y; Buschdorf, Jan Paul; Stünkel, Walter; Kobor, Michael S; Meaney, Michael J; Gluckman, Peter D; Holbrook, Joanna D

2014-07-01

Integrating the genotype with epigenetic marks holds the promise of better understanding the biology that underlies the complex interactions of inherited and environmental components that define the developmental origins of a range of disorders. The quality of the in utero environment significantly influences health over the lifecourse. Epigenetics, and in particular DNA methylation marks, have been postulated as a mechanism for the enduring effects of the prenatal environment. Accordingly, neonate methylomes contain molecular memory of the individual in utero experience. However, interindividual variation in methylation can also be a consequence of DNA sequence polymorphisms that result in methylation quantitative trait loci (methQTLs) and, potentially, the interaction between fixed genetic variation and environmental influences. We surveyed the genotypes and DNA methylomes of 237 neonates and found 1423 punctuate regions of the methylome that were highly variable across individuals, termed variably methylated regions (VMRs), against a backdrop of homogeneity. MethQTLs were readily detected in neonatal methylomes, and genotype alone best explained ∼25% of the VMRs. We found that the best explanation for 75% of VMRs was the interaction of genotype with different in utero environments, including maternal smoking, maternal depression, maternal BMI, infant birth weight, gestational age, and birth order. Our study sheds new light on the complex relationship between biological inheritance as represented by genotype and individual prenatal experience and suggests the importance of considering both fixed genetic variation and environmental factors in interpreting epigenetic variation. © 2014 Teh et al.; Published by Cold Spring Harbor Laboratory Press.

Gene by Environment Interaction and Resilience: Effects of Child Maltreatment and Serotonin, Corticotropin Releasing Hormone, Dopamine, and Oxytocin Genes

PubMed Central

Cicchetti, Dante; Rogosch, Fred A.

2013-01-01

In this investigation, gene-environment interaction effects in predicting resilience in adaptive functioning among maltreated and nonmaltreated low-income children (N = 595) were examined. A multi-component index of resilient functioning was derived and levels of resilient functioning were identified. Variants in four genes, 5-HTTLPR, CRHR1, DRD4 -521C/T, and OXTR, were investigated. In a series of ANCOVAs, child maltreatment demonstrated a strong negative main effect on children’s resilient functioning, whereas no main effects for any of the genotypes of the respective genes were found. However, gene-environment interactions involving genotypes of each of the respective genes and maltreatment status were obtained. For each respective gene, among children with a specific genotype, the relative advantage in resilient functioning of nonmaltreated compared to maltreated children was stronger than was the case for nonmaltreated and maltreated children with other genotypes of the respective gene. Across the four genes, a composite of the genotypes that more strongly differentiated resilient functioning between nonmaltreated and maltreated children provided further evidence of genetic variations influencing resilient functioning in nonmaltreated children, whereas genetic variation had a negligible effect on promoting resilience among maltreated children. Additional effects were observed for children based on the number of subtypes of maltreatment children experienced, as well as for abuse and neglect subgroups. Finally, maltreated and nonmaltreated children with high levels of resilience differed in their average number of differentiating genotypes. These results suggest that differential resilient outcomes are based on the interaction between genes and developmental experiences. PMID:22559122

Evaluation of genotype x environment interactions in cotton using the method proposed by Eberhart and Russell and reaction norm models.

PubMed

Alves, R S; Teodoro, P E; Farias, F C; Farias, F J C; Carvalho, L P; Rodrigues, J I S; Bhering, L L; Resende, M D V

2017-08-17

Cotton produces one of the most important textile fibers of the world and has great relevance in the world economy. It is an economically important crop in Brazil, which is the world's fifth largest producer. However, studies evaluating the genotype x environment (G x E) interactions in cotton are scarce in this country. Therefore, the goal of this study was to evaluate the G x E interactions in two important traits in cotton (fiber yield and fiber length) using the method proposed by Eberhart and Russell (simple linear regression) and reaction norm models (random regression). Eight trials with sixteen upland cotton genotypes, conducted in a randomized block design, were used. It was possible to identify a genotype with wide adaptability and stability for both traits. Reaction norm models have excellent theoretical and practical properties and led to more informative and accurate results than the method proposed by Eberhart and Russell and should, therefore, be preferred. Curves of genotypic values as a function of the environmental gradient, which predict the behavior of the genotypes along the environmental gradient, were generated. These curves make possible the recommendation to untested environmental levels.

Using artificial neural networks to select upright cowpea (Vigna unguiculata) genotypes with high productivity and phenotypic stability.

PubMed

Barroso, L M A; Teodoro, P E; Nascimento, M; Torres, F E; Nascimento, A C C; Azevedo, C F; Teixeira, F R F

2016-11-03

Cowpea (Vigna unguiculata) is grown in three Brazilian regions: the Midwest, North, and Northeast, and is consumed by people on low incomes. It is important to investigate the genotype x environment (GE) interaction to provide accurate recommendations for farmers. The aim of this study was to identify cowpea genotypes with high adaptability and phenotypic stability for growing in the Brazilian Cerrado, and to compare the use of artificial neural networks with the Eberhart and Russell (1966) method. Six trials with upright cowpea genotypes were conducted in 2005 and 2006 in the States of Mato Grosso do Sul and Mato Grosso. The data were subjected to adaptability and stability analysis by the Eberhart and Russell (1966) method and artificial neural networks. The genotypes MNC99-537F-4 and EVX91-2E-2 provided grain yields above the overall environment means, and exhibited high stability according to both methods. Genotype IT93K-93-10 was the most suitable for unfavorable environments. There was a high correlation between the results of both methods in terms of classifying the genotypes by their adaptability and stability. Therefore, this new approach would be effective in quantifying the GE interaction in upright cowpea breeding programs.

Interspecific pine hybrids II. genotype by environment interactions across Australia, Swaziland, and Zimbabwe

Treesearch

H. S. Dungey; M. J. Dieters; D. P. Gwaze; P. G. Toon; D. G. Nikles

2000-01-01

Collaborative research trials of Queensland-bred pine hybrids have been established in many sites outside Australia. These trials enable the estimation of genotype x environment effects, which are important in determining the level of regionalisation needed in any breeding program. Correlations across sites testing hybrids between Pinus caribaea var...

Genetic susceptibility to family environment: BDNF Val66met and 5-HTTLPR influence depressive symptoms.

PubMed

Dalton, Elizabeth D; Hammen, Constance L; Najman, Jake M; Brennan, Patricia A

2014-12-01

Functional genetic polymorphisms associated with Brain-Derived Neurotrophic Factor (BDNF) and serotonin (5-HTTLPR) have demonstrated associations with depression in interaction with environmental stressors. In light of evidence for biological connections between BDNF and serotonin, it is prudent to consider genetic epistasis between variants in these genes in the development of depressive symptoms. The current study examined the effects of val66met, 5-HTTLPR, and family environment quality on youth depressive symptoms in adolescence and young adulthood in a longitudinal sample oversampled for maternal depression history. A differential susceptibility model was tested, comparing the effects of family environment on depression scores across different levels of a cumulative plasticity genotype, defined as presence of both, either, or neither plasticity alleles (defined here as val66met Met and 5-HTTLPR 'S'). Cumulative plasticity genotype interacted with family environment quality to predict depression among males and females at age 15. After age 15, however, the interaction of cumulative plasticity genotype and early family environment quality was only predictive of depression among females. Results supported a differential susceptibility model at age 15, such that plasticity allele presence was associated with more or less depressive symptoms depending on valence of the family environment, and a diathesis-stress model of gene-environment interaction after age 15. These findings, although preliminary because of the small sample size, support prior results indicating interactive effects of 5-HTTLPR, val66met, and environmental stress, and suggest that family environment may have a stronger influence on genetically susceptible women than men.

Genome-wide interaction of genotype by erythrocyte n-3 PUFAs contributes to phenotypic variance of diabetes-related traits

USDA-ARS?s Scientific Manuscript database

While genome-wide association studies (GWAS) and candidate gene approach have identified many genetic variants that contribute to disease risk as main effects, the impact of genotype by environment (GxE) interactions remains rather under-surveyed. The present study aimed to examine variance contribu...

Gender-Specific Gene–Environment Interaction in Alcohol Dependence: The Impact of Daily Life Events and GABRA2

PubMed Central

Perry, Brea L.; Pescosolido, Bernice A.; Bucholz, Kathleen; Edenberg, Howard; Kramer, John; Kuperman, Samuel; Schuckit, Marc Alan; Nurnberger, John I.

2015-01-01

Gender-moderated gene–environment interactions are rarely explored, raising concerns about inaccurate specification of etiological models and inferential errors. The current study examined the influence of gender, negative and positive daily life events, and GABRA2 genotype (SNP rs279871) on alcohol dependence, testing two- and three-way interactions between these variables using multilevel regression models fit to data from 2,281 White participants in the Collaborative Study on the Genetics of Alcoholism. Significant direct effects of variables of interest were identified, as well as gender-specific moderation of genetic risk on this SNP by social experiences. Higher levels of positive life events were protective for men with the high-risk genotype, but not among men with the low-risk genotype or women, regardless of genotype. Our findings support the disinhibition theory of alcohol dependence, suggesting that gender differences in social norms, constraints and opportunities, and behavioral undercontrol may explain men and women’s distinct patterns of association. PMID:23974430

Gender specific gene-environment interactions on laboratory-assessed aggression.

PubMed

Verona, Edelyn; Joiner, Thomas E; Johnson, Frank; Bender, Theodore W

2006-01-01

We examined gene-environment interactive effects on aggressive behavior among men and women genotyped (short versus long alleles) for the serotonin transporter gene. Aggressive behavior was indexed via a laboratory paradigm that measured the intensity and duration of shocks delivered to a putative "employee". Half of the participants were exposed to a physical stressor during the procedure (stress) and half were not (no-stress). Participants' physiological responses were gauged via acoustic startle eyeblink reactions (startle reactivity). Results were that men with the homozygous short (s/s) genotype showed increased aggression only under stress, whereas women and men carrying the long allele did not show differences in aggression in stress versus no-stress. However, although stress exposure produced increases in startle reactivity, there were no genotype or gender differences in physiology. These results replicate longitudinal research findings confirming the interactive effects of genes and environment on behavioral reactivity and on the development of externalizing psychopathological syndromes, at least in men.

Complex Genotype by Environment interactions and changing genetic architectures across thermal environments in the Australian field cricket, Teleogryllus oceanicus

PubMed Central

2011-01-01

Background Biologists studying adaptation under sexual selection have spent considerable effort assessing the relative importance of two groups of models, which hinge on the idea that females gain indirect benefits via mate discrimination. These are the good genes and genetic compatibility models. Quantitative genetic studies have advanced our understanding of these models by enabling assessment of whether the genetic architectures underlying focal phenotypes are congruent with either model. In this context, good genes models require underlying additive genetic variance, while compatibility models require non-additive variance. Currently, we know very little about how the expression of genotypes comprised of distinct parental haplotypes, or how levels and types of genetic variance underlying key phenotypes, change across environments. Such knowledge is important, however, because genotype-environment interactions can have major implications on the potential for evolutionary responses to selection. Results We used a full diallel breeding design to screen for complex genotype-environment interactions, and genetic architectures underlying key morphological traits, across two thermal environments (the lab standard 27°C, and the cooler 23°C) in the Australian field cricket, Teleogryllus oceanicus. In males, complex three-way interactions between sire and dam parental haplotypes and the rearing environment accounted for up to 23 per cent of the scaled phenotypic variance in the traits we measured (body mass, pronotum width and testes mass), and each trait harboured significant additive genetic variance in the standard temperature (27°C) only. In females, these three-way interactions were less important, with interactions between the paternal haplotype and rearing environment accounting for about ten per cent of the phenotypic variance (in body mass, pronotum width and ovary mass). Of the female traits measured, only ovary mass for crickets reared at the cooler temperature (23°C), exhibited significant levels of additive genetic variance. Conclusions Our results show that the genetics underlying phenotypic expression can be complex, context-dependent and different in each of the sexes. We discuss the implications of these results, particularly in terms of the evolutionary processes that hinge on good and compatible genes models. PMID:21791118

Elevated temperature is more effective than elevated [CO2 ] in exposing genotypic variation in Telopea speciosissima growth plasticity: implications for woody plant populations under climate change.

PubMed

Huang, Guomin; Rymer, Paul D; Duan, Honglang; Smith, Renee A; Tissue, David T

2015-10-01

Intraspecific variation in phenotypic plasticity is a critical determinant of plant species capacity to cope with climate change. A long-standing hypothesis states that greater levels of environmental variability will select for genotypes with greater phenotypic plasticity. However, few studies have examined how genotypes of woody species originating from contrasting environments respond to multiple climate change factors. Here, we investigated the main and interactive effects of elevated [CO2 ] (CE ) and elevated temperature (TE ) on growth and physiology of Coastal (warmer, less variable temperature environment) and Upland (cooler, more variable temperature environment) genotypes of an Australian woody species Telopea speciosissima. Both genotypes were positively responsive to CE (35% and 29% increase in whole-plant dry mass and leaf area, respectively), but only the Coastal genotype exhibited positive growth responses to TE . We found that the Coastal genotype exhibited greater growth response to TE (47% and 85% increase in whole-plant dry mass and leaf area, respectively) when compared with the Upland genotype (no change in dry mass or leaf area). No intraspecific variation in physiological plasticity was detected under CE or TE , and the interactive effects of CE and TE on intraspecific variation in phenotypic plasticity were also largely absent. Overall, TE was a more effective climate factor than CE in exposing genotypic variation in our woody species. Our results contradict the paradigm that genotypes from more variable climates will exhibit greater phenotypic plasticity in future climate regimes. © 2015 John Wiley & Sons Ltd.

A Partial Least Square Approach for Modeling Gene-gene and Gene-environment Interactions When Multiple Markers Are Genotyped

PubMed Central

Wang, Tao; Ho, Gloria; Ye, Kenny; Strickler, Howard; Elston, Robert C.

2008-01-01

Genetic association studies achieve an unprecedented level of resolution in mapping disease genes by genotyping dense SNPs in a gene region. Meanwhile, these studies require new powerful statistical tools that can optimally handle a large amount of information provided by genotype data. A question that arises is how to model interactions between two genes. Simply modeling all possible interactions between the SNPs in two gene regions is not desirable because a greatly increased number of degrees of freedom can be involved in the test statistic. We introduce an approach to reduce the genotype dimension in modeling interactions. The genotype compression of this approach is built upon the information on both the trait and the cross-locus gametic disequilibrium between SNPs in two interacting genes, in such a way as to parsimoniously model the interactions without loss of useful information in the process of dimension reduction. As a result, it improves power to detect association in the presence of gene-gene interactions. This approach can be similarly applied for modeling gene-environment interactions. We compare this method with other approaches: the corresponding test without modeling any interaction, that based on a saturated interaction model, that based on principal component analysis, and that based on Tukey’s 1-df model. Our simulations suggest that this new approach has superior power to that of the other methods. In an application to endometrial cancer case-control data from the Women’s Health Initiative (WHI), this approach detected AKT1 and AKT2 as being significantly associated with endometrial cancer susceptibility by taking into account their interactions with BMI. PMID:18615621

A partial least-square approach for modeling gene-gene and gene-environment interactions when multiple markers are genotyped.

PubMed

Wang, Tao; Ho, Gloria; Ye, Kenny; Strickler, Howard; Elston, Robert C

2009-01-01

Genetic association studies achieve an unprecedented level of resolution in mapping disease genes by genotyping dense single nucleotype polymorphisms (SNPs) in a gene region. Meanwhile, these studies require new powerful statistical tools that can optimally handle a large amount of information provided by genotype data. A question that arises is how to model interactions between two genes. Simply modeling all possible interactions between the SNPs in two gene regions is not desirable because a greatly increased number of degrees of freedom can be involved in the test statistic. We introduce an approach to reduce the genotype dimension in modeling interactions. The genotype compression of this approach is built upon the information on both the trait and the cross-locus gametic disequilibrium between SNPs in two interacting genes, in such a way as to parsimoniously model the interactions without loss of useful information in the process of dimension reduction. As a result, it improves power to detect association in the presence of gene-gene interactions. This approach can be similarly applied for modeling gene-environment interactions. We compare this method with other approaches, the corresponding test without modeling any interaction, that based on a saturated interaction model, that based on principal component analysis, and that based on Tukey's one-degree-of-freedom model. Our simulations suggest that this new approach has superior power to that of the other methods. In an application to endometrial cancer case-control data from the Women's Health Initiative, this approach detected AKT1 and AKT2 as being significantly associated with endometrial cancer susceptibility by taking into account their interactions with body mass index.

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.

The Interaction of Genotype and Environment Determines Variation in the Maize Kernel Ionome

PubMed Central

Asaro, Alexandra; Ziegler, Gregory; Ziyomo, Cathrine; Hoekenga, Owen A.; Dilkes, Brian P.; Baxter, Ivan

2016-01-01

Plants obtain soil-resident elements that support growth and metabolism from the water-flow facilitated by transpiration and active transport processes. The availability of elements in the environment interacts with the genetic capacity of organisms to modulate element uptake through plastic adaptive responses, such as homeostasis. These interactions should cause the elemental contents of plants to vary such that the effects of genetic polymorphisms will be dramatically dependent on the environment in which the plant is grown. To investigate genotype by environment interactions underlying elemental accumulation, we analyzed levels of elements in maize kernels of the Intermated B73 × Mo17 (IBM) recombinant inbred population grown in 10 different environments, spanning a total of six locations and five different years. In analyses conducted separately for each environment, we identified a total of 79 quantitative trait loci (QTL) controlling seed elemental accumulation. While a set of these QTL was found in multiple environments, the majority were specific to a single environment, suggesting the presence of genetic by environment interactions. To specifically identify and quantify QTL by environment interactions (QEIs), we implemented two methods: linear modeling with environmental covariates, and QTL analysis on trait differences between growouts. With these approaches, we found several instances of QEI, indicating that elemental profiles are highly heritable, interrelated, and responsive to the environment. PMID:27770027

The Interaction of Genotype and Environment Determines Variation in the Maize Kernel Ionome.

PubMed

Asaro, Alexandra; Ziegler, Gregory; Ziyomo, Cathrine; Hoekenga, Owen A; Dilkes, Brian P; Baxter, Ivan

2016-12-07

Plants obtain soil-resident elements that support growth and metabolism from the water-flow facilitated by transpiration and active transport processes. The availability of elements in the environment interacts with the genetic capacity of organisms to modulate element uptake through plastic adaptive responses, such as homeostasis. These interactions should cause the elemental contents of plants to vary such that the effects of genetic polymorphisms will be dramatically dependent on the environment in which the plant is grown. To investigate genotype by environment interactions underlying elemental accumulation, we analyzed levels of elements in maize kernels of the Intermated B73 × Mo17 (IBM) recombinant inbred population grown in 10 different environments, spanning a total of six locations and five different years. In analyses conducted separately for each environment, we identified a total of 79 quantitative trait loci (QTL) controlling seed elemental accumulation. While a set of these QTL was found in multiple environments, the majority were specific to a single environment, suggesting the presence of genetic by environment interactions. To specifically identify and quantify QTL by environment interactions (QEIs), we implemented two methods: linear modeling with environmental covariates, and QTL analysis on trait differences between growouts. With these approaches, we found several instances of QEI, indicating that elemental profiles are highly heritable, interrelated, and responsive to the environment. Copyright © 2016 Asaro et al.

Development of a QTL-environment-based predictive model for node addition rate in common bean.

PubMed

Zhang, Li; Gezan, Salvador A; Eduardo Vallejos, C; Jones, James W; Boote, Kenneth J; Clavijo-Michelangeli, Jose A; Bhakta, Mehul; Osorno, Juan M; Rao, Idupulapati; Beebe, Stephen; Roman-Paoli, Elvin; Gonzalez, Abiezer; Beaver, James; Ricaurte, Jaumer; Colbert, Raphael; Correll, Melanie J

2017-05-01

This work reports the effects of the genetic makeup, the environment and the genotype by environment interactions for node addition rate in an RIL population of common bean. This information was used to build a predictive model for node addition rate. To select a plant genotype that will thrive in targeted environments it is critical to understand the genotype by environment interaction (GEI). In this study, multi-environment QTL analysis was used to characterize node addition rate (NAR, node day - 1 ) on the main stem of the common bean (Phaseolus vulgaris L). This analysis was carried out with field data of 171 recombinant inbred lines that were grown at five sites (Florida, Puerto Rico, 2 sites in Colombia, and North Dakota). Four QTLs (Nar1, Nar2, Nar3 and Nar4) were identified, one of which had significant QTL by environment interactions (QEI), that is, Nar2 with temperature. Temperature was identified as the main environmental factor affecting NAR while day length and solar radiation played a minor role. Integration of sites as covariates into a QTL mixed site-effect model, and further replacing the site component with explanatory environmental covariates (i.e., temperature, day length and solar radiation) yielded a model that explained 73% of the phenotypic variation for NAR with root mean square error of 16.25% of the mean. The QTL consistency and stability was examined through a tenfold cross validation with different sets of genotypes and these four QTLs were always detected with 50-90% probability. The final model was evaluated using leave-one-site-out method to assess the influence of site on node addition rate. These analyses provided a quantitative measure of the effects on NAR of common beans exerted by the genetic makeup, the environment and their interactions.

Chemical performance of multi-environment trials in lens (Lens culinaris M.).

PubMed

Karadavut, Ufuk; Palta, Cetin

2010-01-15

Genotype-environment (GE) interaction has been a major effect to determine stable lens (Lens culinaris (Medik.) Merr.) cultivars for chemical composition in Turkey. Utilization of the lines depends on their agronomic traits and stability of the chemical composition in diverse environments. The objectives of this study were: (i) to evaluate the influence of year and location on the chemical composition of lens genotypes; and (ii) to determine which cultivar is the most stable. Genotypes were evaluated over 3 years (2005, 2006 and 2007) at four locations in Turkey. Effects of year had the largest impact on all protein contents. GE interaction was analyzed by using linear regression techniques. Stability was estimated using the Eberhart and Russell method. 'Kişlik Kirmizi51' was the most stable cultivar for grain yield. The highest protein was obtained from 'Kişlik Kirmizi51' (4.6%) across environments. According to stability analysis, 'Firat 87' had the most stable chemical composition. This genotype had a regression coefficient (b(i) = 1) around unity, and deviations from regression values (delta(ij) = 0) around zero. Chemical composition was affected by year in this study. Temperature might have an effect on protein, oil, carbohydrate, fibre and ash. Firat 87 could be recommended for favourable environments. Copyright (c) 2009 Society of Chemical Industry.

Stability and adaptability of soybean cultivars in Minas Gerais.

PubMed

Soares, I O; Bruzi, A T; Zambiazzi, E V; Guilherme, S R; Bianchi, M C; Silva, K B; Fronza, V; Teixeira, C M

2017-08-17

Genotypes x environment (G x E) interaction consists of different behavior of genotypes cultivated in different environments. This interaction occurs due to the performance variation of each genotype in different environments. To reduce the effect of the interaction in soybean crops, some studies have been reported in the literature to study their adaptability and stability. However, these studies are still scarce in Minas Gerais State. Thus, the aim of this study was to verify the adaptability and stability of soybean cultivars and identify the cultivars that contribute least to the G x E interaction in Minas Gerais. Six soybean cultivars were evaluated in 9 different environments. The plots were composed of 4 rows of 5 m with a spacing of 0.5 m between rows, and only the two central rows were harvested. The inoculation with Bradyrhizobium japonicum was performed through sowing furrow. The fertilization followed the recommendations of the Soil Fertility Commission of Minas Gerais. Grain yield was evaluated in kg/ha after conversion to 13% moisture. After individual analysis, the joint analysis was performed by grouping the phenotypic means by the Scott and Knott (1974) test. Wricke's ecovalence methodologies and the Annicchiarico confidence index were applied for the adaptability and stability analysis. The interaction was decomposed into a simple and a complex part. The cultivars BRSMG 820RR and BRSMG 760SRR have wide adaptability and stability. The first one presents a better index of confidence and a small contribution to the interaction.

Microbial competition in porous environments can select against rapid biofilm growth

PubMed Central

Coyte, Katharine Z.; Tabuteau, Hervé; Gaffney, Eamonn A.; Durham, William M.

2017-01-01

Microbes often live in dense communities called biofilms, where competition between strains and species is fundamental to both evolution and community function. Although biofilms are commonly found in soil-like porous environments, the study of microbial interactions has largely focused on biofilms growing on flat, planar surfaces. Here, we use microfluidic experiments, mechanistic models, and game theory to study how porous media hydrodynamics can mediate competition between bacterial genotypes. Our experiments reveal a fundamental challenge faced by microbial strains that live in porous environments: cells that rapidly form biofilms tend to block their access to fluid flow and redirect resources to competitors. To understand how these dynamics influence the evolution of bacterial growth rates, we couple a model of flow–biofilm interaction with a game theory analysis. This investigation revealed that hydrodynamic interactions between competing genotypes give rise to an evolutionarily stable growth rate that stands in stark contrast with that observed in typical laboratory experiments: cells within a biofilm can outcompete other genotypes by growing more slowly. Our work reveals that hydrodynamics can profoundly affect how bacteria compete and evolve in porous environments, the habitat where most bacteria live. PMID:28007984

Maternal-by-environment but not genotype-by-environment interactions in a fish without parental care.

PubMed

Vega-Trejo, Regina; Head, Megan L; Jennions, Michael D; Kruuk, Loeske E B

2018-01-01

The impact of environmental conditions on the expression of genetic variance and on maternal effects variance remains an important question in evolutionary quantitative genetics. We investigate here the effects of early environment on variation in seven adult life history, morphological, and secondary sexual traits (including sperm characteristics) in a viviparous poeciliid fish, the mosquitofish Gambusia holbrooki. Specifically, we manipulated food availability during early development and then assessed additive genetic and maternal effects contributions to the overall phenotypic variance in adults. We found higher heritability for female than male traits, but maternal effects variance for traits in both sexes. An interaction between maternal effects variance and rearing environment affected two adult traits (female age at maturity and male size at maturity), but there was no evidence of trade-offs in maternal effects across environments. Our results illustrate (i) the potential for pre-natal maternal effects to interact with offspring environment during development, potentially affecting traits through to adulthood and (ii) that genotype-by-environment interactions might be overestimated if maternal-by-environment interactions are not accounted for, similar to heritability being overestimated if maternal effects are ignored. We also discuss the potential for dominance genetic variance to contribute to the estimate of maternal effects variance.

A novel differential susceptibility gene: CHRNA4 and moderation of the effect of maltreatment on child personality.

PubMed

Grazioplene, Rachael G; Deyoung, Colin G; Rogosch, Fred A; Cicchetti, Dante

2013-08-01

The differential susceptibility hypothesis states that some genetic variants that confer risk in adverse environments are beneficial in normal or nurturing environments. The cholinergic system is promising as a source of susceptibility genes because of its involvement in learning and neural plasticity. The cholinergic receptor gene CHRNA4 has been linked to characteristics related to the personality traits Neuroticism and Openness/Intellect. The effects of interaction between CHRNA4 genotype and maltreatment status on child personality were examined in a well matched sample of 339 maltreated and 275 non-maltreated children (aged 8-13 years). Variation in CHRNA4 interacted with childhood maltreatment to predict personality in a manner indicating differential susceptibility. The interaction of CHRNA4 and maltreatment status predicted Neuroticism and Openness/Intellect. Maltreated children with the rs1044396 T/T genotype scored highest on Neuroticism and showed no effect of genotype on Openness/Intellect. Non-maltreated children with this genotype scored lowest on Neuroticism and highest on Openness/Intellect. Variation in CHRNA4 appears to contribute to personality by affecting degree of developmental sensitivity to both normal and adverse environments. © 2012 The Authors. Journal of Child Psychology and Psychiatry © 2012 Association for Child and Adolescent Mental Health.

Environmental Maternal Effects Mediate the Resistance of Maritime Pine to Biotic Stress

PubMed Central

Vivas, María; Zas, Rafael; Sampedro, Luis; Solla, Alejandro

2013-01-01

The resistance to abiotic stress is increasingly recognised as being impacted by maternal effects, given that environmental conditions experienced by parent (mother) trees affect stress tolerance in offspring. We hypothesised that abiotic environmental maternal effects may also mediate the resistance of trees to biotic stress. The influence of maternal environment and maternal genotype and the interaction of these two factors on early resistance of Pinus pinaster half-sibs to the Fusarium circinatum pathogen was studied using 10 mother genotypes clonally replicated in two contrasting environments. Necrosis length of infected seedlings was 16% shorter in seedlings grown from favourable maternal environment seeds than in seedlings grown from unfavourable maternal environment seeds. Damage caused by F. circinatum was mediated by maternal environment and maternal genotype, but not by seed mass. Mechanisms unrelated to seed provisioning, perhaps of epigenetic nature, were probably involved in the transgenerational plasticity of P. pinaster, mediating its resistance to biotic stress. Our findings suggest that the transgenerational resistance of pines due to an abiotic stress may interact with the defensive response of pines to a biotic stress. PMID:23922944

Interaction of childhood urbanicity and variation in dopamine genes alters adult prefrontal function as measured by functional magnetic resonance imaging (fMRI).

PubMed

Reed, Jessica L; D'Ambrosio, Enrico; Marenco, Stefano; Ursini, Gianluca; Zheutlin, Amanda B; Blasi, Giuseppe; Spencer, Barbara E; Romano, Raffaella; Hochheiser, Jesse; Reifman, Ann; Sturm, Justin; Berman, Karen F; Bertolino, Alessandro; Weinberger, Daniel R; Callicott, Joseph H

2018-01-01

Brain phenotypes showing environmental influence may help clarify unexplained associations between urban exposure and psychiatric risk. Heritable prefrontal fMRI activation during working memory (WM) is such a phenotype. We hypothesized that urban upbringing (childhood urbanicity) would alter this phenotype and interact with dopamine genes that regulate prefrontal function during WM. Further, dopamine has been hypothesized to mediate urban-associated factors like social stress. WM-related prefrontal function was tested for main effects of urbanicity, main effects of three dopamine genes-catechol-O-methyltransferase (COMT), dopamine receptor D1 (DRD1), and dopamine receptor D2 (DRD2)-and, importantly, dopamine gene-by-urbanicity interactions. For COMT, three independent human samples were recruited (total n = 487). We also studied 253 subjects genotyped for DRD1 and DRD2. 3T fMRI activation during the N-back WM task was the dependent variable, while childhood urbanicity, dopamine genotype, and urbanicity-dopamine interactions were independent variables. Main effects of dopamine genes and of urbanicity were found. Individuals raised in an urban environment showed altered prefrontal activation relative to those raised in rural or town settings. For each gene, dopamine genotype-by-urbanicity interactions were shown in prefrontal cortex-COMT replicated twice in two independent samples. An urban childhood upbringing altered prefrontal function and interacted with each gene to alter genotype-phenotype relationships. Gene-environment interactions between multiple dopamine genes and urban upbringing suggest that neural effects of developmental environmental exposure could mediate, at least partially, increased risk for psychiatric illness in urban environments via dopamine genes expressed into adulthood.

Genotype x environment interaction for age at first calving in Brazilian and Colombian Holsteins.

PubMed

Cerón-Muñoz, M F; Tonhati, H; Costa, C N; Maldonado-Estrada, J; Rojas-Sarmiento, D

2004-08-01

The objective was to determine whether there is a genotype x environment interaction for age at first calving (AFC) in Holstein cattle in Brazil and Colombia. Data included 51,239 and 25,569 first-lactation records from Brazil and Colombia, respectively. Of 4230 sires in the data, 530 were North American sires used in both countries. Analyses were done using the REML bi-trait animal model, and AFC was considered as a distinct characteristic in each country. Fixed effects of contemporary group (herd-calving year), sire genetic group, and cow genetic group, and random effects of animal and residual variation were included in the model. Average AFC in Brazil and Colombia were 29.5 +/- 4.0 and 32.1 +/- 3.5 mo, respectively. Additive and residual genetic components and heritability coefficient for AFC in Brazil were 2.21 mo2, 9.41 mo2, and 0.19, respectively, whereas for Colombia, they were 1.02 mo2, 6.84 mo2, and 0.13, respectively. The genetic correlation of AFC between Brazil and Colombia was 0.78, indicating differences in ranking of sires consistent with a genotype x environment interaction. Therefore, in countries with differing environments, progeny of Holstein sires may calve at relatively younger or older ages compared with contemporary herdmates in one environment versus another.

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.

Genetic Variability, Genotype × Environment Interaction, Correlation, and GGE Biplot Analysis for Grain Iron and Zinc Concentration and Other Agronomic Traits in RIL Population of Sorghum (Sorghum bicolor L. Moench)

PubMed Central

Phuke, Rahul M.; Anuradha, Kotla; Radhika, Kommineni; Jabeen, Farzana; Anuradha, Ghanta; Ramesh, Thatikunta; Hariprasanna, K.; Mehtre, Shivaji P.; Deshpande, Santosh P.; Anil, Gaddameedi; Das, Roma R.; Rathore, Abhishek; Hash, Tom; Reddy, Belum V. S.; Kumar, Are Ashok

2017-01-01

The low grain iron and zinc densities are well documented problems in food crops, affecting crop nutritional quality especially in cereals. Sorghum is a major source of energy and micronutrients for majority of population in Africa and central India. Understanding genetic variation, genotype × environment interaction and association between these traits is critical for development of improved cultivars with high iron and zinc. A total of 336 sorghum RILs (Recombinant Inbred Lines) were evaluated for grain iron and zinc concentration along with other agronomic traits for 2 years at three locations. The results showed that large variability exists in RIL population for both micronutrients (Iron = 10.8 to 76.4 mg kg−1 and Zinc = 10.2 to 58.7 mg kg−1, across environments) and agronomic traits. Genotype × environment interaction for both micronutrients (iron and zinc) was highly significant. GGE biplots comparison for grain iron and zinc showed greater variation across environments. The results also showed that G × E was substantial for grain iron and zinc, hence wider testing needed for taking care of G × E interaction to breed micronutrient rich sorghum lines. Iron and zinc concentration showed high significant positive correlation (across environment = 0.79; p < 0.01) indicating possibility of simultaneous effective selection for both the traits. The RIL population showed good variability and high heritabilities (>0.60, in individual environments) for Fe and Zn and other traits studied indicating its suitability to map QTL for iron and zinc. PMID:28529518

Genotype x prenatal and post-weaning nutritional environment interaction in a composite beef cattle breed using reaction norms and multi-trait model

USDA-ARS?s Scientific Manuscript database

Environmental effects have been shown to influence several economically important traits in beef cattle. In this study, genetic x nutritional environment interaction has been evaluated in a composite beef cattle breed (50% Red Angus, 25% Charolais, 25% Tarentaise). Four nutritional environments (MAR...

Genotype x environment interaction and growth stability of several elm clones resistant to Dutch elm disease

Treesearch

Alberto Santini; Francesco Pecori; Alessia L. Pepori; Luisa Ghelardini

2012-01-01

The elm breeding program carried out in Italy at the Institute of Plant Protection - Consiglio Nazionale delle Ricercje (CNR) during the last 40 years aimed to develop Dutch elm disease (DED)-resistant elm selections specific to the Mediterranean environment. The need for genotypes adapted to Mediterranean conditions was evident from the poor performance of the Dutch...

Environment effects for earliness and grain yield traits in F1 diallel populations of maize (Zea mays L.).

PubMed

Ali, Sardar; Khan, Naqib Ullah; Khalil, Iftikhar Hussain; Iqbal, Muhammad; Gul, Samrin; Ahmed, Sheraz; Ali, Naushad; Sajjad, Mohammad; Afridi, Khilwat; Ali, Imtiaz; Khan, Shah Masaud

2017-10-01

Five maize inbred lines, 20 F 1 diallel hybrids and two check genotypes were evaluated through genotype × environment interaction (GEI) and GGE biplot for earliness and yield traits at four locations. Genotype, environment and GEI showed highly significant differences for all the traits. In total sum of squares, environment and genotype played a primary role, followed by GEI. Larger effects of environment and genotype to total variation influence the earliness and yield traits. However, according to the GGE biplot, the first two principal components (PC1 and PC2) explained 95% of the variation caused by GEI. GGE biplot confirmed the differential response of genotypes across environments. F 1 hybrid SWAJK-1 × FRHW-3 had better stability, with a good yield, and was considered an ideal genotype. F 1 hybrid FRHW-2 × FRHW-1 showed more earliness at CCRI and Haripur, followed by PSEV3 × FRHW-2 and its reciprocal at Swat and Mansehra, respectively. F 1 hybrids FRHW-1 × SWAJK-1, PSEV3 × SWAJK-1 and SWAJK-1 × FRHW-3 at Mansehra and Swat produced maximum grain yield, followed by SWAJK-1 × FRHW-1 and PSEV3 × FRHW-1 at Haripur and CCRI, respectively. Overall, maize genotypes showed early maturity in plain areas (CCRI and Haripur) but higher yield in hilly areas (Mansehra and Swat). © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Effects of data structure on the estimation of covariance functions to describe genotype by environment interactions in a reaction norm model

PubMed Central

Calus, Mario PL; Bijma, Piter; Veerkamp, Roel F

2004-01-01

Covariance functions have been proposed to predict breeding values and genetic (co)variances as a function of phenotypic within herd-year averages (environmental parameters) to include genotype by environment interaction. The objective of this paper was to investigate the influence of definition of environmental parameters and non-random use of sires on expected breeding values and estimated genetic variances across environments. Breeding values were simulated as a linear function of simulated herd effects. The definition of environmental parameters hardly influenced the results. In situations with random use of sires, estimated genetic correlations between the trait expressed in different environments were 0.93, 0.93 and 0.97 while simulated at 0.89 and estimated genetic variances deviated up to 30% from the simulated values. Non random use of sires, poor genetic connectedness and small herd size had a large impact on the estimated covariance functions, expected breeding values and calculated environmental parameters. Estimated genetic correlations between a trait expressed in different environments were biased upwards and breeding values were more biased when genetic connectedness became poorer and herd composition more diverse. The best possible solution at this stage is to use environmental parameters combining large numbers of animals per herd, while losing some information on genotype by environment interaction in the data. PMID:15339629

Refining the Candidate Environment: Interpersonal Stress, the Serotonin Transporter Polymorphism, and Gene-Environment Interactions in Major Depression.

PubMed

Vrshek-Schallhorn, Suzanne; Mineka, Susan; Zinbarg, Richard E; Craske, Michelle G; Griffith, James W; Sutton, Jonathan; Redei, Eva E; Wolitzky-Taylor, Kate; Hammen, Constance; Adam, Emma K

2014-05-01

Meta-analytic evidence supports a gene-environment (G×E) interaction between life stress and the serotonin transporter polymorphism (5-HTTLPR) on depression, but few studies have examined factors that influence detection of this effect, despite years of inconsistent results. We propose that the "candidate environment" (akin to a candidate gene) is key. Theory and evidence implicate major stressful life events (SLEs)-particularly major interpersonal SLEs-as well as chronic family stress. Participants ( N = 400) from the Youth Emotion Project (which began with 627 high school juniors oversampled for high neuroticism) completed up to five annual diagnostic and life stress interviews and provided DNA samples. A significant G×E effect for major SLEs and S -carrier genotype was accounted for significantly by major interpersonal SLEs but not significantly by major non-interpersonal SLEs. S -carrier genotype and chronic family stress also significantly interacted. Identifying such candidate environments may facilitate future G×E research in depression and psychopathology more broadly.

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.

Short communication: Improving accuracy of predicting breeding values in Brazilian Holstein population by adding data from Nordic and French Holstein populations.

PubMed

Li, X; Lund, M S; Zhang, Q; Costa, C N; Ducrocq, V; Su, G

2016-06-01

The present study investigated the improvement of prediction reliabilities for 3 production traits in Brazilian Holsteins that had no genotype information by adding information from Nordic and French Holstein bulls that had genotypes. The estimated across-country genetic correlations (ranging from 0.604 to 0.726) indicated that an important genotype by environment interaction exists between Brazilian and Nordic (or Nordic and French) populations. Prediction reliabilities for Brazilian genotyped bulls were greatly increased by including data of Nordic and French bulls, and a 2-trait single-step genomic BLUP performed much better than the corresponding pedigree-based BLUP. However, only a minor improvement in prediction reliabilities was observed in nongenotyped Brazilian cows. The results indicate that although there is a large genotype by environment interaction, inclusion of a foreign reference population can improve accuracy of genetic evaluation for the Brazilian Holstein population. However, a Brazilian reference population is necessary to obtain a more accurate genomic evaluation. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Effect of genotype and environment on the concentrations of starch and protein in, and the physicochemical properties of starch from, field pea and fababean.

PubMed

Hood-Niefer, Shannon D; Warkentin, Thomas D; Chibbar, Ravindra N; Vandenberg, Albert; Tyler, Robert T

2012-01-15

The effects of genotype and environment and their interaction on the concentrations of starch and protein in, and the amylose content and thermal and pasting properties of starch from, pea and fababean are not well known. Differences due to genotype were observed in the concentrations of starch and protein in pea and fababean, in the onset temperature (To) and peak temperature (Tp) of gelatinization of fababean starch, and in the pasting, trough, cooling and final viscosities of pea starch and fababean starch. Significant two-way interactions (location × genotype) were observed for the concentration of starch in fababean and the amylose content, To, endothermic enthalpy of gelatinization (ΔH) and trough viscosity of fababean starch. Significant three-way interactions (location × year × genotype) were observed for the concentration of starch in pea and the pasting, trough, cooling and final viscosities of pea starch. Differences observed in the concentrations of starch and protein in pea and fababean were sufficient to be of practical significance to end-users, but the relatively small differences in amylose content and physicochemical properties of starch from pea and fababean were not. Copyright © 2011 Society of Chemical Industry.

Increased prediction accuracy in wheat breeding trials using a marker x environment interaction genomic selection model

USDA-ARS?s Scientific Manuscript database

Genomic selection (GS) models use genome-wide genetic information to predict genetic values of candidates for selection. Originally these models were developed without considering genotype ' environment interaction (GE). Several authors have proposed extensions of the cannonical GS model that accomm...

The interaction of genotype and environment determines variation in the maize kernal ionome

USDA-ARS?s Scientific Manuscript database

Plants obtain soil-resident elements that support growth and metabolism via water-mediated flow due to transpiration and active transport processes. The availability of elements in the environment can interact with the genetic capacity of the organism to modulate element uptake through plastic adapt...

Genotype x Nutritional Environment Interaction in a Composite Beef Cattle Breed

USDA-ARS?s Scientific Manuscript database

Environmental effects have been shown to influence several economically important traits in beef cattle. In this study, genetic x nutritional environment interaction has been evaluated in a composite beef cattle breed(50% Red Angus, 25% Charolais, 25% Tarentaise).Cows were randomly assigned to be fe...

Use of genotype-environment interactions to elucidate the pattern of maize root plasticity to nitrogen deficiency.

PubMed

Li, Pengcheng; Zhuang, Zhongjuan; Cai, Hongguang; Cheng, Shuai; Soomro, Ayaz Ali; Liu, Zhigang; Gu, Riliang; Mi, Guohua; Yuan, Lixing; Chen, Fanjun

2016-03-01

Maize (Zea mays L.) root morphology exhibits a high degree of phenotypic plasticity to nitrogen (N) deficiency, but the underlying genetic architecture remains to be investigated. Using an advanced BC4 F3 population, we investigated the root growth plasticity under two contrasted N levels and identified the quantitative trait loci (QTLs) with QTL-environment (Q × E) interaction effects. Principal components analysis (PCA) on changes of root traits to N deficiency (ΔLN-HN) showed that root length and biomass contributed for 45.8% in the same magnitude and direction on the first PC, while root traits scattered highly on PC2 and PC3. Hierarchical cluster analysis on traits for ΔLN-HN further assigned the BC4 F3 lines into six groups, in which the special phenotypic responses to N deficiency was presented. These results revealed the complicated root plasticity of maize in response to N deficiency that can be caused by genotype-environment (G × E) interactions. Furthermore, QTL mapping using a multi-environment analysis identified 35 QTLs for root traits. Nine of these QTLs exhibited significant Q × E interaction effects. Taken together, our findings contribute to understanding the phenotypic and genotypic pattern of root plasticity to N deficiency, which will be useful for developing maize tolerance cultivars to N deficiency. © 2015 Institute of Botany, Chinese Academy of Sciences.

Social context influences chemical communication in D. melanogaster males.

PubMed

Kent, Clement; Azanchi, Reza; Smith, Ben; Formosa, Amanda; Levine, Joel D

2008-09-23

Chemical communication mediates social interactions in insects. For the fruit fly, D. melanogaster, the chemical display is a key fitness trait because it leads to mating. An exchange of cues that resembles a dialogue between males and females is enacted by pheromones, chemical signals that pass between individual flies to alter physiology and behavior. Chemical signals also affect the timing of locomotor activity and sleep. We investigated genetic and environmental determinants of chemical communication. To evaluate the role of the social environment, we extracted a chemical blend from individual males selected from groups composed of one genotype and compared these extracts to those from groups of mixed genotypes. To evaluate the role of the physical environment, these comparisons were performed under a light-dark cycle or in constant darkness. Here, we show that chemical signaling is affected by the social environment, light-dark cycle, and genotype as well as the complex interplay of these variables. Gene-by-environment interactions produce highly significant effects on chemical signaling. We also examined individual responses within the groups. Strikingly, the response of one wild-type fly to another is modulated by the genotypic composition of his neighbors. Chemical signaling in D. melanogaster may be a "fickle" trait that depends on the individual's social background.

Gene-Environment Interactions across Development: Exploring DRD2 Genotype and Prenatal Smoking Effects on Self-Regulation

ERIC Educational Resources Information Center

Wiebe, Sandra A.; Espy, Kimberly Andrews; Stopp, Christian; Respass, Jennifer; Stewart, Peter; Jameson, Travis R.; Gilbert, David G.; Huggenvik, Jodi I.

2009-01-01

Genetic factors dynamically interact with both pre- and postnatal environmental influences to shape development. Considerable attention has been devoted to gene-environment interactions (G x E) on important outcomes (A. Caspi & T. E. Moffitt, 2006). It is also important to consider the possibility that these G x E effects may vary across…

Sex-specific genotype-by-environment interactions for cuticular hydrocarbon expression in decorated crickets, Gryllodes sigillatus: implications for the evolution of signal reliability.

PubMed

Weddle, C B; Mitchell, C; Bay, S K; Sakaluk, S K; Hunt, J

2012-10-01

Phenotypic traits that convey information about individual identity or quality are important in animal social interactions, and the degree to which such traits are influenced by environmental variation can have profound effects on the reliability of these cues. Using inbred genetic lines of the decorated cricket, Gryllodes sigillatus, we manipulated diet quality to test how the cuticular hydrocarbon (CHC) profiles of males and females respond across two different nutritional rearing environments. There were significant differences between lines in the CHC profiles of females, but the effect of diet was not quite statistically significant. There was no significant genotype-by-environment interaction (GEI), suggesting that environmental effects on phenotypic variation in female CHCs are independent of genotype. There was, however, a significant effect of GEI for males, with changes in both signal quantity and content, suggesting that environmental effects on phenotypic expression of male CHCs are dependent on genotype. The differential response of male and female CHC expression to variation in the nutritional environment suggests that these chemical cues may be under sex-specific selection for signal reliability. Female CHCs show the characteristics of reliable cues of identity: high genetic variability, low condition dependence and a high degree of genetic determination. This supports earlier work showing that female CHCs are used in self-recognition to identify previous mates and facilitate polyandry. In contrast, male CHCs show the characteristics of reliable cues of quality: condition dependence and a relatively higher degree of environmental determination. This suggests that male CHCs are likely to function as cues of underlying quality during mate choice and/or male dominance interactions. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

The association between the MAOA 2R genotype and delinquency over time among men: the interactive role of parental closeness and parental incarceration

PubMed Central

Roettger, Michael E.; Boardman, Jason D.; Harris, Kathleen Mullan; Guo, Guang

2017-01-01

Using a panel of 6,001 males from the National Longitudinal Study of Adolescent and Adult Health, we examine potential moderation by paternal incarceration and parent-child closeness altering the relationship between the rare 2R MAOA genotype and delinquency. By jointly examining moderation patterns for both the mother and father with the transmission of the MAOA genotype from mother to son, we are able to make inferences about the specific genetic model that best explains these outcomes. In line with prior research, we find a direct relationship between the MAOA 2R genotype and delinquency, independent of parental incarceration and closeness. Examining moderation patterns, we find that delinquency risk for the 2R allele is buffered for males close to their biological or social father, but not their biological mother. We conclude that the 2R delinquency association is not due to passive gene-environment correlation but is best characterized as a social control gene-environment interaction. PMID:29033475

AGT M235T genotype/anxiety interaction and gender in the HyperGEN study.

PubMed

Knox, Sarah S; Guo, Xinxin; Zhang, Yuqing; Weidner, G; Williams, Scott; Ellison, R Curtis

2010-10-13

Both anxiety and elevated heart rate (HR) have been implicated in the development of hypertension. The HyperGen cohort, consisting of siblings with severe and mild hypertension, an age-matched random sample of persons from the same base populations, and unmedicated adult offspring of the hypertensive siblings (N = 1,002 men and 987 women), was analyzed for an association of the angiotenisinogen AGTM235T genotype (TT, MT, MM) with an endophenotype, heart rate (HR) in high and low anxious groups. The interaction of AGTM genotype with anxiety, which has been independently associated with hypertension, was investigated adjusting for age, hypertension status, smoking, alcohol consumption, beta blocker medication, body mass index, physical activity and hours of television viewing (sedentary life style). Although there was no main effect of genotype on HR in men or women, high anxious men with the TT genotype had high HR, whereas high anxious men with the MM genotype had low HR. In women, HR was inversely associated with anxiety but there was no interaction with genotype. The results suggest that high anxiety in men with the TT genotype may increase risk for hypertension whereas the MM genotype may be protective in high anxious men. This type of gene x environment interaction may be one reason why genome wide association studies sometimes fail to replicate. The locus may be important only in combination with certain environmental factors.

Genotype x environmental interaction for mature size and rate of maturing for Angus, Brahman, and reciprocal-cross cows grazing bermudagrass or endophyte infected fescue.

PubMed

Sandelin, B A; Brown, A H; Brown, M A; Johnson, Z B; Kellogg, D W; Stelzleni, A M

2002-12-01

Mature weight and rate of maturing were estimated in 177 Angus, Brahman, and reciprocal-cross cows grazing bermudagrass or endophyte-infected tall fescue over a 4-yr period to evaluate genotype x environment interactions. Data were collected every 28 d until cows were approximately 18 mo of age and then at prebreeding, postcalving, and weaning of calf. All cows with weight data to at least 42 mo of age were included in the analysis. Mature weight and rate of maturing were estimated using the three-parameter growth curve model described by Brody (1945). Data were pooled over year and analyzed by the general linear model procedure of SAS. Included in the models for mature weight and rate of maturing were the independent variables of genotype, environment, and genotype x environment interaction. There was a genotype x environment interaction (P < 0.01) for mature body weight (BW) but not for rate of maturing. Angus cows grazing fescue pastures had greater (P < 0.01) mean mature BW than Angus x Brahman cows grazing bermudagrass (611 +/- 17 vs 546 +/- 16 kg). Angus x Brahman cows grazing bermudagrass had lower (P < 0.05) mean mature BW than Brahman x Angus cows grazing bermudagrass or endophyte-infected fescue and Brahman cows grazing bermudagrass (546 +/- 16 vs 624 +/- 19, 614 +/- 22 and 598 +/- 20 kg, respectively). Brahman cows grazing endophyte-infected fescue had smaller (P < 0.05) mean mature BW than all genotype x forage combinations except for Angus x Brahman cows grazing bermudagrass. Angus cows had a smaller (P < 0.05) mean rate of maturing than Angus x Brahman and Brahman x Angus cows (0.039 +/- 0.002 vs 0.054 +/- 0.002 and 0.049 +/- 0.002%/mo, respectively), respectively, and Angus x Brahman cows had a larger (P < 0.05) mean rate of maturing than Brahman x Angus and Brahman cows (0.054 +/- 0.002 vs 0.049 +/- 0.002 and 0.041 +/- 0.002 %/mo, respectively). There was a direct breed x forage interaction (P < 0.05) for mature BW. These data suggest that the choice of breed type is important in maintaining a crossbreeding program, in that mature BW and rate of maturing are critical to the matching of animal requirements to available production resources.

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.

Gene-environment studies: any advantage over environmental studies?

PubMed

Bermejo, Justo Lorenzo; Hemminki, Kari

2007-07-01

Gene-environment studies have been motivated by the likely existence of prevalent low-risk genes that interact with common environmental exposures. The present study assessed the statistical advantage of the simultaneous consideration of genes and environment to investigate the effect of environmental risk factors on disease. In particular, we contemplated the possibility that several genes modulate the environmental effect. Environmental exposures, genotypes and phenotypes were simulated according to a wide range of parameter settings. Different models of gene-gene-environment interaction were considered. For each parameter combination, we estimated the probability of detecting the main environmental effect, the power to identify the gene-environment interaction and the frequency of environmentally affected individuals at which environmental and gene-environment studies show the same statistical power. The proportion of cases in the population attributable to the modeled risk factors was also calculated. Our data indicate that environmental exposures with weak effects may account for a significant proportion of the population prevalence of the disease. A general result was that, if the environmental effect was restricted to rare genotypes, the power to detect the gene-environment interaction was higher than the power to identify the main environmental effect. In other words, when few individuals contribute to the overall environmental effect, individual contributions are large and result in easily identifiable gene-environment interactions. Moreover, when multiple genes interacted with the environment, the statistical benefit of gene-environment studies was limited to those studies that included major contributors to the gene-environment interaction. The advantage of gene-environment over plain environmental studies also depends on the inheritance mode of the involved genes, on the study design and, to some extend, on the disease prevalence.

Caregiving and 5-HTTLPR Genotype Predict Adolescent Physiological Stress Reactivity: Confirmatory Tests of Gene × Environment Interactions.

PubMed

Sumner, Jennifer A; McLaughlin, Katie A; Walsh, Kate; Sheridan, Margaret A; Koenen, Karestan C

2015-03-03

A theory-driven confirmatory approach comparing diathesis-stress and differential susceptibility models of Gene × Environment (G × E) interactions was applied to examine whether 5-HTTLPR genotype moderated the effect of early maternal caregiving on autonomic nervous system (ANS) stress reactivity in 113 adolescents aged 13-17 years. Findings supported a differential susceptibility, rather than diathesis-stress, framework. Carriers of one or more 5-HTTLPR short alleles (SS/SL carriers) reporting higher quality caregiving exhibited approach ANS responses to a speech task, whereas those reporting lower quality caregiving exhibited withdrawal ANS responses. Carriers of two 5-HTTLPR long alleles (LL carriers) were unaffected by caregiving. Findings suggest that 5-HTTLPR genotype and early caregiving in interaction are associated with ANS stress reactivity in adolescents in a "for better and for worse" fashion, and they demonstrate the promise of confirmatory methods for testing G × E interactions. © 2015 The Authors. Child Development © 2015 Society for Research in Child Development, Inc.

The moderating effect of ANKK1 on the association of family environment with longitudinal executive function following traumatic brain injury in early childhood: A preliminary study.

PubMed

Smith-Paine, Julia; Wade, Shari L; Treble-Barna, Amery; Zhang, Nanhua; Zang, Huaiyu; Martin, Lisa J; Yeates, Keith Owen; Taylor, H Gerry; Kurowski, Brad G

2018-05-02

This study examined whether the ankyrin repeat and kinase domain containing 1 gene (ANKK1) C/T single-nucleotide polymorphism (SNP) rs1800497 moderated the association of family environment with long-term executive function (EF) following traumatic injury in early childhood. Caregivers of children with traumatic brain injury (TBI) and children with orthopedic injury (OI) completed the Behavior Rating Inventory of Executive Function (BRIEF) at post injury visits. DNA was collected to identify the rs1800497 genotype in the ANKK1 gene. General linear models examined gene-environment interactions as moderators of the effects of TBI on EF at two times post injury (12 months and 7 years). At 12 months post injury, analyses revealed a significant 3-way interaction of genotype with level of permissive parenting and injury type. Post-hoc analyses showed genetic effects were more pronounced for children with TBI from more positive family environments, such that children with TBI who were carriers of the risk allele (T-allele) had significantly poorer EF compared to non-carriers only when they were from more advantaged environments. At 7 years post injury, analyses revealed a significant 2-way interaction of genotype with level of authoritarian parenting. Post-hoc analyses found that carriers of the risk allele had significantly poorer EF compared to non-carriers only when they were from more advantaged environments. These results suggest a gene-environment interaction involving the ANKK1 gene as a predictor of EF in a pediatric injury population. The findings highlight the importance of considering environmental influences in future genetic studies on recovery following TBI and other traumatic injuries in childhood.

Infant pathways to externalizing behavior: evidence of Genotype x Environment interaction.

PubMed

Leve, Leslie D; Kerr, David C R; Shaw, Daniel; Ge, Xiaojia; Neiderhiser, Jenae M; Scaramella, Laura V; Reid, John B; Conger, Rand; Reiss, David

2010-01-01

To further the understanding of the effects of early experiences, 9-month-old infants were observed during a frustration task. The analytical sample was composed of 348 linked triads of participants (adoptive parents, adopted child, and birth parent[s]) from a prospective adoption study. It was hypothesized that genetic risk for externalizing problems and affect dysregulation in the adoptive parents would independently and interactively predict a known precursor to externalizing problems: heightened infant attention to frustrating events. Results supported the moderation hypotheses involving adoptive mother affect dysregulation: Infants at genetic risk showed heightened attention to frustrating events only when the adoptive mother had higher levels of anxious and depressive symptoms. The Genotype x Environment interaction pattern held when substance use during pregnancy was considered.

Minor Allele Frequency Changes the Nature of Genotype by Environment Interactions.

PubMed

Verhulst, Brad; Neale, Michael C

2016-09-01

In the classical twin study, phenotypic variation is often partitioned into additive genetic (A), common (C) and specific environment (E) components. From genetical theory, the outcome of genotype by environment interaction is expected to inflate A when the interacting factor is shared (i.e., C) between the members of a twin pair. We show that estimates of both A and C can be inflated. When the shared interacting factor changes the size of the difference between homozygotes' means, the expected sibling or DZ twin correlation is .5 if and only if the minor allele frequency (MAF) is .5; otherwise the expected DZ correlation is greater than this value, consistent (and confounded) with some additional effect of C. This result is considered in the light of the distribution of minor allele frequencies for polygenic traits. Also discussed is whether such interactions take place at the locus level or affect an aggregated biological structure or system. Interactions with structures or endophenotypes that result from the aggregated effects of many loci will generally emerge as part of the A estimate.

Genotype × environment interactions in populations possessing Ga1-s and ga1 alleles for cross incompatibility in maize

USDA-ARS?s Scientific Manuscript database

Pop corn (Zea mays L.) inbred lines with genotype Ga1S/Ga1S are normally cross incompatible to dent corn (Z. mays L.) pollen with genotype ga1/ga1 but the reciprocal cross is fully receptive resulting in full seed set. However, in previous studies the incompatibility reaction of heterozygous plants ...

Stability of fruit quality traits in diverse watermelon cultivars tested in multiple environments

PubMed Central

Dia, Mahendra; Wehner, Todd C; Perkins-Veazie, Penelope; Hassell, Richard; Price, Daniel S; Boyhan, George E; Olson, Stephen M; King, Stephen R; Davis, Angela R; Tolla, Gregory E; Bernier, Jerome; Juarez, Benito

2016-01-01

Lycopene is a naturally occurring red carotenoid compound that is found in watermelon. Lycopene has antioxidant properties. Lycopene content, sugar content and hollowheart resistance are subject to significant genotype×environment interaction (G×E), which makes breeding for these fruit quality traits difficult. The objectives of this study were to (i) evaluate the influence of years and locations on lycopene content, sugar content and hollowheart resistance for a set of watermelon genotypes, and (ii) identify genotypes with high stability for lycopene, sugar, and hollowheart resistance. A diverse set of 40 genotypes was tested over 3 years and 8 locations across the southern United States in replicated, multi-harvest trials. Lycopene was tested in a subset of 10 genotypes. Data were analyzed using univariate and multivariate stability statistics (BLUP-GGE biplot) using SASGxE and RGxE programs. There were strong effects of environment as well as G×E interaction on watermelon quality traits. On the basis of stability measures, genotypes were classified as stable or unstable for each quality trait. 'Crimson Sweet' is an inbred line with high quality trait performance as well as trait stability. 'Stone Mountain', 'Tom Watson', 'Crimson Sweet' and 'Minilee' were among the best genotypes for lycopene content, sugar content and hollowheart resistance. We developed a stability chart based on marketable yield and average ranking generated from different stability measures for yield attributes and quality traits. The chart will assist in choosing parents for improvement of watermelon cultivars. See http://cuke.hort.ncsu.edu/cucurbit/wmelon/wmelonmain.html. PMID:28066557

Assessing the impact of natural service bulls and genotype by environment interactions on genetic gain and inbreeding in organic dairy cattle genomic breeding programs.

PubMed

Yin, T; Wensch-Dorendorf, M; Simianer, H; Swalve, H H; König, S

2014-06-01

The objective of the present study was to compare genetic gain and inbreeding coefficients of dairy cattle in organic breeding program designs by applying stochastic simulations. Evaluated breeding strategies were: (i) selecting bulls from conventional breeding programs, and taking into account genotype by environment (G×E) interactions, (ii) selecting genotyped bulls within the organic environment for artificial insemination (AI) programs and (iii) selecting genotyped natural service bulls within organic herds. The simulated conventional population comprised 148 800 cows from 2976 herds with an average herd size of 50 cows per herd, and 1200 cows were assigned to 60 organic herds. In a young bull program, selection criteria of young bulls in both production systems (conventional and organic) were either 'conventional' estimated breeding values (EBV) or genomic estimated breeding values (GEBV) for two traits with low (h 2=0.05) and moderate heritability (h 2=0.30). GEBV were calculated for different accuracies (r mg), and G×E interactions were considered by modifying originally simulated true breeding values in the range from r g=0.5 to 1.0. For both traits (h 2=0.05 and 0.30) and r mg⩾0.8, genomic selection of bulls directly in the organic population and using selected bulls via AI revealed higher genetic gain than selecting young bulls in the larger conventional population based on EBV; also without the existence of G×E interactions. Only for pronounced G×E interactions (r g=0.5), and for highly accurate GEBV for natural service bulls (r mg>0.9), results suggests the use of genotyped organic natural service bulls instead of implementing an AI program. Inbreeding coefficients of selected bulls and their offspring were generally lower when basing selection decisions for young bulls on GEBV compared with selection strategies based on pedigree indices.

Response to angiotensin-converting enzyme inhibition is selectively blunted by high sodium in angiotensin-converting enzyme DD genotype: evidence for gene-environment interaction in healthy volunteers.

PubMed

Lely, A Titia; Heerspink, Hiddo J Lambers; Zuurman, Mike; Visser, Folkert W; Kocks, Menno J A; Boomsma, Frans; Navis, Gerjan

2010-12-01

Renin-angiotensin-aldosterone system blockade is a cornerstone in cardiovascular protection. Angiotensin-converting enzyme (ACE)-DD genotype has been associated with resistance to angiotensin-converting enzyme inhibition (ACEi), but data are conflicting. As sodium intake modifies the effect of ACEi as well as the genotype-phenotype relationship, we hypothesize gene-environment interaction between sodium-status, the response to ACEi, and ACE genotype. Thirty-five male volunteers (26 ± 9 years; II n = 6, ID n = 18, DD n = 11) were studied during placebo and ACEi (double blind, enalapril 20 mg/day) on low [7 days 50 mmol Na/day (low salt)] and high [7 days 200 mmol Na/day (high salt)] sodium, with a washout of 6 weeks in-between. After each period mean arterial pressure (MAP) was measured before and during graded infusion of angiotensin II (Ang II). During high salt, ACEi reduced MAP in II and ID, but not in DD [II: 88 (78-94) versus 76 (72-88); ID: 87 (84-91) versus 83 (79-87); both P < 0.05 and DD: 86 (82-96) versus 88 (80-90); ns, P < 0.05 between genotypes]. However, during low salt, ACEi reduced MAP in all genotype groups [II: 83 (78-89) versus 77 (72-83); ID: 88 (84-91) versus 82 (78-86); DD: 84 (80-91) versus 81 (75-85); all P < 0.05]. During high salt + ACEi, the Ang II response was blunted in DD, with an 18% rise in MAP during the highest dose versus 22 and 31% in ID and II (P < 0.05). Low salt annihilated these differences. In healthy participants, the MAP response to ACEi is selectively blunted in DD genotype during high salt, accompanied by blunted sensitivity to Ang II. Low salt corrects both abnormalities. Further analysis of this gene-environment interaction in patients may contribute to strategies for improvement of individual treatment efficacy.

Adaptability and phenotypic stability of common bean genotypes through Bayesian inference.

PubMed

Corrêa, A M; Teodoro, P E; Gonçalves, M C; Barroso, L M A; Nascimento, M; Santos, A; Torres, F E

2016-04-27

This study used Bayesian inference to investigate the genotype x environment interaction in common bean grown in Mato Grosso do Sul State, and it also evaluated the efficiency of using informative and minimally informative a priori distributions. Six trials were conducted in randomized blocks, and the grain yield of 13 common bean genotypes was assessed. To represent the minimally informative a priori distributions, a probability distribution with high variance was used, and a meta-analysis concept was adopted to represent the informative a priori distributions. Bayes factors were used to conduct comparisons between the a priori distributions. The Bayesian inference was effective for the selection of upright common bean genotypes with high adaptability and phenotypic stability using the Eberhart and Russell method. Bayes factors indicated that the use of informative a priori distributions provided more accurate results than minimally informative a priori distributions. According to Bayesian inference, the EMGOPA-201, BAMBUÍ, CNF 4999, CNF 4129 A 54, and CNFv 8025 genotypes had specific adaptability to favorable environments, while the IAPAR 14 and IAC CARIOCA ETE genotypes had specific adaptability to unfavorable environments.

Evaluation of the genotype, environment and their interaction on carotenoid and ascorbic acid accumulation in tomato germplasm.

PubMed

Roselló, Salvador; Adalid, Ana Maria; Cebolla-Cornejo, Jaime; Nuez, Fernando

2011-04-01

Tomatoes are an important source of antioxidants (carotenoids, vitamin C, etc.) owing to their high level of consumption. There is great interest in developing cultivars with increased levels of lycopene, β-carotene or L-ascorbic acid. There is necessary to survey new sources of variation. In this study, the potential of improvement for each character in tomato breeding programmes, in a single or joint approach, and the nature of genotype (G), environment (E) and G × E interaction effects in the expression of these characters were investigated. The content of lycopene, β-carotene and ascorbic acid determined was very high in some phenotypes (up to 281, 35 and 346 mg kg(-1) respectively). The important differences in the three environments studied (with some stressing conditions in several situations) had a remarkable influence in the phenotypic expression of the functional characters evaluated. Nevertheless, the major contribution came from the genotypic effect along with a considerable G × E interaction. The joint accumulation of lycopene and β-carotene has a high genetic component. It is possible to select elite genotypes with high content of both carotenoids in tomato breeding programmes but multi-environment trials are recommended. The improvement of ascorbic acid content is more difficult because the interference of uncontrolled factors mask the real genetic potential. Among the accessions evaluated, there are four accessions with an amazing genetic potential for functional properties that can be used as donor parents in tomato breeding programmes or for direct consumption in quality markets. Copyright © 2011 Society of Chemical Industry.

Vernalization response of domesticated× wild chickpea progeny is subject to strong genotype by environment interaction

USDA-ARS?s Scientific Manuscript database

Vernalization insensitivity is a key feature of domesticated chickpea and its genetic basis is not well understood. We studied vernalization response among hybrid progeny derived from two domesticated x wild crosses. The wild parents are vernalization sensitive, late flowering genotypes while both d...

Cat exposure in early life decreases asthma risk from the 17q21 high-risk variant.

PubMed

Stokholm, Jakob; Chawes, Bo L; Vissing, Nadja; Bønnelykke, Klaus; Bisgaard, Hans

2018-05-01

Early-life exposure to cats and dogs has shown diverging associations with childhood asthma risk, and gene-environment interaction is one possible explanation. We investigated interactions between cat and dog exposure and single nucleotide polymorphism rs7216389 variants in the chromosome 17q21 locus, the strongest known genetic risk factor for childhood asthma. Genotyping was performed in 377 children from the at-risk Copenhagen Prospective Studies on Asthma in Childhood 2000 . The primary end point was the development of asthma until age 12 years. The secondary end point was the number of episodes with pneumonia and bronchiolitis from 0 to 3 years of age. Exposures included cat and dog ownership from birth and cat and dog allergen levels in bedding at age 1 year. Replication was performed in the unselected COPSAC 2010 cohort with follow-up until 5 years of age. Cat and/or dog exposure from birth was associated with a lower prevalence of asthma among children with the rs7216389 high-risk TT genotype (adjusted hazard ratio, 0.16; 95% CI, 0.04-0.71; P = .015), with no effect in those with the CC/CT genotype (adjusted P = .283), demonstrating interaction between cat and dog exposure and the rs7216389 genotype (adjusted P = .044). Cat allergen levels were inversely associated with asthma development in children with the TT genotype (adjusted hazard ratio, 0.83; 95% CI, 0.71-0.97; P = .022), supporting the cat-rs7216389 genotype interaction (adjusted P = .008). Dog allergen exposure did not show such interaction. Furthermore, the TT genotype was associated with higher risk of pneumonia and bronchiolitis, and this increased risk was likewise decreased in children exposed to cat. Replication showed similar effects on asthma risk. The observed gene-environment interaction suggests a role of early-life exposure, especially to cat, for attenuating the risk of childhood asthma, pneumonia, and bronchiolitis in genetically susceptible subjects. Copyright © 2017 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

Genotype and growing environment interaction shows a positive correlation between substrates of raffinose family oligosaccharides (RFO) biosynthesis and their accumulation in chickpea ( Cicer arietinum L.) seeds.

PubMed

Gangola, Manu P; Khedikar, Yogendra P; Gaur, Pooran M; Båga, Monica; Chibbar, Ravindra N

2013-05-22

To develop genetic improvement strategies to modulate raffinose family oligosaccharides (RFO) concentration in chickpea ( Cicer arietinum L.) seeds, RFO and their precursor concentrations were analyzed in 171 chickpea genotypes from diverse geographical origins. The genotypes were grown in replicated trials over two years in the field (Patancheru, India) and in the greenhouse (Saskatoon, Canada). Analysis of variance revealed a significant impact of genotype, environment, and their interaction on RFO concentration in chickpea seeds. Total RFO concentration ranged from 1.58 to 5.31 mmol/100 g and from 2.11 to 5.83 mmol/100 g in desi and kabuli genotypes, respectively. Sucrose (0.60-3.59 g/100 g) and stachyose (0.18-2.38 g/100 g) were distinguished as the major soluble sugar and RFO, respectively. Correlation analysis revealed a significant positive correlation between substrate and product concentration in RFO biosynthesis. In chickpea seeds, raffinose, stachyose, and verbascose showed a moderate broad sense heritability (0.25-0.56), suggesting the use of a multilocation trials based approach in chickpea seed quality improvement programs.

AGT M235T Genotype/Anxiety Interaction and Gender in the HyperGEN Study

PubMed Central

Knox, Sarah S.; Guo, Xinxin; Zhang, Yuqing; Weidner, G.; Williams, Scott; Ellison, R. Curtis

2010-01-01

Background Both anxiety and elevated heart rate (HR) have been implicated in the development of hypertension. The HyperGen cohort, consisting of siblings with severe and mild hypertension, an age-matched random sample of persons from the same base populations, and unmedicated adult offspring of the hypertensive siblings (N = 1,002 men and 987 women), was analyzed for an association of the angiotenisinogen AGTM235T genotype (TT, MT, MM) with an endophenotype, heart rate (HR) in high and low anxious groups. Methodology The interaction of AGTM genotype with anxiety, which has been independently associated with hypertension, was investigated adjusting for age, hypertension status, smoking, alcohol consumption, beta blocker medication, body mass index, physical activity and hours of television viewing (sedentary life style). Principal Findings Although there was no main effect of genotype on HR in men or women, high anxious men with the TT genotype had high HR, whereas high anxious men with the MM genotype had low HR. In women, HR was inversely associated with anxiety but there was no interaction with genotype. Conclusion/Significance The results suggest that high anxiety in men with the TT genotype may increase risk for hypertension whereas the MM genotype may be protective in high anxious men. This type of gene x environment interaction may be one reason why genome wide association studies sometimes fail to replicate. The locus may be important only in combination with certain environmental factors. PMID:20967221

Effect of Genetics, Environment, and Phenotype on the Metabolome of Maize Hybrids Using GC/MS and LC/MS.

PubMed

Tang, Weijuan; Hazebroek, Jan; Zhong, Cathy; Harp, Teresa; Vlahakis, Chris; Baumhover, Brian; Asiago, Vincent

2017-06-28

We evaluated the variability of metabolites in various maize hybrids due to the effect of environment, genotype, phenotype as well as the interaction of the first two factors. We analyzed 480 forage and the same number of grain samples from 21 genetically diverse non-GM Pioneer brand maize hybrids, including some with drought tolerance and viral resistance phenotypes, grown at eight North American locations. As complementary platforms, both GC/MS and LC/MS were utilized to detect a wide diversity of metabolites. GC/MS revealed 166 and 137 metabolites in forage and grain samples, respectively, while LC/MS captured 1341 and 635 metabolites in forage and grain samples, respectively. Univariate and multivariate analyses were utilized to investigate the response of the maize metabolome to the environment, genotype, phenotype, and their interaction. Based on combined percentages from GC/MS and LC/MS datasets, the environment affected 36% to 84% of forage metabolites, while less than 7% were affected by genotype. The environment affected 12% to 90% of grain metabolites, whereas less than 27% were affected by genotype. Less than 10% and 11% of the metabolites were affected by phenotype in forage and grain, respectively. Unsupervised PCA and HCA analyses revealed similar trends, i.e., environmental effect was much stronger than genotype or phenotype effects. On the basis of comparisons of disease tolerant and disease susceptible hybrids, neither forage nor grain samples originating from different locations showed obvious phenotype effects. Our findings demonstrate that the combination of GC/MS and LC/MS based metabolite profiling followed by broad statistical analysis is an effective approach to identify the relative impact of environmental, genetic and phenotypic effects on the forage and grain composition of maize hybrids.

Genotype-Based Association Mapping of Complex Diseases: Gene-Environment Interactions with Multiple Genetic Markers and Measurement Error in Environmental Exposures

PubMed Central

Lobach, Irvna; Fan, Ruzone; Carroll, Raymond T.

2011-01-01

With the advent of dense single nucleotide polymorphism genotyping, population-based association studies have become the major tools for identifying human disease genes and for fine gene mapping of complex traits. We develop a genotype-based approach for association analysis of case-control studies of gene-environment interactions in the case when environmental factors are measured with error and genotype data are available on multiple genetic markers. To directly use the observed genotype data, we propose two genotype-based models: genotype effect and additive effect models. Our approach offers several advantages. First, the proposed risk functions can directly incorporate the observed genotype data while modeling the linkage disequihbrium information in the regression coefficients, thus eliminating the need to infer haplotype phase. Compared with the haplotype-based approach, an estimating procedure based on the proposed methods can be much simpler and significantly faster. In addition, there is no potential risk due to haplotype phase estimation. Further, by fitting the proposed models, it is possible to analyze the risk alleles/variants of complex diseases, including their dominant or additive effects. To model measurement error, we adopt the pseudo-likelihood method by Lobach et al. [2008]. Performance of the proposed method is examined using simulation experiments. An application of our method is illustrated using a population-based case-control study of association between calcium intake with the risk of colorectal adenoma development. PMID:21031455

Environmental stress, oxytocin receptor gene (OXTR) polymorphism, and mental health following collective stress.

PubMed

Lucas-Thompson, Rachel G; Holman, E Alison

2013-04-01

We examined whether the oxytocin receptor gene (OXTR) single nucleotide polymorphism (SNP) rs53576 genotype buffers the combined impact of negative social environments (e.g., interpersonal conflict/constraint) and economic stress on post-traumatic stress (PTS) symptoms and impaired daily functioning following collective stress (September 11th terrorist attacks). Saliva was collected by mail and used to genotype 704 respondents. Participants completed Web-based assessments of pre-9/11 mental health, acute stress 9-23 days after 9/11, the quality of social environments 1 year post-9/11, economic stress 18 months post-9/11, and PTS symptoms and impaired functioning 2 and 3 years post-9/11. Interactions between negative social environments and economic stress were examined separately based on OXTR rs53576 genotype (GG vs. any A allele). For individuals with an A allele, a negative social environment significantly increased PTS symptoms without regard to the level of economic stress experienced. However, for respondents with a GG genotype, negative social environments predicted elevated PTS symptoms only for those also experiencing high economic stress. Gender moderated associations between negative social environments, economic stress, and impaired functioning. The functioning of females was most affected by negative social environments regardless of genotype and economic stress, whereas the functioning of males was differentially susceptible to economic stress depending on OXTR genotype and negative social environments. These findings suggest that it is important to consider the combined impact of gender and ongoing stress in different domains as moderators of genetic vulnerability following collective stress. Copyright © 2013 Elsevier Inc. All rights reserved.

Quantifying Wheat Sensitivities to Environmental Constraints to Dissect Genotype × Environment Interactions in the Field1[OPEN

PubMed Central

Maphosa, Lance; Kovalchuk, Alex

2017-01-01

Yield is subject to strong genotype-by-environment (G × E) interactions in the field, especially under abiotic constraints such as soil water deficit (drought [D]) and high temperature (heat [H]). Since environmental conditions show strong fluctuations during the whole crop cycle, geneticists usually do not consider environmental measures as quantitative variables but rather as factors in multienvironment analyses. Based on 11 experiments in a field platform with contrasting temperature and soil water deficit, we determined the periods of sensitivity to drought and heat constraints in wheat (Triticum aestivum) and determined the average sensitivities for major yield components. G × E interactions were separated into their underlying components, constitutive genotypic effect (G), G × D, G × H, and G × H × D, and were analyzed for two genotypes, highlighting contrasting responses to heat and drought constraints. We then tested the constitutive and responsive behaviors of two strong quantitative trait loci (QTLs) associated previously with yield components. This analysis confirmed the constitutive effect of the chromosome 1B QTL and explained the G × E interaction of the chromosome 3B QTL by a benefit of one allele when temperature rises. In addition to the method itself, which can be applied to other data sets and populations, this study will support the cloning of a major yield QTL on chromosome 3B that is highly dependent on environmental conditions and for which the climatic interaction is now quantified. PMID:28546436

Genotype-by-environment interactions leads to variable selection on life-history strategy in Common Evening Primrose (Oenothera biennis).

PubMed

Johnson, M T J

2007-01-01

Monocarpic plant species, where reproduction is fatal, frequently exhibit variation in the length of their prereproductive period prior to flowering. If this life-history variation in flowering strategy has a genetic basis, genotype-by-environment interactions (G x E) may maintain phenotypic diversity in flowering strategy. The native monocarpic plant Common Evening Primrose (Oenothera biennis L., Onagraceae) exhibits phenotypic variation for annual vs. biennial flowering strategies. I tested whether there was a genetic basis to variation in flowering strategy in O. biennis, and whether environmental variation causes G x E that imposes variable selection on flowering strategy. In a field experiment, I randomized more than 900 plants from 14 clonal families (genotypes) into five distinct habitats that represented a natural productivity gradient. G x E strongly affected the lifetime fruit production of O. biennis, with the rank-order in relative fitness of genotypes changing substantially between habitats. I detected genetic variation in annual vs. biennial strategies in most habitats, as well as a G x E effect on flowering strategy. This variation in flowering strategy was correlated with genetic variation in relative fitness, and phenotypic and genotypic selection analyses revealed that environmental variation resulted in variable directional selection on annual vs. biennial strategies. Specifically, a biennial strategy was favoured in moderately productive environments, whereas an annual strategy was favoured in low-productivity environments. These results highlight the importance of variable selection for the maintenance of genetic variation in the life-history strategy of a monocarpic plant.

Best Linear Unbiased Prediction (BLUP) for regional yield trials: a comparison to additive main effects and multiplicative interaction (AMMI) analysis.

PubMed

Piepho, H P

1994-11-01

Multilocation trials are often used to analyse the adaptability of genotypes in different environments and to find for each environment the genotype that is best adapted; i.e. that is highest yielding in that environment. For this purpose, it is of interest to obtain a reliable estimate of the mean yield of a cultivar in a given environment. This article compares two different statistical estimation procedures for this task: the Additive Main Effects and Multiplicative Interaction (AMMI) analysis and Best Linear Unbiased Prediction (BLUP). A modification of a cross validation procedure commonly used with AMMI is suggested for trials that are laid out as a randomized complete block design. The use of these procedure is exemplified using five faba bean datasets from German registration trails. BLUP was found to outperform AMMI in four of five faba bean datasets.

Mixed models identify physic nut genotypes adapted to environments with different phosphorus availability.

PubMed

Teodoro, P E; Laviola, B G; Martins, L D; Amaral, J F T; Rodrigues, W N

2016-08-19

The aim of this study was to screen physic nut (Jatropha curcas) genotypes that differ in their phosphorous (P) use, using mixed models. The experiment was conducted in a greenhouse located in the experimental area of the Centro de Ciências Agrárias of the Universidade Federal do Espírito Santo, in Alegre, ES, Brazil. The experiment was arranged in a randomized block design, using a 10 x 3-factorial scheme, including ten physic nut genotypes and two environments that differed in their levels of soil P availability (10 and 60 mg/dm 3 ), each with four replications. After 100 days of cultivation, we evaluated the plant height, stem diameter, root volume, root dry matter, aerial part dry matter, total dry matter, as well as the efficiency of absorption, and use. The parameters were estimated for combined selection while considering the studied parameters: stability and adaptability for both environments were obtained using the harmonic mean of the relative performance of the predicted genotypic values. High genotype by environment interactions were observed for most physic nut traits, indicating considerable influences of P availability on the phenotypic value. The genotype Paraíso simultaneously presented high adaptability and stability for aerial part dry matter, total dry matter, and P translocation efficiency. The genotype CNPAE-C2 showed a positive response to P fertilization by increasing both the total and aerial part dry matter.

Genomic Prediction Accounting for Genotype by Environment Interaction Offers an Effective Framework for Breeding Simultaneously for Adaptation to an Abiotic Stress and Performance Under Normal Cropping Conditions in Rice.

PubMed

Ben Hassen, Manel; Bartholomé, Jérôme; Valè, Giampiero; Cao, Tuong-Vi; Ahmadi, Nourollah

2018-05-09

Developing rice varieties adapted to alternate wetting and drying water management is crucial for the sustainability of irrigated rice cropping systems. Here we report the first study exploring the feasibility of breeding rice for adaptation to alternate wetting and drying using genomic prediction methods that account for genotype by environment interactions. Two breeding populations (a reference panel of 284 accessions and a progeny population of 97 advanced lines) were evaluated under alternate wetting and drying and continuous flooding management systems. The predictive ability of genomic prediction for response variables (index of relative performance and the slope of the joint regression) and for multi-environment genomic prediction models were compared. For the three traits considered (days to flowering, panicle weight and nitrogen-balance index), significant genotype by environment interactions were observed in both populations. In cross validation, predictive ability for the index was on average lower (0.31) than that of the slope of the joint regression (0.64) whatever the trait considered. Similar results were found for progeny validation. Both cross-validation and progeny validation experiments showed that the performance of multi-environment models predicting unobserved phenotypes of untested entrees was similar to the performance of single environment models with differences in predictive ability ranging from -6% to 4% depending on the trait and on the statistical model concerned. The predictive ability of multi-environment models predicting unobserved phenotypes of entrees evaluated under both water management systems outperformed single environment models by an average of 30%. Practical implications for breeding rice for adaptation to alternate wetting and drying system are discussed. Copyright © 2018, G3: Genes, Genomes, Genetics.

Childhood Temperament: Passive Gene-Environment Correlation, Gene-Environment Interaction, and the Hidden Importance of the Family Environment

PubMed Central

Lemery-Chalfant, Kathryn; Kao, Karen; Swann, Gregory; Goldsmith, H. Hill

2013-01-01

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 (M 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. PMID:23398752

Adaptive capacity of the habitat modifying sea urchin Centrostephanus rodgersii to ocean warming and ocean acidification: performance of early embryos.

PubMed

Foo, Shawna A; Dworjanyn, Symon A; Poore, Alistair G B; Byrne, Maria

2012-01-01

Predicting effects of rapid climate change on populations depends on measuring the effects of climate stressors on performance, and potential for adaptation. Adaptation to stressful climatic conditions requires heritable genetic variance for stress tolerance present in populations. We quantified genetic variation in tolerance of early development of the ecologically important sea urchin Centrostephanus rodgersii to near-future (2100) ocean conditions projected for the southeast Australian global change hot spot. Multiple dam-sire crosses were used to quantify the interactive effects of warming (+2-4 °C) and acidification (-0.3-0.5 pH units) across twenty-seven family lines. Acidification, but not temperature, decreased the percentage of cleavage stage embryos. In contrast, temperature, but not acidification decreased the percentage of gastrulation. Cleavage success in response to both stressors was strongly affected by sire identity. Sire and dam identity significantly affected gastrulation and both interacted with temperature to determine developmental success. Positive genetic correlations for gastrulation indicated that genotypes that did well at lower pH also did well in higher temperatures. Significant genotype (sire) by environment interactions for both stressors at gastrulation indicated the presence of heritable variation in thermal tolerance and the ability of embryos to respond to changing environments. The significant influence of dam may be due to maternal provisioning (maternal genotype or environment) and/or offspring genotype. It appears that early development in this ecologically important sea urchin is not constrained in adapting to the multiple stressors of ocean warming and acidification. The presence of tolerant genotypes indicates the potential to adapt to concurrent warming and acidification, contributing to the resilience of C. rodgersii in a changing ocean.

Adaptive Capacity of the Habitat Modifying Sea Urchin Centrostephanus rodgersii to Ocean Warming and Ocean Acidification: Performance of Early Embryos

PubMed Central

Foo, Shawna A.; Dworjanyn, Symon A.; Poore, Alistair G. B.; Byrne, Maria

2012-01-01

Background Predicting effects of rapid climate change on populations depends on measuring the effects of climate stressors on performance, and potential for adaptation. Adaptation to stressful climatic conditions requires heritable genetic variance for stress tolerance present in populations. Methodology/Principal Findings We quantified genetic variation in tolerance of early development of the ecologically important sea urchin Centrostephanus rodgersii to near-future (2100) ocean conditions projected for the southeast Australian global change hot spot. Multiple dam-sire crosses were used to quantify the interactive effects of warming (+2–4°C) and acidification (−0.3−0.5 pH units) across twenty-seven family lines. Acidification, but not temperature, decreased the percentage of cleavage stage embryos. In contrast, temperature, but not acidification decreased the percentage of gastrulation. Cleavage success in response to both stressors was strongly affected by sire identity. Sire and dam identity significantly affected gastrulation and both interacted with temperature to determine developmental success. Positive genetic correlations for gastrulation indicated that genotypes that did well at lower pH also did well in higher temperatures. Conclusions/Significance Significant genotype (sire) by environment interactions for both stressors at gastrulation indicated the presence of heritable variation in thermal tolerance and the ability of embryos to respond to changing environments. The significant influence of dam may be due to maternal provisioning (maternal genotype or environment) and/or offspring genotype. It appears that early development in this ecologically important sea urchin is not constrained in adapting to the multiple stressors of ocean warming and acidification. The presence of tolerant genotypes indicates the potential to adapt to concurrent warming and acidification, contributing to the resilience of C. rodgersii in a changing ocean. PMID:22880005

Gene-Gene-Environment Interactions of Serotonin Transporter, Monoamine Oxidase A and Childhood Maltreatment Predict Aggressive Behavior in Chinese Adolescents

PubMed Central

Zhang, Yun; Ming, Qing-sen; Yi, Jin-yao; Wang, Xiang; Chai, Qiao-lian; Yao, Shu-qiao

2017-01-01

Gene-environment interactions that moderate aggressive behavior have been identified independently in the serotonin transporter (5-HTT) gene and monoamine oxidase A gene (MAOA). The aim of the present study was to investigate epistasis interactions between MAOA-variable number tandem repeat (VNTR), 5-HTTlinked polymorphism (LPR) and child abuse and the effects of these on aggressive tendencies in a group of otherwise healthy adolescents. A group of 546 Chinese male adolescents completed the Child Trauma Questionnaire and Youth self-report of the Child Behavior Checklist. Buccal cells were collected for DNA analysis. The effects of childhood abuse, MAOA-VNTR, 5-HTTLPR genotypes and their interactive gene-gene-environmental effects on aggressive behavior were analyzed using a linear regression model. The effect of child maltreatment was significant, and a three-way interaction among MAOA-VNTR, 5-HTTLPR and sexual abuse (SA) relating to aggressive behaviors was identified. Chinese male adolescents with high expression of the MAOA-VNTR allele and 5-HTTLPR “SS” genotype exhibited the highest aggression tendencies with an increase in SA during childhood. The findings reported support aggression being a complex behavior involving the synergistic effects of gene-gene-environment interactions. PMID:28203149

Interactive Effects of in Utero Nutrition and Genetic Inheritance on Cognition: New Evidence Using Sibling Comparisons1

PubMed Central

Cook, C. Justin; Fletcher, Jason M.

2013-01-01

A large literature links early environments and later outcomes, such as cognition; however, little is known about the mechanisms. One potential mechanism is sensitivity to early environments that is moderated or amplified by the genotype. With this mechanism in mind, a complementary literature outside economics examines the interaction between genes and environments, but often problems of endogeneity and bias in estimation are uncorrected. A key issue in the literature is exploring environmental variation that is not exogenous, which is potentially problematic if there are gene-environment correlation or gene-gene interactions. Using sibling pairs with genetic data in the Wisconsin Longitudinal Study we extend a previous, and widely cited, gene-environment study that explores an interaction between the FADS2 gene, which is associated with the processing of essential fatty acids related to cognitive development, and early life nutrition in explaining later-life IQ. Our base OLS findings suggest that individuals with specific FADS2 variants gain roughly 0.15 standard deviations in IQ for each standard deviation increase in birth weight, our measure of the early nutrition environment; while, individuals with other variants of FADS2 do not have a statistically significant association with early nutrition, implying the genotype is influencing the effects of environmental exposure. When including family-level fixed effects, however, the magnitude of the gene-environment interaction is reduced by half and statistical significance dissipates, implying the interaction between FADS2 and early nutrition in explaining later life IQ may in part be due to unobserved, family-level factors. The example has wider implications for the practice of investigating gene-environment interactions when the environmental exposure is not exogenous and robustness to unobserved variation in the genome is not controlled for in the analysis. PMID:24172871

Hemiclonal analysis reveals significant genetic, environmental and genotype x environment effects on sperm size in Drosophila melanogaster.

PubMed

Morrow, E H; Leijon, A; Meerupati, A

2008-11-01

Spermatozoa are the most diverse of all animal cells. Variation in size alone is enormous and yet there are still no clear evolutionary explanations that can account for such diversity. The basic genetics of sperm form is also poorly understood, although sperm size is known to have a strong genetic component. Here, using hemiclonal analysis of Drosophila melanogaster, we demonstrate that there is not only a significant additive genetic component contributing to phenotypic variation in sperm length but also a significant environmental effect. Furthermore, the plasticity of sperm size has a significant genetic component to it (a genotype x environment interaction). A genotype x environment interaction could contribute to the maintenance of the substantial genetic variation in this trait and thereby explain the persistent inter-male differences in sperm size seen in numerous taxa. We suggest that the low conditional dependence and high heritability but low evolvability (the coefficient of additive genetic variation) of sperm length is more consistent with a history of stabilizing selection rather than either sexual selection or strong directional selection.

Serotonin-transporter-linked polymorphic region (5-HTTLPR) genotype and stressful life events interact to predict preschool onset depression: A replication and developmental extension

PubMed Central

Bogdan, Ryan; Agrawal, Arpana; Gaffrey, Michael S; Tillman, Rebecca; Luby, Joan L

2013-01-01

Background Scientific enthusiasm about gene x environment interactions, spurred by the 5-HTTLPR (serotonin transporter polymorphic-region) x SLEs (stressful life events) interaction predicting depression, have recently been tempered by sober realizations of small effects and meta-analyses reaching opposing conclusions. These mixed findings highlight the need for further research. Converging evidence suggests that the effects of 5-HTTLPR genotype may be neurodevelopmental in origin but we are not aware of empirical studies that have investigated whether the 5-HTTLPR genotype x SLE interaction predicts preschool-onset depression (PO-MDD), the earliest validated form of depression. Methods Children (n = 234) aged 3–5 were recruited for a longitudinal study designed to examine PO-MDD. In a comprehensive baseline assessment, the child’s primary caregivers completed questionnaires and were interviewed about their child’s behaviors, psychiatric symptoms, and exposure to SLEs. Results A 5-HTTLPR x SLEs interaction emerged, such that children homozygous for the short allele were more susceptible to depression in the context of elevated SLE than long allele carriers. In contrast, at low SLE exposure, short allele homozygotes had fewer depressive symptoms. The data were best fit by a plasticity model with a substantial reduction in fit by diathesis-stress models. Conclusions Extending studies in adult and adolescent populations, these data suggest that 5-HTTLPR genotype may provide plasticity to environmental influence, for better or worse. Specifically, children homozygous for the short allele were more susceptible to the depressogenic effects of SLEs but benefitted, in the form of reduced depressive symptoms, in the context of relatively benign environmental conditions (i.e., relatively low SLE exposure). These data highlight the importance of examining gene x environment interactions across development, environment, and outcome but should be interpreted cautiously given the small sample size. PMID:24117502

Genetic sensitivity to the caregiving context: The influence of 5httlpr and BDNF val66met on indiscriminate social behavior

PubMed Central

Drury, Stacy S; Gleason, Mary Margaret; Theall, Katherine; Smyke, Anna T; Nelson, Charles A; Fox, Nathan A; Zeanah, Charles H

2014-01-01

Evidence that gene x environment interactions can reflect differential sensitivity to the environmental context, rather than risk or resilience, is increasing. To test this model, we examined the genetic contribution to indiscriminate social behavior, in the setting of a randomized controlled trial of foster care compared to institutional rearing. Children enrolled in the Bucharest Early Intervention Project (BEIP) were assessed comprehensively before the age of 30 months and subsequently randomized to either care as usual (CAUG) or high quality foster care (FCG). Indiscriminate social behavior was assessed at four time points, baseline, 30 months, 42 months and 54 months of age, using caregiver report with the Disturbances of Attachment Interview (DAI). General linear mixed-effects models were used to examine the effect of the interaction between group status and functional polymorphisms in Brain Derived Neurotrophic Factor (BDNF) and the Serotonin Transporter (5htt) on levels of indiscriminate behavior over time. Differential susceptibility, relative to levels of indiscriminate behavior, was demonstrated in children with either the s/s 5httlpr genotype or met 66 BDNF allele carriers. Specifically children with either the s/s 5httlpr genotype or met66 carriers in BDNF demonstrated the lowest levels of indiscriminate behavior in the FCG and the highest levels in the CAUG. Children with either the long allele of the 5httlpr or val/val genotype of BDNF demonstrated little difference in levels of indiscriminate behaviors over time and no group x genotype interaction. Children with both plasticity genotypes had the most signs of indiscriminate behavior at 54 months if they were randomized to the CAUG in the institution, while those with both plasticity genotypes randomized to the FCG intervention had the fewest signs at 54 months. Strikingly children with no plasticity alleles demonstrated no intervention effect on levels of indiscriminate behavior at 54 months. These findings represent the first genetic associations reported with Indiscriminate social behavior, replicate previous gene x gene x environment findings with these polymorphisms, and add to the growing body of literature supporting a differential susceptibility model of gene x environment interactions in developmental psychopathology. PMID:22133521

Significant effects of Pgi genotype and body reserves on lifespan in the Glanville fritillary butterfly

PubMed Central

Saastamoinen, Marjo; Ikonen, Suvi; Hanski, Ilkka

2009-01-01

Individuals with a particular variant of the gene phosphoglucose isomerase (Pgi) have been shown to have superior dispersal capacity and fecundity in the Glanville fritillary butterfly (Melitaea cinxia), raising questions about the mechanisms that maintain polymorphism in this gene in the field. Here, we investigate how variation in the Pgi genotype affects female and male life history under controlled conditions. The most striking effect is the longer lifespan of genotypes with high dispersal capacity, especially in non-reproducing females. Butterflies use body reserves for somatic maintenance and reproduction, but different resources (in thorax versus abdomen) are used under dissimilar conditions, with some interactions with the Pgi genotype. These results indicate life-history trade-offs that involve resource allocation and genotype×environment interactions, and these trade-offs are likely to contribute to the maintenance of Pgi polymorphism in the natural populations. PMID:19129143

Maternal Genetic Variants of IL4/IL13 Pathway Genes on IgE With "Western or Eastern Environments/Lifestyles".

PubMed

Zhang, Guicheng; Khoo, Siew-Kim; Mäkelä, Mika J; Candelaria, Pierre; Hayden, Catherine M; von Hertzen, Leena; Laatikainen, Tiina; Vartiainen, Erkki; Goldblatt, Jack; Haahtela, Tari; LeSouëf, Peter N

2014-07-01

We investigated maternal genetic effects of four IL-4/IL-13 pathway genes as well as their interactions with the "Western or Eastern lifestyles/environments" on IgE in Karelian children. This study included 609 children and their mothers. Total IgE levels in children and mothers were measured and 10 single nucleotide polymorphisms (SNPs) in IL-4, IL-4Ra, IL-13, and STAT6 were genotyped in mothers and their children. The maternal G allele of IL-13 130 (rs20541) was significantly (P=0.001) associated with decreased IgE in children in the Karelian population (Pooling Finnish and Russian children), as well as in Finnish (P=0.030) and Russian children (P=0.018). The IgE levels were significantly (P=0.001) higher in Russian children whose mothers were homozygous for the G allele of the IL-4Ra 50 (rs1805010) SNP than that in Russian children of mothers who were AG heterozygotes or AA homozygotes. After accounting for children's genotypes, we observed interactive effects on children's IgE for maternal IL-13 130 genotypes (P=0.014) and maternal IL-4Ra 50 genotypes (P=0.0003) with "Western or Eastern" lifestyles/environments. With the adjustment for multiple comparisons using a false discovery rate (FDR) of 0.05, the interactive effect of the maternal IL-4Ra50 SNP was significant. Maternal genetic variants in IL-4/IL-13 pathway genes, such as IL-13 130 and IL-4Ra50, influenced IgE levels in school children that were independent of the children's genetic effects. These effects differ in "Western or Eastern" environments.

A latent modeling approach to genotype-phenotype relationships: maternal problem behavior clusters, prenatal smoking, and MAOA genotype.

PubMed

McGrath, L M; Mustanski, B; Metzger, A; Pine, D S; Kistner-Griffin, E; Cook, E; Wakschlag, L S

2012-08-01

This study illustrates the application of a latent modeling approach to genotype-phenotype relationships and gene × environment interactions, using a novel, multidimensional model of adult female problem behavior, including maternal prenatal smoking. The gene of interest is the monoamine oxidase A (MAOA) gene which has been well studied in relation to antisocial behavior. Participants were adult women (N = 192) who were sampled from a prospective pregnancy cohort of non-Hispanic, white individuals recruited from a neighborhood health clinic. Structural equation modeling was used to model a female problem behavior phenotype, which included conduct problems, substance use, impulsive-sensation seeking, interpersonal aggression, and prenatal smoking. All of the female problem behavior dimensions clustered together strongly, with the exception of prenatal smoking. A main effect of MAOA genotype and a MAOA × physical maltreatment interaction were detected with the Conduct Problems factor. Our phenotypic model showed that prenatal smoking is not simply a marker of other maternal problem behaviors. The risk variant in the MAOA main effect and interaction analyses was the high activity MAOA genotype, which is discrepant from consensus findings in male samples. This result contributes to an emerging literature on sex-specific interaction effects for MAOA.

Integration of statistical and physiological analyses of adaptation of near-isogenic barley lines.

PubMed

Romagosa, I; Fox, P N; García Del Moral, L F; Ramos, J M; García Del Moral, B; Roca de Togores, F; Molina-Cano, J L

1993-08-01

Seven near-isogenic barley lines, differing for three independent mutant genes, were grown in 15 environments in Spain. Genotype x environment interaction (G x E) for grain yield was examined with the Additive Main Effects and Multiplicative interaction (AMMI) model. The results of this statistical analysis of multilocation yield-data were compared with a morpho-physiological characterization of the lines at two sites (Molina-Cano et al. 1990). The first two principal component axes from the AMMI analysis were strongly associated with the morpho-physiological characters. The independent but parallel discrimination among genotypes reflects genetic differences and highlights the power of the AMMI analysis as a tool to investigate G x E. Characters which appear to be positively associated with yield in the germplasm under study could be identified for some environments.

Parenting and adolescent antisocial behavior and depression: evidence of genotype x parenting environment interaction.

PubMed

Feinberg, Mark E; Button, Tanya M M; Neiderhiser, Jenae M; Reiss, David; Hetherington, E Mavis

2007-04-01

Little is known about the interplay of genotypes and malleable risk factors in influencing adolescent psychiatric symptoms and disorders. Information on these processes is crucial in designing programs for the prevention of psychiatric disorders. To assess whether latent genetic factors and measured parent-child relationships interact (G x E) in predicting adolescent antisocial behavior and depression. We characterized risk of antisocial behavior and depression in adolescents by means of a genetically informed design. We used in-home questionnaire and observational measures of adolescent outcomes and environmental moderators (parenting), and a latent variable behavior genetic analytic model. A nationally distributed sample recruited from random-digit dialing and national market panels. A total of 720 families with at least 2 children, 9 through 18 years old, stratified by genetic relatedness (monozygotic and dizygotic twins, full biological siblings in nondivorced and stepfamilies, and half-siblings and biologically unrelated siblings in stepfamilies). Antisocial behavior and depressive symptoms. There was an interaction of genotype and both parental negativity and low warmth predicting overall antisocial behavior, as well as aggressive and nonaggressive forms of antisocial behavior, but not depression. Genetic influence was greater for adolescent antisocial behavior when parenting was more negative or less warm. Genotype-environment correlation was partialled out in the analysis and thus did not account for the results. This study demonstrates, on the basis of careful measurement and appropriate analytic methods, that a continuous measure of parenting in the normative range moderates the influence of genotype on antisocial behavior.

Asymmetric Evolutionary Games.

PubMed

McAvoy, Alex; Hauert, Christoph

2015-08-01

Evolutionary game theory is a powerful framework for studying evolution in populations of interacting individuals. A common assumption in evolutionary game theory is that interactions are symmetric, which means that the players are distinguished by only their strategies. In nature, however, the microscopic interactions between players are nearly always asymmetric due to environmental effects, differing baseline characteristics, and other possible sources of heterogeneity. To model these phenomena, we introduce into evolutionary game theory two broad classes of asymmetric interactions: ecological and genotypic. Ecological asymmetry results from variation in the environments of the players, while genotypic asymmetry is a consequence of the players having differing baseline genotypes. We develop a theory of these forms of asymmetry for games in structured populations and use the classical social dilemmas, the Prisoner's Dilemma and the Snowdrift Game, for illustrations. Interestingly, asymmetric games reveal essential differences between models of genetic evolution based on reproduction and models of cultural evolution based on imitation that are not apparent in symmetric games.

Genomic Prediction of Genotype × Environment Interaction Kernel Regression Models.

PubMed

Cuevas, Jaime; Crossa, José; Soberanis, Víctor; Pérez-Elizalde, Sergio; Pérez-Rodríguez, Paulino; Campos, Gustavo de Los; Montesinos-López, O A; Burgueño, Juan

2016-11-01

In genomic selection (GS), genotype × environment interaction (G × E) can be modeled by a marker × environment interaction (M × E). The G × E may be modeled through a linear kernel or a nonlinear (Gaussian) kernel. In this study, we propose using two nonlinear Gaussian kernels: the reproducing kernel Hilbert space with kernel averaging (RKHS KA) and the Gaussian kernel with the bandwidth estimated through an empirical Bayesian method (RKHS EB). We performed single-environment analyses and extended to account for G × E interaction (GBLUP-G × E, RKHS KA-G × E and RKHS EB-G × E) in wheat ( L.) and maize ( L.) data sets. For single-environment analyses of wheat and maize data sets, RKHS EB and RKHS KA had higher prediction accuracy than GBLUP for all environments. For the wheat data, the RKHS KA-G × E and RKHS EB-G × E models did show up to 60 to 68% superiority over the corresponding single environment for pairs of environments with positive correlations. For the wheat data set, the models with Gaussian kernels had accuracies up to 17% higher than that of GBLUP-G × E. For the maize data set, the prediction accuracy of RKHS EB-G × E and RKHS KA-G × E was, on average, 5 to 6% higher than that of GBLUP-G × E. The superiority of the Gaussian kernel models over the linear kernel is due to more flexible kernels that accounts for small, more complex marker main effects and marker-specific interaction effects. Copyright © 2016 Crop Science Society of America.

The GP problem: quantifying gene-to-phenotype relationships.

PubMed

Cooper, Mark; Chapman, Scott C; Podlich, Dean W; Hammer, Graeme L

2002-01-01

In this paper we refer to the gene-to-phenotype modeling challenge as the GP problem. Integrating information across levels of organization within a genotype-environment system is a major challenge in computational biology. However, resolving the GP problem is a fundamental requirement if we are to understand and predict phenotypes given knowledge of the genome and model dynamic properties of biological systems. Organisms are consequences of this integration, and it is a major property of biological systems that underlies the responses we observe. We discuss the E(NK) model as a framework for investigation of the GP problem and the prediction of system properties at different levels of organization. We apply this quantitative framework to an investigation of the processes involved in genetic improvement of plants for agriculture. In our analysis, N genes determine the genetic variation for a set of traits that are responsible for plant adaptation to E environment-types within a target population of environments. The N genes can interact in epistatic NK gene-networks through the way that they influence plant growth and development processes within a dynamic crop growth model. We use a sorghum crop growth model, available within the APSIM agricultural production systems simulation model, to integrate the gene-environment interactions that occur during growth and development and to predict genotype-to-phenotype relationships for a given E(NK) model. Directional selection is then applied to the population of genotypes, based on their predicted phenotypes, to simulate the dynamic aspects of genetic improvement by a plant-breeding program. The outcomes of the simulated breeding are evaluated across cycles of selection in terms of the changes in allele frequencies for the N genes and the genotypic and phenotypic values of the populations of genotypes.

Quantifying Wheat Sensitivities to Environmental Constraints to Dissect Genotype × Environment Interactions in the Field.

PubMed

Parent, Boris; Bonneau, Julien; Maphosa, Lance; Kovalchuk, Alex; Langridge, Peter; Fleury, Delphine

2017-07-01

Yield is subject to strong genotype-by-environment (G × E) interactions in the field, especially under abiotic constraints such as soil water deficit (drought [D]) and high temperature (heat [H]). Since environmental conditions show strong fluctuations during the whole crop cycle, geneticists usually do not consider environmental measures as quantitative variables but rather as factors in multienvironment analyses. Based on 11 experiments in a field platform with contrasting temperature and soil water deficit, we determined the periods of sensitivity to drought and heat constraints in wheat ( Triticum aestivum ) and determined the average sensitivities for major yield components. G × E interactions were separated into their underlying components, constitutive genotypic effect (G), G × D, G × H, and G × H × D, and were analyzed for two genotypes, highlighting contrasting responses to heat and drought constraints. We then tested the constitutive and responsive behaviors of two strong quantitative trait loci (QTLs) associated previously with yield components. This analysis confirmed the constitutive effect of the chromosome 1B QTL and explained the G × E interaction of the chromosome 3B QTL by a benefit of one allele when temperature rises. In addition to the method itself, which can be applied to other data sets and populations, this study will support the cloning of a major yield QTL on chromosome 3B that is highly dependent on environmental conditions and for which the climatic interaction is now quantified. © 2017 American Society of Plant Biologists. All Rights Reserved.

Correlation of interactions between NOS3 polymorphisms and oxygen therapy with retinopathy of prematurity susceptibility

PubMed Central

Yu, Chunhong; Yi, Jinglin; Yin, Xiaolong; Deng, Yan; Liao, Yujun; Li, Xiaobing

2015-01-01

Aim: This study was aimed to detect the correlation of nitric oxide synthase 3 (NOS3) gene polymorphisms (T-786C and G894T) and retinopathy of prematurity (ROP) susceptibility. Interaction between NOS3 gene polymorphisms and the duration of oxygen therapy was also explored in ROP babies. Methods: Genotypes of NOS3 gene polymorphisms were genotyped by MassArray method. Hardy-Weinberg equilibrium (HWE) was used to calculate the representativeness of the cases and controls. Crossover analysis was utilized to explore the gene environment interactions. Relative risk of ROP was presented by odds ratios (ORs) with corresponding 95% confidence intervals (95% CIs). Results: Among the subject features, oxygen therapy had obvious difference between case and control groups (P<0.05). There existed significant association between-786C allele and ROP susceptibility (P=0.049, OR=0.669, 95% CI=0.447-0.999). Genotypes of T-786C polymorphism and genotypes and alleles of G894T polymorphism did not related to the susceptibility of ROP. Interactions were existed between NOS3 gene polymorphisms and oxygen therapy duration. When the duration of oxygen therapy was less than 17 days, both -786CC genotype and 894GT genotype were correlated with ROP susceptibility (P=0.020, OR=0.115, 95% CI=0.014-0.960; P=0.011, OR=0.294, 95% CI=0.100-0.784). Conclusion: -786C allele might have a protective effect for ROP. Interactions of -786CC and 894GT genotype with oxygen therapy duration (less than 17 days) were both protection factors of ROP. PMID:26823875

A genome-wide association and gene-environment interaction study for serum triglycerides levels in a healthy Chinese male population.

PubMed

Tan, Aihua; Sun, Jielin; Xia, Ning; Qin, Xue; Hu, Yanling; Zhang, Shijun; Tao, Sha; Gao, Yong; Yang, Xiaobo; Zhang, Haiying; Kim, Seong-Tae; Peng, Tao; Lin, Xiaoling; Li, Li; Mo, Linjian; Liang, Zhengjia; Shi, Deyi; Huang, Zhang; Huang, Xianghua; Liu, Ming; Ding, Qiang; Trent, Jeffrey M; Zheng, S Lilly; Mo, Zengnan; Xu, Jianfeng

2012-04-01

Triglyceride (TG) is a complex phenotype influenced by both genetic and environmental factors. Recent genome-wide association studies (GWAS) have identified genes or loci affecting lipid levels; however, such studies in Chinese populations are limited. A two-stage GWAS were conducted to identify genetic variants that were associated with TG in a Chinese population of 3495 men. Gene-environment interactions on serum TG levels were further investigated for the seven single nucleotide polymorphisms (SNPs) that were studied in both stages. Two previously reported SNPs (rs651821 in APOA5, rs328 in LPL) were replicated in the second stage, and the combined P-values were 9.19 × 10(-26) and 1.41 × 10(-9) for rs651821 and rs328, respectively. More importantly, a significant interaction between aldehyde dehydrogenase 2 (ALDH2) rs671 and alcohol consumption on serum TG levels were observed (P = 3.34 × 10(-5)). Rs671 was significantly associated with serum TG levels in drinkers (P = 1.90 × 10(-10)), while no association was observed in non-drinkers (P > 0.05). For drinkers, men carrying the AA/AG genotype have significantly lower serum TG levels, compared with men carrying the GG genotype. For men with the GG genotype, the serum TG levels increased with the quantity of alcohol intake (P = 1.28 × 10(-8) for trend test). We identified a novel, significant interaction effect between alcohol consumption and the ALDH2 rs671 polymorphism on TG levels, which suggests that the effect of alcohol intake on TG occurs in a two-faceted manner. Just one drink can increase TG level in susceptible individuals who carry the GG genotype, while individuals carrying AA/AG genotypes may actually benefit from moderate drinking.

Interaction between the SLC19A1 gene and maternal first trimester fever on offspring neural tube defects.

PubMed

Pei, Lijun; Zhu, Huiping; Ye, Rongwei; Wu, Jilei; Liu, Jianmeng; Ren, Aiguo; Li, Zhiwen; Zheng, Xiaoying

2015-01-01

Many studies have indicated that the reduced folate carrier gene (SLC19A1) is associated with an increased risk of neural tube defects (NTDs). However, the interaction between the SLC19A1 gene variant and maternal fever exposure and NTD risk remains unknown. The aim of this study was to investigate whether the risk for NTDs was influenced by the interactions between the SLC19A1 (rs1051266) variant and maternal first trimester fever. We investigated the potential interaction between maternal first trimester fever and maternal or offspring SLC19A1 polymorphism through a population-based case-control study. One hundred and four nuclear families with NTDs and 100 control families with nonmal newborns were included in the study. SLC19A1 polymorphism was determined using polymerase chain reaction-restricted fragment length polymorphism. Mothers who had the GG/GA genotype and first trimester fever had an elevated risk of NTDs (adjusted odds ratio, 11.73; 95% confidence interval, 3.02-45.58) as compared to absence of maternal first trimester fever and AA genotype after adjusting for maternal education, paternal education, and age, and had a significant interactive coefficient (γ = 3.17) between maternal GG/GA genotype and first trimester fever. However, there was no interaction between offspring's GG/GA genotype and maternal first trimester fever (the interactive coefficient γ = 0.97) after adjusting for confounding factors. Our findings suggested that the risk of NTDs was potentially influenced by a gene-environment interaction between maternal SLC19A1 rs1051266 GG/GA genotype and first trimester fever. Maternal GG/GA genotype may strengthen the effect of maternal fever exposure on NTD risk in this Chinese population. © 2014 Wiley Periodicals, Inc.

Serotonin transporter gene and childhood trauma--a G × E effect on anxiety sensitivity.

PubMed

Klauke, Benedikt; Deckert, Jürgen; Reif, Andreas; Pauli, Paul; Zwanzger, Peter; Baumann, Christian; Arolt, Volker; Glöckner-Rist, Angelika; Domschke, Katharina

2011-12-21

Genetic factors and environmental factors are assumed to interactively influence the pathogenesis of anxiety disorders. Thus, a gene-environment interaction (G × E) study was conducted with respect to anxiety sensitivity (AS) as a promising intermediate phenotype of anxiety disorders. Healthy subjects (N = 363) were assessed for AS, childhood maltreatment (Childhood Trauma Questionnaire), and genotyped for functional serotonin transporter gene variants (5-HTTLPR/5-HTT rs25531). The influence of genetic and environmental variables on AS and its subdimensions was determined by a step-wise hierarchical regression and a multiple indicator multiple cause (MIMIC) model. A significant G × E effect of the more active 5-HTT genotypes and childhood maltreatment on AS was observed. Furthermore, genotype (LL)-childhood trauma interaction particularly influenced somatic AS subdimensions, whereas cognitive subdimensions were affected by childhood maltreatment only. Results indicate a G × E effect of the more active 5-HTT genotypes and childhood maltreatment on AS, with particular impact on its somatic subcomponent. © 2011 Wiley Periodicals, Inc.

A method to associate all possible combinations of genetic and environmental factors using GxE landscape plot.

PubMed

Nagaie, Satoshi; Ogishima, Soichi; Nakaya, Jun; Tanaka, Hiroshi

2015-01-01

Genome-wide association studies (GWAS) and linkage analysis has identified many single nucleotide polymorphisms (SNPs) related to disease. There are many unknown SNPs whose minor allele frequencies (MAFs) as low as 0.005 having intermediate effects with odds ratio between 1.5~3.0. Low frequency variants having intermediate effects on disease pathogenesis are believed to have complex interactions with environmental factors called gene-environment interactions (GxE). Hence, we describe a model using 3D Manhattan plot called GxE landscape plot to visualize the association of p-values for gene-environment interactions (GxE). We used the Gene-Environment iNteraction Simulator 2 (GENS2) program to simulate interactions between two genetic loci and one environmental factor in this exercise. The dataset used for training contains disease status, gender, 20 environmental exposures and 100 genotypes for 170 subjects, and p-values were calculated by Cochran-Mantel-Haenszel chi-squared test on known data. Subsequently, we created a 3D GxE landscape plot of negative logarithm of the association of p-values for all the possible combinations of genetic and environmental factors with their hierarchical clustering. Thus, the GxE landscape plot is a valuable model to predict association of p-values for GxE and similarity among genotypes and environments in the context of disease pathogenesis. GxE - Gene-environment interactions, GWAS - Genome-wide association study, MAFs - Minor allele frequencies, SNPs - Single nucleotide polymorphisms, EWAS - Environment-wide association study, FDR - False discovery rate, JPT+CHB - HapMap population of Japanese in Tokyo, Japan - Han Chinese in Beijing.

Environmental Moderators of Genetic Influence on Verbal and Nonverbal Abilities in Early Childhood

ERIC Educational Resources Information Center

Asbury, Kathryn; Wachs, Theodore D.; Plomin, Robert

2005-01-01

The study of genotype-environment interaction (G x E) has been dominated by two competing hypotheses, one that heritability is greater in high-risk environments (diathesis-stress) and the other that heritability is greater in permissive environments. The current study examined relationships between verbal and nonverbal abilities and 10 measured…

Preliminary Studies of the Performance of Quinoa (Chenopodium quinoa Willd.) Genotypes under Irrigated and Rainfed Conditions of Central Malawi.

PubMed

Maliro, Moses F A; Guwela, Veronica F; Nyaika, Jacinta; Murphy, Kevin M

2017-01-01

The goal of sustainable intensification of agriculture in Malawi has led to the evaluation of innovative, regionally novel or under-utilized crop species. Quinoa ( Chenopodium quinoa Willd.) has the potential to provide a drought tolerant, nutritious alternative to maize. We evaluated 11 diverse varieties of quinoa for their yield and agronomic performance at two locations, Bunda and Bembeke, in Malawi. The varieties originated from Ecuador, Chile and Bolivia in South America; the United States and Canada in North America; and, Denmark in Europe, and were chosen based on their variation in morphological and agronomic traits, and their potential for adaptation to the climate of Malawi. Plant height, panicle length, days to maturity, harvest index, and seed yield were recorded for each variety under irrigation at Bunda and Bembeke, and under rainfed conditions at Bunda. Plant height was significantly influenced by both genotype and environment. There were also significant differences between the two locations for panicle length whereas genotype and genotype × environment (G × E) interaction were not significantly different. Differences were found for genotype and G × E interaction for harvest index. Notably, differences for genotype, environment and G × E were found for grain yield. Seed yield was higher at Bunda (237-3019 kg/ha) than Bembeke (62-692 kg/ha) under irrigated conditions. The highest yielding genotype at Bunda was Titicaca (3019 kg/ha) whereas Multi-Hued was the highest (692 kg/ha) at Bembeke. Strong positive correlations between seed yield and (1) plant height ( r = 0.74), (2) days to maturity ( r = 0.76), and (3) biomass ( r = 0.87) were found under irrigated conditions. The rainfed evaluations at Bunda revealed significant differences in seed yield, plant biomass, and seed size among the genotypes. The highest yielding genotype was Black Seeded (2050 kg/ha) followed by Multi-Hued (1603 kg/ha) and Bio-Bio (1446 kg/ha). Ecuadorian (257 kg/ha) was the lowest yielding genotype. In general the seed yields of the genotypes were lower under rainfed conditions than under irrigated conditions at Bunda. The results also highlight the need to continue evaluating a diverse number of cultivars to select for genotypes adapted to specific agro-ecological areas and across seasons in Malawi.

Preliminary Studies of the Performance of Quinoa (Chenopodium quinoa Willd.) Genotypes under Irrigated and Rainfed Conditions of Central Malawi

PubMed Central

Maliro, Moses F. A.; Guwela, Veronica F.; Nyaika, Jacinta; Murphy, Kevin M.

2017-01-01

The goal of sustainable intensification of agriculture in Malawi has led to the evaluation of innovative, regionally novel or under-utilized crop species. Quinoa (Chenopodium quinoa Willd.) has the potential to provide a drought tolerant, nutritious alternative to maize. We evaluated 11 diverse varieties of quinoa for their yield and agronomic performance at two locations, Bunda and Bembeke, in Malawi. The varieties originated from Ecuador, Chile and Bolivia in South America; the United States and Canada in North America; and, Denmark in Europe, and were chosen based on their variation in morphological and agronomic traits, and their potential for adaptation to the climate of Malawi. Plant height, panicle length, days to maturity, harvest index, and seed yield were recorded for each variety under irrigation at Bunda and Bembeke, and under rainfed conditions at Bunda. Plant height was significantly influenced by both genotype and environment. There were also significant differences between the two locations for panicle length whereas genotype and genotype × environment (G × E) interaction were not significantly different. Differences were found for genotype and G × E interaction for harvest index. Notably, differences for genotype, environment and G × E were found for grain yield. Seed yield was higher at Bunda (237–3019 kg/ha) than Bembeke (62–692 kg/ha) under irrigated conditions. The highest yielding genotype at Bunda was Titicaca (3019 kg/ha) whereas Multi-Hued was the highest (692 kg/ha) at Bembeke. Strong positive correlations between seed yield and (1) plant height (r = 0.74), (2) days to maturity (r = 0.76), and (3) biomass (r = 0.87) were found under irrigated conditions. The rainfed evaluations at Bunda revealed significant differences in seed yield, plant biomass, and seed size among the genotypes. The highest yielding genotype was Black Seeded (2050 kg/ha) followed by Multi-Hued (1603 kg/ha) and Bio-Bio (1446 kg/ha). Ecuadorian (257 kg/ha) was the lowest yielding genotype. In general the seed yields of the genotypes were lower under rainfed conditions than under irrigated conditions at Bunda. The results also highlight the need to continue evaluating a diverse number of cultivars to select for genotypes adapted to specific agro-ecological areas and across seasons in Malawi. PMID:28289421

Genomic Prediction with Pedigree and Genotype × Environment Interaction in Spring Wheat Grown in South and West Asia, North Africa, and Mexico.

PubMed

Sukumaran, Sivakumar; Crossa, Jose; Jarquin, Diego; Lopes, Marta; Reynolds, Matthew P

2017-02-09

Developing genomic selection (GS) models is an important step in applying GS to accelerate the rate of genetic gain in grain yield in plant breeding. In this study, seven genomic prediction models under two cross-validation (CV) scenarios were tested on 287 advanced elite spring wheat lines phenotyped for grain yield (GY), thousand-grain weight (GW), grain number (GN), and thermal time for flowering (TTF) in 18 international environments (year-location combinations) in major wheat-producing countries in 2010 and 2011. Prediction models with genomic and pedigree information included main effects and interaction with environments. Two random CV schemes were applied to predict a subset of lines that were not observed in any of the 18 environments (CV1), and a subset of lines that were not observed in a set of the environments, but were observed in other environments (CV2). Genomic prediction models, including genotype × environment (G×E) interaction, had the highest average prediction ability under the CV1 scenario for GY (0.31), GN (0.32), GW (0.45), and TTF (0.27). For CV2, the average prediction ability of the model including the interaction terms was generally high for GY (0.38), GN (0.43), GW (0.63), and TTF (0.53). Wheat lines in site-year combinations in Mexico and India had relatively high prediction ability for GY and GW. Results indicated that prediction ability of lines not observed in certain environments could be relatively high for genomic selection when predicting G×E interaction in multi-environment trials. Copyright © 2017 Sukumaran et al.

Interplay of Genes and Early Mother-Child Relationship in the Development of Self-Regulation from Toddler to Preschool Age

ERIC Educational Resources Information Center

Kochanska, Grazyna; Philibert, Robert A.; Barry, Robin A.

2009-01-01

Background: A broad capacity for deliberate self-regulation plays a key role in emotion regulation. This longitudinal investigation from infancy to preschool age examines genotype by environment (G x E) interaction in the development of self-regulation, using molecular measures of children's genotypes and observed measures of the quality of early…

Attachment style and oxytocin receptor gene variation interact in influencing social anxiety.

PubMed

Notzon, S; Domschke, K; Holitschke, K; Ziegler, C; Arolt, V; Pauli, P; Reif, A; Deckert, J; Zwanzger, P

2016-01-01

Social anxiety has been suggested to be promoted by an insecure attachment style. Oxytocin is discussed as a mediator of trust and social bonding as well as a modulator of social anxiety. Applying a gene-environment (G × E) interaction approach, in the present pilot study the main and interactive effects of attachment styles and oxytocin receptor (OXTR) gene variation were probed in a combined risk factor model of social anxiety in healthy probands. Participants (N = 388; 219 females, 169 males; age 24.7 ± 4.7 years) were assessed for anxiety in social situations (Social Phobia and Anxiety Inventory) depending on attachment style (Adult Attachment Scale, AAS) and OXTR rs53576 A/G genotype. A less secure attachment style was significantly associated with higher social anxiety. This association was partly modulated by OXTR genotype, with a stronger negative influence of a less secure attachment style on social anxiety in A allele carriers as compared to GG homozygotes. The present pilot data point to a strong association of less secure attachment and social anxiety as well as to a gene-environment interaction effect of OXTR rs53576 genotype and attachment style on social anxiety possibly constituting a targetable combined risk marker of social anxiety disorder.

Monoamine oxidase A genotype, childhood adversity, and criminal behavior in an incarcerated sample.

PubMed

Armstrong, Todd A; Boutwell, Brian B; Flores, Shahida; Symonds, Mary; Keller, Shawn; Gangitano, David A

2014-08-01

A number of studies have found a functional variable number tandem repeat polymorphism in the upstream regulatory region of the monoamine oxidase A gene (MAOA-uVNTR) interacts with childhood adversity to increase risk for antisocial behavior. Several studies have also reported null findings. Here, we examine the association between MAOA-uVNTR genotype, childhood adversity, and criminal activity in a sample of 99 male volunteers who were incarcerated in a large city jail in the Southern United States. MAOA-uVNTR genotypes were obtained from DNA extracted from buccal swabs. Criminal activity in the year before incarceration and childhood adversity were measured with self-report surveys. Violent arrest rates and property arrest rates were quantified with official records of arrest and accounted for periods of incarceration in local and state correctional facilities. The low expressing allele of the MAOA-uVNTR genotype (MAOAL) interacted with abuse to predict self-reports of less serious criminal and delinquent behavior and had a direct association with serious criminal activity. MAOAL genotype interacted with parental criminality to predict self-reports of serious criminal behavior, property arrest rates, and violent arrest rates. The findings suggest that crime prevention efforts may be improved through attention to the neurodevelopmental consequence of gene-by-environment interactions.

Plant genotypes affect aboveground and belowground herbivore interactions by changing chemical defense.

PubMed

Li, Xiaoqiong; Guo, Wenfeng; Siemann, Evan; Wen, Yuanguang; Huang, Wei; Ding, Jianqing

2016-12-01

Spatially separated aboveground (AG) and belowground (BG) herbivores are closely linked through shared host plants, and both patterns of AG-BG interactions and plant responses may vary among plant genotypes. We subjected invasive (USA) and native (China) genotypes of tallow tree (Triadica sebifera) to herbivory by the AG specialist leaf-rolling weevil Heterapoderopsis bicallosicollis and/or the root-feeding larvae of flea beetle Bikasha collaris. We measured leaf damage and leaves rolled by weevils, quantified beetle survival, and analyzed flavonoid and tannin concentrations in leaves and roots. AG and BG herbivores formed negative feedbacks on both native and invasive genotypes. Leaf damage by weevils and the number of beetle larvae emerging as adults were higher on invasive genotypes. Beetles reduced weevil damage and weevils reduced beetle larval emergence more strongly for invasive genotypes. Invasive genotypes had lower leaf and root tannins than native genotypes. BG beetles decreased leaf tannins of native genotypes but increased root tannins of invasive genotypes. AG herbivory increased root flavonoids of invasive genotypes while BG herbivory decreased leaf flavonoids. Invasive genotypes had lower AG and BG herbivore resistance, and negative AG-BG herbivore feedbacks were much stronger for invasive genotypes. Lower tannin concentrations explained overall better AG and BG herbivore performances on invasive genotypes. However, changes in tannins and flavonoids affected AG and BG herbivores differently. These results suggest that divergent selection on chemical production in invasive plants may be critical in regulating herbivore performances and novel AG and BG herbivore communities in new environments.

Character displacement and the evolution of niche complementarity in a model biofilm community

PubMed Central

Ellis, Crystal N; Traverse, Charles C; Mayo-Smith, Leslie; Buskirk, Sean W; Cooper, Vaughn S

2015-01-01

Colonization of vacant environments may catalyze adaptive diversification and be followed by competition within the nascent community. How these interactions ultimately stabilize and affect productivity are central problems in evolutionary ecology. Diversity can emerge by character displacement, in which selection favors phenotypes that exploit an alternative resource and reduce competition, or by facilitation, in which organisms change the environment and enable different genotypes or species to become established. We previously developed a model of long-term experimental evolution in which bacteria attach to a plastic bead, form a biofilm, and disperse to a new bead. Here, we focus on the evolution of coexisting mutants within a population of Burkholderia cenocepacia and how their interactions affected productivity. Adaptive mutants initially competed for space, but later competition declined, consistent with character displacement and the predicted effects of the evolved mutations. The community reached a stable equilibrium as each ecotype evolved to inhabit distinct, complementary regions of the biofilm. Interactions among ecotypes ultimately became facilitative and enhanced mixed productivity. Observing the succession of genotypes within niches illuminated changing selective forces within the community, including a fundamental role for genotypes producing small colony variants that underpin chronic infections caused by B. cenocepacia. PMID:25494960

Quality of Lupinus albus L. (white lupin) seed: extent of genotypic and environmental effects.

PubMed

Annicchiarico, Paolo; Manunza, Patrizia; Arnoldi, Anna; Boschin, Giovanna

2014-07-16

White lupin seed can be used for traditional and functional foods or as animal feed. This study aimed to support lupin breeders and production stakeholders by assessing the extent of genotypic, environmental, and genotype × environment (GE) interaction effects on seed contents of oil, tocopherols (TOC), and quinolizidine alkaloids (QA), grain yield, and seed weight of eight elite genotypes grown in two climatically contrasting Italian locations for two cropping years. On average, plants in the subcontinental climate site exhibited higher grain yield and seed size, about 8% lower oil content, and almost 85% higher QA content than those in the Mediterranean climate site. The range of genotype means was 2.97-5.14 t/ha for yield, 92-110 mg/g for oil, and 0.121-0.133 mg/g for TOC. TOC amount was largely unpredictable and featured large GE interactions that hinder its genetic improvement. Oil and alkaloid contents and seed size are more predictable and offer potential for selection.

Religion priming and an oxytocin receptor gene (OXTR) polymorphism interact to affect self-control in a social context.

PubMed

Sasaki, Joni Y; Mojaverian, Taraneh; Kim, Heejung S

2015-02-01

Using a genetic moderation approach, this study examines how an experimental prime of religion impacts self-control in a social context, and whether this effect differs depending on the genotype of an oxytocin receptor gene (OXTR) polymorphism (rs53576). People with different genotypes of OXTR seem to have different genetic orientations toward sociality, which may have consequences for the way they respond to religious cues in the environment. In order to determine whether the influence of religion priming on self-control is socially motivated, we examine whether this effect is stronger for people who have OXTR genotypes that should be linked to greater rather than less social sensitivity (i.e., GG vs. AA/AG genotypes). The results showed that experimentally priming religion increased self-control behaviors for people with GG genotypes more so than people with AA/AG genotypes. Furthermore, this Gene × Religion interaction emerged in a social context, when people were interacting face to face with another person. This research integrates genetic moderation and social psychological approaches to address a novel question about religion's influence on self-control behavior, which has implications for coping with distress and psychopathology. These findings also highlight the importance of the social context for understanding genetic moderation of psychological effects.

Genotype x environment interactions in eggplant for fruit phenolic acid content

USDA-ARS?s Scientific Manuscript database

Eggplant fruit are a rich source of phenolic acids that contribute to fruit nutritive value and influence culinary quality. We evaluated the influence of production environment on eggplant fruit phenolic acid content. Ten Solanum melongena accessions including five F1 hybrid cultivars, three open-...

Interaction of child maltreatment and 5-HTT polymorphisms: suicidal ideation among children from low-SES backgrounds.

PubMed

Cicchetti, Dante; Rogosch, Fred A; Sturge-Apple, Melissa; Toth, Sheree L

2010-06-01

To investigate whether genotypic variation of the serotonin transporter gene-linked promoter region (5-HTTLPR) moderates the effect of maltreatment on suicidal ideation in school-aged children. Eight hundred and fifty low-income children (478 maltreated; 372 non-maltreated) provided DNA samples and self-reported depressive and suicidal symptoms. Genotypes of 5-HTTLPR (s/s or s/l vs. l/l) were determined by fragment analyses. Higher suicidal ideation was found among maltreated than non-maltreated children; the groups did not differ in 5-HTTLPR genotype frequencies. Children with one to two maltreatment subtypes and s/s or s/l genotypes had higher suicidal ideation than those with the l/l genotype; suicidal ideation did not differ in non-maltreated children or children with three to four maltreatment subtypes based on 5-HTTLPR variation. The results were applicable to emotionally maltreated/neglected and to physically/sexually abused children. Gene-environment interaction was not found for depressive symptoms. The protective effect of the 5-HTTLPR l/l genotype on suicidal ideation was limited to maltreated children experiencing fewer subtypes.

Impact of thermal stress on evolutionary trajectories of pathogen resistance in three-spined stickleback (Gasterosteus aculeatus).

PubMed

Schade, Franziska M; Shama, Lisa N S; Wegner, K Mathias

2014-07-26

Pathogens are a major regulatory force for host populations, especially under stressful conditions. Elevated temperatures may enhance the development of pathogens, increase the number of transmission stages, and can negatively influence host susceptibility depending on host thermal tolerance. As a net result, this can lead to a higher prevalence of epidemics during summer months. These conditions also apply to marine ecosystems, where possible ecological impacts and the population-specific potential for evolutionary responses to changing environments and increasing disease prevalence are, however, less known. Therefore, we investigated the influence of thermal stress on the evolutionary trajectories of disease resistance in three marine populations of three-spined sticklebacks Gasterosteus aculeatus by combining the effects of elevated temperature and infection with a bacterial strain of Vibrio sp. using a common garden experiment. We found that thermal stress had an impact on fish weight and especially on survival after infection after only short periods of thermal acclimation. Environmental stress reduced genetic differentiation (QST) between populations by releasing cryptic within-population variation. While life history traits displayed positive genetic correlations across environments with relatively weak genotype by environment interactions (GxE), environmental stress led to negative genetic correlations across environments in pathogen resistance. This reversal of genetic effects governing resistance is probably attributable to changing environment-dependent virulence mechanisms of the pathogen interacting differently with host genotypes, i.e. GPathogenxGHostxE or (GPathogenxE)x(GHostxE) interactions, rather than to pure host genetic effects, i.e. GHostxE interactions. To cope with climatic changes and the associated increase in pathogen virulence, host species require wide thermal tolerances and pathogen-resistant genotypes. The higher resistance we found for some families at elevated temperatures showed that there is evolutionary potential for resistance to Vibrio sp. in both thermal environments. The negative genetic correlation of pathogen resistance between thermal environments, on the other hand, indicates that adaptation to current conditions can be a weak predictor for performance in changing environments. The observed feedback on selective gradients exerted on life history traits may exacerbate this effect, as it can also modify the response to selection for other vital components of fitness.

Social Environmental Variation, Plasticity Genes, and Aggression: Evidence for the Differential Susceptibility Hypothesis

PubMed Central

Simons, Ronald L.; Lei, Man Kit; Beach, Steven R.H.; Brody, Gene H.; Philibert, Robert A.; Gibbons, Frederick X.

2011-01-01

Although G×E studies are typically based on the assumption that some individuals possess genetic variants that enhance their vulnerability to environmental adversity, the differential susceptibility perspective posits that these individuals are simply more susceptible to environmental influence than others. An important implication of this model is that those persons most vulnerable to adverse social environments are the same ones who reap the most benefit from environmental support. The present study tested several implications of this proposition. Using longitudinal data from a sample of several hundred African Americans, we found that relatively common variants of the dopamine receptor gene and the serotonin transporter gene interact with social environmental conditions to predict aggression in a manner consonant with differential susceptibility. When the social environment was adverse, individuals with these genetic variants manifested more aggression than other genotypes, whereas when the environment was supportive they demonstrated less aggression than other genotypes. Further, we found that these genetic variants interact with environmental conditions to foster various cognitive schemas and emotions in a manner consistent with differential susceptibility and that a latent construct formed by these schemas and emotions mediated the effect of gene by environment interaction on aggression. PMID:22199399

Plant Taxonomy as a Field Study

ERIC Educational Resources Information Center

Dalby, D. H.

1970-01-01

Suggests methods of teaching plant identification and taxonomic theory using keys, statistical analyses, and biometrics. Population variation, genotype- environment interaction and experimental taxonomy are used in laboratory and field. (AL)

Social environment influences the relationship between genotype and gene expression in wild baboons

PubMed Central

Runcie, Daniel E.; Wiedmann, Ralph T.; Archie, Elizabeth A.; Altmann, Jeanne; Wray, Gregory A.; Alberts, Susan C.; Tung, Jenny

2013-01-01

Variation in the social environment can have profound effects on survival and reproduction in wild social mammals. However, we know little about the degree to which these effects are influenced by genetic differences among individuals, and conversely, the degree to which social environmental variation mediates genetic reaction norms. To better understand these relationships, we investigated the potential for dominance rank, social connectedness and group size to modify the effects of genetic variation on gene expression in the wild baboons of the Amboseli basin. We found evidence for a number of gene–environment interactions (GEIs) associated with variation in the social environment, encompassing social environments experienced in adulthood as well as persistent effects of early life social environment. Social connectedness, maternal dominance rank and group size all interacted with genotype to influence gene expression in at least one sex, and either in early life or in adulthood. These results suggest that social and behavioural variation, akin to other factors such as age and sex, can impact the genotype–phenotype relationship. We conclude that GEIs mediated by the social environment are important in the evolution and maintenance of individual differences in wild social mammals, including individual differences in responses to social stressors. PMID:23569293

Serotonin transporter deficient mice are vulnerable to escape deficits following inescapable shocks.

PubMed

Muller, J M; Morelli, E; Ansorge, M; Gingrich, J A

2011-03-01

Modulation of serotonin transporter (5-HTT) function causes changes in affective behavior, both in humans and rodents. Stressful life events likewise affect emotional behavior. In humans, a low-expressing genetic 5-htt variant, the s allele of the 5-htt linked promoter region, has been associated with increased risk for depression only where there was a history of stressful life events. To investigate this gene by environment interaction in mice, we compared the effects of inescapable shocks on the behavior of wild-type (5-htt+/+), heterozygote (5-htt+/-) and serotonin transporter deficient (5-htt-/-) mice. Inescapable shocks induce behavioral changes including a shock escape deficit, in a subsequent test when escape is possible. Confirming a gene by environment interaction, we found that stress increases escape latencies in a gene-dose dependent manner (5-htt-/->5-htt+/->5-htt +/+), where as there were no differences among the genotypes in the unstressed condition. The vulnerability to increased escape latency could not be accounted for by enhanced fear learning, as 5-htt-/- mice did not show heightened fear conditioning. The interaction of 5-htt genotype and stress appeared to produce a selective behavioral vulnerability, because no interaction of 5-htt genotype and stress was observed in other measures of anxiety and depression-linked behavior, including the open field, novelty suppressed feeding, and forced swim tests. We replicated prior findings that the 5-htt-/- displays heightened anxiety and depression-like behavior at baseline (unstressed condition). In conclusion, our data offer the possibility for future investigation of the neural basis underlying 5-htt genotype-by-stress interaction shown here. © 2010 The Authors. Genes, Brain and Behavior © 2010 Blackwell Publishing Ltd and International Behavioural and Neural Genetics Society.

Eggplant fruit composition as affected by the cultivation environment and genetic constitution.

PubMed

San José, Raquel; Sánchez-Mata, María-Cortes; Cámara, Montaña; Prohens, Jaime

2014-10-01

No comprehensive reports exist on the combined effects of season, cultivation environment and genotype on eggplant (Solanum melongena) composition. We studied proximate composition, carbohydrates, total phenolics and vitamin C of eggplant fruits of three Spanish landraces, three commercial hybrids and three hybrids between landraces cultivated across two environmental conditions (open field, OF; and, greenhouse, GH) for up to four seasons. Season (S) had a larger effect than the genotype (G) for composition traits, except for total phenolics. G × S interaction was generally of low relative magnitude. Orthogonal decomposition of the season effect showed that differences within OF or GH environments were in many instances greater than those between OF and GH. Spanish landraces presented, on average, lower contents of total carbohydrates and starch and higher contents of total vitamin C, ascorbic acid, and total phenolics than commercial hybrids. Hybrids among landraces presented variable levels of heterosis for composition traits. Genotypes grown in the same season cluster together on the graph of multivariate principal components analysis. The cultivation environment has a major role in determining the composition of eggplant fruits. Environmental and genotypic differences can be exploited to obtain high quality eggplant fruits.

Impact of selection on maize root traits and rhizosphere interactions

NASA Astrophysics Data System (ADS)

Schmidt, J. E.; Gaudin, A. C. M.

2017-12-01

Effects of domestication and breeding on maize have been well-characterized aboveground, but impacts on root traits and rhizosphere processes remain unclear. Breeding in high-inorganic-input environments may have negatively affected the ability of modern maize to acquire nutrients through foraging and microbial interactions in marginal and/or organically managed soils. Twelve maize genotypes representing a selection gradient (teosintes, landraces, open-pollinated parents of modern elite germplasm, and modern hybrids released 1934-2015) were grown in three soils varying in intensity of long-term management (unfertilized, organic, conventional) in the greenhouse. Recruitment of rhizosphere microbial communities, nutrient acquisition, and plant productivity were affected by genotype-by-soil interactions. Maize genotypes exhibit significant variation in their ability to obtain nutrients from soils of different management history, indicating the potential for re-integration of beneficial root and rhizosphere traits to increase adaptation to low-input agroecosystems.

Interactions between the vascular endothelial growth factor gene polymorphism and life events in susceptibility to major depressive disorder in a Chinese population.

PubMed

Han, Dong; Qiao, Zhengxue; Chen, Lu; Qiu, Xiaohui; Fang, Deyu; Yang, Xiuxian; Ma, Jingsong; Chen, Mingqi; Yang, Jiarun; Wang, Lin; Zhu, Xiongzhao; Zhang, Congpei; Yang, Yanjie; Pan, Hui

2017-08-01

Recent studies suggest that vascular endothelial growth factor (VEGF) is involved in the development of major depressive disorder. The aim of this study is to investigate the interaction between vascular endothelial growth factor (VEGF) polymorphism (+405G/C, rs2010963) and negative life events in the pathogenesis of major depressive disorder (MDD). DNA genotyping was performed on peripheral blood leukocytes in 274 patients with MDD and 273 age-and sex-matched controls. The frequency and severity of negative life events were assessed by the Life Events Scale (LES). A logistics method was employed to assess the gene-environment interaction (G×E). Differences in rs2010963 genotype distributions were observed between MDD patients and controls. Significant G×E interactions between allelic variation of rs2010963 and negative life events were observed. Individuals carrying the C alleles were susceptible to MDD only when exposed to high-negative life events. These results indicate that interactions between the VEGF rs2010963 polymorphism and environment increases the risk of developing MDD. Copyright © 2017 Elsevier B.V. All rights reserved.

Specific gravity of hybrid poplars in the north-central region, USA: within-tree variability and site × genotype effects

Treesearch

William L. Headlee; Ronald S. Jr. Zalesny; Richard B. Hall; Edmund O. Bauer; Bradford Bender; Bruce A. Birr; Raymond O. Miller; Jesse A. Randall; Adam H. Wiese

2013-01-01

Specific gravity is an important consideration for traditional uses of hybrid poplars for pulp and solid wood products, as well as for biofuels and bioenergy production. While specific gravity has been shown to be under strong genetic control and subject to within-tree variability, the role of genotype × environment interactions is poorly understood. Most...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chung, Chi-Jung; Department of Medical Research, China Medical University Hospital, Taichung, Taiwan; Huang, Chao-Yuan

Inter-individual variation in the metabolism of xenobiotics, caused by factors such as cigarette smoking or inorganic arsenic exposure, is hypothesized to be a susceptibility factor for urothelial carcinoma (UC). Therefore, our study aimed to evaluate the role of gene–environment interaction in the carcinogenesis of UC. A hospital-based case–control study was conducted. Urinary arsenic profiles were measured using high-performance liquid chromatography–hydride generator-atomic absorption spectrometry. Genotyping was performed using a polymerase chain reaction-restriction fragment length polymorphism technique. Information about cigarette smoking exposure was acquired from a lifestyle questionnaire. Multivariate logistic regression was applied to estimate the UC risk associated with certain riskmore » factors. We found that UC patients had higher urinary levels of total arsenic, higher percentages of inorganic arsenic (InAs%) and monomethylarsonic acid (MMA%) and lower percentages of dimethylarsinic acid (DMA%) compared to controls. Subjects carrying the GSTM1 null genotype had significantly increased UC risk. However, no association was observed between gene polymorphisms of CYP1A1, EPHX1, SULT1A1 and GSTT1 and UC risk after adjustment for age and sex. Significant gene–environment interactions among urinary arsenic profile, cigarette smoking, and GSTM1 wild/null polymorphism and UC risk were observed after adjustment for potential risk factors. Overall, gene–environment interactions simultaneously played an important role in UC carcinogenesis. In the future, large-scale studies should be conducted using tag-SNPs of xenobiotic-metabolism-related enzymes for gene determination. -- Highlights: ► Subjects with GSTM1 null genotype had significantly increased UC risk. ► UC patients had poor arsenic metabolic ability compared to controls. ► GSTM1 null genotype may modify arsenic related UC risk.« less

Importance of adaptation and genotype × environment interactions in tropical beef breeding systems.

PubMed

Burrow, H M

2012-05-01

This paper examines the relative importance of productive and adaptive traits in beef breeding systems based on Bos taurus and tropically adapted breeds across temperate and (sub)tropical environments. In the (sub)tropics, differences that exist between breeds in temperate environments are masked by the effects of environmental stressors. Hence in tropical environments, breeds are best categorised into breed types to compare their performance across environments. Because of the presence of environmental stressors, there are more sources of genetic variation in tropical breeding programmes. It is therefore necessary to examine the genetic basis of productive and adaptive traits for breeding programmes in those environments. This paper reviews the heritabilities and genetic relationships between economically important productive and adaptive traits relevant to (sub)tropical breeding programmes. It is concluded that it is possible to simultaneously genetically improve productive and adaptive traits in tropically adapted breeds of beef cattle grazed in tropical environments without serious detrimental consequences for either adaptation or production. However, breed-specific parameters are required for genetic evaluations. The paper also reviews the magnitude of genotype × environment (G × E) interactions impacting on production and adaptation of cattle, where 'genotype' is defined as breed (within a crossbreeding system), sire within breed (in a within-breed selection programme) or associations between economically important traits and single nucleotide polymorphisms (SNPs - within a marker-assisted selection programme). It is concluded that re-ranking of breeds across environments is best managed by the use of the breed type(s) best suited to the particular production environment. Re-ranking of sires across environments is apparent in poorly adapted breed types across extreme tropical and temperate environments or where breeding animals are selected in a temperate environment for use in the (sub)tropics. However, G × E interactions are unlikely to be of major importance in tropically adapted beef cattle grazed in either temperate or (sub)tropical environments, although sex × environment interactions may provide new opportunities for differentially selecting to simultaneously improve steer performance in benign environments and female performance in harsher environments. Early evidence suggests that re-ranking of SNPs occurs across temperate and tropical environments, although their magnitude is still to be confirmed in well-designed experiments. The major limitation to genetic improvement of beef cattle over the next decade is likely to be a deficiency of large numbers of accurately recorded phenotypes for most productive and adaptive traits and, in particular, for difficult-to-measure adaptive traits such as resistance to disease and environmental stressors.

3D Laser Triangulation for Plant Phenotyping in Challenging Environments

PubMed Central

Kjaer, Katrine Heinsvig; Ottosen, Carl-Otto

2015-01-01

To increase the understanding of how the plant phenotype is formed by genotype and environmental interactions, simple and robust high-throughput plant phenotyping methods should be developed and considered. This would not only broaden the application range of phenotyping in the plant research community, but also increase the ability for researchers to study plants in their natural environments. By studying plants in their natural environment in high temporal resolution, more knowledge on how multiple stresses interact in defining the plant phenotype could lead to a better understanding of the interaction between plant responses and epigenetic regulation. In the present paper, we evaluate a commercial 3D NIR-laser scanner (PlantEye, Phenospex B.V., Herleen, The Netherlands) to track daily changes in plant growth with high precision in challenging environments. Firstly, we demonstrate that the NIR laser beam of the scanner does not affect plant photosynthetic performance. Secondly, we demonstrate that it is possible to estimate phenotypic variation amongst the growth pattern of ten genotypes of Brassica napus L. (rapeseed), using a simple linear correlation between scanned parameters and destructive growth measurements. Our results demonstrate the high potential of 3D laser triangulation for simple measurements of phenotypic variation in challenging environments and in a high temporal resolution. PMID:26066990

Family environment interacts with CRHR1 rs17689918 to predict mental health and behavioral outcomes.

PubMed

Roy, Arunima; Laas, Kariina; Kurrikoff, Triin; Reif, Andreas; Veidebaum, Toomas; Lesch, Klaus-Peter; Harro, Jaanus

2018-05-14

Corticotrophin-releasing hormone receptor-1 gene (CRHR1) variants have been implicated in mental health. However, little is known of the effects of CRHR1 on long-term mental health and behavior in presence of environmental stressors. We assess the effects of CRHR1 variant (rs17689918)-by-environment interactions on emotionality and behavioral traits, including anxiety, depression, aggression and antisocial behaviors. We also determine effects of rs17689918-by-environment-by-sex interactions on the above-mentioned outcomes. Genotypic assessments were carried out in 564 children (mean age 10 years, 52.5% females) from the ongoing longitudinal Estonian Children Personality Behaviour and Health Study (ECPBHS). Information on stressful life events and family relationships were available at baseline and information on behavioral and mental health outcomes (self- and parent-reports) were available at follow-up ages of 18 and 25 years. ANOVAs were used to determine associations of two-way CRHR1-by-environment and three-way CRHR1-by-sex-by-environment interactions on behavioral and mental health outcomes. Two-way CRHR1 interaction effects showed associations between low familial warmth and hostility in individuals with the GG genotype. Associations of low familial warmth with aggression, of higher number of stressful life events with aggression, and of stressful live events with anxious-depressive symptoms were noted in male A-allele carriers and female GG homozygotes. CRHR1-by-familial environment interactions influence both outwardly-directed aggression as well as mood and anxiety disorder symptoms in a sex-specific manner. The type of environmental stressor can also influence effects of CRHR1 on behavioral and mental health outcomes. Copyright © 2018 Elsevier Inc. All rights reserved.

Asymmetric Evolutionary Games

PubMed Central

McAvoy, Alex; Hauert, Christoph

2015-01-01

Evolutionary game theory is a powerful framework for studying evolution in populations of interacting individuals. A common assumption in evolutionary game theory is that interactions are symmetric, which means that the players are distinguished by only their strategies. In nature, however, the microscopic interactions between players are nearly always asymmetric due to environmental effects, differing baseline characteristics, and other possible sources of heterogeneity. To model these phenomena, we introduce into evolutionary game theory two broad classes of asymmetric interactions: ecological and genotypic. Ecological asymmetry results from variation in the environments of the players, while genotypic asymmetry is a consequence of the players having differing baseline genotypes. We develop a theory of these forms of asymmetry for games in structured populations and use the classical social dilemmas, the Prisoner’s Dilemma and the Snowdrift Game, for illustrations. Interestingly, asymmetric games reveal essential differences between models of genetic evolution based on reproduction and models of cultural evolution based on imitation that are not apparent in symmetric games. PMID:26308326

High-throughput profiling and analysis of plant responses over time to abiotic stress

USDA-ARS?s Scientific Manuscript database

Energy sorghum (Sorghum bicolor (L.) Moench) is a rapidly growing, high-biomass, annual crop prized for abiotic stress tolerance. Measuring genotype-by-environment (G x E) interactions remains a progress bottleneck. High throughput phenotyping within controlled environments has been proposed as a po...

Envirotyping for deciphering environmental impacts on crop plants.

PubMed

Xu, Yunbi

2016-04-01

Global climate change imposes increasing impacts on our environments and crop production. To decipher environmental impacts on crop plants, the concept "envirotyping" is proposed, as a third "typing" technology, complementing with genotyping and phenotyping. Environmental factors can be collected through multiple environmental trials, geographic and soil information systems, measurement of soil and canopy properties, and evaluation of companion organisms. Envirotyping contributes to crop modeling and phenotype prediction through its functional components, including genotype-by-environment interaction (GEI), genes responsive to environmental signals, biotic and abiotic stresses, and integrative phenotyping. Envirotyping, driven by information and support systems, has a wide range of applications, including environmental characterization, GEI analysis, phenotype prediction, near-iso-environment construction, agronomic genomics, precision agriculture and breeding, and development of a four-dimensional profile of crop science involving genotype (G), phenotype (P), envirotype (E) and time (T) (developmental stage). In the future, envirotyping needs to zoom into specific experimental plots and individual plants, along with the development of high-throughput and precision envirotyping platforms, to integrate genotypic, phenotypic and envirotypic information for establishing a high-efficient precision breeding and sustainable crop production system based on deciphered environmental impacts.

Parental overcontrol x OPRM1 genotype interaction predicts school-aged children's sympathetic nervous system activation in response to performance challenge.

PubMed

Partington, Lindsey C; Borelli, Jessica L; Smiley, Patricia; Jarvik, Ella; Rasmussen, Hannah F; Seaman, Lauren C; Nurmi, Erika L

2018-04-26

Parental overcontrol (OC), the excessive regulation of a child's behavior, cognition, and emotion, is associated with the development of child anxiety. While studies have shown that genetic factors may increase sensitivity to stress, genetic vulnerability to parental OC has not been examined in anxiety etiology. A functional polymorphism in the mu opioid receptor OPRM1 (A118G, rs1799971) has been shown to impact stress reactivity. Using a community sample of children (N = 85, 9-12 years old), we examined the main and interactive effects of maternal OC and child OPRM1 genotype in predicting children's sympathetic nervous system reactivity during a performance stressor. Neither OC nor genotype predicted children's electrodermal activity (EDA); however, the interaction between OC and child genotype significantly predicted stress reactivity, as indexed by EDA, during the challenging task. Among children with the minor G-allele, higher maternal OC was associated with higher reactivity. In A homozygotes, maternal OC was not associated with EDA, suggesting a diathesis-stress pattern of gene x environment interaction. We discuss implications for anxiety etiology and intervention. Copyright © 2018 Elsevier Ltd. All rights reserved.

Life events and borderline personality features: the influence of gene-environment interaction and gene-environment correlation.

PubMed

Distel, M A; Middeldorp, C M; Trull, T J; Derom, C A; Willemsen, G; Boomsma, D I

2011-04-01

Traumatic life events are generally more common in patients with borderline personality disorder (BPD) than in non-patients or patients with other personality disorders. This study investigates whether exposure to life events moderates the genetic architecture of BPD features. As the presence of genotype-environment correlation (rGE) can lead to spurious findings of genotype-environment interaction (G × E), we also test whether BPD features increase the likelihood of exposure to life events. The extent to which an individual is at risk to develop BPD was assessed with the Personality Assessment Inventory - Borderline features scale (PAI-BOR). Life events under study were a divorce/break-up, traffic accident, violent assault, sexual assault, robbery and job loss. Data were available for 5083 twins and 1285 non-twin siblings. Gene-environment interaction and correlation were assessed by using structural equation modelling (SEM) and the co-twin control design. There was evidence for both gene-environment interaction and correlation. Additive genetic influences on BPD features interacted with the exposure to sexual assault, with genetic variance being lower in exposed individuals. In individuals who had experienced a divorce/break-up, violent assault, sexual assault or job loss, environmental variance for BPD features was higher, leading to a lower heritability of BPD features in exposed individuals. Gene-environment correlation was present for some life events. The genes that influence BPD features thus also increased the likelihood of being exposed to certain life events. To our knowledge, this study is the first to test the joint effect of genetic and environmental influences and the exposure to life events on BPD features in the general population. Our results indicate the importance of both genetic vulnerability and life events.

The FOXO1 Gene-Obesity Interaction Increases the Risk of Type 2 Diabetes Mellitus in a Chinese Han Population.

PubMed

Gong, Lilin; Li, Rong; Ren, Wei; Wang, Zengchan; Wang, Zhihong; Yang, Maosheng; Zhang, Suhua

2017-02-01

Here, we aimed to study the effect of the forkhead box O1-insulin receptor substrate 2 (FOXO1-IRS2) gene interaction and the FOXO1 and IRS2 genes-environment interaction for the risk of type 2 diabetes mellitus (T2DM) in a Chinese Han population. We genotyped 7 polymorphism sites of FOXO1 gene and IRS2 gene in 780 unrelated Chinese Han people (474 cases of T2DM, 306 cases of healthy control). The risk of T2DM in individuals with AA genotype for rs7986407 and CC genotype for rs4581585 in FOXO1 gene was 2.092 and 2.57 times higher than that with GG genotype (odds ratio [OR] = 2.092; 95% confidence interval [CI] = 1.178-3.731; P = 0.011) and TT genotype (OR = 2.571; 95% CI = 1.404-4.695; P = 0.002), respectively. The risk of T2DM in individuals with GG genotype for Gly1057Asp in IRS2 gene was 1.42 times higher than that with AA genotype (OR = 1.422; 95% CI = 1.037-1.949; P = 0.029). The other 4 single nucleotide polymorphisms (SNPs) had no significant association with T2DM (P > 0.05). Multifactor dimensionality reduction (MDR) analysis showed that the interaction between SNPs rs7986407 and rs4325426 in FOXO1 gene and waist was the best model confirmed by interaction analysis, closely associating with T2DM. There was an increased risk for T2DM in the case of non-obesity with genotype combined AA/CC, AA/AC or AG/AA for rs7986407 and rs4325426, and obesity with genotype AA for rs7986407 or AA for rs4325426 (OR = 3.976; 95% CI = 1.156-13.675; P value from sign test [P(sign)] = 0.025; P value from permutation test [P(perm)] = 0.000-0.001). Together, this study indicates an association of FOXO1 and IRS2 gene polymorphisms with T2DM in Chinese Han population, supporting FOXO1-obesity interaction as a key factor for the risk of T2DM.

Interaction between parental environment and genotype affects plant and seed performance in Arabidopsis.

PubMed

He, Hanzi; de Souza Vidigal, Deborah; Snoek, L Basten; Schnabel, Sabine; Nijveen, Harm; Hilhorst, Henk; Bentsink, Leónie

2014-12-01

Seed performance after dispersal is highly dependent on parental environmental cues, especially during seed formation and maturation. Here we examine which environmental factors are the most dominant in this respect and whether their effects are dependent on the genotypes under investigation. We studied the influence of light intensity, photoperiod, temperature, nitrate, and phosphate during seed development on five plant attributes and thirteen seed attributes, using 12 Arabidopsis genotypes that have been reported to be affected in seed traits. As expected, the various environments during seed development resulted in changed plant and/or seed performances. Comparative analysis clearly indicated that, overall, temperature plays the most dominant role in both plant and seed performance, whereas light has a prominent impact on plant traits. In comparison to temperature and light, nitrate mildly affected some of the plant and seed traits while phosphate had even less influence on those traits. Moreover, clear genotype-by-environment interactions were identified. This was shown by the fact that individual genotypes responded differentially to the environmental conditions. Low temperature significantly increased seed dormancy and decreased seed longevity of NILDOG1 and cyp707a1-1, whereas low light intensity increased seed dormancy and decreased seed longevity of NILDOG3 and NILDOG6. This also indicates that different genetic and molecular pathways are involved in the plant and seed responses. By identifying environmental conditions that affect the dormancy vs longevity correlation in the same way as previously identified naturally occurring loci, we have identified selective forces that probably shaped evolution for these important seed traits. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Capsaicin consumption, Helicobacter pylori CagA status and IL1B-31C > T genotypes: A host and environment interaction in gastric cancer

PubMed Central

López-Carrillo, Lizbeth; Camargo, M. Constanza; Schneider, Barbara G.; Sicinschi, Liviu A.; Hernández-Ramírez, Raúl U.; Correa, Pelayo; Cebrian, Mariano E.

2013-01-01

Gastric cancer (GC) has been associated with a complex combination of genetic and environmental factors. In contrast to most countries, available information on GC mortality trends showed a gradual increase in Mexico. Our aim was to explore potential interactions among dietary (chili pepper consumption), infectious (Helicobacter pylori) and genetic factors (IL1B-31 genotypes) on GC risk. The study was performed in three areas of Mexico, with different GC mortality rates. We included 158 GC patients and 317 clinical controls. Consumption of capsaicin (Cap), the pungent active substance of chili peppers, was estimated by food frequency questionnaire. H. pylori CagA status was assessed by ELISA, and IL1B-31 genotypes were determined by TaqMan assays and Pyrosequencing in DNA samples. Multivariate unconditional logistic regression was used to estimate potential interactions. Moderate to high Cap consumption synergistically increased GC risk in genetically susceptible individuals (IL1B-31C allele carriers) infected with the more virulent H. pylori (CagA+) strains. The combined presence of these factors might explain the absence of a decreasing trend for GC in Mexico. However, further research on gene–environment interactions is required to fully understand the factors determining GC patterns in susceptible populations, with the aim of recommending preventive measures for high risk individuals. PMID:22414649

Serotonin Transporter-Linked Polymorphic Region (5-HTTLPR) Genotype and Stressful Life Events Interact to Predict Preschool-Onset Depression: A Replication and Developmental Extension

ERIC Educational Resources Information Center

Bogdan, Ryan; Agrawal, Arpana; Gaffrey, Michael S.; Tillman, Rebecca; Luby, Joan L.

2014-01-01

Background: Scientific enthusiasm about gene × environment interactions, spurred by the 5-HTTLPR (serotonin transporter-linked polymorphic region) × SLEs (stressful life events) interaction predicting depression, have recently been tempered by sober realizations of small effects and meta-analyses reaching opposing conclusions. These mixed findings…

BDNF rs6265 methylation and genotype interact on risk for schizophrenia.

PubMed

Ursini, Gianluca; Cavalleri, Tommaso; Fazio, Leonardo; Angrisano, Tiziana; Iacovelli, Luisa; Porcelli, Annamaria; Maddalena, Giancarlo; Punzi, Giovanna; Mancini, Marina; Gelao, Barbara; Romano, Raffaella; Masellis, Rita; Calabrese, Francesca; Rampino, Antonio; Taurisano, Paolo; Di Giorgio, Annabella; Keller, Simona; Tarantini, Letizia; Sinibaldi, Lorenzo; Quarto, Tiziana; Popolizio, Teresa; Caforio, Grazia; Blasi, Giuseppe; Riva, Marco A; De Blasi, Antonio; Chiariotti, Lorenzo; Bollati, Valentina; Bertolino, Alessandro

2016-01-01

Epigenetic mechanisms can mediate gene-environment interactions relevant for complex disorders. The BDNF gene is crucial for development and brain plasticity, is sensitive to environmental stressors, such as hypoxia, and harbors the functional SNP rs6265 (Val(66)Met), which creates or abolishes a CpG dinucleotide for DNA methylation. We found that methylation at the BDNF rs6265 Val allele in peripheral blood of healthy subjects is associated with hypoxia-related early life events (hOCs) and intermediate phenotypes for schizophrenia in a distinctive manner, depending on rs6265 genotype: in ValVal individuals increased methylation is associated with exposure to hOCs and impaired working memory (WM) accuracy, while the opposite is true for ValMet subjects. Also, rs6265 methylation and hOCs interact in modulating WM-related prefrontal activity, another intermediate phenotype for schizophrenia, with an analogous opposite direction in the 2 genotypes. Consistently, rs6265 methylation has a different association with schizophrenia risk in ValVals and ValMets. The relationships of methylation with BDNF levels and of genotype with BHLHB2 binding likely contribute to these opposite effects of methylation. We conclude that BDNF rs6265 methylation interacts with genotype to bridge early environmental exposures to adult phenotypes, relevant for schizophrenia. The study of epigenetic changes in regions containing genetic variation relevant for human diseases may have beneficial implications for the understanding of how genes are actually translated into phenotypes.

Interacting effects of genetic variation for seed dormancy and flowering time on phenology, life history, and fitness of experimental Arabidopsis thaliana populations over multiple generations in the field.

PubMed

Taylor, Mark A; Cooper, Martha D; Sellamuthu, Reena; Braun, Peter; Migneault, Andrew; Browning, Alyssa; Perry, Emily; Schmitt, Johanna

2017-10-01

Major alleles for seed dormancy and flowering time are well studied, and can interact to influence seasonal timing and fitness within generations. However, little is known about how this interaction controls phenology, life history, and population fitness across multiple generations in natural seasonal environments. To examine how seed dormancy and flowering time shape annual plant life cycles over multiple generations, we established naturally dispersing populations of recombinant inbred lines of Arabidopsis thaliana segregating early and late alleles for seed dormancy and flowering time in a field experiment. We recorded seasonal phenology and fitness of each genotype over 2 yr and several generations. Strong seed dormancy suppressed mid-summer germination in both early- and late-flowering genetic backgrounds. Strong dormancy and late-flowering genotypes were both necessary to confer a winter annual life history; other genotypes were rapid-cycling. Strong dormancy increased within-season fecundity in an early-flowering background, but decreased it in a late-flowering background. However, there were no detectable differences among genotypes in population growth rates. Seasonal phenology, life history, and cohort fitness over multiple generations depend strongly upon interacting genetic variation for dormancy and flowering. However, similar population growth rates across generations suggest that different life cycle genotypes can coexist in natural populations. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Population-specific responses to light influence herbivory in the understory shrub Lindera benzoin.

PubMed

Mooney, E H; Niesenbaum, R A

2012-12-01

Plants display photosynthetic plasticity in response to variation in light environment, and the extent of this plasticity often varies with genotype, i.e., genotype x environment interaction. Herbivory may also covary with light environment as a result of light-induced changes in photosynthetic traits. For example, greater levels of photoprotective phenolic compounds in high-light environments may reduce host quality to herbivores. We investigated intraspecific variation in photosynthetic responses to light and its consequences for herbivory in the understory shrub, Lindera benzoin (Lauraceae). We transplanted five plants from eight populations (N = 240) into three replicate sun and shade common gardens. Two years after transplantation, we tested for population x light environment interactions in six photosynthesis-related responses: specific leaf area, water content, chlorophyll content, chlorophyll fluorescence (F(0)), maximum quantum yield (F(v)/F(m)), and total phenolics. We assessed seasonal herbivory and consumption by a specialist lepidopteran herbivore (Epimecis hortaria). This allowed us to test for (1) population-specific patterns of photosynthetic acclimation and photoinhibition, (2) population-specific production of phenolics in response to photoinhibition, and (3) population-specific photosynthetic responses that contribute to population x light environment interactions in herbivory. Population X light environment interactions were insignificant in leaf variables but statistically significant for herbivory measured as consumption by E. hortaria. We found similar trends for population x light environment interactions in seasonal herbivory. Total phenolics and minimum chlorophyll fluorescence (F(0)) were significant covariates with herbivory, but their effects depended on light environment and population of origin. High-light environments eliminated differences among populations in how these leaf variables affected herbivory, while population-specific relationships were apparent in the shade. Analysis of total phenolics revealed that they were likely induced by photoinhibition, but that this response varied among the populations we assessed. However, phenolics increased herbivory in L. benzoin, which would limit the fitness value of this protective response to light-induced photoinhibition. Our results suggest that herbivores could affect evolution of photosynthetic plasticity in L. benzoin.

Common variations in the pretest environment influence genotypic comparisons in models of anxiety.

PubMed

Izídio, G S; Lopes, D M; Spricigo, L; Ramos, A

2005-10-01

The behavioral characterization of rodent strains in different studies and laboratories can provide unreplicable results even when genotypes are kept constant and environmental control is maximized. In the present study, the influence of common laboratory environmental variables and their interaction with genotype on the results of behavioral tests of anxiety/emotionality were investigated. To this end, the inbred rat strains Lewis (LEW) and spontaneously hypertensive rats (SHR), which are known to differ for numerous emotionality-related behaviors, were tested in the open field (OF), elevated plus maze (EPM) and black/white box (BWB), while three environmental factors were systematically controlled and analyzed: (1) the experimenter handling the animal (familiar or unfamiliar); (2) the position of the home cage (top or bottom shelf of the rack) and (3) the behavioral state of the animal immediately before the test (arousal or rest). Experimenter familiarity did not alter the behavior of rats in the OF. Cage position, on the other hand, influenced the behavior in the OF and BWB, with rats housed in top cages appearing less anxious than those housed in the bottom. In the BWB (but not in the OF), these effects were genotype dependent. Finally, the behavioral state of the animals prior to testing altered the results of the EPM in a strain-dependent manner, with some anxiety-related genotypic differences being found only among rats that were aroused in their home cages. This study showed that common variations in the laboratory environment interact with genotype in behavioral tests of anxiety/emotionality. Recognizing and understanding such variations can help in the design of more effective experiments.

Genomic Analysis of Genotype-by-Social Environment Interaction for Drosophila melanogaster Aggressive Behavior.

PubMed

Rohde, Palle Duun; Gaertner, Bryn; Ward, Kirsty; Sørensen, Peter; Mackay, Trudy F C

2017-08-01

Human psychiatric disorders such as schizophrenia, bipolar disorder, and attention-deficit/hyperactivity disorder often include adverse behaviors including increased aggressiveness. Individuals with psychiatric disorders often exhibit social withdrawal, which can further increase the probability of conducting a violent act. Here, we used the inbred, sequenced lines of the Drosophila Genetic Reference Panel (DGRP) to investigate the genetic basis of variation in male aggressive behavior for flies reared in a socialized and socially isolated environment. We identified genetic variation for aggressive behavior, as well as significant genotype-by-social environmental interaction (GSEI); i.e. , variation among DGRP genotypes in the degree to which social isolation affected aggression. We performed genome-wide association (GWA) analyses to identify genetic variants associated with aggression within each environment. We used genomic prediction to partition genetic variants into gene ontology (GO) terms and constituent genes, and identified GO terms and genes with high prediction accuracies in both social environments and for GSEI. The top predictive GO terms significantly increased the proportion of variance explained, compared to prediction models based on all segregating variants. We performed genomic prediction across environments, and identified genes in common between the social environments that turned out to be enriched for genome-wide associated variants. A large proportion of the associated genes have previously been associated with aggressive behavior in Drosophila and mice. Further, many of these genes have human orthologs that have been associated with neurological disorders, indicating partially shared genetic mechanisms underlying aggression in animal models and human psychiatric disorders. Copyright © 2017 by the Genetics Society of America.

Bayesian Genomic Prediction with Genotype × Environment Interaction Kernel Models

PubMed Central

Cuevas, Jaime; Crossa, José; Montesinos-López, Osval A.; Burgueño, Juan; Pérez-Rodríguez, Paulino; de los Campos, Gustavo

2016-01-01

The phenomenon of genotype × environment (G × E) interaction in plant breeding decreases selection accuracy, thereby negatively affecting genetic gains. Several genomic prediction models incorporating G × E have been recently developed and used in genomic selection of plant breeding programs. Genomic prediction models for assessing multi-environment G × E interaction are extensions of a single-environment model, and have advantages and limitations. In this study, we propose two multi-environment Bayesian genomic models: the first model considers genetic effects (u) that can be assessed by the Kronecker product of variance–covariance matrices of genetic correlations between environments and genomic kernels through markers under two linear kernel methods, linear (genomic best linear unbiased predictors, GBLUP) and Gaussian (Gaussian kernel, GK). The other model has the same genetic component as the first model (u) plus an extra component, f, that captures random effects between environments that were not captured by the random effects u. We used five CIMMYT data sets (one maize and four wheat) that were previously used in different studies. Results show that models with G × E always have superior prediction ability than single-environment models, and the higher prediction ability of multi-environment models with u and f over the multi-environment model with only u occurred 85% of the time with GBLUP and 45% of the time with GK across the five data sets. The latter result indicated that including the random effect f is still beneficial for increasing prediction ability after adjusting by the random effect u. PMID:27793970

Bayesian Genomic Prediction with Genotype × Environment Interaction Kernel Models.

PubMed

Cuevas, Jaime; Crossa, José; Montesinos-López, Osval A; Burgueño, Juan; Pérez-Rodríguez, Paulino; de Los Campos, Gustavo

2017-01-05

The phenomenon of genotype × environment (G × E) interaction in plant breeding decreases selection accuracy, thereby negatively affecting genetic gains. Several genomic prediction models incorporating G × E have been recently developed and used in genomic selection of plant breeding programs. Genomic prediction models for assessing multi-environment G × E interaction are extensions of a single-environment model, and have advantages and limitations. In this study, we propose two multi-environment Bayesian genomic models: the first model considers genetic effects [Formula: see text] that can be assessed by the Kronecker product of variance-covariance matrices of genetic correlations between environments and genomic kernels through markers under two linear kernel methods, linear (genomic best linear unbiased predictors, GBLUP) and Gaussian (Gaussian kernel, GK). The other model has the same genetic component as the first model [Formula: see text] plus an extra component, F: , that captures random effects between environments that were not captured by the random effects [Formula: see text] We used five CIMMYT data sets (one maize and four wheat) that were previously used in different studies. Results show that models with G × E always have superior prediction ability than single-environment models, and the higher prediction ability of multi-environment models with [Formula: see text] over the multi-environment model with only u occurred 85% of the time with GBLUP and 45% of the time with GK across the five data sets. The latter result indicated that including the random effect f is still beneficial for increasing prediction ability after adjusting by the random effect [Formula: see text]. Copyright © 2017 Cuevas et al.

The effect of environmental heterogeneity on RPW8-mediated resistance to powdery mildews in Arabidopsis thaliana.

PubMed

Jorgensen, Tove H

2012-03-01

The biotic and abiotic environment of interacting hosts and parasites may vary considerably over small spatial and temporal scales. It is essential to understand how different environments affect host disease resistance because this determines frequency of disease and, importantly, heterogeneous environments can retard direct selection and potentially maintain genetic variation for resistance in natural populations. The effect of different temperatures and soil nutrient conditions on the outcome of infection by a pathogen was quantified in Arabidopsis thaliana. Expression levels of a gene conferring resistance to powdery mildews, RPW8, were compared with levels of disease to test a possible mechanism behind variation in resistance. Most host genotypes changed from susceptible to resistant across environments with the ranking of genotypes differing between treatments. Transcription levels of RPW8 increased after infection and varied between environments, but there was no tight association between transcription and resistance levels. There is a strong potential for a heterogeneous environment to change the resistance capacity of A. thaliana genotypes and hence the direction and magnitude of selection in the presence of the pathogen. Possible causative links between resistance gene expression and disease resistance are discussed in light of the present results on RPW8.

Genes, Culture and Conservatism-A Psychometric-Genetic Approach.

PubMed

Schwabe, Inga; Jonker, Wilfried; van den Berg, Stéphanie M

2016-07-01

The Wilson-Patterson conservatism scale was psychometrically evaluated using homogeneity analysis and item response theory models. Results showed that this scale actually measures two different aspects in people: on the one hand people vary in their agreement with either conservative or liberal catch-phrases and on the other hand people vary in their use of the "?" response category of the scale. A 9-item subscale was constructed, consisting of items that seemed to measure liberalism, and this subscale was subsequently used in a biometric analysis including genotype-environment interaction, correcting for non-homogeneous measurement error. Biometric results showed significant genetic and shared environmental influences, and significant genotype-environment interaction effects, suggesting that individuals with a genetic predisposition for conservatism show more non-shared variance but less shared variance than individuals with a genetic predisposition for liberalism.

Gene-environment interaction of ApoE genotype and combat exposure on PTSD.

PubMed

Lyons, Michael J; Genderson, Margo; Grant, Michael D; Logue, Mark; Zink, Tyler; McKenzie, Ruth; Franz, Carol E; Panizzon, Matthew; Lohr, James B; Jerskey, Beth; Kremen, William S

2013-10-01

Factors determining who develops PTSD following trauma are not well understood. The €4 allele of the apolipoprotein E (apoE) gene is associated with dementia and unfavorable outcome following brain insult. PTSD is also associated with dementia. Given evidence that psychological trauma adversely affects the brain, we hypothesized that the apoE genotype moderates effects of psychological trauma on PTSD pathogenesis. To investigate the moderation of the relationship between PTSD symptoms and combat exposure, we used 172 participants with combat trauma sustained during the Vietnam War. PTSD symptoms were the dependent variable and number of combat experiences, apoE genotype, and the combat experiences × apoE genotype interaction were predictors. We also examined the outcome of a diagnosis of PTSD (n = 39) versus no PTSD diagnosis (n = 131). The combat × apoE genotype interaction was significant for both PTSD symptoms (P = .014) and PTSD diagnosis (P = .009). ApoE genotype moderates the relationship between combat exposure and PTSD symptoms. Although the pathophysiology of PTSD is not well understood, the €4 allele is related to reduced resilience of the brain to insult. Our results are consistent with the €4 allele influencing the effects of psychological trauma on the brain, thereby affecting the risk of PTSD. © 2013 Wiley Periodicals, Inc.

Genotype-by-environment interaction of growth traits in rainbow trout (Oncorhynchus mykiss): A continental scale study

USDA-ARS?s Scientific Manuscript database

Rainbow trout is a globally important fish species for aquaculture. However, fish for most farms worldwide are produced by only a few breeding companies. Selection based solely on fish performance recorded at a nucleus may lead to lower-than-expected genetic gains in other production environments wh...

Directional selection on cold tolerance does not constrain plastic capacity in a butterfly.

PubMed

Franke, Kristin; Dierks, Anneke; Fischer, Klaus

2012-12-05

Organisms may respond to environmental change by means of genetic adaptation, phenotypic plasticity or both, which may result in genotype-environment interactions (G x E) if genotypes differ in their phenotypic response. We here specifically target the latter source of variation (i.e. G x E) by comparing plastic responses among lines of the tropical butterfly Bicyclus anynana that had been selected for increased cold tolerance and according controls. Our main aim here was to test the hypothesis that directional selection on cold tolerance will interfere with plastic capacities. Plastic responses to temperature and feeding treatments were strong, with e.g. higher compared to lower temperatures reducing cold tolerance, longevity, pupal mass, and development time. We report a number of statistically significant genotype-environment interactions (i.e. interactions between selection regime and environmental variables), but most of these were not consistent across treatment groups. We found some evidence though for larger plastic responses to different rearing temperatures in the selection compared to the control lines, while plastic responses to different adult temperatures and feeding treatments were overall very similar across selection regimes. Our results indicate that plastic capacities are not always constrained by directional selection (on cold tolerance) and therefore genetic changes in trait means, but may operate independently.

The serotonin transporter gene is a substrate for age and stress dependent epigenetic regulation in rhesus macaque brain: potential roles in genetic selection and gene × environment interactions.

PubMed

Lindell, Stephen G; Yuan, Qiaoping; Zhou, Zhifeng; Goldman, David; Thompson, Robert C; Lopez, Juan F; Suomi, Stephen J; Higley, J Dee; Barr, Christina S

2012-11-01

In humans, it has been demonstrated that the serotonin transporter linked polymorphic region (5-HTTLPR) genotype moderates risk in the face of adversity. One mechanism by which stress could interact with genotype is via epigenetic modifications. We wanted to examine whether stress interacted with genotype to predict binding of a histone 3 protein trimethylated at lysine 3 (H3K4me3) that marks active promoters. The brains (N = 61) of male rhesus macaques that had been reared in the presence or absence of stress were archived and the hippocampusi dissected. Chromatin immunoprecipitation was performed with an antibody against H3K4me3 followed by sequencing on a SolexaG2A. The effects of age, genotype (5-HTTLPR long/long vs. short), and stress exposure (peer-reared vs. mother-reared) on levels of H3K4me3 binding were determined. We found effects of age and stress exposure. There was a decline in H3K4me3 from preadolescence to postadolescence and lower levels in peer-reared monkeys and no effects of genotype. When we controlled for age, however, we found that there were effects of 5-HTTLPR genotype and rearing condition on H3K4me3 binding. In a larger sample, we observed that cerebrospinal fluid 5-hydroxyindoleacetic acid levels were subject to interactive effects among age, rearing history, and genotype. Genes containing both genetic selection and epigenetic regulation may be particularly important in stress adaptation and development. We find evidence for selection at the solute carrier family C6 member 4 gene and observe epigenetic reorganization according to genotype, stress, and age. These data suggest that developmental stage may moderate effects of stress and serotonin transporter genotype in the emergence of alternative adaptation strategies and in the vulnerability to developmental or psychiatric disorders.

Experimental evidence for the evolution of indirect genetic effects: changes in the interaction effect coefficient, psi (Psi), due to sexual selection.

PubMed

Chenoweth, Stephen F; Rundle, Howard D; Blows, Mark W

2010-06-01

Indirect genetics effects (IGEs)--when the genotype of one individual affects the phenotypic expression of a trait in another--may alter evolutionary trajectories beyond that predicted by standard quantitative genetic theory as a consequence of genotypic evolution of the social environment. For IGEs to occur, the trait of interest must respond to one or more indicator traits in interacting conspecifics. In quantitative genetic models of IGEs, these responses (reaction norms) are termed interaction effect coefficients and are represented by the parameter psi (Psi). The extent to which Psi exhibits genetic variation within a population, and may therefore itself evolve, is unknown. Using an experimental evolution approach, we provide evidence for a genetic basis to the phenotypic response caused by IGEs on sexual display traits in Drosophila serrata. We show that evolution of the response is affected by sexual but not natural selection when flies adapt to a novel environment. Our results indicate a further mechanism by which IGEs can alter evolutionary trajectories--the evolution of interaction effects themselves.

The Impact of Simulated Microgravity on the Growth of Different Genotypes of the Model Legume Plant Medicago truncatula

NASA Astrophysics Data System (ADS)

Lionheart, Gemma; Vandenbrink, Joshua P.; Hoeksema, Jason D.; Kiss, John Z.

2018-05-01

Simulated microgravity has been a useful tool to help understand plant development in altered gravity conditions. Thirty-one genotypes of the legume plant Medicago truncatula were grown in either simulated microgravity on a rotating clinostat, or in a static, vertical environment. Twenty morphological features were measured and compared between these two gravity treatments. Within-species genotypic variation was a significant predictor of the phenotypic response to gravity treatment in 100% of the measured morphological and growth features. In addition, there was a genotype-environment interaction (G × E) for 45% of the response variables, including shoot relative growth rate (p < 0.0005), median number of roots (p ˜ 0.02), and root dry mass (p < 0.005). Our studies demonstrate that genotype does play a significant role in M. truncatula morphology and affects the response of plants to the gravity treatment, influencing both the magnitude and direction of the gravity response. These findings are discussed in the context of improving future studies in plant space biology by controlling for genotypic differences. Thus, manipulation of genotype effects, in combination with M. truncatula's symbiotic relationships with bacteria and fungi, will be important for optimizing legumes for cultivation on long-term space missions.

Interaction of Child Maltreatment and 5-HTT Polymorphisms: Suicidal Ideation among Children from low-SES Backgrounds

PubMed Central

Rogosch, Fred A.; Sturge-Apple, Melissa; Toth, Sheree L.

2010-01-01

Objective To investigate whether genotypic variation of the serotonin transporter gene-linked promoter region (5-HTTLPR) moderates the effect of maltreatment on suicidal ideation in school-aged children. Methods Eight hundred and fifty low-income children (478 maltreated; 372 non-maltreated) provided DNA samples and self-reported depressive and suicidal symptoms. Genotypes of 5-HTTLPR (s/s or s/l vs. l/l) were determined by fragment analyses. Results Higher suicidal ideation was found among maltreated than non-maltreated children; the groups did not differ in 5-HTTLPR genotype frequencies. Children with one to two maltreatment subtypes and s/s or s/l genotypes had higher suicidal ideation than those with the l/l genotype; suicidal ideation did not differ in non-maltreated children or children with three to four maltreatment subtypes based on 5-HTTLPR variation. The results were applicable to emotionally maltreated/neglected and to physically/sexually abused children. Gene–environment interaction was not found for depressive symptoms. Conclusion The protective effect of the 5-HTTLPR l/l genotype on suicidal ideation was limited to maltreated children experiencing fewer subtypes. PMID:19779024

ABCB1 genetic polymorphism and risk of upper aerodigestive tract cancers among smokers, tobacco chewers and alcoholics in an Indian population.

PubMed

Sam, Soya Sisy; Thomas, Vinod; Sivagnanam, Kumaran; Reddy, Kanipakapatanam Sathyanarayana; Surianarayanan, Gopalakrishnan; Chandrasekaran, Adithan

2007-10-01

Upper aerodigestive tract (UADT) cancers are associated with the tobacco use and alcohol consumption. Certain toxins and carcinogens causing UADT cancers are found to be substrates of polymorphic ABCB1 gene encoded P-glycoprotein efflux pump. This study investigates the association between ABCB1 gene polymorphism at exon 26 (3435C>T) and risk to UADT cancers in Tamilians, a population of south India. The study included 219 unrelated histopathologically confirmed cases and 210 population-based controls. Genomic DNA was extracted from peripheral leukocytes and genotyped for ABCB1 3435C>T polymorphism by PCR-restriction fragment length polymorphism method. The multivariate logistic regression analyses demonstrated that the homozygous ABCB1 TT genotype was significantly associated with an overall increased risk for developing UADT cancers [odds ratio (OR): 2.53; 95% confidence interval (CI): 1.28-5.02]. Further, the determination of gene-environment interaction by stratified analyses have revealed a significant interaction between the smoking and homozygous TT genotype [(OR: 7.52; CI: 1.50-37.70) and (OR: 16.89; CI: 3.87-73.79) for 11-20 and >20 pack-years, respectively]. The strongest interaction was observed among the regular tobacco chewers (OR: 45.29; CI: 8.94-130.56) homozygous for TT genotype. No suggestion, however, of an interaction between the genotypes and the alcohol consumption on the multiplicative scale was made. The ABCB1 gene polymorphism at exon 26 (3435C>T) may be one of the risk factors for susceptibility to UADT cancers. Furthermore, the significant interaction among habitual smokers and tobacco chewers, homozygous for TT genotype modulates the risk to UADT cancers in the Tamilian population of south India.

Interacting effect of MAOA genotype and maternal prenatal smoking on aggressive behavior in young adulthood.

PubMed

Hohmann, Sarah; Zohsel, Katrin; Buchmann, Arlette F; Blomeyer, Dorothea; Holz, Nathalie; Boecker-Schlier, Regina; Jennen-Steinmetz, Christine; Rietschel, Marcella; Witt, Stephanie H; Schmidt, Martin H; Esser, Günter; Meyer-Lindenberg, Andreas; Banaschewski, Tobias; Brandeis, Daniel; Hohm, Erika; Laucht, Manfred

2016-08-01

Findings on the etiology of aggressive behavior have provided evidence for an effect both of genetic factors, such as variation in the monoamine oxidase A (MAOA) gene, and adverse environmental factors. Recent studies have supported the existence of gene × environment interactions, with early experiences playing a key role. In the present study, the effects of prenatal nicotine exposure, MAOA genotype and their interaction on aggressive behavior during young adulthood were examined. In a sample of 272 young adults (129 males, 143 females) from an epidemiological cohort study, smoking during pregnancy was measured with a standardized parent interview at the offspring's age of 3 months. Aggressive behavior was assessed between the ages of 19 and 25 years using the Young Adult Self-Report. DNA was genotyped for the MAOA 5' untranslated region variable number of tandem repeats polymorphism (VNTR). Results revealed a significant interaction between MAOA and smoking during pregnancy, indicating higher levels of aggressive behavior in young adults carrying the MAOA low-expressing genotype who had experienced prenatal nicotine exposure (n = 8, p = .025). In contrast, in carriers of the MAOA high-expressing genotype, maternal smoking during pregnancy had no effect on aggressive behavior during young adulthood (n = 20, p = .145). This study extends earlier findings demonstrating an interaction between MAOA genotype and prenatal nicotine exposure on aggressive behavior into young adulthood. The results point to the long-term adverse effects of smoking during pregnancy on the offspring's mental health, possibly underlining the importance of smoking cessation during pregnancy. According to the nature of the study (particularly sample size and power), analyses are exploratory and results need to be interpreted cautiously.

Within-host competitive interactions as a mechanism for the maintenance of parasite diversity

PubMed Central

Bashey, Farrah

2015-01-01

Variation among parasite strains can affect the progression of disease or the effectiveness of treatment. What maintains parasite diversity? Here I argue that competition among parasites within the host is a major cause of variation among parasites. The competitive environment within the host can vary depending on the parasite genotypes present. For example, parasite strategies that target specific competitors, such as bacteriocins, are dependent on the presence and susceptibility of those competitors for success. Accordingly, which parasite traits are favoured by within-host selection can vary from host to host. Given the fluctuating fitness landscape across hosts, genotype by genotype (G×G) interactions among parasites should be prevalent. Moreover, selection should vary in a frequency-dependent manner, as attacking genotypes select for resistance and genotypes producing public goods select for cheaters. I review competitive coexistence theory with regard to parasites and highlight a few key examples where within-host competition promotes diversity. Finally, I discuss how within-host competition affects host health and our ability to successfully treat infectious diseases. PMID:26150667

Eco-evolutionary processes affecting plant-herbivore interactions during early community succession.

PubMed

Howard, Mia M; Kalske, Aino; Kessler, André

2018-06-01

The quality and outcome of organismal interactions are not only a function of genotypic composition of the interacting species, but also the surrounding environment. Both the strength and direction of natural selection on interacting populations vary with the community context, which itself is changed by these interactions. Here, we test for the role of interacting evolutionary and ecological processes in plant-herbivore interactions during early community succession in the tall goldenrod, Solidago altissima. We use surveys in a large-scale field experiment with repeated plots representing 6 years of early oldfield succession and reciprocal transplant common garden experiments to test for the relative importance of rapid evolution (genetic) and environmental changes (soil quality) in affecting mean plant resistance and growth phenotypes during community succession. While plant growth varied strongly with soil quality over the first 5 years of agricultural abandonment, plant secondary metabolism, and herbivore resistance varied minimally with the soil environment. Instead, mean composition and abundance of plant secondary compound bouquets differed between S. altissima plants from populations collected in communities in the first ("early") and sixth ("intermediate") years of oldfield succession, which was reflected in the feeding preference of the specialist herbivore, Trirhabda virgata, for early succession lines. Moreover, this preference was most pronounced on poorer quality, early succession soils. Overall, our data demonstrate that plant quality varies for insect herbivores during the course of early succession and this change is a combination of altered genotypic composition of the population and phenotypic plasticity in different soil environments.

The influence of urban/rural residency on depressive symptoms is moderated by the serotonin receptor 2A gene.

PubMed

Jokela, Markus; Lehtimäki, Terho; Keltikangas-Järvinen, Liisa

2007-10-05

Gene-environment interactions are thought to be involved in the development of depression. Here we examined the interaction effect between urban/rural residency and the serotonin receptor 2A (HTR2A) gene on subclinical depressive symptoms. The participants were 1,224 Finnish men and women being followed in the on-going population-based study of "Cardiovascular Risk in Young Finns". Urban/rural residency was determined on the basis of a (1) subjective report and (2) the population density of the residential area. Depressive symptoms were measured in two test settings four years apart. There was a significant gene-environment interaction, such that the urban residency was associated with low depressive symptoms in individuals carrying the T/T or T/C genotype of the T102C polymorphism, but not in those carrying the C/C genotype. The T allele was associated with high depressive symptoms in remote rural areas, but with low depressive symptoms in urban or suburban areas. The gene-environment interaction was not accounted by level of education, social support, unemployment, or partnership status. The HTR2A gene may be involved in the development of depression by influencing how individuals respond to environmental conditions. (c) 2007 Wiley-Liss, Inc.

Sex-specific selection under environmental stress in seed beetles.

PubMed

Martinossi-Allibert, I; Arnqvist, G; Berger, D

2017-01-01

Sexual selection can increase rates of adaptation by imposing strong selection in males, thereby allowing efficient purging of the mutation load on population fitness at a low demographic cost. Indeed, sexual selection tends to be male-biased throughout the animal kingdom, but little empirical work has explored the ecological sensitivity of this sex difference. In this study, we generated theoretical predictions of sex-specific strengths of selection, environmental sensitivities and genotype-by-environment interactions and tested them in seed beetles by manipulating either larval host plant or rearing temperature. Using fourteen isofemale lines, we measured sex-specific reductions in fitness components, genotype-by-environment interactions and the strength of selection (variance in fitness) in the juvenile and adult stage. As predicted, variance in fitness increased with stress, was consistently greater in males than females for adult reproductive success (implying strong sexual selection), but was similar in the sexes in terms of juvenile survival across all levels of stress. Although genetic variance in fitness increased in magnitude under severe stress, heritability decreased and particularly so in males. Moreover, genotype-by-environment interactions for fitness were common but specific to the type of stress, sex and life stage, suggesting that new environments may change the relative alignment and strength of selection in males and females. Our study thus exemplifies how environmental stress can influence the relative forces of natural and sexual selection, as well as concomitant changes in genetic variance in fitness, which are predicted to have consequences for rates of adaptation in sexual populations. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Genotype-environment interaction and stability in ten-year height growth of Norway spruce Clones (Picea abies Karst.).

Treesearch

J.B. St. Clair; J. Kleinschmit

1986-01-01

Norway spruce cuttings of 40 clones were tested on seven contrasting sites in northern Germany. Analysis of variance for ten-year height growth indicate a highly significant clone x site interaction. This interaction may be reduced by selection of stable clones. Several measures of stability were calculated and discussed. Characterization of sites by the method of...

Host genotype and age shape the leaf and root microbiomes of a wild perennial plant

DOE PAGES

Wagner, Maggie R.; Lundberg, Derek S.; del Rio, Tijana G.; ...

2016-07-12

Bacteria living on and in leaves and roots influence many aspects of plant health, so the extent of a plant's genetic control over its microbiota is of great interest to crop breeders and evolutionary biologists. Laboratory-based studies, because they poorly simulate true environmental heterogeneity, may misestimate or totally miss the influence of certain host genes on the microbiome. Here we report a large-scale field experiment to disentangle the effects of genotype, environment, age and year of harvest on bacterial communities associated with leaves and roots of Boechera stricta (Brassicaceae), a perennial wild mustard. Host genetic control of the microbiome ismore » evident in leaves but not roots, and varies substantially among sites. Microbiome composition also shifts as plants age. Furthermore, a large proportion of leaf bacterial groups are shared with roots, suggesting inoculation from soil. Our results demonstrate how genotype-by-environment interactions contribute to the complexity of microbiome assembly in natural environments.« less

Accounting for Genotype-by-Environment Interactions and Residual Genetic Variation in Genomic Selection for Water-Soluble Carbohydrate Concentration in Wheat.

PubMed

Ovenden, Ben; Milgate, Andrew; Wade, Len J; Rebetzke, Greg J; Holland, James B

2018-05-31

Abiotic stress tolerance traits are often complex and recalcitrant targets for conventional breeding improvement in many crop species. This study evaluated the potential of genomic selection to predict water-soluble carbohydrate concentration (WSCC), an important drought tolerance trait, in wheat under field conditions. A panel of 358 varieties and breeding lines constrained for maturity was evaluated under rainfed and irrigated treatments across two locations and two years. Whole-genome marker profiles and factor analytic mixed models were used to generate genomic estimated breeding values (GEBVs) for specific environments and environment groups. Additive genetic variance was smaller than residual genetic variance for WSCC, such that genotypic values were dominated by residual genetic effects rather than additive breeding values. As a result, GEBVs were not accurate predictors of genotypic values of the extant lines, but GEBVs should be reliable selection criteria to choose parents for intermating to produce new populations. The accuracy of GEBVs for untested lines was sufficient to increase predicted genetic gain from genomic selection per unit time compared to phenotypic selection if the breeding cycle is reduced by half by the use of GEBVs in off-season generations. Further, genomic prediction accuracy depended on having phenotypic data from environments with strong correlations with target production environments to build prediction models. By combining high-density marker genotypes, stress-managed field evaluations, and mixed models that model simultaneously covariances among genotypes and covariances of complex trait performance between pairs of environments, we were able to train models with good accuracy to facilitate genetic gain from genomic selection. Copyright © 2018 Ovenden et al.

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.

Genotype-by-Environment Interactions for Female Mate Choice of Male Cuticular Hydrocarbons in Drosophila simulans

PubMed Central

Ingleby, Fiona C.; Hunt, John; Hosken, David J.

2013-01-01

Recent research has highlighted the potential importance of environmental and genotype-by-environment (G×E) variation in sexual selection, but most studies have focussed on the expression of male sexual traits. Consequently, our understanding of genetic variation for plasticity in female mate choice is extremely poor. In this study we examine the genetics of female mate choice in Drosophila simulans using isolines reared across two post-eclosion temperatures. There was evidence for G×Es in female choosiness and preference, which suggests that the evolution of female mate choice behaviour could differ across environments. However, the ranked order of preferred males was consistent across females and environments, so the same males are favoured by mate choice in spite of G×Es. Our study highlights the importance of taking cross-environment perspectives in order to gain a more comprehensive understanding of the operation of sexual selection. PMID:23825675

Impact of thermal stress on evolutionary trajectories of pathogen resistance in three-spined stickleback (Gasterosteus aculeatus)

PubMed Central

2014-01-01

Background Pathogens are a major regulatory force for host populations, especially under stressful conditions. Elevated temperatures may enhance the development of pathogens, increase the number of transmission stages, and can negatively influence host susceptibility depending on host thermal tolerance. As a net result, this can lead to a higher prevalence of epidemics during summer months. These conditions also apply to marine ecosystems, where possible ecological impacts and the population-specific potential for evolutionary responses to changing environments and increasing disease prevalence are, however, less known. Therefore, we investigated the influence of thermal stress on the evolutionary trajectories of disease resistance in three marine populations of three-spined sticklebacks Gasterosteus aculeatus by combining the effects of elevated temperature and infection with a bacterial strain of Vibrio sp. using a common garden experiment. Results We found that thermal stress had an impact on fish weight and especially on survival after infection after only short periods of thermal acclimation. Environmental stress reduced genetic differentiation (QST) between populations by releasing cryptic within-population variation. While life history traits displayed positive genetic correlations across environments with relatively weak genotype by environment interactions (GxE), environmental stress led to negative genetic correlations across environments in pathogen resistance. This reversal of genetic effects governing resistance is probably attributable to changing environment-dependent virulence mechanisms of the pathogen interacting differently with host genotypes, i.e. GPathogenxGHostxE or (GPathogenxE)x(GHostxE) interactions, rather than to pure host genetic effects, i.e. GHostxE interactions. Conclusion To cope with climatic changes and the associated increase in pathogen virulence, host species require wide thermal tolerances and pathogen-resistant genotypes. The higher resistance we found for some families at elevated temperatures showed that there is evolutionary potential for resistance to Vibrio sp. in both thermal environments. The negative genetic correlation of pathogen resistance between thermal environments, on the other hand, indicates that adaptation to current conditions can be a weak predictor for performance in changing environments. The observed feedback on selective gradients exerted on life history traits may exacerbate this effect, as it can also modify the response to selection for other vital components of fitness. PMID:25927537

Antagonistic interactions peak at intermediate genetic distance in clinical and laboratory strains of Pseudomonas aeruginosa.

PubMed

Schoustra, Sijmen E; Dench, Jonathan; Dali, Rola; Aaron, Shawn D; Kassen, Rees

2012-03-22

Bacteria excrete costly toxins to defend their ecological niche. The evolution of such antagonistic interactions between individuals is expected to depend on both the social environment and the strength of resource competition. Antagonism is expected to be weak among highly similar genotypes because most individuals are immune to antagonistic agents and among dissimilar genotypes because these are unlikely to be competing for the same resources and antagonism should not yield much benefit. The strength of antagonism is therefore expected to peak at intermediate genetic distance. We studied the ability of laboratory strains of Pseudomonas aeruginosa to prevent growth of 55 different clinical P. aeruginosa isolates derived from cystic fibrosis patients. Genetic distance was determined using genetic fingerprints. We found that the strength of antagonism was maximal among genotypes of intermediate genetic distance and we show that genetic distance and resource use are linked. Our results suggest that the importance of social interactions like antagonism may be modulated by the strength of resource competition.

Stability Performance of Inductively Coupled Plasma Mass Spectrometry-Phenotyped Kernel Minerals Concentration and Grain Yield in Maize in Different Agro-Climatic Zones

PubMed Central

Mallikarjuna, Mallana Gowdra; Thirunavukkarasu, Nepolean; Hossain, Firoz; Bhat, Jayant S.; Jha, Shailendra K.; Rathore, Abhishek; Agrawal, Pawan Kumar; Pattanayak, Arunava; Reddy, Sokka S.; Gularia, Satish Kumar; Singh, Anju Mahendru; Manjaiah, Kanchikeri Math; Gupta, Hari Shanker

2015-01-01

Deficiency of iron and zinc causes micronutrient malnutrition or hidden hunger, which severely affects ~25% of global population. Genetic biofortification of maize has emerged as cost effective and sustainable approach in addressing malnourishment of iron and zinc deficiency. Therefore, understanding the genetic variation and stability of kernel micronutrients and grain yield of the maize inbreds is a prerequisite in breeding micronutrient-rich high yielding hybrids to alleviate micronutrient malnutrition. We report here, the genetic variability and stability of the kernel micronutrients concentration and grain yield in a set of 50 maize inbred panel selected from the national and the international centres that were raised at six different maize growing regions of India. Phenotyping of kernels using inductively coupled plasma mass spectrometry (ICP-MS) revealed considerable variability for kernel minerals concentration (iron: 18.88 to 47.65 mg kg–1; zinc: 5.41 to 30.85 mg kg–1; manganese: 3.30 to17.73 mg kg–1; copper: 0.53 to 5.48 mg kg–1) and grain yield (826.6 to 5413 kg ha–1). Significant positive correlation was observed between kernel iron and zinc within (r = 0.37 to r = 0.52, p < 0.05) and across locations (r = 0.44, p < 0.01). Variance components of the additive main effects and multiplicative interactions (AMMI) model showed significant genotype and genotype × environment interaction for kernel minerals concentration and grain yield. Most of the variation was contributed by genotype main effect for kernel iron (39.6%), manganese (41.34%) and copper (41.12%), and environment main effects for both kernel zinc (40.5%) and grain yield (37.0%). Genotype main effect plus genotype-by-environment interaction (GGE) biplot identified several mega environments for kernel minerals and grain yield. Comparison of stability parameters revealed AMMI stability value (ASV) as the better representative of the AMMI stability parameters. Dynamic stability parameter GGE distance (GGED) showed strong and positive correlation with both mean kernel concentrations and grain yield. Inbreds (CM-501, SKV-775, HUZM-185) identified from the present investigation will be useful in developing micronutrient-rich as well as stable maize hybrids without compromising grain yield. PMID:26406470

Stability Performance of Inductively Coupled Plasma Mass Spectrometry-Phenotyped Kernel Minerals Concentration and Grain Yield in Maize in Different Agro-Climatic Zones.

PubMed

Mallikarjuna, Mallana Gowdra; Thirunavukkarasu, Nepolean; Hossain, Firoz; Bhat, Jayant S; Jha, Shailendra K; Rathore, Abhishek; Agrawal, Pawan Kumar; Pattanayak, Arunava; Reddy, Sokka S; Gularia, Satish Kumar; Singh, Anju Mahendru; Manjaiah, Kanchikeri Math; Gupta, Hari Shanker

2015-01-01

Deficiency of iron and zinc causes micronutrient malnutrition or hidden hunger, which severely affects ~25% of global population. Genetic biofortification of maize has emerged as cost effective and sustainable approach in addressing malnourishment of iron and zinc deficiency. Therefore, understanding the genetic variation and stability of kernel micronutrients and grain yield of the maize inbreds is a prerequisite in breeding micronutrient-rich high yielding hybrids to alleviate micronutrient malnutrition. We report here, the genetic variability and stability of the kernel micronutrients concentration and grain yield in a set of 50 maize inbred panel selected from the national and the international centres that were raised at six different maize growing regions of India. Phenotyping of kernels using inductively coupled plasma mass spectrometry (ICP-MS) revealed considerable variability for kernel minerals concentration (iron: 18.88 to 47.65 mg kg(-1); zinc: 5.41 to 30.85 mg kg(-1); manganese: 3.30 to 17.73 mg kg(-1); copper: 0.53 to 5.48 mg kg(-1)) and grain yield (826.6 to 5413 kg ha(-1)). Significant positive correlation was observed between kernel iron and zinc within (r = 0.37 to r = 0.52, p < 0.05) and across locations (r = 0.44, p < 0.01). Variance components of the additive main effects and multiplicative interactions (AMMI) model showed significant genotype and genotype × environment interaction for kernel minerals concentration and grain yield. Most of the variation was contributed by genotype main effect for kernel iron (39.6%), manganese (41.34%) and copper (41.12%), and environment main effects for both kernel zinc (40.5%) and grain yield (37.0%). Genotype main effect plus genotype-by-environment interaction (GGE) biplot identified several mega environments for kernel minerals and grain yield. Comparison of stability parameters revealed AMMI stability value (ASV) as the better representative of the AMMI stability parameters. Dynamic stability parameter GGE distance (GGED) showed strong and positive correlation with both mean kernel concentrations and grain yield. Inbreds (CM-501, SKV-775, HUZM-185) identified from the present investigation will be useful in developing micronutrient-rich as well as stable maize hybrids without compromising grain yield.

Design and analysis issues in gene and environment studies

PubMed Central

2012-01-01

Both nurture (environmental) and nature (genetic factors) play an important role in human disease etiology. Traditionally, these effects have been thought of as independent. This perspective is ill informed for non-mendelian complex disorders which result as an interaction between genetics and environment. To understand health and disease we must study how nature and nurture interact. Recent advances in human genomics and high-throughput biotechnology make it possible to study large numbers of genetic markers and gene products simultaneously to explore their interactions with environment. The purpose of this review is to discuss design and analytic issues for gene-environment interaction studies in the “-omics” era, with a focus on environmental and genetic epidemiological studies. We present an expanded environmental genomic disease paradigm. We discuss several study design issues for gene-environmental interaction studies, including confounding and selection bias, measurement of exposures and genotypes. We discuss statistical issues in studying gene-environment interactions in different study designs, such as choices of statistical models, assumptions regarding biological factors, and power and sample size considerations, especially in genome-wide gene-environment studies. Future research directions are also discussed. PMID:23253229

Design and analysis issues in gene and environment studies.

PubMed

Liu, Chen-yu; Maity, Arnab; Lin, Xihong; Wright, Robert O; Christiani, David C

2012-12-19

Both nurture (environmental) and nature (genetic factors) play an important role in human disease etiology. Traditionally, these effects have been thought of as independent. This perspective is ill informed for non-mendelian complex disorders which result as an interaction between genetics and environment. To understand health and disease we must study how nature and nurture interact. Recent advances in human genomics and high-throughput biotechnology make it possible to study large numbers of genetic markers and gene products simultaneously to explore their interactions with environment. The purpose of this review is to discuss design and analytic issues for gene-environment interaction studies in the "-omics" era, with a focus on environmental and genetic epidemiological studies. We present an expanded environmental genomic disease paradigm. We discuss several study design issues for gene-environmental interaction studies, including confounding and selection bias, measurement of exposures and genotypes. We discuss statistical issues in studying gene-environment interactions in different study designs, such as choices of statistical models, assumptions regarding biological factors, and power and sample size considerations, especially in genome-wide gene-environment studies. Future research directions are also discussed.

BDNF rs6265 methylation and genotype interact on risk for schizophrenia

PubMed Central

Ursini, Gianluca; Cavalleri, Tommaso; Fazio, Leonardo; Angrisano, Tiziana; Iacovelli, Luisa; Porcelli, Annamaria; Maddalena, Giancarlo; Punzi, Giovanna; Mancini, Marina; Gelao, Barbara; Romano, Raffaella; Masellis, Rita; Calabrese, Francesca; Rampino, Antonio; Taurisano, Paolo; Giorgio, Annabella Di; Keller, Simona; Tarantini, Letizia; Sinibaldi, Lorenzo; Quarto, Tiziana; Popolizio, Teresa; Caforio, Grazia; Blasi, Giuseppe; Riva, Marco A.; De Blasi, Antonio; Chiariotti, Lorenzo; Bollati, Valentina; Bertolino, Alessandro

2016-01-01

Abstract Epigenetic mechanisms can mediate gene-environment interactions relevant for complex disorders. The BDNF gene is crucial for development and brain plasticity, is sensitive to environmental stressors, such as hypoxia, and harbors the functional SNP rs6265 (Val66Met), which creates or abolishes a CpG dinucleotide for DNA methylation. We found that methylation at the BDNF rs6265 Val allele in peripheral blood of healthy subjects is associated with hypoxia-related early life events (hOCs) and intermediate phenotypes for schizophrenia in a distinctive manner, depending on rs6265 genotype: in ValVal individuals increased methylation is associated with exposure to hOCs and impaired working memory (WM) accuracy, while the opposite is true for ValMet subjects. Also, rs6265 methylation and hOCs interact in modulating WM-related prefrontal activity, another intermediate phenotype for schizophrenia, with an analogous opposite direction in the 2 genotypes. Consistently, rs6265 methylation has a different association with schizophrenia risk in ValVals and ValMets. The relationships of methylation with BDNF levels and of genotype with BHLHB2 binding likely contribute to these opposite effects of methylation. We conclude that BDNF rs6265 methylation interacts with genotype to bridge early environmental exposures to adult phenotypes, relevant for schizophrenia. The study of epigenetic changes in regions containing genetic variation relevant for human diseases may have beneficial implications for the understanding of how genes are actually translated into phenotypes. PMID:26889735

Influence of 5-HTT variation, childhood trauma and self-efficacy on anxiety traits: a gene-environment-coping interaction study.

PubMed

Schiele, Miriam A; Ziegler, Christiane; Holitschke, Karoline; Schartner, Christoph; Schmidt, Brigitte; Weber, Heike; Reif, Andreas; Romanos, Marcel; Pauli, Paul; Zwanzger, Peter; Deckert, Jürgen; Domschke, Katharina

2016-08-01

Environmental vulnerability factors such as adverse childhood experiences in interaction with genetic risk variants, e.g., the serotonin transporter gene linked polymorphic region (5-HTTLPR), are assumed to play a role in the development of anxiety and affective disorders. However, positive influences such as general self-efficacy (GSE) may exert a compensatory effect on genetic disposition, environmental adversity, and anxiety traits. We, thus, assessed childhood trauma (Childhood Trauma Questionnaire, CTQ) and GSE in 678 adults genotyped for 5-HTTLPR/rs25531 and their interaction on agoraphobic cognitions (Agoraphobic Cognitions Questionnaire, ACQ), social anxiety (Liebowitz Social Anxiety Scale, LSAS), and trait anxiety (State-Trait Anxiety Inventory, STAI-T). The relationship between anxiety traits and childhood trauma was moderated by self-efficacy in 5-HTTLPR/rs25531 LALA genotype carriers: LALA probands maltreated as children showed high anxiety scores when self-efficacy was low, but low anxiety scores in the presence of high self-efficacy despite childhood maltreatment. Our results extend previous findings regarding anxiety-related traits showing an interactive relationship between 5-HTT genotype and adverse childhood experiences by suggesting coping-related measures to function as an additional dimension buffering the effects of a gene-environment risk constellation. Given that anxiety disorders manifest already early in childhood, this insight could contribute to the improvement of psychotherapeutic interventions by including measures strengthening self-efficacy and inform early targeted preventive interventions in at-risk populations, particularly within the crucial time window of childhood and adolescence.

The effect of environmental heterogeneity on RPW8-mediated resistance to powdery mildews in Arabidopsis thaliana

PubMed Central

Jorgensen, Tove H.

2012-01-01

Background and Aims The biotic and abiotic environment of interacting hosts and parasites may vary considerably over small spatial and temporal scales. It is essential to understand how different environments affect host disease resistance because this determines frequency of disease and, importantly, heterogeneous environments can retard direct selection and potentially maintain genetic variation for resistance in natural populations. Methods The effect of different temperatures and soil nutrient conditions on the outcome of infection by a pathogen was quantified in Arabidopsis thaliana. Expression levels of a gene conferring resistance to powdery mildews, RPW8, were compared with levels of disease to test a possible mechanism behind variation in resistance. Key Results Most host genotypes changed from susceptible to resistant across environments with the ranking of genotypes differing between treatments. Transcription levels of RPW8 increased after infection and varied between environments, but there was no tight association between transcription and resistance levels. Conclusions There is a strong potential for a heterogeneous environment to change the resistance capacity of A. thaliana genotypes and hence the direction and magnitude of selection in the presence of the pathogen. Possible causative links between resistance gene expression and disease resistance are discussed in light of the present results on RPW8. PMID:22234559

The interaction of early life experiences with COMT val158met affects anxiety sensitivity.

PubMed

Baumann, C; Klauke, B; Weber, H; Domschke, K; Zwanzger, P; Pauli, P; Deckert, J; Reif, A

2013-11-01

The pathogenesis of anxiety disorders is considered to be multifactorial with a complex interaction of genetic factors and individual environmental factors. Therefore, the aim of this study was to examine gene-by-environment interactions of the genes coding for catechol-O-methyltransferase (COMT) and monoamine oxidase A (MAOA) with life events on measures related to anxiety. A sample of healthy subjects (N = 782; thereof 531 women; mean age M = 24.79, SD = 6.02) was genotyped for COMT rs4680 and MAOA-uVNTR (upstream variable number of tandem repeats), and was assessed for childhood adversities [Childhood Trauma Questionnaire (CTQ)], anxiety sensitivity [Anxiety Sensitivity Index (ASI)] and anxious apprehension [Penn State Worry Questionnaire (PSWQ)]. Main and interaction effects of genotype, environment and gender on measures related to anxiety were assessed by means of regression analyses. Association analysis showed no main gene effect on either questionnaire score. A significant interactive effect of childhood adversities and COMT genotype was observed: Homozygosity for the low-active met allele and high CTQ scores was associated with a significant increment of explained ASI variance [R(2) = 0.040, false discovery rate (FDR) corrected P = 0.04]. A borderline interactive effect with respect to MAOA-uVNTR was restricted to the male subgroup. Carriers of the low-active MAOA allele who reported more aversive experiences in childhood exhibited a trend for enhanced anxious apprehension (R(2) = 0.077, FDR corrected P = 0.10). Early aversive life experiences therefore might increase the vulnerability to anxiety disorders in the presence of homozygosity for the COMT 158met allele or low-active MAOA-uVNTR alleles. © 2013 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.

Global cytosine methylation in Daphnia magna depends on genotype, environment, and their interaction.

PubMed

Asselman, Jana; De Coninck, Dieter I M; Vandegehuchte, Michiel B; Jansen, Mieke; Decaestecker, Ellen; De Meester, Luc; Vanden Bussche, Julie; Vanhaecke, Lynn; Janssen, Colin R; De Schamphelaere, Karel A C

2015-05-01

The authors characterized global cytosine methylation levels in 2 different genotypes of the ecotoxicological model organism Daphnia magna after exposure to a wide array of biotic and abiotic environmental stressors. The present study aimed to improve the authors' understanding of the role of cytosine methylation in the organism's response to environmental conditions. The authors observed a significant genotype effect, an environment effect, and a genotype × environment effect. In particular, global cytosine methylation levels were significantly altered after exposure to Triops predation cues, Microcystis, and sodium chloride compared with control conditions. Significant differences between the 2 genotypes were observed when animals were exposed to Triops predation cues, Microcystis, Cryptomonas, and sodium chloride. Despite the low global methylation rate under control conditions (0.49-0.52%), global cytosine methylation levels upon exposure to Triops demonstrated a 5-fold difference between the genotypes (0.21% vs 1.02%). No effects were found in response to arsenic, cadmium, fish, lead, pH of 5.5, pH of 8, temperature, hypoxia, and white fat cell disease. The authors' results point to the potential role of epigenetic effects under changing environmental conditions such as predation (i.e., Triops), diet (i.e., Cryptomonas and Microcystis), and salinity. The results of the present study indicate that, despite global cytosine methylation levels being low, epigenetic effects may be important in environmental studies on Daphnia. © 2015 SETAC.

Host Genotype and Microbiota Contribute Asymmetrically to Transcriptional Variation in the Threespine Stickleback Gut

PubMed Central

Small, Clayton M.; Milligan-Myhre, Kathryn; Bassham, Susan; Guillemin, Karen

2017-01-01

Recent studies of interactions between hosts and their resident microbes have revealed important ecological and evolutionary consequences that emerge from these complex interspecies relationships, including diseases that occur when the interactions go awry. Given the preponderance of these interactions, we hypothesized that effects of the microbiota on gene expression in the developing gut—an important aspect of host biology—would be pervasive, and that these effects would be both comparable in magnitude to and contingent on effects of the host genetic background. To evaluate the effects of the microbiota, host genotype, and their interaction on gene expression in the gut of a genetically diverse, gnotobiotic host model, the threespine stickleback (Gasterosteus aculeatus), we compared RNA-seq data among 84 larval fish. Surprisingly, we found that stickleback population and family differences explained substantially more gene expression variation than the presence of microbes. Expression levels of 72 genes, however, were affected by our microbiota treatment. These genes, including many associated with innate immunity, comprise a tractable subset of host genetic factors for precise, systems-level study of host–microbe interactions in the future. Importantly, our data also suggest subtle signatures of a statistical interaction between host genotype and the microbiota on expression patterns of genetic pathways associated with innate immunity, coagulation and complement cascades, focal adhesion, cancer, and peroxisomes. These genotype-by-environment interactions may prove to be important leads to the understanding of host genetic mechanisms commonly at the root of sometimes complex molecular relationships between hosts and their resident microbes. PMID:28391321

Character displacement and the evolution of niche complementarity in a model biofilm community.

PubMed

Ellis, Crystal N; Traverse, Charles C; Mayo-Smith, Leslie; Buskirk, Sean W; Cooper, Vaughn S

2015-02-01

Colonization of vacant environments may catalyze adaptive diversification and be followed by competition within the nascent community. How these interactions ultimately stabilize and affect productivity are central problems in evolutionary ecology. Diversity can emerge by character displacement, in which selection favors phenotypes that exploit an alternative resource and reduce competition, or by facilitation, in which organisms change the environment and enable different genotypes or species to become established. We previously developed a model of long-term experimental evolution in which bacteria attach to a plastic bead, form a biofilm, and disperse to a new bead. Here, we focus on the evolution of coexisting mutants within a population of Burkholderia cenocepacia and how their interactions affected productivity. Adaptive mutants initially competed for space, but later competition declined, consistent with character displacement and the predicted effects of the evolved mutations. The community reached a stable equilibrium as each ecotype evolved to inhabit distinct, complementary regions of the biofilm. Interactions among ecotypes ultimately became facilitative and enhanced mixed productivity. Observing the succession of genotypes within niches illuminated changing selective forces within the community, including a fundamental role for genotypes producing small colony variants that underpin chronic infections caused by B. cenocepacia. © 2014 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Traits Explaining Durum Wheat (Triticum turgidum L. spp. Durum) Yield in Dry Chilean Mediterranean Environments

PubMed Central

González-Ribot, Gerlitt; Opazo, Marcela; Silva, Paola; Acevedo, Edmundo

2017-01-01

Yield under water stress (YS) is used as the main criterion in the selection of wheat varieties for dry Mediterranean environments. It has been proposed that selection of genotypes using YS assisted by morphological and physiological traits associated with YS is more efficient in selecting high yielding genotypes for dry environments. A study was carried out at the Antumapu Experiment Station of the University of Chile, located in Santiago, Chile (33° 40′S and 70° 38′ W). The objective was to evaluate the extent to which morpho physiological traits could explain YS. For this purpose, grain yield and yield components of 185 durum wheat genotypes from ICARDA (International Center for Agricultural Research in the Dry Areas) and INIA (Chilean National Institute for Agricultural Research) were evaluated along with seed size and weight, days to heading (DH), glaucousness (GLAU), plant height (PH) and 13C discrimination (Δ). The design was an α-lattice with two replications, the genotypes were grown in two different water conditions (high and low irrigation) during two seasons (2011-2012/2012-2013). Grain weight (GW) was the only yield component with high H associated with YS, but it was not associated with yield under high irrigation (YI). The combination of YI with DH+GLAU+PH+Δ+GW obtained in LI environments explained a greater fraction of YS (38%) across years; these traits had lower genotype x environment interaction than YS, they also explained a higher proportion of yield under drought than YI. None of the traits studied could replace YS in selections for grain yield. It is concluded that these traits could aid in the selection of durum wheat subject to water stress, particularly in early generations. PMID:29104578

Child Dopamine Transporter Genotype and Parenting: Evidence for Evocative Gene-Environment Correlations

PubMed Central

Hayden, Elizabeth P.; Hanna, Brigitte; Sheikh, Haroon I.; Laptook, Rebecca S.; Kim, Jiyon; Singh, Shiva M.; Klein, Daniel N.

2017-01-01

The dopamine transporter (DAT1) gene is implicated in psychopathology risk. While the processes by which this gene exerts its effects on risk are poorly understood, a small body of research suggests that DAT1 influences early emerging negative emotionality (NE), a marker of children’s psychopathology risk. As child NE evokes negative parenting practices, the DAT1 may also play a role in gene-environment correlations. To test this model, children (N = 365) were genotyped for DAT1 and participated in standardized parent-child interaction tasks with their primary caregiver. The DAT1 9-repeat variant was associated with child negative affect expressed toward the parent during parent-child interactions, and parents of children with a 9-repeat allele exhibited more hostility and lower guidance/engagement than parents of children without a 9-repeat allele. These gene-environment associations were partially mediated by child negative affect toward the parent. Findings implicate a specific polymorphism in eliciting negative parenting, suggesting that evocative associations play a role in elevating children’s risk for emotional trajectories toward psychopathology risk. PMID:23398760

Family by environment interactions for loblolly and slash pine plantations in the southeastern United States

Treesearch

Brian E. Roth; Eric J. Jokela; Timothy A. Martin; Dudley A. Huber; Timothy L. White

2010-01-01

Few studies have quantified the combined effects of silvicultural treatments and genetic improvement on unit area production of full-sib family blocks of loblolly and slash pine. We examined genotype (family) by environmental interactions (G x E) through age five years using a factorial experiment consisting of silvicultural treatment intensity, planting density and...

Childhood and adolescent anxiety and depression: beyond heritability.

PubMed

Franić, Sanja; Middeldorp, Christel M; Dolan, Conor V; Ligthart, Lannie; Boomsma, Dorret I

2010-08-01

To review the methodology of behavior genetics studies addressing research questions that go beyond simple heritability estimation and illustrate these using representative research on childhood and adolescent anxiety and depression. The classic twin design and its extensions may be used to examine age and gender differences in the genetic determinants of complex traits and disorders, the role of genetic factors in explaining comorbidity, the interaction of genes and the environment, and the effect of social interaction among family members. An overview of the methods typically employed to address such questions is illustrated by a review of 34 recent studies on childhood anxiety and depression. The review provides relatively consistent evidence for small to negligible sex differences in the genetic etiology of childhood anxiety and depression, a substantial role of genetic factors in accounting for the temporal stability of these disorders, a partly genetic basis of the comorbidity between anxiety and depression, a possible role of the interaction between genotype and the environment in affecting liability to these disorders, a role of genotype-environment correlation, and a minor, if any, etiological role of sibling interaction. The results clearly demonstrate a role for genetic factors in the etiology and temporal stability of individual differences in childhood anxiety and depression. Clinical implications of the findings are discussed. 2010 American Academy of Child and Adolescent Psychiatry. Published by Elsevier Inc. All rights reserved.

Does selection in a challenging environment produce Nile tilapia genotypes that can thrive in a range of production systems?

PubMed Central

Thoa, Ngo Phu; Ninh, Nguyen Huu; Knibb, Wayne; Nguyen, Nguyen Hong

2016-01-01

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. PMID:26892814

Genotype by environment interaction for stayability of Red Angus in the United States.

PubMed

Fennewald, Dennis J; Weaber, Robert L; Lamberson, William R

2018-03-06

Bulls are used across a wide variety of environments through the use of artificial insemination. However, not all bulls rank the same for genetic merit in all environments. Sire selection could be more accurate via improved methods of characterization. The objective of this study was to evaluate the presence of genotype by environment (GxE) interaction for stayability in Red Angus in the United States. Environments were defined as nine regions within the continental United States with similar temperature-humidity indices. Stayability was defined as having a calf at age 4 given that the cow had a calf at age 2. A probit sire model was used to determine the heritability on the underlying scale. The percentage of females that calved at age 2 that also calved at age 4 ranged from 32.9 to 58.5% across regions and was 55.0% for the national data set. The heritability of stayability ranged from 0.10 to 0.57 across regions and was 0.12 for the national data set. Genetic correlations were estimated for stayability between all pairs of regions. An estimate of less than 0.80 indicates GxE at a level for concern. Genetic correlations between regions ranged from 0.32 to 0.87 and were <0.80 for 29 of 36 region pairs.

Optimization of multi-environment trials for genomic selection based on crop models.

PubMed

Rincent, R; Kuhn, E; Monod, H; Oury, F-X; Rousset, M; Allard, V; Le Gouis, J

2017-08-01

We propose a statistical criterion to optimize multi-environment trials to predict genotype × environment interactions more efficiently, by combining crop growth models and genomic selection models. Genotype × environment interactions (GEI) are common in plant multi-environment trials (METs). In this context, models developed for genomic selection (GS) that refers to the use of genome-wide information for predicting breeding values of selection candidates need to be adapted. One promising way to increase prediction accuracy in various environments is to combine ecophysiological and genetic modelling thanks to crop growth models (CGM) incorporating genetic parameters. The efficiency of this approach relies on the quality of the parameter estimates, which depends on the environments composing this MET used for calibration. The objective of this study was to determine a method to optimize the set of environments composing the MET for estimating genetic parameters in this context. A criterion called OptiMET was defined to this aim, and was evaluated on simulated and real data, with the example of wheat phenology. The MET defined with OptiMET allowed estimating the genetic parameters with lower error, leading to higher QTL detection power and higher prediction accuracies. MET defined with OptiMET was on average more efficient than random MET composed of twice as many environments, in terms of quality of the parameter estimates. OptiMET is thus a valuable tool to determine optimal experimental conditions to best exploit MET and the phenotyping tools that are currently developed.

Caffeine, creatine, GRIN2A and Parkinson's disease progression.

PubMed

Simon, David K; Wu, Cai; Tilley, Barbara C; Lohmann, Katja; Klein, Christine; Payami, Haydeh; Wills, Anne-Marie; Aminoff, Michael J; Bainbridge, Jacquelyn; Dewey, Richard; Hauser, Robert A; Schaake, Susen; Schneider, Jay S; Sharma, Saloni; Singer, Carlos; Tanner, Caroline M; Truong, Daniel; Wei, Peng; Wong, Pei Shieen; Yang, Tianzhong

2017-04-15

Caffeine is neuroprotective in animal models of Parkinson's disease (PD) and caffeine intake is inversely associated with the risk of PD. This association may be influenced by the genotype of GRIN2A, which encodes an NMDA-glutamate-receptor subunit. In two placebo-controlled studies, we detected no association of caffeine intake with the rate of clinical progression of PD, except among subjects taking creatine, for whom higher caffeine intake was associated with more rapid progression. We now have analyzed data from 420 subjects for whom DNA samples and caffeine intake data were available from a placebo-controlled study of creatine in PD. The GRIN2A genotype was not associated with the rate of clinical progression of PD in the placebo group. However, there was a 4-way interaction between GRIN2A genotype, caffeine, creatine and the time since baseline. Among subjects in the creatine group with high levels of caffeine intake, but not among those with low caffeine intake, the GRIN2A T allele was associated with more rapid progression (p=0.03). These data indicate that the deleterious interaction between caffeine and creatine with respect to rate of progression of PD is influenced by GRIN2A genotype. This example of a genetic factor interacting with environmental factors illustrates the complexity of gene-environment interactions in the progression of PD. Copyright © 2017 Elsevier B.V. All rights reserved.

Genetic predispositions and parental bonding interact to shape adults' physiological responses to social distress.

PubMed

Esposito, Gianluca; Truzzi, Anna; Setoh, Peipei; Putnick, Diane L; Shinohara, Kazuyuki; Bornstein, Marc H

2017-05-15

Parental bonding and oxytocin receptor (OXTR) gene genotype each influences social abilities in adulthood. Here, we hypothesized an interaction between the two - environmental experience (parental bonding history) and genetic factors (OXTR gene genotype) - in shaping adults' social sensitivity (physiological response to distress). We assessed heart rate and peripheral temperature (tip of the nose) in 42 male adults during presentation of distress vocalizations (distress cries belonging to female human infants and adults as well as bonobo). The two physiological responses index, respectively, state of arousal and readiness to action. Participants' parental bonding in childhood was assessed through the self-report Parental Bonding Instrument. To assess participants' genetic predispositions, buccal mucosa cell samples were collected, and region rs2254298 of the oxytocin receptor gene was analyzed: previous OXTR gene findings point to associations between the G allele and better sociality (protective factor) and the A allele and poorer sociality (risk factor). We found a gene * environment interaction for susceptibility to social distress: Participants with a genetic risk factor (A carriers) with a history of high paternal overprotection showed higher heart rate increase than those without this risk factor (G/G genotype) to social distress.Also, a significant effect of the interaction between paternal care and genotype on nose temperature changes was found. This susceptibility appears to represent an indirect pathway through which genes and experiences interact to shape mature social sensitivity in males. Copyright © 2016 Elsevier B.V. All rights reserved.

Children’s genotypes interact with maternal responsive care in predicting children’s competence: Diathesis–stress or differential susceptibility?

PubMed Central

KOCHANSKA, GRAZYNA; KIM, SANGHAG; BARRY, ROBIN A.; PHILIBERT, ROBERT A.

2012-01-01

We examined Genotype × Environment (G × E) interactions between children’s genotypes (the serotonin transporter linked promoter region [5-HTTLPR] gene) and maternal responsive care observed at 15, 25, 38, and 52 months on three aspects of children’s competence at 67 months: academic skills and school engagement, social functioning with peers, and moral internalization that encompassed prosocial moral cognition and the moral self. Academic and social competence outcomes were reported by both parents, and moral internalization was observed in children’s narratives elicited by hypothetical stories and in a puppet interview. Analyses revealed robust G × E interactions, such that children’s genotype moderated the effects of maternal responsive care on all aspects of children’s competence. Among children with a short 5-HTTLPR allele (ss/sl), those whose mothers were more responsive were significantly more competent than those whose mothers were less responsive. Responsiveness had no effect for children with two long alleles (ll). For academic and social competence, the G × E interactions resembled the diathesis–stress model: ss/sl children of unresponsive mothers had particularly unfavorable outcomes, but ss/sl children of responsive mothers had no worse outcomes than ll children. For moral internalization, the G × E interaction reflected the differential susceptibility model: whereas ss/sl children of unresponsive mothers again had particularly unfavorable outcomes, ss/sl children of responsive mothers had significantly better outcomes than ll children. PMID:23786699

Genetic predispositions and parental bonding interact to shape adults’ physiological responses to social distress

PubMed Central

Esposito, Gianluca; Truzzi, Anna; Setoh, Peipei; Putnick, Diane L.; Shinohara, Kazuyuki; Bornstein, Marc H.

2018-01-01

Parental bonding and oxytocin receptor (OXTR) gene genotype each influences social abilities in adulthood. Here, we hypothesized an interaction between the two – environmental experience (parental bonding history) and genetic factors (OXTR gene genotype) – in shaping adults’ social sensitivity (physiological response to distress). We assessed heart rate and peripheral temperature (tip of the nose) in 42 male adults during presentation of distress vocalizations (distress cries belonging to female human infants and adults as well as bonobo). The two physiological responses index, respectively, state of arousal and readiness to action. Participants’ parental bonding in childhood was assessed through the self-report Parental Bonding Instrument. To assess participants’ genetic predispositions, buccal mucosa cell samples were collected, and region rs2254298 of the oxytocin receptor gene was analyzed: previous OXTR gene findings point to associations between the G allele and better sociality (protective factor) and the A allele and poorer sociality (risk factor). We found a gene * environment interaction for susceptibility to social distress: Participants with a genetic risk factor (A carriers) with a history of high paternal overprotection showed higher heart rate increase than those without this risk factor (G/G genotype) to social distress. Also, a significant effect of the interaction between paternal care and genotype on nose temperature changes was found. This susceptibility appears to represent an indirect pathway through which genes and experiences interact to shape mature social sensitivity in males. PMID:27343933

Identification of genetic loci associated with crude protein and mineral concentrations in alfalfa (Medicago sativa) using association mapping.

PubMed

Jia, Congjun; Wu, Xinming; Chen, Min; Wang, Yunqi; Liu, Xiqiang; Gong, Pan; Xu, Qingfang; Wang, Xuemin; Gao, Hongwen; Wang, Zan

2017-06-06

Alfalfa (Medicago sativa) is one of the most important legume forage species in China and many other countries of the world. It provides a quality source of proteins and minerals to animals. Genetic underpinnings for these important traits, however, are elusive. An alfalfa (M. sativa) association mapping study for six traits, namely crude protein (CP), rumen undegraded protein (RUP), and four mineral elements (Ca, K, Mg and P), was conducted in three consecutive years using a large collection encompassing 336 genotypes genotyped with 85 simple sequence repeat (SSR) markers. All the traits were significantly influenced by genotype, environment, and genotype × environment interaction. Eight-five significant associations (P < 0.005) were identified. Among these, five associations with Ca were repeatedly observed and six co-localized associations were identified. The identified marker alleles significantly associated with the traits provided important information for understanding genetic controls of alfalfa quality. The markers could be used in assisting selection for the individual traits in breeding populations for developing new alfalfa cultivars.

Fruit metabolite networks in engineered and non-engineered tomato genotypes reveal fluidity in a hormone and agroecosystem specific manner.

PubMed

Fatima, Tahira; Sobolev, Anatoly P; Teasdale, John R; Kramer, Matthew; Bunce, Jim; Handa, Avtar K; Mattoo, Autar K

Metabolomics provides a view of endogenous metabolic patterns not only during plant growth, development and senescence but also in response to genetic events, environment and disease. The effects of the field environment on plant hormone-specific metabolite profiles are largely unknown. Few studies have analyzed useful phenotypes generated by introducing single or multiple gene events alongside the non-engineered wild type control at field scale to determine the robustness of the genetic trait and its modulation in the metabolome as a function of specific agroecosystem environments. We evaluated the influence of genetic background (high polyamine lines; low methyl jasmonate line; low ethylene line; and isogenic genotypes carrying double transgenic events) and environments (hairy vetch, rye, plastic black mulch and bare soil mulching systems) on the metabolomic profile of isogenic reverse genetic mutations and selected mulch based cropping systems in tomato fruit. Net photosynthesis and fruit yield were also determined. NMR spectroscopy was used for quantifying metabolites that are central to primary metabolism. We analyzed both the first moment (means) of metabolic response to genotypes and agroecosystems by traditional univariate/multivariate methods, and the second moment (covariances) of responses by creating networks that depicted changes in correlations of paired metabolites. This particular approach is novel and was necessary because our experimental material yielded highly variable metabolic responses that could not be easily understood using the traditional analytical approaches for first moment statistics. High endogenous spermidine and spermine content exhibited strong effects on amino acids, Krebs cycle intermediates and energy molecules (ADP + ATP) in ripening fruits of plants grown under different agroecosystem environments. The metabolic response to high polyamine genotypes was similar to the response to hairy vetch cover crop mulch; supported by the pattern of changes in correlation between metabolites. Changes in primary metabolites of genotypes mutated for the deficiency of ethylene or methyl jasmonate were unique under all growth conditions and opposite of high polyamine genotype results. The high polyamine trait was found to dominate the low ethylene and low jasmonate mutations under field conditions. For several metabolites low ethylene and low methyl jasmonate genotypes had an inverse relationship. Collectively, these results affirm that interactions between metabolite pathways and growth environments are affected by genotype, and influence the metabolite quality of a crop. This study portrays how metabolite relationships change, both in mean and in correlation, under different genotypic and environmental conditions. Although these networks are surprisingly dynamic, we also find examples of selectively conserved associations.

Genotype × environment interaction on tocochromanol and plastochromanol-8 content in seeds of doubled haploids obtained from F1 hybrid black × yellow seeds of winter oilseed rape (Brassica napus L.).

PubMed

Siger, Aleksander; Michalak, Michał; Lembicz, Justyna; Nogala-Kałucka, Małgorzata; Cegielska-Taras, Teresa; Szała, Laurencja

2018-07-01

The aim of the study was to determine the effect of genotype × environment interaction on the levels of α-, β-, γ- and δ-tocopherol (α-T, β-T, γ-T and δ-T, respectively) and plastochromanol-8 (PC-8) in seeds of 17 doubled haploids (DHs) obtained from the F1 hybrid derived from crossing black (DH H 2 -26) × yellow (DH Z-114) seeds of winter oilseed rape. The content of tocopherols in the tested DH lines ranged from 415.6 to 540.1 mg kg -1 seeds, while PC-8 content ranged from 56.3 to 89.0 mg kg -1 seeds. The α-T/γ-T ratio reached a level of 0.78-1.29. Studies have shown that heritability for α-T, β-T, γ-T, total-T and PC-8 is mainly due to genotypic variation. For the δ-T homologue the level was dependent on environmental effect. The obtained DH lines population of oilseed rape is characterized by high heritability coefficients for α-T, β-T, γ-T, total-T and PC-8 levels, which indicates a greater influence of genotype than the environment on the content of these compounds. Among all studied doubled haploids, seven DHs were selected which were characterized by stable contents of α-T, β-T, γ-T, δ-T and total-T with the simultaneous stable content of PC-8. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Camelina Seed Yield and Fatty Acids as Influenced by Genotype and Environment

DOE PAGES

Obour, Augustine K.; Obeng, Eric; Mohammed, Yesuf A.; ...

2017-05-05

Camelina (Camelina sativa L. Crantz) is an alternative oilseed crop with potential for fallow replacement in dryland cereal-based crop production systems in the semiarid Great Plains. The interaction between genotype and environment was investigated on camelina seed yield, oil content, and fatty acid composition across two locations in the U.S. Great Plains. Treatments were three spring camelina genotypes (cultivars Blaine Creek, Pronghorn, and Shoshone), three growing seasons (2013, 2014, and 2015) and two locations (at Hays, KS, and Moccasin, MT). Our results showed camelina grown at Hays yielded 54% less than that at Moccasin. Blaine Creek yielded 17 and 42%more » more than Pronghorn and Shoshone at Hays but yields were not different among genotypes at Moccasin. Oil content ranged from 262 g kg -1 at Hays to 359 g kg -1 at Moccasin. The proportion of polyunsaturated fatty acids (PUFAs) ranged from 51% at Hays to 55% at Moccasin, whereas monounsaturated fatty acid (MUFA) and saturated fatty acid (SFA) contents were greater at Hays. The linolenic acid content ranged from 26% when Pronghorn was planted at Hays to 35% when planted at Moccasin. In general, the variations in seed yield and fatty acid profile corresponded well with growing season precipitation and temperatures at each environment.« less

Camelina Seed Yield and Fatty Acids as Influenced by Genotype and Environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Obour, Augustine K.; Obeng, Eric; Mohammed, Yesuf A.

Camelina (Camelina sativa L. Crantz) is an alternative oilseed crop with potential for fallow replacement in dryland cereal-based crop production systems in the semiarid Great Plains. The interaction between genotype and environment was investigated on camelina seed yield, oil content, and fatty acid composition across two locations in the U.S. Great Plains. Treatments were three spring camelina genotypes (cultivars Blaine Creek, Pronghorn, and Shoshone), three growing seasons (2013, 2014, and 2015) and two locations (at Hays, KS, and Moccasin, MT). Our results showed camelina grown at Hays yielded 54% less than that at Moccasin. Blaine Creek yielded 17 and 42%more » more than Pronghorn and Shoshone at Hays but yields were not different among genotypes at Moccasin. Oil content ranged from 262 g kg -1 at Hays to 359 g kg -1 at Moccasin. The proportion of polyunsaturated fatty acids (PUFAs) ranged from 51% at Hays to 55% at Moccasin, whereas monounsaturated fatty acid (MUFA) and saturated fatty acid (SFA) contents were greater at Hays. The linolenic acid content ranged from 26% when Pronghorn was planted at Hays to 35% when planted at Moccasin. In general, the variations in seed yield and fatty acid profile corresponded well with growing season precipitation and temperatures at each environment.« less

Host Genotype and Harvest Practices Shape the Leaf and Root Microbiomes of the Biofuel Crop Switchgrass

NASA Astrophysics Data System (ADS)

Singer, E.; Gonzalez, J.; Juenger, T. E.; Woyke, T.

2016-12-01

Growing energy demands and concerns for climate change have urgently pushed forward the timeline for the implementation of biofuel energies. Switchgrass (Panicum virgatum) is a leading biofuel crop in the United States. Bacteria living on and inside leaves and roots affect plant health, hence a plant's genetic control over its microbiota is of great interest to crop breeders and evolutionary biologists. We present a large-scale field experiment to untangle the effects of genotype, environment, soil horizon and harvest treatment practices on prokaryotic and fungal communities associated with leaves and roots of switchgrass. Using V4 16S rRNA and ITS gene as well as metagenome sequencing, we show that host genotype is significant in both, leaves and roots, and varies among sites. Microbiome composition along the rhizosphere also shifts with soil depth. Furthermore, plant harvest significantly changes both, leaf surface and rhizosphere communities, which can be seen a year after the harvest event. Gene function analysis shows that rhizosphere communities are enriched in genes encoding nitrate reduction, carbohydrate transport and metabolism, motility, and sensory and signal transduction proteins relative to leaf surface communities. Our results demonstrate how genotype-environment interactions contribute to the complexity of microbiome assembly in natural environments.

Water Deficit and Salinity Stress Reveal Many Specific QTL for Plant Growth and Fruit Quality Traits in Tomato

PubMed Central

Diouf, Isidore A.; Derivot, Laurent; Bitton, Frédérique; Pascual, Laura; Causse, Mathilde

2018-01-01

Quality is a key trait in plant breeding, especially for fruit and vegetables. Quality involves several polygenic components, often influenced by environmental conditions with variable levels of genotype × environment interaction that must be considered in breeding strategies aiming to improve quality. In order to assess the impact of water deficit and salinity on tomato fruit quality, we evaluated a multi-parent advanced generation intercross (MAGIC) tomato population in contrasted environmental conditions over 2 years, one year in control vs. drought condition and the other in control vs. salt condition. Overall 250 individual lines from the MAGIC population—derived from eight parental lines covering a large diversity in cultivated tomato—were used to identify QTL in both experiments for fruit quality and yield component traits (fruit weight, number of fruit, Soluble Solid Content, firmness), phenology traits (time to flower and ripe) and a vegetative trait, leaf length. All the traits showed a large genotype variation (33–86% of total phenotypic variation) in both experiments and high heritability whatever the year or treatment. Significant genotype × treatment interactions were detected for five of the seven traits over the 2 years of experiments. QTL were mapped using 1,345 SNP markers. A total of 54 QTL were found among which 15 revealed genotype × environment interactions and 65% (35 QTL) were treatment specific. Confidence intervals of the QTL were projected on the genome physical map and allowed identifying regions carrying QTL co-localizations, suggesting pleiotropic regulation. We then applied a strategy for candidate gene detection based on the high resolution mapping offered by the MAGIC population, the allelic effect of each parental line at the QTL and the sequence information of the eight parental lines. PMID:29559986

Cultivar evaluation and essential test locations identification for sugarcane breeding in China.

PubMed

Luo, Jun; Pan, Yong-Bao; Xu, Liping; Zhang, Hua; Yuan, Zhaonian; Deng, Zuhu; Chen, Rukai; Que, Youxiong

2014-01-01

The discrepancies across test sites and years, along with the interaction between cultivar and environment, make it difficult to accurately evaluate the differences of the sugarcane cultivars. Using a genotype main effect plus genotype-environment interaction (GGE) Biplot software, the yield performance data of seven sugarcane cultivars in the 8th Chinese National Sugarcane Regional Tests were analyzed to identify cultivars recommended for commercial release. Fn38 produced a high and stable sugar yield. Gn02-70 had the lowest cane yield with high stability. Yz06-407 was a high cane yield cultivar with poor stability in sugar yield. Yz05-51 and Lc03-1137 had an unstable cane yield but relatively high sugar yield. Fn39 produced stable high sugar yield with low and unstable cane production. Significantly different sugar and cane yields were observed across seasons due to strong cultivar-environment interactions. Three areas, Guangxi Chongzuo, Guangxi Baise, and Guangxi Hechi, showed better representativeness of cane yield and sugar content than the other four areas. On the other hand, the areas Guangxi Chongzuo, Yunnan Lincang, and Yunnan Baoshan showed strong discrimination ability, while the areas Guangxi Hechi and Guangxi Liuzhou showed poor discrimination ability. This study provides a reference for cultivar evaluation and essential test locations identification for sugarcane breeding in China.

Cultivar Evaluation and Essential Test Locations Identification for Sugarcane Breeding in China

PubMed Central

Luo, Jun; Xu, Liping; Zhang, Hua; Yuan, Zhaonian; Deng, Zuhu; Chen, Rukai

2014-01-01

The discrepancies across test sites and years, along with the interaction between cultivar and environment, make it difficult to accurately evaluate the differences of the sugarcane cultivars. Using a genotype main effect plus genotype-environment interaction (GGE) Biplot software, the yield performance data of seven sugarcane cultivars in the 8th Chinese National Sugarcane Regional Tests were analyzed to identify cultivars recommended for commercial release. Fn38 produced a high and stable sugar yield. Gn02-70 had the lowest cane yield with high stability. Yz06-407 was a high cane yield cultivar with poor stability in sugar yield. Yz05-51 and Lc03-1137 had an unstable cane yield but relatively high sugar yield. Fn39 produced stable high sugar yield with low and unstable cane production. Significantly different sugar and cane yields were observed across seasons due to strong cultivar-environment interactions. Three areas, Guangxi Chongzuo, Guangxi Baise, and Guangxi Hechi, showed better representativeness of cane yield and sugar content than the other four areas. On the other hand, the areas Guangxi Chongzuo, Yunnan Lincang, and Yunnan Baoshan showed strong discrimination ability, while the areas Guangxi Hechi and Guangxi Liuzhou showed poor discrimination ability. This study provides a reference for cultivar evaluation and essential test locations identification for sugarcane breeding in China. PMID:24982939

Using low energy x-ray radiography to evaluate root initiation and growth of Populus

Treesearch

Ronald S., Jr. Zalesny; A. L. Friend; B. Kodrzycki; D.W. McDonald; R. Michaels; A.H. Wiese; J.W. Powers

2007-01-01

Populus roots have been studied less than aboveground tissues. However, there is an overwhelming need to evaluate root initiation and growth in order to understand the genetics and physiology of rooting, along with genotype x environment interactions.

Epistasis × environment interactions among Arabidopsis thaliana glucosinolate genes impact complex traits and fitness in the field.

PubMed

Kerwin, Rachel E; Feusier, Julie; Muok, Alise; Lin, Catherine; Larson, Brandon; Copeland, Daniel; Corwin, Jason A; Rubin, Matthew J; Francisco, Marta; Li, Baohua; Joseph, Bindu; Weinig, Cynthia; Kliebenstein, Daniel J

2017-08-01

Despite the growing number of studies showing that genotype × environment and epistatic interactions control fitness, the influences of epistasis × environment interactions on adaptive trait evolution remain largely uncharacterized. Across three field trials, we quantified aliphatic glucosinolate (GSL) defense chemistry, leaf damage, and relative fitness using mutant lines of Arabidopsis thaliana varying at pairs of causal aliphatic GSL defense genes to test the impact of epistatic and epistasis × environment interactions on adaptive trait variation. We found that aliphatic GSL accumulation was primarily influenced by additive and epistatic genetic variation, leaf damage was primarily influenced by environmental variation and relative fitness was primarily influenced by epistasis and epistasis × environment interactions. Epistasis × environment interactions accounted for up to 48% of the relative fitness variation in the field. At a single field site, the impact of epistasis on relative fitness varied significantly over 2 yr, showing that epistasis × environment interactions within a location can be temporally dynamic. These results suggest that the environmental dependency of epistasis can profoundly influence the response to selection, shaping the adaptive trajectories of natural populations in complex ways, and deserves further consideration in future evolutionary studies. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Does the FTO gene interact with the socioeconomic status on the obesity development among young European children? Results from the IDEFICS study.

PubMed

Foraita, R; Günther, F; Gwozdz, W; Reisch, L A; Russo, P; Lauria, F; Siani, A; Veidebaum, T; Tornaritis, M; Iacoviello, L; Vyncke, K; Pitsiladis, Y; Mårild, S; Molnár, D; Moreno, L A; Bammann, K; Pigeot, I

2015-01-01

Various twin studies revealed that the influence of genetic factors on psychological diseases or behaviour is more expressed in socioeconomically advantaged environments. Other studies predominantly show an inverse association between socioeconomic status (SES) and childhood obesity in Western developed countries. The aim of this study is to investigate whether the fat mass and obesity-associated (FTO) gene interacts with the SES on childhood obesity in a subsample (N = 4406) of the IDEFICS (Identification and prevention of Dietary- and lifestyle-induced health EFfects In Children and infantS) cohort. A structural equation model (SEM) is applied with the latent constructs obesity, dietary intakes, physical activity and fitness habits, and parental SES to estimate the main effects of the latter three variables and a FTO polymorphism on childhood obesity. Further, a multiple group SEM is used to explore whether an interaction effect exists between the single nucleotide polymorphism rs9939609 within the FTO gene and SES. Significant main effects are shown for physical activity and fitness (standardised [betacrc ](s) = -0.113), SES ([betacrc ](s) = -0.057) and the FTO homozygous AA risk genotype ([betacrc ](s) = -0.177). The explained variance of obesity is ~9%. According to the multiple group approach of SEM, we see an interaction between SES and FTO with respect to their effect on childhood obesity (Δχ(2) = 7.3, df = 2, P = 0.03). Children carrying the protective FTO genotype TT seem to be more protected by a favourable social environment regarding the development of obesity than children carrying the AT or AA genotype.

Grain of environment explains variation in the strength of genotype × environment interaction.

PubMed

Rodríguez, R L

2012-09-01

Theory predicts that genetic variation in phenotypic plasticity (genotype × environment interaction or G × E) should be eroded by selection acting across environments. However, it appears that G × E is often maintained under selection, although not universally. This variation in the presence and strength of G × E requires explanation. Here I ask whether the explanation may lie in the grain of the environment at which G × E is expressed. The grain (or grain size) of the environment refers to the scale of environmental heterogeneity relative to generation time - that is, relative to the window of operation of selection - with higher rates of heterogeneity occurring in finer-grained environments. The hypothesis that the grain of the environment explains variation in the expression of G × E encapsulates variation in the power of selection to shape reaction norms: selection should be able to erode G × E in fine-grained environments but lose its power as the grain becomes coarser. I survey studies of G × E in sexual traits and demonstrate that the strength of G × E varies with the grain of the environment across which it is expressed, with G × E being stronger in coarser-grained environments. This result elucidates when G × E is most likely to be sustained in the reaction norms of fitness-related traits and when its evolutionary consequences will be most pronounced. © 2012 The Author. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

The interactions among organophosphate pesticide exposure, oxidative stress, and genetic polymorphisms of dopamine receptor D4 increase the risk of attention deficit/hyperactivity disorder in children.

PubMed

Chang, Chia-Huang; Yu, Ching-Jung; Du, Jung-Chieh; Chiou, Hsien-Chih; Chen, Hsin-Chang; Yang, Winnie; Chung, Ming-Yi; Chen, Ying-Sheue; Hwang, Betau; Mao, I-Fang; Chen, Mei-Lien

2018-01-01

The aim of this study was to clarify the association between organophosphate pesticides (OPs) and attention-deficit/hyperactivity disorder (ADHD) related to oxidative stress and genetic polymorphisms. This case-control study enrolled 93 children with ADHD and 112 control children in north Taiwan. Six dialkyl phosphate (DAP) metabolites of OPs and oxidative stress biomarkers were analyzed. Polymorphisms of the dopamine receptor D4 gene (DRD4) were identified. Children with ADHD had significantly higher dimethylphosphate (DMP, 236.69nmol/g cre. vs. 186.84nmol/g cre., p value = 0.01) and 4-hydroxy-2-nonenal-mercapturic acid (HNE-MA, 28.95µg/g cre. vs. 16.55µg/g cre., p value<0.01) concentrations than control children. Children who carried DRD4 GA/AA genotypes (rs752306) were less likely than those who carried the DRD4 GG genotype to have ADHD (odds ratio [OR]: 0.45, 95% CI: 0.24-0.84). The estimated value of the AP (attributable proportion due to interaction) was 0.59 (95% CI: 0.13-1.05), indicating that 59% of ADHD cases in DMP-exposed children with the DRD4 GG genotype were due to the gene-environment interaction. After adjustment for other covariates, children who carried the DRD4 GG genotype, had been exposed to high DMP levels (more than the median), and had high HNE-MA levels had a significantly increased risk for developing ADHD (OR = 11.74, 95% CI: 2.12-65.04). This study indicated a gene-environment interaction in the risk of ADHD in children. The association between DMP and ADHD in children might relate to the mechanism of lipid peroxidation. Dose-response relationships and the combined effects of OPs, oxidative stress, and genetic polymorphism on ADHD should not be neglected. Copyright © 2017 Elsevier Inc. All rights reserved.

Serotonin transporter 5-HTTLPR genotype is associated with intrusion and avoidance symptoms of DSM-5 posttraumatic stress disorder (PTSD) in Chinese earthquake survivors.

PubMed

Liu, Luobing; Wang, Li; Cao, Chengqi; Cao, Xing; Zhu, Ye; Liu, Ping; Luo, Shu; Zhang, Jianxin

2018-05-01

Prior studies have found that the serotonin transporter gene-linked polymorphic region (5-HTTLPR) interacts with trauma exposure to increase general risk for Posttraumatic Stress Disorder (PTSD). However, there is little knowledge about the effects of the interaction on distinct symptom clusters of PTSD. This study aimed to investigate the relation between the interaction of 5-HTTLPR and earthquake-related exposures and a contemporary phenotypic model of DSM-5 PTSD symptoms in a traumatised adult sample from China. A cross-sectional design with gene-environment interaction (G × E) approach was adopted. Participants were 1131 survivors who experienced 2008 Wenchuan earthquake. PTSD symptoms were assessed with the PTSD Checklist for DSM-5 (PCL-5). The 5-HTTLPR polymorphism was genotyped with capillary electrophoresis (CE) in ABI 3730xl genetic Analyzer. Although there was no significant interaction between 5-HTTLPR and traumatic exposure on total PTSD symptoms, respondents with the LL genotype of 5-HTTLPR who were highly exposed to the earthquake experienced lower intrusion and avoidance symptoms than those with the S-allele carriers. The findings suggest that the 5-HTTLPR may have an important impact on the development of PTSD and add to the extant knowledge on understanding and treating of posttraumatic psychopathology.

Differential accumulation of polyphenolics in black bean genotypes grown in four environments.

PubMed

Marles, M A Susan; Balasubramanian, Parthiba; Bett, Kirstin E

2010-06-09

Environmental effects on polyphenolic composition of pigmented seed coat tissue were examined in four black bean genotypes, grown in four locations in Canada. Genotype was the most significant determinant in the phenotypic expression of flavonoid traits across four locations (p < 0.0001). The genotype x environment interaction was not significantly different for anthocyanin or extractable condensed tannin (syn. proanthocyanidin) but was significant for the bound anthocyanidin concentration (p < 0.05). One trace metabolite, (-)-epicatechin, was identified, but no flavonols were detected in the seed coats. Sequestration of anthocyanin in the seed coat was genotype-dependent and predominantly consisted of delphinidin with lesser amounts of petunidin and malvidin. Pigment sequestration in the two integument layers of the seed coat appeared to be mutually exclusive across all genotypes in terms of the pigment chemical character. Tissue-specific accumulation of extractable and bound anthocyanin in the outer integument was observed. The inner integument was devoid of anthocyanin, and the pigment consisted solely of condensed tannin inclusions. The occurrence of condensed tannin together with anthocyanin pigments, whether extractable or bound either by oxidation or by cross-linking, influenced the visual uniformity of seeds of bean cultivars. The co-occurrence of these compounds could have an effect on postharvest appearance during storage, on canning quality, and on the dietary effects of the putative functional food profile in the black bean market class.

Phenotypic plasticity in a population of odonates.

PubMed

Bowman, Randi M; Schmidt, Sharol; Weeks, Chelsea; Clark, Hunter; Brown, Christopher; Latta, Leigh C; Edgehouse, Michael

2018-05-31

The maintenance of phenotypic plasticity within a species ensures survival through environmental flux. Plastic strategies are increasingly important given the number and magnitude of modern anthropogenic threats to the environment. We tested for phenotypic plasticity in the odonate Argia vivida in response to resource limitation. By limiting food availability, effectively inducing hunger, we were able to quantify shifts in agonistic behavior during intraspecific interactions. Scoring behavior in one-on-one combat trials after 1 and 4 days without food revealed phenotypic plasticity. Three classes of genotypes were identified, genotypes exhibiting either increased aggression, decreased aggression, or no phenotypic plasticity, in response to resource limitation. The variable plastic strategies in this population of odonates likely aids in maintaining fitness in fluctuating environments.

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

Interaction between genotypes, environment and season (G x E x S) on anthocyanin corn in lowland zone of Indonesia

NASA Astrophysics Data System (ADS)

G, M. Yasin H.; Isnaeni, M.; Faesal; Azrai, M.

2018-05-01

Interaction between genotypes (G), environment (E) and season (S) on anthocyanin corn has been studied under lowland zone in Indonesia. The experiment were conducted using Randomized Complete Block Design (RCBD) based on location namely Maros, Bajeng, and Polman with three replications. Ten populations of open pollinated variety (OPV) of anthocyanins purple corn included checks were used in two planting seasons (dry and rainy) in 2015/2016. The objective of the experiment is to determine which of the population is stable and has high yield to be promoted as candidate for new OPV varieties. Genotypes were planted in four rows of 5.0 m length, spacing of 75 cm x 20 cm, one plant per hill, and applied with Urea, Ponska (300 and 200 kg Ha-1). Population was then selected by t test in model Yij=µ+βiIj+δij, i≠j (Y: yield, µ: mean, β: regression coefficient, I: environmental index, δ: deviation from regression), and stability parameter bi=ΣYiIj/I2 j. The results show that there was a significant interaction of GxExS on PMU(S1).Synth.F.C1 and PPU(S1).F.C1 with yield ranging between 6.70-8.48 t ha-1 and grain potential found in the locations of Maros and Bajeng in the rainy season. Content of anthocyanins were between 37.15 and 51.92 µg per 100 g sample.

Simulating the yield impacts of organ-level quantitative trait loci associated with drought response in maize: a "gene-to-phenotype" modeling approach.

PubMed

Chenu, Karine; Chapman, Scott C; Tardieu, François; McLean, Greg; Welcker, Claude; Hammer, Graeme L

2009-12-01

Under drought, substantial genotype-environment (G x E) interactions impede breeding progress for yield. Identifying genetic controls associated with yield response is confounded by poor genetic correlations across testing environments. Part of this problem is related to our inability to account for the interplay of genetic controls, physiological traits, and environmental conditions throughout the crop cycle. We propose a modeling approach to bridge this "gene-to-phenotype" gap. For maize under drought, we simulated the impact of quantitative trait loci (QTL) controlling two key processes (leaf and silk elongation) that influence crop growth, water use, and grain yield. Substantial G x E interaction for yield was simulated for hypothetical recombinant inbred lines (RILs) across different seasonal patterns of drought. QTL that accelerated leaf elongation caused an increase in crop leaf area and yield in well-watered or preflowering water deficit conditions, but a reduction in yield under terminal stresses (as such "leafy" genotypes prematurely exhausted the water supply). The QTL impact on yield was substantially enhanced by including pleiotropic effects of these QTL on silk elongation and on consequent grain set. The simulations obtained illustrated the difficulty of interpreting the genetic control of yield for genotypes influenced only by the additive effects of QTL associated with leaf and silk growth. The results highlight the potential of integrative simulation modeling for gene-to-phenotype prediction and for exploiting G x E interactions for complex traits such as drought tolerance.

The development of exploratory behaviour in the african striped mouse rhabdomys reflects a gene × environment compromise.

PubMed

Rymer, Tasmin L; Pillay, Neville

2012-09-01

Behaviour results from the interaction of an individual's genotype with prevailing environmental conditions, resulting in local adaptation to specific habitats. We investigated the development of exploratory behaviour in two closely-related species of African striped mice from the semi-arid Succulent Karoo (Rhabdomys pumilio) and moist grassland (R. dilectus chakae) localities. Irrespective of sex, R. pumilio displayed greater exploratory behaviour (open field) and greater use of the open arms of a modified plus maze, and thus were less anxious and bolder than R. d. chakae. When pups were cross-fostered between species, fostered individuals of both species showed an intermediate behavioural pattern between their foster and biological siblings: fostered R. pumilio explored more than their foster siblings but less than their biological siblings, whereas fostered R. d. chakae explored more than their biological siblings, but less than their foster siblings. Our study is one of the first to address how the underlying genotype and early postnatal experience interact to influence the expression of exploratory behaviour and personality. In particular, we showed that, in striped mice, the early postnatal environment shapes the anxiety responses and concomitant exploratory behaviour, but the genotype apparently modulates the phenotype and constrains the limit of behavioural flexibility.

Interactions of central obesity with rs3918242 on risk of non-alcoholic fat liver disease: a preliminary case-control study.

PubMed

Wu, Pengbo; Hua, Yonglong; Tan, Shiyun; Li, Ming; Shu, Yongxiang; Fang, Guo

2015-01-01

NAFLD is a complex disease characterized by inflammation and insulin resistance which is determined by an interaction of genetics and environmental factors. MMP gene has been implicated in relation to inflammation and insulin resistance. The preliminary case-control study aimed to investigate the association between Matrix metalloproteinase (MMP)-9-1562C/T (rs3918242), MMP-2-1306C/T (rs243865) and risk of NAFLD and to further evaluate the interactions of central obesity with rs3918242 and rs243865. Two variants, rs3918242 and rs243865, were genotyped by polymerase chain reaction -restriction fragment length polymorphism. Gene-environment interactions on risk of NAFLD was preliminarily investigated by generalized multifactor dimensionality reduction (GMDR) and further confirmed by unconditional logistic regression methods. After adjusting for covariates, increased risk of NAFLD were observed in subjects carrying TT/CT genotypes in rs3918242 ((Adjust)OR=1.64, 95% CI: 1.24, 2.11, P=0.006). However, decreased risk of non-alcoholic fat liver disease was found when MMP-2 rs243865 (TT/CT) genotype carriers compared with CC carrier ((Adjust)OR=0.65, 95% CI: 0.47, 0.72, P=0.000).Interactions of central obesity with rs3918242 was preliminarily found by GMDR, with a maximum prediction accuracy (67.61%) and a maximum Cross-validation Consistency (10/10).The unconditional logistic regression method indicated central obesity-positive subject with genotype TT/CT had 4.54 times risk of NAFLD compared to central obesity-negative subjects with genotype CC (OR(add)(a)=4.54, 95% CI: 2.81, 7.21, P(add)(a)=0.000), which further confirmed the interactions. The results indicate that both rs3918242 and rs243865 is associated with risk of NAFLD. Furthermore, rs3918242 and central obesity have synergistic effects on risk of NAFLD.

The TreadWheel: A Novel Apparatus to Measure Genetic Variation in Response to Gently Induced Exercise for Drosophila

PubMed Central

Mendez, Sean; Watanabe, Louis; Hill, Rachel; Owens, Meredith; Moraczewski, Jason; Rowe, Glenn C.; Riddle, Nicole C.

2016-01-01

Obesity is one of the dramatic health issues affecting developed and developing nations, and exercise is a well-established intervention strategy. While exercise-by-genotype interactions have been shown in humans, overall little is known. Using the natural negative geotaxis of Drosophila melanogaster, an important model organism for the study of genetic interactions, a novel exercise machine, the TreadWheel, can be used to shed light on this interaction. The mechanism for inducing exercise with the TreadWheel is inherently gentle, thus minimizing possible confounding effects of other stressors. Using this machine, we were able to assess large cohorts of adult flies from eight genetic lines for their response to exercise after one week of training. We measured their triglyceride, glycerol, protein, glycogen, glucose content, and body weight, as well as their climbing ability and feeding behavior in response to exercise. Exercised flies showed decreased stored triglycerides, glycogen, and body weight, and increased stored protein and climbing ability. In addition to demonstrating an overall effect of TreadWheel exercise on flies, we found significant interactions of exercise with genotype, sex, or genotype-by-sex effects for most of the measured phenotypes. We also observed interaction effects between exercise, genotype, and tissue (abdomen or thorax) for metabolite profiles, and those differences can be partially linked to innate differences in the flies' persistence in maintaining activity during exercise bouts. In addition, we assessed gene expression levels for a panel of 13 genes known to be associated with respiratory fitness and found that many responded to exercise. With this study, we have established the TreadWheel as a useful tool to study the effect of exercise in flies, shown significant genotype-specific and sex-specific impacts of exercise, and have laid the ground work for more extensive studies of how genetics, sex, environment, and aging interact with exercise to influence metabolic fitness in Drosophila. PMID:27736996

A modern amplelography: A genetic basis for leaf shape and venation patterning in grape

USDA-ARS?s Scientific Manuscript database

Terroir, the unique interaction between genotype, environment, and culture, is highly refined in domesticated grape (Vitis vinifera). Toward cultivating terroir, the science of ampelography tried to distinguish thousands of grape cultivars without the aid of genetics. This led to sophisticated pheno...

Magnitude of genotype x environment interactions affecting tomato fruit quality

USDA-ARS?s Scientific Manuscript database

There is a growing interest by consumers to purchase fresh tomato with improved quality traits including lycopene, total soluble solids (TSS), vitamin C and titratable acid (TA) content. Therefore, there are considerable efforts by tomato breeders to improve tomato for these traits. However, suitabl...

Genotype by environment interaction for plant density response in maize

USDA-ARS?s Scientific Manuscript database

Increased adaptation to high plant density has been an important factor in improvements in grain yield in maize. Despite extensive public literature on variation in plant density response among maize varieties, almost no public information is available on environmental effects on plant density respo...

A modern ampelography: A genetic basis for leaf shape and venation patterning in grape

USDA-ARS?s Scientific Manuscript database

Terroir, the unique interaction between genotype, environment, and culture, is highly refined in domesticated grape (Vitis vinifera). Toward cultivating terroir, the science of ampelography tried to distinguish thousands of grape cultivars without the aid of genetics. This led to sophisticated pheno...

Sleep Duration and Body Mass Index in Twins: A Gene-Environment Interaction

PubMed Central

Watson, Nathaniel F.; Harden, Kathryn Paige; Buchwald, Dedra; Vitiello, Michael V.; Pack, Allan I.; Weigle, David S.; Goldberg, Jack

2012-01-01

Study Objectives: To examine whether sleep duration modifies genetic and environmental influences on body mass index (BMI). Design: Genotype-environment interaction twin study. Setting: University of Washington Twin Registry. Patients or Participants: A population-based sample of US twins (1,088 pairs, 604 monozygotic, 484 dizygotic; 66% female; mean age = 36.6 yr, standard deviation (SD) = 15.9 yr). Interventions: N/A. Measurements and Results: Participants self-reported information on height, weight, and sleep. Mean BMI was calculated as 25.3 kg/m2 (SD = 5.4) and mean habitual sleep duration was 7.2 hr/night (SD = 1.2). Data were analyzed using biometric genetic interaction models. Overall the heritability of sleep duration was 34%. Longer sleep duration was associated with decreased BMI (P < 0.05). The heritability of BMI when sleep duration was < 7 hr (h2 = 70%) was more than twice as large as the heritability of BMI when sleep duration was ≥ 9 hr (h2 = 32%); this interaction was significant (P < 0.05). Conclusions: Shorter sleep duration is associated with increased BMI and increased genetic influences on BMI, suggesting that shorter sleep duration increases expression of genetic risks for high body weight. At the same time, longer sleep duration may suppress genetic influences on body weight. Future research aiming to identify specific genotypes for BMI may benefit by considering the moderating role of sleep duration. Citation: Watson NF; Harden KP; Buchwald D; Vitiello MV; Pack AI; Weigle DS; Goldberg J. Sleep duration and body mass index in twins: a gene-environment interaction. SLEEP 2012;35(5):597-603. PMID:22547885

Cortico-limbic connectivity in MAOA-L carriers is vulnerable to acute tryptophan depletion.

PubMed

Eisner, Patrick; Klasen, Martin; Wolf, Dhana; Zerres, Klaus; Eggermann, Thomas; Eisert, Albrecht; Zvyagintsev, Mikhail; Sarkheil, Pegah; Mathiak, Krystyna A; Zepf, Florian; Mathiak, Klaus

2017-03-01

A gene-environment interaction between expression genotypes of the monoamine oxidase A (MAOA) and adverse childhood experience increases the risk of antisocial behavior. However, the neural underpinnings of this interaction remain uninvestigated. A cortico-limbic circuit involving the prefrontal cortex (PFC) and the amygdala is central to the suppression of aggressive impulses and is modulated by serotonin (5-HT). MAOA genotypes may modulate the vulnerability of this circuit and increase the risk for emotion regulation deficits after specific life events. Acute tryptophan depletion (ATD) challenges 5-HT regulation and may identify vulnerable neuronal circuits, contributing to the gene-environment interaction. Functional magnetic resonance imaging measured the resting-state state activity in 64 healthy males in a double-blind, placebo-controlled study. Cortical maps of amygdala correlation identified the impact of ATD and its interaction with low- (MAOA-L) and high-expression variants (MAOA-H) of MAOA on cortico-limbic connectivity. Across all Regions of Interest (ROIs) exhibiting an ATD effect on cortico-limbic connectivity, MAOA-L carriers were more susceptible to ATD than MAOA-H carriers. In particular, the MAOA-L group exhibited a larger reduction of amygdala connectivity with the right prefrontal cortex and a larger increase of amygdala connectivity with the insula and dorsal PCC. MAOA-L carriers were more susceptable to a central 5-HT challenge in cortico-limbic networks. Such vulnerability of the cortical serotonergic system may contribute to the emergence of antisocial behavior after systemic challenges, observed as gene-environment interaction. Hum Brain Mapp 38:1622-1635, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Genotype by environment interactions for behavioral reactivity in sheep.

PubMed

Hazard, D; Bouix, J; Chassier, M; Delval, E; Foulquié, D; Fassier, T; Bourdillon, Y; François, D; Boissy, A

2016-04-01

In sheep, social reactivity and reactivity to humans are relevant behavioral responses that are used to investigate the behavioral adaptation of farm animals to various rearing conditions. Such traits were previously reported as heritable and associated with several QTLs. However, few behavior-related genotype by environment (G × E) interactions have been reported to date. The experiment was performed on 2,989 male and female lambs issued from 30 sires. Every sire had progeny reared under both intensive and extensive conditions. After weaning, all lambs were individually exposed to two standardized behavioral tests. A broad range of behaviors including vocalizations, locomotion, localization, vigilance, and flight distance were assessed. Two complementary statistic approaches, with and without assumptions on the biological significance of behaviors, were performed to investigate social reactivity and reactivity to humans. G × E interactions were investigated based on the genetic correlations estimated for each factor or trait between farming conditions; those significantly different from 1 indicating a G × E. Environmental effects showed that social reactivity and reactivity to humans were higher in intensively reared lambs. The heritability of factors or traits used to measure social reactivity and reactivity to humans was similar in both rearing conditions. Estimated heritabilities were high for vocalizations in response to social isolation, moderate for locomotion and vigilance in response to social isolation, and low for both flight distance to an approaching human and proximity to a motionless human. No significant G × E interaction was found for vocalizations. G × E interactions were found for locomotion, vigilance and flight distance. Genetic correlations between both environments were low to moderate for vigilance, locomotion and flight distance. Vocalization in response to social isolation with or without human presence was identified as a robust trait and could be used to improve sheep sociability, independently of the environment. A G × E interaction was observed for behavioral reactivity to humans. Although moderate, the genetic correlation for this trait between intensive and extensive conditions could be used to select sires in the same environment by taking into account the G × E and to produce in different environments progenies that are less reactive to humans.

Responses of alloplasmic (cytoplasm=Triticum timopheevii) and euplasmic wheats (Triticum aestivum) to photoperiod and vernalization.

PubMed

Ward, R W; Heyne, E G; Paulsen, G M

1983-07-01

Studies were conducted to determine the influence of the male sterility-inducing cytoplasm of Triticum timopheevii (Zhuk.) Zhuk. on response of several common winter wheat (T. aestivum L.) nuclear genotypes to photoperiod and vernalization. Comparative studies of cytoplasmic substitution lines provide information on the role of the cytoplasmic genetic mechanism in growth and development. In the case of cytoplasmic male sterility-based hybrid production systems, ubiquity of sterility-inducing cytoplasm in derived hybrids warrants thorough characterization of its influence on plant phenotype. Factorial combinations of cytoplasm (T. timopheevii and T. aestivum), nuclear genotype, and photoperiod or vernalization treatments were evaluated under hydroponic conditions in controlled environment chambers. Interaction of cytoplasm, photoperiod, and nuclear genotype was significant in one or more experiments for days to anthesis and potential spikelet number, and interaction of cytoplasm, vernalization, and nuclear genotype was significant for days to spike emergence. Long day length was associated with increased percentage seed set in one study, but interactions of photoperiod and cytoplasm were not detected for percentage seed set. Interactions involving cytoplasm and photoperiod or vernalization were interpreted as evidence of the existence of genetic factors in cytoplsam of T. timopheevii which alter photoperiod or vernalization responses of alloplasmic plants relative to responses exhibited by euplasmic plants. Since photoperiod and vernalization responses are critical to adaptation, T. timopheevii cytoplasm can alter adaptability of T. aestivum. The specific effect would be nuclear genotype dependent, and does not appear to be of a magnitude greater than that induced by nuclear genetic variability at loci conditioning photoperiod or vernalization responses or other adaptation-determining characteristics. Normal multilocation/year testing of alloplasmic hybrids should therefore adequately identify zones of adaptation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wagner, Maggie R.; Lundberg, Derek S.; del Rio, Tijana G.

Bacteria living on and in leaves and roots influence many aspects of plant health, so the extent of a plant's genetic control over its microbiota is of great interest to crop breeders and evolutionary biologists. Laboratory-based studies, because they poorly simulate true environmental heterogeneity, may misestimate or totally miss the influence of certain host genes on the microbiome. Here we report a large-scale field experiment to disentangle the effects of genotype, environment, age and year of harvest on bacterial communities associated with leaves and roots of Boechera stricta (Brassicaceae), a perennial wild mustard. Host genetic control of the microbiome ismore » evident in leaves but not roots, and varies substantially among sites. Microbiome composition also shifts as plants age. Furthermore, a large proportion of leaf bacterial groups are shared with roots, suggesting inoculation from soil. Our results demonstrate how genotype-by-environment interactions contribute to the complexity of microbiome assembly in natural environments.« less

The serotonin transporter gene polymorphism 5-HTTLPR moderates the effects of stress on attention-deficit/hyperactivity disorder.

PubMed

van der Meer, Dennis; Hartman, Catharina A; Richards, Jennifer; Bralten, Janita B; Franke, Barbara; Oosterlaan, Jaap; Heslenfeld, Dirk J; Faraone, Stephen V; Buitelaar, Jan K; Hoekstra, Pieter J

2014-12-01

The role of the serotonin transporter gene polymorphism 5-HTTLPR in attention-deficit/hyperactivity disorder (ADHD) is unclear. Heterogeneity of findings may be explained by gene-environment interactions (GxE), as it has been suggested that S-allele carriers are more reactive to psychosocial stress than L-allele homozygotes. This study aimed to investigate whether 5-HTTLPR genotype moderates the effects of stress on ADHD in a multisite prospective ADHD cohort study. 5-HTTLPR genotype, as well as the number of stressful life events in the past 5 years and ongoing long-term difficulties, was determined in 671 adolescents and young adults with ADHD, their siblings, and healthy controls (57.4% male, average age 17.3 years). Linear mixed models, accounting for family relatedness, were applied to investigate the effects of genotype, experienced stress, and their interaction on ADHD severity at time point T2, while controlling for ADHD severity at T1 (mean follow-up time 5.9 years) and for comorbid internalizing problems at T2. The interaction between genotype and stress significantly predicted ADHD severity at T2 (p = .006), which was driven by the effect on hyperactivity-impulsivity (p = .004). Probing of the interaction effect made clear that S-allele carriers had a significantly more positive correlation between stress and ADHD severity than L-allele homozygotes. The results show that the interaction between 5-HTTLPR and stress is a mechanism involved particularly in the hyperactivity/impulsivity dimension of ADHD, and that this is independent of comorbid internalizing problems. Further research into the neurobiological mechanisms underlying this interaction effect is warranted. © 2014 The Authors. Journal of Child Psychology and Psychiatry. © 2014 Association for Child and Adolescent Mental Health.

Relations between three dopaminergic system genes, school attachment, and adolescent delinquency.

PubMed

Fine, Adam; Mahler, Alissa; Simmons, Cortney; Chen, Chuansheng; Moyzis, Robert; Cauffman, Elizabeth

2016-11-01

Both environmental factors and genetic variation, particularly in genes responsible for the dopaminergic system such as DRD4, DRD2, and DAT1 (SLC6A3), affect adolescent delinquency. The school context, despite its developmental importance, has been overlooked in gene-environment research. Using data from the National Institute of Child Health and Human Development Study of Early Child Care and Youth Development (NICHD ECCYD), this study examined key interactions between school attachment and (a) each of the DRD4, DRD2, and DAT1 (SLC6A3) genotypes; and (b) a polygenic score. Results indicate that there is a main effect of school attachment, unlike genetic variation, on delinquency. Interestingly, there are important interactive effects of school attachment and dopaminergic genotypes on delinquency. Carriers of the DRD2-A1 allele were differentially affected by both positive and negative school environments, whereas DAT1-10R carriers fared the same as 9R homozygotes in poorer and moderate school environments, but fared disproportionately better in more positive environments. Contrary to expectations, youth without the DRD4-7R allele were particularly affected by the school environment. These findings contribute to the literature considering the roles of both context and genes in delinquency research, and inform our understanding of the individual-level traits that influence sensitivity to particular contexts. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Interaction of CD38 Variant and Chronic Interpersonal Stress Prospectively Predicts Social Anxiety and Depression Symptoms Over Six Years

PubMed Central

Tabak, Benjamin A.; Vrshek-Schallhorn, Suzanne; Zinbarg, Richard E.; Prenoveau, Jason M.; Mineka, Susan; Redei, Eva E.; Adam, Emma K.; Craske, Michelle G.

2015-01-01

Variation in the CD38 gene, which regulates secretion of the neuropeptide oxytocin, has been associated with several social phenotypes. Specifically, rs3796863 A allele carriers have demonstrated increased social sensitivity. In 400 older adolescents, we used trait-state-occasion modeling to investigate how rs3796863 genotype, baseline ratings of chronic interpersonal stress, and their gene-environment (GxE) interaction predicted trait social anxiety and depression symptoms over six years. We found significant GxE effects for CD38 A-carrier genotypes and chronic interpersonal stress at baseline predicting greater social anxiety and depression symptoms. A significant GxE effect of smaller magnitude was also found for C/C genotype and chronic interpersonal stress predicting greater depression; however, this effect was small compared to the main effect of chronic interpersonal stress. Thus, in the context of chronic interpersonal stress, heightened social sensitivity associated with the rs3796863 A allele may prospectively predict risk for social anxiety and (to a lesser extent) depression. PMID:26958455

The trans-generational impact of population density signals on host-parasite interactions.

PubMed

Michel, Jessica; Ebert, Dieter; Hall, Matthew D

2016-11-25

The density of a host population is a key parameter underlying disease transmission, but it also has implications for the expression of disease through its effect on host physiology. In response to higher densities, individuals are predicted to either increase their immune investment in response to the elevated risk of parasitism, or conversely to decrease their immune capacity as a consequence of the stress of a crowded environment. However, an individual's health is shaped by many different factors, including their genetic background, current environmental conditions, and maternal effects. Indeed, population density is often sensed through the presence of info-chemicals in the environment, which may influence a host's interaction with parasites, and also those of its offspring. All of which may alter the expression of disease, and potentially uncouple the presumed link between changes in host density and disease outcomes. In this study, we used the water flea Daphnia magna and its obligate bacterial parasite Pasteuria ramosa, to investigate how signals of high host density impact on host-parasite interactions over two consecutive generations. We found that the chemical signals from crowded treatments induced phenotypic changes in both the parental and offspring generations. In the absence of a pathogen, life-history changes were genotype-specific, but consistent across generations, even when the signal of density was removed. In contrast, the influence of density on infected animals depended on the trait and generation of exposure. When directly exposed to signals of high-density, host genotypes responded differently in how they minimised the severity of disease. Yet, in the subsequent generation, the influence of density was rarely genotype-specific and instead related to ability of the host to minimise the onset of infection. Our findings reveal that population level correlations between host density and infection capture only part of the complex relationship between crowding and the severity of disease. We suggest that besides its role in horizontal transmission, signals of density can influence parasite epidemiology by modifying mechanisms of resistance across multiple generations, and elevating variability via genotype-by-environment interactions. Our results help resolve why some studies are able to find a positive correlation between high density and resistance, while others uncover a negative correlation, or even no direct relationship at all.

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

Genotype, environment, seeding rate, and top-dressed nitrogen effects on end-use quality of modern Nebraska winter wheat.

PubMed

Bhatta, Madhav; Regassa, Teshome; Rose, Devin J; Baenziger, P Stephen; Eskridge, Kent M; Santra, Dipak K; Poudel, Rachana

2017-12-01

Fine-tuning production inputs such as seeding rate, nitrogen (N), and genotype may improve end-use quality of hard red winter wheat (Triticum aestivium L.) when growing conditions are unpredictable. Studies were conducted at the Agronomy Research Farm (ARF; Lincoln, NE, USA) and the High Plains Agricultural Laboratory (HPAL; Sidney, NE, USA) in 2014 and 2015 in Nebraska, USA, to determine the effects of genotype (6), environment (4), seeding rate (3), and flag leaf top-dressed N (0 and 34 kg N ha -1 ) on the end-use quality of winter wheat. End-use quality traits were influenced by environment, genotype, seeding rate, top-dressed N, and their interactions. Mixograph parameters had a strong correlation with grain volume weight and flour yield. Doubling the recommended seeding rate and N at the flag leaf stage increased grain protein content by 8.1% in 2014 and 1.5% in 2015 at ARF and 4.2% in 2014 and 8.4% in 2015 at HPAL. The key finding of this research is that increasing seeding rates up to double the current recommendations with N at the flag leaf stage improved most of the end-use quality traits. This will have a significant effect on the premium for protein a farmer could receive when marketing wheat. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Lead in rice: analysis of baseline lead levels in market and field collected rice grains.

PubMed

Norton, Gareth J; Williams, Paul N; Adomako, Eureka E; Price, Adam H; Zhu, Yongguan; Zhao, Fang-Jie; McGrath, Steve; Deacon, Claire M; Villada, Antia; Sommella, Alessia; Lu, Ying; Ming, Lei; De Silva, P Mangala C S; Brammer, Hugh; Dasgupta, Tapash; Islam, M Rafiqul; Meharg, Andrew A

2014-07-01

In a large scale survey of rice grains from markets (13 countries) and fields (6 countries), a total of 1578 rice grain samples were analysed for lead. From the market collected samples, only 0.6% of the samples exceeded the Chinese and EU limit of 0.2 μg g(-1) lead in rice (when excluding samples collected from known contaminated/mine impacted regions). When evaluating the rice grain samples against the Food and Drug Administration's (FDA) provisional total tolerable intake (PTTI) values for children and pregnant women, it was found that only people consuming large quantities of rice were at risk of exceeding the PTTI from rice alone. Furthermore, 6 field experiments were conducted to evaluate the proportion of the variation in lead concentration in rice grains due to genetics. A total of 4 of the 6 field experiments had significant differences between genotypes, but when the genotypes common across all six field sites were assessed, only 4% of the variation was explained by genotype, with 9.5% and 11% of the variation explained by the environment and genotype by environment interaction respectively. Further work is needed to identify the sources of lead contamination in rice, with detailed information obtained on the locations and environments where the rice is sampled, so that specific risk assessments can be performed. Copyright © 2014 Elsevier B.V. All rights reserved.

Investigation of genotype x environment interactions for weaning weight for Herefords in three countries.

PubMed

de Mattos, D; Bertrand, J K; Misztal, I

2000-08-01

The objective of this study was to investigate the possibility of genotype x environment interactions for weaning weight (WWT) between different regions of the United States (US) and between Canada (CA), Uruguay (UY), and US for populations of Hereford cattle. Original data were composed of 487,661, 102,986, and 2,322,722 edited weaning weight records from CA, UY, and US, respectively. A total of 359 sires were identified as having progeny across all three countries; 240 of them had at least one progeny with a record in each environment. The data sets within each country were reduced by retaining records from herds with more than 500 WWT records, with an average contemporary group size of greater than nine animals, and that contained WWT records from progeny or maternal grand-progeny of the across-country sires. Data sets within each country were further reduced by randomly selecting among remaining herds. Four regions within US were defined: Upper Plains (UP), Cornbelt (CB), South (S), and Gulf Coast (GC). Similar sampling criteria and common international sires were used to form the within-US regional data sets. A pairwise analysis was done between countries and regions within US (UP-CB vs S-GC, UP vs CB, and S vs GC) for the estimation of (co)variance components and genetic correlation between environments. An accelerated EM-REML algorithm and a multiple-trait animal model that considered WWT as a different trait in each environment were used to estimate parameters in each pairwise analysis. Direct and maternal (in parentheses) estimated genetic correlations for CA vs UY, CA vs US, US vs UY, UP-CB vs S-GC, UP vs CB, and S vs GC were .88 (.84), .86 (.82), .90 (.85), .88 (.87), .88 (.84), and .87 (.85), respectively. The general absence of genotype x country interactions observed in this study, together with a prior study that showed the similarity of genetic and environmental parameters across the three countries, strongly indicates that a joint WWT genetic evaluation for Hereford cattle could be conducted using a model that treated the information from CA, UY, and US as a single population using single population-wide genetic parameters.

Genotype by environment interaction effects of propagation and defoliation on meadow bromegrass

USDA-ARS?s Scientific Manuscript database

Sixty-three meadow bromegrass (Bromus riparius Rehm.) half-sib families were evaluated over two years at Millville, UT location for biomass production and nutritive value. Families were evaluated under either space-plant or sward conditions combined with either grazed or cut management. The objectiv...

A First Life with Computerized Business Simulations

ERIC Educational Resources Information Center

Thavikulwat, Precha

2011-01-01

The author discusses the theoretical lens, origins, and environment of his work on computerized business simulations. Key ideas that inform his work include the two dimensions (control and interaction) of computerized simulation, the two ways of representing a natural process (phenotypical and genotypical) in a simulation, which he defines as a…

Simulation of genotype-by-environment interactions on irrigated soybean yields in the U.S. Midsouth

USDA-ARS?s Scientific Manuscript database

Dynamic crop models that incorporate the effect of environmental variables can potentially explain yield differences associated with location, year, planting date, and cultivars with different growing cycles. Soybean (Glycine max (L.) Mer.) cultivar coefficients for the DSSAT-CROPGRO model were cali...

QTL and drought effects on leaf physiology in lowland Panicum virgatum

USDA-ARS?s Scientific Manuscript database

Switchgrass is a key component of plans to develop sustainable cellulosic ethanol production for bioenergy in the U.S. We sought quantitative trait loci (QTL) for leaf structure and function, and tested for genotype × environment interactions in response to drought using the Albany full-sib mapping...

Genotypes Do Not Confer Risk For Delinquency ut Rather Alter Susceptibility to Positive and Negative Environmental Factors: Gene-Environment Interactions of BDNF Val66Met, 5-HTTLPR, and MAOA-uVNTR

PubMed Central

Comasco, Erika; Hodgins, Sheilagh; Oreland, Lars; Åslund, Cecilia

2015-01-01

Background: Previous evidence of gene-by-environment interactions associated with emotional and behavioral disorders is contradictory. Differences in findings may result from variation in valence and dose of the environmental factor, and/or failure to take account of gene-by-gene interactions. The present study investigated interactions between the brain-derived neurotrophic factor gene (BDNF Val66Met), the serotonin transporter gene-linked polymorphic region (5-HTTLPR), the monoamine oxidase A (MAOA-uVNTR) polymorphisms, family conflict, sexual abuse, the quality of the child-parent relationship, and teenage delinquency. Methods: In 2006, as part of the Survey of Adolescent Life in Västmanland, Sweden, 1 337 high-school students, aged 17–18 years, anonymously completed questionnaires and provided saliva samples for DNA analyses. Results: Teenage delinquency was associated with two-, three-, and four-way interactions of each of the genotypes and the three environmental factors. Significant four-way interactions were found for BDNF Val66Met × 5-HTTLPR×MAOA-uVNTR × family conflicts and for BDNF Val66Met × 5-HTTLPR×MAOA-uVNTR × sexual abuse. Further, the two genotype combinations that differed the most in expression levels (BDNF Val66Met Val, 5-HTTLPR LL, MAOA-uVNTR LL [girls] and L [boys] vs BDNF Val66Met Val/Met, 5-HTTLPR S/LS, MAOA-uVNTR S/SS/LS) in interaction with family conflict and sexual abuse were associated with the highest delinquency scores. The genetic variants previously shown to confer vulnerability for delinquency (BDNF Val66Met Val/Met × 5-HTTLPR S × MAOA-uVNTR S) were associated with the lowest delinquency scores in interaction with a positive child-parent relationship. Conclusions: Functional variants of the MAOA-uVNTR, 5-HTTLPR, and BDNF Val66Met, either alone or in interaction with each other, may be best conceptualized as modifying sensitivity to environmental factors that confer either risk or protection for teenage delinquency. PMID:25522433

Factors that cause genotype by environment interaction and use of a multiple-trait herd-cluster model for milk yield of Holstein cattle from Brazil and Colombia.

PubMed

Cerón-Muñoz, M F; Tonhati, H; Costa, C N; Rojas-Sarmiento, D; Echeverri Echeverri, D M

2004-08-01

Descriptive herd variables (DVHE) were used to explain genotype by environment interactions (G x E) for milk yield (MY) in Brazilian and Colombian production environments and to develop a herd-cluster model to estimate covariance components and genetic parameters for each herd environment group. Data consisted of 180,522 lactation records of 94,558 Holstein cows from 937 Brazilian and 400 Colombian herds. Herds in both countries were jointly grouped in thirds according to 8 DVHE: production level, phenotypic variability, age at first calving, calving interval, percentage of imported semen, lactation length, and herd size. For each DVHE, REML bivariate animal model analyses were used to estimate genetic correlations for MY between upper and lower thirds of the data. Based on estimates of genetic correlations, weights were assigned to each DVHE to group herds in a cluster analysis using the FASTCLUS procedure in SAS. Three clusters were defined, and genetic and residual variance components were heterogeneous among herd clusters. Estimates of heritability in clusters 1 and 3 were 0.28 and 0.29, respectively, but the estimate was larger (0.39) in Cluster 2. The genetic correlations of MY from different clusters ranged from 0.89 to 0.97. The herd-cluster model based on DVHE properly takes into account G x E by grouping similar environments accordingly and seems to be an alternative to simply considering country borders to distinguish between environments.

A latent modeling approach to genotype–phenotype relationships: maternal problem behavior clusters, prenatal smoking, and MAOA genotype

PubMed Central

Mustanski, B.; Metzger, A.; Pine, D. S.; Kistner-Griffin, E.; Cook, E.; Wakschlag, L. S.

2013-01-01

This study illustrates the application of a latent modeling approach to genotype–phenotype relationships and gene×environment interactions, using a novel, multidimensional model of adult female problem behavior, including maternal prenatal smoking. The gene of interest is the mono-amine oxidase A (MAOA) gene which has been well studied in relation to antisocial behavior. Participants were adult women (N=192) who were sampled from a prospective pregnancy cohort of non-Hispanic, white individuals recruited from a neighborhood health clinic. Structural equation modeling was used to model a female problem behavior phenotype, which included conduct problems, substance use, impulsive-sensation seeking, interpersonal aggression, and prenatal smoking. All of the female problem behavior dimensions clustered together strongly, with the exception of prenatal smoking. A main effect of MAOA genotype and a MAOA× physical maltreatment interaction were detected with the Conduct Problems factor. Our phenotypic model showed that prenatal smoking is not simply a marker of other maternal problem behaviors. The risk variant in the MAOA main effect and interaction analyses was the high activity MAOA genotype, which is discrepant from consensus findings in male samples. This result contributes to an emerging literature on sex-specific interaction effects for MAOA. PMID:22610759

Mitigating aggressiveness through education? The monoamine oxidase A genotype and mental health in general population.

PubMed

Kiive, Evelyn; Laas, Kariina; Akkermann, Kirsti; Comasco, Erika; Oreland, Lars; Veidebaum, Toomas; Harro, Jaanus

2014-02-01

Monoamine oxidase A (MAOA) gene promoter region includes a variable number of tandem repeat (VNTR) associated with antisocial behaviour in adverse environment. We have examined the effect of the MAOA-uVNTR on mental health and academic success by using a population representative sample and a longitudinal design. The data of the older cohort (n = 593, aged 15 years at the original sampling) of the longitudinal Estonian Children Personality, Behaviour and Health Study (ECPBHS) were used. Follow-ups were conducted at ages 18 and 25 years. Aggressiveness, inattention and hyperactivity were reported by class teachers or, at older age, self-reported. Stressful life events, psychological environment in the family and interactions between family members were self-reported. Data of general mental abilities and education were obtained at the age of 25, and lifetime psychiatric disorder assessment was carried out with the Mini-International Neuropsychiatric Interview (MINI) interview. MAOA-uVNTR genotype had no independent effect on aggressiveness, hyperactive and inattentive symptoms, and neither was there a genotype interaction with adverse life events. Interestingly, the proportion of male subjects with higher education by the age of 25 was significantly larger among those with MAOA low-activity alleles (χ² = 7.13; p = 0.008). Logistic regression revealed that MAOA low-activity alleles, higher mental abilities, occurrence of anxiety disorders and absence of substance-use disorder were significant independent predictors for higher education in male subjects. In a population representative sample of young subjects, the MAOA-uVNTR 'risk genotype' predicted better life outcomes as expressed in higher level of education.

A structuralist theory of evolution reconsidered.

PubMed

van der Hammen, L

1997-01-01

The structuralist theory of evolution is reconsidered in the light of new discoveries. According to this theory, the evolutionary potentialities are in the genotype (a hierarchically ordered set of interacting elements) and manifest themselves in the course of morphogenesis in association with changes in the environment. It is demonstrated that this theory is in fact the development of a long philosophical tradition, in which Darwin and Neo-Darwinism did not participate. New discoveries in the field of molecular cytogenetics confirm the ideas of evolutionary potentiality and hierarchical genotypic ordering. It is demonstrated that gene regulation can manifest itself in association with instabilities of the morphogenetic field and the attainment of a new equilibrium; this change could be connected with changes in the environment, but has nothing to do with natural selection.

The effect of myostatin genotype on body temperature during extreme temperature events.

PubMed

Howard, J T; Kachman, S D; Nielsen, M K; Mader, T L; Spangler, M L

2013-07-01

Extreme heat and cold events can create deleterious physiological changes in cattle as they attempt to cope. The genetic background of animals can influence their response to these events. The objective of the current study was to determine the impact of myostatin genotype (MG) on body temperature during periods of heat and cold stress. Two groups of crossbred steers and heifers of unknown pedigree and breed fraction with varying percentages of Angus, Simmental, and Piedmontese were placed in a feedlot over 2 summers and 2 winters. Before arrival, animals were genotyped for the Piedmontese-derived myostatin mutation (C313Y) to determine their MG as either homozygous normal (0 copy; n = 84), heterozygous (1 copy; n = 96), or homozygous for inactive myostatin (2 copy; n = 59). Hourly tympanic and vaginal temperature measurements were collected for steers and heifers, respectively, for 5 d during times of anticipated heat and cold stress. Mean (±SD) ambient temperature for summer and winter stress events were 24.4 (±4.64) and -1.80 (±11.71), respectively. A trigonometric function (sine + cosine) with periods of 12 and 24 h was used to describe the diurnal cyclical pattern. Hourly body temperature was analyzed within a season, and fixed effects included MG, group, trigonometric functions nested within group, and interaction of MG with trigonometric functions nested within group; random effects were animal and residual (Model [I]). A combined analysis of season and group was also investigated with the inclusion of season as a main effect and the nesting of effects within both group and season (Model [C]). In both models, the residual was fitted using an autoregressive covariance structure. A 3-way interaction of MG, season, and trigonometric function periodicities of 24 h (P < 0.001) and 12 h (P < 0.02) for Model [C] indicate that a genotype × environment interaction exists for MG. For MG during summer stress events the additive estimate was 0.10°C (P < 0.01) and dominance estimate was -0.12°C (P < 0.001). During winter stress events the additive estimate was 0.10°C (P < 0.001) and dominance estimate was 0.054°C (P > 0.05). The current study illustrated that a genotype × environment interaction exists for MG and 1-copy animals were more robust to environmental extremes in comparison with 0- or 2-copy animals.

A Variational Bayes Genomic-Enabled Prediction Model with Genotype × Environment Interaction

PubMed Central

Montesinos-López, Osval A.; Montesinos-López, Abelardo; Crossa, José; Montesinos-López, José Cricelio; Luna-Vázquez, Francisco Javier; Salinas-Ruiz, Josafhat; Herrera-Morales, José R.; Buenrostro-Mariscal, Raymundo

2017-01-01

There are Bayesian and non-Bayesian genomic models that take into account G×E interactions. However, the computational cost of implementing Bayesian models is high, and becomes almost impossible when the number of genotypes, environments, and traits is very large, while, in non-Bayesian models, there are often important and unsolved convergence problems. The variational Bayes method is popular in machine learning, and, by approximating the probability distributions through optimization, it tends to be faster than Markov Chain Monte Carlo methods. For this reason, in this paper, we propose a new genomic variational Bayes version of the Bayesian genomic model with G×E using half-t priors on each standard deviation (SD) term to guarantee highly noninformative and posterior inferences that are not sensitive to the choice of hyper-parameters. We show the complete theoretical derivation of the full conditional and the variational posterior distributions, and their implementations. We used eight experimental genomic maize and wheat data sets to illustrate the new proposed variational Bayes approximation, and compared its predictions and implementation time with a standard Bayesian genomic model with G×E. Results indicated that prediction accuracies are slightly higher in the standard Bayesian model with G×E than in its variational counterpart, but, in terms of computation time, the variational Bayes genomic model with G×E is, in general, 10 times faster than the conventional Bayesian genomic model with G×E. For this reason, the proposed model may be a useful tool for researchers who need to predict and select genotypes in several environments. PMID:28391241

A Variational Bayes Genomic-Enabled Prediction Model with Genotype × Environment Interaction.

PubMed

Montesinos-López, Osval A; Montesinos-López, Abelardo; Crossa, José; Montesinos-López, José Cricelio; Luna-Vázquez, Francisco Javier; Salinas-Ruiz, Josafhat; Herrera-Morales, José R; Buenrostro-Mariscal, Raymundo

2017-06-07

There are Bayesian and non-Bayesian genomic models that take into account G×E interactions. However, the computational cost of implementing Bayesian models is high, and becomes almost impossible when the number of genotypes, environments, and traits is very large, while, in non-Bayesian models, there are often important and unsolved convergence problems. The variational Bayes method is popular in machine learning, and, by approximating the probability distributions through optimization, it tends to be faster than Markov Chain Monte Carlo methods. For this reason, in this paper, we propose a new genomic variational Bayes version of the Bayesian genomic model with G×E using half-t priors on each standard deviation (SD) term to guarantee highly noninformative and posterior inferences that are not sensitive to the choice of hyper-parameters. We show the complete theoretical derivation of the full conditional and the variational posterior distributions, and their implementations. We used eight experimental genomic maize and wheat data sets to illustrate the new proposed variational Bayes approximation, and compared its predictions and implementation time with a standard Bayesian genomic model with G×E. Results indicated that prediction accuracies are slightly higher in the standard Bayesian model with G×E than in its variational counterpart, but, in terms of computation time, the variational Bayes genomic model with G×E is, in general, 10 times faster than the conventional Bayesian genomic model with G×E. For this reason, the proposed model may be a useful tool for researchers who need to predict and select genotypes in several environments. Copyright © 2017 Montesinos-López et al.

Dopamine receptor D2 (DRD2), dopamine transporter solute carrier family C6, member 4 (SLC6A3), and catechol-O-methyltransferase (COMT) genes as moderators of the relation between maternal history of maltreatment and infant emotion regulation.

PubMed

Villani, Vanessa; Ludmer, Jaclyn; Gonzalez, Andrea; Levitan, Robert; Kennedy, James; Masellis, Mario; Basile, Vincenzo S; Wekerle, Christine; Atkinson, Leslie

2018-05-01

Although infants less than 18 months old are capable of engaging in self-regulatory behavior (e.g., avoidance, withdrawal, and orienting to other aspects of their environment), the use of self-regulatory strategies at this age (as opposed to relying on caregivers) is associated with elevated behavioral and physiological distress. This study investigated infant dopamine-related genotypes (dopamine receptor D2 [DRD2], dopamine transporter solute carrier family C6, member 4 [SLC6A3], and catechol-O-methyltransferase [COMT]) as they interact with maternal self-reported history of maltreatment to predict observed infant independent emotion regulation behavior. A community sample (N = 193) of mother-infant dyads participated in a toy frustration challenge at infant age 15 months, and infant emotion regulation behavior was coded. Buccal cells were collected for genotyping. Maternal maltreatment history significantly interacted with infant SLC6A3 and COMT genotypes, such that infants with more 10-repeat and valine alleles of SLC6A3 and COMT, respectively, relative to infants with fewer or no 10-repeat and valine alleles, utilized more independent (i.e., maladaptive) regulatory behavior if mother reported a more extensive maltreatment history, as opposed to less. The findings indicate that child genetic factors moderate the intergenerational impact of maternal maltreatment history. The results are discussed in terms of potential mechanism of Gene × Environment interaction.

Gene-environment interactions linking air pollution and inflammation in Parkinson's disease.

PubMed

Lee, Pei-Chen; Raaschou-Nielsen, Ole; Lill, Christina M; Bertram, Lars; Sinsheimer, Janet S; Hansen, Johnni; Ritz, Beate

2016-11-01

Both air pollution exposure and systemic inflammation have been linked to Parkinson's disease (PD). In the PASIDA study, 408 incident cases of PD diagnosed in 2006-2009 and their 495 population controls were interviewed and provided DNA samples. Markers of long term traffic related air pollution measures were derived from geographic information systems (GIS)-based modeling. Furthermore, we genotyped functional polymorphisms in genes encoding proinflammatory cytokines, namely rs1800629 in TNFα (tumor necrosis factor alpha) and rs16944 in IL1B (interleukin-1β). In logistic regression models, long-term exposure to NO 2 increased PD risk overall (odds ratio (OR)=1.06 per 2.94μg/m 3 increase, 95% CI=1.00-1.13). The OR for PD in individuals with high NO 2 exposure (≧75th percentile) and the AA genotype of IL1B rs16944 was 3.10 (95% CI=1.14-8.38) compared with individuals with lower NO 2 exposure (<75th percentile) and the GG genotype. The interaction term was nominally significant on the multiplicative scale (p=0.01). We did not find significant gene-environment interactions with TNF rs1800629. Our finds may provide suggestive evidence that a combination of traffic-related air pollution and genetic variation in the proinflammatory cytokine gene IL1B contribute to risk of developing PD. However, as statistical evidence was only modest in this large sample we cannot rule out that these results represent a chance finding, and additional replication efforts are warranted. Copyright © 2016 Elsevier Inc. All rights reserved.

Genotype by energy expenditure interaction with metabolic syndrome traits: the Portuguese healthy family study.

PubMed

Santos, Daniel M V; Katzmarzyk, Peter T; Diego, Vincent P; Souza, Michele C; Chaves, Raquel N; Blangero, John; Maia, José A R

2013-01-01

Moderate-to-high levels of physical activity are established as preventive factors in metabolic syndrome development. However, there is variability in the phenotypic expression of metabolic syndrome under distinct physical activity conditions. In the present study we applied a Genotype X Environment interaction method to examine the presence of GxEE interaction in the phenotypic expression of metabolic syndrome. A total of 958 subjects, from 294 families of The Portuguese Healthy Family study, were included in the analysis. Total daily energy expenditure was assessed using a 3 day physical activity diary. Six metabolic syndrome related traits, including waist circumference, systolic blood pressure, glucose, HDL cholesterol, total cholesterol and triglycerides, were measured and adjusted for age and sex. GxEE examination was performed on SOLAR 4.3.1. All metabolic syndrome indicators were significantly heritable. The GxEE interaction model fitted the data better than the polygenic model (p<0.001) for waist circumference, systolic blood pressure, glucose, total cholesterol and triglycerides. For waist circumference, glucose, total cholesterol and triglycerides, the significant GxEE interaction was due to rejection of the variance homogeneity hypothesis. For waist circumference and glucose, GxEE was also significant by the rejection of the genetic correlation hypothesis. The results showed that metabolic syndrome traits expression is significantly influenced by the interaction established between total daily energy expenditure and genotypes. Physical activity may be considered an environmental variable that promotes metabolic differences between individuals that are distinctively active.

Early establishment response of different Pinus nigra ssp. salzmanii seed sources on contrasting environments: Implications for future reforestation programs and assisted population migration.

PubMed

Taïbi, K; del Campo, A D; Aguado, A; Mulet, J M

2016-04-15

Forest restoration constitutes an important issue within adaptive environmental management for climate change at global scale. However, effective implementation of these programs can only be achieved by revising current seed transfer guidelines, as they lack inherent spatial and temporal dynamics associated with climate change. In this sense, provenance trials may provide key information on the relative performance of different populations and/or genotypes under changing ecological conditions. This study addresses a methodological approach to evaluate early plantation performance and the consequent phenotypic plasticity and the pattern of the adaptation of different seed sources in contrasting environments. To this end, six seed sources of Salzmann pine were tested at three contrasting trial sites testing a hypothetical assisted population migration. Adaptation at each site was assessed through Joint Regression and Additive Main effect and Multiplication Interaction (AMMI) models. Most of the observed variation was attributed to the environment (above 90% for all traits), even so genotype and genotype by environment interaction (GxE) were significant. Seedlings out-planted under better site conditions did not differ in survival but in height growth. However, on sites with higher constraints, survival differed among seed sources and diameter growth was high. The adaptation analyses (AMMI) indicated that the cold-continental seed source 'Soria' performed as a generalist seed source, whereas 'Cordilleras Béticas', the southernmost seed source, was more adapted to harsh environments (frost and drought) in terms of survival. The results supported partially the hypothesis that assisted migration of seed sources makes sense within limited transfer distances, and this was reinforced by the GxE results. The present study could be valuable to address adaptive transfer of seedings in ecological restoration and to determine the suitable seed sources for reforestation programs and assisted population migration under climatic changes. The reported results are based on 3 years' data and need to be considered in this context. Copyright © 2016 Elsevier Ltd. All rights reserved.

MAOA genotype, social exclusion and aggression: an experimental test of a gene-environment interaction.

PubMed

Gallardo-Pujol, D; Andrés-Pueyo, A; Maydeu-Olivares, A

2013-02-01

In 2002, Caspi and colleagues provided the first epidemiological evidence that genotype may moderate individuals' responses to environmental determinants. However, in a correlational study great care must be taken to ensure the proper estimation of the causal relationship. Here, a randomized experiment was performed to test the hypothesis that the MAOA gene promoter polymorphism (MAOA-LPR) interacts with environmental adversity in determining aggressive behavior using laboratory analogs of real-life conditions. A sample of 57 Caucasian male students of Catalan and Spanish origin was recruited at the University of Barcelona. Ostracism, or social exclusion, was induced as environmental adversity using the Cyberball software. Laboratory aggression was assessed with the Point Subtraction Aggression Paradigm (PSAP), which was used as an analog of antisocial behavior. We also measured aggressiveness by means of the reduced version of the Aggression Questionnaire. The MAOA-LPR polymorphism showed a significant effect on the number of aggressive responses in the PSAP (F(1,53) = 4.63, P = 0.03, partial η(2) = 0.08), as well as social exclusion (F(1,53) = 8.03, P = 0.01, partial η(2) = 0.13). Most notably, however, we found that the MAOA-LPR polymorphism interacts significantly with social exclusion in order to provoke aggressive behavior (F(1,53) = 4.42, P = 0.04, partial η(2) = 0.08), remarkably, the low-activity allele of the MAOA-LPR polymorphism carriers in the ostracized group show significantly higher aggression scores than the rest. Our results support the notion that gene-environment interactions can be successfully reproduced within a laboratory using analogs and an appropriate design. We provide guidelines to test gene-environment interactions hypotheses under controlled, experimental settings. © 2012 The Authors. Genes, Brain and Behavior © 2012 Blackwell Publishing Ltd and International Behavioural and Neural Genetics Society.

Selection of common bean genotypes for the Cerrado/Pantanal ecotone via mixed models and multivariate analysis.

PubMed

Corrêa, A M; Pereira, M I S; de Abreu, H K A; Sharon, T; de Melo, C L P; Ito, M A; Teodoro, P E; Bhering, L L

2016-10-17

The common bean, Phaseolus vulgaris, is predominantly grown on small farms and lacks accurate genotype recommendations for specific micro-regions in Brazil. This contributes to a low national average yield. The aim of this study was to use the methods of the harmonic mean of the relative performance of genetic values (HMRPGV) and the centroid, for selecting common bean genotypes with high yield, adaptability, and stability for the Cerrado/Pantanal ecotone region in Brazil. We evaluated 11 common bean genotypes in three trials carried out in the dry season in Aquidauana in 2013, 2014, and 2015. A likelihood ratio test detected a significant interaction between genotype x year, contributing 54% to the total phenotypic variation in grain yield. The three genotypes selected by the joint analysis of genotypic values in all years (Carioca Precoce, BRS Notável, and CNFC 15875) were the same as those recommended by the HMRPGV method. Using the centroid method, genotypes BRS Notável and CNFC 15875 were considered ideal genotypes based on their high stability to unfavorable environments and high responsiveness to environmental improvement. We identified a high association between the methods of adaptability and stability used in this study. However, the use of centroid method provided a more accurate and precise recommendation of the behavior of the evaluated genotypes.

Infant Pathways to Externalizing Behavior: Evidence of Genotype x Environment Interaction

ERIC Educational Resources Information Center

Leve, Leslie D.; Kerr, David C. R.; Shaw, Daniel; Ge, Xiaojia; Neiderhiser, Jenae M.; Scaramella, Laura V.; Reid, John B.; Conger, Rand; Reiss, David

2010-01-01

To further the understanding of the effects of early experiences, 9-month-old infants were observed during a frustration task. The analytical sample was composed of 348 linked triads of participants (adoptive parents, adopted child, and birth parent[s]) from a prospective adoption study. It was hypothesized that genetic risk for externalizing…

Genotype x shade effects for western hemlock.

Treesearch

G.R. Johnson; C. Cartwright

2005-01-01

Western hemlock (Tsuga heterophylla (Raf.) Sarg.) families were grown under different levels of shade for 2 or 3 years at two nursery sites to determine whether families performed differently relative to one another in the different shade environments. Differences were found both for levels of shade and families, but no family x shade interaction...

Toward understanding genotype x environment interactions in black raspberry (Rubus occidentalis L.)

USDA-ARS?s Scientific Manuscript database

Over the last 75 years, the black raspberry industry in the United States has undergone a slow but steady contraction because of a lack of adapted, disease resistant cultivars. Recent research about the health benefits of a diet rich in polyphenolics, and black raspberries in particular, has led to ...

Reliability of measurement and genotype x environment 1 interaction for potato specific gravity

USDA-ARS?s Scientific Manuscript database

The dry matter content of potatoes used to make potato chips and French fries strongly influences fry oil absorption and texture of the finished product. Specific gravity (SpGr) is often used to assess the processing quality of potatoes tubers because of its strong correlation with dry matter conten...

Genotype by Environment Interactions in Cognitive Ability: A Survey of 14 Studies from 4 Countries covering 4 Age Groups

PubMed Central

Molenaar, Dylan; van der Sluis, Sophie; Boomsma, Dorret I.; Haworth, Claire M. A.; Hewitt, John K.; Martin, Nicholas G.; Plomin, Robert; Wright, Margie J.; Dolan, Conor V.

2014-01-01

A large part of the variation in cognitive ability is known to be due to genetic factors. Researchers have tried to identify modifiers that influence the heritability of cognitive ability, indicating a genotype by environment interaction (GxE). To date, such modifiers include measured variables like income and socioeconomic status. The present paper focuses on GxE in cognitive ability where the environmental variable is an unmeasured environmental factor that is uncorrelated in family members. We examined this type of GxE in the GHCA-database (Haworth et al., 2009), which comprises data of 14 different cognition studies from 4 different countries including participants of different ages. Results indicate that for younger participants (4–13 years), the strength of E decreases across the additive genetic factor A, but that this effect reverts for older participants (17–34 years). However, a clear and general conclusion about the presence of a genuine GxE is hampered by differences between the individual studies with respect to environmental and genetic influences on cognitive ability. PMID:23397253

Welcome to the neighbourhood: interspecific genotype by genotype interactions in Solidago influence above- and belowground biomass and associated communities.

PubMed

Genung, Mark A; Bailey, Joseph K; Schweitzer, Jennifer A

2012-01-01

Intra- and interspecific plant-plant interactions are fundamental to patterns of community assembly and to the mixture effects observed in biodiversity studies. Although much research has been conducted at the species level, very little is understood about how genetic variation within and among interacting species may drive these processes. Using clones of both Solidago altissima and Solidago gigantea, we found that genotypic variation in a plant's neighbours affected both above- and belowground plant traits, and that genotype by genotype interactions between neighbouring plants impacted associated pollinator communities. The traits for which focal plant genotypic variation explained the most variation varied by plant species, whereas neighbour genotypic variation explained the most variation in coarse root biomass. Our results provide new insight into genotypic and species diversity effects in plant-neighbour interactions, the extended consequences of diversity effects, and the potential for evolution in response to competitive or to facilitative plant-neighbour interactions. © 2011 Blackwell Publishing Ltd/CNRS.

Plasticity in Vegetative Growth over Contrasted Growing Sites of an F1 Olive Tree Progeny during Its Juvenile Phase.

PubMed

Ben Sadok, Inès; Martinez, Sebastien; Moutier, Nathalie; Garcia, Gilbert; Leon, Lorenzo; Belaj, Angelina; De La Rosa, Raúl; Khadari, Bouchaib; Costes, Evelyne

2015-01-01

Climatic changes impact fruit tree growth and severely limit their production. Investigating the tree ability to cope with environmental variations is thus necessary to adapt breeding and management strategies in order to ensure sustainable production. In this study, we assessed the genetic parameters and genotype by environment interaction (GxE) during the early tree growth. One hundred and twenty olive seedlings derived from the cross 'Olivière' x 'Arbequina' were examined across two sites with contrasted environments, accounting for ontogenetic trends over three years. Models including the year of growth, branching order, environment, genotype effects, and their interactions were built with variance function and covariance structure of residuals when necessary. After selection of a model, broad sense heritabilities were estimated. Despite strong environmental effect on most traits, no GxE was found. Moreover, the internal structure of traits co-variation was similar in both sites. Ontogenetic growth variation, related to (i) the overall tree form and (ii) the growth and branching habit at growth unit scale, was not altered by the environment. Finally, a moderate to strong genetic control was identified for traits at the whole tree scale and at internode scale. Among all studied traits, the maximal internode length exhibited the highest heritability (H2 = 0.74). Considering the determinant role of this trait in tree architecture and its stability across environments, this study consolidates its relevance for breeding.

Plasticity in Vegetative Growth over Contrasted Growing Sites of an F1 Olive Tree Progeny during Its Juvenile Phase

PubMed Central

Ben Sadok, Inès; Martinez, Sebastien; Moutier, Nathalie; Garcia, Gilbert; Leon, Lorenzo; Belaj, Angelina; De La Rosa, Raúl; Khadari, Bouchaib; Costes, Evelyne

2015-01-01

Climatic changes impact fruit tree growth and severely limit their production. Investigating the tree ability to cope with environmental variations is thus necessary to adapt breeding and management strategies in order to ensure sustainable production. In this study, we assessed the genetic parameters and genotype by environment interaction (GxE) during the early tree growth. One hundred and twenty olive seedlings derived from the cross ‘Olivière’ x ‘Arbequina’ were examined across two sites with contrasted environments, accounting for ontogenetic trends over three years. Models including the year of growth, branching order, environment, genotype effects, and their interactions were built with variance function and covariance structure of residuals when necessary. After selection of a model, broad sense heritabilities were estimated. Despite strong environmental effect on most traits, no GxE was found. Moreover, the internal structure of traits co-variation was similar in both sites. Ontogenetic growth variation, related to (i) the overall tree form and (ii) the growth and branching habit at growth unit scale, was not altered by the environment. Finally, a moderate to strong genetic control was identified for traits at the whole tree scale and at internode scale. Among all studied traits, the maximal internode length exhibited the highest heritability (H2 = 0.74). Considering the determinant role of this trait in tree architecture and its stability across environments, this study consolidates its relevance for breeding. PMID:26062090

Critical environmental and genotypic factors for Fusarium verticillioides infection, fungal growth and fumonisin contamination in maize grown in northwestern Spain.

PubMed

Cao, Ana; Santiago, Rogelio; Ramos, Antonio J; Souto, Xosé C; Aguín, Olga; Malvar, Rosa Ana; Butrón, Ana

2014-05-02

In northwestern Spain, where weather is rainy and mild throughout the year, Fusarium verticillioides is the most prevalent fungus in kernels and a significant risk of fumonisin contamination has been exposed. In this study, detailed information about environmental and maize genotypic factors affecting F. verticillioides infection, fungal growth and fumonisin content in maize kernels was obtained in order to establish control points to reduce fumonisin contamination. Evaluations were conducted in a total of 36 environments and factorial regression analyses were performed to determine the contribution of each factor to variability among environments, genotypes, and genotype × environment interactions for F. verticillioides infection, fungal growth and fumonisin content. Flowering and kernel drying were the most critical periods throughout the growing season for F. verticillioides infection and fumonisin contamination. Around flowering, wetter and cooler conditions limited F. verticillioides infection and growth, and high temperatures increased fumonisin contents. During kernel drying, increased damaged kernels favored fungal growth, and higher ear damage by corn borers and hard rainfall favored fumonisin accumulation. Later planting dates and especially earlier harvest dates reduced the risk of fumonisin contamination, possibly due to reduced incidence of insects and accumulation of rainfall during the kernel drying period. The use of maize varieties resistant to Sitotroga cerealella, with good husk coverage and non-excessive pericarp thickness could also be useful to reduce fumonisin contamination of maize kernels. Copyright © 2014 Elsevier B.V. All rights reserved.

Genomic-Enabled Prediction in Maize Using Kernel Models with Genotype × Environment Interaction

PubMed Central

Bandeira e Sousa, Massaine; Cuevas, Jaime; de Oliveira Couto, Evellyn Giselly; Pérez-Rodríguez, Paulino; Jarquín, Diego; Fritsche-Neto, Roberto; Burgueño, Juan; Crossa, Jose

2017-01-01

Multi-environment trials are routinely conducted in plant breeding to select candidates for the next selection cycle. In this study, we compare the prediction accuracy of four developed genomic-enabled prediction models: (1) single-environment, main genotypic effect model (SM); (2) multi-environment, main genotypic effects model (MM); (3) multi-environment, single variance G×E deviation model (MDs); and (4) multi-environment, environment-specific variance G×E deviation model (MDe). Each of these four models were fitted using two kernel methods: a linear kernel Genomic Best Linear Unbiased Predictor, GBLUP (GB), and a nonlinear kernel Gaussian kernel (GK). The eight model-method combinations were applied to two extensive Brazilian maize data sets (HEL and USP data sets), having different numbers of maize hybrids evaluated in different environments for grain yield (GY), plant height (PH), and ear height (EH). Results show that the MDe and the MDs models fitted with the Gaussian kernel (MDe-GK, and MDs-GK) had the highest prediction accuracy. For GY in the HEL data set, the increase in prediction accuracy of SM-GK over SM-GB ranged from 9 to 32%. For the MM, MDs, and MDe models, the increase in prediction accuracy of GK over GB ranged from 9 to 49%. For GY in the USP data set, the increase in prediction accuracy of SM-GK over SM-GB ranged from 0 to 7%. For the MM, MDs, and MDe models, the increase in prediction accuracy of GK over GB ranged from 34 to 70%. For traits PH and EH, gains in prediction accuracy of models with GK compared to models with GB were smaller than those achieved in GY. Also, these gains in prediction accuracy decreased when a more difficult prediction problem was studied. PMID:28455415

Genomic-Enabled Prediction in Maize Using Kernel Models with Genotype × Environment Interaction.

PubMed

Bandeira E Sousa, Massaine; Cuevas, Jaime; de Oliveira Couto, Evellyn Giselly; Pérez-Rodríguez, Paulino; Jarquín, Diego; Fritsche-Neto, Roberto; Burgueño, Juan; Crossa, Jose

2017-06-07

Multi-environment trials are routinely conducted in plant breeding to select candidates for the next selection cycle. In this study, we compare the prediction accuracy of four developed genomic-enabled prediction models: (1) single-environment, main genotypic effect model (SM); (2) multi-environment, main genotypic effects model (MM); (3) multi-environment, single variance G×E deviation model (MDs); and (4) multi-environment, environment-specific variance G×E deviation model (MDe). Each of these four models were fitted using two kernel methods: a linear kernel Genomic Best Linear Unbiased Predictor, GBLUP (GB), and a nonlinear kernel Gaussian kernel (GK). The eight model-method combinations were applied to two extensive Brazilian maize data sets (HEL and USP data sets), having different numbers of maize hybrids evaluated in different environments for grain yield (GY), plant height (PH), and ear height (EH). Results show that the MDe and the MDs models fitted with the Gaussian kernel (MDe-GK, and MDs-GK) had the highest prediction accuracy. For GY in the HEL data set, the increase in prediction accuracy of SM-GK over SM-GB ranged from 9 to 32%. For the MM, MDs, and MDe models, the increase in prediction accuracy of GK over GB ranged from 9 to 49%. For GY in the USP data set, the increase in prediction accuracy of SM-GK over SM-GB ranged from 0 to 7%. For the MM, MDs, and MDe models, the increase in prediction accuracy of GK over GB ranged from 34 to 70%. For traits PH and EH, gains in prediction accuracy of models with GK compared to models with GB were smaller than those achieved in GY. Also, these gains in prediction accuracy decreased when a more difficult prediction problem was studied. Copyright © 2017 Bandeira e Sousa et al.

Feasibility for improving phytonutrient content in vegetable crops using conventional breeding strategies: case study with carotenoids and tocopherols in sweet corn and broccoli.

PubMed

Ibrahim, Khalid E; Juvik, John A

2009-06-10

Among vegetables, sweet corn ( Zea mays L.) and broccoli ( Brassica oleracea L. ssp. italica) are important sources of dietary carotenoids and tocopherols. Because medical evidence suggests that carotenoid and tocopherol health-promoting activity acts in a dose-dependent manner, conventional breeding to develop elite sweet corn and broccoli germplasm with enhanced levels of these phytochemicals will potentially promote health among the consuming public. This investigation includes the quantitative analysis of carotenoid and tocopherol contents of 41 corn and 24 broccoli genotypes grown in multiple environments (years and seasons in one location) to partition the variation into genetic, environment, and genotype by environment interaction (GxE) components and measure the phenotypic stability of genotypes for these phytochemicals. The primary carotenoids and tocopherols in corn were lutein and gamma-tocopherol (65 and 73% of total carotenoid and tocopherol, respectively), whereas beta-carotene and alpha-tocopherol were dominant in broccoli (65 and 79% of total carotenoid and tocopherol, respectively). Partitioning of the variance indicated that genetic differences among the genotypes averaged for the primary compounds in corn (lutein, zeaxanthin, and alpha- and gamma-tocopherol) and broccoli (beta-carotene, lutein, and alpha- and gamma-tocopherol) accounted for the largest proportion of the variation (67 and 55% of total phenotypic variation averaged across the phytochemicals in sweet corn and broccoli, respectively). Stability analysis identified several corn (IL451b sh2 and IL2027-8 sh2) and broccoli ('Pirate' and 'Baccus') genotypes with relatively high mean concentrations for the various carotenoids and tocopherols that were comparatively stable across seasons and years. The results of this investigation suggest that sweet corn and broccoli germplasm with enhanced concentrations of carotenoids and tocopherols can be developed using conventional breeding protocols.

Condition-dependence, genotype-by-environment interactions and the lek paradox.

PubMed

Kokko, Hanna; Heubel, Katja

2008-09-01

The lek paradox states that maintaining genetic variation necessary for 'indirect benefit' models of female choice is difficult, and two interrelated solutions have been proposed. 'Genic capture' assumes condition-dependence of sexual traits, while genotype-by-environment interactions (GEIs) offer an additional way to maintain diversity. However, condition-dependence, particularly with GEIs, implies that environmental variation can blur the relationship between male displays and offspring fitness. These issues have been treated separately in the past. Here we combine them in a population genetic model, and show that predictions change not only in magnitude but also in direction when the timing of dispersal between environments relative to the life cycle is changed. GEIs can dramatically improve the evolution of costly female preferences, but also hamper it if much dispersal occurs between the life history stage where condition is determined and mating. This situation also arises if selection or mutation rates are too high. In general, our results highlight that when evaluating any mechanism promoted as a potential resolution of the lek paradox, it is not sufficient to focus on its effects on genetic variation. It also has to be assessed to what extent the proposed mechanism blurs the association between male attractiveness and offspring fitness; the net balance of these two effects can be positive or negative, and often strongly context-dependent.

Condition-dependence, genotype-by-environment interactions and the lek paradox.

PubMed

Kokko, Hanna; Heubel, Katja

2008-02-01

The lek paradox states that maintaining genetic variation necessary for 'indirect benefit' models of female choice is difficult, and two interrelated solutions have been proposed. 'Genic capture' assumes condition-dependence of sexual traits, while genotype-by-environment interactions (GEIs) offer an additional way to maintain diversity. However, condition-dependence, particularly with GEIs, implies that environmental variation can blur the relationship between male displays and offspring fitness. These issues have been treated separately in the past. Here we combine them in a population genetic model, and show that predictions change not only in magnitude but also in direction when the timing of dispersal between environments relative to the life cycle is changed. GEIs can dramatically improve the evolution of costly female preferences, but also hamper it if much dispersal occurs between the life history stage where condition is determined and mating. This situation also arises if selection or mutation rates are too high. In general, our results highlight that when evaluating any mechanism promoted as a potential resolution of the lek paradox, it is not sufficient to focus on its effects on genetic variation. It also has to be assessed to what extent the proposed mechanism blurs the association between male attractiveness and offspring fitness; the net balance of these two effects can be positive or negative, and often strongly context-dependent.

Disentangling the influence of parasite genotype, host genotype and maternal environment on different stages of bacterial infection in Daphnia magna.

PubMed

Hall, Matthew D; Ebert, Dieter

2012-08-22

Individuals naturally vary in the severity of infectious disease when exposed to a parasite. Dissecting this variation into genetic and environmental components can reveal whether or not this variation depends on the host genotype, parasite genotype or a range of environmental conditions. Complicating this task, however, is that the symptoms of disease result from the combined effect of a series of events, from the initial encounter between a host and parasite, through to the activation of the host immune system and the exploitation of host resources. Here, we use the crustacean Daphnia magna and its parasite Pasteuria ramosa to show how disentangling genetic and environmental factors at different stages of infection improves our understanding of the processes shaping infectious disease. Using compatible host-parasite combinations, we experimentally exclude variation in the ability of a parasite to penetrate the host, from measures of parasite clearance, the reduction in host fecundity and the proliferation of the parasite. We show how parasite resistance consists of two components that vary in environmental sensitivity, how the maternal environment influences all measured aspects of the within-host infection process and how host-parasite interactions following the penetration of the parasite into the host have a distinct temporal component.

Disentangling the influence of parasite genotype, host genotype and maternal environment on different stages of bacterial infection in Daphnia magna

PubMed Central

Hall, Matthew D.; Ebert, Dieter

2012-01-01

Individuals naturally vary in the severity of infectious disease when exposed to a parasite. Dissecting this variation into genetic and environmental components can reveal whether or not this variation depends on the host genotype, parasite genotype or a range of environmental conditions. Complicating this task, however, is that the symptoms of disease result from the combined effect of a series of events, from the initial encounter between a host and parasite, through to the activation of the host immune system and the exploitation of host resources. Here, we use the crustacean Daphnia magna and its parasite Pasteuria ramosa to show how disentangling genetic and environmental factors at different stages of infection improves our understanding of the processes shaping infectious disease. Using compatible host–parasite combinations, we experimentally exclude variation in the ability of a parasite to penetrate the host, from measures of parasite clearance, the reduction in host fecundity and the proliferation of the parasite. We show how parasite resistance consists of two components that vary in environmental sensitivity, how the maternal environment influences all measured aspects of the within-host infection process and how host–parasite interactions following the penetration of the parasite into the host have a distinct temporal component. PMID:22593109

Resolving the infection process reveals striking differences in the contribution of environment, genetics and phylogeny to host-parasite interactions.

PubMed

Duneau, David; Luijckx, Pepijn; Ben-Ami, Frida; Laforsch, Christian; Ebert, Dieter

2011-02-22

Infection processes consist of a sequence of steps, each critical for the interaction between host and parasite. Studies of host-parasite interactions rarely take into account the fact that different steps might be influenced by different factors and might, therefore, make different contributions to shaping coevolution. We designed a new method using the Daphnia magna - Pasteuria ramosa system, one of the rare examples where coevolution has been documented, in order to resolve the steps of the infection and analyse the factors that influence each of them. Using the transparent Daphnia hosts and fluorescently-labelled spores of the bacterium P. ramosa, we identified a sequence of infection steps: encounter between parasite and host; activation of parasite dormant spores; attachment of spores to the host; and parasite proliferation inside the host. The chances of encounter had been shown to depend on host genotype and environment. We tested the role of genetic and environmental factors in the newly described activation and attachment steps. Hosts of different genotypes, gender and species were all able to activate endospores of all parasite clones tested in different environments; suggesting that the activation cue is phylogenetically conserved. We next established that parasite attachment occurs onto the host oesophagus independently of host species, gender and environmental conditions. In contrast to spore activation, attachment depended strongly on the combination of host and parasite genotypes. Our results show that different steps are influenced by different factors. Host-type-independent spore activation suggests that this step can be ruled out as a major factor in Daphnia-Pasteuria coevolution. On the other hand, we show that the attachment step is crucial for the pronounced genetic specificities of this system. We suggest that this one step can explain host population structure and could be a key force behind coevolutionary cycles. We discuss how different steps can explain different aspects of the coevolutionary dynamics of the system: the properties of the attachment step, explaining the rapid evolution of infectivity and the properties of later parasite proliferation explaining the evolution of virulence. Our study underlines the importance of resolving the infection process in order to better understand host-parasite interactions.

Challenges and opportunities for quantifying roots and rhizosphere interactions through imaging and image analysis.

PubMed

Downie, H F; Adu, M O; Schmidt, S; Otten, W; Dupuy, L X; White, P J; Valentine, T A

2015-07-01

The morphology of roots and root systems influences the efficiency by which plants acquire nutrients and water, anchor themselves and provide stability to the surrounding soil. Plant genotype and the biotic and abiotic environment significantly influence root morphology, growth and ultimately crop yield. The challenge for researchers interested in phenotyping root systems is, therefore, not just to measure roots and link their phenotype to the plant genotype, but also to understand how the growth of roots is influenced by their environment. This review discusses progress in quantifying root system parameters (e.g. in terms of size, shape and dynamics) using imaging and image analysis technologies and also discusses their potential for providing a better understanding of root:soil interactions. Significant progress has been made in image acquisition techniques, however trade-offs exist between sample throughput, sample size, image resolution and information gained. All of these factors impact on downstream image analysis processes. While there have been significant advances in computation power, limitations still exist in statistical processes involved in image analysis. Utilizing and combining different imaging systems, integrating measurements and image analysis where possible, and amalgamating data will allow researchers to gain a better understanding of root:soil interactions. © 2014 John Wiley & Sons Ltd.

Genotypic variability-based genome-wide association study identifies non-additive loci HLA-C and IL12B for psoriasis.

PubMed

Wei, Wen-Hua; Massey, Jonathan; Worthington, Jane; Barton, Anne; Warren, Richard B

2018-03-01

Genome-wide association studies (GWASs) have identified a number of loci for psoriasis but largely ignored non-additive effects. We report a genotypic variability-based GWAS (vGWAS) that can prioritize non-additive loci without requiring prior knowledge of interaction types or interacting factors in two steps, using a mixed model to partition dichotomous phenotypes into an additive component and non-additive environmental residuals on the liability scale and then the Levene's (Brown-Forsythe) test to assess equality of the residual variances across genotype groups genome widely. The vGWAS identified two genome-wide significant (P < 5.0e-08) non-additive loci HLA-C and IL12B that were also genome-wide significant in an accompanying GWAS in the discovery cohort. Both loci were statistically replicated in vGWAS of an independent cohort with a small sample size. HLA-C and IL12B were reported in moderate gene-gene and/or gene-environment interactions in several occasions. We found a moderate interaction with age-of-onset of psoriasis, which was replicated indirectly. The vGWAS also revealed five suggestive loci (P < 6.76e-05) including FUT2 that was associated with psoriasis with environmental aspects triggered by virus infection and/or metabolic factors. Replication and functional investigation are needed to validate the suggestive vGWAS loci.

The effects of MAOA genotype, childhood trauma, and sex on trait and state-dependent aggression

PubMed Central

Verhoeven, Floor E A; Booij, Linda; Kruijt, Anne-Wil; Cerit, Hilâl; Antypa, Niki; Does, Willem

2012-01-01

Monoamine oxidase A (MAOA) genotypic variation has been associated with variation in aggression, especially in interaction with childhood trauma or other early adverse events. Male carriers of the low-expressing variant (MAOA-L) with childhood trauma or other early adverse events seem to be more aggressive, whereas female carriers with the high-expressing variant (MAOA-H) with childhood trauma or other early adverse events may be more aggressive. We further investigated the effects of MAOA genotype and its interaction with sex and childhood trauma or other early adverse events on aggression in a young adult sample. We hypothesized that the association between genotype, childhood trauma, and aggression would be different for men and women. We also explored whether this association is different for dispositional (trait) aggression versus aggression in the context of dysphoric mood. In all, 432 Western European students (332 women, 100 men; mean age 20.2) were genotyped for the MAOA gene. They completed measures of childhood trauma, state and trait measures of aggression-related behaviors (STAXI), and cognitive reactivity to sad mood (LEIDS-R), including aggression reactivity. Women with the MAOA-H had higher aggression reactivity scores than women with the MAOA-L. This effect was not observed in men, although the nonsignificant findings in men may be a result of low power. Effects on the STAXI were not observed, nor were there gene by environment interactions on any of the aggression measures. A protective effect of the low-expression variant in women on aggression reactivity is consistent with previous observations in adolescent girls. In females, the MAOA-H may predispose to aggression-related problems during sad mood. PMID:23170243

Interaction between serotonin transporter gene-linked polymorphic region (5-HTTLPR) and job-related stress in insomnia: a cross-sectional study in Sichuan, China.

PubMed

Huang, Chan; Li, Ju; Lu, Lingeng; Ren, Xiaohui; Li, Yongru; Huang, Qian; Lan, Yajia; Wang, Yongwei

2014-10-01

Insomnia, a widely occurring sleep disorder in modern society, has a large impact on life quality and work safety. A cross-sectional study was conducted to explore the possible link between serotonin transporter-linked polymorphic region (5-HTTLPR), job-related stress, and insomnia in West China. Of the total 462 workers recruited, 177 had insomnia according to the Athens Insomnia Scale (AIS-5). The 5-HTTLPR genotypes were determined by polymerase chain reaction. Job-related stress was assessed for each participant by the General Job Stress Questionnaire. Unconditional logistic regression models showed that the 5-HTTLPR genotype was significantly associated with insomnia, and >80% increased risk per S allele was observed. High job-related stress had a higher risk for insomnia than low job-related stress (odds ratio [OR], 6.14; 95% confidence interval [CI], 3.94-9.59). Crossover analysis found significant job-related stress × 5-HTTLPR interaction. Compared to individuals with both low job-related stress and SL/LL genotype, those with both higher job-related stress and SS genotype had a higher risk of insomnia (OR, 5.16; 95% CI, 3.13-8.54), whereas those with both low job-related stress and SS genotype showed a lower risk of insomnia (OR, 0.26; 95% CI, 0.08-0.74). The interaction remained statistically significant after adjusting for potential confounding factors. The findings indicated that 5-HTTLPR could modify the effect of job-related stress on employees' insomnia, suggesting that a work environment-based personalized intervention may be applied to prevent employees' insomnia by alleviating job-related stress in the workplace. Copyright © 2014. Published by Elsevier B.V.

The effects of MAOA genotype, childhood trauma, and sex on trait and state-dependent aggression.

PubMed

Verhoeven, Floor E A; Booij, Linda; Kruijt, Anne-Wil; Cerit, Hilâl; Antypa, Niki; Does, Willem

2012-11-01

Monoamine oxidase A (MAOA) genotypic variation has been associated with variation in aggression, especially in interaction with childhood trauma or other early adverse events. Male carriers of the low-expressing variant (MAOA-L) with childhood trauma or other early adverse events seem to be more aggressive, whereas female carriers with the high-expressing variant (MAOA-H) with childhood trauma or other early adverse events may be more aggressive. We further investigated the effects of MAOA genotype and its interaction with sex and childhood trauma or other early adverse events on aggression in a young adult sample. We hypothesized that the association between genotype, childhood trauma, and aggression would be different for men and women. We also explored whether this association is different for dispositional (trait) aggression versus aggression in the context of dysphoric mood. In all, 432 Western European students (332 women, 100 men; mean age 20.2) were genotyped for the MAOA gene. They completed measures of childhood trauma, state and trait measures of aggression-related behaviors (STAXI), and cognitive reactivity to sad mood (LEIDS-R), including aggression reactivity. Women with the MAOA-H had higher aggression reactivity scores than women with the MAOA-L. This effect was not observed in men, although the nonsignificant findings in men may be a result of low power. Effects on the STAXI were not observed, nor were there gene by environment interactions on any of the aggression measures. A protective effect of the low-expression variant in women on aggression reactivity is consistent with previous observations in adolescent girls. In females, the MAOA-H may predispose to aggression-related problems during sad mood.

Moderating role of the MAOA genotype in antisocial behaviour.

PubMed

Fergusson, David M; Boden, Joseph M; Horwood, L John; Miller, Allison; Kennedy, Martin A

2012-02-01

Recent studies have examined gene×environment (G×E) interactions involving the monoamine oxidase A (MAOA) gene in moderating the associations between exposure to adversity and antisocial behaviour. The present study examined a novel method for assessing interactions between a single gene and multiple risk factors related to environmental and personal adversity. To test the hypothesis that the presence of the low-activity MAOA genotype was associated with an increased response to a series of risk factors. Participants were 399 males from the Christchurch Health and Development Study who had complete data on: (a) MAOA promoter region variable number tandem repeat genotype; (b) antisocial behaviour (criminal offending) to age 30 and convictions to age 21; and (c) maternal smoking during pregnancy, IQ, childhood maltreatment and school failure. Poisson regression models were fitted to three antisocial behaviour outcomes (property/violent offending ages 15-30; and convictions ages 17-21), using measures of exposure to adverse childhood circumstances. The analyses revealed consistent evidence of G x E interactions, such that those with the low-activity MAOA variant who were exposed to adversity in childhood were significantly more likely to report offending in late adolescence and early adulthood. The present findings add to the evidence suggesting that there is a stable G x E interaction involving MAOA, a range of adverse environmental and personal factors, and antisocial behaviour across the life course. These analyses also demonstrate the utility of using multiple environmental/personal exposures to test G×E interactions.

5-HTTLPR Expression Outside the Skin: An Experimental Test of the Emotional Reactivity Hypothesis in Children.

PubMed

Weeland, Joyce; Slagt, Meike; Brummelman, Eddie; Matthys, Walter; de Castro, Bram Orobio; Overbeek, Geertjan

2015-01-01

There is increasing evidence that variation in the promoter region of the serotonin transporter gene SLC6A4 (i.e., the 5-HTTLPR polymorphism) moderates the impact of environmental stressors on child psychopathology. Emotional reactivity -the intensity of an individual's response to other's emotions- has been put forward as a possible mechanism underlying these gene-by-environment interactions (i.e., G×E). Compared to children homozygous for the L-allele (LL-genotypes), children carrying an S-allele (SS/SL-genotypes), specifically when they have been frequently exposed to negative emotions in the family environment, might be more emotionally reactive and therefore more susceptible to affective environmental stressors. However, the association between 5-HTTLPR and emotional reactivity in children has not yet been empirically tested. Therefore, the goal of this study was to test this association in a large-scale experiment. Children (N = 521, 52.5% boys, Mage = 9.72 years) were genotyped and randomly assigned to happy, angry or neutral dynamic facial expressions and vocalizations. Motor and affective emotional reactivity were assessed through children's self-reported negative and positive affect (n = 460) and facial electromyography activity (i.e., fEMG: the zygomaticus or "smile" muscle and the corrugator or "frown" muscle, n = 403). Parents reported on their negative and positive parenting behaviors. Children mimicked and experienced the emotion they were exposed to. However, neither motor reactivity nor affective reactivity to these emotions depended on children's 5-HTTLPR genotype: SS/SL-genotypes did not manifest any stronger response to emotional stimuli than LL-genotypes. This finding remained the same when taking the broader family environment into account, controlling for kinship, age, gender and genetic ancestry, and when including a tri-allelic factor. We found no evidence for an association between the 5-HTTLPR polymorphism and children's emotional reactivity. This finding is important, in discounting one potential underlying endophenotype of G×E between the 5-HTTLPR and affective environmental stressors.

Genotype by environment interaction for activity-based estrus traits in relation to production level for Danish Holstein.

PubMed

Ismael, Ahmed; Strandberg, Erling; Berglund, Britt; Kargo, Morten; Fogh, Anders; Løvendahl, Peter

2016-12-01

The objective of this study was to investigate whether genotype by environment interaction exists for female fertility traits and production of energy-corrected milk at 70d in milk (ECM70). Fertility traits considered were the activity-based estrus traits interval from calving to first high activity (CFHA), duration of high activity episode (DHA), as an indicator for first estrus duration, and strength of high activity episode (SHA), as an indicator for first estrus strength. The physical activity traits were derived from electronic activity tags for 11,522 first-parity cows housed in 125 commercial dairy herds. Data were analyzed using a univariate random regression animal model (URRM), by regressing the phenotypic performance on the average herd ECM70 as an environmental gradient. Furthermore, the genetic correlations between CFHA and ECM70 as a function of production level were estimated using a bivariate random regression animal model (BRRM). For all traits, heterogeneity of additive genetic variances and heritability estimates was observed. The heritability estimate for CFHA decreased from 0.25 to 0.10 with increasing production level and the heritability estimate for ECM70 decreased from 0.35 to 0.15 with increasing production level using URRM. The genetic correlation of the same trait in low and high production levels was around 0.74 for CFHA and 0.80 for ECM70 using URRM, but when data were analyzed using the multiple-trait analysis (MT), genetic correlation estimates between low and high production levels were not significantly different from unity. Furthermore, the genetic correlation of SHA between low and high production level was 0.22 using URRM, but the corresponding correlation estimate had large standard error when data were analyzed using MT. The genetic correlation between CFHA and ECM70 as a function of production environment was weak but unfavorable and decreased slightly from 0.09 to 0.04 with increasing production level using BRRM. Moreover, the same trend was observed when the data were analyzed using MT where the genetic correlation between CFHA and ECM70 in the low production environment was 0.29 compared with -0.13 in the high production environment, but these estimates had large standard errors. In conclusion, regardless of the trait used, in relation to average herd ECM70 production, the results indicated no clear evidence of strong genotype by environment interaction that would cause significant re-ranking of sires between low and high production environments. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Gene-Lifestyle Interactions in Complex Diseases: Design and Description of the GLACIER and VIKING Studies

PubMed Central

Kurbasic, Azra; Poveda, Alaitz; Chen, Yan; Ågren, Åsa; Engberg, Elisabeth; Hu, Frank B.; Johansson, Ingegerd; Barroso, Ines; Brändström, Anders; Hallmans, Göran; Renström, Frida; Franks, Paul W.

2014-01-01

Most complex diseases have well-established genetic and non-genetic risk factors. In some instances, these risk factors are likely to interact, whereby their joint effects convey a level of risk that is either significantly more or less than the sum of these risks. Characterizing these gene-environment interactions may help elucidate the biology of complex diseases, as well as to guide strategies for their targeted prevention. In most cases, the detection of gene-environment interactions will require sample sizes in excess of those needed to detect the marginal effects of the genetic and environmental risk factors. Although many consortia have been formed, comprising multiple diverse cohorts to detect gene-environment interactions, few robust examples of such interactions have been discovered. This may be because combining data across studies, usually through meta-analysis of summary data from the contributing cohorts, is often a statistically inefficient approach for the detection of gene-environment interactions. Ideally, single, very large and well-genotyped prospective cohorts, with validated measures of environmental risk factor and disease outcomes should be used to study interactions. The presence of strong founder effects within those cohorts might further strengthen the capacity to detect novel genetic effects and gene-environment interactions. Access to accurate genealogical data would also aid in studying the diploid nature of the human genome, such as genomic imprinting (parent-of-origin effects). Here we describe two studies from northern Sweden (the GLACIER and VIKING studies) that fulfill these characteristics. PMID:25396097

Gene-Lifestyle Interactions in Complex Diseases: Design and Description of the GLACIER and VIKING Studies.

PubMed

Kurbasic, Azra; Poveda, Alaitz; Chen, Yan; Agren, Asa; Engberg, Elisabeth; Hu, Frank B; Johansson, Ingegerd; Barroso, Ines; Brändström, Anders; Hallmans, Göran; Renström, Frida; Franks, Paul W

2014-12-01

Most complex diseases have well-established genetic and non-genetic risk factors. In some instances, these risk factors are likely to interact, whereby their joint effects convey a level of risk that is either significantly more or less than the sum of these risks. Characterizing these gene-environment interactions may help elucidate the biology of complex diseases, as well as to guide strategies for their targeted prevention. In most cases, the detection of gene-environment interactions will require sample sizes in excess of those needed to detect the marginal effects of the genetic and environmental risk factors. Although many consortia have been formed, comprising multiple diverse cohorts to detect gene-environment interactions, few robust examples of such interactions have been discovered. This may be because combining data across studies, usually through meta-analysis of summary data from the contributing cohorts, is often a statistically inefficient approach for the detection of gene-environment interactions. Ideally, single, very large and well-genotyped prospective cohorts, with validated measures of environmental risk factor and disease outcomes should be used to study interactions. The presence of strong founder effects within those cohorts might further strengthen the capacity to detect novel genetic effects and gene-environment interactions. Access to accurate genealogical data would also aid in studying the diploid nature of the human genome, such as genomic imprinting (parent-of-origin effects). Here we describe two studies from northern Sweden (the GLACIER and VIKING studies) that fulfill these characteristics.

Genotype by environment interaction and the use of unbalanced historical data for genomic selection in an international wheat breeding program

USDA-ARS?s Scientific Manuscript database

Genomic selection (GS) offers breeders the possibility of using historic data and unbalanced breeding trials to form training populations for predicting the performance of new lines. However, in using datasets that are unbalanced over time and space, there is increasing exposure to particular genoty...

Serotonin Transporter (5-HTTLPR) Genotype, Childhood Abuse, and Suicide Attempts in Adult Psychiatric Inpatients

ERIC Educational Resources Information Center

Gibb, Brandon E.; McGeary, John E.; Beevers, Christopher G.; Miller, Ivan W.

2006-01-01

There is growing evidence that a functional polymorphism in the serotonin transporter gene (5-HTTLPR) moderates the impact of negative life events (e.g., childhood abuse) on the development of depression. However, it is unclear whether the gene x environment interaction predicts suicide attempts specifically. In addition, previous studies have not…

Genetic variation in ponderosa pine: A 15-year test of provenances in the Great Plains

Treesearch

David F. Van Haverbeke

1986-01-01

Survival was highest and height growth greatest in ponderosa pine provenances from northcentral Nebraska, southwest South Dakota, and the High Plains region. Genotype x environment interaction was minimal in central and northern Great Plains plantations. Age/age correlations indicate provenances expressing superior height growth can be identified after 5 or 10 years....

Curli fimbriae are conditionally required in Escherichia coli O157:H7 for initial attachment and biofilm formation

USDA-ARS?s Scientific Manuscript database

Several species of enteric pathogens produce curli fimbriae, which may affect their interaction with surfaces and other microbes in nonhost environments. Here we used two E. coli O157:H7 outbreak strains with distinct genotypes to understand the role of curli in surface attachment and biofilm format...

Repeatability and Genotype x Environment Interaction of Intermediate Stage Sugarcane Selection Conducted on Sand and Organic soils

USDA-ARS?s Scientific Manuscript database

The Florida cooperative sugarcane cultivar development program conducts all of its early selection stages on muck (organic) soils at the USDA-ARS Sugarcane Field Station in Canal Point. About 25% of the locations in the final two stages (Stages 3 and 4) are conducted on sand soils, after a reduction...

Combining quantitative trait loci analysis with physiological models to predict genotype-specific transpiration rates.

PubMed

Reuning, Gretchen A; Bauerle, William L; Mullen, Jack L; McKay, John K

2015-04-01

Transpiration is controlled by evaporative demand and stomatal conductance (gs ), and there can be substantial genetic variation in gs . A key parameter in empirical models of transpiration is minimum stomatal conductance (g0 ), a trait that can be measured and has a large effect on gs and transpiration. In Arabidopsis thaliana, g0 exhibits both environmental and genetic variation, and quantitative trait loci (QTL) have been mapped. We used this information to create a genetically parameterized empirical model to predict transpiration of genotypes. For the parental lines, this worked well. However, in a recombinant inbred population, the predictions proved less accurate. When based only upon their genotype at a single g0 QTL, genotypes were less distinct than our model predicted. Follow-up experiments indicated that both genotype by environment interaction and a polygenic inheritance complicate the application of genetic effects into physiological models. The use of ecophysiological or 'crop' models for predicting transpiration of novel genetic lines will benefit from incorporating further knowledge of the genetic control and degree of independence of core traits/parameters underlying gs variation. © 2014 John Wiley & Sons Ltd.

Interaction of ACE genotype and salt intake on hypertension among Chinese Kazakhs: results from a population-based cross-sectional study.

PubMed

Wang, Yuyan; Zhang, Biao; Hou, Lei; Han, Wei; Xue, Fang; Wang, Yanhong; Tang, Yong; Liang, Shaohua; Wang, Weizhi; Asaiti, Kuliqian; Wang, Zixing; Hu, Yaoda; Wang, Lei; Qiu, Changchun; Zhang, Mingtao; Jiang, Jingmei

2017-05-17

To explore the effect of interaction between ACE genotype and salt intake on hypertension among Chinese Kazakhs, and to compare applications of interactions between logistic model and generalised partially linear tree-based regression (GPLTR) model. Population-based cross-sectional study. Hong Dun, North Xinjiang, China. Non-consanguineous Chinese Kazakh participants (n=916, 342 men and 574 women) aged ≥30 years. Association between ACE genotype and hypertension, association between salt intake and hypertension, and interaction of ACE genotype and salt intake on hypertension in two models. Associations between salt intake and hypertension were different in ACE genotype of II and ID+DD. Under the logistic models, main and interaction effects were not observed for men, but effects were present in opposite directions for women (main effect of ACE: OR=0.20, p=0.003; interaction effect: OR=1.07, p=0.027). Under the GPLTR model, Bayesian information criterion trees included both salt intake and ACE genotype as split variables. Individuals with a salt intake ≥19.5 g/day and ID+DD genotypes had a 3.99-fold (p=0.004) higher risk of hypertension compared with the II genotype for men, whereas salt intake <20.1 g/day and ID+DD genotypes had an OR=0.55 (p=0.014) compared with the II genotype for women. An interaction of ACE genotype and salt intake on hypertension was observed among Chinese Kazakhs but in different ways according to sex. The GPLTR model appears to be more suitable for an exploration of interactions in complex diseases. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Maltreatment, MAOA, and delinquency: sex differences in gene-environment interaction in a large population-based cohort of adolescents.

PubMed

Aslund, C; Nordquist, N; Comasco, E; Leppert, J; Oreland, L; Nilsson, K W

2011-03-01

The present study investigated a possible interaction between a functional polymorphism in the MAOA gene promoter (MAOA-VNTR) and childhood maltreatment in the prediction of adolescent male and female delinquency. A cohort of 1,825 high school students, 17-18 years old, completed an anonymous questionnaire during class hours which included questions on childhood maltreatment, sexual abuse, and delinquency. Saliva samples were collected for DNA isolation, and analyzed for the MAOA-VNTR polymorphism. Self-reported maltreatment was a strong risk factor for adolescent delinquent behavior. The MAOA genotype also showed a significant main effect when controlled for maltreatment. Boys with a short variant and girls with one or two long variants of the polymorphism showed a higher risk for delinquency when exposed to maltreatment. Our results confirm previous findings of an interaction between the MAOA-VNTR polymorphism and self-reported maltreatment. Results for boys and girls differ according to MAOA-VNTR genotype and direction of phenotypic expression.

The functional cytotoxic T lymphocyte-associated Protein 4 49G-to-A genetic variant and risk of pancreatic cancer.

PubMed

Yang, Ming; Sun, Tong; Zhou, Yifeng; Wang, Li; Liu, Li; Zhang, Xiaojiao; Tang, Xiaohu; Zhou, Mo; Kuang, Pengqun; Tan, Wen; Li, Hui; Yuan, Qipeng; Yu, Dianke

2012-10-01

Antitumor T lymphocytes play an essential part in immune surveillance of cancer cells. Cytotoxic T lymphocyte-associated Protein 4 (CTLA-4) is a negative regulator of T cell activation and proliferation and therefore influences immune surveillance of carcinogenesis of pancreas. Thus, this study examined the association between functional CTLA-4 49G-to-A (49G>A) single-nucleotide polymorphism and pancreatic cancer risk. Genotypes were determined in 368 patients with pancreatic cancer and 926 controls, and odds ratios (ORs) and 95% confidence intervals (CIs) were estimated by logistic regression. A significant increased risk of pancreatic cancer was found to be associated with the CTLA-4 49G>A single-nucleotide polymorphism. Compared with noncarriers, the OR of developing pancreatic cancer for CTLA-4 49 GA or AA carriers was 1.75 (95% CI = 1.34-2.30, P = 4.83 × 10(-5) ) or 2.54 (95% CI = 1.67-3.87, P = 1.36 × 10(-5) ), respectively. In stratified analyses, the association was more pronounced in GA and AA carriers aged ≤60 years (OR = 3.10, 95% CI = 2.15-4.47, P(interaction) = .002), smokers with GA and AA genotypes (OR = 3.92, 95% CI = 2.39-6.43, P(interaction) = .037), and drinkers with GA and AA genotypes (OR = 4.55, 95% CI = 2.65-7.82, P(interaction) = .042), compared with GG carriers. Moreover, a supermultiplicative interaction between the CTLA-4 49AA genotype and smoking plus drinking was also evident in intensifying risk of pancreatic cancer (P(interaction) = 5.64 × 10(-12) ). These results suggest that CTLA-4 49G>A polymorphism is involved in susceptibility to developing pancreatic cancer, alone and in a gene-environment interaction manner. Copyright © 2012 American Cancer Society.

Genotype by environment interactions on culling rates and 305-day milk yield of Holstein cows in 3 US regions.

PubMed

Tsuruta, S; Lourenco, D A L; Misztal, I; Lawlor, T J

2015-08-01

The objective of this study was to investigate genotype by environment interactions for culling rates and milk production in large and small dairy herds in 3 US regions, using genotypes, pedigree, and phenotypes. Single nucleotide polymorphism (SNP) marker variances were also estimated in these different environments. Culling rates including cow mortality were based on 6 Dairy Herd Improvement termination codes reported by dairy producers. Separate data sets for culling rates and 305-d milk yield were created for large and small dairy herds in the US regions of the Southeast (SE), Southwest (SW), and Northeast (NE) for the first 3 lactation cows that calved between 1999 and 2008. Genomic information from 42,503 SNP markers on 34,506 bulls was included in the analysis to predict genomic estimated breeding value (GEBV) of culling rates and 305-d milk yield with a single-step genomic BLUP using a bivariate threshold-linear model. Cow replacement rates in large SE and NE herds were higher. Heritability estimates of culling rates ranged from 0.03 to 0.11, but the differences were small between large and small herds and among the 3 US regions. Genetic correlations between culling rates and 305-d milk yield were medium to high for cows sold for poor production and reproduction problems. Correlations of GEBV for culling rates among the 3 US regions ranged from 0.34 to 0.92 and were lower between the SW and the other regions, especially in small herds. Correlations of GEBV between large and small herds ranged from 0.44 to 0.90 and were lower in the SW. These results indicate genotype by environment interactions of cow culling rate between the US regions and between large and small herds. Correlations of top 30 SNP marker effects for culling rates between 2 US regions ranged from 0.64 to 0.98 and were higher than those of more SNP marker effects except for a culling reason "sold for dairy purpose." Those correlations between large and small herds ranged from 0.67 to 0.98. High correlations of top SNP marker effects on culling reasons between the US regions and between large and small herds suggest that major markers can be useful for selection in different environments. The SNP variance shown in a marker gene segment on chromosome 14 was strongly associated with milk production in large and small herds in the NE but not in the SE and SW. Marker genes on chromosome 14 also showed a strong association with cow culling rates due to poor production and mortality in large herds in the NE. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

War exposure, 5-HTTLPR genotype and lifetime risk of depression

PubMed Central

Artero, Sylvaine; Touchon, Jacques; Dupuy, Anne-Marie; Malafosse, Alain; Ritchie, Karen

2011-01-01

Background in 1962, during the Algerian war, approximately one and a half million French people living in Algeria were repatriated to France in very poor and often life-threatening conditions. These subjects constitute a cohort for the study of the long term impact of gene-environment interaction on depression. Aims To examine the interaction between a highly stressful life event and subsequent depression, and its modulation by the serotonin transporter gene (5-HTTLPR). Method A community sample of elderly persons aged 65 years and over residing in the Montpellier region of the South of France was randomly recruited from electoral rolls. Genotyping was performed on 248 repatriated persons and 632 controls. Current and lifetime major and minor depressions were assessed according to DSM-IV criteria. Results A significant relationship was observed between exposure to repatriation and subsequent depression (p<0.002), but there was no significant effect of gene alone (p=0.62). After controlling for age, gender, education, disability, recent life events and cognitive function, the gene-environment interaction (Repatriation X 5-HTTLPR) was globally significant (p<0.002; OR= 3.21 [2.48–5.12]). Subjects carrying the two short ( S ) alleles of 5-HTTLPR were observed to be at higher risk (p<0.005; OR=2.34 [1.24–4.32]) and particularly when the repatriation occurred before the age of 35 (p<0.002; OR=2.91 [1.44–5.88]) but did not reach significance in subjects who were older at the time of the event (p=0.067). Conclusion The association between depression and war repatriation is significantly modulated by 5-HTTLPR genotype but this appears to occur only in persons who were younger at the time of exposure. PMID:21593514

A multi-environmental study of recent breeding progress on nitrogen use efficiency in wheat (Triticum aestivum L.).

PubMed

Cormier, Fabien; Faure, Sébastien; Dubreuil, Pierre; Heumez, Emmanuel; Beauchêne, Katia; Lafarge, Stéphane; Praud, Sébastien; Le Gouis, Jacques

2013-12-01

By comparing 195 varieties in eight trials, this study assesses nitrogen use efficiency improvement in high and low nitrogen conditions in European winter wheat over the last 25 years. In a context where European agriculture practices have to deal with environmental concerns and nitrogen (N) fertiliser cost, nitrogen use efficiency (NUE) has to be improved. This study assessed genetic progress in winter wheat (Triticum aestivum L.) NUE. Two hundred and twenty-five European elite varieties were tested in four environments under two levels of N. Global genetic progress was assessed on additive genetic values and on genotype × N interaction, covering 25 years of European breeding. To avoid sampling bias, quality, precocity and plant height were added as covariates in the analyses when needed. Genotype × environment interactions were highly significant for all the traits studied to such an extent that no additive genetic effect was detected on N uptake. Genotype × N interactions were significant for yield, grain protein content (GPC), N concentration in straw, N utilisation, and NUE. Grain yield improvement (+0.45 % year(-1)) was independent of the N treatment. GPC was stable, thus grain nitrogen yield was improved (+0.39 % year(-1)). Genetic progress on N harvest index (+0.12 % year(-1)) and on N concentration in straw (-0.52 % year(-1)) possibly revealed improvement in N remobilisation. There has been an improvement of NUE additive genetic value (+0.33 % year(-1)) linked to better N utilisation (+0.20 % year(-1)). Improved yield stability was detected as a significant improvement of NUE in low compared to high N conditions. The application of these results to breeding programs is discussed.

War exposure, 5-HTTLPR genotype and lifetime risk of depression.

PubMed

Artero, Sylvaine; Touchon, Jacques; Dupuy, Anne-Marie; Malafosse, Alain; Ritchie, Karen

2011-07-01

In 1962 approximately 1.5 million French people living in Algeria were repatriated to France in very poor and often life-threatening conditions. These people constitute a cohort for the study of the long-term impact of gene-environment interaction on depression. To examine the interaction between a highly stressful life event and subsequent depression, and its modulation by a length polymorphism of the serotonin transporter gene (5-HTTLPR). A community sample of people aged 65 years and over residing in the Montpellier region of the south of France was randomly recruited from electoral rolls. Genotyping was performed on 248 repatriated persons and 632 controls. Current and lifetime major and minor depressive disorders were assessed according to DSM-IV criteria. A significant relationship was observed between exposure to repatriation and subsequent depression (P<0.002), but there was no significant effect of gene alone (P = 0.62). After controlling for age, gender, education, disability, recent life events and cognitive function, the gene-environment interaction (repatriation × 5-HTTLPR) was globally significant (P<0.002; OR = 3.21, 95% CI 2.48-5.12). Individuals carrying the two short (s) alleles of 5-HTTLPR were observed to be at higher risk (P<0.005; OR = 2.34, 95% CI 1.24-4.32), particularly when repatriation occurred before age 35 years (P<0.002; OR = 2.91, 95% CI 1.44-5.88), but this did not reach significance in those who were older at the time of the event (P = 0.067). The association between depression and war repatriation was significantly modulated by 5-HTTLPR genotype but this appeared to occur only in people who were younger at the time of exposure.

Interaction effects between the 5-hydroxy tryptamine transporter-linked polymorphic region (5-HTTLPR) genotype and family conflict on adolescent alcohol use and misuse.

PubMed

Kim, Jueun; Park, Aesoon; Glatt, Stephen J; Eckert, Tanya L; Vanable, Peter A; Scott-Sheldon, Lori A J; Carey, Kate B; Ewart, Craig K; Carey, Michael P

2015-02-01

To investigate whether the effects of family conflict on adolescent drinking differed as a function of 5-hydroxy tryptamine transporter-linked polymorphic region (5-HTTLPR) genotype cross-sectionally and prospectively in two independent samples of adolescents. Path analysis and multi-group analysis of two prospective datasets were conducted. United States and United Kingdom. Sample 1 was 175 adolescents in the United States (mean age = 15 at times 1 and 2 with a 6-month interval); Sample 2 was 4916 adolescents in the United Kingdon (mean age = 12 at time 1 and 15 at time 2). In both samples, demographics, tri-allelic 5-HTTLPR genotype and perceived family conflict were assessed at time 1. Alcohol use (frequency of drinking) and alcohol misuse (frequency of intoxication, frequency of drinking three or more drinks, maximum number of drinks) were assessed at times 1 and 2. A significant gene-environment interaction on alcohol misuse at time 1 was found in both sample 1 (β = 0.57, P = 0.001) and sample 2 (β = 0.19, P = 0.01), indicating that the 5-HTTLPR low-activity allele carriers exposed to higher levels of family conflict were more likely to engage in alcohol misuse than non-carriers. A significant gene-environment interaction effect on change in alcohol misuse over time was found only in sample 1 (β = 0.48, P = 0.04) but not in sample 2. Compared with non-carriers, adolescents carrying the 5-HTTLPR low-activity allele are more susceptible to the effects of family conflict on alcohol misuse. © 2014 Society for the Study of Addiction.

Linear reaction norm models for genetic merit prediction of Angus cattle under genotype by environment interaction.

PubMed

Cardoso, F F; Tempelman, R J

2012-07-01

The objectives of this work were to assess alternative linear reaction norm (RN) models for genetic evaluation of Angus cattle in Brazil. That is, we investigated the interaction between genotypes and continuous descriptors of the environmental variation to examine evidence of genotype by environment interaction (G×E) in post-weaning BW gain (PWG) and to compare the environmental sensitivity of national and imported Angus sires. Data were collected by the Brazilian Angus Improvement Program from 1974 to 2005 and consisted of 63,098 records and a pedigree file with 95,896 animals. Six models were implemented using Bayesian inference and compared using the Deviance Information Criterion (DIC). The simplest model was M(1), a traditional animal model, which showed the largest DIC and hence the poorest fit when compared with the 4 alternative RN specifications accounting for G×E. In M(2), a 2-step procedure was implemented using the contemporary group posterior means of M(1) as the environmental gradient, ranging from -92.6 to +265.5 kg. Moreover, the benefits of jointly estimating all parameters in a 1-step approach were demonstrated by M(3). Additionally, we extended M(3) to allow for residual heteroskedasticity using an exponential function (M(4)) and the best fitting (smallest DIC) environmental classification model (M(5)) specification. Finally, M(6) added just heteroskedastic residual variance to M(1). Heritabilities were less at harsh environments and increased with the improvement of production conditions for all RN models. Rank correlations among genetic merit predictions obtained by M(1) and by the best fitting RN models M(3) (homoskedastic) and M(5) (heteroskedastic) at different environmental levels ranged from 0.79 and 0.81, suggesting biological importance of G×E in Brazilian Angus PWG. These results suggest that selection progress could be optimized by adopting environment-specific genetic merit predictions. The PWG environmental sensitivity of imported North American origin bulls (0.046 ± 0.009) was significantly larger (P < 0.05) than that of local sires (0.012 ± 0.013). Moreover, PWG of progeny of imported sires exceeded that of native sires in medium and superior production levels. On the other hand, Angus cattle locally selected in Brazil tended to be more robust to environmental changes and hence be more suitable when production environments for potential progeny is uncertain.

European cowpea landraces for a more sustainable agriculture system and novel foods.

PubMed

Carvalho, Márcia; Bebeli, Penelope J; Pereira, Graça; Castro, Isaura; Egea-Gilabert, Catalina; Matos, Manuela; Lazaridi, Efstathia; Duarte, Isabel; Lino-Neto, Teresa; Ntatsi, Georgia; Rodrigues, Miguel; Savvas, Dimitrios; Rosa, Eduardo; Carnide, Valdemar

2017-10-01

Genetic diversity is fundamental to breeding programs and consequently has an important role in obtaining new varieties. To properly use the genetic diversity present in germplasm collections, a good knowledge of the agro-morphological traits of each accession is needed. The aim of this study was to explore the production capacity of 24 cowpea landraces from southern Europe, through phenotypic characterization and evaluation in three different locations in Greece and Portugal. Most qualitative parameters tested showed a high stability among the three locations. A wide difference was observed among the three locations with respect to number of days to flowering, ranging from 55 to 99 days. Quantitative traits showed a higher genotype × environment than genetic variance component. In general, an inverse relationship between σ 2 ge /σ 2 g ratio (where σ 2 ge is genotype × genotype interaction and σ 2 g is genotype impact) and heritability value was observed. Principal component analysis was able to group accessions based on their origin. The first two principal components explained 97.52% of variation, being the number of seeds per plant, plant height and seed protein content, the traits which contributed most to variability. The results show that sufficient variation exists in different traits within landraces in the studied cowpea germplasm to pursue a breeding program. However, the quantitative traits showed a higher genotype × environment component. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

COMT Val(158)Met genotype and cannabis use in people with an At Risk Mental State for psychosis: Exploring Gene x Environment interactions.

PubMed

Nieman, Dorien H; Dragt, Sara; van Duin, Esther D A; Denneman, Nadine; Overbeek, Jozefien M; de Haan, Lieuwe; Rietdijk, Judith; Ising, Helga K; Klaassen, Rianne M C; van Amelsvoort, Thérèse; Wunderink, Lex; van der Gaag, Mark; Linszen, Don H

2016-07-01

Epidemiological and retrospective studies suggest a cannabis x catechol-O-methyltransferase (COMT) Val(158)Met interaction effect on development of psychosis. The aim of this study was to examine this interaction and its association with severity of subclinical symptoms in people with an At Risk Mental State (ARMS) for psychosis. Severity of symptoms, cannabis use and genotype were assessed at baseline in 147 help-seeking young adults who met the ARMS criteria and agreed to participate in the Dutch Early Detection and Intervention (EDIE-NL) trial. Cannabis use and COMT Val-allele showed an interaction effect in ARMS subjects. Subjects who were weekly cannabis users at some point prior to entering the study showed more severe positive symptoms. This effect increased if they were carriers of the COMT Val-allele and even more so if they were homozygous for the Val-allele. Our results suggest that the COMT Val(158)Met polymorphism moderates the effect of regular cannabis use on severity of subclinical psychotic symptoms. Copyright © 2016 Elsevier B.V. All rights reserved.

Genotyping of Single Nucleotide Polymorphisms in DNA Isolated from Serum Using Sequenom MassARRAY Technology.

PubMed

Clendenen, Tess V; Rendleman, Justin; Ge, Wenzhen; Koenig, Karen L; Wirgin, Isaac; Currie, Diane; Shore, Roy E; Kirchhoff, Tomas; Zeleniuch-Jacquotte, Anne

2015-01-01

Large epidemiologic studies have the potential to make valuable contributions to the assessment of gene-environment interactions because they prospectively collected detailed exposure data. Some of these studies, however, have only serum or plasma samples as a low quantity source of DNA. We examined whether DNA isolated from serum can be used to reliably and accurately genotype single nucleotide polymorphisms (SNPs) using Sequenom multiplex SNP genotyping technology. We genotyped 81 SNPs using samples from 158 participants in the NYU Women's Health Study. Each participant had DNA from serum and at least one paired DNA sample isolated from a high quality source of DNA, i.e. clots and/or cell precipitates, for comparison. We observed that 60 of the 81 SNPs (74%) had high call frequencies (≥95%) using DNA from serum, only slightly lower than the 85% of SNPs with high call frequencies in DNA from clots or cell precipitates. Of the 57 SNPs with high call frequencies for serum, clot, and cell precipitate DNA, 54 (95%) had highly concordant (>98%) genotype calls across all three sample types. High purity was not a critical factor to successful genotyping. Our results suggest that this multiplex SNP genotyping method can be used reliably on DNA from serum in large-scale epidemiologic studies.

Genotype, soil type, and locale effects on reciprocal transplant vigor, endophyte growth, and microbial functional diversity of a narrow sagebrush hybrid zone in Salt Creek Canyon, Utah

USGS Publications Warehouse

Miglia, K.J.; McArthur, E.D.; Redman, R.S.; Rodriguez, R.J.; Zak, J.C.; Freeman, D.C.

2007-01-01

When addressing the nature of ecological adaptation and environmental factors limiting population ranges and contributing to speciation, it is important to consider not only the plant's genotype and its response to the environment, but also any close interactions that it has with other organisms, specifically, symbiotic microorganisms. To investigate this, soils and seedlings were reciprocally transplanted into common gardens of the big sagebrush hybrid zone in Salt Creek Canyon, Utah, to determine location and edaphic effects on the fitness of parental and hybrid plants. Endophytic symbionts and functional microbial diversity of indigenous and transplanted soils and sagebrush plants were also examined. Strong selection occurred against the parental genotypes in the middle hybrid zone garden in middle hybrid zone soil; F1 hybrids had the highest fitness under these conditions. Neither of the parental genotypes had superior fitness in their indigenous soils and habitats; rather F1 hybrids with the nonindigenous maternal parent were superiorly fit. Significant garden-by-soil type interactions indicate adaptation of both plant and soil microorganisms to their indigenous soils and habitats, most notably in the middle hybrid zone garden in middle hybrid zone soil. Contrasting performances of F1 hybrids suggest asymmetrical gene flow with mountain, rather than basin, big sagebrush acting as the maternal parent. We showed that the microbial community impacted the performance of parental and hybrid plants in different soils, likely limiting the ranges of the different genotypes.

Gene-environment interaction in the etiology of mathematical ability using SNP sets.

PubMed

Docherty, Sophia J; Kovas, Yulia; Plomin, Robert

2011-01-01

Mathematics ability and disability is as heritable as other cognitive abilities and disabilities, however its genetic etiology has received relatively little attention. In our recent genome-wide association study of mathematical ability in 10-year-old children, 10 SNP associations were nominated from scans of pooled DNA and validated in an individually genotyped sample. In this paper, we use a 'SNP set' composite of these 10 SNPs to investigate gene-environment (GE) interaction, examining whether the association between the 10-SNP set and mathematical ability differs as a function of ten environmental measures in the home and school in a sample of 1888 children with complete data. We found two significant GE interactions for environmental measures in the home and the school both in the direction of the diathesis-stress type of GE interaction: The 10-SNP set was more strongly associated with mathematical ability in chaotic homes and when parents are negative.

Genome-wide association analysis to identify genotype × environment interaction for milk protein yield and level of somatic cell score as environmental descriptors in German Holsteins.

PubMed

Streit, M; Reinhardt, F; Thaller, G; Bennewitz, J

2013-01-01

Genotype by environment interaction (G × E) has been widely reported in dairy cattle. If the environment can be measured on a continuous scale, reaction norms can be applied to study G × E. The average herd milk production level has frequently been used as an environmental descriptor because it is influenced by the level of feeding or the feeding regimen. Another important environmental factor is the level of udder health and hygiene, for which the average herd somatic cell count might be a descriptor. In the present study, we conducted a genome-wide association analysis to identify single nucleotide polymorphisms (SNP) that affect intercept and slope of milk protein yield reaction norms when using the average herd test-day solution for somatic cell score as an environmental descriptor. Sire estimates for intercept and slope of the reaction norms were calculated from around 12 million daughter records, using linear reaction norm models. Sires were genotyped for ~54,000 SNP. The sire estimates were used as observations in the association analysis, using 1,797 sires. Significant SNP were confirmed in an independent validation set consisting of 500 sires. A known major gene affecting protein yield was included as a covariable in the statistical model. Sixty (21) SNP were confirmed for intercept with P ≤ 0.01 (P ≤ 0.001) in the validation set, and 28 and 11 SNP, respectively, were confirmed for slope. Most but not all SNP affecting slope also affected intercept. Comparison with an earlier study revealed that SNP affecting slope were, in general, also significant for slope when the environment was modeled by the average herd milk production level, although the two environmental descriptors were poorly correlated. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Association of FKBP5 Polymorphisms and Childhood Abuse With Risk of Posttraumatic Stress Disorder Symptoms in Adults

PubMed Central

Binder, Elisabeth B.; Bradley, Rebekah G.; Liu, Wei; Epstein, Michael P.; Deveau, Todd C.; Mercer, Kristina B.; Tang, Yilang; Gillespie, Charles F.; Heim, Christine M.; Nemeroff, Charles B.; Schwartz, Ann C.; Cubells, Joseph F.; Ressler, Kerry J.

2008-01-01

Context In addition to trauma exposure, other factors contribute to risk for development of posttraumatic stress disorder (PTSD) in adulthood. Both genetic and environmental factors are contributory, with child abuse providing significant risk liability. Objective To increase understanding of genetic and environmental risk factors as well as their interaction in the development of PTSD by gene × environment interactions of child abuse, level of non–child abuse trauma exposure, and genetic polymorphisms at the stress-related gene FKBP5. Design, Setting, and Participants A cross-sectional study examining genetic and psychological risk factors in 900 non psychiatric clinic patients (762 included for all genotype studies) with significant levels of childhood abuse as well as non–child abuse trauma using a verbally presented survey combined with single-nucleotide polymorphism (SNP) genotyping. Participants were primarily urban, low-income, black (>95%) men and women seeking care in the general medical care and obstetrics-gynecology clinics of an urban public hospital in Atlanta, Georgia, between 2005 and 2007. Main Outcome Measures Severity of adult PTSD symptomatology, measured with the modified PTSD Symptom Scale, non–child abuse (primarily adult) trauma exposure and child abuse measured using the traumatic events inventory and 8 SNPs spanning the FKBP5 locus. Results Level of child abuse and non–child abuse trauma each separately predicted level of adult PTSD symptomatology (mean [SD], PTSD Symptom Scale for no child abuse, 8.03 [10.48] vs ≥2 types of abuse, 20.93 [14.32]; and for no non–child abuse trauma, 3.58 [6.27] vs ≥4 types, 16.74 [12.90]; P<.001). Although FKBP5 SNPs did not directly predict PTSD symptom outcome or interact with level of non–child abuse trauma to predict PTSD symptom severity, 4 SNPs in the FKBP5 locus significantly interacted (rs9296158, rs3800373, rs1360780, and rs9470080; minimum P=.0004) with the severity of child abuse to predict level of adult PTSD symptoms after correcting for multiple testing. This gene × environment interaction remained significant when controlling for depression severity scores, age, sex, levels of non–child abuse trauma exposure, and genetic ancestry. This genetic interaction was also paralleled by FKBP5 genotype-dependent and PTSD-dependent effects on glucocorticoid receptor sensitivity, measured by the dexamethasone suppression test. Conclusions Four SNPs of the FKBP5 gene interacted with severity of child abuse as a predictor of adult PTSD symptoms. There were no main effects of the SNPs on PTSD symptoms and no significant genetic interactions with level of non–child abuse trauma as predictor of adult PTSD symptoms, suggesting a potential gene-childhood environment interaction for adult PTSD. PMID:18349090

The effects of genotype, age, and social environment on male ornamentation, mating behavior, and attractiveness.

PubMed

Miller, Lisa K; Brooks, Robert

2005-11-01

The traits thought to advertise genetic quality are often highly susceptible to environmental variation and prone to change with age. These factors may either undermine or reinforce the potential for advertisement traits to signal quality depending on the magnitude of age-dependent expression, environmental variation, and genotype-age and genotype-environment interaction. Measurements of the magnitude of these effects are thus a necessary step toward assessing the implications of age dependence and environmental variability for the evolution of signals of quality. We conducted a longitudinal study of male guppies (Poecilia reticulata) from 22 full-sibling families. Each fish was assigned at maturity to one of three treatments in order to manipulate his allocation of resources to reproduction: a control in which the male was kept alone, a courtship-only treatment in which he could see and court a female across a clear partition, and a mating treatment in which he interacted freely with a female. We measured each male's size, ornamental color patterns, courtship, attractiveness to females, and mating success at three ages. Size was influenced by treatment and age-treatment interactions, indicating that courtship and mating may impose costs on growth. Tail size and color patterns were influenced by age but not by treatment, suggesting fixed age-dependent trajectories in these advertisement traits. By contrast, display rate and attempted sneak copulation rate differed among treatments but not among ages, suggesting greater plasticity of these behavioral traits. As a result of the different patterns of variation in ornamentation and behavior, male attractiveness and mating success responded to male age, treatment, and the interaction between age and treatment. Neither age nor treatment obscured the presence of genetic variation, and the genetic relationship between male ornamentation and attractiveness remained the same among treatments. Our findings suggest that neither age-dependent variation nor environmentally induced variation in reproductive effort is likely to undermine the reliability of male signaling.

Tissue Culture as a Source of Replicates in Nonmodel Plants: Variation in Cold Response in Arabidopsis lyrata ssp. petraea.

PubMed

Kenta, Tanaka; Edwards, Jessica E M; Butlin, Roger K; Burke, Terry; Quick, W Paul; Urwin, Peter; Davey, Matthew P

2016-12-07

While genotype-environment interaction is increasingly receiving attention by ecologists and evolutionary biologists, such studies need genetically homogeneous replicates-a challenging hurdle in outcrossing plants. This could be potentially overcome by using tissue culture techniques. However, plants regenerated from tissue culture may show aberrant phenotypes and "somaclonal" variation. Here, we examined somaclonal variation due to tissue culturing using the response to cold treatment of photosynthetic efficiency (chlorophyll fluorescence measurements for F v /F m , F v '/F m ', and Φ PSII , representing maximum efficiency of photosynthesis for dark- and light-adapted leaves, and the actual electron transport operating efficiency, respectively, which are reliable indicators of photoinhibition and damage to the photosynthetic electron transport system). We compared this to variation among half-sibling seedlings from three different families of Arabidopsis lyrata ssp. petraea Somaclonal variation was limited, and we could detect within-family variation in change in chlorophyll fluorescence due to cold shock successfully with the help of tissue-culture derived replicates. Icelandic and Norwegian families exhibited higher chlorophyll fluorescence, suggesting higher performance after cold shock, than a Swedish family. Although the main effect of tissue culture on F v /F m , F v '/F m ', and Φ PSII was small, there were significant interactions between tissue culture and family, suggesting that the effect of tissue culture is genotype-specific. Tissue-cultured plantlets were less affected by cold treatment than seedlings, but to a different extent in each family. These interactive effects, however, were comparable to, or much smaller than the single effect of family. These results suggest that tissue culture is a useful method for obtaining genetically homogenous replicates for studying genotype-environment interaction related to adaptively-relevant phenotypes, such as cold response, in nonmodel outcrossing plants. Copyright © 2016 Kenta et al.

The variety mixture strategy assessed in a G × G experiment with rice and the blast fungus Magnaporthe oryzae

PubMed Central

Gallet, Romain; Bonnot, François; Milazzo, Joëlle; Tertois, Christophe; Adreit, Henri; Ravigné, Virginie; Tharreau, Didier; Fournier, Elisabeth

2014-01-01

Frequent and devastating epidemics of parasites are one of the major issues encountered by modern agriculture. To manage the impact of pathogens, resistant plant varieties have been selected. However, resistances are overcome by parasites requiring the use of pesticides and causing new economical and food safety issues. A promising strategy to maintain the epidemic at a low level and hamper pathogen's adaptation to varietal resistance is the use of mixtures of varieties such that the mix will form a heterogeneous environment for the parasite. A way to find the good combination of varieties that will actually constitute a heterogeneous environment for pathogens is to look for genotype × genotype (G × G) interactions between pathogens and plant varieties. A pattern in which pathogens have a high fitness on one variety and a poor fitness on other varieties guarantees the efficiency of the mixture strategy. In the present article, we inoculated 18 different genotypes of the fungus Magnaporthe oryzae on three rice plant varieties showing different levels of partial resistance in order to find a variety combination compatible with the requirements of the variety mixture strategy, i.e., showing appropriate G × G interactions. We estimated the success of each plant-fungus interaction by measuring fungal fitness and three fungal life history traits: infection success, within-host growth, sporulation capacity. Our results show the existence of G × G interactions between the two varieties Ariete and CO39 on all measured traits and fungal fitness. We also observed that these varieties have different resistance mechanisms; Ariete is good at controlling infection success of the parasite but is not able to control its growth when inside the leaf, while CO39 shows the opposite pattern. We also found that Maratelli's resistance has been eroded. Finally, correlation analyses demonstrated that not all infectious traits are positively correlated. PMID:24474958

The variety mixture strategy assessed in a G × G experiment with rice and the blast fungus Magnaporthe oryzae.

PubMed

Gallet, Romain; Bonnot, François; Milazzo, Joëlle; Tertois, Christophe; Adreit, Henri; Ravigné, Virginie; Tharreau, Didier; Fournier, Elisabeth

2013-01-01

Frequent and devastating epidemics of parasites are one of the major issues encountered by modern agriculture. To manage the impact of pathogens, resistant plant varieties have been selected. However, resistances are overcome by parasites requiring the use of pesticides and causing new economical and food safety issues. A promising strategy to maintain the epidemic at a low level and hamper pathogen's adaptation to varietal resistance is the use of mixtures of varieties such that the mix will form a heterogeneous environment for the parasite. A way to find the good combination of varieties that will actually constitute a heterogeneous environment for pathogens is to look for genotype × genotype (G × G) interactions between pathogens and plant varieties. A pattern in which pathogens have a high fitness on one variety and a poor fitness on other varieties guarantees the efficiency of the mixture strategy. In the present article, we inoculated 18 different genotypes of the fungus Magnaporthe oryzae on three rice plant varieties showing different levels of partial resistance in order to find a variety combination compatible with the requirements of the variety mixture strategy, i.e., showing appropriate G × G interactions. We estimated the success of each plant-fungus interaction by measuring fungal fitness and three fungal life history traits: infection success, within-host growth, sporulation capacity. Our results show the existence of G × G interactions between the two varieties Ariete and CO39 on all measured traits and fungal fitness. We also observed that these varieties have different resistance mechanisms; Ariete is good at controlling infection success of the parasite but is not able to control its growth when inside the leaf, while CO39 shows the opposite pattern. We also found that Maratelli's resistance has been eroded. Finally, correlation analyses demonstrated that not all infectious traits are positively correlated.

In Black South Africans from Rural and Urban Communities, the 4G/5G PAI-1 Polymorphism Influences PAI-1 Activity, but Not Plasma Clot Lysis Time

PubMed Central

de Lange, Zelda; Rijken, Dingeman C.; Hoekstra, Tiny; Conradie, Karin R.; Jerling, Johann C.; Pieters, Marlien

2013-01-01

Data on genetic and environmental factors influencing PAI-1 levels and their consequent effect on clot lysis in black African populations are limited. We identified polymorphisms in the promoter area of the PAI-1 gene and determined their influence on PAI-1act levels and plasma clot lysis time (CLT). We also describe gene-environment interactions and the effect of urbanisation. Data from 2010 apparently healthy urban and rural black participants from the South African arm of the PURE study were cross-sectionally analysed. The 5G allele frequency of the 4G/5G polymorphism was 0.85. PAI-1act increased across genotypes in the urban subgroup (p = 0.009) but not significantly in the rural subgroup, while CLT did not differ across genotypes. Significant interaction terms were found between the 4G/5G polymorphism and BMI, waist circumference and triglycerides in determining PAI-1act, and between the 4G/5G polymorphism and fibrinogen and fibrinogen gamma prime in determining CLT. The C428T and G429A polymorphisms did not show direct relationships with PAI-1act or CLT but they did influence the association of other environmental factors with PAI-1act and CLT. Several of these interactions differed significantly between rural and urban subgroups, particularly in individuals harbouring the mutant alleles. In conclusion, although the 4G/5G polymorphism significantly affected PAI-1act, it contributed less than 1% to the PAI-1act variance. (Central) obesity was the biggest contributor to PAI-1act variance (12.5%). Urbanisation significantly influenced the effect of the 4G/5G polymorphism on PAI-1act as well as gene-environment interactions for the C428T and G429A genotypes in determining PAI-1act and CLT. PMID:24386152

In black South Africans from rural and urban communities, the 4G/5G PAI-1 polymorphism influences PAI-1 activity, but not plasma clot lysis time.

PubMed

de Lange, Zelda; Rijken, Dingeman C; Hoekstra, Tiny; Conradie, Karin R; Jerling, Johann C; Pieters, Marlien

2013-01-01

Data on genetic and environmental factors influencing PAI-1 levels and their consequent effect on clot lysis in black African populations are limited. We identified polymorphisms in the promoter area of the PAI-1 gene and determined their influence on PAI-1act levels and plasma clot lysis time (CLT). We also describe gene-environment interactions and the effect of urbanisation. Data from 2010 apparently healthy urban and rural black participants from the South African arm of the PURE study were cross-sectionally analysed. The 5G allele frequency of the 4G/5G polymorphism was 0.85. PAI-1act increased across genotypes in the urban subgroup (p = 0.009) but not significantly in the rural subgroup, while CLT did not differ across genotypes. Significant interaction terms were found between the 4G/5G polymorphism and BMI, waist circumference and triglycerides in determining PAI-1act, and between the 4G/5G polymorphism and fibrinogen and fibrinogen gamma prime in determining CLT. The C428T and G429A polymorphisms did not show direct relationships with PAI-1act or CLT but they did influence the association of other environmental factors with PAI-1act and CLT. Several of these interactions differed significantly between rural and urban subgroups, particularly in individuals harbouring the mutant alleles. In conclusion, although the 4G/5G polymorphism significantly affected PAI-1act, it contributed less than 1% to the PAI-1act variance. (Central) obesity was the biggest contributor to PAI-1act variance (12.5%). Urbanisation significantly influenced the effect of the 4G/5G polymorphism on PAI-1act as well as gene-environment interactions for the C428T and G429A genotypes in determining PAI-1act and CLT.

Phenotypic Evolution With and Beyond Genome Evolution.

PubMed

Félix, M-A

2016-01-01

DNA does not make phenotypes on its own. In this volume entitled "Genes and Phenotypic Evolution," the present review draws the attention on the process of phenotype construction-including development of multicellular organisms-and the multiple interactions and feedbacks between DNA, organism, and environment at various levels and timescales in the evolutionary process. First, during the construction of an individual's phenotype, DNA is recruited as a template for building blocks within the cellular context and may in addition be involved in dynamical feedback loops that depend on the environmental and organismal context. Second, in the production of phenotypic variation among individuals, stochastic, environmental, genetic, and parental sources of variation act jointly. While in controlled laboratory settings, various genetic and environmental factors can be tested one at a time or in various combinations, they cannot be separated in natural populations because the environment is not controlled and the genotype can rarely be replicated. Third, along generations, genotype and environment each have specific properties concerning the origin of their variation, the hereditary transmission of this variation, and the evolutionary feedbacks. Natural selection acts as a feedback from phenotype and environment to genotype. This review integrates recent results and concrete examples that illustrate these three points. Although some themes are shared with recent calls and claims to a new conceptual framework in evolutionary biology, the viewpoint presented here only means to add flesh to the standard evolutionary synthesis. © 2016 Elsevier Inc. All rights reserved.

Individual diet has sex-dependent effects on vertebrate gut microbiota

PubMed Central

Bolnick, Daniel I.; Snowberg, Lisa K.; Hirsch, Philipp E.; Lauber, Christian L.; Org, Elin; Parks, Brian; Lusis, Aldons J.; Knight, Rob; Caporaso, J. Gregory; Svanbäck, Richard

2014-01-01

Vertebrates harbour diverse communities of symbiotic gut microbes. Host diet is known to alter microbiota composition, implying that dietary treatments might alleviate diseases arising from altered microbial composition (‘dysbiosis’). However, it remains unclear whether diet effects are general or depend on host genotype. Here we show that gut microbiota composition depends on interactions between host diet and sex within populations of wild and laboratory fish, laboratory mice and humans. Within each of two natural fish populations (threespine stickleback and Eurasian perch), among-individual diet variation is correlated with individual differences in gut microbiota. However, these diet–microbiota associations are sex dependent. We document similar sex-specific diet–microbiota correlations in humans. Experimental diet manipulations in laboratory stickleback and mice confirmed that diet affects microbiota differently in males versus females. The prevalence of such genotype by environment (sex by diet) interactions implies that therapies to treat dysbiosis might have sex-specific effects. PMID:25072318

Individual diet has sex-dependent effects on vertebrate gut microbiota.

PubMed

Bolnick, Daniel I; Snowberg, Lisa K; Hirsch, Philipp E; Lauber, Christian L; Org, Elin; Parks, Brian; Lusis, Aldons J; Knight, Rob; Caporaso, J Gregory; Svanbäck, Richard

2014-07-29

Vertebrates harbour diverse communities of symbiotic gut microbes. Host diet is known to alter microbiota composition, implying that dietary treatments might alleviate diseases arising from altered microbial composition ('dysbiosis'). However, it remains unclear whether diet effects are general or depend on host genotype. Here we show that gut microbiota composition depends on interactions between host diet and sex within populations of wild and laboratory fish, laboratory mice and humans. Within each of two natural fish populations (threespine stickleback and Eurasian perch), among-individual diet variation is correlated with individual differences in gut microbiota. However, these diet-microbiota associations are sex dependent. We document similar sex-specific diet-microbiota correlations in humans. Experimental diet manipulations in laboratory stickleback and mice confirmed that diet affects microbiota differently in males versus females. The prevalence of such genotype by environment (sex by diet) interactions implies that therapies to treat dysbiosis might have sex-specific effects.

Will crown ideotype help determine optimum varietal silviculture?

Treesearch

Timothy J. Albaugh; Thomas R. Fox; Marco A. Yanez; Rafael A. Rubilar; Barry Goldfarb

2016-01-01

Recent advances in somatic embryogenesis permit large numbers of clonal loblolly pine (Pinus taeda L.) to be produced and deployed. Clones may have greater growth (mean annual increment exceeding 30 cubic meters per hectare per year), greater stand uniformity and may be more susceptible to genotype by environment interactions when they are deployed in intensively...

Toward understanding genotype x environment interactions on flowering and fruiting in black raspberry (Rubus occidentalis L.)

USDA-ARS?s Scientific Manuscript database

The black raspberry (Rubus occidentalis)industry in the United States has declined over the past 75 years due to a lack of new cultivars to meet the needs of the growers and consumers. The health benefits of dark fruits, especially black raspberry, are well documented and this has led to renewed int...

A mutualistic interaction between a fungivorous nematode and a fungus within the endophytic community of Bromus tectorum

Treesearch

Melissa A. Baynes; Danelle M. Russell; George Newcombe; Lynn K. Carta; Amy Y. Rossman; Adnan Ismaiel

2012-01-01

In its invaded range in western North America, Bromus tectorum (cheatgrass) can host more than 100 sequence-based, operational taxonomic units of endophytic fungi, of which an individual plant hosts a subset. Research suggests that the specific subset is determined by plant genotype, environment, dispersal of locally available endophytes, and mycorrhizal associates....

Effects of genotype and environment on the contents of betaine, choline, and trigonelline in cereal grains.

PubMed

Corol, Delia-Irina; Ravel, Catherine; Raksegi, Mariann; Bedo, Zoltan; Charmet, Gilles; Beale, Michael H; Shewry, Peter R; Ward, Jane L

2012-05-30

This study examined the environmental and genetic variation in methyl donor contents and compositions of 200 cereal genotypes. Glycine betaine, choline, and trigonelline contents were determined by (1)H NMR, and significant differences were observed between cereal types (G) and across harvesting years and growing locations (E). Glycine betaine was the most abundant methyl donor in all of the 200 lines grown on a single site, and concentrations ranged from 0.43 ± 0.09 mg/g dm in oats to 2.57 ± 0.25 mg/g dm in diploid Einkorn varieties. In bread wheat genotypes there was a 3-fold difference in glycine betaine content. Choline contents, in the same lines, were substantially lower, and mean concentrations ranged from 0.17 mg/g dm in oats to 0.27 mg/g dm in durum wheat. Trigonelline was by far the least abundant of the methyl donors studied. Despite this, however, there were large differences between cereal types. Twenty-six wheat genotypes were grown in additional years at four European locations. The average glycine betaine content was highest in grains grown in Hungary and lowest in those grown in the United Kingdom. Across the six environments, there was a 3.8-fold difference in glycine betaine content. Glycine betaine levels, although moderately heritable (0.36), were found to be the most susceptible to the environmental conditions. Free choline concentrations were less variable across genotypes, but heritability of this component was the lowest of all methyl donor components (0.25) and showed a high G × E interaction. Trigonelline showed the most variation due to genotype. Heritability of this metabolite was the highest (0.59), but given that it is at a very low concentration in wheat, it is probably not attractive to plant breeders.

Genotype by environment interactions for growth in Red Angus.

PubMed

Fennewald, D J; Weaber, R L; Lamberson, W R

2017-02-01

Accuracy of sire selection is limited by how well animals are characterized for their environment. The objective of this study was to evaluate the presence of genotype × environment interactions (G×E) for birth weight (BiW) and weaning weight (WW) for Red Angus in the United States. Adjusted weights were provided by the Red Angus Association of America. Environments were defined as 9 regions within the continental United States with similar temperature-humidity indices. Mean weights of calves were determined for each region and for each sire's progeny within each region. A reaction norm (RN) for each bull was estimated by regressing the sire means on the region means weighted for the number of progeny of each sire. The range for BiW and WW RN was -1.3 to 4.0 and -1.7 to 2.8, respectively. The heritabilities of BiW and WW RN were 0.40 and 0.39, respectively. Phenotypic and genetic correlations between BiW and WW RN were 0.19 and 0.54, respectively. The phenotypic correlation of the progeny mean to the RN was -0.20 ( <0.05) and suggests that sires with higher means are more stable in progeny performance across environments. Weights in different regions were considered separate traits and genetic correlations were estimated between all pairs of regions as another method to determine G×E. Genetic correlations < 0.80 indicate G×E at a level for concern, but existed for only 2 of 36 estimates for BiW and 12 of 36 estimates for WW. Genetic correlations between different regions ranged from 0.74 to 0.96 for BiW and 0.62 to 0.99 for WW and indicate that sires tend to rank similarly across environments for these traits.

An experimental study of catechol-o-methyltransferase Val158Met moderation of delta-9-tetrahydrocannabinol-induced effects on psychosis and cognition.

PubMed

Henquet, Cécile; Rosa, Araceli; Krabbendam, Lydia; Papiol, Sergi; Fananás, Lourdes; Drukker, Marjan; Ramaekers, Johannes G; van Os, Jim

2006-12-01

Observational studies have suggested that psychometric psychosis liability and a functional polymorphism in the catechol-O-methyltransferase (COMT Val(158)Met) gene moderate the psychosis-inducing effect of cannabis. To replicate and extend this finding, a double-blind, placebo-controlled cross-over design was used in which patients with a psychotic disorder (n=30), relatives of patients with a psychotic disorder (n=12), and healthy controls (n=32) were exposed to Delta-9-tetrahydrocannabinol (Delta-9-THC, the principal component of cannabis) or placebo, followed by cognitive assessment and assessment of current psychotic experiences. Previous expression of psychometric psychosis liability was also assessed. Models of current psychotic experiences and cognition were examined with multilevel random regression analyses to assess (i) main effects of genotype and condition, (ii) interactions between condition and genotype, and (iii) three-way interactions between condition, genotype, and psychometric psychosis liability. Carriers of the Val allele were most sensitive to Delta-9-THC-induced psychotic experiences, but this was conditional on prior evidence of psychometric psychosis liability. Delta-9-THC impacted negatively on cognitive measures. Carriers of the Val allele were also more sensitive to Delta-9-THC-induced memory and attention impairments compared to carriers of the Met allele. Experimental effects of Delta-9-THC on cognition and psychosis are moderated by COMT Val(158)Met genotype, but the effects may in part be conditional on the additional presence of pre-existing psychosis liability. The association between cannabis and psychosis may represent higher order gene-environment and gene-gene interactions.

Interaction of FKBP5 with Childhood Adversity on Risk for Post-Traumatic Stress Disorder

PubMed Central

Xie, Pingxing; Kranzler, Henry R; Poling, James; Stein, Murray B; Anton, Raymond F; Farrer, Lindsay A; Gelernter, Joel

2010-01-01

FKBP5 regulates the cortisol-binding affinity and nuclear translocation of the glucocorticoid receptor. Polymorphisms at the FKBP5 locus have been associated with increased recurrence risk of depressive episodes and rapid response to antidepressant treatment. A recent study showed that FKBP5 genotypes moderated the risk of post-traumatic stress disorder (PTSD) symptoms associated with childhood maltreatment. One thousand one hundred forty-three European Americans (EAs) and 1284 African Americans (AAs) recruited for studies of the genetics of substance dependence were also screened for lifetime PTSD. Four single-nucleotide polymorphisms (SNPs) in FKBP5, rs3800373, rs9296158, rs1360780, and rs9470080, were genotyped on the complete sample. Logistic regression analyses were performed to explore the interactive effect of FKBP5 polymorphisms and childhood adversity on the risk for PTSD. After correction for multiple testing, childhood adversity significantly increased the risk for PTSD. FKBP5 genotypes were not associated with the development of the disorder. In AAs, one of the SNPs, rs9470080, moderated the risk of PTSD that was associated with childhood abuse. Without childhood adverse experiences, participants with the TT genotype of this SNP had the lowest risk for PTSD, whereas they had the highest risk for PTSD after childhood adversity exposure. In addition, in EAs, alcohol dependence was observed to interact with childhood adverse experiences, and also FKBP5 polymorphisms, to increase the risk for PTSD. This study provides further evidence of a gene × environment effect of FKBP5 and childhood abuse on the risk for PTSD in AAs. Further study is required in other populations. PMID:20393453

Strategy and model building in the fourth dimension: a null model for genotype x age interaction as a Gaussian stationary stochastic process.

PubMed

Diego, Vincent P; Almasy, Laura; Dyer, Thomas D; Soler, Júlia M P; Blangero, John

2003-12-31

Using univariate and multivariate variance components linkage analysis methods, we studied possible genotype x age interaction in cardiovascular phenotypes related to the aging process from the Framingham Heart Study. We found evidence for genotype x age interaction for fasting glucose and systolic blood pressure. There is polygenic genotype x age interaction for fasting glucose and systolic blood pressure and quantitative trait locus x age interaction for a linkage signal for systolic blood pressure phenotypes located on chromosome 17 at 67 cM.

Genotype by environment interaction and breeding for robustness in livestock

PubMed Central

Rauw, Wendy M.; Gomez-Raya, Luis

2015-01-01

The increasing size of the human population is projected to result in an increase in meat consumption. However, at the same time, the dominant position of meat as the center of meals is on the decline. Modern objections to the consumption of meat include public concerns with animal welfare in livestock production systems. Animal breeding practices have become part of the debate since it became recognized that animals in a population that have been selected for high production efficiency are more at risk for behavioral, physiological and immunological problems. As a solution, animal breeding practices need to include selection for robustness traits, which can be implemented through the use of reaction norms analysis, or though the direct inclusion of robustness traits in the breeding objective and in the selection index. This review gives an overview of genotype × environment interactions (the influence of the environment, reaction norms, phenotypic plasticity, canalization, and genetic homeostasis), reaction norms analysis in livestock production, options for selection for increased levels of production and against environmental sensitivity, and direct inclusion of robustness traits in the selection index. Ethical considerations of breeding for improved animal welfare are discussed. The discussion on animal breeding practices has been initiated and is very alive today. This positive trend is part of the sustainable food production movement that aims at feeding 9.15 billion people not just in the near future but also beyond. PMID:26539207

Moderating role of the MAOA genotype in antisocial behaviour

PubMed Central

Fergusson, David M.; Boden, Joseph M.; Horwood, L. John; Miller, Allison; Kennedy, Martin A.

2012-01-01

Background Recent studies have examined gene×environment (G×E) interactions involving the monoamine oxidase A (MAOA) gene in moderating the associations between exposure to adversity and antisocial behaviour. The present study examined a novel method for assessing interactions between a single gene and multiple risk factors related to environmental and personal adversity. Aims To test the hypothesis that the presence of the low-activity MAOA genotype was associated with an increased response to a series of risk factors. Method Participants were 399 males from the Christchurch Health and Development Study who had complete data on: (a) MAOA promoter region variable number tandem repeat genotype; (b) antisocial behaviour (criminal offending) to age 30 and convictions to age 21; and (c) maternal smoking during pregnancy, IQ, childhood maltreatment and school failure. Results Poisson regression models were fitted to three antisocial behaviour outcomes (property/violent offending ages 15–30; and convictions ages 17–21), using measures of exposure to adverse childhood circumstances. The analyses revealed consistent evidence of G x E interactions, such that those with the low-activity MAOA variant who were exposed to adversity in childhood were significantly more likely to report offending in late adolescence and early adulthood. Conclusions The present findings add to the evidence suggesting that there is a stable G x E interaction involving MAOA, a range of adverse environmental and personal factors, and antisocial behaviour across the life course. These analyses also demonstrate the utility of using multiple environmental/personal exposures to test G×E interactions. PMID:22297589

Brain-derived neurotrophic factor as a model system for examining gene by environment interactions across development.

PubMed

Casey, B J; Glatt, C E; Tottenham, N; Soliman, F; Bath, K; Amso, D; Altemus, M; Pattwell, S; Jones, R; Levita, L; McEwen, B; Magariños, A M; Gunnar, M; Thomas, K M; Mezey, J; Clark, A G; Hempstead, B L; Lee, F S

2009-11-24

There has been a dramatic rise in gene x environment studies of human behavior over the past decade that have moved the field beyond simple nature versus nurture debates. These studies offer promise in accounting for more variability in behavioral and biological phenotypes than studies that focus on genetic or experiential factors alone. They also provide clues into mechanisms of modifying genetic risk or resilience in neurodevelopmental disorders. Yet, it is rare that these studies consider how these interactions change over the course of development. In this paper, we describe research that focuses on the impact of a polymorphism in a brain-derived neurotrophic factor (BDNF) gene, known to be involved in learning and development. Specifically we present findings that assess the effects of genotypic and environmental loadings on neuroanatomic and behavioral phenotypes across development. The findings illustrate the use of a genetic mouse model that mimics the human polymorphism, to constrain the interpretation of gene-environment interactions across development in humans.

Genotype by environment interaction in Nelore cattle from five Brazilian states

PubMed Central

Diaz, Iara Del Pilar Solar; de Oliveira, Henrique Nunes; Bezerra, Luis Antônio Framartino; Lôbo, Raysildo Barbosa

2011-01-01

Records from 75,941 Nelore cattle were used to determine the importance of genotype by environment interaction (GEI) in five Brazilian states. (Co)variance components were estimated by single-trait analysis (with yearling weight, W450, considered to be the same trait in all states) and multiple-trait analysis (with the record from each state considered to be a different trait). The direct heritability estimates for yearling weight were 0.51, 0.39, 0.44, 0.37 and 0.41 in the states of Goiás, Mato Grosso, São Paulo, Mato Grosso do Sul and Minas Gerais, respectively. The across-state genetic correlation estimates between Goiás and Mato Grosso, Goiás and Minas Gerais, São Paulo and Minas Gerais, and Mato Grosso do Sul and Minas Gerais ranged from 0.67 to 0.75. These estimates indicate that GEIs are biologically important. No interactions were observed between Goiás and São Paulo, Goiás and Mato Grosso do Sul, Mato Grosso and São Paulo, Mato Grosso and Mato Grosso do Sul, Mato Grosso and Minas Gerais, or São Paulo and Mato Grosso do Sul (0.82 to 0.97). Comparison of single and multiple-trait analyses showed that selection based on the former was less efficient in the presence of GEI, with substantial losses (up to 10%) during selection. PMID:21931516

Influence of apolipoprotein E genotype on the transmission of Alzheimer disease in a community-based sample

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jarvik, G.P.; Larson, E.B.; Goddard, K.

1996-01-01

The {epsilon}4 allele of the apolipoprotein E locus (APOE) has been found to be an important predictor of Alzheimer disease (AD). However, linkage analysis has not clarified the role of APOE in the transmission of AD. The results of the current study provide evidence that the pattern of transmission of memory disorders differs in nuclear families in which the AD-affected proband did carry an {epsilon}4 allele versus those families in which the AD-affected proband did not carry an {epsilon}4 allele. Further, risk of AD due to APOE genotype in the probands is modified by family history of memory disorders, suggestingmore » gene-by-gene interactions. Family history remained a significant predictor of AD for affected probands with some, but not all, APOE genotypes in a logistic regression analysis. Though nonadditive in the prediction of AD, APOE genotype and family history acted additively in the prediction of age at AD onset. The results of complex segregation analysis were inconsistent with Mendelian segregation of memory disorders both in families of affected probands who did or did not carry an {epsilon}4 allele, yet these two groups had significantly different parameter estimates for their transmission models. These results are consistent with gene-by-gene interactions, but also could result from common elements in the familial environment. 41 refs., 1 fig., 7 tabs.« less

Genetic variation for leaf morphology, leaf structure and leaf carbon isotope discrimination in European populations of black poplar (Populus nigra L.).

PubMed

Guet, Justine; Fabbrini, Francesco; Fichot, Régis; Sabatti, Maurizio; Bastien, Catherine; Brignolas, Franck

2015-08-01

To buffer against the high spatial and temporal heterogeneity of the riparian habitat, riparian tree species, such as black poplar (Populus nigra L.), may display a high level of genetic variation and phenotypic plasticity for functional traits. Using a multisite common garden experiment, we estimated the relative contribution of genetic and environmental effects on the phenotypic variation expressed for individual leaf area, leaf shape, leaf structure and leaf carbon isotope discrimination (Δ(13)C) in natural populations of black poplar. Twenty-four to 62 genotypes were sampled in nine metapopulations covering a latitudinal range from 48 °N to 42 °N in France and in Italy and grown in two common gardens at Orléans (ORL) and at Savigliano (SAV). In the two common gardens, substantial genetic variation was expressed for leaf traits within all metapopulations, but its expression was modulated by the environment, as attested by the genotype × environment (G × E) interaction variance being comparable to or even greater than genetic effects. For LA, G × E interactions were explained by both changes in genotype ranking between common gardens and increased variation in SAV, while these interactions were mainly attributed to changes in genotype ranking for Δ(13)C. The nine P. nigra metapopulations were highly differentiated for LA, as attested by the high coefficient of genetic differentiation (QST = 0.50 at ORL and 0.51 at SAV), and the pattern of metapopulation differentiation was highly conserved between the two common gardens. In contrast, they were moderately differentiated for Δ(13)C (QST = 0.24 at ORL and 0.25 at SAV) and the metapopulation clustering changed significantly between common gardens. Our results evidenced that the nine P. nigra metapopulations present substantial genetic variation and phenotypic plasticity for leaf traits, which both represent potentially significant determinants of populations' capacities to respond, on a short-term basis and over generations, to environmental variations. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

ACE insertion/deletion polymorphism and submaximal exercise hemodynamics in postmenopausal women.

PubMed

Hagberg, James M; McCole, Steve D; Brown, Michael D; Ferrell, Robert E; Wilund, Kenneth R; Huberty, Andrea; Douglass, Larry W; Moore, Geoffrey E

2002-03-01

We sought to determine whether the angiotensin-converting enzyme (ACE) insertion (I)/deletion (D) polymorphism is associated with submaximal exercise cardiovascular hemodynamics. Postmenopausal healthy women (20 sedentary, 20 physically active, 22 endurance athletes) had cardiac output (acetylene rebreathing) measured during 40, 60, and 80% VO(2 max) exercise. The interaction of ACE genotype and habitual physical activity (PA) level was significantly associated with submaximal exercise systolic blood pressure, with only sedentary women exhibiting differences among genotypes. No significant effects of ACE genotype or its interaction with PA levels was observed for submaximal exercise diastolic blood pressure. ACE genotype was significantly associated with submaximal exercise heart rate (HR) with ACE II having approximately 10 beats/min higher HR than ACE ID/DD genotype women. ACE genotype did not interact significantly with habitual PA level to associate with submaximal exercise HR. ACE genotype was not independently, but was interactively with habitual PA levels, associated with differences in submaximal exercise cardiac output and stroke volume. For cardiac output, ACE II genotype women athletes had ~25% greater cardiac output than ACE DD genotype women athletes, whereas for stroke volume genotype-dependent differences were observed in both the physically active and athletic women. ACE genotype was not significantly associated, either independently or interactively with habitual PA levels, with submaximal exercise total peripheral resistance or arteriovenous O(2) difference. Thus the common ACE locus polymorphic variation is associated with many submaximal exercise cardiovascular hemodynamic responses.

Genetic Basis for Variation in Wheat Grain Yield in Response to Varying Nitrogen Application.

PubMed

Mahjourimajd, Saba; Taylor, Julian; Sznajder, Beata; Timmins, Andy; Shahinnia, Fahimeh; Rengel, Zed; Khabaz-Saberi, Hossein; Kuchel, Haydn; Okamoto, Mamoru; Langridge, Peter

2016-01-01

Nitrogen (N) is a major nutrient needed to attain optimal grain yield (GY) in all environments. Nitrogen fertilisers represent a significant production cost, in both monetary and environmental terms. Developing genotypes capable of taking up N early during development while limiting biomass production after establishment and showing high N-use efficiency (NUE) would be economically beneficial. Genetic variation in NUE has been shown previously. Here we describe the genetic characterisation of NUE and identify genetic loci underlying N response under different N fertiliser regimes in a bread wheat population of doubled-haploid lines derived from a cross between two Australian genotypes (RAC875 × Kukri) bred for a similar production environment. NUE field trials were carried out at four sites in South Australia and two in Western Australia across three seasons. There was genotype-by-environment-by-treatment interaction across the sites and also good transgressive segregation for yield under different N supply in the population. We detected some significant Quantitative Trait Loci (QTL) associated with NUE and N response at different rates of N application across the sites and years. It was also possible to identify lines showing positive N response based on the rankings of their Best Linear Unbiased Predictions (BLUPs) within a trial. Dissecting the complexity of the N effect on yield through QTL analysis is a key step towards elucidating the molecular and physiological basis of NUE in wheat.

Genetic variation for resistance to ergot (Claviceps purpurea [Fr.] Tul.) among full-sib families of five populations of winter rye (Secale cereale L.).

PubMed

Mirdita, V; Dhillon, B S; Geiger, H H; Miedaner, T

2008-12-01

Ergot (Claviceps purpurea [Fr.] Tul.) is a serious disease of rye (Secale cereale L.) and it adversely affects the quality of grain. The present investigation was undertaken to study genotypic variability among full-sib families (FSF) of five open-pollinated (OP) winter rye populations of highly diverse origin, namely Dankovskie Selekcyine (Poland), Charkovskaja (Ukraine), NEM4 (Russia), Halo and Carokurz, both from Germany. About 50 FSF were developed at random in each population, and the FSF of each population were evaluated in separate but adjacent experiments conducted in four environments under artificial inoculation. A mixture of conidia of C. purpurea isolates was sprayed thrice during the flowering period. The materials were manually harvested at yellow-ripe stage. Resistance trait recorded was disease severity, i.e. percent ergot sclerotia in grain by weight. Mean ergot severity ranged from 2.29 to 4.08% for the five populations across environments. Significant genotypic variation (P < 0.01) due to FSF and FSF x environment interaction was observed within each population. Genotypic variation within all populations was higher than that among five populations. All populations showed high estimates of heritability (0.72-0.89). The study indicated that the evaluated OP populations are rich reservoirs of genetic variation that should also be used in hybrid breeding. Recurrent selection to further improve ergot resistance should be successful.

Crop epigenetics and the molecular hardware of genotype × environment interactions.

PubMed

King, Graham J

2015-01-01

Crop plants encounter thermal environments which fluctuate on a diurnal and seasonal basis. Future climate resilient cultivars will need to respond to thermal profiles reflecting more variable conditions, and harness plasticity that involves regulation of epigenetic processes and complex genomic regulatory networks. Compartmentalization within plant cells insulates the genomic central processing unit within the interphase nucleus. This review addresses the properties of the chromatin hardware in which the genome is embedded, focusing on the biophysical and thermodynamic properties of DNA, histones and nucleosomes. It explores the consequences of thermal and ionic variation on the biophysical behavior of epigenetic marks such as DNA cytosine methylation (5mC), and histone variants such as H2A.Z, and how these contribute to maintenance of chromatin integrity in the nucleus, while enabling specific subsets of genes to be regulated. Information is drawn from theoretical molecular in vitro studies as well as model and crop plants and incorporates recent insights into the role epigenetic processes play in mediating between environmental signals and genomic regulation. A preliminary speculative framework is outlined, based on the evidence of what appears to be a cohesive set of interactions at molecular, biophysical and electrostatic level between the various components contributing to chromatin conformation and dynamics. It proposes that within plant nuclei, general and localized ionic homeostasis plays an important role in maintaining chromatin conformation, whilst maintaining complex genomic regulation that involves specific patterns of epigenetic marks. More generally, reversible changes in DNA methylation appear to be consistent with the ability of nuclear chromatin to manage variation in external ionic and temperature environment. Whilst tentative, this framework provides scope to develop experimental approaches to understand in greater detail the internal environment of plant nuclei. It is hoped that this will generate a deeper understanding of the molecular mechanisms underlying genotype × environment interactions that may be beneficial for long-term improvement of crop performance in less predictable climates.

Crop epigenetics and the molecular hardware of genotype × environment interactions

PubMed Central

King, Graham J.

2015-01-01

Crop plants encounter thermal environments which fluctuate on a diurnal and seasonal basis. Future climate resilient cultivars will need to respond to thermal profiles reflecting more variable conditions, and harness plasticity that involves regulation of epigenetic processes and complex genomic regulatory networks. Compartmentalization within plant cells insulates the genomic central processing unit within the interphase nucleus. This review addresses the properties of the chromatin hardware in which the genome is embedded, focusing on the biophysical and thermodynamic properties of DNA, histones and nucleosomes. It explores the consequences of thermal and ionic variation on the biophysical behavior of epigenetic marks such as DNA cytosine methylation (5mC), and histone variants such as H2A.Z, and how these contribute to maintenance of chromatin integrity in the nucleus, while enabling specific subsets of genes to be regulated. Information is drawn from theoretical molecular in vitro studies as well as model and crop plants and incorporates recent insights into the role epigenetic processes play in mediating between environmental signals and genomic regulation. A preliminary speculative framework is outlined, based on the evidence of what appears to be a cohesive set of interactions at molecular, biophysical and electrostatic level between the various components contributing to chromatin conformation and dynamics. It proposes that within plant nuclei, general and localized ionic homeostasis plays an important role in maintaining chromatin conformation, whilst maintaining complex genomic regulation that involves specific patterns of epigenetic marks. More generally, reversible changes in DNA methylation appear to be consistent with the ability of nuclear chromatin to manage variation in external ionic and temperature environment. Whilst tentative, this framework provides scope to develop experimental approaches to understand in greater detail the internal environment of plant nuclei. It is hoped that this will generate a deeper understanding of the molecular mechanisms underlying genotype × environment interactions that may be beneficial for long-term improvement of crop performance in less predictable climates. PMID:26594221

The Influence of Nutritional Factors on Verbal Deficits and Psychopathic Personality Traits: Evidence of the Moderating Role of the MAOA Genotype

PubMed Central

Jackson, Dylan B.; Beaver, Kevin M.

2015-01-01

The current study explores whether: (a) nutritional factors among adolescent males predict their risk of exhibiting verbal deficits and psychopathic traits during adulthood and (b) the link between nutritional factors and these outcomes is conditioned by the MAOA genotype. The study analyzes data from the U.S. National Longitudinal Study of Adolescent Health (Add Health), a nationally representative, genetically informative sample. We find evidence that meal deprivation increases the likelihood of both verbal deficits and psychopathic personality traits, whereas poor quality nutrition increases the risk of verbal deficits. We detect the presence of a number of gene-environment interactions between measures of food quality and MAOA genotype, but no evidence of GxE in the case of meal deprivation. Limitations are noted and avenues for future research are discussed. PMID:26690459

Dopamine D4 receptor gene and religious affiliation correlate with dictator game altruism in males and not females: evidence for gender-sensitive gene × culture interaction.

PubMed

Jiang, Yushi; Bachner-Melman, Rachel; Chew, Soo Hong; Ebstein, Richard P

2015-01-01

On a large sample of 2288 Han Chinese undergraduates, we investigated how religion and DRD4 are related to human altruistic giving behavior as measured with the Andreoni-Miller Dictator Game. This game enables us to clearly specify (non-)selfishness, efficiency, and fairness motives for sharing. Participants were further classified into religious categories (Christian, Buddhist-Tao, and No Religion) based on self-reports, and genotyped for the dopamine D4 receptor (DRD4) gene exon III VNTR. Our analysis revealed a significant interaction between religion and DRD4 correlated with giving behavior solely among males: Whereas no significant association between religion and sharing decisions was observed in the majority 4R/4R genotype group, a significant difference in giving behavior between Christian and non-Christian males was seen in the non-4R/4R group, with Christian men being overall more altruistic (less selfish and fairer) than non-Christian men. These results support the vantage sensitivity hypothesis regarding DRD4 that the non-4R/4R "susceptibility" genotype is more responsive to a positive environment provided by some religions.

Dopamine D4 receptor gene and religious affiliation correlate with dictator game altruism in males and not females: evidence for gender-sensitive gene × culture interaction

PubMed Central

Jiang, Yushi; Bachner-Melman, Rachel; Chew, Soo Hong; Ebstein, Richard P.

2015-01-01

On a large sample of 2288 Han Chinese undergraduates, we investigated how religion and DRD4 are related to human altruistic giving behavior as measured with the Andreoni-Miller Dictator Game. This game enables us to clearly specify (non-)selfishness, efficiency, and fairness motives for sharing. Participants were further classified into religious categories (Christian, Buddhist-Tao, and No Religion) based on self-reports, and genotyped for the dopamine D4 receptor (DRD4) gene exon III VNTR. Our analysis revealed a significant interaction between religion and DRD4 correlated with giving behavior solely among males: Whereas no significant association between religion and sharing decisions was observed in the majority 4R/4R genotype group, a significant difference in giving behavior between Christian and non-Christian males was seen in the non-4R/4R group, with Christian men being overall more altruistic (less selfish and fairer) than non-Christian men. These results support the vantage sensitivity hypothesis regarding DRD4 that the non-4R/4R “susceptibility” genotype is more responsive to a positive environment provided by some religions. PMID:26441510

Evolutionary history, immigration history, and the extent of diversification in community assembly.

PubMed

Knope, Matthew L; Forde, Samantha E; Fukami, Tadashi

2011-01-01

During community assembly, species may accumulate not only by immigration, but also by in situ diversification. Diversification has intrigued biologists because its extent varies even among closely related lineages under similar ecological conditions. Recent research has suggested that some of this puzzling variation may be caused by stochastic differences in the history of immigration (relative timing and order of immigration by founding populations), indicating that immigration and diversification may affect community assembly interactively. However, the conditions under which immigration history affects diversification remain unclear. Here we propose the hypothesis that whether or not immigration history influences the extent of diversification depends on the founding populations' prior evolutionary history, using evidence from a bacterial experiment. To create genotypes with different evolutionary histories, replicate populations of Pseudomonas fluorescens were allowed to adapt to a novel environment for a short or long period of time (approximately 10 or 100 bacterial generations) with or without exploiters (viral parasites). Each evolved genotype was then introduced to a new habitat either before or after a standard competitor genotype. Most genotypes diversified to a greater extent when introduced before, rather than after, the competitor. However, introduction order did not affect the extent of diversification when the evolved genotype had previously adapted to the environment for a long period of time without exploiters. Diversification of these populations was low regardless of introduction order. These results suggest that the importance of immigration history in diversification can be predicted by the immigrants' evolutionary past. The hypothesis proposed here may be generally applicable in both micro- and macro-organisms.

Defining a genetic ideotype for crop improvement.

PubMed

Trethowan, Richard M

2014-01-01

While plant breeders traditionally base selection on phenotype, the development of genetic ideotypes can help focus the selection process. This chapter provides a road map for the establishment of a refined genetic ideotype. The first step is an accurate definition of the target environment including the underlying constraints, their probability of occurrence, and impact on phenotype. Once the environmental constraints are established, the wealth of information on plant physiological responses to stresses, known gene information, and knowledge of genotype ×environment and gene × environment interaction help refine the target ideotype and form a basis for cross prediction.Once a genetic ideotype is defined the challenge remains to build the ideotype in a plant breeding program. A number of strategies including marker-assisted recurrent selection and genomic selection can be used that also provide valuable information for the optimization of genetic ideotype. However, the informatics required to underpin the realization of the genetic ideotype then becomes crucial. The reduced cost of genotyping and the need to combine pedigree, phenotypic, and genetic data in a structured way for analysis and interpretation often become the rate-limiting steps, thus reducing genetic gain. Systems for managing these data and an example of ideotype construction for a defined environment type are discussed.

The Oxytocin Receptor Gene (OXTR) in Relation to State Levels of Loneliness in Adolescence: Evidence for Micro-Level Gene-Environment Interactions

PubMed Central

van Roekel, Eeske; Verhagen, Maaike; Scholte, Ron H. J.; Kleinjan, Marloes; Goossens, Luc; Engels, Rutger C. M. E.

2013-01-01

Previous research has shown that the rs53576 variant of the oxytocin receptor gene (OXTR) is associated with trait levels of loneliness, but results are inconsistent. The aim of the present study is to examine micro-level effects of the OXTR rs53576 variant on state levels of loneliness in early adolescents. In addition, gene-environment interactions are examined between this OXTR variant and positive and negative perceptions of company. Data were collected in 278 adolescents (58% girls), by means of the Experience Sampling Method (ESM). Sampling periods consisted of six days with nine assessments per day. A relation was found between the OXTR rs53576 variant and state loneliness, in girls only. Girls carrying an A allele had higher levels of state loneliness than girls carrying the GG genotype. In addition, adolescents with an A allele were more affected by negative perceptions of company than GG carriers, on weekend days only. No significant gene-environment interactions were found with positive company. Adolescents carrying an A allele were more susceptible to negative environments during weekend days than GG carriers. Our findings emphasize the importance of operationalizing the phenotype and the environment accurately. PMID:24223720

The oxytocin receptor gene (OXTR) in relation to state levels of loneliness in adolescence: evidence for micro-level gene-environment interactions.

PubMed

van Roekel, Eeske; Verhagen, Maaike; Scholte, Ron H J; Kleinjan, Marloes; Goossens, Luc; Engels, Rutger C M E

2013-01-01

Previous research has shown that the rs53576 variant of the oxytocin receptor gene (OXTR) is associated with trait levels of loneliness, but results are inconsistent. The aim of the present study is to examine micro-level effects of the OXTR rs53576 variant on state levels of loneliness in early adolescents. In addition, gene-environment interactions are examined between this OXTR variant and positive and negative perceptions of company. Data were collected in 278 adolescents (58% girls), by means of the Experience Sampling Method (ESM). Sampling periods consisted of six days with nine assessments per day. A relation was found between the OXTR rs53576 variant and state loneliness, in girls only. Girls carrying an A allele had higher levels of state loneliness than girls carrying the GG genotype. In addition, adolescents with an A allele were more affected by negative perceptions of company than GG carriers, on weekend days only. No significant gene-environment interactions were found with positive company. Adolescents carrying an A allele were more susceptible to negative environments during weekend days than GG carriers. Our findings emphasize the importance of operationalizing the phenotype and the environment accurately.

Culture as a mediator of gene-environment interaction: Cultural consonance, childhood adversity, a 2A serotonin receptor polymorphism, and depression in urban Brazil.

PubMed

Dressler, William W; Balieiro, Mauro C; Ferreira de Araújo, Luiza; Silva, Wilson A; Ernesto Dos Santos, José

2016-07-01

Research on gene-environment interaction was facilitated by breakthroughs in molecular biology in the late 20th century, especially in the study of mental health. There is a reliable interaction between candidate genes for depression and childhood adversity in relation to mental health outcomes. The aim of this paper is to explore the role of culture in this process in an urban community in Brazil. The specific cultural factor examined is cultural consonance, or the degree to which individuals are able to successfully incorporate salient cultural models into their own beliefs and behaviors. It was hypothesized that cultural consonance in family life would mediate the interaction of genotype and childhood adversity. In a study of 402 adult Brazilians from diverse socioeconomic backgrounds, conducted from 2011 to 2014, the interaction of reported childhood adversity and a polymorphism in the 2A serotonin receptor was associated with higher depressive symptoms. Further analysis showed that the gene-environment interaction was mediated by cultural consonance in family life, and that these effects were more pronounced in lower social class neighborhoods. The findings reinforce the role of the serotonergic system in the regulation of stress response and learning and memory, and how these processes in turn interact with environmental events and circumstances. Furthermore, these results suggest that gene-environment interaction models should incorporate a wider range of environmental experience and more complex pathways to better understand how genes and the environment combine to influence mental health outcomes. Copyright © 2016 Elsevier Ltd. All rights reserved.

5HTT genotype moderates the influence of early institutional deprivation on emotional problems in adolescence: evidence from the English and Romanian Adoptee (ERA) study.

PubMed

Kumsta, Robert; Stevens, Suzanne; Brookes, Keeley; Schlotz, Wolff; Castle, Jenny; Beckett, Celia; Kreppner, Jana; Rutter, Michael; Sonuga-Barke, Edmund

2010-07-01

A common polymorphism in the serotonin transporter gene (SLC6A4, 5HTT) has been repeatedly shown to moderate the influence of childhood adversity and stressful life events on the development of psychopathology. Using data from the English and Romanian Adoptee Study, a prospective-longitudinal study of individuals (n = 125) exposed to severe early institutional deprivation (ID), we tested whether the effect of ID on adolescent emotional problems is moderated by 5HTT genotype and stressful life events in adolescence. Emotional problems were assessed using questionnaire data (age 11), and on the basis of the CAPA diagnostic interview (age 15). Additionally, the number of stressful life events was measured. There was a significant effect for genotype (p = .003) and a gene x environment interaction (p = .008) that was independent of age at testing. Carriers of the s/l and s/s genotype who experienced severe ID showed the highest emotional problem scores, while l/l homozygotes in the severe ID group showed the lowest overall levels. Furthermore, s/s carriers in the severe ID group who experienced a high number of stressful life events between 11 and 15 years had the largest increases in emotional problem scores, while a low number of stressful life events was associated with the largest decrease (4-way interaction: p = .05). The effects of severe early ID on emotional problems in adolescence are moderated by 5HTT genotype, and influenced by stressful life events in adolescence.

MAOA genotype, childhood maltreatment, and their interaction in the etiology of adult antisocial behaviors.

PubMed

Haberstick, Brett C; Lessem, Jeffrey M; Hewitt, John K; Smolen, Andrew; Hopfer, Christian J; Halpern, Carolyn T; Killeya-Jones, Ley A; Boardman, Jason D; Tabor, Joyce; Siegler, Ilene C; Williams, Redford B; Mullan Harris, Kathleen

2014-01-01

Maltreatment by an adult or caregiver during childhood is a prevalent and important predictor of antisocial behaviors in adulthood. A functional promoter polymorphism in the monoamine oxidase A (MAOA) gene has been implicated as a moderating factor in the relationship between childhood maltreatment and antisocial behaviors. Although there have been numerous attempts at replicating this observation, results remain inconclusive. We examined this gene-environment interaction hypothesis in a sample of 3356 white and 960 black men (aged 24-34) participating in the National Longitudinal Study of Adolescent Health. Primary analysis indicated that childhood maltreatment was a significant risk factor for later behaviors that violate rules and the rights of others (p < .05), there were no main effects of MAOA genotype, and MAOA genotype was not a significant moderator of the relationship between maltreatment and antisocial behaviors in our white sample. Post hoc analyses identified a similar pattern of results among our black sample in which maltreatment was not a significant predictor of antisocial behavior. Post hoc analyses also revealed a main effect of MAOA genotype on having a disposition toward violence in both samples and for violent convictions among our black sample. None of these post hoc findings, however, survived correction for multiple testing (p > .05). Power analyses indicated that these results were not due to insufficient statistical power. We could not confirm the hypothesis that MAOA genotype moderates the relationship between childhood maltreatment and adult antisocial behaviors. Copyright © 2014 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Genetic composition of social groups influences male aggressive behaviour and fitness in natural genotypes of Drosophila melanogaster.

PubMed

Saltz, Julia B

2013-11-22

Indirect genetic effects (IGEs) describe how an individual's behaviour-which is influenced by his or her genotype-can affect the behaviours of interacting individuals. IGE research has focused on dyads. However, insights from social networks research, and other studies of group behaviour, suggest that dyadic interactions are affected by the behaviour of other individuals in the group. To extend IGE inferences to groups of three or more, IGEs must be considered from a group perspective. Here, I introduce the 'focal interaction' approach to study IGEs in groups. I illustrate the utility of this approach by studying aggression among natural genotypes of Drosophila melanogaster. I chose two natural genotypes as 'focal interactants': the behavioural interaction between them was the 'focal interaction'. One male from each focal interactant genotype was present in every group, and I varied the genotype of the third male-the 'treatment male'. Genetic variation in the treatment male's aggressive behaviour influenced the focal interaction, demonstrating that IGEs in groups are not a straightforward extension of IGEs measured in dyads. Further, the focal interaction influenced male mating success, illustrating the role of IGEs in behavioural evolution. These results represent the first manipulative evidence for IGEs at the group level.

Genotype by environment (climate) interaction improves genomic prediction for production traits in US Holstein cattle.

PubMed

Tiezzi, F; de Los Campos, G; Parker Gaddis, K L; Maltecca, C

2017-03-01

Genotype by environment interaction (G × E) in dairy cattle productive traits has been shown to exist, but current genetic evaluation methods do not take this component into account. As several environmental descriptors (e.g., climate, farming system) are known to vary within the United States, not accounting for the G × E could lead to reranking of bulls and loss in genetic gain. Using test-day records on milk yield, somatic cell score, fat, and protein percentage from all over the United States, we computed within herd-year-season daughter yield deviations for 1,087 Holstein bulls and regressed them on genetic and environmental information to estimate variance components and to assess prediction accuracy. Genomic information was obtained from a 50k SNP marker panel. Environmental effect inputs included herd (160 levels), geographical region (7 levels), geographical location (2 variables), climate information (7 variables), and management conditions of the herds (16 total variables divided in 4 subgroups). For each set of environmental descriptors, environmental, genomic, and G × E components were sequentially fitted. Variance components estimates confirmed the presence of G × E on milk yield, with its effect being larger than main genetic effect and the environmental effect for some models. Conversely, G × E was moderate for somatic cell score and small for milk composition. Genotype by environment interaction, when included, partially eroded the genomic effect (as compared with the models where G × E was not included), suggesting that the genomic variance could at least in part be attributed to G × E not appropriately accounted for. Model predictive ability was assessed using 3 cross-validation schemes (new bulls, incomplete progeny test, and new environmental conditions), and performance was compared with a reference model including only the main genomic effect. In each scenario, at least 1 of the models including G × E was able to perform better than the reference model, although it was not possible to find the overall best-performing model that included the same set of environmental descriptors. In general, the methodology used is promising in accounting for G × E in genomic predictions, but challenges exist in identifying a unique set of covariates capable of describing the entire variety of environments. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Family variation in photosynthesis of 22-year-old black spruce: a test of two models of physiological response to water stress

Treesearch

John E. Major; Kurt H. Johnsen

1996-01-01

Gas exchange and water potential were measured in 22-year-old black spruce (Piceamariana (Mill.) BSP) trees from four full-sib families on two sites (one drier and one wetter) at the Petawawa National Forestry Institute, Ontario. Based on an observed genotype × environment interaction and earlier work with seedlings, a...

Modification of the association between early adversity and obsessive-compulsive disorder by polymorphisms in the MAOA, MAOB and COMT genes.

PubMed

McGregor, N W; Hemmings, S M J; Erdman, L; Calmarza-Font, I; Stein, D J; Lochner, C

2016-12-30

The monoamine oxidases (MAOA/B) and catechol-O-methyltransferase (COMT) enzymes break down regulatory components within serotonin and dopamine pathways, and polymorphisms within these genes are candidates for OCD susceptibility. Childhood trauma has been linked OCD psychopathology, but little attention has been paid to the interactions between genes and environment in OCD aetiology. This pilot study investigated gene-by-environment interactions between childhood trauma and polymorphisms in the MAOA, MAOB and COMT genes in OCD. Ten polymorphisms (MAOA: 3 variants, MAOB: 4 variants, COMT: 3 variants) were genotyped in a cohort of OCD patients and controls. Early-life trauma was assessed using the Childhood Trauma Questionnaire (CTQ). Gene-by-gene (GxG) and gene-by-environment interactions (GxE) of the variants and childhood trauma were assessed using logistic regression models. Significant GxG interactions were found between rs362204 (COMT) and two independent polymorphisms in the MAOB gene (rs1799836 and rs6651806). Haplotype associations for OCD susceptibility were found for MAOB. Investigation of GxE interactions indicated that the sexual abuse sub-category was significantly associated with all three genes in haplotype x environment interaction analyses. Preliminary findings indicate that polymorphisms within the MAOB and COMT genes interact resulting in risk for OCD. Childhood trauma interacts with haplotypes in COMT, MAOA and MAOB, increasing risk for OCD. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Microbial interactions: ecology in a molecular perspective.

PubMed

Braga, Raíssa Mesquita; Dourado, Manuella Nóbrega; Araújo, Welington Luiz

2016-12-01

The microorganism-microorganism or microorganism-host interactions are the key strategy to colonize and establish in a variety of different environments. These interactions involve all ecological aspects, including physiochemical changes, metabolite exchange, metabolite conversion, signaling, chemotaxis and genetic exchange resulting in genotype selection. In addition, the establishment in the environment depends on the species diversity, since high functional redundancy in the microbial community increases the competitive ability of the community, decreasing the possibility of an invader to establish in this environment. Therefore, these associations are the result of a co-evolution process that leads to the adaptation and specialization, allowing the occupation of different niches, by reducing biotic and abiotic stress or exchanging growth factors and signaling. Microbial interactions occur by the transference of molecular and genetic information, and many mechanisms can be involved in this exchange, such as secondary metabolites, siderophores, quorum sensing system, biofilm formation, and cellular transduction signaling, among others. The ultimate unit of interaction is the gene expression of each organism in response to an environmental (biotic or abiotic) stimulus, which is responsible for the production of molecules involved in these interactions. Therefore, in the present review, we focused on some molecular mechanisms involved in the microbial interaction, not only in microbial-host interaction, which has been exploited by other reviews, but also in the molecular strategy used by different microorganisms in the environment that can modulate the establishment and structuration of the microbial community. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Resolving the infection process reveals striking differences in the contribution of environment, genetics and phylogeny to host-parasite interactions

PubMed Central

2011-01-01

Background Infection processes consist of a sequence of steps, each critical for the interaction between host and parasite. Studies of host-parasite interactions rarely take into account the fact that different steps might be influenced by different factors and might, therefore, make different contributions to shaping coevolution. We designed a new method using the Daphnia magna - Pasteuria ramosa system, one of the rare examples where coevolution has been documented, in order to resolve the steps of the infection and analyse the factors that influence each of them. Results Using the transparent Daphnia hosts and fluorescently-labelled spores of the bacterium P. ramosa, we identified a sequence of infection steps: encounter between parasite and host; activation of parasite dormant spores; attachment of spores to the host; and parasite proliferation inside the host. The chances of encounter had been shown to depend on host genotype and environment. We tested the role of genetic and environmental factors in the newly described activation and attachment steps. Hosts of different genotypes, gender and species were all able to activate endospores of all parasite clones tested in different environments; suggesting that the activation cue is phylogenetically conserved. We next established that parasite attachment occurs onto the host oesophagus independently of host species, gender and environmental conditions. In contrast to spore activation, attachment depended strongly on the combination of host and parasite genotypes. Conclusions Our results show that different steps are influenced by different factors. Host-type-independent spore activation suggests that this step can be ruled out as a major factor in Daphnia-Pasteuria coevolution. On the other hand, we show that the attachment step is crucial for the pronounced genetic specificities of this system. We suggest that this one step can explain host population structure and could be a key force behind coevolutionary cycles. We discuss how different steps can explain different aspects of the coevolutionary dynamics of the system: the properties of the attachment step, explaining the rapid evolution of infectivity and the properties of later parasite proliferation explaining the evolution of virulence. Our study underlines the importance of resolving the infection process in order to better understand host-parasite interactions. PMID:21342515

Evolutionary process of Bos taurus cattle in favourable versus unfavourable environments and its implications for genetic selection

PubMed Central

O'Neill, Christopher J; Swain, David L; Kadarmideen, Haja N

2010-01-01

The evolutionary processes that have enabled Bos taurus cattle to establish around the globe are at the core to the future success of livestock production. Our study focuses on the history of cattle domestication including the last 60 years of B. taurus breeding programmes in both favourable and unfavourable environments and its consequences on evolution and fitness of cattle. We discuss the emergence of ‘production diseases’ in temperate production systems and consider the evolutionary genetics of tropical adaptation in cattle and conclude that the Senepol, N'Dama, Adaptaur and Criollo breeds, among others with similar evolutionary trajectories, would possess genes capable of improving the productivity of cattle in challenging environments. Using our own experimental evidence from northern Australia, we review the evolution of the Adaptaur cattle breed which has become resistant to cattle tick. We emphasize that the knowledge of interactions between genotype, environment and management in the livestock systems will be required to generate genotypes for efficient livestock production that are both economically and environmentally sustainable. Livestock producers in the 21st century will have less reliance on infrastructure and veterinary products to alleviate environmental stress and more on the animal's ability to achieve fitness in a given production environment. PMID:25567936

Evolutionary process of Bos taurus cattle in favourable versus unfavourable environments and its implications for genetic selection.

PubMed

O'Neill, Christopher J; Swain, David L; Kadarmideen, Haja N

2010-09-01

The evolutionary processes that have enabled Bos taurus cattle to establish around the globe are at the core to the future success of livestock production. Our study focuses on the history of cattle domestication including the last 60 years of B. taurus breeding programmes in both favourable and unfavourable environments and its consequences on evolution and fitness of cattle. We discuss the emergence of 'production diseases' in temperate production systems and consider the evolutionary genetics of tropical adaptation in cattle and conclude that the Senepol, N'Dama, Adaptaur and Criollo breeds, among others with similar evolutionary trajectories, would possess genes capable of improving the productivity of cattle in challenging environments. Using our own experimental evidence from northern Australia, we review the evolution of the Adaptaur cattle breed which has become resistant to cattle tick. We emphasize that the knowledge of interactions between genotype, environment and management in the livestock systems will be required to generate genotypes for efficient livestock production that are both economically and environmentally sustainable. Livestock producers in the 21st century will have less reliance on infrastructure and veterinary products to alleviate environmental stress and more on the animal's ability to achieve fitness in a given production environment.

5-HTTLPR Expression Outside the Skin: An Experimental Test of the Emotional Reactivity Hypothesis in Children

PubMed Central

Weeland, Joyce; Slagt, Meike; Brummelman, Eddie; Matthys, Walter; de Castro, Bram Orobio; Overbeek, Geertjan

2015-01-01

Background There is increasing evidence that variation in the promoter region of the serotonin transporter gene SLC6A4 (i.e., the 5-HTTLPR polymorphism) moderates the impact of environmental stressors on child psychopathology. Emotional reactivity −the intensity of an individual’s response to other’s emotions− has been put forward as a possible mechanism underlying these gene-by-environment interactions (i.e., G×E). Compared to children homozygous for the L-allele (LL-genotypes), children carrying an S-allele (SS/SL-genotypes), specifically when they have been frequently exposed to negative emotions in the family environment, might be more emotionally reactive and therefore more susceptible to affective environmental stressors. However, the association between 5-HTTLPR and emotional reactivity in children has not yet been empirically tested. Therefore, the goal of this study was to test this association in a large-scale experiment. Methods Children (N = 521, 52.5% boys, Mage = 9.72 years) were genotyped and randomly assigned to happy, angry or neutral dynamic facial expressions and vocalizations. Motor and affective emotional reactivity were assessed through children’s self-reported negative and positive affect (n = 460) and facial electromyography activity (i.e., fEMG: the zygomaticus or “smile” muscle and the corrugator or “frown” muscle, n = 403). Parents reported on their negative and positive parenting behaviors. Results Children mimicked and experienced the emotion they were exposed to. However, neither motor reactivity nor affective reactivity to these emotions depended on children’s 5-HTTLPR genotype: SS/SL-genotypes did not manifest any stronger response to emotional stimuli than LL-genotypes. This finding remained the same when taking the broader family environment into account, controlling for kinship, age, gender and genetic ancestry, and when including a tri-allelic factor. Conclusions We found no evidence for an association between the 5-HTTLPR polymorphism and children’s emotional reactivity. This finding is important, in discounting one potential underlying endophenotype of G×E between the 5-HTTLPR and affective environmental stressors. PMID:26560754

Natural genetic variation in social environment choice: context-dependent gene-environment correlation in Drosophila melanogaster.

PubMed

Saltz, Julia B

2011-08-01

Gene-environment correlation (rGE) occurs when an individual's genotype determines its choice of environment, generating a correlation between environment and genotype frequency. In particular, social rGE, caused by genetic variation in social environment choice, can critically determine both individual development and the course of social selection. Despite its foundational role in social evolution and developmental psychology theory, natural genetic variation in social environment choice has scarcely been examined empirically. Drosophila melanogaster provides an ideal system for investigating social rGE. Flies live socially in nature and have many opportunities to make social decisions; and natural, heterozygous genotypes may be replicated, enabling comparisons between genotypes across environments. Using this approach, I show that all aspects of social environment choice vary among natural genotypes, demonstrating pervasive social rGE. Surprisingly, genetic variation in group-size preference was density dependent, indicating that the behavioral and evolutionary consequences of rGE may depend on the context in which social decisions are made. These results provide the first detailed investigation of social rGE, and illustrate that that genetic variation may influence organismal performance by specifying the environment in which traits are expressed. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Conservation of social effects (Ψ) between two species of Drosophila despite reversal of sexual dimorphism.

PubMed

Signor, Sarah A; Abbasi, Mohammad; Marjoram, Paul; Nuzhdin, Sergey V

2017-12-01

Indirect genetic effects (IGEs) describe the effect of the genes of social partners on the phenotype of a focal individual. Here, we measure indirect genetic effects using the "coefficient of interaction" (Ψ) to test whether Ψ evolved between Drosophila melanogaster and D. simulans . We compare Ψ for locomotion between ethanol and nonethanol environments in both species, but only D. melanogaster utilizes ethanol ecologically. We find that while sexual dimorphism for locomotion has been reversed in D. simulans , there has been no evolution of social effects between these two species. What did evolve was the interaction between genotype-specific Ψ and the environment, as D. melanogaster  varies unpredictably between environments and D. simulans  does not. In this system, this suggests evolutionary lability of sexual dimorphism but a conservation of social effects, which brings forth interesting questions about the role of the social environment in sexual selection.

Quantification of the effects of VRN1 and Ppd-D1 to predict spring wheat (Triticum aestivum) heading time across diverse environments

PubMed Central

Zheng, Bangyou; Biddulph, Ben; Li, Dora; Kuchel, Haydn; Chapman, Scott

2013-01-01

Heading time is a major determinant of the adaptation of wheat to different environments, and is critical in minimizing risks of frost, heat, and drought on reproductive development. Given that major developmental genes are known in wheat, a process-based model, APSIM, was modified to incorporate gene effects into estimation of heading time, while minimizing degradation in the predictive capability of the model. Model parameters describing environment responses were replaced with functions of the number of winter and photoperiod (PPD)-sensitive alleles at the three VRN1 loci and the Ppd-D1 locus, respectively. Two years of vernalization and PPD trials of 210 lines (spring wheats) at a single location were used to estimate the effects of the VRN1 and Ppd-D1 alleles, with validation against 190 trials (~4400 observations) across the Australian wheatbelt. Compared with spring genotypes, winter genotypes for Vrn-A1 (i.e. with two winter alleles) had a delay of 76.8 degree days (°Cd) in time to heading, which was double the effect of the Vrn-B1 or Vrn-D1 winter genotypes. Of the three VRN1 loci, winter alleles at Vrn-B1 had the strongest interaction with PPD, delaying heading time by 99.0 °Cd under long days. The gene-based model had root mean square error of 3.2 and 4.3 d for calibration and validation datasets, respectively. Virtual genotypes were created to examine heading time in comparison with frost and heat events and showed that new longer-season varieties could be heading later (with potential increased yield) when sown early in season. This gene-based model allows breeders to consider how to target gene combinations to current and future production environments using parameters determined from a small set of phenotyping treatments. PMID:23873997

Quantification of the effects of VRN1 and Ppd-D1 to predict spring wheat (Triticum aestivum) heading time across diverse environments.

PubMed

Zheng, Bangyou; Biddulph, Ben; Li, Dora; Kuchel, Haydn; Chapman, Scott

2013-09-01

Heading time is a major determinant of the adaptation of wheat to different environments, and is critical in minimizing risks of frost, heat, and drought on reproductive development. Given that major developmental genes are known in wheat, a process-based model, APSIM, was modified to incorporate gene effects into estimation of heading time, while minimizing degradation in the predictive capability of the model. Model parameters describing environment responses were replaced with functions of the number of winter and photoperiod (PPD)-sensitive alleles at the three VRN1 loci and the Ppd-D1 locus, respectively. Two years of vernalization and PPD trials of 210 lines (spring wheats) at a single location were used to estimate the effects of the VRN1 and Ppd-D1 alleles, with validation against 190 trials (~4400 observations) across the Australian wheatbelt. Compared with spring genotypes, winter genotypes for Vrn-A1 (i.e. with two winter alleles) had a delay of 76.8 degree days (°Cd) in time to heading, which was double the effect of the Vrn-B1 or Vrn-D1 winter genotypes. Of the three VRN1 loci, winter alleles at Vrn-B1 had the strongest interaction with PPD, delaying heading time by 99.0 °Cd under long days. The gene-based model had root mean square error of 3.2 and 4.3 d for calibration and validation datasets, respectively. Virtual genotypes were created to examine heading time in comparison with frost and heat events and showed that new longer-season varieties could be heading later (with potential increased yield) when sown early in season. This gene-based model allows breeders to consider how to target gene combinations to current and future production environments using parameters determined from a small set of phenotyping treatments.

Plant genetics and interspecific competitive interactions determine ectomycorrhizal fungal community responses to climate change.

PubMed

Gehring, Catherine; Flores-Rentería, Dulce; Sthultz, Christopher M; Leonard, Tierra M; Flores-Rentería, Lluvia; Whipple, Amy V; Whitham, Thomas G

2014-03-01

Although the importance of plant-associated microbes is increasingly recognized, little is known about the biotic and abiotic factors that determine the composition of that microbiome. We examined the influence of plant genetic variation, and two stressors, one biotic and one abiotic, on the ectomycorrhizal (EM) fungal community of a dominant tree species, Pinus edulis. During three periods across 16 years that varied in drought severity, we sampled the EM fungal communities of a wild stand of P. edulis in which genetically based resistance and susceptibility to insect herbivory was linked with drought tolerance and the abundance of competing shrubs. We found that the EM fungal communities of insect-susceptible trees remained relatively constant as climate dried, while those of insect-resistant trees shifted significantly, providing evidence of a genotype by environment interaction. Shrub removal altered the EM fungal communities of insect-resistant trees, but not insect-susceptible trees, also a genotype by environment interaction. The change in the EM fungal community of insect-resistant trees following shrub removal was associated with greater shoot growth, evidence of competitive release. However, shrub removal had a 7-fold greater positive effect on the shoot growth of insect-susceptible trees than insect-resistant trees when shrub density was taken into account. Insect-susceptible trees had higher growth than insect-resistant trees, consistent with the hypothesis that the EM fungi associated with susceptible trees were superior mutualists. These complex, genetic-based interactions among species (tree-shrub-herbivore-fungus) argue that the ultimate impacts of climate change are both ecological and evolutionary. © 2013 John Wiley & Sons Ltd.

A family-based study of gene variants and maternal folate and choline in neuroblastoma: A Report from the Children’s Oncology Group

PubMed Central

Mazul, Angela L; Siega-Riz, Anna Maria; Weinberg, Clarice R; Engel, Stephanie M.; Zou, Fei; Carrier, Kathryn S.; Basta, Patricia V; Vaksman, Zalman; Maris, John M; Diskin, Sharon J; Maxen, Charlene; Naranjo, Arlene; Olshan, Andrew F

2016-01-01

Purpose Neuroblastoma is a childhood cancer of the sympathetic nervous system with embryonic origins. Previous epidemiologic studies suggest maternal vitamin supplementation during pregnancy reduces the risk of neuroblastoma. We hypothesized offspring and maternal genetic variants in folate-related and choline-related genes are associated with neuroblastoma and modify the effects of maternal intake of folate, choline and folic acid. Methods The Neuroblastoma Epidemiology in North America (NENA) study recruited 563 affected children and their parents through the Children’s Oncology Group’s Childhood Cancer Research Network. We used questionnaires to ascertain pre-pregnancy supplementation and estimate usual maternal dietary intake of folate, choline and folic acid. We genotyped 955 genetic variants related to folate or choline using DNA extracted from saliva samples and used a log-linear model to estimate both child and maternal risk ratios and stratum-specific risk ratios for gene-environment interactions. Results Overall, no maternal or offspring genotypic results met criteria for a false discovery rate (FDR) Q-value <0.2. Associations were also null for gene-environment interaction with pre-pregnancy vitamin supplementation, dietary folic acid and folate. FDR significant gene-choline interactions were found for offspring SNPs rs10489810 and rs9966612 located in MTHFD1L and TYMS, respectively, with maternal choline dietary intake dichotomized at the first quartile. Conclusion These results suggest that variants related to one-carbon metabolism are not strongly associated with neuroblastoma. Choline-related variants may play a role; however, the functional consequences of the interacting variants are unknown and require independent replication. PMID:27541142

A family-based study of gene variants and maternal folate and choline in neuroblastoma: a report from the Children's Oncology Group.

PubMed

Mazul, Angela L; Siega-Riz, Anna Maria; Weinberg, Clarice R; Engel, Stephanie M; Zou, Fei; Carrier, Kathryn S; Basta, Patricia V; Vaksman, Zalman; Maris, John M; Diskin, Sharon J; Maxen, Charlene; Naranjo, Arlene; Olshan, Andrew F

2016-10-01

Neuroblastoma is a childhood cancer of the sympathetic nervous system with embryonic origins. Previous epidemiologic studies suggest maternal vitamin supplementation during pregnancy reduces the risk of neuroblastoma. We hypothesized offspring and maternal genetic variants in folate-related and choline-related genes are associated with neuroblastoma and modify the effects of maternal intake of folate, choline, and folic acid. The Neuroblastoma Epidemiology in North America (NENA) study recruited 563 affected children and their parents through the Children's Oncology Group's Childhood Cancer Research Network. We used questionnaires to ascertain pre-pregnancy supplementation and estimate usual maternal dietary intake of folate, choline, and folic acid. We genotyped 955 genetic variants related to folate or choline using DNA extracted from saliva samples and used a log-linear model to estimate both child and maternal risk ratios and stratum-specific risk ratios for gene-environment interactions. Overall, no maternal or offspring genotypic results met criteria for a false discovery rate (FDR) Q-value <0.2. Associations were also null for gene-environment interaction with pre-pregnancy vitamin supplementation, dietary folic acid, and folate. FDR-significant gene-choline interactions were found for offspring SNPs rs10489810 and rs9966612 located in MTHFD1L and TYMS, respectively, with maternal choline dietary intake dichotomized at the first quartile. These results suggest that variants related to one-carbon metabolism are not strongly associated with neuroblastoma. Choline-related variants may play a role; however, the functional consequences of the interacting variants are unknown and require independent replication.

Genotype-based association models of complex diseases to detect gene-gene and gene-environment interactions.

PubMed

Lobach, Iryna; Fan, Ruzong; Manga, Prashiela

A central problem in genetic epidemiology is to identify and rank genetic markers involved in a disease. Complex diseases, such as cancer, hypertension, diabetes, are thought to be caused by an interaction of a panel of genetic factors, that can be identified by markers, which modulate environmental factors. Moreover, the effect of each genetic marker may be small. Hence, the association signal may be missed unless a large sample is considered, or a priori biomedical data are used. Recent advances generated a vast variety of a priori information, including linkage maps and information about gene regulatory dependence assembled into curated pathway databases. We propose a genotype-based approach that takes into account linkage disequilibrium (LD) information between genetic markers that are in moderate LD while modeling gene-gene and gene-environment interactions. A major advantage of our method is that the observed genetic information enters a model directly thus eliminating the need to estimate haplotype-phase. Our approach results in an algorithm that is inexpensive computationally and does not suffer from bias induced by haplotype-phase ambiguity. We investigated our model in a series of simulation experiments and demonstrated that the proposed approach results in estimates that are nearly unbiased and have small variability. We applied our method to the analysis of data from a melanoma case-control study and investigated interaction between a set of pigmentation genes and environmental factors defined by age and gender. Furthermore, an application of our method is demonstrated using a study of Alcohol Dependence.

Variation in cassava germplasm for tolerance to post-harvest physiological deterioration.

PubMed

Venturini, M T; Santos, L R; Vildoso, C I A; Santos, V S; Oliveira, E J

2016-05-06

Tolerant varieties can effectively control post-harvest physiological deterioration (PPD) of cassava, although knowledge on the genetic variability and inheritance of this trait is needed. The objective of this study was to estimate genetic parameters and identify sources of tolerance to PPD and their stability in cassava accessions. Roots from 418 cassava accessions, grown in four independent experiments, were evaluated for PPD tolerance 0, 2, 5, and 10 days post-harvest. Data were transformed into area under the PPD-progress curve (AUP-PPD) to quantify tolerance. Genetic parameters, stability (Si), adaptability (Ai), and the joint analysis of stability and adaptability (Zi) were obtained via residual maximum likelihood (REML) and best linear unbiased prediction (BLUP) methods. Variance in the genotype (G) x environment (E) interaction and genotypic variance were important for PPD tolerance. Individual broad-sense heritability (hg(2)= 0.38 ± 0.04) and average heritability in accessions (hmg(2)= 0.52) showed high genetic control of PPD tolerance. Genotypic correlation of AUP-PPD in different experiments was of medium magnitude (ȓgA = 0.42), indicating significant G x E interaction. The predicted genotypic values o f G x E free of interaction (û + ĝi) showed high variation. Of the 30 accessions with high Zi, 19 were common to û + ĝi, Si, and Ai parameters. The genetic gain with selection of these 19 cassava accessions was -55.94, -466.86, -397.72, and -444.03% for û + ĝi, Si, Ai, and Zi, respectively, compared with the overall mean for each parameter. These results demonstrate the variability and potential of cassava germplasm to introduce PPD tolerance in commercial varieties.

Gene-Environment Interaction in the Etiology of Mathematical Ability Using SNP Sets

PubMed Central

Kovas, Yulia; Plomin, Robert

2010-01-01

Mathematics ability and disability is as heritable as other cognitive abilities and disabilities, however its genetic etiology has received relatively little attention. In our recent genome-wide association study of mathematical ability in 10-year-old children, 10 SNP associations were nominated from scans of pooled DNA and validated in an individually genotyped sample. In this paper, we use a ‘SNP set’ composite of these 10 SNPs to investigate gene-environment (GE) interaction, examining whether the association between the 10-SNP set and mathematical ability differs as a function of ten environmental measures in the home and school in a sample of 1888 children with complete data. We found two significant GE interactions for environmental measures in the home and the school both in the direction of the diathesis-stress type of GE interaction: The 10-SNP set was more strongly associated with mathematical ability in chaotic homes and when parents are negative. PMID:20978832

Interactions between ultraviolet light and MC1R and OCA2 variants are determinants of childhood nevus and freckle phenotypes

PubMed Central

Barón, Anna E.; Asdigian, Nancy L.; Gonzalez, Victoria; Aalborg, Jenny; Terzian, Tamara; Stiegmann, Regan A.; C.Torchia, Enrique; Berwick, Marianne; Dellavalle, Robert P.; G.Morelli, Joseph; Mokrohisky, Stefan T.; Crane, Lori A.; Box, Neil F.

2014-01-01

Background Melanocytic nevi (moles) and freckles are well known biomarkers of melanoma risk, and they are influenced by similar ultraviolet (UV) light exposures and genetic susceptibilities to those that increase melanoma risk. Nevertheless, the selective interactions between UV exposures and nevus and freckling genes remain largely undescribed. Methods We conducted a longitudinal study from ages 6 through 10 in 477 Colorado children who had annual information collected for sun exposure, sun protection behaviors, and full body skin exams. MC1R and HERC2/OCA2 rs12913832 were genotyped and linear mixed models were used to identify main and interaction effects. Results All measures of sun exposure (chronic, sunburns and waterside vacations) contributed to total nevus counts, and cumulative chronic exposure acted as the major driver of nevus development. Waterside vacations strongly increased total nevus counts in children with rs12913832 blue eye color alleles and facial freckling scores in those with MC1R red hair color variants. Sunburns increased numbers of larger nevi (≥2 mm) in subjects with certain MC1R and rs12913832 genotypes. Conclusions Complex interactions between different UV exposure profiles and genotype combinations determine nevus numbers and size, and the degree of facial freckling. Impact Our findings emphasize the importance of implementing sun-protective behavior in childhood regardless of genetic make-up; although children with particular genetic variants may benefit from specifically targeted preventive measures to counteract their inherent risk of melanoma. Moreover, we demonstrate, for the first time, that longitudinal studies are a highly powered tool to uncover new gene-environment interactions that increase cancer risk. PMID:25410285

Interactions between ultraviolet light and MC1R and OCA2 variants are determinants of childhood nevus and freckle phenotypes.

PubMed

Barón, Anna E; Asdigian, Nancy L; Gonzalez, Victoria; Aalborg, Jenny; Terzian, Tamara; Stiegmann, Regan A; Torchia, Enrique C; Berwick, Marianne; Dellavalle, Robert P; Morelli, Joseph G; Mokrohisky, Stefan T; Crane, Lori A; Box, Neil F

2014-12-01

Melanocytic nevi (moles) and freckles are well known biomarkers of melanoma risk, and they are influenced by similar UV light exposures and genetic susceptibilities to those that increase melanoma risk. Nevertheless, the selective interactions between UV exposures and nevus and freckling genes remain largely undescribed. We conducted a longitudinal study from ages 6 through 10 years in 477 Colorado children who had annual information collected for sun exposure, sun protection behaviors, and full body skin exams. MC1R and HERC2/OCA2 rs12913832 were genotyped and linear mixed models were used to identify main and interaction effects. All measures of sun exposure (chronic, sunburns, and waterside vacations) contributed to total nevus counts, and cumulative chronic exposure acted as the major driver of nevus development. Waterside vacations strongly increased total nevus counts in children with rs12913832 blue eye color alleles and facial freckling scores in those with MC1R red hair color variants. Sunburns increased the numbers of larger nevi (≥2 mm) in subjects with certain MC1R and rs12913832 genotypes. Complex interactions between different UV exposure profiles and genotype combinations determine nevus numbers and size, and the degree of facial freckling. Our findings emphasize the importance of implementing sun-protective behavior in childhood regardless of genetic make-up, although children with particular genetic variants may benefit from specifically targeted preventive measures to counteract their inherent risk of melanoma. Moreover, we demonstrate, for the first time, that longitudinal studies are a highly powered tool to uncover new gene-environment interactions that increase cancer risk. ©2014 American Association for Cancer Research.

Strategies in identifying individuals in a segregant population of common bean and implications of genotype x environment interaction in the success of selection.

PubMed

Mendes, M P; Ramalho, M A P; Abreu, A F B

2012-04-10

The objective of this study was to compare the BLUP selection method with different selection strategies in F(2:4) and assess the efficiency of this method on the early choice of the best common bean (Phaseolus vulgaris) lines. Fifty-one F(2:4) progenies were produced from a cross between the CVIII8511 x RP-26 lines. A randomized block design was used with 20 replications and one-plant field plots. Character data on plant architecture and grain yield were obtained and then the sum of the standardized variables was estimated for simultaneous selection of both traits. Analysis was carried out by mixed models (BLUP) and the least squares method to compare different selection strategies, like mass selection, stratified mass selection and between and within progeny selection. The progenies selected by BLUP were assessed in advanced generations, always selecting the greatest and smallest sum of the standardized variables. Analyses by the least squares method and BLUP procedure ranked the progenies in the same way. The coincidence of the individuals identified by BLUP and between and within progeny selection was high and of the greatest magnitude when BLUP was compared with mass selection. Although BLUP is the best estimator of genotypic value, its efficiency in the response to long term selection is not different from any of the other methods, because it is also unable to predict the future effect of the progenies x environments interaction. It was inferred that selection success will always depend on the most accurate possible progeny assessment and using alternatives to reduce the progenies x environments interaction effect.

Genotype and local environment dynamically influence growth, disturbance response and survivorship in the threatened coral, Acropora cervicornis.

PubMed

Drury, Crawford; Manzello, Derek; Lirman, Diego

2017-01-01

The relationship between the coral genotype and the environment is an important area of research in degraded coral reef ecosystems. We used a reciprocal outplanting experiment with 930 corals representing ten genotypes on each of eight reefs to investigate the influence of genotype and the environment on growth and survivorship in the threatened Caribbean staghorn coral, Acropora cervicornis. Coral genotype and site were strong drivers of coral growth and individual genotypes exhibited flexible, non-conserved reaction norms, complemented by ten-fold differences in growth between specific G-E combinations. Growth plasticity may diminish the influence of local adaptation, where foreign corals grew faster than native corals at their home sites. Novel combinations of environment and genotype also significantly affected disturbance response during and after the 2015 bleaching event, where these factors acted synergistically to drive variation in bleaching and recovery. Importantly, small differences in temperature stress elicit variable patterns of survivorship based on genotype and illustrate the importance of novel combinations of coral genetics and small differences between sites representing habitat refugia. In this context, acclimatization and flexibility is especially important given the long lifespan of corals coping with complex environmental change. The combined influence of site and genotype creates short-term differences in growth and survivorship, contributing to the standing genetic variation needed for adaptation to occur over longer timescales and the recovery of degraded reefs through natural mechanisms.

Effect of 5-HT2A receptor polymorphisms and occupational stress on self-reported sleep quality: a cross-sectional study in Xinjiang, China.

PubMed

Jiang, Yu; Cui, Changyong; Ge, Hua; Guan, Suzhen; Lian, Yulong; Liu, Jiwen

2016-04-01

Occupational stress and the serotonin receptor (5-HTR) play a key role in the regulation of sleep quality. Previous studies on the relationship between work-related stress, 5-HTR2A polymorphism, and sleep complaints found that 5-HTR2A modulates the response of the hypothalamic-pituitary-adrenal axis to stress and the maintenance of circadian rhythm. However, the effect of 5-HTR2A polymorphism and occupational stress on sleep quality has not been reported. The present study investigated the effects of 5-HTR2A genotypes, occupational stress, and gene-environment interactions on the sleep quality. Using a three-stage stratified sampling method, 1181 participants were recruited. Then, according to the study exclusion criteria, 810 subjects remained eligible. Finally, because some of subjects did not agree to being involved in this study, 700 workers were included. Of 700 workers finally included in the study, 251 had poor sleep quality based on the Pittsburgh Sleep Quality Index. The 5-HTR2A genotypes were determined with the SNaPshot single nucleotide polymorphism assay. Occupational stress was assessed with the Occupational Stress Inventory-Revised questionnaire. 5-HTR2A genotype was significantly associated with sleep quality. The CT genotype of rs1923884 was detected at a higher frequency among individuals with low sleep efficiency; the AA genotype of rs2070040 was associated with long sleep duration and more daytime dysfunction; and the CC genotype of rs6313 was linked to long sleep latency and duration and poor sleep quality. A high level of occupational stress was linked to higher risk of poor sleep quality than low or moderate levels (odds ratio [OR] = 12.55, 95% confidence interval [CI]: 7.02-22.43). A crossover analysis demonstrated an occupational stress × 5-HTR2A interaction. Compared to participants with low occupational stress and a CT/TT genotype, those with high occupational stress and a CC genotype had a higher risk of poor sleep quality (OR = 7.93, 95% CI: 3.41-18.43), whereas those with low occupational stress and a CC genotype had a lower risk of poor sleep quality (OR = 1.53, 95% CI: 1.07-2.19). Occupational stress and 5-HTR2A genotypes in workers are associated both independently and in combination with increased risk of poor sleep quality. Our data provide evidence that occupational stress contributes to the risk of poor sleep quality through interaction with 5-HTR2A gene polymorphism. Copyright © 2016 Elsevier B.V. All rights reserved.

[The role of genotype in the intergenerational transmission of experiences of childhood adversity].

PubMed

Reichl, Corinna; Kaess, Michael; Resch, Franz; Brunner, Romuald

2014-09-01

The prevalence of childhood abuse and maltreatment is estimated to lie at about 15% in the overall German population. Previous research suggested that about one third of all individuals who had experienced childhood adversity subsequently maltreated their own children or responded insensitively to their children's needs. Empirical studies imply that interindividual differences in the responsiveness to childhood adversity can partially be explained by gene-environment interactions. This article discusses the potential interplay of genes and environment in the context of transmitting maltreating behavior and (in)sensitive parenting against the background of current challenges in genetic research. Selected studies on gene × environment interactions are presented and relevant gene polymorphisms are identified. Overall, previous studies reported interactions between polymorphisms of the serotonergic, dopaminergic, oxytocin-related, and arginine vasopressin-related systems and childhood experiences of care and abuse in the prediction of social behaviors during mother-child interactions. The results indicate a differential susceptibility toward both negative and positive environments which is dependent on genetic characteristics. Future research should thus investigate the effects of children's presumed risk gene variants toward negative as well as positive parenting. This could contribute to a deeper understanding of the underlying mechanisms of the intergenerational transmission of abusive and beneficial parenting behavior and help to avoid false stigmatizations.

Poplar breeding and testing strategies in the north-central U.S.: Demonstration of potential yield and consideration of future research needs1

Treesearch

Don E. Riemenschneider; William E. Berguson; Donald I. Dickmann; Richard B. Hall; J. G. Isebrands; Carl A. Mohn; Glen R. Stanosz; Gerald A. Tuskan

2001-01-01

We present results from a Populus Regional Testing Program that has been conducted in Minnesota, Iowa, Wisconsin, and Michigan over the past six years. Our objectives have been to: 1) identify highly productive, disease resistant intra- and inter-specific clonal selections and 2) understand patterns of genotype x environment interactions within the region that would,...

Gene-Environment Interplay, Family Relationships, and Child Adjustment

ERIC Educational Resources Information Center

Horwitz, Briana N.; Neiderhiser, Jenae M.

2011-01-01

This paper reviews behavioral genetic research from the past decade that has moved beyond simply studying the independent influences of genes and environments. The studies considered in this review have instead focused on understanding gene-environment interplay, including genotype-environment correlation (rGE) and genotype x environment…

Challenges Facing Crop Production And (Some) Potential Solutions

NASA Astrophysics Data System (ADS)

Schnable, P. S.

2017-12-01

To overcome some of the myriad challenges facing sustainable crop production we are seeking to develop statistical models that will predict crop performance in diverse agronomic environments. Crop phenotypes such as yield and drought tolerance are controlled by genotype, environment (considered broadly) and their interaction (GxE). As a consequence of the next generation sequencing revolution genotyping data are now available for a wide diversity of accessions in each of the major crops. The necessary volumes of phenotypic data, however, remain limiting and our understanding of molecular basis of GxE is minimal. To address this limitation, we are collaborating with engineers to construct new sensors and robots to automatically collect large volumes of phenotypic data. Two types of high-throughput, high-resolution, field-based phenotyping systems and new sensors will be described. Some of these technologies will be introduced within the context of the Genomes to Fields Initiative. Progress towards developing predictive models will be briefly summarized. An administrative structure that fosters transdisciplinary collaborations will be briefly described.

Quantitative proteomics reveals a role of JAZ7 in plant defense response to Pseudomonas syringae DC3000.

PubMed

Zhang, Tong; Meng, Li; Kong, Wenwen; Yin, Zepeng; Wang, Yang; Schneider, Jacqueline D; Chen, Sixue

2018-03-20

Jasmonate ZIM-domain (JAZ) proteins are key transcriptional repressors regulating various biological processes. Although many studies have studied JAZ proteins by genetic and biochemical analyses, little is known about JAZ7-associated global protein networks and how JAZ7 contributes to bacterial pathogen defense. In this study, we aim to fill this knowledge gap by conducting unbiased large-scale quantitative proteomics using tandem mass tags (TMT). We compared the proteomes of a JAZ7 knock-out line, a JAZ7 overexpression line, as well as the wild type Arabidopsis plants in the presence and absence of Pseudomonas syringae DC3000 infection. Both pairwise comparison and multi-factor analysis of variance reveal that differential proteins are enriched in biological processes such as primary and secondary metabolism, redox regulation, and response to stress. The differential regulation in these pathways may account for the alterations in plant size, redox homeostasis and accumulation of glucosinolates. In addition, possible interplay between genotype and environment is suggested as the abundance of seven proteins is influenced by the interaction of the two factors. Collectively, we demonstrate a role of JAZ7 in pathogen defense and provide a list of proteins that are uniquely responsive to genetic disruption, pathogen infection, or the interaction between genotypes and environmental factors. We report proteomic changes as a result of genetic perturbation of JAZ7, and the contribution of JAZ7 in plant immunity. Specifically, the similarity between the proteomes of a JAZ7 knockout mutant and the wild type plants confirmed the functional redundancy of JAZs. In contrast, JAZ7 overexpression plants were much different, and proteomic analysis of the JAZ7 overexpression plants under Pst DC3000 infection revealed that JAZ7 may regulate plant immunity via ROS modulation, energy balance and glucosinolate biosynthesis. Multiple variate analysis for this two-factor proteomics experiment suggests that protein abundance is determined by genotype, environment and the interaction between them. Copyright © 2018 Elsevier B.V. All rights reserved.

Using Extended Genealogy to Estimate Components of Heritability for 23 Quantitative and Dichotomous Traits

PubMed Central

Zaitlen, Noah; Kraft, Peter; Patterson, Nick; Pasaniuc, Bogdan; Bhatia, Gaurav; Pollack, Samuela; Price, Alkes L.

2013-01-01

Important knowledge about the determinants of complex human phenotypes can be obtained from the estimation of heritability, the fraction of phenotypic variation in a population that is determined by genetic factors. Here, we make use of extensive phenotype data in Iceland, long-range phased genotypes, and a population-wide genealogical database to examine the heritability of 11 quantitative and 12 dichotomous phenotypes in a sample of 38,167 individuals. Most previous estimates of heritability are derived from family-based approaches such as twin studies, which may be biased upwards by epistatic interactions or shared environment. Our estimates of heritability, based on both closely and distantly related pairs of individuals, are significantly lower than those from previous studies. We examine phenotypic correlations across a range of relationships, from siblings to first cousins, and find that the excess phenotypic correlation in these related individuals is predominantly due to shared environment as opposed to dominance or epistasis. We also develop a new method to jointly estimate narrow-sense heritability and the heritability explained by genotyped SNPs. Unlike existing methods, this approach permits the use of information from both closely and distantly related pairs of individuals, thereby reducing the variance of estimates of heritability explained by genotyped SNPs while preventing upward bias. Our results show that common SNPs explain a larger proportion of the heritability than previously thought, with SNPs present on Illumina 300K genotyping arrays explaining more than half of the heritability for the 23 phenotypes examined in this study. Much of the remaining heritability is likely to be due to rare alleles that are not captured by standard genotyping arrays. PMID:23737753

Using extended genealogy to estimate components of heritability for 23 quantitative and dichotomous traits.

PubMed

Zaitlen, Noah; Kraft, Peter; Patterson, Nick; Pasaniuc, Bogdan; Bhatia, Gaurav; Pollack, Samuela; Price, Alkes L

2013-05-01

Important knowledge about the determinants of complex human phenotypes can be obtained from the estimation of heritability, the fraction of phenotypic variation in a population that is determined by genetic factors. Here, we make use of extensive phenotype data in Iceland, long-range phased genotypes, and a population-wide genealogical database to examine the heritability of 11 quantitative and 12 dichotomous phenotypes in a sample of 38,167 individuals. Most previous estimates of heritability are derived from family-based approaches such as twin studies, which may be biased upwards by epistatic interactions or shared environment. Our estimates of heritability, based on both closely and distantly related pairs of individuals, are significantly lower than those from previous studies. We examine phenotypic correlations across a range of relationships, from siblings to first cousins, and find that the excess phenotypic correlation in these related individuals is predominantly due to shared environment as opposed to dominance or epistasis. We also develop a new method to jointly estimate narrow-sense heritability and the heritability explained by genotyped SNPs. Unlike existing methods, this approach permits the use of information from both closely and distantly related pairs of individuals, thereby reducing the variance of estimates of heritability explained by genotyped SNPs while preventing upward bias. Our results show that common SNPs explain a larger proportion of the heritability than previously thought, with SNPs present on Illumina 300K genotyping arrays explaining more than half of the heritability for the 23 phenotypes examined in this study. Much of the remaining heritability is likely to be due to rare alleles that are not captured by standard genotyping arrays.

Genotype-by-environment effect on bioactive compounds in strawberry (Fragaria x ananassa Duch.).

PubMed

Palmieri, Luisa; Masuero, Domenico; Martinatti, Paolo; Baratto, Giuseppe; Martens, Stefan; Vrhovsek, Urska

2017-09-01

The assessment of the relative contribution of genotype, environment and the genotype-by-environmental (G × E) interaction to the performance of varieties is necessary when determining adaptation capacity. The influence of temperature, ultraviolet (UV)-irradiation and sunshine duration on the quality and the composition of fruits was investigated in nine strawberry cultivars grown at three different altitudes. The UV-radiation intensity affected both pH and sugar content, which were higher for most of the varieties at low altitudes, whereas total titratable acidity was less. Fruits from plants grown at low elevation generally had a higher benzoic acid derivative content. A significant correlation was found between phenylpropanoid content and UV-radiation and sunshine duration. The flavone class appeared to be affected most by the variety effect, in contrast to flavonols and ellagitannins, which were highly affected by the environment. The accumulation of a number of secondary metabolites in strawberry fruits grown in an unusual environmental condition highlighted the acclimation effects in terms of the response of plants to abiotic stress. Finally, the genetic factor only appears to be more influential for the varieties 'Sveva' and 'Marmolada' with respect to all of the parameters considered. A 'plant environmental metabolomics' approach has been used successfully to assess the phenotypic plasticity of varieties that showed different magnitudes with respect to the relationship between environmental conditions and the accumulation of healthy compounds. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Genetic Basis for Variation in Wheat Grain Yield in Response to Varying Nitrogen Application

PubMed Central

Mahjourimajd, Saba; Taylor, Julian; Sznajder, Beata; Timmins, Andy; Shahinnia, Fahimeh; Rengel, Zed; Khabaz-Saberi, Hossein; Kuchel, Haydn; Okamoto, Mamoru

2016-01-01

Nitrogen (N) is a major nutrient needed to attain optimal grain yield (GY) in all environments. Nitrogen fertilisers represent a significant production cost, in both monetary and environmental terms. Developing genotypes capable of taking up N early during development while limiting biomass production after establishment and showing high N-use efficiency (NUE) would be economically beneficial. Genetic variation in NUE has been shown previously. Here we describe the genetic characterisation of NUE and identify genetic loci underlying N response under different N fertiliser regimes in a bread wheat population of doubled-haploid lines derived from a cross between two Australian genotypes (RAC875 × Kukri) bred for a similar production environment. NUE field trials were carried out at four sites in South Australia and two in Western Australia across three seasons. There was genotype-by-environment-by-treatment interaction across the sites and also good transgressive segregation for yield under different N supply in the population. We detected some significant Quantitative Trait Loci (QTL) associated with NUE and N response at different rates of N application across the sites and years. It was also possible to identify lines showing positive N response based on the rankings of their Best Linear Unbiased Predictions (BLUPs) within a trial. Dissecting the complexity of the N effect on yield through QTL analysis is a key step towards elucidating the molecular and physiological basis of NUE in wheat. PMID:27459317

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).

Methylation of the oxytocin receptor gene in clinically depressed patients compared to controls: The role of OXTR rs53576 genotype.

PubMed

Reiner, I; Van IJzendoorn, M H; Bakermans-Kranenburg, M J; Bleich, S; Beutel, M; Frieling, H

2015-06-01

The emerging field of epigenetics provides a biological basis for gene-environment interactions relevant to depression. We focus on DNA methylation of exon 1 and 2 of the oxytocin receptor gene (OXTR) promoter. The research aims of the current study were to compare OXTR DNA methylation of depressed patients with healthy control subjects and to investigate possible influences of the OXTR rs53576 genotype. The sample of the present study consisted of 43 clinically depressed women recruited from a psychosomatic inpatient unit and 42 healthy, female control subjects - mean age 30 years (SD = 9). DNA methylation profiles of the OXTR gene were assessed from leukocyte DNA by means of bisulfite sequencing. Depressed female patients had decreased OXTR exon 1 DNA methylation compared to non-depressed women. The association between depression and methylation level was moderated by OXTR rs53576 genotype. Exon 2 methylation was associated with OXTR rs53576 genotype but not with depression. Our findings suggest exon-specific methylation mechanisms. Exon 1 methylation appears to be associated with depressive phenotypes whereas exon 2 methylation is influenced by genotype. Previously reported divergent associations between OXTR genotype and depression might be explained by varying exon 1 methylation. In order to further understand the etiology of depression, research on the interplay between genotype, environmental influences and exon-specific methylation patterns is needed. Copyright © 2015 Elsevier Ltd. All rights reserved.

Gene by Social-Context Interactions for Number of Sexual Partners Among White Male Youths: Genetics-informed Sociology

PubMed Central

Guo, Guang; Tong, Yuying; Cai, Tianji

2010-01-01

In this study, we set out to investigate whether introducing molecular genetic measures into an analysis of sexual partner variety will yield novel sociological insights. The data source is the white male DNA sample in the National Longitudinal Study of Adolescent Health. Our empirical analysis has produced a robust protective effect of the 9R/9R genotype relative to the Any10R genotype in the dopamine transporter gene (DAT1). The gene-environment interaction analysis demonstrates that the protective effect of 9R/9R tends to be lost in schools in which higher proportions of students start having sex early or among those with relatively low levels of cognitive ability. Our genetics-informed sociological analysis suggests that the “one size” of a single social theory may not fit all. Explaining a human trait or behavior may require a theory that accommodates the complex interplay between social contextual and individual influences and genetic predispositions. PMID:19569400

Indirect genetic effects and sexual conflicts: Partner genotype influences multiple morphological and behavioral reproductive traits in a flatworm.

PubMed

Marie-Orleach, Lucas; Vogt-Burri, Nadja; Mouginot, Pierick; Schlatter, Aline; Vizoso, Dita B; Bailey, Nathan W; Schärer, Lukas

2017-05-01

The expression of an individual's phenotypic traits can be influenced by genes expressed in its social partners. Theoretical models predict that such indirect genetic effects (IGEs) on reproductive traits should play an important role in determining the evolutionary outcome of sexual conflict. However, empirical tests of (i) whether reproductive IGEs exist, (ii) how they vary among genotypes, and (iii) whether they are uniform for different types of reproductive traits are largely lacking. We addressed this in a series of experiments in the simultaneously hermaphroditic flatworm Macrostomum lignano. We found strong evidence for IGEs on both morphological and behavioral reproductive traits. Partner genotype had a significant impact on the testis size of focal individuals-varying up to 2.4-fold-suggesting that IGEs could mediate sexual conflicts that target the male sex function. We also found that time to first copulation was affected by a genotype × genotype interaction between mating partners, and that partner genotype affected the propensity to copulate and perform the postcopulatory suck behavior, which may mediate conflicts over the fate of received ejaculate components. These findings provide clear empirical evidence for IGEs on multiple behavioral and morphological reproductive traits, which suggests that the evolutionary dynamics of these traits could be altered by genes contained in the social environment. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Absence of deficits in social behaviors and ultrasonic vocalizations in later generations of mice lacking neuroligin4.

PubMed

Ey, E; Yang, M; Katz, A M; Woldeyohannes, L; Silverman, J L; Leblond, C S; Faure, P; Torquet, N; Le Sourd, A-M; Bourgeron, T; Crawley, J N

2012-11-01

Mutations in NLGN4X have been identified in individuals with autism spectrum disorders and other neurodevelopmental disorders. A previous study reported that adult male mice lacking neuroligin4 (Nlgn4) displayed social approach deficits in the three-chambered test, altered aggressive behaviors and reduced ultrasonic vocalizations. To replicate and extend these findings, independent comprehensive analyses of autism-relevant behavioral phenotypes were conducted in later generations of the same line of Nlgn4 mutant mice at the National Institute of Mental Health in Bethesda, MD, USA and at the Institut Pasteur in Paris, France. Adult social approach was normal in all three genotypes of Nlgn4 mice tested at both sites. Reciprocal social interactions in juveniles were similarly normal across genotypes. No genotype differences were detected in ultrasonic vocalizations in pups separated from the nest or in adults during reciprocal social interactions. Anxiety-like behaviors, self-grooming, rotarod and open field exploration did not differ across genotypes, and measures of developmental milestones and general health were normal. Our findings indicate an absence of autism-relevant behavioral phenotypes in subsequent generations of Nlgn4 mice tested at two locations. Testing environment and methods differed from the original study in some aspects, although the presence of normal sociability was seen in all genotypes when methods taken from Jamain et al. (2008) were used. The divergent results obtained from this study indicate that phenotypes may not be replicable across breeding generations, and highlight the significant roles of environmental, generational and/or procedural factors on behavioral phenotypes. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.

Partial automation of database processing of simulation outputs from L-systems models of plant morphogenesis.

PubMed

Chen, Yi- Ping Phoebe; Hanan, Jim

2002-01-01

Models of plant architecture allow us to explore how genotype environment interactions effect the development of plant phenotypes. Such models generate masses of data organised in complex hierarchies. This paper presents a generic system for creating and automatically populating a relational database from data generated by the widely used L-system approach to modelling plant morphogenesis. Techniques from compiler technology are applied to generate attributes (new fields) in the database, to simplify query development for the recursively-structured branching relationship. Use of biological terminology in an interactive query builder contributes towards making the system biologist-friendly.

Association Between Four Polymorphisms in lncRNA and Risk of Lung Cancer in a Chinese Never-Smoking Female Population.

PubMed

Gao, Min; Li, Hang; Lv, Xiaoting; Zhou, Baosen; Yin, Zhihua

2018-06-07

Long noncoding RNAs (lncRNAs) play important roles in the development of human cancers. This is the first case-control study of the association between specific polymorphisms in lncRNA genes and the risk of lung cancer, as well as the gene-environment interaction between the polymorphisms and cooking oil fume exposure in Chinese never-smoking females. A hospital-based case-control study was carried out in Shenyang, Liaoning province. The study included 395 cases and 556 controls. The polymorphisms of rs4785367, rs3803662, rs10750417, and rs1814343 in lncRNA genes were analyzed. The gene-environment interactions were explored on both additive and multiplicative scale. In addition, the results were listed as follows: for rs3803662, compared with the individuals carrying homozygous TT genotype, those with homozygous CC genotype had the decreased risk of lung cancer (adjusted odds ratio [OR] = 0.61, 95% confidence interval [CI] = 0.40-0.92, p = 0.018). As for rs4785367, compared with homozygous TT, homozygous CC could lessen the risk of lung cancer (adjusted OR = 0.54, 95% CI = 0.33-0.89, p = 0.016). The recessive models of rs3803662 and rs4785367 showed significant association (adjusted OR = 0.65, 95% CIs = 0.44-0.97, p = 0.033; adjusted OR = 0.54, 95% CIs = 0.33-0.88, p = 0.014). The C allele of rs3803662 was suggested to be protective allele of lung cancer (adjusted OR = 0.80, 95% CI = 0.66-0.97, p = 0.023). However, rs10750417 and rs1814343 polymorphisms were not significantly associated with lung cancer risks. The measures of additive interaction and logistic models suggested that the gene-environment interactions were not statistically significant on both additive and multiplicative scales.

Genotype x environment interactions in postweaning performance to yearling in Angus, Brahman, and reciprocal-cross calves.

PubMed

Brown, M A; Brown, A H; Jackson, W G; Miesner, J R

1993-12-01

Data from 431 Angus, Brahman, and reciprocal-cross calves were used to evaluate performance from weaning to yearling in calves managed during the winter on dormant common bermudagrass or endophyte-infected tall fescue (backgrounding environments). Calves on bermudagrass were weaned at heavier weights (P < .01) but gained less postweaning (P < .01). Weights at 365 d, 365-d hip heights, and 365-d weight:height ratios were similar between calves on different backgrounding environments averaged over breed. There was evidence that heterosis for postweaning ADG was larger in calves managed on endophyte-infected tall fescue (P < .05), but heterosis estimates for 205-d weight, 365-d weight, 365-d hip height, and 365-d weight:height were similar between backgrounding environments. Maternal and direct effects did not significantly interact with backgrounding environment, but there was a trend for maternal effects of 205-d weight, 365-d weight, and 365-d weight:height to be larger on the common bermudagrass environment than on the tall fescue environment. There was also a trend for direct breed effects for postweaning ADG and 365-d hip height to be larger on the common bermudagrass environment. These data indicated that genetic effects may vary with production environment and that consideration should be given to environment when developing crossbreeding systems.

Genetic variation for maternal effects on parasite susceptibility.

PubMed

Stjernman, M; Little, T J

2011-11-01

The expression of infectious disease is increasingly recognized to be impacted by maternal effects, where the environmental conditions experienced by mothers alter resistance to infection in offspring, independent of heritability. Here, we studied how maternal effects (high or low food availability to mothers) mediated the resistance of the crustacean Daphnia magna to its bacterial parasite Pasteuria ramosa. We sought to disentangle maternal effects from the effects of host genetic background by studying how maternal effects varied across 24 host genotypes sampled from a natural population. Under low-food conditions, females produced offspring that were relatively resistant, but this maternal effect varied strikingly between host genotypes, i.e. there were genotype by maternal environment interactions. As infection with P. ramosa causes a substantial reduction in host fecundity, this maternal effect had a large effect on host fitness. Maternal effects were also shown to impact parasite fitness, both because they prevented the establishment of the parasites and because even when parasites did establish in the offspring of poorly fed mothers, and they tended to grow more slowly. These effects indicate that food stress in the maternal generation can greatly influence parasite susceptibility and thus perhaps the evolution and coevolution of host-parasite interactions. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

[Association between anxiety-depression and 5-HTTLPR gene polymorphism in school-aged twins].

PubMed

Zhao, Qiao; Li, Yu-Ling; Enherbayaer; Liu, Yan; Ding, Yi

2016-01-01

To investigate the association between anxiety-depression and 5-HTTLPR gene polymorphism in school-aged twins. A total of 147 pairs of twins (47 pairs of monozygotic twins, 100 pairs of dizygotic twins) aged 8-12 years from Baotou and Hohhot were selected as respondents. The Achenbach Child Behavior Checklist (CBCL) was used to calculate the scores of anxiety-depression factors in school-aged twins. The DNA was extracted from oral epithelial cells, and polymerase chain reaction was applied for 5-HTTLPR genotyping. The generalized estimating equation (GEE) was used to analyze the effect of 5-HTTLPR polymorphism and family environment on anxiety-depression in school-aged twins. The children with LS and SS genotypes had significantly higher scores of anxiety-depression factors than those with LL genotype (χ2=3.938, P<0.05). The interaction of 5-HTTLPR genotype with family cohesion and family rearing patterns had a significant impact on the scores of anxiety-depression factors in twins (χ2=6.129 and 7.665, both P<0.05). 5-HTTLPR genotype is significantly correlated with the scores of anxiety-depression factors in school-aged twins. In the family with high cohesion and an autocratic family rearing pattern, S allele may increase the possibility of anxiety-depression in twin children.

Accuracy of Genomic Prediction in a Commercial Perennial Ryegrass Breeding Program.

PubMed

Fè, Dario; Ashraf, Bilal H; Pedersen, Morten G; Janss, Luc; Byrne, Stephen; Roulund, Niels; Lenk, Ingo; Didion, Thomas; Asp, Torben; Jensen, Christian S; Jensen, Just

2016-11-01

The implementation of genomic selection (GS) in plant breeding, so far, has been mainly evaluated in crops farmed as homogeneous varieties, and the results have been generally positive. Fewer results are available for species, such as forage grasses, that are grown as heterogenous families (developed from multiparent crosses) in which the control of the genetic variation is far more complex. Here we test the potential for implementing GS in the breeding of perennial ryegrass ( L.) using empirical data from a commercial forage breeding program. Biparental F and multiparental synthetic (SYN) families of diploid perennial ryegrass were genotyped using genotyping-by-sequencing, and phenotypes for five different traits were analyzed. Genotypes were expressed as family allele frequencies, and phenotypes were recorded as family means. Different models for genomic prediction were compared by using practically relevant cross-validation strategies. All traits showed a highly significant level of genetic variance, which could be traced using the genotyping assay. While there was significant genotype × environment (G × E) interaction for some traits, accuracies were high among F families and between biparental F and multiparental SYN families. We have demonstrated that the implementation of GS in grass breeding is now possible and presents an opportunity to make significant gains for various traits. Copyright © 2016 Crop Science Society of America.

Paraoxonase 1 (PON1) Q192R genotypes and their interaction with smoking strongly increase atherogenicity and the Framingham risk score.

PubMed

Souza-Nogueira, Andre de; Camargo, Alissana Ester; Remondi, Felipe Assan; Paoliello, Monica Maria Bastos; Richter, Rebecca J; Furlong, Clement E; Barbosa, Decio Sabbatini; Maes, Michael; Moreira, Estefania Gastaldello

2016-10-01

Paraoxonase 1 (PON1) polymorphisms are associated with an increased susceptibility to cardiovascular disease. PON1 Q192R polymorphism (rs662) partially determine PON1 hydrolytic activity and protect against oxidation of LDL and HDL. This study aimed to delineate the association of PON1 status (functional 192 genotype and plasma activity levels) and atherogenicity in urbans residents aged 40 years or more. Anthropometric data, lipid profiles, the atherogenic index of the plasma (AIP) and Framingham score risk were measured. Three kinetic assays were conducted to assay PON1 status using phenylacetate and 4-(chloromethyl)phenyl acetate as substrates. Smoking per se did not significantly impact the AIP but the interaction PON1 genotype by smoking significantly increased the AIP. In subjects with the RR genotype smoking increased the AIP index from (estimated mean ± SEM) -0.038 ± 0.039 to 0.224 ± 0.094. The QR genotype increased the Framingham risk index by around 1.3 points. Smoking by RR genotype carriers significantly increased the Framingham risk score (17.23 ± 2.04) as compared to smoking (13.00 ± 1.06) and non-smoking (7.79 ± 0.70) by QQ+QR genotype carriers. The interaction RR genotype by smoking was a more important predictor (odds ratio = 7.90) of an increased Framingham risk score (> 20) than smoking per se (odds ratio = 2.73). The interaction smoking by RR genotype carriers significantly increased triglycerides and lowered HDL cholesterol. Smoking per se has no (AIP) or a mild (Framingham risk score) effect on atherogenicity, while the interaction smoking by PON1 RR genotype has a clinically highly significant impact on atherogenicity.

Genotype and local environment dynamically influence growth, disturbance response and survivorship in the threatened coral, Acropora cervicornis

PubMed Central

Drury, Crawford; Manzello, Derek; Lirman, Diego

2017-01-01

The relationship between the coral genotype and the environment is an important area of research in degraded coral reef ecosystems. We used a reciprocal outplanting experiment with 930 corals representing ten genotypes on each of eight reefs to investigate the influence of genotype and the environment on growth and survivorship in the threatened Caribbean staghorn coral, Acropora cervicornis. Coral genotype and site were strong drivers of coral growth and individual genotypes exhibited flexible, non-conserved reaction norms, complemented by ten-fold differences in growth between specific G-E combinations. Growth plasticity may diminish the influence of local adaptation, where foreign corals grew faster than native corals at their home sites. Novel combinations of environment and genotype also significantly affected disturbance response during and after the 2015 bleaching event, where these factors acted synergistically to drive variation in bleaching and recovery. Importantly, small differences in temperature stress elicit variable patterns of survivorship based on genotype and illustrate the importance of novel combinations of coral genetics and small differences between sites representing habitat refugia. In this context, acclimatization and flexibility is especially important given the long lifespan of corals coping with complex environmental change. The combined influence of site and genotype creates short-term differences in growth and survivorship, contributing to the standing genetic variation needed for adaptation to occur over longer timescales and the recovery of degraded reefs through natural mechanisms. PMID:28319134

Gene Polymorphism Association with Type 2 Diabetes and Related Gene-Gene and Gene-Environment Interactions in a Uyghur Population

PubMed Central

Xiao, Shan; Zeng, Xiaoyun; Fan, Yong; Su, Yinxia; Ma, Qi; Zhu, Jun; Yao, Hua

2016-01-01

Background We investigated the association between 8 single-nucleotide polymorphisms (SNPs) at 3 genetic loci (CDKAL1, CDKN2A/2B and FTO) with type 2 diabetes (T2D) in a Uyghur population. Material/Methods A case-control study of 879 Uyghur patients with T2D and 895 non-diabetic Uyghur controls was conducted at the Hospital of Xinjiang Medical University between 2010 and 2013. Eight SNPs in CDKAL1, CDKN2A/2B and FTO were analyzed using Sequenom MassARRAY®SNP genotyping. Factors associated with T2D were assessed by logistic regression analyses. Gene-gene and gene-environment interactions were analyzed by generalized multifactor dimensionality reduction. Results Genotype distributions of rs10811661 (CDKN2A/2B), rs7195539, rs8050136, and rs9939609 (FTO) and allele frequencies of rs8050136 and rs9939609 differed significantly between diabetes and control groups (all P<0.05). While rs10811661, rs8050136, and rs9939609 were eliminated after adjusting for covariates (P>0.05), rs7195539 distribution differed significantly in co-dominant and dominant models (P<0.05). In gene-gene interaction analysis, after adjusting for covariates the two-locus rs10811661-rs7195539 interaction model had a cross-validation consistency of 10/10 and the highest balanced accuracy of 0.5483 (P=0.014). In gene-environment interaction analysis, the 3-locus interaction model TG-HDL-family history of diabetes had a cross-validation consistency of 10/10 and the highest balanced accuracy of 0.7072 (P<0.001). The 4-locus interaction model, rs7195539-TG-HDL-family history of diabetes had a cross-validation consistency of 8/10 (P<0.001). Conclusions Polymorphisms in CDKN2A/2B and FTO, but not CDKAL1, may be associated with T2D, and alleles rs8050136 and rs9939609 are likely risk alleles for T2D in this population. There were potential interactions among CDKN2A/2B (rs10811661) – FTO (rs7195539) or FTO (rs7195539)-TG-HDL-family history of diabetes in the pathogenesis of T2D in a Uyghur population. PMID:26873362

Paternal identity influences response of Acanthaster planci embryos to ocean acidification and warming

NASA Astrophysics Data System (ADS)

Sparks, Kate M.; Foo, Shawna A.; Uthicke, Sven; Byrne, Maria; Lamare, Miles

2017-03-01

The crown-of-thorns sea star Acanthaster planci is a key predator of corals and has had a major influence on the decrease in coral cover across the Indo-Pacific. To understand how this species may adapt to ocean warming and acidification, this study used a quantitative genetic approach to examine the response in offspring of 24 half-sib A. planci families raised in fully crossed treatment combinations of temperature (27, 29 and 31 °C) and pCO2 (450 and 900 ppm) to the gastrulation stage (26 h post-fertilisation). Interactions between genotype and environment were tested using a permutational multivariate ANOVA and restricted error maximum likelihood calculations of variance. High temperature (31 °C) significantly reduced normal (symmetrical, intact) development by 15% at the 16-cell stage. Increased temperature (from 29 to 31 °C) reduced normal gastrulation from 65 to 30%. The extent to which each genotype was affected depended on sire identity, which explained 15% of variation. pCO2 did not significantly influence development at gastrulation. To explore the importance of individual mating pairs, response ratios were calculated for offspring of each family across all treatments. Response ratios demonstrated that the majority of genotypes experienced the highest percentage of normal development to gastrulation in the control treatment, and that family (sire × dam) is important in determining the response to ocean warming and acidification. A positive genetic correlation (overall r* G = 0.76) from sire × environment interactions, however, indicated that individuals which develop `better' at both high temperature and high pCO2 may cope better with near-future predicted warm and acidified conditions for eastern Australia.

Volatile organic compounds as non-invasive markers for plant phenotyping.

PubMed

Niederbacher, B; Winkler, J B; Schnitzler, J P

2015-09-01

Plants emit a great variety of volatile organic compounds (VOCs) that can actively participate in plant growth and protection against biotic and abiotic stresses. VOC emissions are strongly dependent on environmental conditions; the greatest ambiguity is whether or not the predicted change in climate will influence and modify plant-pest interactions that are mediated by VOCs. The constitutive and induced emission patterns between plant genotypes, species, and taxa are highly variable and can be used as pheno(chemo)typic markers to distinguish between different origins and provenances. In recent years significant progress has been made in molecular and genetic plant breeding. However, there is actually a lack of knowledge in functionally linking genotypes and phenotypes, particularly in analyses of plant-environment interactions. Plant phenotyping, the assessment of complex plant traits such as growth, development, tolerance, resistance, etc., has become a major bottleneck, and quantitative information on genotype-environment relationships is the key to addressing major future challenges. With increasing demand to support and accelerate progress in breeding for novel traits, the plant research community faces the need to measure accurately increasingly large numbers of plants and plant traits. In this review article, we focus on the promising outlook of VOC phenotyping as a fast and non-invasive measure of phenotypic dynamics. The basic principle is to define plant phenotypes according to their disease resistance and stress tolerance, which in turn will help in improving the performance and yield of economically relevant plants. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Threshold models for genome-enabled prediction of ordinal categorical traits in plant breeding.

PubMed

Montesinos-López, Osval A; Montesinos-López, Abelardo; Pérez-Rodríguez, Paulino; de Los Campos, Gustavo; Eskridge, Kent; Crossa, José

2014-12-23

Categorical scores for disease susceptibility or resistance often are recorded in plant breeding. The aim of this study was to introduce genomic models for analyzing ordinal characters and to assess the predictive ability of genomic predictions for ordered categorical phenotypes using a threshold model counterpart of the Genomic Best Linear Unbiased Predictor (i.e., TGBLUP). The threshold model was used to relate a hypothetical underlying scale to the outward categorical response. We present an empirical application where a total of nine models, five without interaction and four with genomic × environment interaction (G×E) and genomic additive × additive × environment interaction (G×G×E), were used. We assessed the proposed models using data consisting of 278 maize lines genotyped with 46,347 single-nucleotide polymorphisms and evaluated for disease resistance [with ordinal scores from 1 (no disease) to 5 (complete infection)] in three environments (Colombia, Zimbabwe, and Mexico). Models with G×E captured a sizeable proportion of the total variability, which indicates the importance of introducing interaction to improve prediction accuracy. Relative to models based on main effects only, the models that included G×E achieved 9-14% gains in prediction accuracy; adding additive × additive interactions did not increase prediction accuracy consistently across locations. Copyright © 2015 Montesinos-López et al.

Improving accuracies of genomic predictions for drought tolerance in maize by joint modeling of additive and dominance effects in multi-environment trials.

PubMed

Dias, Kaio Olímpio Das Graças; Gezan, Salvador Alejandro; Guimarães, Claudia Teixeira; Nazarian, Alireza; da Costa E Silva, Luciano; Parentoni, Sidney Netto; de Oliveira Guimarães, Paulo Evaristo; de Oliveira Anoni, Carina; Pádua, José Maria Villela; de Oliveira Pinto, Marcos; Noda, Roberto Willians; Ribeiro, Carlos Alexandre Gomes; de Magalhães, Jurandir Vieira; Garcia, Antonio Augusto Franco; de Souza, João Cândido; Guimarães, Lauro José Moreira; Pastina, Maria Marta

2018-07-01

Breeding for drought tolerance is a challenging task that requires costly, extensive, and precise phenotyping. Genomic selection (GS) can be used to maximize selection efficiency and the genetic gains in maize (Zea mays L.) breeding programs for drought tolerance. Here, we evaluated the accuracy of genomic selection (GS) using additive (A) and additive + dominance (AD) models to predict the performance of untested maize single-cross hybrids for drought tolerance in multi-environment trials. Phenotypic data of five drought tolerance traits were measured in 308 hybrids along eight trials under water-stressed (WS) and well-watered (WW) conditions over two years and two locations in Brazil. Hybrids' genotypes were inferred based on their parents' genotypes (inbred lines) using single-nucleotide polymorphism markers obtained via genotyping-by-sequencing. GS analyses were performed using genomic best linear unbiased prediction by fitting a factor analytic (FA) multiplicative mixed model. Two cross-validation (CV) schemes were tested: CV1 and CV2. The FA framework allowed for investigating the stability of additive and dominance effects across environments, as well as the additive-by-environment and the dominance-by-environment interactions, with interesting applications for parental and hybrid selection. Results showed differences in the predictive accuracy between A and AD models, using both CV1 and CV2, for the five traits in both water conditions. For grain yield (GY) under WS and using CV1, the AD model doubled the predictive accuracy in comparison to the A model. Through CV2, GS models benefit from borrowing information of correlated trials, resulting in an increase of 40% and 9% in the predictive accuracy of GY under WS for A and AD models, respectively. These results highlight the importance of multi-environment trial analyses using GS models that incorporate additive and dominance effects for genomic predictions of GY under drought in maize single-cross hybrids.

The divergent impact of catechol-O-methyltransferase (COMT) Val158Met genetic polymorphisms on executive function in adolescents with discrete patterns of childhood adversity.

PubMed

Zhang, Huihui; Li, Jie; Yang, Bei; Ji, Tao; Long, Zhouting; Xing, Qiquan; Shao, Di; Bai, Huayu; Sun, Jiwei; Cao, Fenglin

2018-02-01

Catechol-O-methyltransferase (COMT) Val 158 Met functional polymorphisms play a crucial role in the development of executive function (EF), but their effect may be moderated by environmental factors such as childhood adversity. The present study aimed at testing the divergent impact of the COMT Val 158 Met genotype on EF in non-clinical adolescents with discrete patterns of childhood adversity. A total of 341 participants completed the Childhood Trauma Questionnaire, the self-reported version of the Behavior Rating Inventory of Executive Function, and self-administered questionnaires on familial function. The participants' COMT Val 158 Met genotype was determined. Associations among the variables were explored using latent class analysis and general linear models. We found that Val/Val homozygotes showed significantly worse performance on behavioral shift, relative to Met allele carriers (F=5.921, p=0.015, Partial η 2 =0.018). Moreover, three typical patterns of childhood adversity, namely, low childhood adversity (23.5%), childhood neglect (59.8%), and high childhood adversity (16.7%), were found. Both childhood neglect and high childhood adversity had a negative impact on each aspect of EF and on global EF performance. Importantly, these results provided evidence for significant interaction effects, as adolescents with the Val/Val genotype showed inferior behavioral shift performance than Met carriers (F=6.647, p=0.010, Partial η 2 =0.020) in the presence of high childhood adversity. Furthermore, there were no differences between the genotypes for childhood neglect and low childhood adversity. Overall, this is the first study to show that an interaction between the COMT genotype and childhood adversity affects EF in non-clinical adolescents. These results suggest that the COMT genotype may operate as a susceptibility gene vulnerable to an adverse environment. Copyright © 2017 Elsevier Inc. All rights reserved.

The influence of gene-environment interactions on GHR and IGF-1 expression and their association with growth in brook charr, Salvelinus fontinalis (Mitchill)

PubMed Central

Côté, Guillaume; Perry, Guy; Blier, Pierre; Bernatchez, Louis

2007-01-01

Background Quantitative reaction norm theory proposes that genotype-by-environment interaction (GxE) results from inter-individual differences of expression in adaptive suites of genes in distinct environments. However, environmental norms for actual gene suites are poorly documented. In this study, we investigated the effects of GxE interactions on levels of gene transcription and growth by documenting the impact of rearing environment (freshwater vs. saltwater), sex and genotypic (low vs. high estimated breeding value EBV) effects on the transcription level of insulin-like growth factor (IGF-1) and growth hormone receptor (GHR) in brook charr (Salvelinus fontinalis). Results Males grew faster than females (μ♀ = 1.20 ± 0.07 g·d-1, μ♂ = 1.46 ± 0.06 g·d-1) and high-EBV fish faster than low-EBV fish (μLOW = 0.97 ± 0.05 g·d-1, μHIGH = 1.58 ± 0.07 g·d-1; p < 0.05). However, growth was markedly lower in saltwater-reared fish than freshwater sibs (μFW = 1.52 ± 0.07 g·d-1, μSW = 1.15 ± 0.06 g·d-1), yet GHR mRNA transcription level was significantly higher in saltwater than in freshwater (μSW = 0.85 ± 0.05, μFW = 0.61 ± 0.05). The ratio of actual growth to units in assayed mRNA ('individual transcript efficiency', iTE; g·d-1·u-1) also differed among EBV groups (μLOW = 2.0 ± 0.24 g·d-1·u-1; μHIGH = 3.7 ± 0.24 g·d-1·u-1) and environments (μSW = 2.0 ± 0.25 g·d-1·u-1; μFW = 3.7 ± 0.25 g·d-1·u-1) for GHR. Males had a lower iTE for GHR than females (μ♂ = 2.4 ± 0.29 g·d-1·u-1; μ♀ = 3.1 ± 0.23 g·d-1·u-1). There was no difference in IGF-1 transcription level between environments (p > 0.7) or EBV groups (p > 0.15) but the level of IGF-1 was four times higher in males than females (μ♂ = 2.4 ± 0.11, μ♀ = 0.58 ± 0.09; p < 0.0001). We detected significant sexual differences in iTE (μ♂ = 1.3 ± 0.59 g·d-1·u-1; μ♀ = 3.9 ± 0.47 g·d-1·u-1), salinities (μSW = 2.3 ± 0.52 g·d-1·u-1; μFW = 3.7 ± 0.53 g·d-1·u-1) and EBV-groups (μLOW = 2.4 ± 0.49 g·d-1·u-1; μHIGH = 3.8 ± 0.49 g·d-1·u-1). Interaction between EBV-group and environment was detected for both GHR (p = 0.027) and IGF-1 (p = 0.019), and for iTE in the two genes (p < 0.0001; p < 0.05, respectively), where increased divergence in levels of GHR and IGF-1 transcription occurred among EBV-groups in the saltwater environment. Conclusion Our results show that both environment and sex have major impacts on the expression of mRNA for two key genes involved in the physiological pathway for growth. We also demonstrate for the first time, at least in fish, genotype-by-environment interaction at the level of individual gene transcription. This work contributes significantly to ongoing efforts towards documenting environmentally and sexually induced variance of gene activity and understanding the resulting phenotypes. PMID:18154679

Differential Susceptibility: The Genetic Moderation of Peer Pressure on Alcohol Use

PubMed Central

Cleveland, H. Harrington; Schlomer, Gabriel L.; Vandenbergh, David J.; Feinberg, Mark E.

2016-01-01

Although peer pressure can influence adolescents’ alcohol use, individual susceptibility to these pressures varies across individuals. The dopamine receptor D4 gene (DRD4) is a potential candidate gene that may influence adolescents’ susceptibility to their peer environment due to the role dopamine plays in reward sensation during social interaction. We hypothesized that DRD4 genotype status would moderate the impact of 7th-grade antisocial peer pressure on 12th-grade lifetime alcohol use (n = 414; 58.7 % female; 92.8 % White). The results revealed significant main effects for antisocial peer pressure, but no main effects for DRD4 genotype on lifetime alcohol use. Adolescent DRD4 genotype moderated the association between peer pressure and lifetime alcohol use. For individuals who carried at least one copy of the DRD4 7-repeat allele (7+), antisocial peer pressure was associated with increased lifetime alcohol use. These findings indicate that genetic sensitivity to peer pressure confers increased alcohol use in late adolescence. PMID:26307243

Differential Susceptibility: The Genetic Moderation of Peer Pressure on Alcohol Use.

PubMed

Griffin, Amanda M; Cleveland, H Harrington; Schlomer, Gabriel L; Vandenbergh, David J; Feinberg, Mark E

2015-10-01

Although peer pressure can influence adolescents' alcohol use, individual susceptibility to these pressures varies across individuals. The dopamine receptor D4 gene (DRD4) is a potential candidate gene that may influence adolescents' susceptibility to their peer environment due to the role dopamine plays in reward sensation during social interaction. We hypothesized that DRD4 genotype status would moderate the impact of 7th-grade antisocial peer pressure on 12th-grade lifetime alcohol use (n = 414; 58.7% female; 92.8% White). The results revealed significant main effects for antisocial peer pressure, but no main effects for DRD4 genotype on lifetime alcohol use. Adolescent DRD4 genotype moderated the association between peer pressure and lifetime alcohol use. For individuals who carried at least one copy of the DRD4 7-repeat allele (7+), antisocial peer pressure was associated with increased lifetime alcohol use. These findings indicate that genetic sensitivity to peer pressure confers increased alcohol use in late adolescence.

Bad nature, bad nurture, and testimony regarding MAOA and SLC6A4 genotyping at murder trials.

PubMed

Bernet, William; Vnencak-Jones, Cindy L; Farahany, Nita; Montgomery, Stephen A

2007-11-01

Recent research-in which subjects were studied longitudinally from childhood until adulthood-has started to clarify how a child's environment and genetic makeup interact to create a violent adolescent or adult. For example, male subjects who were born with a particular allele of the monoamine oxidase A gene and also were maltreated as children had a much greater likelihood of manifesting violent antisocial behavior as adolescents and adults. Also, individuals who were born with particular alleles of the serotonin transporter gene and also experienced multiple stressful life events were more likely to manifest serious depression and suicidality. This research raises the question of whether testimony regarding a defendant's genotype, exposure to child maltreatment, and experience of unusual stress is appropriate to present during the guilt or penalty phases of criminal trials, especially when capital punishment is a consideration. The authors present their experience in genotyping criminal defendants and presenting genetic information at criminal trials.

Social disorder, APOE-E4 genotype, and change in cognitive function among older adults living in Chicago

PubMed Central

Boardman, Jason D.; Barnes, Lisa L.; Wilson, Robert S.; Evans, Denis A.; Mendes de Leon, Carlos F.

2013-01-01

The goal of this paper is to describe the simultaneous influence of social and genetic risk factors on declines in cognitive functioning among older American adults. We use detailed information about the social characteristics of older adults' neighborhoods from the Chicago Health and Aging Project (n = 1655; ages 65+) in conjunction with information about respondent's APOE genotype to predict changes in cognitive function over time. Results indicate that the presence of the ɛ4 allele is associated with a significantly lower cognitive function score at baseline and greater declines in cognitive function compared to those without this risk allele. Importantly, we also show significant variation in the effect of the ɛ4 allele across neighborhoods and our results indicate that this genotype is more strongly associated with cognitive function for residents of neighborhoods with the lowest levels of social disorder. Our findings support the non-causal social push gene–environment interaction model. PMID:22465377

The case-only test for gene-environment interaction is not uniformly powerful: an empirical example

PubMed Central

Wu, Chen; Chang, Jiang; Ma, Baoshan; Miao, Xiaoping; Zhou, Yifeng; Liu, Yu; Li, Yun; Wu, Tangchun; Hu, Zhibin; Shen, Hongbing; Jia, Weihua; Zeng, Yixin; Lin, Dongxin; Kraft, Peter

2016-01-01

The case-only test has been proposed as a more powerful approach to detect gene-environment (G×E) interactions. This approach assumes that the genetic and environmental factors are independent. While it is well known that Type I error rate will increase if this assumption is violated, it is less widely appreciated that gene-environment correlation can also lead to power loss. We illustrate this phenomenon by comparing the performance of the case-only test to other approaches to detect G×E interactions in a genome-wide association study of esophageal squamous carcinoma (ESCC) in Chinese populations. Some of these approaches do not use information on the correlation between exposure and genotype (standard logistic regression), while others seek to use this information in a robust fashion to boost power without increasing Type I error (two-step, empirical Bayes and cocktail methods). G×E interactions were identified involving drinking status and two regions containing genes in the alcohol metabolism pathway, 4q23 and 12q24. Although the case-only test yielded the most significant tests of G×E interaction in the 4q23 region, the case-only test failed to identify significant interactions in the 12q24 region which were readily identified using other approaches. The low power of the case-only test in the 12q24 region is likely due to the strong inverse association between the SNPs in this region and drinking status. This example underscores the need to consider multiple approaches to detect gene-environment interactions, as different tests are more or less sensitive to different alternative hypotheses and violations of the gene-environment independence assumption. PMID:23595356

Host Genetics and Environment Drive Divergent Responses of Two Resource Sharing Gall-Formers on Norway Spruce: A Common Garden Analysis.

PubMed

Axelsson, E Petter; Iason, Glenn R; Julkunen-Tiitto, Riitta; Whitham, Thomas G

2015-01-01

A central issue in the field of community genetics is the expectation that trait variation among genotypes play a defining role in structuring associated species and in forming community phenotypes. Quantifying the existence of such community phenotypes in two common garden environments also has important consequences for our understanding of gene-by-environment interactions at the community level. The existence of community phenotypes has not been evaluated in the crowns of boreal forest trees. In this study we address the influence of tree genetics on needle chemistry and genetic x environment interactions on two gall-inducing adelgid aphids (Adelges spp. and Sacchiphantes spp.) that share the same elongating bud/shoot niche. We examine the hypothesis that the canopies of different genotypes of Norway spruce (Picea abies L.) support different community phenotypes. Three patterns emerged. First, the two gallers show clear differences in their response to host genetics and environment. Whereas genetics significantly affected the abundance of Adelges spp. galls, Sacchiphantes spp. was predominately affected by the environment suggesting that the genetic influence is stronger in Adelges spp. Second, the among family variation in genetically controlled resistance was large, i.e. fullsib families differed as much as 10 fold in susceptibility towards Adelges spp. (0.57 to 6.2 galls/branch). Also, the distribution of chemical profiles was continuous, showing both overlap as well as examples of significant differences among fullsib families. Third, despite the predicted effects of host chemistry on galls, principal component analyses using 31 different phenolic substances showed only limited association with galls and a similarity test showed that trees with similar phenolic chemical characteristics, did not host more similar communities of gallers. Nonetheless, the large genetic variation in trait expression and clear differences in how community members respond to host genetics supports our hypothesis that the canopies of Norway spruce differ in their community phenotypes.

Gene-Gene and Gene-Environment Interactions in the Etiology of Breast Cancer

DTIC Science & Technology

2007-06-01

When you eat fried or baked pork or beef , you normally prefer that: Entire surface is brown with a slight burnt flavor 1...Uridine diphospho-glucuronosyltransferase 1A1 (UGT1A1) is involved in catalyzing estrogen, the hormone that plays a central role in the etiology of...relationship of UGT1A1 genotypes with plasma levels of estrone, estrone sulfate, estradiol, testosterone, and sex hormone binding globulins (SHBG

Shoot water relations of mature black spruce families displaying a genotype x environment interaction in growth rate. II. Temporal trends and response to varying soil water conditions

Treesearch

John E. Major; Kurt H. Johnsen

1999-01-01

Pressure-volume curves and shoot water potentials were determined for black spruce (Picea mariana (Mill.) BSP) trees from four full-sib families at the Petawawa Research Forest, Ontario, Canada. Trees were sampled from a dry site in 1992 and from the dry site and a wet site in 1993. Modulus of elasticity (e ), osmotic potential at...

Shoot water relations of mature black spruce families displaying a genotype x environment interaction in growth rate. I. Family and site effects over three growing seasons

Treesearch

Kurt H. Johnsen; John E Major

1999-01-01

Pressure-volume curves were determined for black spruce (Picea mariana (Mill.) BSP) trees from four full-sib families. During the first two years, trees were measured from a plantation on a dry site. In the third year, trees were sampled from the dry site and a wet site. Diurnal measurements of shoot water potential allowed in situ ...

Genotype by watering regime interaction in cultivated tomato: lessons from linkage mapping and gene expression.

PubMed

Albert, Elise; Gricourt, Justine; Bertin, Nadia; Bonnefoi, Julien; Pateyron, Stéphanie; Tamby, Jean-Philippe; Bitton, Frédérique; Causse, Mathilde

2016-02-01

In tomato, genotype by watering interaction resulted from genotype re-ranking more than scale changes. Interactive QTLs according to watering regime were detected. Differentially expressed genes were identified in some intervals. As a result of climate change, drought will increasingly limit crop production in the future. Studying genotype by watering regime interactions is necessary to improve plant adaptation to low water availability. In cultivated tomato (Solanum lycopersicum L.), extensively grown in dry areas, well-mastered water deficits can stimulate metabolite production, increasing plant defenses and concentration of compounds involved in fruit quality, at the same time. However, few tomato Quantitative Trait Loci (QTLs) and genes involved in response to drought are identified or only in wild species. In this study, we phenotyped a population of 119 recombinant inbred lines derived from a cross between a cherry tomato and a large fruit tomato, grown in greenhouse under two watering regimes, in two locations. A large genetic variability was measured for 19 plant and fruit traits, under the two watering treatments. Highly significant genotype by watering regime interactions were detected and resulted from re-ranking more than scale changes. The population was genotyped for 679 SNP markers to develop a genetic map. In total, 56 QTLs were identified among which 11 were interactive between watering regimes. These later mainly exhibited antagonist effects according to watering treatment. Variation in gene expression in leaves of parental accessions revealed 2259 differentially expressed genes, among which candidate genes presenting sequence polymorphisms were identified under two main interactive QTLs. Our results provide knowledge about the genetic control of genotype by watering regime interactions in cultivated tomato and the possible use of deficit irrigation to improve tomato quality.

Interaction between MTHFR 677C>T and periconceptional folic acid supplementation in the risk of Hypospadias.

PubMed

Dokter, Elisabeth M J; van Rooij, Iris A L M; Wijers, Charlotte H W; Groothuismink, Johanne M; van der Biezen, Jan Jaap; Feitz, Wout F J; Roeleveld, Nel; van der Zanden, Loes F M

2016-04-01

Hypospadias is a congenital malformation with both environmental factors and genetic predisposition involved in the pathogenesis. The role of maternal periconceptional folic acid supplement use in the development of hypospadias is unclear. As folate levels may also be influenced by the C677T polymorphism in the methylenetetrahydrofolate reductase (MTHFR) gene, we hypothesize that a gene-environment interaction between this polymorphism and folic acid use is involved in the etiology of hypospadias. We conducted a case-control study among 855 hypospadias cases and 713 population-based controls from the AGORA data- and biobank. Folic acid supplement use was derived from maternal questionnaires and infant and maternal DNA was used to determine the MTHFR C677T polymorphism using Taqman assays. We performed separate analyses for different hypospadias phenotypes (anterior/middle/posterior). Hypospadias was neither associated with folic acid use or the MTHFR C677T polymorphism, nor with their interaction. However, we did find an association with middle hypospadias when no supplements were used (odds ratio = 1.6; 95% confidence interval, 1.1-2.4), especially in infants carrying the CT/TT genotype (odds ratio = 2.5; 95% confidence interval, 1.4-4.7). In addition, more infants with these genotypes seemed to have posterior hypospadias, regardless of folic acid use. Our study does not suggest a major role for folic acid supplements or the MTHFR C677T polymorphism in the etiology of hypospadias in general, but not using folic acid and/or carrying the MTHFR C677T polymorphism may be associated with middle and posterior hypospadias. Therefore, we stress the importance of studying gene-environment interactions preferably in stratified analyses for different hypospadias phenotypes. © 2016 Wiley Periodicals, Inc.

Genotype × Adiposity Interaction Linkage Analyses Reveal a Locus on Chromosome 1 for Lipoprotein-Associated Phospholipase A2, a Marker of Inflammation and Oxidative Stress

PubMed Central

Diego, Vincent P.; Rainwater, David L.; Wang, Xing-Li; Cole, Shelley A.; Curran, Joanne E.; Johnson, Matthew P.; Jowett, Jeremy B. M.; Dyer, Thomas D.; Williams, Jeff T.; Moses, Eric K.; Comuzzie, Anthony G.; MacCluer, Jean W.; Mahaney, Michael C.; Blangero, John

2007-01-01

Because obesity leads to a state of chronic, low-grade inflammation and oxidative stress, we hypothesized that the contribution of genes to variation in a biomarker of these two processes may be influenced by the degree of adiposity. We tested this hypothesis using samples from the San Antonio Family Heart Study that were assayed for activity of lipoprotein-associated phospholipase A2 (Lp-PLA2), a marker of inflammation and oxidative stress. Using an approach to model discrete genotype×environment (G×E) interaction, we assigned individuals to one of two discrete diagnostic states (or “adiposity environments”): nonobese or obese, according to criteria suggested by the World Health Organization. We found a genomewide maximum LOD of 3.39 at 153 cM on chromosome 1 for Lp-PLA2. Significant G×E interaction for Lp-PLA2 at the genomewide maximum (P=1.16×10-4) was also found. Microarray gene-expression data were analyzed within the 1-LOD interval of the linkage signal on chromosome 1. We found two transcripts—namely, for Fc gamma receptor IIA and heat-shock protein (70 kDa)—that were significantly associated with Lp-PLA2 (P<.001 for both) and showed evidence of cis-regulation with nominal LOD scores of 2.75 and 13.82, respectively. It would seem that there is a significant genetic response to the adiposity environment in this marker of inflammation and oxidative stress. Additionally, we conclude that G×E interaction analyses can improve our ability to identify and localize quantitative-trait loci. PMID:17160904

The serotonin transporter gene polymorphism (5HTTLPR) moderates the effect of adolescent environmental conditions on self-esteem in young adulthood: A structural equation modeling approach

PubMed Central

Jonassaint, Charles R.; Ashley-Koch, Allison; Whitfield, Keith E.; Hoyle, Rick H.; Richman, Laura Smart; Siegler, Ilene C.; Royal, Charmaine D.; Williams, Redford

2013-01-01

Here we examine the effects of both self-reported and independent observer-reported environmental risk indices, the serotonin transporter gene promoter (5HTTLPR) polymorphism, and their interaction on self-esteem. This trait was assessed during early and mid adolescence (mean age = 14 and 16.5, respectively) and young adulthood (mean age = 21.8) in a prospective cohort of 1214 unrelated participants in the Longitudinal Study of Adolescent Health (Add Health). Using structural equation modeling we identified a gene–environment (G × E) interaction using observer-report but not self-report measures of environmental stress exposure during adolescence: 5HTTLPR genotype and observer-reports of home and neighborhood quality (HNQ) during adolescence interacted to predict self-esteem levels in young adulthood (p < .004). Carriers of the s allele who lived in poor HNQ conditions during adolescence reported lower self-esteem in young adulthood than those with a good HNQ during adolescence. In contrast, among individuals with the l/l genotype, adolescent HNQ did not predict adulthood self-esteem. Genes may moderate the effect of adolescent environmental conditions on adulthood self-esteem. PMID:22659377

Gendering Genetics: Biological Contingencies in the Protective Effects of Social Integration for Men and Women.

PubMed

Perry, Brea L

2016-05-01

Evidence that social and biological processes are intertwined in producing health and human behavior is rapidly accumulating. Using a feminist approach, this research explores how gender moderates the interaction between biological processes and men's and women's behavioral and emotional responses to similar social environments. Using data from the Collaborative Study on the Genetics of Alcoholism, the influence of gender, social integration, and genetic risk on nicotine and alcohol dependence is examined. Three-way interaction models reveal gender-specific moderation of interactions between genetic risk score and social integration. Namely, being currently married and reporting positive social psychological integration are predictive of reduced risk of nicotine dependence among men with genetic susceptibility to strong nicotine cravings in the presence of social cues like stress. In contrast, the protective effects of marital status and social integration are substantially attenuated and absent, respectively, among women with high-risk genotypes. This pattern reflects the dualism (i.e., simultaneous costs and benefits) inherent in social integration for women, which may disproportionately affect those with a genetic sensitivity to stress. These findings contest the notion of genotype as static biological hardwiring that is independent from social and cultural systems of gender difference.

[An ADAA model and its analysis method for agronomic traits based on the double-cross mating design].

PubMed

Xu, Z C; Zhu, J

2000-01-01

According to the double-cross mating design and using principles of Cockerham's general genetic model, a genetic model with additive, dominance and epistatic effects (ADAA model) was proposed for the analysis of agronomic traits. Components of genetic effects were derived for different generations. Monte Carlo simulation was conducted for analyzing the ADAA model and its reduced AD model by using different generations. It was indicated that genetic variance components could be estimated without bias by MINQUE(1) method and genetic effects could be predicted effectively by AUP method; at least three generations (including parent, F1 of single cross and F1 of double-cross) were necessary for analyzing the ADAA model and only two generations (including parent and F1 of double-cross) were enough for the reduced AD model. When epistatic effects were taken into account, a new approach for predicting the heterosis of agronomic traits of double-crosses was given on the basis of unbiased prediction of genotypic merits of parents and their crosses. In addition, genotype x environment interaction effects and interaction heterosis due to G x E interaction were discussed briefly.

Cloning of the unculturable parasite Pasteuria ramosa and its Daphnia host reveals extreme genotype-genotype interactions.

PubMed

Luijckx, Pepijn; Ben-Ami, Frida; Mouton, Laurence; Du Pasquier, Louis; Ebert, Dieter

2011-02-01

The degree of specificity in host-parasite interactions has important implications for ecology and evolution. Unfortunately, specificity can be difficult to determine when parasites cannot be cultured. In such cases, studies often use isolates of unknown genetic composition, which may lead to an underestimation of specificity. We obtained the first clones of the unculturable bacterium Pasteuria ramosa, a parasite of Daphnia magna. Clonal genotypes of the parasite exhibited much more specific interactions with host genotypes than previous studies using isolates. Clones of P. ramosa infected fewer D. magna genotypes than isolates and host clones were either fully susceptible or fully resistant to the parasite. Our finding enhances our understanding of the evolution of virulence and coevolutionary dynamics in this system. We recommend caution when using P. ramosa isolates as the presence of multiple genotypes may influence the outcome and interpretation of some experiments. © 2010 Blackwell Publishing Ltd/CNRS.

Genome-environment associations in sorghum landraces predict adaptive traits

PubMed Central

Lasky, Jesse R.; Upadhyaya, Hari D.; Ramu, Punna; Deshpande, Santosh; Hash, C. Tom; Bonnette, Jason; Juenger, Thomas E.; Hyma, Katie; Acharya, Charlotte; Mitchell, Sharon E.; Buckler, Edward S.; Brenton, Zachary; Kresovich, Stephen; Morris, Geoffrey P.

2015-01-01

Improving environmental adaptation in crops is essential for food security under global change, but phenotyping adaptive traits remains a major bottleneck. If associations between single-nucleotide polymorphism (SNP) alleles and environment of origin in crop landraces reflect adaptation, then these could be used to predict phenotypic variation for adaptive traits. We tested this proposition in the global food crop Sorghum bicolor, characterizing 1943 georeferenced landraces at 404,627 SNPs and quantifying allelic associations with bioclimatic and soil gradients. Environment explained a substantial portion of SNP variation, independent of geographical distance, and genic SNPs were enriched for environmental associations. Further, environment-associated SNPs predicted genotype-by-environment interactions under experimental drought stress and aluminum toxicity. Our results suggest that genomic signatures of environmental adaptation may be useful for crop improvement, enhancing germplasm identification and marker-assisted selection. Together, genome-environment associations and phenotypic analyses may reveal the basis of environmental adaptation. PMID:26601206

Genetic benefits of a female mating preference in gray tree frogs are context-dependent.

PubMed

Welch, Allison M

2003-04-01

"Good genes" models of sexual selection predict that male courtship displays can advertise genetic quality and that, by mating with males with extreme displays, females can obtain genetic benefits for their offspring. However, because the relative performance of different genotypes can vary across environments, these genetic benefits may depend on the environmental context; in which case, static mating preferences may not be adaptive. To better understand how selection acts on the preference that female gray tree frogs (Hyla versicolor) express for long advertisement calls, I tested for genetic benefits in two realistic natural environments, by comparing the performance of half-sibling offspring sired by males with long versus short calls. Tadpoles from twelve such maternal half-sibships were raised in enclosures in their natal pond at two densities. In the low-density treatment, offspring of long-call males were larger at metamorphosis than were offspring of short-call males, whereas in the high-density treatment, offspring of males with long calls tended to metamorphose later than offspring of males with short calls. Thus, although the genes indicated by long calls were advantageous under low-density conditions, they were not beneficial under all conditions, suggesting that a static preference for long calls may not be adaptive in all environments. Such a genotype-by-environment interaction in the genetic consequences of mate choice predicts that when the environment is variable, selection may favor plasticity in female preferences or female selectivity among environments to control the conditions experienced by the offspring.

Genetic Parameters And Selection Response For Yield Traits In Bread Wheat Under Irrigated And Rainfed Environments

NASA Astrophysics Data System (ADS)

Khalil, Iftikhar Hussain; at-ur-Rahman, Hiday; Khan, Imran

2008-01-01

A set of 22 F5:7 experimental wheat lines along with four check cultivars (Dera-98, Fakhr-e-Sarhad, Ghaznavi-98 and Tatara) were evaluated as independent experiments under irrigated and rainfed environments using a randomized complete block design at NWFP Agricultural University, Peshawar during 2004-05. The two environments were statistically different for days to heading and spike length only. Highly significant genetic variability existed among the wheat lines (P<0.01) in the combined analysis across environments for all traits. Genotype×environment interactions were non-significant for all traits except 1000-grain weight indicating consistent performance of wheat genotypes across the two environments. Wheat lines and check cultivars were 2 to 5 days early in heading under rainfed environment compared to the irrigated. Plant height, spike length, 1000-grain weight, biological and grain yields were generally reduced under rainfed environment. Genetic variances were of greater magnitude than environmental variances for most of the traits in both environments. The heritability estimates were of higher magnitude (0.74 to 0.96) for days to heading, plant height, spike length, biological and grain yield, while medium (0.31 to 0.51) for 1000-grain weight. Selection differentials were negative for heading (-7.3 days in irrigated vs -9.4 days in rainfed) and plant height (-9.0 cm in irrigated vs -8.7 cm in rainfed) indicating possibility of selecting wheat genotypes with early heading and short plant stature. Positive selection differentials of 1.3 vs 1.6 cm for spike length, 3.8 vs 3.4 g for 1000-grain weight, 2488.2 vs 3139.7 kg ha-1 for biological yield and 691.6 vs 565.4 kg ha-1 for grain yield at 20% selection intensity were observed under irrigated and rainfed environments, respectively. Expected selection responses were 7.98 vs 8.91 days for heading, 8.20 vs 9.52 cm for plant height, 1.01 vs 1.61 cm for spike length, 2.12 vs 1.15 g for 1000-grain weight, 1655.8 vs 2317.2 kg ha-1 for biological yield and 691.6 vs 565.4 kg ha-1 for grain yield under the two test environments, respectively. The differential heritability and selection responses for yield and related traits suggest the simultaneous evaluation and selection of wheat lines under the two environments.

Angiotensinogen M235T polymorphism associates with exercise hemodynamics in postmenopausal women.

PubMed

McCole, Steve D; Brown, Michael D; Moore, Geoffrey E; Ferrell, Robert E; Wilund, Kenneth R; Huberty, Andrea; Douglass, Larry W; Hagberg, James M

2002-08-14

We sought to determine whether the M235T angiotensinogen (AGT) polymorphism, either interacting with habitual physical activity (PA) levels or independently, was associated with cardiovascular (CV) hemodynamics during maximal and submaximal exercise. Sixty-one healthy postmenopausal women (16 sedentary, 21 physically active, and 24 endurance athletes) had heart rate (HR), blood pressure (BP), cardiac output, stroke volume (SV), total peripheral resistance (TPR), and arteriovenous O2 difference (a-vDO2) assessed during 40, 60, 80, and approximately 100% of VO2 max treadmill exercise. VO2 max did not differ among AGT genotype groups; however, maximal HR was 14 beats/min higher in AGT TT than MM genotype women (P < 0.05). AGT TT genotype women also had 19 beats/min higher HR during approximately 100% VO2 max exercise than AGT MM genotype women (P = 0.008). AGT genotype also interacted with habitual PA levels to associate with systolic BP and a-vDO2 during approximately 100% VO2 max exercise (both P < 0.01). AGT TT genotype women had 11 beats/min higher HR during submaximal exercise than MM genotype women (P < 0.05). AGT genotype interacted with habitual PA levels to associate with systolic BP during submaximal exercise (P = 0.009). AGT genotype, independently or interacting with habitual PA levels, did not associate significantly with diastolic BP, cardiac output, SV, or TPR during maximal or submaximal exercise. Thus this common genetic variant in the renin-angiotensin system appears to associate, both interactively with habitual PA levels and independently, with HR, systolic BP, and a-vDO2 responses to maximal and submaximal exercise in postmenopausal women.

Shift Work in Nurses: Contribution of Phenotypes and Genotypes to Adaptation

PubMed Central

Gamble, Karen L.; Motsinger-Reif, Alison A.; Hida, Akiko; Borsetti, Hugo M.; Servick, Stein V.; Ciarleglio, Christopher M.; Robbins, Sam; Hicks, Jennifer; Carver, Krista; Hamilton, Nalo; Wells, Nancy; Summar, Marshall L.; McMahon, Douglas G.; Johnson, Carl Hirschie

2011-01-01

Background Daily cycles of sleep/wake, hormones, and physiological processes are often misaligned with behavioral patterns during shift work, leading to an increased risk of developing cardiovascular/metabolic/gastrointestinal disorders, some types of cancer, and mental disorders including depression and anxiety. It is unclear how sleep timing, chronotype, and circadian clock gene variation contribute to adaptation to shift work. Methods Newly defined sleep strategies, chronotype, and genotype for polymorphisms in circadian clock genes were assessed in 388 hospital day- and night-shift nurses. Results Night-shift nurses who used sleep deprivation as a means to switch to and from diurnal sleep on work days (∼25%) were the most poorly adapted to their work schedule. Chronotype also influenced efficacy of adaptation. In addition, polymorphisms in CLOCK, NPAS2, PER2, and PER3 were significantly associated with outcomes such as alcohol/caffeine consumption and sleepiness, as well as sleep phase, inertia and duration in both single- and multi-locus models. Many of these results were specific to shift type suggesting an interaction between genotype and environment (in this case, shift work). Conclusions Sleep strategy, chronotype, and genotype contribute to the adaptation of the circadian system to an environment that switches frequently and/or irregularly between different schedules of the light-dark cycle and social/workplace time. This study of shift work nurses illustrates how an environmental “stress” to the temporal organization of physiology and metabolism can have behavioral and health-related consequences. Because nurses are a key component of health care, these findings could have important implications for health-care policy. PMID:21533241

Host genotype by parasite genotype interactions underlying the resistance of anopheline mosquitoes to Plasmodium falciparum.

PubMed

Lambrechts, Louis; Halbert, Jean; Durand, Patrick; Gouagna, Louis C; Koella, Jacob C

2005-01-11

Most studies on the resistance of mosquitoes to their malaria parasites focus on the response of a mosquito line or colony against a single parasite genotype. In natural situations, however, it may be expected that mosquito-malaria relationships are based, as are many other host-parasite systems, on host genotype by parasite genotype interactions. In such systems, certain hosts are resistant to one subset of the parasite's genotypes, while other hosts are resistant to a different subset. To test for genotype by genotype interactions between malaria parasites and their anopheline vectors, different genetic backgrounds (families consisting of the F1 offspring of individual females) of the major African vector Anopheles gambiae were challenged with several isolates of the human malaria parasite Plasmodium falciparum (obtained from naturally infected children in Kenya). Averaged across all parasites, the proportion of infected mosquitoes and the number of oocysts found in their midguts were similar in all mosquito families. Both indices of resistance, however, differed considerably among isolates of the parasite. In particular, no mosquito family was most resistant to all parasites, and no parasite isolate was most infectious to all mosquitoes. These results suggest that the level of mosquito resistance depends on the interaction between its own and the parasite's genotype. This finding thus emphasizes the need to take into account the range of genetic diversity exhibited by mosquito and malaria field populations in ideas and studies concerning the control of malaria.

The Influence of Gene-Environment Interactions on Alcohol Consumption and Alcohol Use Disorders: A Comprehensive Review

PubMed Central

Young-Wolff, Kelly C.; Enoch, Mary-Anne; Prescott, Carol A.

2011-01-01

Since 2005, a rapidly expanding literature has evaluated whether environmental factors such as socio-cultural context and environmental adversity interact with genetic influences on drinking behaviors. This article critically reviews empirical research on alcohol-related genotype-environment interactions (GxE) and provides a contextual framework for understanding how genetic factors combine with (or are shaped by) environmental influences to influence the development of drinking behaviors and alcohol use disorders. Collectively, evidence from twin, adoption, and molecular genetic studies indicates that the degree of importance of genetic influences on risk for drinking outcomes can vary in different populations and under different environmental circumstances. However, methodological limitations and lack of consistent replications in this literature make it difficult to draw firm conclusions regarding the nature and effect size of alcohol-related GxE. On the basis of this review, we describe several methodological challenges as they relate to current research on GxE in drinking behaviors and provide recommendations to aid future research. PMID:21530476

Genotypes of Brassica rapa respond differently to plant-induced variation in air CO2 concentration in growth chambers with standard and enhanced venting.

PubMed

Edwards, Christine E; Haselhorst, Monia S H; McKnite, Autumn M; Ewers, Brent E; Williams, David G; Weinig, Cynthia

2009-10-01

Growth chambers allow measurement of phenotypic differences among genotypes under controlled environment conditions. However, unintended variation in growth chamber air CO2 concentration ([CO2]) may affect the expression of diverse phenotypic traits, and genotypes may differ in their response to variation in [CO2]. We monitored [CO2] and quantified phenotypic responses of 22 Brassica rapa genotypes in growth chambers with either standard or enhanced venting. [CO2] in chambers with standard venting dropped to 280 micromol mol(-1) during the period of maximum canopy development, approximately 80 micromol mol(-1) lower than in chambers with enhanced venting. The stable carbon isotope ratio of CO2 in chamber air (delta13C(air)) was negatively correlated with [CO2], suggesting that photosynthesis caused observed [CO2] decreases. Significant genotype x chamber-venting interactions were detected for 12 of 20 traits, likely due to differences in the extent to which [CO2] changed in relation to genotypes' phenology or differential sensitivity of genotypes to low [CO2]. One trait, 13C discrimination (delta13C), was particularly influenced by unaccounted-for fluctuations in delta13C(air) and [CO2]. Observed responses to [CO2] suggest that genetic variance components estimated in poorly vented growth chambers may be influenced by the expression of genes involved in CO2 stress responses; genotypic values estimated in these chambers may likewise be misleading such that some mapped quantitative trait loci may regulate responses to CO2 stress rather than a response to the environmental factor of interest. These results underscore the importance of monitoring, and where possible, controlling [CO2].

A simulation study of gene-by-environment interactions in GWAS implies ample hidden effects

PubMed Central

Marigorta, Urko M.; Gibson, Greg

2014-01-01

The switch to a modern lifestyle in recent decades has coincided with a rapid increase in prevalence of obesity and other diseases. These shifts in prevalence could be explained by the release of genetic susceptibility for disease in the form of gene-by-environment (GxE) interactions. Yet, the detection of interaction effects requires large sample sizes, little replication has been reported, and a few studies have demonstrated environmental effects only after summing the risk of GWAS alleles into genetic risk scores (GRSxE). We performed extensive simulations of a quantitative trait controlled by 2500 causal variants to inspect the feasibility to detect gene-by-environment interactions in the context of GWAS. The simulated individuals were assigned either to an ancestral or a modern setting that alters the phenotype by increasing the effect size by 1.05–2-fold at a varying fraction of perturbed SNPs (from 1 to 20%). We report two main results. First, for a wide range of realistic scenarios, highly significant GRSxE is detected despite the absence of individual genotype GxE evidence at the contributing loci. Second, an increase in phenotypic variance after environmental perturbation reduces the power to discover susceptibility variants by GWAS in mixed cohorts with individuals from both ancestral and modern environments. We conclude that a pervasive presence of gene-by-environment effects can remain hidden even though it contributes to the genetic architecture of complex traits. PMID:25101110

Role of folate-homocysteine pathway gene polymorphisms and nutritional cofactors in Down syndrome: A triad study.

PubMed

Sukla, K K; Jaiswal, S K; Rai, A K; Mishra, O P; Gupta, V; Kumar, A; Raman, R

2015-08-01

Do gene-gene and gene-environment interactions in folate-homocysteine (Hcy) pathway have a predisposing role for Down syndrome (DS)? The study provides evidence that in addition to advanced age, maternal genotype, micronutrient deficiency and elevated Hcy levels, individually and in combination, are risk factors for Down syndrome. Polymorphisms in certain folate-Hcy-pathway genes (especially the T allele of MTHFR C677T), elevated Hcy and poor folate levels in mothers during pregnancy have been shown to be risk factors for Down syndrome in certain Asian populations (including the eastern region of India), while the same SNPs are not a risk factor in European populations. This conflicting situation alludes to differential gene-environment (nutrition) interactions in different populations which needs to be explored. Between 2008 and 2012, 151 Down syndrome triads and 200 age-matched controls (Control mothers n = 186) were included in the study. Seven polymorphisms in six genes of folate-Hcy metabolic pathway, along with Hcy, cysteine (Cys), vitamin B12 (vit-B12) and folate levels, were analysed and compared among the case and control groups. Genotyping was performed by the PCR-RFLP technique. Levels of homocysteine and cysteine were measured by HPLC while vitamin B12 and folate were estimated by chemiluminescence. We demonstrate that polymorphisms in the folate-Hcy pathway genes in mothers collectively constitute a genotypic risk for DS which is effectively modified by interactions among genes and by the environment affecting folate, Hcy and vitamin B12 levels. The study also supports the idea that these maternal risk factors provide an adaptive advantage during pregnancy supporting live birth of the DS child. Our inability to obtain genotype and nutritional assessments of unaffected siblings of the DS children was an important limitation of the study. Also, its confinement to a specific geographic region (the eastern part) of India, and relatively small sample size is a limitation. A parallel investigation on another population could add greater authenticity to the data. For mothers genetically susceptible to deliver a DS child (particularly in South Asia), peri-conceptional nutritional supplementation and antenatal care could potentially reduce the risk of a DS child. Additionally, nutritional strategies could possibly be used for better management of the symptoms of DS children. The work is funded through Programme support for Genetic disorders by Department of Biotechnology, Government of India to R.R. The authors declare no conflict of interest. © The Author 2015. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Screening toll-like receptor markers to predict latent tuberculosis infection and subsequent tuberculosis disease in a Chinese population.

PubMed

Wu, Linlin; Hu, Yi; Li, Dange; Jiang, Weili; Xu, Biao

2015-04-01

We investigated whether polymorphisms in the toll-like receptor genes or gene-gene interactions are associated with susceptibility to latent tuberculosis infection (LTBI) or subsequent pulmonary tuberculosis (PTB) in a Chinese population. Two matched case-control studies were undertaken. Previously reported polymorphisms in the toll-like receptors (TLRs) were compared between 422 healthy controls (HC) and 205 LTBI patients and between 205 LTBI patients and 109 PTB patients, to assess whether these polymorphisms and their interactions are associated with LTBI or PTB. A PCR-based restriction fragment length polymorphism analysis was used to detect genetic polymorphisms in the TLR genes. Nonparametric multifactor dimensionality reduction (MDR) was used to analyze the effects of interactions between complex disease genes and other genes or environmental factors. Sixteen markers in TLR1, TLR2, TLR4, TLR6, TLR8, TLR9, and TIRAP were detected. In TLR2, the frequencies of the CC genotype (OR = 2.262; 95% CI: 1.433-3.570) and C allele (OR = 1.566; 95% CI: 1.223-1.900) in single-nucleotide polymorphism (SNP) rs3804100 were significantly higher in the LTBI group than in the HC group, whereas the GA genotype of SNP rs5743708 was associated with PTB (OR = 6.087; 95% CI: 1.687-21.968). The frequencies of the GG genotype of SNP rs7873784 in TLR4 (OR = 2.136; 95% CI: 1.312-3.478) and the CC genotype of rs3764879 in TLR8 (OR = 1.982; 95% CI: 1.292-3.042) were also significantly higher in the PTB group than in the HC group. The TC genotype frequency of SNP rs5743836 in TLR9 was significantly higher in the LTBI group than in the HC group (OR = 1.664; 95% CI: 1.201-2.306). An MDR analysis of gene-gene and gene-environment interactions identified three SNPs (rs10759932, rs7873784, and rs10759931) that predicted LTBI with 84% accuracy (p = 0.0004) and three SNPs (rs3804100, rs1898830, and rs10759931) that predicted PTB with 80% accuracy (p = 0.0001). Our results suggest that genetic variation in TLR2, 4, 8 and 9, implicating TLR-related pathways affecting the innate immunity response, modulate LTBI and PTB susceptibility in Chinese.

Genotype × environment interaction is weaker in genitalia than in mating signals and body traits in Enchenopa treehoppers (Hemiptera: Membracidae).

PubMed

Rodríguez, Rafael L; Al-Wathiqui, Nooria

2011-07-01

Theory predicts that selection acting across environments should erode genetic variation in reaction norms; i.e., selection should weaken genotype × environment interaction (G × E). In spite of this expectation, G × E is often detected in fitness-related traits. It thus appears that G × E is at least sometimes sustained under selection, a possibility that highlights the need for theory that can account for variation in the presence and strength of G × E. We tested the hypothesis that trait differences in developmental architecture contribute to variation in the expression of G × E. Specifically, we assessed the influence of canalization (robustness to genetic or environmental perturbations) and condition-dependence (association between trait expression and prior resource acquisition or vital cellular processes). We compared G × E across three trait types expected to differ in canalization and condition-dependence: mating signals, body size-related traits, and genitalia. Because genitalia are expected to show the least condition-dependence and the most canalization, they should express weaker G × E than the other trait types. Our study species was a member of the Enchenopa binotata species complex of treehoppers. We found significant G × E in most traits; G × E was strongest in signals and body traits, and weakest in genitalia. These results support the hypothesis that trait differences in developmental architecture (canalization and condition-dependence) contribute to variation in the expression of G × E. We discuss implications for the dynamics of sexual selection on different trait types.

Gene-Gene and Gene-Environment Interactions in Ulcerative Colitis

PubMed Central

Wang, Ming-Hsi; Fiocchi, Claudio; Zhu, Xiaofeng; Ripke, Stephan; Kamboh, M. Ilyas; Rebert, Nancy; Duerr, Richard H.; Achkar, Jean-Paul

2014-01-01

Genome-wide association studies (GWAS) have identified at least 133 ulcerative colitis (UC) associated loci. The role of genetic factors in clinical practice is not clearly defined. The relevance of genetic variants to disease pathogenesis is still uncertain because of not characterized gene-gene and gene-environment interactions. We examined the predictive value of combining the 133 UC risk loci with genetic interactions in an ongoing inflammatory bowel disease (IBD) GWAS. The Wellcome Trust Case-Control Consortium (WTCCC) IBD GWAS was used as a replication cohort. We applied logic regression (LR), a novel adaptive regression methodology, to search for high order interactions. Exploratory genotype correlations with UC sub-phenotypes (extent of disease, need of surgery, age of onset, extra-intestinal manifestations and primary sclerosing cholangitis (PSC)) were conducted. The combination of 133 UC loci yielded good UC risk predictability (area under the curve [AUC] of 0.86). A higher cumulative allele score predicted higher UC risk. Through LR, several lines of evidence for genetic interactions were identified and successfully replicated in the WTCCC cohort. The genetic interactions combined with the gene-smoking interaction significantly improved predictability in the model (AUC, from 0.86 to 0.89, P=3.26E-05). Explained UC variance increased from 37% to 42% after adding the interaction terms. A within case analysis found suggested genetic association with PSC. Our study demonstrates that the LR methodology allows the identification and replication of high order genetic interactions in UC GWAS datasets. UC risk can be predicted by a 133 loci and improved by adding gene-gene and gene-environment interactions. PMID:24241240

Observed positive parenting behaviors and youth genotype: evidence for gene-environment correlations and moderation by parent personality traits.

PubMed

Oppenheimer, Caroline W; Hankin, Benjamin L; Jenness, Jessica L; Young, Jami F; Smolen, Andrew

2013-02-01

Gene-environment correlations (rGE) have been demonstrated in behavioral genetic studies, but rGE have proven elusive in molecular genetic research. Significant gene-environment correlations may be difficult to detect because potential moderators could reduce correlations between measured genetic variants and the environment. Molecular genetic studies investigating moderated rGE are lacking. This study examined associations between child catechol-O-methyltransferase genotype and aspects of positive parenting (responsiveness and warmth), and whether these associations were moderated by parental personality traits (neuroticism and extraversion) among a general community sample of third, sixth, and ninth graders (N = 263) and their parents. Results showed that parent personality traits moderated the rGE association between youths' genotype and coded observations of positive parenting. Parents with low levels of neuroticism and high levels of extraversion exhibited greater sensitive responsiveness and warmth, respectively, to youth with the valine/valine genotype. Moreover, youth with this genotype exhibited lower levels of observed anger. There was no association between the catechol-O-methyltransferase genotype and parenting behaviors for parents high on neuroticism and low on extraversion. Findings highlight the importance of considering moderating variables that may influence child genetic effects on the rearing environment. Implications for developmental models of maladaptive and adaptive child outcomes, and interventions for psychopathology, are discussed within a developmental psychopathology framework.

Observed positive parenting behaviors and youth genotype: Evidence for gene–environment correlations and moderation by parent personality traits

PubMed Central

OPPENHEIMER, CAROLINE W.; HANKIN, BENJAMIN L.; JENNESS, JESSICA L.; YOUNG, JAMI F.; SMOLEN, ANDREW

2013-01-01

Gene–environment correlations (rGE) have been demonstrated in behavioral genetic studies, but rGE have proven elusive in molecular genetic research. Significant gene–environment correlations may be difficult to detect because potential moderators could reduce correlations between measured genetic variants and the environment. Molecular genetic studies investigating moderated rGE are lacking. This study examined associations between child catechol-O-methyltransferase genotype and aspects of positive parenting (responsiveness and warmth), and whether these associations were moderated by parental personality traits (neuroticism and extraversion) among a general community sample of third, sixth, and ninth graders (N = 263) and their parents. Results showed that parent personality traits moderated the rGE association between youths’ genotype and coded observations of positive parenting. Parents with low levels of neuroticism and high levels of extraversion exhibited greater sensitive responsiveness and warmth, respectively, to youth with the valine/valine genotype. Moreover, youth with this genotype exhibited lower levels of observed anger. There was no association between the catechol-O-methyltransferase genotype and parenting behaviors for parents high on neuroticism and low on extraversion. Findings highlight the importance of considering moderating variables that may influence child genetic effects on the rearing environment. Implications for developmental models of maladaptive and adaptive child outcomes, and interventions for psychopathology, are discussed within a developmental psychopathology framework. PMID:23398761

Simulating the Yield Impacts of Organ-Level Quantitative Trait Loci Associated With Drought Response in Maize: A “Gene-to-Phenotype” Modeling Approach

PubMed Central

Chenu, Karine; Chapman, Scott C.; Tardieu, François; McLean, Greg; Welcker, Claude; Hammer, Graeme L.

2009-01-01

Under drought, substantial genotype–environment (G × E) interactions impede breeding progress for yield. Identifying genetic controls associated with yield response is confounded by poor genetic correlations across testing environments. Part of this problem is related to our inability to account for the interplay of genetic controls, physiological traits, and environmental conditions throughout the crop cycle. We propose a modeling approach to bridge this “gene-to-phenotype” gap. For maize under drought, we simulated the impact of quantitative trait loci (QTL) controlling two key processes (leaf and silk elongation) that influence crop growth, water use, and grain yield. Substantial G × E interaction for yield was simulated for hypothetical recombinant inbred lines (RILs) across different seasonal patterns of drought. QTL that accelerated leaf elongation caused an increase in crop leaf area and yield in well-watered or preflowering water deficit conditions, but a reduction in yield under terminal stresses (as such “leafy” genotypes prematurely exhausted the water supply). The QTL impact on yield was substantially enhanced by including pleiotropic effects of these QTL on silk elongation and on consequent grain set. The simulations obtained illustrated the difficulty of interpreting the genetic control of yield for genotypes influenced only by the additive effects of QTL associated with leaf and silk growth. The results highlight the potential of integrative simulation modeling for gene-to-phenotype prediction and for exploiting G × E interactions for complex traits such as drought tolerance. PMID:19786622

Shoot water relations of mature black spruce families displaying a genotype × environment interaction in growth rate. III. Diurnal patterns as influenced by vapor pressure deficit and internal water status

Treesearch

John E. Major; Kurt H. Johnsen

2001-01-01

Pressure­volume curves were constructed and shoot water potentials measured for +20-year-old black spruce (Picea mariana (Mill.) BSP) trees from four full-sib families growing on a moist site and a dry site at the Petawawa Research Forest, Ontario, to determine whether differences in diurnal water relations traits were related to productivity. To...

QTL analysis of genotype x environment interactions affecting cotton fiber quality.

PubMed

Paterson, A H; Saranga, Y; Menz, M; Jiang, C-X; Wright, R J

2003-02-01

Cotton is unusual among major crops in that large acreages are grown under both irrigated and rainfed conditions, making genotype x environment interactions of even greater importance than usual in designing crop-improvement strategies. We describe the impact of well-watered versus water-limited growth conditions on the genetic control of fiber quality, a complex suite of traits that collectively determine the utility of cotton. Fiber length, length uniformity, elongation, strength, fineness, and color (yellowness) were influenced by 6, 7, 9, 21, 25 and 11 QTLs (respectively) that could be detected in one or more treatments. The genetic control of cotton fiber quality was markedly affected both by general differences between growing seasons ("years") and by specific differences in water management regimes. Seventeen QTLs were detected only in the water-limited treatment while only two were specific to the well-watered treatment, suggesting that improvement of fiber quality under water stress may be even more complicated than improvement of this already complex trait under well-watered conditions. In crops such as cotton with widespread use of both irrigated and rainfed production systems, the need to manipulate larger numbers of genes to confer adequate quality under both sets of conditions will reduce the expected rate of genetic gain. These difficulties may be partly ameliorated by efficiencies gained through identification and use of diagnostic DNA markers, including those identified herein.

Cross-cultural gene by environment interactions in depression, posttraumatic stress disorder, and the cortisol awakening response: FKBP5 polymorphisms and childhood trauma in South Asia

PubMed Central

Kohrt, Brandon A.; Worthman, Carol M.; Ressler, Kerry J.; Mercer, Kristina B.; Upadhaya, Nawaraj; Koirala, Suraj; Nepal, Mahendra K.; Sharma, Vidya Dev; Binder, Elisabeth B.

2015-01-01

Background Despite increased attention to global mental health, psychiatric genetic research has been dominated by studies in high-income countries, especially with populations of European descent. The objective of this study was to assess single nucleotide polymorphisms (SNPs) in the FKBP5 gene in a population living in South Asia. Methods Among adults in Nepal, depression was assessed with the Beck Depression Inventory (BDI), posttraumatic stress disorder (PTSD) with the PTSD Checklist-Civilian Version (PCL-C), and childhood maltreatment with the Childhood Trauma Questionnaire (CTQ). FKBP5 SNPs were genotyped for 682 participants. Cortisol awakening response (CAR) was assessed in a subsample of 118 participants over three days. Results The FKBP5 tag-SNP rs9296158 showed a main effect on depressive symptoms (p=0.03). Interaction of rs9296158 and childhood maltreatment predicted adult depressive symptoms (p=0.02) but not PTSD. Childhood maltreatment associated with endocrine response in individuals homozygous for the A allele, demonstrated by a negative CAR and overall hypocortisolemia in the rs9296158 AA genotype and childhood maltreatment group (p<0.001). Conclusions This study replicated findings related to FKBP5 and depression but not PTSD. Gene by environment studies should take differences in prevalence and cultural significance of phenotypes and exposures into account when interpreting cross-cultural findings. PMID:26100613

Polymorphism in the two-locus Levene model with nonepistatic directional selection.

PubMed

Bürger, Reinhard

2009-11-01

For the Levene model with soft selection in two demes, the maintenance of polymorphism at two diallelic loci is studied. Selection is nonepistatic and dominance is intermediate. Thus, there is directional selection in every deme and at every locus. We assume that selection is in opposite directions in the two demes because otherwise no polymorphism is possible. If at one locus there is no dominance, then a complete analysis of the dynamical and equilibrium properties is performed. In particular, a simple necessary and sufficient condition for the existence of an internal equilibrium and sufficient conditions for global asymptotic stability are obtained. These results are extended to deme-independent degree of dominance at one locus. A perturbation analysis establishes structural stability within the full parameter space. In the absence of genotype-environment interaction, which requires deme-independent dominance at both loci, nongeneric equilibrium behavior occurs, and the introduction of arbitrarily small genotype-environment interaction changes the equilibrium structure and may destroy stable polymorphism. The volume of the parameter space for which a (stable) two-locus polymorphism is maintained is computed numerically. It is investigated how this volume depends on the strength of selection and on the dominance relations. If the favorable allele is (partially) dominant in its deme, more than 20% of all parameter combinations lead to a globally asymptotically stable, fully polymorphic equilibrium.

Oxytocin receptor gene (OXTR) in relation to loneliness in adolescence: interactions with sex, parental support, and DRD2 and 5-HTTLPR genotypes.

PubMed

van Roekel, Eeske; Verhagen, Maaike; Engels, Rutger C M E; Goossens, Luc; Scholte, Ron H J

2013-10-01

Recent research has shown that loneliness, a common problem in adolescence, may have a genetic basis. The evidence, though, was limited mostly to serotonin-related and dopamine-related genes. In the present study, we focused on the oxytocin receptor gene (OXTR). Associations were examined in a longitudinal study spanning five annual waves (N=307). The relations between OXTR and loneliness were examined, as well as interactions between OXTR and sex, parental support, 5-HTTLPR genotype, and DRD2 genotype. Using Latent Growth Curve Modeling, the OXTR genotype was not directly related to loneliness. An OXTR×sex interaction was found. Girls showed a steeper decline in loneliness when they had an A allele compared with girls who were homozygous for the G allele. In addition, a gene-gene interaction or epistasis was observed. Both boys and girls who had at least one A1 allele for the DRD2 gene and also had the GG genotype for the OXTR gene showed stable levels of loneliness over time. The present study is the first to show that the GG genotype for the OXTR gene is linked to the development of loneliness in adolescence and that this association is moderated by participants' sex and their genotype for a dopamine-related gene.

Genotypes do not confer risk for delinquency but rather alter susceptibility to positive and negative environmental factors: gene-environmentinteractions of BDNF Val66Met, 5-HTTLPR, and MAOA-uVNTR [corrected].

PubMed

Nilsson, Kent W; Comasco, Erika; Hodgins, Sheilagh; Oreland, Lars; Åslund, Cecilia

2014-12-10

Previous evidence of gene-by-environment interactions associated with emotional and behavioral disorders is contradictory. Differences in findings may result from variation in valence and dose of the environmental factor, and/or failure to take account of gene-by-gene interactions. The present study investigated interactions between the brain-derived neurotrophic factor gene (BDNF Val66Met), the serotonin transporter gene-linked polymorphic region (5-HTTLPR), the monoamine oxidase A (MAOA-uVNTR) polymorphisms, family conflict, sexual abuse, the quality of the child-parent relationship, and teenage delinquency. In 2006, as part of the Survey of Adolescent Life in Västmanland, Sweden, 1 337 high-school students, aged 17-18 years, anonymously completed questionnaires and provided saliva samples for DNA analyses. Teenage delinquency was associated with two-, three-, and four-way interactions of each of the genotypes and the three environmental factors. Significant four-way interactions were found for BDNF Val66Met × 5-HTTLPR×MAOA-uVNTR × family conflicts and for BDNF Val66Met × 5-HTTLPR×MAOA-uVNTR × sexual abuse. Further, the two genotype combinations that differed the most in expression levels (BDNF Val66Met Val, 5-HTTLPR LL, MAOA-uVNTR LL [girls] and L [boys] vs BDNF Val66Met Val/Met, 5-HTTLPR S/LS, MAOA-uVNTR S/SS/LS) in interaction with family conflict and sexual abuse were associated with the highest delinquency scores. The genetic variants previously shown to confer vulnerability for delinquency (BDNF Val66Met Val/Met × 5-HTTLPR S × MAOA-uVNTR S) were associated with the lowest delinquency scores in interaction with a positive child-parent relationship. Functional variants of the MAOA-uVNTR, 5-HTTLPR, and BDNF Val66Met, either alone or in interaction with each other, may be best conceptualized as modifying sensitivity to environmental factors that confer either risk or protection for teenage delinquency. © The Author 2015. Published by Oxford University Press on behalf of CINP.

Amygdala Volume in Offspring from Multiplex for Alcohol Dependence Families: The Moderating Influence of Childhood Environment and 5-HTTLPR Variation.

PubMed

Hill, Shirley Y; Wang, Shuhui; Carter, Howard; McDermott, Michael D; Zezza, Nicholas; Stiffler, Scott

2013-12-12

The increased susceptibility for developing alcohol dependence seen in offspring from families with alcohol dependence may be related to structural and functional differences in brain circuits that influence emotional processing. Early childhood environment, genetic variation in the serotonin transporter-linked polymorphic region (5-HTTLPR) of the SLCA4 gene and allelic variation in the Brain Derived Neurotrophic Factor (BDNF) gene have each been reported to be related to volumetric differences in the temporal lobe especially the amygdala. Magnetic resonance imaging was used to obtain amygdala volumes for 129 adolescent/young adult individuals who were either High-Risk (HR) offspring from families with multiple cases of alcohol dependence (N=71) or Low-Risk (LR) controls (N=58). Childhood family environment was measured prospectively using age-appropriate versions of the Family Environment Scale during a longitudinal follow-up study. The subjects were genotyped for Brain-Derived Neurotrophic Factor (BDNF) Val66Met and the serotonin transporter polymorphism (5-HTTLPR). Two family environment scale scores (Cohesion and Conflict), genotypic variation, and their interaction were tested for their association with amygdala volumes. Personal and prenatal exposure to alcohol and drugs were considered in statistical analyses in order to more accurately determine the effects of familial risk group differences. Amygdala volume was reduced in offspring from families with multiple alcohol dependent members in comparison to offspring from control families. High-Risk offspring who were carriers of the S variant of the 5-HTTLPR polymorphism had reduced amygdala volume in comparison to those with an LL genotype. Larger amygdala volume was associated with greater family cohesion but only in Low-Risk control offspring. Familial risk for alcohol dependence is an important predictor of amygdala volume even when removing cases with significant personal exposure and covarying for prenatal exposure effects. The present study provides new evidence that amygdala volume is modified by 5-HTTLPR variation in High-Risk families.

Interaction of rearing environment and reproductive tactic on gene expression profiles in Atlantic salmon

USGS Publications Warehouse

Aubin-Horth, N.; Letcher, B.H.; Hofmann, H.A.

2005-01-01

Organisms that share the same genotype can develop into divergent phenotypes, depending on environmental conditions. In Atlantic salmon, young males of the same age can be found either as sneakers or immature males that are future anadromous fish. Just as the organism-level phenotype varies between divergent male developmental trajectories, brain gene expression is expected to vary as well. We hypothesized that rearing environment can also have an important effect on gene expression in the brain and possibly interact with the reproductive tactic adopted. We tested this hypothesis by comparing brain gene expression profiles of the two male tactics in fish from the same population that were reared in either a natural stream or under laboratory conditions. We found that expression of certain genes was affected by rearing environment only, while others varied between male reproductive tactics independent of rearing environment. Finally, more than half of all genes that showed variable expression varied between the two male tactics only in one environment. Thus, in these fish, very different molecular pathways can give rise to similar macro-phenotypes depending on rearing environment. This result gives important insights into the molecular underpinnings of developmental plasticity in relationship to the environment. ?? 2005 The American Genetic Association.

Analysis of hepatitis B virus preS1 variability and prevalence of the rs2296651 polymorphism in a Spanish population

PubMed Central

Casillas, Rosario; Tabernero, David; Gregori, Josep; Belmonte, Irene; Cortese, Maria Francesca; González, Carolina; Riveiro-Barciela, Mar; López, Rosa Maria; Quer, Josep; Esteban, Rafael; Buti, Maria; Rodríguez-Frías, Francisco

2018-01-01

AIM To determine the variability/conservation of the domain of hepatitis B virus (HBV) preS1 region that interacts with sodium-taurocholate cotransporting polypeptide (hereafter, NTCP-interacting domain) and the prevalence of the rs2296651 polymorphism (S267F, NTCP variant) in a Spanish population. METHODS Serum samples from 246 individuals were included and divided into 3 groups: patients with chronic HBV infection (CHB) (n = 41, 73% Caucasians), patients with resolved HBV infection (n = 100, 100% Caucasians) and an HBV-uninfected control group (n = 105, 100% Caucasians). Variability/conservation of the amino acid (aa) sequences of the NTCP-interacting domain, (aa 2-48 in viral genotype D) and a highly conserved preS1 domain associated with virion morphogenesis (aa 92-103 in viral genotype D) were analyzed by next-generation sequencing and compared in 18 CHB patients with viremia > 4 log IU/mL. The rs2296651 polymorphism was determined in all individuals in all 3 groups using an in-house real-time PCR melting curve analysis. RESULTS The HBV preS1 NTCP-interacting domain showed a high degree of conservation among the examined viral genomes especially between aa 9 and 21 (in the genotype D consensus sequence). As compared with the virion morphogenesis domain, the NTCP-interacting domain had a smaller proportion of HBV genotype-unrelated changes comprising > 1% of the quasispecies (25.5% vs 31.8%), but a larger proportion of genotype-associated viral polymorphisms (34% vs 27.3%), according to consensus sequences from GenBank patterns of HBV genotypes A to H. Variation/conservation in both domains depended on viral genotype, with genotype C being the most highly conserved and genotype E the most variable (limited finding, only 2 genotype E included). Of note, proline residues were highly conserved in both domains, and serine residues showed changes only to threonine or tyrosine in the virion morphogenesis domain. The rs2296651 polymorphism was not detected in any participant. CONCLUSION In our CHB population, the NTCP-interacting domain was highly conserved, particularly the proline residues and essential amino acids related with the NTCP interaction, and the prevalence of rs2296651 was low/null. PMID:29456407

Abiotic stress growth conditions induce different responses in kernel iron concentration across genotypically distinct maize inbred varieties

PubMed Central

Kandianis, Catherine B.; Michenfelder, Abigail S.; Simmons, Susan J.; Grusak, Michael A.; Stapleton, Ann E.

2013-01-01

The improvement of grain nutrient profiles for essential minerals and vitamins through breeding strategies is a target important for agricultural regions where nutrient poor crops like maize contribute a large proportion of the daily caloric intake. Kernel iron concentration in maize exhibits a broad range. However, the magnitude of genotype by environment (GxE) effects on this trait reduces the efficacy and predictability of selection programs, particularly when challenged with abiotic stress such as water and nitrogen limitations. Selection has also been limited by an inverse correlation between kernel iron concentration and the yield component of kernel size in target environments. Using 25 maize inbred lines for which extensive genome sequence data is publicly available, we evaluated the response of kernel iron density and kernel mass to water and nitrogen limitation in a managed field stress experiment using a factorial design. To further understand GxE interactions we used partition analysis to characterize response of kernel iron and weight to abiotic stressors among all genotypes, and observed two patterns: one characterized by higher kernel iron concentrations in control over stress conditions, and another with higher kernel iron concentration under drought and combined stress conditions. Breeding efforts for this nutritional trait could exploit these complementary responses through combinations of favorable allelic variation from these already well-characterized genetic stocks. PMID:24363659

Effect of genotype and environment on branching in weedy green millet (Setaria viridis) and domesticated foxtail millet (Setaria italica) (Poaceae).

PubMed

Doust, Andrew N; Kellogg, Elizabeth A

2006-04-01

Many domesticated crops are derived from species whose life history includes weedy characteristics, such as the ability to vary branching patterns in response to environmental conditions. However, domesticated crop plants are characterized by less variable plant architecture, as well as by a general reduction in vegetative branching compared to their progenitor species. Here we examine weedy green millet and its domesticate foxtail millet that differ in the number of tillers (basal branches) and axillary branches along each tiller. Branch number in F(2:3) progeny of a cross between the two species varies with genotype, planting density, and other environmental variables, with significant genotype-environment interactions (GEI). This is shown by a complex pattern of reaction norms and by variation in the pattern of significant quantitative trait loci (QTL) amongst trials. Individual and joint analyses of high and low density trials indicate that most QTL have significant GEI. Dominance and epistasis also explain some variation in branching. Likely candidate genes underlying the QTL (based on map position and phenotypic effect) include teosinte branched1 and barren stalk1. Phytochrome B, which has been found to affect response to shading in other plants, explains little or no variation. Much variation in branching is explained by QTL that do not have obvious candidate genes from maize or rice.

Personality and serotonin transporter genotype interact with social context to affect immunity and viral set-point in simian immunodeficiency virus disease

PubMed Central

Capitanio, John P.; Abel, Kristina; Mendoza, Sally P.; Blozis, Shelley A.; McChesney, Michael B.; Cole, Steve W.; Mason, William A.

2008-01-01

From the beginning of the AIDS epidemic, stress has been a suspected contributor to the wide variation seen in disease progression, and some evidence supports this idea. Not all individuals respond to a stressor in the same way, however, and little is known about the biological mechanisms by which variations in individuals’ responses to their environment affect disease-relevant immunologic processes. Using the simian immunodeficiency virus/rhesus macaque model of AIDS, we explored how personality (sociability) and genotype (serotonin transporter promoter) independently interact with social context (stable or unstable social conditions) to influence behavioral expression, plasma cortisol concentrations, SIV-specific IgG, and expression of genes associated with Type I interferon early in infection. SIV viral RNA set-point was strongly and negatively correlated with survival as expected. Set-point was also associated with expression of interferon-stimulated genes, with CXCR3 expression, and with SIV-specific IgG titers. Poorer immune responses, in turn, were associated with display of sustained aggression and submission. Personality and genotype acted independently as well as in interaction with social condition to affect behavioral responses. Together, the data support an “interactionist” perspective (Eysenck, 1991) on disease. Given that an important goal of HIV treatment is to maintain viral set-point as low as possible, our data suggest that supplementing anti-retroviral therapy with behavioral or pharmacologic modulation of other aspects of an organism’s functioning might prolong survival, particularly among individuals living under conditions of threat or uncertainty. PMID:17719201

Has the "Equal Environments" assumption been tested in twin studies?

PubMed

Eaves, Lindon; Foley, Debra; Silberg, Judy

2003-12-01

A recurring criticism of the twin method for quantifying genetic and environmental components of human differences is the necessity of the so-called "equal environments assumption" (EEA) (i.e., that monozygotic and dizygotic twins experience equally correlated environments). It has been proposed to test the EEA by stratifying twin correlations by indices of the amount of shared environment. However, relevant environments may also be influenced by genetic differences. We present a model for the role of genetic factors in niche selection by twins that may account for variation in indices of the shared twin environment (e.g., contact between members of twin pairs). Simulations reveal that stratification of twin correlations by amount of contact can yield spurious evidence of large shared environmental effects in some strata and even give false indications of genotype x environment interaction. The stratification approach to testing the equal environments assumption may be misleading and the results of such tests may actually be consistent with a simpler theory of the role of genetic factors in niche selection.

GxG epistasis in growth and condition and the maintenance of genetic polymorphism in Gambusia holbrooki.

PubMed

Culumber, Zachary W; Kraft, Brittany; Lemakos, Valerie; Hoffner, Erika; Travis, Joseph; Hughes, Kimberly A

2018-05-01

Theory on indirect genetic effects (IGEs) indicates that variation in the genetic composition of social groups can generate GxG epistasis that may promote the evolution of stable polymorphisms. Using a livebearing fish with a genetic polymorphism in coloration and associated behavioral differences, we tested whether genotypes of social partners interacted with focal individual genotypes to influence growth and condition over 16 weeks of development. We found that IGEs had a significant influence on patterns of feeding, regardless of focal fish genotype. There was no influence of social environment on juvenile length, but there was significant GxG epistasis for body condition. Each focal juvenile was in better condition when its own genotype was not present in adult social partners. These data are consistent with negative frequency-dependent selection in which each morph performs better when it is rare. Neither variation in feeding nor activity-related behaviors explained variation in body condition, suggesting that GxG epistasis for condition was caused by physiological differences between the two genotypes. These findings indicate that GxG epistasis in a given polymorphism can generate fitness landscapes that contribute to the maintenance of that polymorphism and to maintenance of genetic variation for additional fitness-related traits. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Genetic polymorphism in leaf-cutting ants is phenotypically plastic.

PubMed

Hughes, William O H; Boomsma, Jacobus J

2007-07-07

Advanced societies owe their success to an efficient division of labour that, in some social insects, is based on specialized worker phenotypes. The system of caste determination in such species is therefore critical. Here, we examine in a leaf-cutting ant (Acromyrmex echinatior) how a recently discovered genetic influence on caste determination interacts with the social environment. By removing most of one phenotype (large workers; LW) from test colonies, we increased the stimulus for larvae to develop into this caste, while for control colonies we removed a representative sample of all workers so that the stimulus was unchanged. We established the relative tendencies of genotypes to develop into LW by genotyping workers before and after the manipulation. In the control colonies, genotypes were similarly represented in the large worker caste before and after worker removal. In the test colonies, however, this relationship was significantly weaker, demonstrating that the change in environmental stimuli had altered the caste propensity of at least some genotypes. The results indicate that the genetic influence on worker caste determination acts via genotypes differing in their response thresholds to environmental cues and can be conceptualized as a set of overlapping reaction norms. A plastic genetic influence on division of labour has thus evolved convergently in two distantly related polyandrous taxa, the leaf-cutting ants and the honeybees, suggesting that it may be a common, potentially adaptive, property of complex, genetically diverse societies.

Genotype-specific physiological and transcriptomic responses to drought stress in Setaria italica (an emerging model for Panicoideae grasses).

PubMed

Tang, Sha; Li, Lin; Wang, Yongqiang; Chen, Qiannan; Zhang, Wenying; Jia, Guanqing; Zhi, Hui; Zhao, Baohua; Diao, Xianmin

2017-08-30

Understanding drought-tolerance mechanisms and identifying genetic dominance are important for crop improvement. Setaria italica, which is extremely drought-tolerant, has been regarded as a model plant for studying stress biology. Moreover, different genotypes of S. italica have evolved various drought-tolerance/avoidance mechanisms that should be elucidated. Physiological and transcriptomic comparisons between drought-tolerant S. italica cultivar 'Yugu1' and drought-sensitive 'An04' were conducted. 'An04' had higher yields and more efficient photosystem activities than 'Yugu1' under well-watered conditions, and this was accompanied by positive brassinosteroid regulatory actions. However, 'An04's growth advantage was severely repressed by drought, while 'Yugu1' maintained normal growth under a water deficiency. High-throughput sequencing suggested that the S. italica transcriptome was severely remodelled by genotype × environment interactions. Expression profiles of genes related to phytohormone metabolism and signalling, transcription factors, detoxification, and other stress-related proteins were characterised, revealing genotype-dependent and -independent drought responses in different S. italica genotypes. Combining our data with drought-tolerance-related QTLs, we identified 20 candidate genes that contributed to germination and early seedling' drought tolerance in S. italica. Our analysis provides a comprehensive picture of how different S. italica genotypes respond to drought, and may be used for the genetic improvement of drought tolerance in Poaceae crops.

Genetic variation in social environment construction influences the development of aggressive behavior in Drosophila melanogaster

PubMed Central

Saltz, J B

2017-01-01

Individuals are not merely subject to their social environments; they choose and create them, through a process called social environment (or social niche) construction. When genotypes differ in social environment-constructing behaviors, different genotypes are expected to experience different social environments. As social experience often affects behavioral development, quantitative genetics and psychology theories predict that genetic variation in social environment construction should have an important role in determining phenotypic variation; however, this hypothesis has not been tested directly. I identify multiple mechanisms of social environment construction that differ among natural genotypes of Drosophila melanogaster and investigate their consequences for the development of aggressive behavior. Male genotypes differed in the group sizes that they preferred and in their aggressive behavior; both of these behaviors influenced social experience, demonstrating that these behaviors function as social environment-constructing traits. Further, the effects of social experience—as determined in part by social environment construction—carried over to affect focal male aggression at a later time and with a new opponent. These results provide manipulative experimental support for longstanding hypotheses in psychology, that genetic variation in social environment construction has a causal role in behavioral development. More broadly, these results imply that studies of the genetic basis of complex traits should be expanded to include mechanisms by which genetic variation shapes the environments that individuals experience. PMID:27848947

Interacting effect of BDNF Val66Met polymorphism and stressful life events on adolescent depression.

PubMed

Chen, J; Li, X; McGue, M

2012-11-01

There is a strong etiological link between brain-derived neurotrophic factor and depression, but the neurocellular mechanisms and gene-environment interactions remain obscure. This study investigated whether one functional polymorphism in the brain-derived neurotrophic factor gene (BDNF Val66Met) modulates the influence of stressful life events on adolescent depressive symptoms. A total of 780 pairs of ethnic Han Chinese adolescent twins, 11-17 years of age, were randomly assigned to one of two subgroups (twin1 and twin2). All subjects were genotyped as Val/Val, Val/Met or Met/Met, and assessed for depressive symptoms using the Children's Depression Inventory. The level of environmental stress was estimated by the frequency of stressful life events using the Life Events Checklist. The frequency of stressful life events was significantly correlated with depressive symptoms (twin1: β = 0.21, P = 0.01; twin2: β = 0.27, P < 0.01), but there was no significant main effect of the BDNF Val66Met genotype on depressive symptoms. In both subgroups, however, the interaction between the BDNF Val66Met genotype and stressful life event frequency was significant (twin1: β = 0.19, P = 0.01; twin2: β = 0.15, P = 0.04); individuals with one or two Val alleles demonstrated a greater susceptibility to both the detrimental effects of higher stress and the beneficial effects of lower stress compared to the Met/Met genotype. These findings support the 'differential-susceptibility' hypothesis, whereby the BDNF Val allele modulates the influence of environmental stress on depression by enhancing the neuroplastic response to all life events. © 2012 The Authors. Genes, Brain and Behavior © 2012 Blackwell Publishing Ltd and International Behavioural and Neural Genetics Society.

Computational identification of gene–social environment interaction at the human IL6 locus

PubMed Central

Cole, Steven W.; Arevalo, Jesusa M. G.; Takahashi, Rie; Sloan, Erica K.; Lutgendorf, Susan K.; Sood, Anil K.; Sheridan, John F.; Seeman, Teresa E.

2010-01-01

To identify genetic factors that interact with social environments to impact human health, we used a bioinformatic strategy that couples expression array–based detection of environmentally responsive transcription factors with in silico discovery of regulatory polymorphisms to predict genetic loci that modulate transcriptional responses to stressful environments. Tests of one predicted interaction locus in the human IL6 promoter (SNP rs1800795) verified that it modulates transcriptional response to β-adrenergic activation of the GATA1 transcription factor in vitro. In vivo validation studies confirmed links between adverse social conditions and increased transcription of GATA1 target genes in primary neural, immune, and cancer cells. Epidemiologic analyses verified the health significance of those molecular interactions by documenting increased 10-year mortality risk associated with late-life depressive symptoms that occurred solely for homozygous carriers of the GATA1-sensitive G allele of rs1800795. Gating of depression-related mortality risk by IL6 genotype pertained only to inflammation-related causes of death and was associated with increased chronic inflammation as indexed by plasma C-reactive protein. Computational modeling of molecular interactions, in vitro biochemical analyses, in vivo animal modeling, and human molecular epidemiologic analyses thus converge in identifying β-adrenergic activation of GATA1 as a molecular pathway by which social adversity can alter human health risk selectively depending on individual genetic status at the IL6 locus. PMID:20176930

A multilevel prediction of physiological response to challenge: Interactions among child maltreatment, neighborhood crime, endothelial nitric oxide synthase gene (eNOS), and GABA(A) receptor subunit alpha-6 gene (GABRA6).

PubMed

Lynch, Michael; Manly, Jody Todd; Cicchetti, Dante

2015-11-01

Physiological response to stress has been linked to a variety of healthy and pathological conditions. The current study conducted a multilevel examination of interactions among environmental toxins (i.e., neighborhood crime and child maltreatment) and specific genetic polymorphisms of the endothelial nitric oxide synthase gene (eNOS) and GABA(A) receptor subunit alpha-6 gene (GABRA6). One hundred eighty-six children were recruited at age 4. The presence or absence of child maltreatment as well as the amount of crime that occurred in their neighborhood during the previous year were determined at that time. At age 9, the children were brought to the lab, where their physiological response to a cognitive challenge (i.e., change in the amplitude of the respiratory sinus arrhythmia) was assessed and DNA samples were collected for subsequent genotyping. The results confirmed that complex Gene × Gene, Environment × Environment, and Gene × Environment interactions were associated with different patterns of respiratory sinus arrhythmia reactivity. The implications for future research and evidence-based intervention are discussed.

The maternal environment interacts with genetic variation in regulating seed dormancy in Swedish Arabidopsis thaliana

PubMed Central

Nordborg, Magnus

2017-01-01

Seed dormancy is a complex adaptive trait that controls the timing of seed germination, one of the major fitness components in many plant species. Despite being highly heritable, seed dormancy is extremely plastic and influenced by a wide range of environmental cues. Here, using a set of 92 Arabidopsis thaliana lines from Sweden, we investigate the effect of seed maturation temperature on dormancy variation at the population level. The response to temperature differs dramatically between lines, demonstrating that genotype and the maternal environment interact in controlling the trait. By performing a genome-wide association study (GWAS), we identified several candidate genes that could presumably account for this plasticity, two of which are involved in the photoinduction of germination. Altogether, our results provide insight into both the molecular mechanisms and the evolution of dormancy plasticity, and can serve to improve our understanding of environmentally dependent life-history transitions. PMID:29281703

Epistasis and Its Implications for Personal Genetics

PubMed Central

Moore, Jason H.; Williams, Scott M.

2009-01-01

The widespread availability of high-throughput genotyping technology has opened the door to the era of personal genetics, which brings to consumers the promise of using genetic variations to predict individual susceptibility to common diseases. Despite easy access to commercial personal genetics services, our knowledge of the genetic architecture of common diseases is still very limited and has not yet fulfilled the promise of accurately predicting most people at risk. This is partly because of the complexity of the mapping relationship between genotype and phenotype that is a consequence of epistasis (gene-gene interaction) and other phenomena such as gene-environment interaction and locus heterogeneity. Unfortunately, these aspects of genetic architecture have not been addressed in most of the genetic association studies that provide the knowledge base for interpreting large-scale genetic association results. We provide here an introductory review of how epistasis can affect human health and disease and how it can be detected in population-based studies. We provide some thoughts on the implications of epistasis for personal genetics and some recommendations for improving personal genetics in light of this complexity. PMID:19733727

Epistasis and its implications for personal genetics.

PubMed

Moore, Jason H; Williams, Scott M

2009-09-01

The widespread availability of high-throughput genotyping technology has opened the door to the era of personal genetics, which brings to consumers the promise of using genetic variations to predict individual susceptibility to common diseases. Despite easy access to commercial personal genetics services, our knowledge of the genetic architecture of common diseases is still very limited and has not yet fulfilled the promise of accurately predicting most people at risk. This is partly because of the complexity of the mapping relationship between genotype and phenotype that is a consequence of epistasis (gene-gene interaction) and other phenomena such as gene-environment interaction and locus heterogeneity. Unfortunately, these aspects of genetic architecture have not been addressed in most of the genetic association studies that provide the knowledge base for interpreting large-scale genetic association results. We provide here an introductory review of how epistasis can affect human health and disease and how it can be detected in population-based studies. We provide some thoughts on the implications of epistasis for personal genetics and some recommendations for improving personal genetics in light of this complexity.

Genetic moderation of transactional relations between parenting practices and child self-regulation.

PubMed

Cho, Junhan; Kogan, Steven M; Brody, Gene H

2016-10-01

The present study addressed the ways in which parent and child dopamine D4 receptor (DRD4) genotypes jointly moderate the transactional relations between parenting practices and child self-regulation. African American children (N = 309) and their parents provided longitudinal data spanning child ages 11 to 15 years and a saliva sample from which variation at DRD4 was genotyped. Based on the differential susceptibility perspective, this study examined moderation effects of DRD4 status on (a) the extent to which parenting practices affect child self-regulation and (b) the extent to which child self-regulation, as an environmental influence on the parent, affects parenting behavior. Results indicated that responsive-supportive parenting interacted with children's DRD4 status to influence increases in child self-regulation. Also, child self-regulation interacted with parent's DRD4 status to predict changes in parenting practices. Both Gene × Environment effects conformed to a differential susceptibility model in which parents' and children's DRD4 genes operated to increase environmental sensitivity "for better and for worse." (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Angiotensin-converting enzyme gene polymorphisms and hypertension in occupational noise exposure in Egypt

PubMed Central

Zawilla, Nermin; Shaker, Dalia; Abdelaal, Amaal; Aref, Wael

2014-01-01

Background: The gene–environment interaction in the pathogenesis of hypertension has not been extensively studied in occupational noise. Objectives: The aim of this study was to determine the relationship between noise and hypertension in Egyptian workers, the interaction of angiotensin-converting enzyme (ACE) gene polymorphisms as modifiers, and the possible relationship between noise hearing impairment and hypertension. Methods: Study subjects were divided into two groups depending on noise exposure level. The control group (n = 161) was exposed to noise intensity <85 dB and the exposed group (n = 217) was exposed to noise intensity ≧85 dB. A polymerase chain reaction was used to differentiate the various genotypes of ACE insertion/deletion (I/D) and ACE G2350A. Results: Noise significantly increased the likelihood of hypertension. Carriers of the genotypes AG, GG, and DD were vulnerable to hypertension on noise exposure. No association between hypertension and hearing impairment or noise-induced hearing loss (NIHL) was found. Conclusion: Our results support the association between ACE gene polymorphisms and occurrence of hypertension in noise-exposed workers. PMID:25000107