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Sample records for quantitative phenotypic variation

  1. Beyond Punnett Squares: Student Word Association and Explanations of Phenotypic Variation through an Integrative Quantitative Genetics Unit Investigating Anthocyanin Inheritance and Expression in "Brassica rapa" Fast Plants

    ERIC Educational Resources Information Center

    Batzli, Janet M.; Smith, Amber R.; Williams, Paul H.; McGee, Seth A.; Dosa, Katalin; Pfammatter, Jesse

    2014-01-01

    Genetics instruction in introductory biology is often confined to Mendelian genetics and avoids the complexities of variation in quantitative traits. Given the driving question "What determines variation in phenotype (Pv)? (Pv=Genotypic variation Gv + environmental variation Ev)," we developed a 4-wk unit for an inquiry-based laboratory…

  2. Quantitative phenotypic analysis of multistress response in Zygosaccharomyces rouxii complex.

    PubMed

    Solieri, Lisa; Dakal, Tikam C; Bicciato, Silvio

    2014-06-01

    Zygosaccharomyces rouxii complex comprises three yeasts clusters sourced from sugar- and salt-rich environments: haploid Zygosaccharomyces rouxii, diploid Zygosaccharomyces sapae and allodiploid/aneuploid strains of uncertain taxonomic affiliations. These yeasts have been characterized with respect to gene copy number variation, karyotype variability and change in ploidy, but functional diversity in stress responses has not been explored yet. Here, we quantitatively analysed the stress response variation in seven strains of the Z. rouxii complex by modelling growth variables via model and model-free fitting methods. Based on the spline fit as most reliable modelling method, we resolved different interstrain responses to 15 environmental perturbations. Compared with Z. rouxii CBS 732(T) and Z. sapae strains ABT301(T) and ABT601, allodiploid strain ATCC 42981 and aneuploid strains CBS 4837 and CBS 4838 displayed higher multistress resistance and better performance in glycerol respiration even in the presence of copper. ?-based logarithmic phenotypic index highlighted that ABT601 is a slow-growing strain insensitive to stress, whereas ABT301(T) grows fast on rich medium and is sensitive to suboptimal conditions. Overall, the differences in stress response could imply different adaptation mechanisms to sugar- and salt-rich niches. The obtained phenotypic profiling contributes to provide quantitative insights for elucidating the adaptive mechanisms to stress in halo- and osmo-tolerant Zygosaccharomyces yeasts. PMID:24533625

  3. Bayesian causal phenotype network incorporating genetic variation and biological knowledge

    E-print Network

    Yandell, Brian S.

    to improve the inference of causal phenotype networks. Genetic variation information in a segregating genetic architectures may compromise the inference of causal relationships among phenotypes. To address this issue, several researchers [16,17] proposed to jointly infer causal phenotype networks and genetic

  4. ALCES VOL. 47, 2011 PETERSON ET AL. PHENOTYPIC VARIATION IN MOOSE PHENOTYPIC VARIATION IN MOOSE: THE ISLAND RULE AND THE

    E-print Network

    ALCES VOL. 47, 2011 PETERSON ET AL. ­ PHENOTYPIC VARIATION IN MOOSE 125 PHENOTYPIC VARIATION IN MOOSE: THE ISLAND RULE AND THE MOOSE OF ISLE ROYALE Rolf O. Peterson1 , John A. Vucetich1 , Dean Beyer2 limitation. We found that metatarsal length of moose (Alces alces) from Isle Royale National Park in Lake

  5. Linking Post-Translational Modifications and Variation of Phenotypic Traits*

    PubMed Central

    Albertin, Warren; Marullo, Philippe; Bely, Marina; Aigle, Michel; Bourgais, Aurélie; Langella, Olivier; Balliau, Thierry; Chevret, Didier; Valot, Benoît; da Silva, Telma; Dillmann, Christine; de Vienne, Dominique; Sicard, Delphine

    2013-01-01

    Enzymes can be post-translationally modified, leading to isoforms with different properties. The phenotypic consequences of the quantitative variability of isoforms have never been studied. We used quantitative proteomics to dissect the relationships between the abundances of the enzymes and isoforms of alcoholic fermentation, metabolic traits, and growth-related traits in Saccharomyces cerevisiae. Although the enzymatic pool allocated to the fermentation proteome was constant over the culture media and the strains considered, there was variation in abundance of individual enzymes and sometimes much more of their isoforms, which suggests the existence of selective constraints on total protein abundance and trade-offs between isoforms. Variations in abundance of some isoforms were significantly associated to metabolic traits and growth-related traits. In particular, cell size and maximum population size were highly correlated to the degree of N-terminal acetylation of the alcohol dehydrogenase. The fermentation proteome was found to be shaped by human selection, through the differential targeting of a few isoforms for each food-processing origin of strains. These results highlight the importance of post-translational modifications in the diversity of metabolic and life-history traits. PMID:23271801

  6. Epigenetics and phenotypic variation in mammals Anne E. Peaston,1

    E-print Network

    Epigenetics and phenotypic variation in mammals Anne E. Peaston,1 * Emma Whitelaw2 1 School and environment, in addition to variation not readily attributable to either. Epigenetic phe- nomena associated and are likely to contribute to the ``intangible variation'' alluded to. While it is clear that epigenetic

  7. Geographical Variation in Selection, from Phenotypes to Molecules

    E-print Network

    Kelly, John K.

    2006-04-01

    sequence evolution within genomic regions that harbor QTLs. The QTLs influence a trait experiencing geographical variation in selection, which is common in nature and produces obvious differentiation at the phenotypic level. Counter to expectations...

  8. Hormones, life-history, and phenotypic variation: Opportunities in evolutionary avian endocrinology

    E-print Network

    Review Hormones, life-history, and phenotypic variation: Opportunities in evolutionary avian 2011 Keywords: Phenotypic variation Breeding Clutch size Hormonal pleiotropy Hormonal conflict a b. We have only a rudimentary understanding of the physiological and hormonal basis of phenotypic

  9. Phenotypic divergence and population variation in cuphea

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Morphological and seed-related traits in populations of a semi-domesticated, potential oilseed crop (PSR23), selected from an inter-specific Cuphea spp. cross, were used in quantifying levels of divergence from its wild parents and levels of variation among and within its populations. Multivariate a...

  10. Adaptive basis of geographic variation: genetic, phenotypic and environmental

    E-print Network

    Hoekstra, Hopi E.

    Adaptive basis of geographic variation: genetic, phenotypic and environmental differences among a novel habitat. A classical example of adaptation is the pale colour of beach mice, relative at other genetic loci. Together, these results suggest that natural selection for camouflage--via changes

  11. Mining Natural Variation for Maize Improvement: Selection on Phenotypes

    E-print Network

    Flint-Garcia, Sherry

    Chapter 25 Mining Natural Variation for Maize Improvement: Selection on Phenotypes and Genes Shilpa Sood, Sherry Flint-Garcia, Martha C. Willcox and James B. Holland Contents 25.1 Maize History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 623 25.5 Linkage and Association Analysis in Nested Association Mapping Populations . . . . . 625 25

  12. Phenotypic Variation in Infants, Not Adults, Reflects Genotypic Variation among Chimpanzees and Bonobos

    PubMed Central

    Morimoto, Naoki; Ponce de León, Marcia S.; Zollikofer, Christoph P. E.

    2014-01-01

    Studies comparing phenotypic variation with neutral genetic variation in modern humans have shown that genetic drift is a main factor of evolutionary diversification among populations. The genetic population history of our closest living relatives, the chimpanzees and bonobos, is now equally well documented, but phenotypic variation among these taxa remains relatively unexplored, and phenotype-genotype correlations are not yet documented. Also, while the adult phenotype is typically used as a reference, it remains to be investigated how phenotype-genotye correlations change during development. Here we address these questions by analyzing phenotypic evolutionary and developmental diversification in the species and subspecies of the genus Pan. Our analyses focus on the morphology of the femoral diaphysis, which represents a functionally constrained element of the locomotor system. Results show that during infancy phenotypic distances between taxa are largely congruent with non-coding (neutral) genotypic distances. Later during ontogeny, however, phenotypic distances deviate from genotypic distances, mainly as an effect of heterochronic shifts between taxon-specific developmental programs. Early phenotypic differences between Pan taxa are thus likely brought about by genetic drift while late differences reflect taxon-specific adaptations. PMID:25013970

  13. Impact of DISC1 variation on neuroanatomical and neurocognitive phenotypes

    PubMed Central

    Carless, M.A.; Glahn, D.C.; Johnson, M.P.; Curran, J.E.; Bozaoglu, K.; Dyer, T.D.; Winkler, A.M.; Cole, S.A.; Almasy, L.; MacCluer, J.W.; Duggirala, R.; Moses, E.K.; Göring, H.H.H.; Blangero, J.

    2011-01-01

    Although DISC1 has been implicated in many psychiatric disorders, including schizophrenia, bipolar disorder, schizoaffective disorder and major depression, its biological role in these disorders is unclear. To better understand this gene and its role in psychiatric disease, we conducted transcriptional profiling and genome-wide association analysis in 1 232 pedigreed Mexican American individuals for whom we have neuroanatomic images, neurocognitive assessments and neuropsychiatric diagnoses. SOLAR was used to determine heritability, identify gene expression patterns and perform association analyses on 188 quantitative brain-related phenotypes. We found that the DISC1 transcript is highly heritable (h2=0.50; p=1.97 × 10?22), and that gene expression is strongly cis-regulated (cis-LOD=3.89) but is also influenced by trans-effects. We identified several DISC1 polymorphisms that were associated with cortical gray-matter thickness within the parietal, temporal and frontal lobes. Associated regions affiliated with memory included the entorhinal cortex (rs821639, p=4.11 × 10?5; rs2356606, p=4.71 × 10?4), cingulate cortex (rs16856322, p=2.88 × 10?4) and parahippocampal gyrus (rs821639, p=4.95 × 10?4); those affiliated with executive and other cognitive processing included the transverse temporal gyrus (rs9661837, p=5.21 × 10?4; rs17773946, p=6.23 × 10?4), anterior cingulate cortex (rs2487453, p=; 4.79 × 10?4; rs3738401, p= 5.43 × 10?4) and medial orbitofrontal cortex (rs9661837; p=7.40 × 10?4). Cognitive measures of working memory (rs2793094, p=3.38 × 10?4), as well as lifetime history of depression (rs4658966, p=4.33 × 10?4; rs12137417, p=4.93 × 10?4) and panic (rs12137417, p=7.41 × 10?4) were associated with DISC1 sequence variation. DISC1 has well-defined genetic regulation and clearly influences important phenotypes related to psychiatric disease. PMID:21483430

  14. Catch Me if You Can: Adaptation from Standing Genetic Variation to a Moving Phenotypic Optimum

    PubMed Central

    Matuszewski, Sebastian; Hermisson, Joachim; Kopp, Michael

    2015-01-01

    Adaptation lies at the heart of Darwinian evolution. Accordingly, numerous studies have tried to provide a formal framework for the description of the adaptive process. Of these, two complementary modeling approaches have emerged: While so-called adaptive-walk models consider adaptation from the successive fixation of de novo mutations only, quantitative genetic models assume that adaptation proceeds exclusively from preexisting standing genetic variation. The latter approach, however, has focused on short-term evolution of population means and variances rather than on the statistical properties of adaptive substitutions. Our aim is to combine these two approaches by describing the ecological and genetic factors that determine the genetic basis of adaptation from standing genetic variation in terms of the effect-size distribution of individual alleles. Specifically, we consider the evolution of a quantitative trait to a gradually changing environment. By means of analytical approximations, we derive the distribution of adaptive substitutions from standing genetic variation, that is, the distribution of the phenotypic effects of those alleles from the standing variation that become fixed during adaptation. Our results are checked against individual-based simulations. We find that, compared to adaptation from de novo mutations, (i) adaptation from standing variation proceeds by the fixation of more alleles of small effect and (ii) populations that adapt from standing genetic variation can traverse larger distances in phenotype space and, thus, have a higher potential for adaptation if the rate of environmental change is fast rather than slow. PMID:26038348

  15. Deciphering Genomic Underpinnings of Quantitative MRI-based Radiomic Phenotypes of Invasive Breast Carcinoma

    PubMed Central

    Zhu, Yitan; Li, Hui; Guo, Wentian; Drukker, Karen; Lan, Li; Giger, Maryellen L.; Ji, Yuan

    2015-01-01

    Magnetic Resonance Imaging (MRI) has been routinely used for the diagnosis and treatment of breast cancer. However, the relationship between the MRI tumor phenotypes and the underlying genetic mechanisms remains under-explored. We integrated multi-omics molecular data from The Cancer Genome Atlas (TCGA) with MRI data from The Cancer Imaging Archive (TCIA) for 91 breast invasive carcinomas. Quantitative MRI phenotypes of tumors (such as tumor size, shape, margin, and blood flow kinetics) were associated with their corresponding molecular profiles (including DNA mutation, miRNA expression, protein expression, pathway gene expression and copy number variation). We found that transcriptional activities of various genetic pathways were positively associated with tumor size, blurred tumor margin, and irregular tumor shape and that miRNA expressions were associated with the tumor size and enhancement texture, but not with other types of radiomic phenotypes. We provide all the association findings as a resource for the research community (available at http://compgenome.org/Radiogenomics/). These findings pave potential paths for the discovery of genetic mechanisms regulating specific tumor phenotypes and for improving MRI techniques as potential non-invasive approaches to probe the cancer molecular status. PMID:26639025

  16. Evolution of adaptive phenotypic variation patterns by direct selection for evolvability

    PubMed Central

    Pavlicev, Mihaela; Cheverud, James M.; Wagner, Günter P.

    2011-01-01

    A basic assumption of the Darwinian theory of evolution is that heritable variation arises randomly. In this context, randomness means that mutations arise irrespective of the current adaptive needs imposed by the environment. It is broadly accepted, however, that phenotypic variation is not uniformly distributed among phenotypic traits, some traits tend to covary, while others vary independently, and again others barely vary at all. Furthermore, it is well established that patterns of trait variation differ among species. Specifically, traits that serve different functions tend to be less correlated, as for instance forelimbs and hind limbs in bats and humans, compared with the limbs of quadrupedal mammals. Recently, a novel class of genetic elements has been identified in mouse gene-mapping studies that modify correlations among quantitative traits. These loci are called relationship loci, or relationship Quantitative Trait Loci (rQTL), and affect trait correlations by changing the expression of the existing genetic variation through gene interaction. Here, we present a population genetic model of how natural selection acts on rQTL. Contrary to the usual neo-Darwinian theory, in this model, new heritable phenotypic variation is produced along the selected dimension in response to directional selection. The results predict that selection on rQTL leads to higher correlations among traits that are simultaneously under directional selection. On the other hand, traits that are not simultaneously under directional selection are predicted to evolve lower correlations. These results and the previously demonstrated existence of rQTL variation, show a mechanism by which natural selection can directly enhance the evolvability of complex organisms along lines of adaptive change. PMID:21106581

  17. ACETYLATION PHENOTYPE VARIATION IN PEDIATRIC PATIENTS WITH ATOPIC DERMATITIS

    PubMed Central

    Majeed Al-Razzuqi, Rafi A; Al-Jeboori, Ali A; Al-Waiz, Makram M

    2011-01-01

    Background: Few studies have been done on the relation between acetylator status and allergic diseases. Aim: To determine any possible association between acetylating phenotype in pediatric patients with atopic dermatitis (AD) and the disease prognosis. Patients and Methods: Thirty-six pediatric patients and forty two healthy children as a control group were participated in the study. All participants received a single oral dose of dapsone of 1.54 mg/kg body weight, after an overnight fast. Using high performance liquid chromatography (HPLC), plasma concentrations of dapsone and its metabolite (monoacetyldapsone) were estimated to phenotype the participants as slow and rapid acetylators according to their acetylation ratio (ratio of monoacetyldapsone to dapsone). Results: 72.2% of pediatric patients with AD showed slow acetylating status as compared to 69.4% of control individuals. Also, 73% of AD patients with slow acetylating phenotype had familial history of allergy. The severity of AD occurred only in slow acetylator patients. The eczematous lesions in slow acetylators presented mainly in the limbs, while in rapid acetylators, they were found mostly in face and neck. Conclusion: This study shows an association between the N-acetylation phenotype variation and clinical aspects of AD. PMID:21716538

  18. Post-transcriptional Mechanisms Contribute Little to Phenotypic Variation in Snake Venoms

    PubMed Central

    Rokyta, Darin R.; Margres, Mark J.; Calvin, Kate

    2015-01-01

    Protein expression is a major link in the genotype–phenotype relationship, and processes affecting protein abundances, such as rates of transcription and translation, could contribute to phenotypic evolution if they generate heritable variation. Recent work has suggested that mRNA abundances do not accurately predict final protein abundances, which would imply that post-transcriptional regulatory processes contribute significantly to phenotypes. Post-transcriptional processes also appear to buffer changes in transcriptional patterns as species diverge, suggesting that the transcriptional changes have little or no effect on the phenotypes undergoing study. We tested for concordance between mRNA and protein expression levels in snake venoms by means of mRNA-seq and quantitative mass spectrometry for 11 snakes representing 10 species, six genera, and three families. In contrast to most previous work, we found high correlations between venom gland transcriptomes and venom proteomes for 10 of our 11 comparisons. We tested for protein-level buffering of transcriptional changes during species divergence by comparing the difference between transcript abundance and protein abundance for three pairs of species and one intraspecific pair. We found no evidence for buffering during divergence of our three species pairs but did find evidence for protein-level buffering for our single intraspecific comparison, suggesting that buffering, if present, was a transient phenomenon in venom divergence. Our results demonstrated that post-transcriptional mechanisms did not contribute significantly to phenotypic evolution in venoms and suggest a more prominent and direct role for cis-regulatory evolution in phenotypic variation, particularly for snake venoms. PMID:26358130

  19. Post-transcriptional Mechanisms Contribute Little to Phenotypic Variation in Snake Venoms.

    PubMed

    Rokyta, Darin R; Margres, Mark J; Calvin, Kate

    2015-01-01

    Protein expression is a major link in the genotype-phenotype relationship, and processes affecting protein abundances, such as rates of transcription and translation, could contribute to phenotypic evolution if they generate heritable variation. Recent work has suggested that mRNA abundances do not accurately predict final protein abundances, which would imply that post-transcriptional regulatory processes contribute significantly to phenotypes. Post-transcriptional processes also appear to buffer changes in transcriptional patterns as species diverge, suggesting that the transcriptional changes have little or no effect on the phenotypes undergoing study. We tested for concordance between mRNA and protein expression levels in snake venoms by means of mRNA-seq and quantitative mass spectrometry for 11 snakes representing 10 species, six genera, and three families. In contrast to most previous work, we found high correlations between venom gland transcriptomes and venom proteomes for 10 of our 11 comparisons. We tested for protein-level buffering of transcriptional changes during species divergence by comparing the difference between transcript abundance and protein abundance for three pairs of species and one intraspecific pair. We found no evidence for buffering during divergence of our three species pairs but did find evidence for protein-level buffering for our single intraspecific comparison, suggesting that buffering, if present, was a transient phenomenon in venom divergence. Our results demonstrated that post-transcriptional mechanisms did not contribute significantly to phenotypic evolution in venoms and suggest a more prominent and direct role for cis-regulatory evolution in phenotypic variation, particularly for snake venoms. PMID:26358130

  20. The Evolution of Human Genetic and Phenotypic Variation in Africa

    PubMed Central

    Campbell, Michael C.

    2010-01-01

    Africa is the birthplace of modern humans, and is the source of the geographic expansion of ancestral populations into other regions of the world. Indigenous Africans are characterized by high levels of genetic diversity within and between populations. The pattern of genetic variation in these populations has been shaped by demographic events occurring over the last 200,000 years. The dramatic variation in climate, diet, and exposure to infectious disease across the continent has also resulted in novel genetic and phenotypic adaptations in extant Africans. This review summarizes some recent advances in our understanding of the demographic history and selective pressures that have influenced levels and patterns of diversity in African populations. PMID:20178763

  1. Intraspecific phenotypic variation among alewife populations drives parallel phenotypic shifts in bluegill

    PubMed Central

    Huss, Magnus; Howeth, Jennifer G.; Osterman, Julia I.; Post, David M.

    2014-01-01

    Evolutionary diversification within consumer species may generate selection on local ecological communities, affecting prey community structure. However, the extent to which this niche construction can propagate across food webs and shape trait variation in competing species is unknown. Here, we tested whether niche construction by different life-history variants of the planktivorous fish alewife (Alosa pseudoharengus) can drive phenotypic divergence and resource use in the competing species bluegill (Lepomis macrochirus). Using a combination of common garden experiments and a comparative field study, we found that bluegill from landlocked alewife lakes grew relatively better when fed small than large zooplankton, had gill rakers better adapted for feeding on small-bodied prey and selected smaller zooplankton compared with bluegill from lakes with anadromous or no alewife. Observed shifts in bluegill foraging traits in lakes with landlocked alewife parallel those in alewife, suggesting interspecific competition leading to parallel phenotypic changes rather than to divergence (which is commonly predicted). Our findings suggest that species may be locally adapted to prey communities structured by different life-history variants of a competing dominant species. PMID:24920478

  2. Genetic interactions contribute less than additive effects to quantitative trait variation in yeast

    PubMed Central

    Bloom, Joshua S.; Kotenko, Iulia; Sadhu, Meru J.; Treusch, Sebastian; Albert, Frank W.; Kruglyak, Leonid

    2015-01-01

    Genetic mapping studies of quantitative traits typically focus on detecting loci that contribute additively to trait variation. Genetic interactions are often proposed as a contributing factor to trait variation, but the relative contribution of interactions to trait variation is a subject of debate. Here we use a very large cross between two yeast strains to accurately estimate the fraction of phenotypic variance due to pairwise QTL–QTL interactions for 20 quantitative traits. We find that this fraction is 9% on average, substantially less than the contribution of additive QTL (43%). Statistically significant QTL–QTL pairs typically have small individual effect sizes, but collectively explain 40% of the pairwise interaction variance. We show that pairwise interaction variance is largely explained by pairs of loci at least one of which has a significant additive effect. These results refine our understanding of the genetic architecture of quantitative traits and help guide future mapping studies. PMID:26537231

  3. Classification of Human Chromosome 21 Gene-Expression Variations in Down Syndrome: Impact on Disease Phenotypes

    PubMed Central

    Aït Yahya-Graison, E. ; Aubert, J. ; Dauphinot, L. ; Rivals, I. ; Prieur, M. ; Golfier, G. ; Rossier, J. ; Personnaz, L. ; Créau, N. ; Bléhaut, H. ; Robin, S. ; Delabar, J. M. ; Potier, M.-C. 

    2007-01-01

    Down syndrome caused by chromosome 21 trisomy is the most common genetic cause of mental retardation in humans. Disruption of the phenotype is thought to be the result of gene-dosage imbalance. Variations in chromosome 21 gene expression in Down syndrome were analyzed in lymphoblastoid cells derived from patients and control individuals. Of the 359 genes and predictions displayed on a specifically designed high-content chromosome 21 microarray, one-third were expressed in lymphoblastoid cells. We performed a mixed-model analysis of variance to find genes that are differentially expressed in Down syndrome independent of sex and interindividual variations. In addition, we identified genes with variations between Down syndrome and control samples that were significantly different from the gene-dosage effect (1.5). Microarray data were validated by quantitative polymerase chain reaction. We found that 29% of the expressed chromosome 21 transcripts are overexpressed in Down syndrome and correspond to either genes or open reading frames. Among these, 22% are increased proportional to the gene-dosage effect, and 7% are amplified. The other 71% of expressed sequences are either compensated (56%, with a large proportion of predicted genes and antisense transcripts) or highly variable among individuals (15%). Thus, most of the chromosome 21 transcripts are compensated for the gene-dosage effect. Overexpressed genes are likely to be involved in the Down syndrome phenotype, in contrast to the compensated genes. Highly variable genes could account for phenotypic variations observed in patients. Finally, we show that alternative transcripts belonging to the same gene are similarly regulated in Down syndrome but sense and antisense transcripts are not. PMID:17701894

  4. A Multi-Objective Program for Quantitative Subtyping of Clinically Relevant Phenotypes

    E-print Network

    Chandy, John A.

    , PA, USA kranzler h@mail.trc.upenn.edu Abstract--Identifying genetic variations that underlie human-objective programming that is capable of clinically categorizing a disease phenotype so as to discover genetically at the molecular and clinical syndrome levels [1]. Categorizing a disease phenotype clinically has been hindered

  5. Disentangling the phylogenetic and ecological components of spider phenotypic variation.

    PubMed

    Gonçalves-Souza, Thiago; Diniz-Filho, José Alexandre Felizola; Romero, Gustavo Quevedo

    2014-01-01

    An understanding of how the degree of phylogenetic relatedness influences the ecological similarity among species is crucial to inferring the mechanisms governing the assembly of communities. We evaluated the relative importance of spider phylogenetic relationships and ecological niche (plant morphological variables) to the variation in spider body size and shape by comparing spiders at different scales: (i) between bromeliads and dicot plants (i.e., habitat scale) and (ii) among bromeliads with distinct architectural features (i.e., microhabitat scale). We partitioned the interspecific variation in body size and shape into phylogenetic (that express trait values as expected by phylogenetic relationships among species) and ecological components (that express trait values independent of phylogenetic relationships). At the habitat scale, bromeliad spiders were larger and flatter than spiders associated with the surrounding dicots. At this scale, plant morphology sorted out close related spiders. Our results showed that spider flatness is phylogenetically clustered at the habitat scale, whereas it is phylogenetically overdispersed at the microhabitat scale, although phylogenic signal is present in both scales. Taken together, these results suggest that whereas at the habitat scale selective colonization affect spider body size and shape, at fine scales both selective colonization and adaptive evolution determine spider body shape. By partitioning the phylogenetic and ecological components of phenotypic variation, we were able to disentangle the evolutionary history of distinct spider traits and show that plant architecture plays a role in the evolution of spider body size and shape. We also discussed the relevance in considering multiple scales when studying phylogenetic community structure. PMID:24651264

  6. Disentangling the Phylogenetic and Ecological Components of Spider Phenotypic Variation

    PubMed Central

    Gonçalves-Souza, Thiago; Diniz-Filho, José Alexandre Felizola; Romero, Gustavo Quevedo

    2014-01-01

    An understanding of how the degree of phylogenetic relatedness influences the ecological similarity among species is crucial to inferring the mechanisms governing the assembly of communities. We evaluated the relative importance of spider phylogenetic relationships and ecological niche (plant morphological variables) to the variation in spider body size and shape by comparing spiders at different scales: (i) between bromeliads and dicot plants (i.e., habitat scale) and (ii) among bromeliads with distinct architectural features (i.e., microhabitat scale). We partitioned the interspecific variation in body size and shape into phylogenetic (that express trait values as expected by phylogenetic relationships among species) and ecological components (that express trait values independent of phylogenetic relationships). At the habitat scale, bromeliad spiders were larger and flatter than spiders associated with the surrounding dicots. At this scale, plant morphology sorted out close related spiders. Our results showed that spider flatness is phylogenetically clustered at the habitat scale, whereas it is phylogenetically overdispersed at the microhabitat scale, although phylogenic signal is present in both scales. Taken together, these results suggest that whereas at the habitat scale selective colonization affect spider body size and shape, at fine scales both selective colonization and adaptive evolution determine spider body shape. By partitioning the phylogenetic and ecological components of phenotypic variation, we were able to disentangle the evolutionary history of distinct spider traits and show that plant architecture plays a role in the evolution of spider body size and shape. We also discussed the relevance in considering multiple scales when studying phylogenetic community structure. PMID:24651264

  7. Detection and characterisation of quantitative trait loci affecting muscle and growth phenotypes in sheep 

    E-print Network

    Hadjipavlou, Georgia

    2010-01-01

    This thesis addresses the dissection and characterisation of quantitative trait loci (QTL) affecting production traits in sheep. Firstly, the association between specific genetic polymorphisms and complex variation in ...

  8. Alzheimer's Disease Neuroimaging Initiative biomarkers as quantitative phenotypes: Genetics core aims, progress, and plans

    E-print Network

    Thompson, Paul

    Alzheimer's Disease Neuroimaging Initiative biomarkers as quantitative phenotypes: Genetics core C. Greenj , Lars Bertramk , Clifford R. Jack, Jr.l , Michael W. Weinerm,n,o,p ; and the Alzheimer of Veterans Affairs Medical Center, San Francisco, CA, USA Abstract The role of the Alzheimer's Disease

  9. Quantitative phenotyping via deep barcode Andrew M. Smith,1,2,3

    E-print Network

    Roth, Frederick

    Methods Quantitative phenotyping via deep barcode sequencing Andrew M. Smith,1,2,3 Lawrence E collections in parallel. This method, Barcode analysis by Sequencing, or ``Bar-seq,'' outperforms the current benchmark barcode microarray assay in terms of both dynamic range and throughput. When applied to a complex

  10. Application of quantitative metabolomics in systems genetics in rodent models of complex phenotypes.

    PubMed

    Gauguier, Dominique

    2016-01-01

    Genome-wide association studies (GWAS) have provided remarkable advances in our understanding of the etiology of complex diseases in humans and have underlined the need to improve patients' phenotype characterization with intermediate molecular phenotypes. High resolution metabolomics is becoming an increasingly popular and robust strategy for metabolic phenotyping large cohorts of patients and controls in genetic studies, in order to map the genetic control of metabotypes in various biological matrices (organ extracts and biofluids) through Quantitative Trait Locus (mQTL) analysis. This article reviews results from ongoing research in mQTL mapping in rodent models of human complex traits, with a specific focus on the cardiometabolic syndrome, and prospects of applications of untargeted metabolomics to improve knowledge of multilevel genome expression control in health and disease and to detect potential novel biomarkers for complex phenotypes in experimental systems in mice and rats. PMID:26391925

  11. PhenoChipping of psychotic disorders: a novel approach for deconstructing and quantitating psychiatric phenotypes.

    PubMed

    Niculescu, Alexander B; Lulow, Len L; Ogden, Corey A; Le-Niculescu, Helen; Salomon, Daniel R; Schork, Nicholas J; Caligiuri, Michael P; Lohr, James B

    2006-09-01

    Psychiatric phenotypes as currently defined are primarily the result of clinical consensus criteria rather than empirical research. We propose, and present initial proof of principle for, a novel approach to characterizing psychiatric phenotypes. We have termed our approach PhenoChipping, by analogy with, and borrowing paradigms and tools from, gene expression microarray studies (GeneChipping). A massive parallel profiling of cognitive and affective state is done with a PhenoChip composed of a battery of existing and new quantitative psychiatric rating scales, as well as hand neuromotor measures. We present preliminary data from 104 subjects, 72 with psychotic disorders (bipolar disorder-41, schizophrenia-17, schizoaffective disorder-14), and 32 normal controls. Microarray data analysis software and visualization tools were used to investigate: 1. relationships between phenotypic items ("phenes"), including with objective motor measures, and 2. relationships between subjects. Our analyses revealed phenotypic overlap among, as well as phenotypic heterogeneity within, the three major psychotic disorders studied. This approach may be useful in helping us move beyond current diagnostic classifications, and suggests a combinatorial building-block (Lego-like) structure underlies psychiatric syndromes. The adaptation of microarray informatic tools for phenotypic analysis readily facilitates direct integration with gene expression profiling of lymphocytes in the same individuals, a strategy for molecular biomarker identification. Empirically derived clusterings of (endo)phenotypes and of patients will better serve genetic, pharmacological, and imaging research, as well as clinical practice. PMID:16838358

  12. Quantitative Molecular Phenotyping of Gill Remodeling in a Cichlid Fish Responding to Salinity Stress*

    PubMed Central

    Kültz, Dietmar; Li, Johnathon; Gardell, Alison; Sacchi, Romina

    2013-01-01

    A two-tiered label-free quantitative (LFQ) proteomics workflow was used to elucidate how salinity affects the molecular phenotype, i.e. proteome, of gills from a cichlid fish, the euryhaline tilapia (Oreochromis mossambicus). The workflow consists of initial global profiling of relative tryptic peptide abundances in treated versus control samples followed by targeted identification (by MS/MS) and quantitation (by chromatographic peak area integration) of validated peptides for each protein of interest. Fresh water acclimated tilapia were independently exposed in separate experiments to acute short-term (34 ppt) and gradual long-term (70 ppt, 90 ppt) salinity stress followed by molecular phenotyping of the gill proteome. The severity of salinity stress can be deduced with high technical reproducibility from the initial global label-free quantitative profiling step alone at both peptide and protein levels. However, an accurate regulation ratio can only be determined by targeted label-free quantitative profiling because not all peptides used for protein identification are also valid for quantitation. Of the three salinity challenges, gradual acclimation to 90 ppt has the most pronounced effect on gill molecular phenotype. Known salinity effects on tilapia gills, including an increase in the size and number of mitochondria-rich ionocytes, activities of specific ion transporters, and induction of specific molecular chaperones are reflected in the regulation of abundances of the corresponding proteins. Moreover, specific protein isoforms that are responsive to environmental salinity change are resolved and it is revealed that salinity effects on the mitochondrial proteome are nonuniform. Furthermore, protein NDRG1 has been identified as a novel key component of molecular phenotype restructuring during salinity-induced gill remodeling. In conclusion, besides confirming known effects of salinity on gills of euryhaline fish, molecular phenotyping reveals novel insight into proteome changes that underlie the remodeling of tilapia gill epithelium in response to environmental salinity change. PMID:24065692

  13. The molecular basis of phenotypic variation in yeast Justin C Fay

    E-print Network

    Fay, Justin

    effect [3]. The first example of such in yeast involved a major effect high temperature growth QTLThe molecular basis of phenotypic variation in yeast Justin C Fay The power of yeast genetics has considerable phenotypic effects and alter conserved amino acid positions within protein coding sequences. When

  14. Decoupled phenotypic variation between floral and vegetative traits: distinguishing between developmental and environmental correlations

    PubMed Central

    Pélabon, Christophe; Osler, Nora C.; Diekmann, Martin; Graae, Bente J.

    2013-01-01

    Background and Aims In species with specialized pollination, floral traits are expected to be relatively invariant and decoupled from the phenotypic variation affecting vegetative traits. However, inferring the degree of decoupling between morphological characters from patterns of phenotypic correlations is difficult because phenotypic correlations result from the superimposition of several sources of covariance. In this study it is hypothesized that, in some cases, negative environmental correlations generated by non-congruent reaction norms across traits overshadow positive developmental correlations and generate a decoupling of the phenotypic variation between vegetative and floral traits. Methods To test this hypothesis, Campanula rotundifolia were grown from two distinct populations under two temperature treatments, and patterns of correlation were analysed between leaf size and flower size within and among treatments. Key Results Flower size was less sensitive to temperature variation than leaf size. Furthermore, flower size and leaf size showed temperature-induced reaction norms in opposite directions. Flower size decreased with an increasing temperature, while leaf size increased. Consequently, among treatments, correlations between leaf size and flower size were negative or absent, while, within treatments, these correlations were positive or absent in the cold and warm environments, respectively. Conclusions These results confirm that the decoupling of the phenotypic variation between vegetative and floral traits can be dependent on the environment. They also underline the importance of distinguishing sources of phenotypic covariance when testing hypotheses about phenotypic integration. PMID:23471008

  15. Phenotypic variation and genotype-phenotype discordance in canine cone-rod dystrophy with an RPGRIP1 mutation

    PubMed Central

    Kato, Kumiko; Aguirre-Hernández, Jesús; Tokuriki, Tsuyoshi; Morimoto, Kyohei; Busse, Claudia; Barnett, Keith; Holmes, Nigel; Ogawa, Hiroyuki; Sasaki, Nobuo; Mellersh, Cathryn S.; Sargan, David R.

    2009-01-01

    Purpose Previously, a 44 bp insertion in exon 2 of retinitis pigmentosa GTPase interacting protein 1 (RPGRIP1) was identified as the cause of cone-rod dystrophy 1 (cord1), a recessive form of progressive retinal atrophy (PRA) in the Miniature Longhaired Dachshund (MLHD), a dog model for Leber congenital amaurosis. The cord1 locus was mapped using MLHDs from an inbred colony with a homogeneous early onset disease phenotype. In this paper, the MLHD pet population was studied to investigate phenotypic variation and genotype-phenotype correlation. Further, the cord1 locus was fine-mapped using PRA cases from the MLHD pet population to narrow the critical region. Other dog breeds were also screened for the RGPRIP1 insertion. Methods This study examined phenotypic variation in an MLHD pet population that included 59 sporadic PRA cases and 18 members of an extended family with shared environment and having six PRA cases. Ophthalmologic evaluations included behavioral abnormalities, responses to menace and light, fundoscopy, and electroretinography (ERG). The RPGRIP1 insertion was screened for in all cases and 200 apparently normal control MLHDs and in 510 dogs from 66 other breed. To fine-map the cord1 locus in the MLHD, 74 PRA cases and 86 controls aged 4 years or more were genotyped for 24 polymorphic markers within the previously mapped cord1 critical region of 14.15 Mb. Results Among sporadic PRA cases from the MLHD pet population, the age of onset varied from 4 months to 15 years old; MLHDs from the extended family also showed variable onset and rate of progression. Screening for the insertion in RPGRIP1 identified substantial genotype-phenotype discordance: 16% of controls were homozygous for the insertion (RPGRIP1?/?), while 20% of PRA cases were not homozygous for it. Four other breeds were identified to carry the insertion including English Springer Spaniels and Beagles with insertion homozygotes. The former breed included both controls and PRA cases, yet in the latter breed, cone ERG was undetectable in two dogs with no clinically apparent visual dysfunction. Notably, the insertion in the Beagles was a longer variant of that seen in the other breeds. Fine-mapping of the cord1 locus narrowed the critical region on CFA15 from 14.15 Mb to 1.74 Mb which still contains the RPGRIP1 gene. Conclusions Extensive phenotypic variations of onset age and progression rate were observed in PRA cases of the MLHD pet population. The insertion in RPGRIP1 showed the strongest association with the disease, yet additional as well as alternative factors may account for the substantial genotype-phenotype discordance. PMID:19936303

  16. Quantitative characterization of planarian wild-type behavior as a platform for screening locomotion phenotypes.

    PubMed

    Talbot, Jared; Schötz, Eva-Maria

    2011-04-01

    Changes in animal behavior resulting from genetic or chemical intervention are frequently used for phenotype characterizations. The majority of these studies are qualitative in nature, especially in systems that go beyond the classical model organisms. Here, we introduce a quantitative method to characterize behavior in the freshwater planarian Schmidtea mediterranea. Wild-type locomotion in confinement was quantified using a wide set of parameters, and the influences of intrinsic intra-worm versus inter-worm variability on our measurements was studied. We also examined the effect of substrate, confinement geometry and the interactions with the boundary on planarian behavior. The method is based on a simple experimental setup, using automated center-of-mass tracking and image analysis, making it an easily implemented alternative to current methods for screening planarian locomotion phenotypes. As a proof of principle, two drug-induced behavioral phenotypes were generated to show the capacity of this method. PMID:21389189

  17. Gene Expression in Transformed Lymphocytes Reveals Variation in Endomembrane and HLA Pathways Modifying Cystic Fibrosis Pulmonary Phenotypes

    PubMed Central

    O’Neal, Wanda K.; Gallins, Paul; Pace, Rhonda G.; Dang, Hong; Wolf, Whitney E.; Jones, Lisa C.; Guo, XueLiang; Zhou, Yi-Hui; Madar, Vered; Huang, Jinyan; Liang, Liming; Moffatt, Miriam F.; Cutting, Garry R.; Drumm, Mitchell L.; Rommens, Johanna M.; Strug, Lisa J.; Sun, Wei; Stonebraker, Jaclyn R.; Wright, Fred A.; Knowles, Michael R.

    2015-01-01

    Variation in cystic fibrosis (CF) phenotypes, including lung disease severity, age of onset of persistent Pseudomonas aeruginosa (P. aeruginosa) lung infection, and presence of meconium ileus (MI), has been partially explained by genome-wide association studies (GWASs). It is not expected that GWASs alone are sufficiently powered to uncover all heritable traits associated with CF phenotypic diversity. Therefore, we utilized gene expression association from lymphoblastoid cells lines from 754 p.Phe508del CF-affected homozygous individuals to identify genes and pathways. LPAR6, a G protein coupled receptor, associated with lung disease severity (false discovery rate q value = 0.0006). Additional pathway analyses, utilizing a stringent permutation-based approach, identified unique signals for all three phenotypes. Pathways associated with lung disease severity were annotated in three broad categories: (1) endomembrane function, containing p.Phe508del processing genes, providing evidence of the importance of p.Phe508del processing to explain lung phenotype variation; (2) HLA class I genes, extending previous GWAS findings in the HLA region; and (3) endoplasmic reticulum stress response genes. Expression pathways associated with lung disease were concordant for some endosome and HLA pathways, with pathways identified using GWAS associations from 1,978 CF-affected individuals. Pathways associated with age of onset of persistent P. aeruginosa infection were enriched for HLA class II genes, and those associated with MI were related to oxidative phosphorylation. Formal testing demonstrated that genes showing differential expression associated with lung disease severity were enriched for heritable genetic variation and expression quantitative traits. Gene expression provided a powerful tool to identify unrecognized heritable variation, complementing ongoing GWASs in this rare disease. PMID:25640674

  18. Modulating the frequency and bias of stochastic switching to control phenotypic variation.

    PubMed

    Hung, Michelle; Chang, Emily; Hussein, Razika; Frazier, Katya; Shin, Jung-Eun; Sagawa, Shiori; Lim, Han N

    2014-01-01

    Mechanisms that control cell-to-cell variation in gene expression ('phenotypic variation') can determine a population's growth rate, robustness, adaptability and capacity for complex behaviours. Here we describe a general strategy (termed FABMOS) for tuning the phenotypic variation and mean expression of cell populations by modulating the frequency and bias of stochastic transitions between 'OFF' and 'ON' expression states of a genetic switch. We validated the strategy experimentally using a synthetic fim switch in Escherichia coli. Modulating the frequency of switching can generate a bimodal (low frequency) or a unimodal (high frequency) population distribution with the same mean expression. Modulating the bias as well as the frequency of switching can generate a spectrum of bimodal and unimodal distributions with the same mean expression. This remarkable control over phenotypic variation, which cannot be easily achieved with standard gene regulatory mechanisms, has many potential applications for synthetic biology, engineered microbial ecosystems and experimental evolution. PMID:25087841

  19. Impact of temporal variation on design and analysis of mouse knockout phenotyping studies.

    PubMed

    Karp, Natasha A; Speak, Anneliese O; White, Jacqueline K; Adams, David J; Hrabé de Angelis, Martin; Hérault, Yann; Mott, Richard F

    2014-01-01

    A significant challenge facing high-throughput phenotyping of in-vivo knockout mice is ensuring phenotype calls are robust and reliable. Central to this problem is selecting an appropriate statistical analysis that models both the experimental design (the workflow and the way control mice are selected for comparison with knockout animals) and the sources of variation. Recently we proposed a mixed model suitable for small batch-oriented studies, where controls are not phenotyped concurrently with mutants. Here we evaluate this method both for its sensitivity to detect phenotypic effects and to control false positives, across a range of workflows used at mouse phenotyping centers. We found the sensitivity and control of false positives depend on the workflow. We show that the phenotypes in control mice fluctuate unexpectedly between batches and this can cause the false positive rate of phenotype calls to be inflated when only a small number of batches are tested, when the effect of knockout becomes confounded with temporal fluctuations in control mice. This effect was observed in both behavioural and physiological assays. Based on this analysis, we recommend two approaches (workflow and accompanying control strategy) and associated analyses, which would be robust, for use in high-throughput phenotyping pipelines. Our results show the importance in modelling all sources of variability in high-throughput phenotyping studies. PMID:25343444

  20. Variation in selection, phenotypic plasticity, and the ecology of sexual

    E-print Network

    Fox, Charles W.

    on female reproduction. For example, studies manipulating female mating fre- quency generally demonstrate that differ in the direc- tion of dimorphism (female-biased and male-biased) and that show substantial variation in dimorphism among populations within species. Seed beetles are an excellent system for studies

  1. Life history as a constraint on plasticity: developmental timing is correlated with phenotypic variation in birds.

    PubMed

    Snell-Rood, E C; Swanson, E M; Young, R L

    2015-10-01

    Understanding why organisms vary in developmental plasticity has implications for predicting population responses to changing environments and the maintenance of intraspecific variation. The epiphenotype hypothesis posits that the timing of development can constrain plasticity-the earlier alternate phenotypes begin to develop, the greater the difference that can result amongst the final traits. This research extends this idea by considering how life history timing shapes the opportunity for the environment to influence trait development. We test the prediction that the earlier an individual begins to actively interact with and explore their environment, the greater the opportunity for plasticity and thus variation in foraging traits. This research focuses on life history variation across four groups of birds using museum specimens and measurements from the literature. We reasoned that greater phenotypic plasticity, through either environmental effects or genotype-by-environment interactions in development, would be manifest in larger trait ranges (bills and tarsi) within species. Among shorebirds and ducks, we found that species with relatively shorter incubation times tended to show greater phenotypic variation. Across warblers and sparrows, we found little support linking timing of flight and trait variation. Overall, our results also suggest a pattern between body size and trait variation, consistent with constraints on egg size that might result in larger species having more environmental influences on development. Taken together, our results provide some support for the hypothesis that variation in life histories affects how the environment shapes development, through either the expression of plasticity or the release of cryptic genetic variation. PMID:26039409

  2. Optimizing experimental procedures for quantitative evaluation of crop plant performance in high throughput phenotyping systems

    PubMed Central

    Junker, Astrid; Muraya, Moses M.; Weigelt-Fischer, Kathleen; Arana-Ceballos, Fernando; Klukas, Christian; Melchinger, Albrecht E.; Meyer, Rhonda C.; Riewe, David; Altmann, Thomas

    2015-01-01

    Detailed and standardized protocols for plant cultivation in environmentally controlled conditions are an essential prerequisite to conduct reproducible experiments with precisely defined treatments. Setting up appropriate and well defined experimental procedures is thus crucial for the generation of solid evidence and indispensable for successful plant research. Non-invasive and high throughput (HT) phenotyping technologies offer the opportunity to monitor and quantify performance dynamics of several hundreds of plants at a time. Compared to small scale plant cultivations, HT systems have much higher demands, from a conceptual and a logistic point of view, on experimental design, as well as the actual plant cultivation conditions, and the image analysis and statistical methods for data evaluation. Furthermore, cultivation conditions need to be designed that elicit plant performance characteristics corresponding to those under natural conditions. This manuscript describes critical steps in the optimization of procedures for HT plant phenotyping systems. Starting with the model plant Arabidopsis, HT-compatible methods were tested, and optimized with regard to growth substrate, soil coverage, watering regime, experimental design (considering environmental inhomogeneities) in automated plant cultivation and imaging systems. As revealed by metabolite profiling, plant movement did not affect the plants' physiological status. Based on these results, procedures for maize HT cultivation and monitoring were established. Variation of maize vegetative growth in the HT phenotyping system did match well with that observed in the field. The presented results outline important issues to be considered in the design of HT phenotyping experiments for model and crop plants. It thereby provides guidelines for the setup of HT experimental procedures, which are required for the generation of reliable and reproducible data of phenotypic variation for a broad range of applications. PMID:25653655

  3. Combined mass quantitation and phenotyping of intact extracellular vesicles by a microarray platform.

    PubMed

    Gagni, Paola; Cretich, Marina; Benussi, Luisa; Tonoli, Elisa; Ciani, Miriam; Ghidoni, Roberta; Santini, Benedetta; Galbiati, Elisabetta; Prosperi, Davide; Chiari, Marcella

    2016-01-01

    The interest towards extracellular vesicles (EVs) has grown exponentially over the last few years; being involved in intercellular communication and serving as reservoirs for biomarkers for tumors, they have a great potential for liquid biopsy development, possibly replacing many costly and invasive tissue biopsies. Here we propose, for the first time, the use of a Si/SiO2 interferometric, microarray platform for multiparametric intact EVs analysis combining label-free EVs mass quantitation and high sensitivity fluorescence based phenotyping. Label free interferometric measurement allows to quantify the amount of vesicles captured by printed antibodies while, on the same chip, EVs are also detected by fluorescence in a sandwich immunoassay. The proposed method simultaneously detects, quantify and phenotype intact EVs in a microarray format. PMID:26703266

  4. Relevance of phenotypic variation in risk assessment: The scientific viewpoint

    SciTech Connect

    Setlow, R.B.

    1986-01-01

    A number of examples are presented indicating the types of variation that may be expected in the responses of the human population to deleterious agents of an endogeneous or exogenous nature. If one assumes that the variations in repair in the normal population are reflected in large variations in carcinogenic risk per unit of exposure, then the dose-response curves at low doses cannot be extrapolated from high doeses without knowing the distribution of sensitivities among humans. The probability of determining this range by ecpidemiological studies on a random population by small. On the other hand, the probability of determining the range by careful genetic and molecular studies appears high enough so that such experiments now are being carried out. They cannot be carried out on real populations, using chronic exposures. Hence, the ability to estimate dose-response relations in the low dose region on human populations can only be by making theoretical constructs that, in turn, are dependent on fundamental research. 12 refs., 2 tabs.

  5. KRN4 Controls Quantitative Variation in Maize Kernel Row Number

    PubMed Central

    Liu, Lei; Du, Yanfang; Shen, Xiaomeng; Li, Manfei; Sun, Wei; Huang, Juan; Liu, Zhijie; Tao, Yongsheng; Zheng, Yonglian; Yan, Jianbing; Zhang, Zuxin

    2015-01-01

    Kernel row number (KRN) is an important component of yield during the domestication and improvement of maize and controlled by quantitative trait loci (QTL). Here, we fine-mapped a major KRN QTL, KRN4, which can enhance grain productivity by increasing KRN per ear. We found that a ~3-Kb intergenic region about 60 Kb downstream from the SBP-box gene Unbranched3 (UB3) was responsible for quantitative variation in KRN by regulating the level of UB3 expression. Within the 3-Kb region, the 1.2-Kb Presence-Absence variant was found to be strongly associated with quantitative variation in KRN in diverse maize inbred lines, and our results suggest that this 1.2-Kb transposon-containing insertion is likely responsible for increased KRN. A previously identified A/G SNP (S35, also known as Ser220Asn) in UB3 was also found to be significantly associated with KRN in our association-mapping panel. Although no visible genetic effect of S35 alone could be detected in our linkage mapping population, it was found to genetically interact with the 1.2-Kb PAV to modulate KRN. The KRN4 was under strong selection during maize domestication and the favorable allele for the 1.2-Kb PAV and S35 has been significantly enriched in modern maize improvement process. The favorable haplotype (Hap1) of 1.2-Kb-PAV-S35 was selected during temperate maize improvement, but is still rare in tropical and subtropical maize germplasm. The dissection of the KRN4 locus improves our understanding of the genetic basis of quantitative variation in complex traits in maize. PMID:26575831

  6. Statistical equivalent of the classical TDT for quantitative traits and multivariate phenotypes.

    PubMed

    Haldar, Tanushree; Ghosh, Saurabh

    2015-12-01

    Clinical end-point traits are usually governed by quantitative precursors. Hence, there is active research interest in developing statistical methods for association mapping of quantitative traits. Unlike population-based tests for association, family-based tests for transmission disequilibrium are protected against population stratification. In this study, we propose a logistic regression model to test the association for quantitative traits based on a trio design. We show that the method can be viewed as a direct extension of the classical transmission diequilibrium test for binary traits to quantitative traits. We evaluate the performance of our method usingextensive simulations and compare it with an existing method, family-based association test. We found that the two methods yield comparable powers if all families are considered. However, unlike FBAT, which yields an inflated rate of false positives when noninformative trios with all three individuals' heterozygous are removed, our method maintains the correct size without compromising too much on power. We show that our method can be easily modified to incorporate multivariate phenotypes. Here, we applied this method to analyse a quantitative endophenotype associated with alcoholism. PMID:26690516

  7. Localised intraspecific variation in the swimming phenotype of a coral reef fish across different wave exposures.

    PubMed

    Binning, Sandra A; Roche, Dominique G; Fulton, Christopher J

    2014-03-01

    Wave-driven water flow is a major force structuring marine communities. Species distributions are partly determined by the ability to cope with variation in water flow, such as differences in the assemblage of fish species found in a given water flow environment being linked to swimming ability (based on fin shape and mode of locomotion). It remains unclear, however, whether similar assembly rules apply within a species. Here we show phenotypic variation among sites in traits functionally linked to swimming ability in the damselfish Acanthochromis polyacanthus. These sites differ in wave energy and the observed patterns of phenotypic differences within A. polyacanthus closely mirrored those seen at the interspecific level. Fish from high-exposure sites had more tapered fins and higher maximum metabolic rates than conspecifics from sheltered sites. This translates to a 36% larger aerobic scope and 33% faster critical swimming speed for fish from exposed sites. Our results suggest that functional relationships among swimming phenotypes and water flow not only structure species assemblages, but can also shape patterns of phenotypic divergence within species. Close links between locomotor phenotype and local water flow conditions appear to be important for species distributions as well as phenotypic divergence across environmental gradients. PMID:24132502

  8. Molecular and quantitative trait variation within and among small fragmented populations of the endangered plant species Psilopeganum sinense

    PubMed Central

    Ye, Qigang; Tang, Feiyan; Wei, Na; Yao, Xiaohong

    2014-01-01

    Background and Aims Natural selection and genetic drift are important evolutionary forces in determining genetic and phenotypic differentiation in plant populations. The extent to which these two distinct evolutionary forces affect locally adaptive quantitative traits has been well studied in common plant and animal species. However, we know less about how quantitative traits respond to selection pressures and drift in endangered species that have small population sizes and fragmented distributions. To address this question, this study assessed the relative strengths of selection and genetic drift in shaping population differentiation of phenotypic traits in Psilopeganum sinense, a naturally rare and recently endangered plant species. Methods Population differentiation at five quantitative traits (QST) obtained from a common garden experiment was compared with differentiation at putatively neutral microsatellite markers (FST) in seven populations of P. sinense. QST estimates were derived using a Bayesian hierarchical variance component method. Key Results Trait-specific QST values were equal to or lower than FST. Neutral genetic diversity was not correlated with quantitative genetic variation within the populations of P. sinense. Conclusions Despite the prevalent empirical evidence for QST > FST, the results instead suggest a definitive role of stabilizing selection and drift leading to phenotypic differentiation among small populations. Three traits exhibited a significantly lower QST relative to FST, suggesting that populations of P. sinense might have experienced stabilizing selection for the same optimal phenotypes despite large geographical distances between populations and habitat fragmentation. For the other two traits, QST estimates were of the same magnitude as FST, indicating that divergence in these traits could have been achieved by genetic drift alone. The lack of correlation between molecular marker and quantitative genetic variation suggests that sophisticated considerations are required for the inference of conservation measures of P. sinense from neutral genetic markers. PMID:24265350

  9. Estimation Of The Proportion Of Variation Accounted For By DNA Tests. II: Phenotypic Variance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The proportion of phenotypic variation accounted for (Rp2) is an important characteristic of a DNA test. Therefore, several estimators of this quantity were evaluated by simulation of 500 replicates of a population of 1000 progeny of 100 sires (3 levels of narrow sense heritability and 4 levels of ...

  10. Phenotypic flexibility in passerine birds: Seasonal variation of aerobic enzyme activities in skeletal muscle

    E-print Network

    Swanson, David L.

    Phenotypic flexibility in passerine birds: Seasonal variation of aerobic enzyme activities activities of the key aerobic enzymes citrate synthase (CS) and b-hydroxyacyl CoA-dehydrogenase (HOAD and cellular aerobic capacity in muscle contribute to seasonal metabolic flexibility in some species

  11. A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness

    PubMed Central

    Katsonis, Panagiotis

    2014-01-01

    The relationship between genotype mutations and phenotype variations determines health in the short term and evolution over the long term, and it hinges on the action of mutations on fitness. A fundamental difficulty in determining this action, however, is that it depends on the unique context of each mutation, which is complex and often cryptic. As a result, the effect of most genome variations on molecular function and overall fitness remains unknown and stands apart from population genetics theories linking fitness effect to polymorphism frequency. Here, we hypothesize that evolution is a continuous and differentiable physical process coupling genotype to phenotype. This leads to a formal equation for the action of coding mutations on fitness that can be interpreted as a product of the evolutionary importance of the mutated site with the difference in amino acid similarity. Approximations for these terms are readily computable from phylogenetic sequence analysis, and we show mutational, clinical, and population genetic evidence that this action equation predicts the effect of point mutations in vivo and in vitro in diverse proteins, correlates disease-causing gene mutations with morbidity, and determines the frequency of human coding polymorphisms, respectively. Thus, elementary calculus and phylogenetics can be integrated into a perturbation analysis of the evolutionary relationship between genotype and phenotype that quantitatively links point mutations to function and fitness and that opens a new analytic framework for equations of biology. In practice, this work explicitly bridges molecular evolution with population genetics with applications from protein redesign to the clinical assessment of human genetic variations. PMID:25217195

  12. A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness.

    PubMed

    Katsonis, Panagiotis; Lichtarge, Olivier

    2014-12-01

    The relationship between genotype mutations and phenotype variations determines health in the short term and evolution over the long term, and it hinges on the action of mutations on fitness. A fundamental difficulty in determining this action, however, is that it depends on the unique context of each mutation, which is complex and often cryptic. As a result, the effect of most genome variations on molecular function and overall fitness remains unknown and stands apart from population genetics theories linking fitness effect to polymorphism frequency. Here, we hypothesize that evolution is a continuous and differentiable physical process coupling genotype to phenotype. This leads to a formal equation for the action of coding mutations on fitness that can be interpreted as a product of the evolutionary importance of the mutated site with the difference in amino acid similarity. Approximations for these terms are readily computable from phylogenetic sequence analysis, and we show mutational, clinical, and population genetic evidence that this action equation predicts the effect of point mutations in vivo and in vitro in diverse proteins, correlates disease-causing gene mutations with morbidity, and determines the frequency of human coding polymorphisms, respectively. Thus, elementary calculus and phylogenetics can be integrated into a perturbation analysis of the evolutionary relationship between genotype and phenotype that quantitatively links point mutations to function and fitness and that opens a new analytic framework for equations of biology. In practice, this work explicitly bridges molecular evolution with population genetics with applications from protein redesign to the clinical assessment of human genetic variations. PMID:25217195

  13. Integrating environmental variation, predation pressure, phenotypic plasticity and locomotor performance.

    PubMed

    Fu, Shi-Jian; Cao, Zhen-Dong; Yan, Guan-Jie; Fu, Cheng; Pang, Xu

    2013-10-01

    The Wujiang River, a tributary of the Three Gorges Reservoir, has many dams along its length. These dams alter the river's natural habitat and produce various flow regimes and degrees of predator stress. To test whether the swimming performance and external body shape of pale chub (Zacco platypus) have changed as a result of alterations in the flow regime and predator conditions, we measured the steady (U(crit)) and unsteady (fast-start) swimming performances and morphological characteristics of fish collected from different sites along the Wujiang River. We also calculated the maximum respiratory capacity and cost of transport (COT). We demonstrated significant differences in swimming performance and morphological traits among the sampling sites. Steady swimming performance was positively correlated with water velocity and negatively correlated with the abundance of predators, whereas unsteady swimming performance was negatively correlated with water velocity. The body shape was significantly correlated with both swimming performance and ecological parameters. These findings suggested that selection pressure on swimming performance results in a higher U(crit) and a more streamlined body shape in fast-flow and (or) in habitats with low predator stress and subsequently results in a lower COT. These characteristics were accompanied by a poorer fast-start performance than that of the fish from the slow-flow and (or) high-predator habitats. The divergence in U(crit) may also be due in part to variation in respiratory capacity. PMID:23463244

  14. Exploration of methods to identify polymorphisms associated with variation in DNA repair capacity phenotypes

    SciTech Connect

    Jones, I M; Thomas, C B; Xi, T; Mohrenweiser, H W; Nelson, D O

    2006-07-03

    Elucidating the relationship between polymorphic sequences and risk of common disease is a challenge. For example, although it is clear that variation in DNA repair genes is associated with familial cancer, aging and neurological disease, progress toward identifying polymorphisms associated with elevated risk of sporadic disease has been slow. This is partly due to the complexity of the genetic variation, the existence of large numbers of mostly low frequency variants and the contribution of many genes to variation in susceptibility. There has been limited development of methods to find associations between genotypes having many polymorphisms and pathway function or health outcome. We have explored several statistical methods for identifying polymorphisms associated with variation in DNA repair phenotypes. The model system used was 80 cell lines that had been resequenced to identify variation; 191 single nucleotide substitution polymorphisms (SNPs) are included, of which 172 are in 31 base excision repair pathway genes, 19 in 5 anti-oxidation genes, and DNA repair phenotypes based on single strand breaks measured by the alkaline Comet assay. Univariate analyses were of limited value in identifying SNPs associated with phenotype variation. Of the multivariable model selection methods tested: the easiest that provided reduced error of prediction of phenotype was simple counting of the variant alleles predicted to encode proteins with reduced activity, which led to a genotype including 52 SNPs; the best and most parsimonious model was achieved using a two-step analysis without regard to potential functional relevance: first SNPs were ranked by importance determined by Random Forests Regression (RFR), followed by cross-validation in a second round of RFR modeling that included ever more SNPs in declining order of importance. With this approach 6 SNPs were found to minimize prediction error. The results should encourage research into utilization of multivariate analytical methods for epidemiological studies of the association of genetic variation in complex genotypes with risk of common diseases.

  15. Phenotypic variation and spatial structure of secondary chemistry in a natural population of a tropical tree species

    E-print Network

    Coley, Phyllis

    Phenotypic variation and spatial structure of secondary chemistry in a natural population. Phenotypic variation and spatial structure of secondary chemistry in a natural population of a tropical tree chemistry of the tropical tree Quararibea asterolepis, Pitt. (Bombacaceae) in a natural population on Barro

  16. Stressful environments induce novel phenotypic variation: hierarchical reaction norms for sperm performance of a pervasive invader

    PubMed Central

    Purchase, Craig F; Moreau, Darek T R

    2012-01-01

    Genetic variation for phenotypic plasticity is ubiquitous and important. However, the scale of such variation including the relative variability present in reaction norms among different hierarchies of biological organization (e.g., individuals, populations, and closely related species) is unknown. Complicating interpretation is a trade-off in environmental scale. As plasticity can only be inferred over the range of environments tested, experiments focusing on fine tuned responses to normal or benign conditions may miss cryptic phenotypic variation expressed under novel or stressful environments. Here, we sought to discern the presence and shape of plasticity in the performance of brown trout sperm as a function of optimal to extremely stressful river pH, and demarcate if the reaction norm varies among genotypes. Our overarching goal was to determine if deteriorating environmental quality increases expressed variation among individuals. A more applied aim was to ascertain whether maintaining sperm performance over a wide pH range could help explain how brown trout are able to invade diverse river systems when transplanted outside of their native range. Individuals differed in their reaction norms of phenotypic expression of an important trait in response to environmental change. Cryptic variation was revealed under stressful conditions, evidenced through increasing among-individual variability. Importantly, data on population averages masked this variability in plasticity. In addition, canalized reaction norms in sperm swimming velocities of many individuals over a very large range in water chemistry may help explain why brown trout are able to colonize a wide variety of habitats. PMID:23145341

  17. Region and site conditions affect phenotypic trait variation in five forest herbs

    NASA Astrophysics Data System (ADS)

    Lemke, Isgard Holle; Kolb, Annette; Diekmann, Martin Reemt

    2012-02-01

    Phenotypic plasticity is the ability of organisms to express different phenotypes under different environmental conditions. It may buffer individuals both against short-term environmental fluctuations and long-term effects of global change. A plastic behaviour in response to changes in the environment may be especially important in species with low migration rates and colonization capacities, such as in many forest plants in present-day fragmented landscapes. We compared the phenotypic trait variation (used as a proxy for the amount of phenotypic plasticity) of five forest herbs (Brachypodium sylvaticum, Circaea lutetiana, Impatiens noli-tangere, Sanicula europaea and Stachys sylvatica) between two regions in Germany that differ in their overall environmental conditions (Bremen in the northwest, Freiburg in the southwest; 5 species × 2 regions × 8-15 populations × 25-50 individuals). In addition, we measured light intensity and important soil parameters (soil pH, moisture, K, P and N) in all populations. We found consistent differences in trait variability between the two regions in several species. In Brachypodium and Stachys both vegetative and reproductive traits were more variable in Freiburg. Similarly, reproductive traits of Impatiens and Sanicula appeared to be more variable in Freiburg, while in both species at least one of the vegetative traits was more variable in Bremen. Mean local environmental conditions also affected trait variation; in most of the species both vegetative and reproductive traits were more variable in sites with higher nutrient contents and higher light availability. Across all traits and both regions, seed or fruit production was most variable. In summary, at least some of the studied forest herbs appear to respond strongly to large-scale environmental differences, showing a higher trait variability in the more southern region. Given the assumption that phenotypic trait variation is positively associated with phenotypic plasticity, we conclude that these populations may more easily respond to changes in the environment.

  18. Intraspecific phenotypic variation in a fish predator affects multitrophic lake metacommunity structure

    PubMed Central

    Howeth, Jennifer G; Weis, Jerome J; Brodersen, Jakob; Hatton, Elizabeth C; Post, David M

    2013-01-01

    Contemporary insights from evolutionary ecology suggest that population divergence in ecologically important traits within predators can generate diversifying ecological selection on local community structure. Many studies acknowledging these effects of intraspecific variation assume that local populations are situated in communities that are unconnected to similar communities within a shared region. Recent work from metacommunity ecology suggests that species dispersal among communities can also influence species diversity and composition but can depend upon the relative importance of the local environment. Here, we study the relative effects of intraspecific phenotypic variation in a fish predator and spatial processes related to plankton species dispersal on multitrophic lake plankton metacommunity structure. Intraspecific diversification in foraging traits and residence time of the planktivorous fish alewife (Alosa pseudoharengus) among coastal lakes yields lake metacommunities supporting three lake types which differ in the phenotype and incidence of alewife: lakes with anadromous, landlocked, or no alewives. In coastal lakes, plankton community composition was attributed to dispersal versus local environmental predictors, including intraspecific variation in alewives. Local and beta diversity of zooplankton and phytoplankton was additionally measured in response to intraspecific variation in alewives. Zooplankton communities were structured by species sorting, with a strong influence of intraspecific variation in A. pseudoharengus. Intraspecific variation altered zooplankton species richness and beta diversity, where lake communities with landlocked alewives exhibited intermediate richness between lakes with anadromous alewives and without alewives, and greater community similarity. Phytoplankton diversity, in contrast, was highest in lakes with landlocked alewives. The results indicate that plankton dispersal in the region supplied a migrant pool that was strongly structured by intraspecific variation in alewives. This is one of the first studies to demonstrate that intraspecific phenotypic variation in a predator can maintain contrasting patterns of multitrophic diversity in metacommunities. PMID:24455134

  19. Phenotypic and Genetic Variations in Obligate Parthenogenetic Populations of Eriosoma lanigerum Hausmann (Hemiptera: Aphididae).

    PubMed

    Ruiz-Montoya, L; Zúñiga, G; Cisneros, R; Salinas-Moreno, Y; Peña-Martínez, R; Machkour-M'Rabet, S

    2015-12-01

    The study of phenotypic and genetic variation of obligate parthenogenetic organisms contributes to an understanding of evolution in the absence of genetic variation produced by sexual reproduction. Eriosoma lanigerum Hausmann undergoes obligate parthenogenesis in Mexico City, Mexico, due to the unavailability of the host plants required for sexual reproduction. We analysed the phenotypic and genetic variation of E. lanigerum in relation to the dry and wet season and plant phenology. Aphids were collected on two occasions per season on a secondary host plant, Pyracantha koidzumii, at five different sites in the southern area of Mexico City, Mexico. Thirteen morphological characteristics were measured from 147 to 276 individuals per site and per season. A multivariate analysis of variance was performed to test the effect of the season, site and their interaction on morphological traits. Morphological variation was summarised using a principal component analysis. Genetic variation was described using six enzymatic loci, four of which were polymorphic. Our study showed that the site and season has a significant effect on morphological trait variation. The largest aphids were recorded during cold temperatures with low relative humidity and when the plant was at the end of the fruiting period. The mean genetic diversity was low (mean H e?=?0.161), and populations were genetically structured by season and site. Morphological and genetic variations appear to be associated with environmental factors that directly affect aphid development and/or indirectly by host plant phenology. PMID:26272633

  20. Divergence in a master variator generates distinct phenotypes and transcriptional responses

    PubMed Central

    Gallagher, Jennifer E.G.; Zheng, Wei; Rong, Xiaoqing; Miranda, Noraliz; Lin, Zhixiang; Dunn, Barbara; Zhao, Hongyu; Snyder, Michael P.

    2014-01-01

    Genetic basis of phenotypic differences in individuals is an important area in biology and personalized medicine. Analysis of divergent Saccharomyces cerevisiae strains grown under different conditions revealed extensive variation in response to both drugs (e.g., 4-nitroquinoline 1-oxide [4NQO]) and different carbon sources. Differences in 4NQO resistance were due to amino acid variation in the transcription factor Yrr1. Yrr1YJM789 conferred 4NQO resistance but caused slower growth on glycerol, and vice versa with Yrr1S96, indicating that alleles of Yrr1 confer distinct phenotypes. The binding targets of Yrr1 alleles from diverse yeast strains varied considerably among different strains grown under the same conditions as well as for the same strain under different conditions, indicating that distinct molecular programs are conferred by the different Yrr1 alleles. Our results demonstrate that genetic variations in one important control gene (YRR1), lead to distinct regulatory programs and phenotypes in individuals. We term these polymorphic control genes “master variators.” PMID:24532717

  1. Genotypic and phenotypic variation in transmission traits of a complex life cycle parasite

    PubMed Central

    Louhi, Katja-Riikka; Karvonen, Anssi; Rellstab, Christian; Jokela, Jukka

    2013-01-01

    Characterizing genetic variation in parasite transmission traits and its contribution to parasite vigor is essential for understanding the evolution of parasite life-history traits. We measured genetic variation in output, activity, survival, and infection success of clonal transmission stages (cercaria larvae) of a complex life cycle parasite (Diplostomum pseudospathaceum). We further tested if variation in host nutritional stage had an effect on these traits by keeping hosts on limited or ad libitum diet. The traits we measured were highly variable among parasite genotypes indicating significant genetic variation in these life-history traits. Traits were also phenotypically variable, for example, there was significant variation in the measured traits over time within each genotype. However, host nutritional stage had no effect on the parasite traits suggesting that a short-term reduction in host resources was not limiting the cercarial output or performance. Overall, these results suggest significant interclonal and phenotypic variation in parasite transmission traits that are not affected by host nutritional status. PMID:23919156

  2. Quantitative trait loci mapping of phenotypic plasticity and genotype–environment interactions in plant and insect performance

    PubMed Central

    Tétard-Jones, C.; Kertesz, M. A.; Preziosi, R. F.

    2011-01-01

    Community genetic studies generally ignore the plasticity of the functional traits through which the effect is passed from individuals to the associated community. However, the ability of organisms to be phenotypically plastic allows them to rapidly adapt to changing environments and plasticity is commonly observed across all taxa. Owing to the fitness benefits of phenotypic plasticity, evolutionary biologists are interested in its genetic basis, which could explain how phenotypic plasticity is involved in the evolution of species interactions. Two current ideas exist: (i) phenotypic plasticity is caused by environmentally sensitive loci associated with a phenotype; (ii) phenotypic plasticity is caused by regulatory genes that simply influence the plasticity of a phenotype. Here, we designed a quantitative trait loci (QTL) mapping experiment to locate QTL on the barley genome associated with barley performance when the environment varies in the presence of aphids, and the composition of the rhizosphere. We simultaneously mapped aphid performance across variable rhizosphere environments. We mapped main effects, QTL × environment interaction (QTL×E), and phenotypic plasticity (measured as the difference in mean trait values) for barley and aphid performance onto the barley genome using an interval mapping procedure. We found that QTL associated with phenotypic plasticity were co-located with main effect QTL and QTL×E. We also located phenotypic plasticity QTL that were located separately from main effect QTL. These results support both of the current ideas of how phenotypic plasticity is genetically based and provide an initial insight into the functional genetic basis of how phenotypically plastic traits may still be important sources of community genetic effects. PMID:21444311

  3. Phenotypic Variation and Fitness in a Metapopulation of Tubeworms (Ridgeia piscesae Jones) at Hydrothermal Vents

    PubMed Central

    Tunnicliffe, Verena; St. Germain, Candice; Hilário, Ana

    2014-01-01

    We examine the nature of variation in a hot vent tubeworm, Ridgeia piscesae, to determine how phenotypes are maintained and how reproductive potential is dictated by habitat. This foundation species at northeast Pacific hydrothermal sites occupies a wide habitat range in a highly heterogeneous environment. Where fluids supply high levels of dissolved sulphide for symbionts, the worm grows rapidly in a “short-fat” phenotype characterized by lush gill plumes; when plumes are healthy, sperm package capture is higher. This form can mature within months and has a high fecundity with continuous gamete output and a lifespan of about three years in unstable conditions. Other phenotypes occupy low fluid flux habitats that are more stable and individuals grow very slowly; however, they have low reproductive readiness that is hampered further by small, predator cropped branchiae, thus reducing fertilization and metabolite uptake. Although only the largest worms were measured, only 17% of low flux worms were reproductively competent compared to 91% of high flux worms. A model of reproductive readiness illustrates that tube diameter is a good predictor of reproductive output and that few low flux worms reached critical reproductive size. We postulate that most of the propagules for the vent fields originate from the larger tubeworms that live in small, unstable habitat patches. The large expanses of worms in more stable low flux habitat sustain a small, but long-term, reproductive output. Phenotypic variation is an adaptation that fosters both morphological and physiological responses to differences in chemical milieu and predator pressure. This foundation species forms a metapopulation with variable growth characteristics in a heterogeneous environment where a strategy of phenotypic variation bestows an advantage over specialization. PMID:25337895

  4. Adaptive basis of geographic variation: genetic, phenotypic and environmental differences among beach mouse populations

    PubMed Central

    Mullen, Lynne M.; Vignieri, Sacha N.; Gore, Jeffery A.; Hoekstra, Hopi E.

    2009-01-01

    A major goal in evolutionary biology is to understand how and why populations differentiate, both genetically and phenotypically, as they invade a novel habitat. A classical example of adaptation is the pale colour of beach mice, relative to their dark mainland ancestors, which colonized the isolated sandy dunes and barrier islands on Florida's Gulf Coast. However, much less is known about differentiation among the Gulf Coast beach mice, which comprise five subspecies linearly arrayed on Florida's shoreline. Here, we test the role of selection in maintaining variation among these beach mouse subspecies at multiple levels—phenotype, genotype and the environments they inhabit. While all beach subspecies have light pelage, they differ significantly in colour pattern. These subspecies are also genetically distinct: pair-wise Fst-values range from 0.23 to 0.63 and levels of gene flow are low. However, we did not find a correlation between phenotypic and genetic distance. Instead, we find a significant association between the average ‘lightness’ of each subspecies and the brightness of the substrate it inhabits: the two most genetically divergent subspecies occupy the most similar habitats and have converged on phenotype, whereas the most genetically similar subspecies occupy the most different environments and have divergent phenotypes. Moreover, allelic variation at the pigmentation gene, Mc1r, is statistically correlated with these colour differences but not with variation at other genetic loci. Together, these results suggest that natural selection for camouflage—via changes in Mc1r allele frequency—contributes to pigment differentiation among beach mouse subspecies. PMID:19656790

  5. Digital holographic microscopy: a quantitative label-free microscopy technique for phenotypic screening.

    PubMed

    Rappaz, Benjamin; Breton, Billy; Shaffer, Etienne; Turcatti, Gerardo

    2014-01-01

    Digital Holographic Microscopy (DHM) is a label-free imaging technique allowing visualization of transparent cells with classical imaging cell culture plates. The quantitative DHM phase contrast image provided is related both to the intracellular refractive index and to cell thickness. DHM is able to distinguish cellular morphological changes on two representative cell lines (HeLa and H9c2) when treated with doxorubicin and chloroquine, two cytotoxic compounds yielding distinct phenotypes. We analyzed parameters linked to cell morphology and to the intracellular content in endpoint measurements and further investigated them with timelapse recording. The results obtained by DHM were compared with other optical label-free microscopy techniques, namely Phase Contrast, Differential Interference Contrast and Transport of Intensity Equation (reconstructed from three bright-field images). For comparative purposes, images were acquired in a common 96-well plate format on the different motorized microscopes. In contrast to the other microscopies assayed, images generated with DHM can be easily quantified using a simple automatized on-the-fly analysis method for discriminating the different phenotypes generated in each cell line. The DHM technology is suitable for the development of robust and unbiased image-based assays. PMID:24152227

  6. Earlier Migration Timing, Decreasing Phenotypic Variation, and Biocomplexity in Multiple Salmonid Species

    PubMed Central

    Kovach, Ryan P.; Joyce, John E.; Echave, Jesse D.; Lindberg, Mark S.; Tallmon, David A.

    2013-01-01

    Climate-induced phenological shifts can influence population, evolutionary, and ecological dynamics, but our understanding of these phenomena is hampered by a lack of long-term demographic data. We use a multi-decade census of 5 salmonid species representing 14 life histories in a warming Alaskan stream to address the following key questions about climate change and phenology: How consistent are temporal patterns and drivers of phenology for similar species and alternative life histories? Are shifts in phenology associated with changes in phenotypic variation? How do phenological changes influence the availability of resource subsidies? For most salmonid species, life stages, and life histories, freshwater temperature influences migration timing – migration events are occurring earlier in time (mean?=?1.7 days earlier per decade over the 3–5 decades), and the number of days over which migration events occur is decreasing (mean?=?1.5 days per decade). Temporal trends in migration timing were not correlated with changes in intra-annual phenotypic variation, suggesting that these components of the phenotypic distribution have responded to environmental change independently. Despite commonalities across species and life histories, there was important biocomplexity in the form of disparate shifts in migration timing and variation in the environmental factors influencing migration timing for alternative life history strategies in the same population. Overall, adult populations have been stable during these phenotypic and environmental changes (? ?1.0), but the temporal availability of salmon as a resource in freshwater has decreased by nearly 30 days since 1971 due to changes in the median date of migration timing and decreases in intra-annual variation in migration timing. These novel observations advance our understanding of phenological change in response to climate warming, and indicate that climate change has influenced the ecology of salmon populations, which will have important consequences for the numerous species that depend on this resource. PMID:23326513

  7. Earlier migration timing, decreasing phenotypic variation, and biocomplexity in multiple salmonid species.

    PubMed

    Kovach, Ryan P; Joyce, John E; Echave, Jesse D; Lindberg, Mark S; Tallmon, David A

    2013-01-01

    Climate-induced phenological shifts can influence population, evolutionary, and ecological dynamics, but our understanding of these phenomena is hampered by a lack of long-term demographic data. We use a multi-decade census of 5 salmonid species representing 14 life histories in a warming Alaskan stream to address the following key questions about climate change and phenology: How consistent are temporal patterns and drivers of phenology for similar species and alternative life histories? Are shifts in phenology associated with changes in phenotypic variation? How do phenological changes influence the availability of resource subsidies? For most salmonid species, life stages, and life histories, freshwater temperature influences migration timing--migration events are occurring earlier in time (mean?=?1.7 days earlier per decade over the 3-5 decades), and the number of days over which migration events occur is decreasing (mean?=?1.5 days per decade). Temporal trends in migration timing were not correlated with changes in intra-annual phenotypic variation, suggesting that these components of the phenotypic distribution have responded to environmental change independently. Despite commonalities across species and life histories, there was important biocomplexity in the form of disparate shifts in migration timing and variation in the environmental factors influencing migration timing for alternative life history strategies in the same population. Overall, adult populations have been stable during these phenotypic and environmental changes (? ? 1.0), but the temporal availability of salmon as a resource in freshwater has decreased by nearly 30 days since 1971 due to changes in the median date of migration timing and decreases in intra-annual variation in migration timing. These novel observations advance our understanding of phenological change in response to climate warming, and indicate that climate change has influenced the ecology of salmon populations, which will have important consequences for the numerous species that depend on this resource. PMID:23326513

  8. Phenotypic variation and covariation indicate high evolvability of acoustic communication in crickets.

    PubMed

    Blankers, T; Lübke, A K; Hennig, R M

    2015-09-01

    Studying the genetic architecture of sexual traits provides insight into the rate and direction at which traits can respond to selection. Traits associated with few loci and limited genetic and phenotypic constraints tend to evolve at high rates typically observed for secondary sexual characters. Here, we examined the genetic architecture of song traits and female song preferences in the field crickets Gryllus rubens and Gryllus texensis. Song and preference data were collected from both species and interspecific F1 and F2 hybrids. We first analysed phenotypic variation to examine interspecific differentiation and trait distributions in parental and hybrid generations. Then, the relative contribution of additive and additive-dominance variation was estimated. Finally, phenotypic variance-covariance (P) matrices were estimated to evaluate the multivariate phenotype available for selection. Song traits and preferences had unimodal trait distributions, and hybrid offspring were intermediate with respect to the parents. We uncovered additive and dominance variation in song traits and preferences. For two song traits, we found evidence for X-linked inheritance. On the one hand, the observed genetic architecture does not suggest rapid divergence, although sex linkage may have allowed for somewhat higher evolutionary rates. On the other hand, P matrices revealed that multivariate variation in song traits aligned with major dimensions in song preferences, suggesting a strong selection response. We also found strong covariance between the main traits that are sexually selected and traits that are not directly selected by females, providing an explanation for the striking multivariate divergence in male calling songs despite limited divergence in female preferences. PMID:26134540

  9. Vertically transmitted fecal IgA levels distinguish extra-chromosomal phenotypic variation

    PubMed Central

    Wallace, Meghan A.; D, Carey-Ann; Burnham; Virgin, Herbert W.; Stappenbeck, Thaddeus S.

    2014-01-01

    Summary The proliferation of genetically modified mouse models has exposed phenotypic variation between investigators and institutions that has been challenging to control1-5. In many cases, the microbiota is the presumed culprit of the variation. Current solutions to account for phenotypic variability include littermate and maternal controls or defined microbial consortia in gnotobiotic mice6,7. In conventionally raised mice, the microbiome is transmitted from the dam2,8,9. Here we show that microbially–driven dichotomous fecal IgA levels in WT mice within the same facility mimic the effects of chromosomal mutations. We observed in multiple facilities that vertically-transmissible bacteria in IgA-Low mice dominantly lowered fecal IgA levels in IgA-High mice after cohousing or fecal transplantation. In response to injury, IgA-Low mice showed increased damage that was transferable by fecal transplantation and driven by fecal IgA differences. We found that bacteria from IgA-Low mice degraded the secretory component (SC) of SIgA as well as IgA itself. These data indicate that phenotypic comparisons between mice must take into account the non-chromosomal hereditary variation between different breeders. We propose fecal IgA as one marker of microbial variability and conclude that cohousing and/or fecal transplantation enables analysis of progeny from different dams. PMID:25686606

  10. Diurnal variation in the quantitative EEG in healthy adult volunteers

    PubMed Central

    Cummings, L; Dane, A; Rhodes, J; Lynch, P; Hughes, A M

    2000-01-01

    Aims To define the change in power in standard waveband frequencies of quantitative cortical electroencephalogram (EEG) data over a 24 h period, in a drug free representative healthy volunteer population. Methods This was an open, non randomised study in which 18 volunteers (9 male and 9 female) were studied on 1 study day, over a 24 h period. Volunteers had a cortical EEG recording taken at 0, 2, 4, 6, 8, 10, 12, 16 and 24 h. Each recording lasted for 6 min (3 min eyes open, 3 min eyes closed). All EEG recordings were taken in a quietened ward environment with the curtains drawn round the bed and the volunteer supine. During the 3 min eyes open, volunteers were asked to look at a red circle on a screen at the foot of the bed, and refrain from talking. Results Plots produced of geometric mean power by time of the standard wave band frequencies gave some indication of a circadian rhythm over the 24 h period for ? (4.75–6.75 Hz), ?1 (7.0–9.5 Hz) and ?1 (12.75–18.50 Hz) wavebands. Mixed models were fitted to both the eyes open and eyes closed data which confirmed a change in mean waveband power with time with statistical significance at the conventional 5% level (P < 0.05). Conclusions These data indicate the presence of a diurnal variation in the cortical quantitative EEG. They support the use of a placebo control group when designing clinical trials which utilize quantitative EEG to screen for central nervous system (CNS) activity of pharmaceutical agents, to control for the confounding variable of time of day at which the EEG recordings were made. PMID:10886113

  11. Metabolome 2.0: quantitative genetics and network biology of metabolic phenotypes.

    PubMed

    Dumas, Marc-Emmanuel

    2012-10-01

    The characterization of the metabolome has rapidly evolved over two decades, from early developments in analytical chemistry to systems biology. Metabolites and small molecules are not independent; they are organized in biochemical pathways and in a wider metabolic network, which is itself dependent on various genetic and signaling networks for its regulation. Recent advances in genomics, transcriptomics, proteomics and metabolomics have been matched by the development of publicly available repositories, which have helped shaping a new generation of integrative studies using metabolite measurements in molecular epidemiology and genetic studies. Although the environment influences metabolism, the identification of the genetic determinants of metabolic phenotypes (metabotypes) was made possible by the development of metabotype quantitative trait locus (mQTL) mapping and metabolomic genome-wide association studies (mGWAS) in a rigorous statistical genetics framework, deriving associations between metabolite concentrations and genetic polymorphisms. However, given the complexity of the biomolecular events involved in the regulation of metabolic patterns, alternative network biology approaches have also been recently introduced, such as integrated metabolome and interactome mapping (iMIM). This unprecedented convergence of metabolic biochemistry, quantitative genetics and network biology already has had a strong impact on the role of the metabolome in biomedical sciences, and this review gives a foretaste of its anticipated successes in eventually delivering personalized medicine. PMID:22868675

  12. Differential Expression of Ecdysone Receptor Leads to Variation in Phenotypic Plasticity across Serial Homologs

    PubMed Central

    Tong, Xiaoling; Bear, Ashley; Liew, Seng Fatt; Bhardwaj, Shivam; Wasik, Bethany R.; Dinwiddie, April; Bastianelli, Carole; Cheong, Wei Fun; Wenk, Markus R.; Cao, Hui

    2015-01-01

    Bodies are often made of repeated units, or serial homologs, that develop using the same core gene regulatory network. Local inputs and modifications to this network allow serial homologs to evolve different morphologies, but currently we do not understand which modifications allow these repeated traits to evolve different levels of phenotypic plasticity. Here we describe variation in phenotypic plasticity across serial homologous eyespots of the butterfly Bicyclus anynana, hypothesized to be under selection for similar or different functions in the wet and dry seasonal forms. Specifically, we document the presence of eyespot size and scale brightness plasticity in hindwing eyespots hypothesized to vary in function across seasons, and reduced size plasticity and absence of brightness plasticity in forewing eyespots hypothesized to have the same function across seasons. By exploring the molecular and physiological causes of this variation in plasticity across fore and hindwing serial homologs we discover that: 1) temperature experienced during the wandering stages of larval development alters titers of an ecdysteroid hormone, 20-hydroxyecdysone (20E), in the hemolymph of wet and dry seasonal forms at that stage; 2) the 20E receptor (EcR) is differentially expressed in the forewing and hindwing eyespot centers of both seasonal forms during this critical developmental stage; and 3) manipulations of EcR signaling disproportionately affected hindwing eyespots relative to forewing eyespots. We propose that differential EcR expression across forewing and hindwing eyespots at a critical stage of development explains the variation in levels of phenotypic plasticity across these serial homologues. This finding provides a novel signaling pathway, 20E, and a novel molecular candidate, EcR, for the regulation of levels of phenotypic plasticity across body parts or serial homologs. PMID:26405828

  13. Differential Expression of Ecdysone Receptor Leads to Variation in Phenotypic Plasticity across Serial Homologs.

    PubMed

    Monteiro, Antónia; Tong, Xiaoling; Bear, Ashley; Liew, Seng Fatt; Bhardwaj, Shivam; Wasik, Bethany R; Dinwiddie, April; Bastianelli, Carole; Cheong, Wei Fun; Wenk, Markus R; Cao, Hui; Prudic, Kathleen L

    2015-09-01

    Bodies are often made of repeated units, or serial homologs, that develop using the same core gene regulatory network. Local inputs and modifications to this network allow serial homologs to evolve different morphologies, but currently we do not understand which modifications allow these repeated traits to evolve different levels of phenotypic plasticity. Here we describe variation in phenotypic plasticity across serial homologous eyespots of the butterfly Bicyclus anynana, hypothesized to be under selection for similar or different functions in the wet and dry seasonal forms. Specifically, we document the presence of eyespot size and scale brightness plasticity in hindwing eyespots hypothesized to vary in function across seasons, and reduced size plasticity and absence of brightness plasticity in forewing eyespots hypothesized to have the same function across seasons. By exploring the molecular and physiological causes of this variation in plasticity across fore and hindwing serial homologs we discover that: 1) temperature experienced during the wandering stages of larval development alters titers of an ecdysteroid hormone, 20-hydroxyecdysone (20E), in the hemolymph of wet and dry seasonal forms at that stage; 2) the 20E receptor (EcR) is differentially expressed in the forewing and hindwing eyespot centers of both seasonal forms during this critical developmental stage; and 3) manipulations of EcR signaling disproportionately affected hindwing eyespots relative to forewing eyespots. We propose that differential EcR expression across forewing and hindwing eyespots at a critical stage of development explains the variation in levels of phenotypic plasticity across these serial homologues. This finding provides a novel signaling pathway, 20E, and a novel molecular candidate, EcR, for the regulation of levels of phenotypic plasticity across body parts or serial homologs. PMID:26405828

  14. Natural diversity in daily rhythms of gene expression contributes to phenotypic variation.

    PubMed

    de Montaigu, Amaury; Giakountis, Antonis; Rubin, Matthew; Tóth, Réka; Cremer, Frédéric; Sokolova, Vladislava; Porri, Aimone; Reymond, Matthieu; Weinig, Cynthia; Coupland, George

    2015-01-20

    Daily rhythms of gene expression provide a benefit to most organisms by ensuring that biological processes are activated at the optimal time of day. Although temporal patterns of expression control plant traits of agricultural importance, how natural genetic variation modifies these patterns during the day and how precisely these patterns influence phenotypes is poorly understood. The circadian clock regulates the timing of gene expression, and natural variation in circadian rhythms has been described, but circadian rhythms are measured in artificial continuous conditions that do not reflect the complexity of biologically relevant day/night cycles. By studying transcriptional rhythms of the evening-expressed gene gigantea (GI) at high temporal resolution and during day/night cycles, we show that natural variation in the timing of GI expression occurs mostly under long days in 77 Arabidopsis accessions. This variation is explained by natural alleles that alter light sensitivity of GI, specifically in the evening, and that act at least partly independent of circadian rhythms. Natural alleles induce precise changes in the temporal waveform of GI expression, and these changes have detectable effects on phytochrome interacting factor 4 expression and growth. Our findings provide a paradigm for how natural alleles act within day/night cycles to precisely modify temporal gene expression waveforms and cause phenotypic diversity. Such alleles could confer an advantage by adjusting the activity of temporally regulated processes without severely disrupting the circadian system. PMID:25548158

  15. The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease

    PubMed Central

    Shimoyama, Mary; De Pons, Jeff; Hayman, G. Thomas; Laulederkind, Stanley J.F.; Liu, Weisong; Nigam, Rajni; Petri, Victoria; Smith, Jennifer R.; Tutaj, Marek; Wang, Shur-Jen; Worthey, Elizabeth; Dwinell, Melinda; Jacob, Howard

    2015-01-01

    The Rat Genome Database (RGD, http://rgd.mcw.edu) provides the most comprehensive data repository and informatics platform related to the laboratory rat, one of the most important model organisms for disease studies. RGD maintains and updates datasets for genomic elements such as genes, transcripts and increasingly in recent years, sequence variations, as well as map positions for multiple assemblies and sequence information. Functional annotations for genomic elements are curated from published literature, submitted by researchers and integrated from other public resources. Complementing the genomic data catalogs are those associated with phenotypes and disease, including strains, QTL and experimental phenotype measurements across hundreds of strains. Data are submitted by researchers, acquired through bulk data pipelines or curated from published literature. Innovative software tools provide users with an integrated platform to query, mine, display and analyze valuable genomic and phenomic datasets for discovery and enhancement of their own research. This update highlights recent developments that reflect an increasing focus on: (i) genomic variation, (ii) phenotypes and diseases, (iii) data related to the environment and experimental conditions and (iv) datasets and software tools that allow the user to explore and analyze the interactions among these and their impact on disease. PMID:25355511

  16. Propagule Limitation, Disparate Habitat Quality, and Variation in Phenotypic Selection at a Local Species Range Boundary

    PubMed Central

    Moore, Kara A.; Stanton, Maureen L.

    2014-01-01

    Adaptation to novel conditions beyond current range boundaries requires the presence of suitable sites within dispersal range, but may be impeded when emigrants encounter poor habitat and sharply different selection pressures. We investigated fine-scale spatial heterogeneity in ecological dynamics and selection at a local population boundary of the annual plant Gilia tricolor. In two years, we planted G. tricolor seeds in core habitat, margin habitat at the edge of the local range, and exterior habitat in order to measure spatial and temporal variation in habitat quality, opportunity for selection, and selection on phenotypic traits. We found a striking decline in average habitat quality with distance from the population core, yet some migrant seeds were successful in suitable, unoccupied microsites at and beyond the range boundary. Total and direct selection on four out of five measured phenotypic traits varied across habitat zones, as well as between years. Moreover, the margin habitat often exerted unique selection pressures that were not intermediate between core and exterior habitats. This study reveals that a combination of ecological and evolutionary forces, including propagule limitation, variation in habitat quality and spatial heterogeneity in phenotypic selection may reduce opportunities for adaptive range expansion, even across a very local population boundary. PMID:24717472

  17. Effects of genotypic and phenotypic variation on establishment are important for conservation, invasion, and infection biology

    PubMed Central

    Forsman, Anders

    2014-01-01

    There is abundant evidence that the probability of successful establishment in novel environments increases with number of individuals in founder groups and with number of repeated introductions. Theory posits that the genotypic and phenotypic variation among individuals should also be important, but few studies have examined whether founder diversity influences establishment independent of propagule pressure, nor whether the effect is model or context dependent. I summarize the results of 18 experimental studies and report on a metaanalysis that provides strong evidence that higher levels of genotypic and phenotypic diversity in founder groups increase establishment success in plants and animals. The effect of diversity is stronger in experiments carried out under natural conditions in the wild than under seminatural or standardized laboratory conditions. The realization that genetic and phenotypic variation is key to successful establishment may improve the outcome of reintroduction and translocation programs used to vitalize or restore declining and extinct populations. Founder diversity may also improve the ability of invasive species to establish and subsequently spread in environments outside of their native community, and enhance the ability of pathogens and parasites to colonize and invade the environment constituted by their hosts. It is argued that exchange of ideas, methodological approaches, and insights of the role of diversity for establishment in different contexts may further our knowledge, vitalize future research, and improve management plans in different disciplines. PMID:24367109

  18. The alignment between phenotypic plasticity, the major axis of genetic variation and the response to selection.

    PubMed

    Lind, Martin I; Yarlett, Kylie; Reger, Julia; Carter, Mauricio J; Beckerman, Andrew P

    2015-10-01

    Phenotypic plasticity is the ability of a genotype to produce more than one phenotype in order to match the environment. Recent theory proposes that the major axis of genetic variation in a phenotypically plastic population can align with the direction of selection. Therefore, theory predicts that plasticity directly aids adaptation by increasing genetic variation in the direction favoured by selection and reflected in plasticity. We evaluated this theory in the freshwater crustacean Daphnia pulex, facing predation risk from two contrasting size-selective predators. We estimated plasticity in several life-history traits, the G matrix of these traits, the selection gradients on reproduction and survival, and the predicted responses to selection. Using these data, we tested whether the genetic lines of least resistance and the predicted response to selection aligned with plasticity. We found predator environment-specific G matrices, but shared genetic architecture across environments resulted in more constraint in the G matrix than in the plasticity of the traits, sometimes preventing alignment of the two. However, as the importance of survival selection increased, the difference between environments in their predicted response to selection increased and resulted in closer alignment between the plasticity and the predicted selection response. Therefore, plasticity may indeed aid adaptation to new environments. PMID:26423845

  19. The alignment between phenotypic plasticity, the major axis of genetic variation and the response to selection

    PubMed Central

    Lind, Martin I.; Yarlett, Kylie; Reger, Julia; Carter, Mauricio J.; Beckerman, Andrew P.

    2015-01-01

    Phenotypic plasticity is the ability of a genotype to produce more than one phenotype in order to match the environment. Recent theory proposes that the major axis of genetic variation in a phenotypically plastic population can align with the direction of selection. Therefore, theory predicts that plasticity directly aids adaptation by increasing genetic variation in the direction favoured by selection and reflected in plasticity. We evaluated this theory in the freshwater crustacean Daphnia pulex, facing predation risk from two contrasting size-selective predators. We estimated plasticity in several life-history traits, the G matrix of these traits, the selection gradients on reproduction and survival, and the predicted responses to selection. Using these data, we tested whether the genetic lines of least resistance and the predicted response to selection aligned with plasticity. We found predator environment-specific G matrices, but shared genetic architecture across environments resulted in more constraint in the G matrix than in the plasticity of the traits, sometimes preventing alignment of the two. However, as the importance of survival selection increased, the difference between environments in their predicted response to selection increased and resulted in closer alignment between the plasticity and the predicted selection response. Therefore, plasticity may indeed aid adaptation to new environments. PMID:26423845

  20. Quantitative DNA methylation analysis improves epigenotype-phenotype correlations in Beckwith-Wiedemann syndrome

    PubMed Central

    Calvello, Mariarosaria; Tabano, Silvia; Colapietro, Patrizia; Maitz, Silvia; Pansa, Alessandra; Augello, Claudia; Lalatta, Faustina; Gentilin, Barbara; Spreafico, Filippo; Calzari, Luciano; Perotti, Daniela; Larizza, Lidia; Russo, Silvia; Selicorni, Angelo; Sirchia, Silvia M; Miozzo, Monica

    2013-01-01

    Beckwith-Wiedemann syndrome (BWS) is a rare disorder characterized by overgrowth and predisposition to embryonal tumors. BWS is caused by various epigenetic and/or genetic alterations that dysregulate the imprinted genes on chromosome region 11p15.5. Molecular analysis is required to reinforce the clinical diagnosis of BWS and to identify BWS patients with cancer susceptibility. This is particularly crucial prenatally because most signs of BWS cannot be recognized in utero. We established a reliable molecular assay by pyrosequencing to quantitatively evaluate the methylation profiles of ICR1 and ICR2. We explored epigenotype-phenotype correlations in 19 patients that fulfilled the clinical diagnostic criteria for BWS, 22 patients with suspected BWS, and three fetuses with omphalocele. Abnormal methylation was observed in one prenatal case and 19 postnatal cases, including seven suspected BWS. Seven cases showed ICR1 hypermethylation, five cases showed ICR2 hypomethylation, and eight cases showed abnormal methylation of ICR1 and ICR2 indicating paternal uniparental disomy (UPD). More cases of ICR1 alterations and UPD were found than expected. This is likely due to the sensitivity of this approach, which can detect slight deviations in methylation from normal levels. There was a significant correlation (p < 0.001) between the percentage of ICR1 methylation and BWS features: severe hypermethylation (range: 75–86%) was associated with macroglossia, macrosomia, and visceromegaly, whereas mild hypermethylation (range: 55–59%) was associated with umbilical hernia and diastasis recti. Evaluation of ICR1 and ICR2 methylation by pyrosequencing in BWS can improve epigenotype-phenotype correlations, detection of methylation alterations in suspected cases, and identification of UPD. PMID:23917791

  1. The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The choice of populations for quantitative genetics experiments impacts inferences about genetic architecture and prospective selection gains. Plant breeding and quantitative genetics studies are often conducted in one or a few among many possible biparental families. Trait genotypic variation withi...

  2. Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping.

    PubMed

    Vaysse, Amaury; Ratnakumar, Abhirami; Derrien, Thomas; Axelsson, Erik; Rosengren Pielberg, Gerli; Sigurdsson, Snaevar; Fall, Tove; Seppälä, Eija H; Hansen, Mark S T; Lawley, Cindy T; Karlsson, Elinor K; Bannasch, Danika; Vilà, Carles; Lohi, Hannes; Galibert, Francis; Fredholm, Merete; Häggström, Jens; Hedhammar, Ake; André, Catherine; Lindblad-Toh, Kerstin; Hitte, Christophe; Webster, Matthew T

    2011-10-01

    The extraordinary phenotypic diversity of dog breeds has been sculpted by a unique population history accompanied by selection for novel and desirable traits. Here we perform a comprehensive analysis using multiple test statistics to identify regions under selection in 509 dogs from 46 diverse breeds using a newly developed high-density genotyping array consisting of >170,000 evenly spaced SNPs. We first identify 44 genomic regions exhibiting extreme differentiation across multiple breeds. Genetic variation in these regions correlates with variation in several phenotypic traits that vary between breeds, and we identify novel associations with both morphological and behavioral traits. We next scan the genome for signatures of selective sweeps in single breeds, characterized by long regions of reduced heterozygosity and fixation of extended haplotypes. These scans identify hundreds of regions, including 22 blocks of homozygosity longer than one megabase in certain breeds. Candidate selection loci are strongly enriched for developmental genes. We chose one highly differentiated region, associated with body size and ear morphology, and characterized it using high-throughput sequencing to provide a list of variants that may directly affect these traits. This study provides a catalogue of genomic regions showing extreme reduction in genetic variation or population differentiation in dogs, including many linked to phenotypic variation. The many blocks of reduced haplotype diversity observed across the genome in dog breeds are the result of both selection and genetic drift, but extended blocks of homozygosity on a megabase scale appear to be best explained by selection. Further elucidation of the variants under selection will help to uncover the genetic basis of complex traits and disease. PMID:22022279

  3. Inferring metabolic phenotypes from the exometabolome through a thermodynamic variational principle

    NASA Astrophysics Data System (ADS)

    De Martino, Daniele; Capuani, Fabrizio; De Martino, Andrea

    2014-11-01

    Networks of biochemical reactions, like cellular metabolic networks, are kept in non-equilibrium steady states by the exchange fluxes connecting them to the environment. In most cases, feasible flux configurations can be derived from minimal mass-balance assumptions upon prescribing in- and outtake fluxes. Here we consider the problem of inferring intracellular flux patterns from extracellular metabolite levels. Resorting to a thermodynamic out of equilibrium variational principle to describe the network at steady state, we show that the switch from fermentative to oxidative phenotypes in cells can be characterized in terms of the glucose, lactate, oxygen and carbon dioxide concentrations. Results obtained for an exactly solvable toy model are fully recovered for a large scale reconstruction of human catabolism. Finally we argue that, in spite of the many approximations involved in the theory, available data for several human cell types are well described by the predicted phenotypic map of the problem.

  4. Functional Coding Variation in Recombinant Inbred Mouse Lines Reveals Novel Serotonin Transporter-Associated Phenotypes

    SciTech Connect

    Carneiro, Ana; Airey, David; Thompson, Brent; Zhu, C; Rinchik, Eugene M; Lu, Lu; Chesler, Elissa J; Erikson, Keith; Blakely, Randy

    2009-01-01

    The human serotonin (5-hydroxytryptamine, 5-HT) transporter (hSERT, SLC6A4) figures prominently in the etiology or treatment of many prevalent neurobehavioral disorders including anxiety, alcoholism, depression, autism and obsessive-compulsive disorder (OCD). Here we utilize naturally occurring polymorphisms in recombinant inbred (RI) lines to identify novel phenotypes associated with altered SERT function. The widely used mouse strain C57BL/6J, harbors a SERT haplotype defined by two nonsynonymous coding variants (Gly39 and Lys152 (GK)). At these positions, many other mouse lines, including DBA/2J, encode Glu39 and Arg152 (ER haplotype), assignments found also in hSERT. Synaptosomal 5-HT transport studies revealed reduced uptake associated with the GK variant. Heterologous expression studies confirmed a reduced SERT turnover rate for the GK variant. Experimental and in silico approaches using RI lines (C57Bl/6J X DBA/2J=BXD) identifies multiple anatomical, biochemical and behavioral phenotypes specifically impacted by GK/ER variation. Among our findings are multiple traits associated with anxiety and alcohol consumption, as well as of the control of dopamine (DA) signaling. Further bioinformatic analysis of BXD phenotypes, combined with biochemical evaluation of SERT knockout mice, nominates SERT-dependent 5-HT signaling as a major determinant of midbrain iron homeostasis that, in turn, dictates ironregulated DA phenotypes. Our studies provide a novel example of the power of coordinated in vitro, in vivo and in silico approaches using murine RI lines to elucidate and quantify the system-level impact of gene variation.

  5. The skeletal phenotype of "negritos" from the Andaman Islands and Philippines relative to global variation among hunter-gatherers.

    PubMed

    Stock, Jay T

    2013-01-01

    The "negrito hypothesis" suggests that populations of small-bodied foragers in South and Southeast Asia who share common phenotypic characteristics may also share a common, ancient origin. The key defining characteristics of the "negrito" phenotype, small body size, dark skin, and tightly curled hair, have been interpreted as linking these populations to sub-Saharan Africans. The underlying assumption of this interpretation is that the observed phenotypic similarities likely reflect shared ancestry rather than phenotypic convergence. Current genetic evidence is inconclusive, as it both demonstrates that negrito populations have genetic affinities with neighboring populations but also rare and ancient variation that suggests considerable isolation. This study investigates the skeletal phenotype of Andaman Islanders and Aeta foragers from the Philippines in the context of the phenotypic variation among other hunter-gatherers globally, to test whether they show a common, unique physique apart from small body size. Particular emphasis is placed on the comparison of negrito phenotypes to African, Asian, and Australian hunter-gatherer diversity to investigate phenotypic similarities to other populations globally. The results demonstrate that despite sharing small adult stature, the Andaman Islanders and Aeta show variation in body dimensions. In particular, the Andaman Islanders share a pattern of narrow bi-iliac breadth and short upper limbs with the Khoisan (Later Stone Age Southern Africans), whereas the Aeta and Efé show broader bi-iliac breadths relative to lower limb lengths. Although general similarities in size and proportions remain between the Andamanese and Aeta, differences in humero-femoral indices and arm length between these groups and the Efé demonstrate that there is not a generic "pygmy" phenotype. Our interpretations of negrito origins and adaptation must account for this phenotypic variation. PMID:24297221

  6. Epigenetic marks: regulators of livestock phenotypes and conceivable sources of missing variation in livestock improvement programs

    PubMed Central

    Ibeagha-Awemu, Eveline M.; Zhao, Xin

    2015-01-01

    Improvement in animal productivity has been achieved over the years through careful breeding and selection programs. Today, variations in the genome are gaining increasing importance in livestock improvement strategies. Genomic information alone, however, explains only a part of the phenotypic variance in traits. It is likely that a portion of the unaccounted variance is embedded in the epigenome. The epigenome encompasses epigenetic marks such as DNA methylation, histone tail modifications, chromatin remodeling, and other molecules that can transmit epigenetic information such as non-coding RNA species. Epigenetic factors respond to external or internal environmental cues such as nutrition, pathogens, and climate, and have the ability to change gene expression leading to emergence of specific phenotypes. Accumulating evidence shows that epigenetic marks influence gene expression and phenotypic outcome in livestock species. This review examines available evidence of the influence of epigenetic marks on livestock (cattle, sheep, goat, and pig) traits and discusses the potential for consideration of epigenetic markers in livestock improvement programs. However, epigenetic research activities on farm animal species are currently limited partly due to lack of recognition, funding and a global network of researchers. Therefore, considerable less attention has been given to epigenetic research in livestock species in comparison to extensive work in humans and model organisms. Elucidating therefore the epigenetic determinants of animal diseases and complex traits may represent one of the principal challenges to use epigenetic markers for further improvement of animal productivity. PMID:26442116

  7. Phenotypic Variation and Sexual Size Dimorphism in Dichroplus elongatus (Orthoptera: Acrididae).

    PubMed

    Rosetti, N; Remis, M I

    2015-08-01

    Patterns of body size evolution are of particular interest because body size can affect virtually all the physiological and life history traits of an organism. Sexual size dimorphism (SSD), a difference in body size between males and females, is a widespread phenomenon in insects. Much of the variation in SSD is genetically based and likely due to differential selection acting on males and females. The importance of environmental variables and evolutionary processes affecting phenotypeic variation in both sexes may be useful to gain insights into insect ecology and evolution. Dichroplus elongatus Giglio-Tos is a South American grasshopper widely distributed throughout Argentina, Uruguay, most of Chile, and southern Brazil. In this study, we analyzed 122 adult females of D. elongatus collected in eight natural populations from central-east Argentina. Females show large body size variation among the analyzed populations and this variation exhibits a strong relationship with fecundity. Our results have shown that larger females were more fecund than smaller ones. We found that ovariole number varied along a latitudinal gradient, with higher ovariole numbers in populations from warmer locations. A considerable female-biased SSD was detected. SSD for three analyzed morphometric traits scaled isometrically. However, SSD for thorax length displayed a considerable variation across the studied area, indicating a larger relative increase in female size than in male size in warmer environmental conditions. PMID:26314070

  8. Quantitative Genomics of 30 Complex Phenotypes in Wagyu x Angus F1 Progeny

    PubMed Central

    Zhang, Lifan; Michal, Jennifer J.; O'Fallon, James V.; Pan, Zengxiang; Gaskins, Charles T.; Reeves, Jerry J.; Busboom, Jan R.; Zhou, Xiang; Ding, Bo; Dodson, Michael V.; Jiang, Zhihua

    2012-01-01

    In the present study, a total of 91 genes involved in various pathways were investigated for their associations with six carcass traits and twenty-four fatty acid composition phenotypes in a Wagyu×Angus reference population, including 43 Wagyu bulls and their potential 791 F1 progeny. Of the 182 SNPs evaluated, 102 SNPs that were in Hardy-Weinberg equilibrium with minor allele frequencies (MAF>0.15) were selected for parentage assignment and association studies with these quantitative traits. The parentage assignment revealed that 40 of 43 Wagyu sires produced over 96.71% of the calves in the population. Linkage disequilibrium analysis identified 75 of 102 SNPs derived from 54 genes as tagged SNPs. After Bonferroni correction, single-marker analysis revealed a total of 113 significant associations between 44 genes and 29 phenotypes (adjusted P<0.05). Multiple-marker analysis confirmed single-gene associations for 10 traits, but revealed two-gene networks for 9 traits and three-gene networks for 8 traits. Particularly, we observed that TNF (tumor necrosis factor) gene is significantly associated with both beef marbling score (P=0.0016) and palmitic acid (C16:0) (P=0.0043), RCAN1 (regulator of calcineurin 1) with rib-eye area (P=0.0103), ASB3 (ankyrin repeat and SOCS box-containing 3) with backfat (P=0.0392), ABCA1 (ATP-binding cassette A1) with both palmitic acid (C16:0) (P=0.0025) and oleic acid (C18:1n9) (P=0.0114), SLC27A1(solute carrier family 27 A1) with oleic acid (C18:1n9) (P=0.0155), CRH (corticotropin releasing hormone) with both linolenic acid (OMEGA-3) (P=0.0200) and OMEGA 6:3 RATIO (P=0.0054), SLC27A2 (solute carrier family 27 A2) with both linoleic acid (OMEGA-6) (P=0.0121) and FAT (P=0.0333), GNG3 (guanine nucleotide binding protein gamma 3 with desaturase 9 (P=0.0115), and EFEMP1 (EGF containing fibulin-like extracellular matrix protein 1), PLTP (phospholipid transfer protein) and DSEL (dermatan sulfate epimerase-like) with conjugated linoleic acid (P=0.0042-0.0044), respectively, in the Wagyu x Angus F1 population. In addition, we observed an interesting phenomenon that crossbreeding of different breeds might change gene actions to dominant and overdominant modes, thus explaining the origin of heterosis. The present study confirmed that these important families or pathway-based genes are useful targets for improving meat quality traits and healthful beef products in cattle. PMID:22745575

  9. Phenotypic variation of Pseudomonas brassicacearum as a plant root-colonization strategy.

    PubMed

    Achouak, Wafa; Conrod, Sandrine; Cohen, Valérie; Heulin, Thierry

    2004-08-01

    Pseudomonas brassicacearum was isolated as a major root-colonizing population from Arabidopsis thaliana. The strain NFM421 of P. brassicacearum undergoes phenotypic variation during A. thaliana and Brassica napus root colonization in vitro as well as in soil, resulting in different colony appearance on agar surfaces. Bacteria forming translucent colonies (phase II cells) essentially were localized at the surface of young roots and root tips, whereas wild-type cells (phase I cells) were localized at the basal part of roots. The ability of phase II cells to spread and colonize new sites on root surface correlates with over-production of flagellin as evidenced by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of surface proteins and microsequencing. Moreover, phase II cells showed a higher ability to swim and to swarm on semisolid agar medium. Phase I and phase II cells of P. brassicacearum NFM421 were tagged genetically with green fluorescent protein and red fluorescent protein. Confocal scanning laser microscopy was used to localize phase II cells on secondary roots and root tips of A. thaliana, whereas phase I cells essentially were localized at the basal part of roots. These experiments were conducted in vitro and in soil. Phenotypic variation on plant roots is likely to be a colonization strategy that may explain the high colonization power of P. brassicacearum. PMID:15305608

  10. Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology

    E-print Network

    Oellrich, Anika; Gkoutos, Georgios V.; Hoehndorf, Robert; Rebholz-Schuhmann, Dietrich

    2012-09-21

    analyses, phenotype ontologies were created to standardize the terminology used in describing phenotypes, e.g. [5,6]. We are now facing the challenge to enable the translation of these species-specific standardized phenotypic information across various... -disease associations We used two community-wide established resources containing manually verified gene and disease related data: the Mouse Genome Informatics (MGI) [15] and the Online Mendelian Inheritance in Man (OMIM) [16] database. The MGI database integrates...

  11. Selective Sweep at a Quantitative Trait Locus in the Presence of Background Genetic Variation

    PubMed Central

    Chevin, Luis-Miguel; Hospital, Frédéric

    2008-01-01

    We model selection at a locus affecting a quantitative trait (QTL) in the presence of genetic variance due to other loci. The dynamics at the QTL are related to the initial genotypic value and to the background genetic variance of the trait, assuming that background genetic values are normally distributed, under three different forms of selection on the trait. Approximate dynamics are derived under the assumption of small mutation effect. For similar strengths of selection on the trait (i.e, gradient of directional selection ?) the way background variation affects the dynamics at the QTL critically depends on the shape of the fitness function. It generally causes the strength of selection on the QTL to decrease with time. The resulting neutral heterozygosity pattern resembles that of a selective sweep with a constant selection coefficient corresponding to the early conditions. The signature of selection may also be blurred by mutation and recombination in the later part of the sweep. We also study the race between the QTL and its genetic background toward a new optimum and find the conditions for a complete sweep. Overall, our results suggest that phenotypic traits exhibiting clear-cut molecular signatures of selection may represent a biased subset of all adaptive traits. PMID:18832353

  12. Natural variation in RPS2-mediated resistance among Arabidopsis accessions: correlation between gene expression profiles and phenotypic responses.

    PubMed

    Van Poecke, Remco M P; Sato, Masanao; Lenarz-Wyatt, Lisa; Weisberg, Sanford; Katagiri, Fumiaki

    2007-12-01

    Natural variation in gene expression (expression traits or e-traits) is increasingly used for the discovery of genes controlling traits. An important question is whether a particular e-trait is correlated with a phenotypic trait. Here, we examined the correlations between phenotypic traits and e-traits among 10 Arabidopsis thaliana accessions. We studied defense against Pseudomonas syringae pv tomato DC3000 (Pst), with a focus on resistance gene-mediated resistance triggered by the type III effector protein AvrRpt2. As phenotypic traits, we measured growth of the bacteria and extent of the hypersensitive response (HR) as measured by electrolyte leakage. Genetic variation among accessions affected growth of Pst both with (Pst avrRpt2) and without (Pst) the AvrRpt2 effector. Variation in HR was not correlated with variation in bacterial growth. We also collected gene expression profiles 6 h after mock and Pst avrRpt2 inoculation using a custom microarray. Clusters of genes whose expression levels are correlated with bacterial growth or electrolyte leakage were identified. Thus, we demonstrated that variation in gene expression profiles of Arabidopsis accessions collected at one time point under one experimental condition has the power to explain variation in phenotypic responses to pathogen attack. PMID:18083910

  13. Semi-quantitative and structural metabolic phenotyping by direct infusion ion trap mass spectrometry and its application in genetical metabolomics.

    PubMed

    Koulman, Albert; Cao, Mingshu; Faville, Marty; Lane, Geoff; Mace, Wade; Rasmussen, Susanne

    2009-08-01

    The identification of quantitative trait loci (QTL) for plant metabolites requires the quantitation of these metabolites across a large range of progeny. We developed a rapid metabolic profiling method using both untargeted and targeted direct infusion tandem mass spectrometry (DIMSMS) with a linear ion trap mass spectrometer yielding sufficient precision and accuracy for the quantification of a large number of metabolites in a high-throughput environment. The untargeted DIMSMS method uses top-down data-dependent fragmentation yielding MS(2) and MS(3) spectra. We have developed software tools to assess the structural homogeneity of the MS(2) and MS(3) spectra hence their utility for phenotyping and genetical metabolomics. In addition we used a targeted DIMS(MS) method for rapid quantitation of specific compounds. This method was compared with targeted LC/MS/MS methods for these compounds. The DIMSMS methods showed sufficient precision and accuracy for QTL discovery. We phenotyped 200 individual Lolium perenne genotypes from a mapping population harvested in two consecutive years. Computational and statistical analyses identified 246 nominal m/z bins with sufficient precision and homogeneity for QTL discovery. Comparison of the data for specific metabolites obtained by DIMSMS with the results from targeted LC/MS/MS analysis showed that quantitation by this metabolic profiling method is reasonably accurate. Of the top 100 MS(1) bins, 22 ions gave one or more reproducible QTL across the 2 years. PMID:19551846

  14. Human MAMLD1 Gene Variations Seem Not Sufficient to Explain a 46,XY DSD Phenotype.

    PubMed

    Camats, Núria; Fernández-Cancio, Mónica; Audí, Laura; Mullis, Primus E; Moreno, Francisca; González Casado, Isabel; López-Siguero, Juan Pedro; Corripio, Raquel; Bermúdez de la Vega, José Antonio; Blanco, José Antonio; Flück, Christa E

    2015-01-01

    MAMLD1 is thought to cause disordered sex development in 46,XY patients. But its role is controversial because some MAMLD1 variants are also detected in normal individuals, several MAMLD1 mutations have wild-type activity in functional tests, and the male Mamld1-knockout mouse has normal genitalia and reproduction. Our aim was to search for MAMLD1 variations in 108 46,XY patients with disordered sex development, and to test them functionally. We detected MAMDL1 variations and compared SNP frequencies in controls and patients. We tested MAMLD1 transcriptional activity on promoters involved in sex development and assessed the effect of MAMLD1 on androgen production. MAMLD1 expression in normal steroid-producing tissues and mutant MAMLD1 protein expression were also assessed. Nine MAMLD1 mutations (7 novel) were characterized. In vitro, most MAMLD1 variants acted similarly to wild type. Only the L210X mutation showed loss of function in all tests. We detected no effect of wild-type or MAMLD1 variants on CYP17A1 enzyme activity in our cell experiments, and Western blots revealed no significant differences for MAMLD1 protein expression. MAMLD1 was expressed in human adult testes and adrenals. In conclusion, our data support the notion that MAMLD1 sequence variations may not suffice to explain the phenotype in carriers and that MAMLD1 may also have a role in adult life. PMID:26580071

  15. Human MAMLD1 Gene Variations Seem Not Sufficient to Explain a 46,XY DSD Phenotype

    PubMed Central

    Audí, Laura; Mullis, Primus E.; Moreno, Francisca; González Casado, Isabel; López-Siguero, Juan Pedro; Corripio, Raquel; Bermúdez de la Vega, José Antonio; Blanco, José Antonio; Flück, Christa E.

    2015-01-01

    MAMLD1 is thought to cause disordered sex development in 46,XY patients. But its role is controversial because some MAMLD1 variants are also detected in normal individuals, several MAMLD1 mutations have wild-type activity in functional tests, and the male Mamld1-knockout mouse has normal genitalia and reproduction. Our aim was to search for MAMLD1 variations in 108 46,XY patients with disordered sex development, and to test them functionally. We detected MAMDL1 variations and compared SNP frequencies in controls and patients. We tested MAMLD1 transcriptional activity on promoters involved in sex development and assessed the effect of MAMLD1 on androgen production. MAMLD1 expression in normal steroid-producing tissues and mutant MAMLD1 protein expression were also assessed. Nine MAMLD1 mutations (7 novel) were characterized. In vitro, most MAMLD1 variants acted similarly to wild type. Only the L210X mutation showed loss of function in all tests. We detected no effect of wild-type or MAMLD1 variants on CYP17A1 enzyme activity in our cell experiments, and Western blots revealed no significant differences for MAMLD1 protein expression. MAMLD1 was expressed in human adult testes and adrenals. In conclusion, our data support the notion that MAMLD1 sequence variations may not suffice to explain the phenotype in carriers and that MAMLD1 may also have a role in adult life. PMID:26580071

  16. Variation at range margins across multiple spatial scales: environmental temperature, population genetics and metabolomic phenotype

    PubMed Central

    Kunin, William E.; Vergeer, Philippine; Kenta, Tanaka; Davey, Matthew P.; Burke, Terry; Ian Woodward, F.; Quick, Paul; Mannarelli, Maria-Elena; Watson-Haigh, Nathan S.; Butlin, Roger

    2009-01-01

    Range margins are spatially complex, with environmental, genetic and phenotypic variations occurring across a range of spatial scales. We examine variation in temperature, genes and metabolomic profiles within and between populations of the subalpine perennial plant Arabidopsis lyrata ssp. petraea from across its northwest European range. Our surveys cover a gradient of fragmentation from largely continuous populations in Iceland, through more fragmented Scandinavian populations, to increasingly widely scattered populations at the range margin in Scotland, Wales and Ireland. Temperature regimes vary substantially within some populations, but within-population variation represents a larger fraction of genetic and especially metabolomic variances. Both physical distance and temperature differences between sites are found to be associated with genetic profiles, but not metabolomic profiles, and no relationship was found between genetic and metabolomic population structures in any region. Genetic similarity between plants within populations is the highest in the fragmented populations at the range margin, but differentiation across space is the highest there as well, suggesting that regional patterns of genetic diversity may be scale dependent. PMID:19324821

  17. Phenotypic flexibility in passerine birds: seasonal variation in fuel storage, mobilization and transport.

    PubMed

    Liknes, Eric T; Guglielmo, Christopher G; Swanson, David L

    2014-08-01

    Winter acclimatization in small birds living in cold climates produces a winter phenotype characterized by upregulation of metabolic rates to meet enhanced thermoregulatory demands. We measured several key aspects of fuel storage, mobilization and transport in summer and winter to determine whether black-capped chickadees (Poecile atricapillus), white-breasted nuthatches (Sitta carolinensis), and house sparrows (Passer domesticus) seasonally modulate these attributes to meet enhanced winter thermoregulatory demands. In addition, we exposed birds to thermoneutral (control) and severe cold exposure treatments to determine whether acute cold exposure influenced fuel storage, mobilization or transport. Carcass lipid mass and pectoralis intramuscular lipid did not vary significantly between seasons or temperature treatments for any of the study species. Muscle glycogen varied significantly seasonally only for chickadee supracoracoideus and leg muscles, and did not vary among warm or cold treatments for any species. Pectoralis fatty acid binding protein (FABPc) was significantly elevated in winter for chickadees and nuthatches, but not for sparrows. Plasma metabolites showed little consistent variation in response to season or acute cold exposure. Thus, fuel storage and mobilization do not appear to be major targets of adjustment associated with seasonal metabolic flexibility in these species, but modulation of intracellular lipid transport by FABPc may be an important contributor to seasonal phenotypes in some species of small birds. PMID:24704472

  18. Integrating candidate gene and quantitative genetic approaches to understand variation in timing of breeding in wild tit populations.

    PubMed

    Liedvogel, Miriam; Cornwallis, Charlie K; Sheldon, Ben C

    2012-05-01

    Two commonly used techniques for estimating the effect of genes on traits in wild populations are the candidate gene approach and quantitative genetic analyses. However, whether these two approaches measure the same underlying processes remains unresolved. Here, we use these two methods to test whether they are alternative or complementary approaches to understanding genetic variation in the timing of reproduction - a key trait involved in adaptation to climate change - in wild tit populations. Our analyses of the candidate gene Clock show weak correlates with timing variables in blue tits, but no association in great tits, confirming earlier results. Quantitative genetic analyses revealed very low levels of both direct (female) and indirect (male) additive genetic variation in timing traits for both species, in contrast to previous studies on these traits, and much lower than generally assumed. Hence, neither method suggests strong genetic effects on the timing of breeding in birds, and further work should seek to assess the generality of these conclusions. We discuss how differences in the genetic control of traits, species life-history and confounding environmental variables may determine how useful integrating these two techniques is to understand the phenotypic variation in wild populations. PMID:22409177

  19. Quantitative multi-parametric evaluation of centrosome declustering drugs: centrosome amplification, mitotic phenotype, cell cycle and death

    PubMed Central

    Ogden, A; Cheng, A; Rida, P C G; Pannu, V; Osan, R; Clewley, R; Aneja, R

    2014-01-01

    Unlike normal cells, cancer cells contain amplified centrosomes and rely on centrosome clustering mechanisms to form a pseudobipolar spindle that circumvents potentially fatal spindle multipolarity (MP). Centrosome clustering also promotes low-grade chromosome missegregation, which can drive malignant transformation and tumor progression. Putative ‘centrosome declustering drugs' represent a cancer cell-specific class of chemotherapeutics that produces a common phenotype of centrosome declustering and spindle MP. However, differences between individual agents in terms of efficacy and phenotypic nuances remain unexplored. Herein, we have developed a conceptual framework for the quantitative evaluation of centrosome declustering drugs by investigating their impact on centrosomes, clustering, spindle polarity, cell cycle arrest, and death in various cancer cell lines at multiple drug concentrations over time. Surprisingly, all centrosome declustering drugs evaluated in our study were also centrosome-amplifying drugs to varying extents. Notably, all declustering drugs induced spindle MP, and the peak extent of MP positively correlated with the induction of hypodiploid DNA-containing cells. Our data suggest acentriolar spindle pole amplification as a hitherto undescribed activity of some declustering drugs, resulting in spindle MP in cells that may not have amplified centrosomes. In general, declustering drugs were more toxic to cancer cell lines than non-transformed ones, with some exceptions. Through a comprehensive description and quantitative analysis of numerous phenotypes induced by declustering drugs, we propose a novel framework for the assessment of putative centrosome declustering drugs and describe cellular characteristics that may enhance susceptibility to them. PMID:24787016

  20. Patterns of quantitative genetic variation in multiple dimensions.

    PubMed

    Kirkpatrick, Mark

    2009-06-01

    A fundamental question for both evolutionary biologists and breeders is the extent to which genetic correlations limit the ability of populations to respond to selection. Here I view this topic from three perspectives. First, I propose several nondimensional statistics to quantify the genetic variation present in a suite of traits and to describe the extent to which correlations limit their selection response. A review of five data sets suggests that the total variation differs substantially between populations. In all cases analyzed, however, the "effective number of dimensions" is less than two: more than half of the total genetic variation is explained by a single combination of traits. Second, I consider how patterns of variation affect the average evolutionary response to selection in a random direction. When genetic variation lies in a small number of dimensions but there are a large number of traits under selection, then the average selection response will be reduced substantially from its potential maximum. Third, I discuss how a low genetic correlation between male fitness and female fitness limits the ability of populations to adapt. Data from two recent studies of natural populations suggest this correlation can diminish or even erase any genetic benefit to mate choice. Together these results suggest that adaptation (in natural populations) and genetic improvement (in domesticated populations) may often be as much constrained by patterns of genetic correlation as by the overall amount of genetic variation. PMID:18695991

  1. Temporal patterns of genetic and phenotypic variation in the epidemiologically important drone fly, Eristalis tenax.

    PubMed

    Francuski, Lj; Mati?, I; Ludoški, J; Milankov, V

    2011-06-01

    Eristalis tenax L. (Diptera: Syrphidae) is commonly known as the drone fly (adult) or rat-tailed maggot (immature). Both adults and immature stages are identified as potential mechanical vectors of mycobacterial pathogens, and early-stage maggots cause accidental myiasis. We compared four samples from Mount Fruška Gora, Serbia, with the aim of obtaining insights into the temporal variations and sexual dimorphism in the species. This integrative approach was based on allozyme loci, morphometric wing parameters (shape and size) and abdominal colour patterns. Consistent sexual dimorphism was observed, indicating that male specimens had lighter abdomens and smaller and narrower wings than females. The distribution of genetic diversity at polymorphic loci indicated genetic divergence among collection dates. Landmark-based geometric morphometrics revealed, contrary to the lack of divergence in wing size, significant wing shape variation throughout the year. In addition, temporal changes in the frequencies of the abdominal patterns observed are likely to relate to the biology of the species and ecological factors in the locality. Hence, the present study expands our knowledge of the genetic diversity and phenotypic plasticity of E. tenax. The quantification of such variability represents a step towards the evaluation of the adaptive potential of this species of medical and epidemiological importance. PMID:21414022

  2. Characterization of phenotypic variation for dermo resistance among selectively-bred families of the Eastern oyster, Crassostrea virginica

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dermo disease impacts nearly every region where oysters are cultured in the Eastern U.S. and is a significant concern to industry stakeholders. Efforts to breed for Dermo resistance in the Eastern Oyster have had modest success, yet the range of existing phenotypic variation with respect to Dermo r...

  3. Assessing the extent of phenotypic variation for dermo resistance among selectively-bred families of the Eastern Oyster, Crassostrea virginica

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dermo disease impacts nearly every region where oysters are cultured in the Eastern U.S. and is a significant concern to industry stakeholders. Efforts to breed for Dermo resistance in the Eastern Oyster have had modest success, yet the range of existing phenotypic variation with respect to Dermo ...

  4. A Quantitative Investigation of Stakeholder Variation in Training Program Evaluation.

    ERIC Educational Resources Information Center

    Michalski, Greg V.

    A survey was conducted to investigate variation in stakeholder perceptions of training results and evaluation within the context of a high-technology product development firm (the case organization). A scannable questionnaire survey booklet was developed and scanned data were exported and analyzed. Based on an achieved sample of 280 (70% response…

  5. From phenotypes to causal sequences: using genome wide association studies to dissect the sequence basis for variation of plant development.

    PubMed

    Ogura, Takehiko; Busch, Wolfgang

    2015-02-01

    Tremendous natural variation of growth and development exists within species. Uncovering the molecular mechanisms that tune growth and development promises to shed light on a broad set of biological issues including genotype to phenotype relations, regulatory mechanisms of biological processes and evolutionary questions. Recent progress in sequencing and data processing capabilities has enabled Genome Wide Association Studies (GWASs) to identify DNA sequence polymorphisms that underlie the variation of biological traits. In the last years, GWASs have proven powerful in revealing the complex genetic bases of many phenotypes in various plant species. Here we highlight successful recent GWASs that uncovered mechanistic and sequence bases of trait variation related to plant growth and development and discuss important considerations for conducting successful GWASs. PMID:25449733

  6. Localized versus generalist phenotypes in a broadly distributed tropical mammal: how is intraspecific variation distributed across disparate environments?

    PubMed Central

    2013-01-01

    Background The extent of phenotypic differentiation in response to local environmental conditions is a key component of species adaptation and persistence. Understanding the structuring of phenotypic diversity in response to local environmental pressures can provide important insights into species evolutionary dynamics and responses to environmental change. This work examines the influence of steep environmental gradients on intraspecific phenotypic variation and tests two hypotheses about how the tropical soft grass mouse, Akodon mollis (Cricetidae, Rodentia), contends with the disparate environmental conditions encompassed by its broad distribution. Specifically, we test if the species expresses a geographically unstructured, or generalist, phenotype throughout its range or if it shows geographically localized morphological differentiation across disparate environments. Results Using geometric morphometric and ecomorphological analyses of skull shape variation we found that despite distinct environmental conditions, geographically structured morphological variation is limited, with the notable exception of a distinct morphological disjunction at the high-elevation forest-grassland transition in the southern portion of A. mollis distribution. Based on genetic analyses, geographic isolation alone does not explain this localized phenotype, given that similar levels of genetic differentiation were also observed among individuals inhabiting other ecosystems that are nonetheless not distinct morphologically. Conclusions Instead of phenotypic specialization across environments in these tropical mountains, there was limited differentiation of skull shape and size across the broad range of A. mollis, with the exception of individuals from the puna, the highest-elevation ecosystem. The high morphological variance among individuals, together with a weak association with local environmental conditions, not only highlights the flexibility of A. mollis’ skull, but also highlights the need for further study to understand what maintains the observed morphological patterns. The work also indicates that mechanisms other than processes linked to local ecological specialization as a driver of diversification may contribute to the high diversity of this tropical region. PMID:23899319

  7. Consistency and variation in phenotypic selection exerted by a community of seed predators.

    PubMed

    Benkman, Craig W; Smith, Julie W; Maier, Monika; Hansen, Leif; Talluto, Matt V

    2013-01-01

    Phenotypic selection that is sustained over time underlies both anagenesis and cladogenesis, but the conditions that lead to such selection and what causes variation in selection are not well known. We measured the selection exerted by three species of predispersal seed predators of lodgepole pine (Pinus contorta latifolia) in the South Hills, Idaho, and found that net selection on different cone and seed traits exerted by red crossbills (Loxia curvirostra) and cone borer moths (Eucosma recissoriana) over 10 years of seed crops was similar to that measured in another mountain range. We also found that the strength of selection increased as seed predation increased, which provides a mechanism for the correlation between the escalation of seed defenses and the density of seed predators. Red crossbills consume the most seeds and selection they exert accounts for much of the selection experienced by lodgepole pine, providing additional support for a coevolutionary arms race between crossbills and lodgepole pine in the South Hills. The third seed predator, hairy woodpeckers (Picoides villosus), consumed less than one-sixth as many seeds as crossbills. Across the northern Rocky Mountains, woodpecker abundance and therefore selective impact appears limited by the elevated seed defenses of lodgepole pine. PMID:23289569

  8. Genomic Analysis of Natural Selection and Phenotypic Variation in High-Altitude Mongolians

    PubMed Central

    Watkins, W. Scott; Witherspoon, David J.; Wu, Wilfred; Qin, Ga; Huff, Chad D.; Jorde, Lynn B.; Ge, Ri-Li

    2013-01-01

    Deedu (DU) Mongolians, who migrated from the Mongolian steppes to the Qinghai-Tibetan Plateau approximately 500 years ago, are challenged by environmental conditions similar to native Tibetan highlanders. Identification of adaptive genetic factors in this population could provide insight into coordinated physiological responses to this environment. Here we examine genomic and phenotypic variation in this unique population and present the first complete analysis of a Mongolian whole-genome sequence. High-density SNP array data demonstrate that DU Mongolians share genetic ancestry with other Mongolian as well as Tibetan populations, specifically in genomic regions related with adaptation to high altitude. Several selection candidate genes identified in DU Mongolians are shared with other Asian groups (e.g., EDAR), neighboring Tibetan populations (including high-altitude candidates EPAS1, PKLR, and CYP2E1), as well as genes previously hypothesized to be associated with metabolic adaptation (e.g., PPARG). Hemoglobin concentration, a trait associated with high-altitude adaptation in Tibetans, is at an intermediate level in DU Mongolians compared to Tibetans and Han Chinese at comparable altitude. Whole-genome sequence from a DU Mongolian (Tianjiao1) shows that about 2% of the genomic variants, including more than 300 protein-coding changes, are specific to this individual. Our analyses of DU Mongolians and the first Mongolian genome provide valuable insight into genetic adaptation to extreme environments. PMID:23874230

  9. Phenotypic variation in metamorphosis and paedomorphosis in the salamander Ambystoma talpoideum

    SciTech Connect

    Semlitsch, R.D.; Gibbons, J.W.

    1985-08-01

    Phenotypic variation in metamorphosis and paedomorphosis in the salamander Ambystoma talpoideum was examined to determine its environmental or genetic basis. Eight artificial ponds were maintained, four at each of two environmental treatments: constant water level, to simulate fish-free permanent breeding ponds, and gradual drying out, to simulate temporary breeding ponds. Two populations of salamanders were used, derived from two breeding ponds having different frequencies of paedomorphosis. The water level in the drying treatment was lowered during the last 10 wk of the experimental period with no apparent differences in water chemistry parameters between treatments and only a slight change in water temperature during the last 2 wk. The effects of water level were potentially confounded by those of water temperature, density of larvae, and amount food. Population differences in the frequency of metamorphosis and paedomorphosis could potentially represent genetic differences resulting from the different selective regimes that individuals encounter in breeding ponds varying in drying frequency. 35 references, 3 figures, 4 tables.

  10. Speciation, Phenotypic Variation and Plasticity: What Can Endocrine Disruptors Tell Us?

    PubMed Central

    Ayala-García, Braulio; López-Santibáñez Guevara, Marta; Marcos-Camacho, Lluvia I.; Fuentes-Farías, Alma L.; Meléndez-Herrera, Esperanza; Gutiérrez-Ospina, Gabriel

    2013-01-01

    Phenotype variability, phenotypic plasticity, and the inheritance of phenotypic traits constitute the fundamental ground of processes such as individuation, individual and species adaptation and ultimately speciation. Even though traditional evolutionary thinking relies on genetic mutations as the main source of intra- and interspecies phenotypic variability, recent studies suggest that the epigenetic modulation of gene transcription and translation, epigenetic memory, and epigenetic inheritance are by far the most frequent reliable sources of transgenerational variability among viable individuals within and across organismal species. Therefore, individuation and speciation should be considered as nonmutational epigenetic phenomena. PMID:23762055

  11. Phenotypic Variation Is Almost Entirely Independent of the Host-Pathogen Relationship in Clinical Isolates of S. aureus

    PubMed Central

    Land, Adrian D.; Hogan, Patrick; Fritz, Stephanie; Levin, Petra Anne

    2015-01-01

    Background A key feature of Staphylococcus aureus biology is its ability to switch from an apparently benign colonizer of ~30% of the population to a cutaneous pathogen, to a deadly invasive pathogen. Little is known about the mechanisms driving this transition or the propensity of different S. aureus strains to engender different types of host-pathogen interactions. At the same time, significant weight has been given to the role of specific in vitro phenotypes in S. aureus virulence. Biofilm formation, hemolysis and pigment formation have all been associated with virulence in mice. Design To determine if there is a correlation between in vitro phenotype and the three types of host-pathogen relationships commonly exhibited by S. aureus in the context of its natural human host, we assayed 300 clinical isolates for phenotypes implicated in virulence including hemolysis, sensitivity to autolysis, and biofilm formation. For comparative purposes, we also assayed phenotype in 9 domesticated S. aureus strains routinely used for analysis of virulence determinants in laboratory settings. Results Strikingly, the clinical strains exhibited significant phenotypic uniformity in each of the assays evaluated in this study. One exception was a small, but significant, correlation between an increased propensity for biofilm formation and isolation from skin and soft tissue infections (SSTIs). In contrast, we observed a high degree of phenotypic variation between common laboratory strains that exhibit virulence in mouse models. These data suggest the existence of significant evolutionary pressure on the S. aureus genome and highlight a role for host factors as a strong determinant of the host-pathogen relationship. In addition, the high degree of variation between laboratory strains emphasizes the need for caution when applying data obtained in one lab strain to the analysis of another. PMID:26098551

  12. Phenotypic Variation in Fitness Traits of a Managed Solitary Bee, Osmia ribifloris (Hymenoptera: Megachilidae).

    PubMed

    Sampson, B J; Rinehart, T A; Kirker, G T; Stringer, S J; Werle, C T

    2015-12-01

    We investigated fitness in natural populations of a managed solitary bee Osmia ribifloris Cockerell (Hymenoptera: Megachilidae) from sites separated from 400 to 2,700 km. Parental wild bees originated in central Texas (TX), central-northern Utah (UT), and central California (CA). They were then intercrossed and raised inside a mesh enclosure in southern Mississippi (MS). Females from all possible mated pairs of O. ribifloris produced F1 broods with 30-40% female cocoons and outcrossed progeny were 30% heavier. Mitochondrial (COI) genomes of the four populations revealed three distinct clades, a TX-CA clade, a UT clade, and an MS clade, the latter (MS) representing captive progeny of CA and UT bees. Although classified as separate subspecies, TX and CA populations from 30° N to 38° N latitude shared 98% similarity in COI genomes and the greatest brood biomass per nest straw (600- to 700-mg brood). Thus, TX and CA bees show greater adaptation for southern U.S. sites. In contrast, UT-sourced bees were more distantly related to TX and CA bees and also produced ?50% fewer brood. These results, taken together, confirm that adult O. ribifloris from all trap-nest sites are genetically compatible, but some phenotypic variation exists that could affect this species performance as a commercial blueberry pollinator. Males, their sperm, or perhaps a substance in their sperm helped stabilize our captive bee population by promoting legitimate nesting over nest usurpation. Otherwise, without insemination, 50% fewer females nested (they nested 14 d late) and 20% usurped nests, killing 33-67% of brood in affected nests. PMID:26470379

  13. Identification of genes related to the phenotypic variations of a synthesized Paulownia (Paulownia tomentosa×Paulownia fortunei) autotetraploid.

    PubMed

    Li, Yongsheng; Fan, Guoqiang; Dong, Yanpeng; Zhao, Zhenli; Deng, Minjie; Cao, Xibing; Xu, Enkai; Niu, Suyan

    2014-12-15

    Paulownia is a fast-growing deciduous tree native to China. It has great economic importance for the pulp and paper industries, as well as ecological prominence in forest ecosystems. Paulownia is of much interest to plant breeder keen to explore new plant varieties by selecting on the basis of phenotype. A newly synthesized autotetraploid Paulownia exhibited advanced characteristics, such as greater yield, and higher resistance than the diploid tree. However, tissue-specific transcriptome and genomic data in public databases are not sufficient to understand the molecular mechanisms associated with genome duplication. To evaluate the effects of genome duplication on the phenotypic variations in Paulownia tomentosa×Paulownia fortunei, the transcriptomes of the autotetraploid and diploid Paulownia were compared. Using Illumina sequencing technology, a total of 82,934 All-unigenes with a mean length of 1109 bp were assembled. The data revealed numerous differences in gene expression between the two transcriptomes, including 718 up-regulated and 667 down-regulated differentially expressed genes between the two Paulownia trees. An analysis of the pathway and gene annotations revealed that genes involved in nucleotide sugar metabolism in plant cell walls were down-regulated, and genes involved in the light signal pathway and the biosynthesis of structural polymers were up-regulated in autotetraploid Paulownia. The differentially expressed genes may contribute to the observed phenotypic variations between diploid and autotetraploid Paulownia. These results provide a significant resource for understanding the variations in Paulownia polyploidization and will benefit future breeding work. PMID:25300252

  14. Quantitative Analysis of Adventitious Root Growth Phenotypes in Carnation Stem Cuttings.

    PubMed

    Birlanga, Virginia; Villanova, Joan; Cano, Antonio; Cano, Emilio A; Acosta, Manuel; Pérez-Pérez, José Manuel

    2015-01-01

    Carnation is one of the most important species on the worldwide market of cut flowers. Commercial carnation cultivars are vegetatively propagated from terminal stem cuttings that undergo a rooting and acclimation process. For some of the new cultivars that are being developed by ornamental breeders, poor adventitious root (AR) formation limits its commercial scaling-up, due to a significant increase in the production costs. We have initiated a genetical-genomics approach to determine the molecular basis of the differences found between carnation cultivars during adventitious rooting. The detailed characterization of AR formation in several carnation cultivars differing in their rooting losses has been performed (i) during commercial production at a breeders' rooting station and (ii) on a defined media in a controlled environment. Our study reveals the phenotypic signatures that distinguishes the bad-rooting cultivars and provides the appropriate set-up for the molecular identification of the genes involved in AR development in this species. PMID:26230608

  15. Quantitative Analysis of Adventitious Root Growth Phenotypes in Carnation Stem Cuttings

    PubMed Central

    Birlanga, Virginia; Villanova, Joan; Cano, Antonio; Cano, Emilio A.; Acosta, Manuel; Pérez-Pérez, José Manuel

    2015-01-01

    Carnation is one of the most important species on the worldwide market of cut flowers. Commercial carnation cultivars are vegetatively propagated from terminal stem cuttings that undergo a rooting and acclimation process. For some of the new cultivars that are being developed by ornamental breeders, poor adventitious root (AR) formation limits its commercial scaling-up, due to a significant increase in the production costs. We have initiated a genetical-genomics approach to determine the molecular basis of the differences found between carnation cultivars during adventitious rooting. The detailed characterization of AR formation in several carnation cultivars differing in their rooting losses has been performed (i) during commercial production at a breeders’ rooting station and (ii) on a defined media in a controlled environment. Our study reveals the phenotypic signatures that distinguishes the bad-rooting cultivars and provides the appropriate set-up for the molecular identification of the genes involved in AR development in this species. PMID:26230608

  16. Quadratic Optimization to Identify Highly Heritable Quantitative Traits from Complex Phenotypic Features

    E-print Network

    Chandy, John A.

    Features Jiangwen Sun Department of Computer Science and Engineering University of Connecticut Storrs, CT, USA javon@engr.uconn.edu Jinbo Bi Department of Computer Science and Engineering University of Pennsylvania Philadelphia, PA, USA kranzler_h@mail.trc.upenn.edu ABSTRACT Identifying genetic variation

  17. Genetic variation in the oxytocin receptor gene is associated with a social phenotype in autism spectrum disorders.

    PubMed

    Harrison, Ashley J; Gamsiz, Ece D; Berkowitz, Isaac C; Nagpal, Shailender; Jerskey, Beth A

    2015-12-01

    Oxytocin regulates social behavior in animal models. Research supports an association between genetic variation in the oxytocin receptor gene (OXTR) and autism spectrum disorders (ASD). In this study, we examine the association between the OXTR gene and a specific social phenotype within ASD. This genotype-phenotype investigation may provide insight into how OXTR conveys risk for social impairment. The current study investigated 10 SNPS in the OXTR gene that have been previously shown to be associated with ASD. We examine the association of these SNPs with both a social phenotype and a repetitive behavior phenotype comprised of behaviors commonly impaired in ASD in the Simons simplex collection (SSC). Using a large sample to examine the association between OXTR and ASD (n?=?range: 485-1002), we find evidence to support a relation between two OXTR SNPs and the examined social phenotype among children diagnosed with ASD. Greater impairment on the social responsiveness scale standardized total score and on several subdomains was observed among individuals with one or more copies of the minor frequency allele in both rs7632287 and rs237884. Linkage disequilibrium (LD) mapping suggests that these two SNPs are in LD within and overlapping the 3' untranslated region (3'-UTR) of the OXTR gene. These two SNPs were also associated with greater impairment on the repetitive behavior scale. Results of this study indicate that social impairment and repetitive behaviors in ASD are associated with genomic variation in the 3'UTR of the OXTR gene. These variants may be linked to an allele that alters stability of the mRNA message although further work is necessary to test this hypothesis. © 2015 Wiley Periodicals, Inc. PMID:26365303

  18. Quantitative variation as a tool for detecting human-induced impacts on genetic diversity

    E-print Network

    Carvajal-Rodríguez, Antonio

    Quantitative variation as a tool for detecting human-induced impacts on genetic diversity A some human-induced environmental or genetic impacts on diversity, both at intra and interpopulation extinction or after recolonisation. Genetic diversity is overwhelmingly monitored by neutral molec- ular

  19. Identification of Genomic Regions Associated with Phenotypic Variation between Dog Breeds using Selection Mapping

    E-print Network

    Vaysse, Amaury

    The extraordinary phenotypic diversity of dog breeds has been sculpted by a unique population history accompanied by selection for novel and desirable traits. Here we perform a comprehensive analysis using multiple test ...

  20. Co-localization of quantitative trait loci regulating resistance to Salmonella typhimurium infection and specific antibody production phenotypes.

    PubMed

    Trezena, Aryene Goes; Souza, Carla Martins; Borrego, Andrea; Massa, Solange; Siqueira, Maria; De Franco, Marcelo; Sant'Anna, Osvaldo Augusto

    2002-11-01

    Salmonella enterica serotype typhimurium is a facultative intracellular bacteria that induces systemic infection in mice. Resistance to this pathogen is under polygenic control in which Nramp1 is the major gene involved. Lines of mice obtained by selective breeding for high (HIII) or low (LIII) antibody response to flagellar antigens of salmonellae showed significant susceptibility differences, although both the lines display Nramp1(R) alleles. The HIII line was extremely susceptible to infection, while the LIII line was resistant. In order to examine the cellular and genetic mechanisms involved in this distinct pattern of resistance, HIII and LIII mice were analyzed for IFNgamma and IL4 production and screened for quantitative trait loci involved in S. typhimurium infection, using several polymorphic microsatellites. In the present work, HIII mice showed an IFNgamma downregulation in the early phase of infection when compared with LIII animals. No interline differences in IL4 production were verified. The loci screening was performed on immunized F2 intercrosses obtained from HIII and LIII mice. Three antibody-controlling chromosomal regions were coincident, and another was mapped near one of the four loci known to affect susceptibility to S. typhimurium. These results indicate a major role of IFNgamma in our model, and suggest the co-localization of quantitative trait loci modulating both infection and antibody production phenotypes. PMID:12475631

  1. Phenotypic Variation across Chromosomal Hybrid Zones of the Common Shrew (Sorex araneus) Indicates Reduced Gene Flow

    PubMed Central

    Polly, P. David; Polyakov, Andrei V.; Ilyashenko, Vadim B.; Onischenko, Sergei S.; White, Thomas A.; Shchipanov, Nikolay A.; Bulatova, Nina S.; Pavlova, Svetlana V.; Borodin, Pavel M.; Searle, Jeremy B.

    2013-01-01

    Sorex araneus, the Common shrew, is a species with more than 70 karyotypic races, many of which form parapatric hybrid zones, making it a model for studying chromosomal speciation. Hybrids between races have reduced fitness, but microsatellite markers have demonstrated considerable gene flow between them, calling into question whether the chromosomal barriers actually do contribute to genetic divergence. We studied phenotypic clines across two hybrid zones with especially complex heterozygotes. Hybrids between the Novosibirsk and Tomsk races produce chains of nine and three chromosomes at meiosis, and hybrids between the Moscow and Seliger races produce chains of eleven. Our goal was to determine whether phenotypes show evidence of reduced gene flow at hybrid zones. We used maximum likelihood to fit tanh cline models to geometric shape data and found that phenotypic clines in skulls and mandibles across these zones had similar centers and widths as chromosomal clines. The amount of phenotypic differentiation across the zones is greater than expected if it were dissipating due to unrestricted gene flow given the amount of time since contact, but it is less than expected to have accumulated from drift during allopatric separation in glacial refugia. Only if heritability is very low, Ne very high, and the time spent in allopatry very short, will the differences we observe be large enough to match the expectation of drift. Our results therefore suggest that phenotypic differentiation has been lost through gene flow since post-glacial secondary contact, but not as quickly as would be expected if there was free gene flow across the hybrid zones. The chromosomal tension zones are confirmed to be partial barriers that prevent differentiated races from becoming phenotypically homogenous. PMID:23874420

  2. Variation in Plasmodium falciparum erythrocyte invasion phenotypes and merozoite ligand gene expression across different populations in areas of malaria endemicity.

    PubMed

    Bowyer, Paul W; Stewart, Lindsay B; Aspeling-Jones, Harvey; Mensah-Brown, Henrietta E; Ahouidi, Ambroise D; Amambua-Ngwa, Alfred; Awandare, Gordon A; Conway, David J

    2015-06-01

    Plasmodium falciparum merozoites use diverse alternative erythrocyte receptors for invasion and variably express cognate ligands encoded by the erythrocyte binding antigen (eba) and reticulocyte binding-like homologue (Rh) gene families. Previous analyses conducted on parasites from single populations in areas of endemicity revealed a wide spectrum of invasion phenotypes and expression profiles, although comparisons across studies have been limited by the use of different protocols. For direct comparisons within and among populations, clinical isolates from three different West African sites of endemicity (in Ghana, Guinea, and Senegal) were cryopreserved and cultured ex vivo after thawing in a single laboratory to assay invasion of target erythrocytes pretreated with enzymes affecting receptor subsets. Complete invasion assay data from 67 isolates showed no differences among the populations in the broad range of phenotypes measured by neuraminidase treatment (overall mean, 40.6% inhibition) or trypsin treatment (overall mean, 83.3% inhibition). The effects of chymotrypsin treatment (overall mean, 79.2% inhibition) showed heterogeneity across populations (Kruskall-Wallis P = 0.023), although the full phenotypic range was seen in each. Schizont-stage transcript data for a panel of 8 invasion ligand genes (eba175, eba140, eba181, Rh1, Rh2a, Rh2b, Rh4, and Rh5) were obtained for 37 isolates, showing similar ranges of variation in each population except that eba175 levels tended to be higher in parasites from Ghana than in those from Senegal (whereas levels of eba181 and Rh2b were lower in parasites from Ghana). The broad diversity in invasion phenotypes and gene expression seen within each local population, with minimal differences among them, is consistent with a hypothesis of immune selection maintaining parasite variation. PMID:25870227

  3. Quantitative Fundus Autofluorescence and Optical Coherence Tomography in PRPH2/RDS- and ABCA4-Associated Disease Exhibiting Phenotypic Overlap

    PubMed Central

    Duncker, Tobias; Tsang, Stephen H.; Woods, Russell L.; Lee, Winston; Zernant, Jana; Allikmets, Rando; Delori, François C.; Sparrow, Janet R.

    2015-01-01

    Purpose. To assess whether quantitative fundus autofluorescence (qAF), a measure of RPE lipofuscin, and spectral-domain optical coherence tomography (SD-OCT) can aid in the differentiation of patients with fundus features that could either be related to ABCA4 mutations or be part of the phenotypic spectrum of pattern dystrophies. Methods. Autofluorescence images (30°, 488-nm excitation) from 39 patients (67 eyes) were acquired with a confocal scanning laser ophthalmoscope equipped with an internal fluorescent reference and were quantified as previously described. In addition, horizontal SD-OCT images through the fovea were obtained. Patients were screened for ABCA4 and PRPH2/RDS mutations. Results. ABCA4 mutations were identified in 19 patients (mean age, 37 ± 12 years) and PRPH2/RDS mutations in 8 patients (mean age, 48 ± 13 years); no known ABCA4 or PRPH2/RDS mutations were found in 12 patients (mean age, 48 ± 9 years). Differentiation of the groups using phenotypic SD-OCT and AF features (e.g., peripapillary sparing, foveal sparing) was not reliable. However, patients with ABCA4 mutations could be discriminated reasonably well from other patients when qAF values were corrected for age and race. In general, ABCA4 patients had higher qAF values than PRPH2/RDS patients, while most patients without mutations in PRPH2/RDS or ABCA4 had qAF levels within the normal range. Conclusions. The high qAF levels of ABCA4-positive patients are a hallmark of ABCA4-related disease. The reason for high qAF among many PRPH2/RDS-positive patients is not known; higher RPE lipofuscin accumulation may be a primary or secondary effect of the PRPH2/RDS mutation. PMID:26024099

  4. Fleece variation in alpaca (Vicugna pacos): a two-locus model for the Suri/Huacaya phenotype

    PubMed Central

    2010-01-01

    Background Genetic improvement of fibre-producing animal species has often induced transition from double coated to single coated fleece, accompanied by dramatic changes in skin follicles and hair composition, likely implying variation at multiple loci. Huacaya, the more common fleece phenotype in alpaca (Vicugna pacos), is characterized by a thick dense coat growing perpendicularly from the body, whereas the alternative rare and more prized single-coated Suri phenotype is distinguished by long silky fibre that grows parallel to the body and hangs in separate, distinctive pencil locks. A single-locus genetic model has been proposed for the Suri-Huacaya phenotype, where Huacaya is recessive. Results Two reciprocal experimental test-crosses (Suri × Huacaya) were carried out, involving a total of 17 unrelated males and 149 unrelated females. An additional dataset of 587 offspring of Suri × Suri crosses was analyzed. Segregation ratios, population genotype frequencies, and/or recombination fraction under different genetic models were estimated by maximum likelihood. The single locus model for the Suri/Huacaya phenotype was rejected. In addition, we present two unexpected observations: 1) a large proportion (about 3/4) of the Suri animals are segregating (with at least one Huacaya offspring), even in breeding conditions where the Huacaya trait would have been almost eliminated; 2) a model with two different values of the segregation ratio fit the data significantly better than a model with a single parameter. Conclusions The data support a genetic model in which two linked loci must simultaneously be homozygous for recessive alleles in order to produce the Huacaya phenotype. The estimated recombination rate between these loci was 0.099 (95% C.L. = 0.029-0.204). Our genetic analysis may be useful for other species whose breeding system produces mainly half-sib families. PMID:20646304

  5. Quantitative measurement of phase variation amplitude of ultrasonic diffraction grating based on diffraction spectral analysis

    SciTech Connect

    Pan, Meiyan Zeng, Yingzhi; Huang, Zuohua

    2014-09-15

    A new method based on diffraction spectral analysis is proposed for the quantitative measurement of the phase variation amplitude of an ultrasonic diffraction grating. For a traveling wave, the phase variation amplitude of the grating depends on the intensity of the zeroth- and first-order diffraction waves. By contrast, for a standing wave, this amplitude depends on the intensity of the zeroth-, first-, and second-order diffraction waves. The proposed method is verified experimentally. The measured phase variation amplitude ranges from 0 to 2?, with a relative error of approximately 5%. A nearly linear relation exists between the phase variation amplitude and driving voltage. Our proposed method can also be applied to ordinary sinusoidal phase grating.

  6. Clonal Expansion of the Pseudogymnoascus destructans Genotype in North America Is Accompanied by Significant Variation in Phenotypic Expression

    PubMed Central

    Khankhet, Jordan; Vanderwolf, Karen J.; McAlpine, Donald F.; McBurney, Scott; Overy, David P.; Slavic, Durda; Xu, Jianping

    2014-01-01

    Pseudogymnoascus destructans is the causative agent of an emerging infectious disease that threatens populations of several North American bat species. The fungal disease was first observed in 2006 and has since caused the death of nearly six million bats. The disease, commonly known as white-nose syndrome, is characterized by a cutaneous infection with P. destructans causing erosions and ulcers in the skin of nose, ears and/or wings of bats. Previous studies based on sequences from eight loci have found that isolates of P. destructans from bats in the US all belong to one multilocus genotype. Using the same multilocus sequence typing method, we found that isolates from eastern and central Canada also had the same genotype as those from the US, consistent with the clonal expansion of P. destructans into Canada. However, our PCR fingerprinting revealed that among the 112 North American isolates we analyzed, three, all from Canada, showed minor genetic variation. Furthermore, we found significant variations among isolates in mycelial growth rate; the production of mycelial exudates; and pigment production and diffusion into agar media. These phenotypic differences were influenced by culture medium and incubation temperature, indicating significant variation in environmental condition - dependent phenotypic expression among isolates of the clonal P. destructans genotype in North America. PMID:25122221

  7. recA mediated spontaneous deletions of the icaADBC operon of clinical Staphylococcus epidermidis isolates: a new mechanism of phenotypic variations

    PubMed Central

    Nuryastuti, Titik; van der Mei, Henny C.; Busscher, Henk J.; Kuijer, Roel; Aman, Abu T.

    2008-01-01

    Phenotypic variation of Staphylococcus epidermidis involving the slime related ica operon results in heterogeneity in surface characteristics of individual bacteria in axenic cultures. Five clinical S. epidermidis isolates demonstrated phenotypic variation, i.e. both black and red colonies on Congo Red agar. Black colonies displayed bi-modal electrophoretic mobility distributions at pH 2, but such phenotypic variation was absent in red colonies of the same strain as well as in control strains without phenotypic variation. All red colonies had lost ica and the ability to form biofilms, in contrast to black colonies of the same strain. Real time PCR targeting icaA indicated a reduction in gene copy number within cultures exhibiting phenotypic variation, which correlated with phenotypic variations in biofilm formation and electrophoretic mobility distribution of cells within a culture. Loss of ica was irreversible and independent of the mobile element IS256. Instead, in high frequency switching strains, spontaneous mutations in lexA were found which resulted in deregulation of recA expression, as shown by real time PCR. RecA is involved in genetic deletions and rearrangements and we postulate a model representing a new mechanism of phenotypic variation in clinical isolates of S. epidermidis. This is the first report of S. epidermidis strains irreversibly switching from biofilm-positive to biofilm-negative phenotype by spontaneous deletion of icaADBC. Electronic supplementary material The online version of this article (doi:10.1007/s10482-008-9249-8) contains supplementary material, which is available to authorized users. PMID:18454346

  8. Mining natural variation for maize improvement: Selection on phenotypes and genes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Maize is highly genetically and phenotypically diverse. Tropical maize and teosinte are important genetic resources that harbor unique alleles not found in temperate maize hybrids. To access these resources, breeders must be able to extract favorable unique alleles from tropical maize and teosinte f...

  9. Continuous variation rather than specialization in the egg phenotypes of cuckoos (Cuculus canorus) parasitizing two sympatric reed warbler species.

    PubMed

    Drobniak, Szymon M; Dyrcz, Andrzej; Sudyka, Joanna; Cicho?, Mariusz

    2014-01-01

    The evolution of brood parasitism has long attracted considerable attention among behavioural ecologists, especially in the common cuckoo system. Common cuckoos (Cuculus canorus) are obligatory brood parasites, laying eggs in nests of passerines and specializing on specific host species. Specialized races of cuckoos are genetically distinct. Often in a given area, cuckoos encounter multiple hosts showing substantial variation in egg morphology. Exploiting different hosts should lead to egg-phenotype specialization in cuckoos to match egg phenotypes of the hosts. Here we test this assumption using a wild population of two sympatrically occurring host species: the great reed warbler (Acrocephalus arundinaceus) and reed warbler (A. scirpaceus). Using colour spectrophotometry, egg shell dynamometry and egg size measurements, we studied egg morphologies of cuckoos parasitizing these two hosts. In spite of observing clear differences between host egg phenotypes, we found no clear differences in cuckoo egg morphologies. Interestingly, although chromatically cuckoo eggs were more similar to reed warbler eggs, after taking into account achromatic differences, cuckoo eggs seemed to be equally similar to both host species. We hypothesize that such pattern may represent an initial stage of an averaging strategy of cuckoos, that--instead of specializing for specific hosts or exploiting only one host--adapt to multiple hosts. PMID:25180796

  10. Continuous Variation Rather than Specialization in the Egg Phenotypes of Cuckoos (Cuculus canorus) Parasitizing Two Sympatric Reed Warbler Species

    PubMed Central

    Drobniak, Szymon M.; Dyrcz, Andrzej; Sudyka, Joanna; Cicho?, Mariusz

    2014-01-01

    The evolution of brood parasitism has long attracted considerable attention among behavioural ecologists, especially in the common cuckoo system. Common cuckoos (Cuculus canorus) are obligatory brood parasites, laying eggs in nests of passerines and specializing on specific host species. Specialized races of cuckoos are genetically distinct. Often in a given area, cuckoos encounter multiple hosts showing substantial variation in egg morphology. Exploiting different hosts should lead to egg-phenotype specialization in cuckoos to match egg phenotypes of the hosts. Here we test this assumption using a wild population of two sympatrically occurring host species: the great reed warbler (Acrocephalus arundinaceus) and reed warbler (A. scirpaceus). Using colour spectrophotometry, egg shell dynamometry and egg size measurements, we studied egg morphologies of cuckoos parasitizing these two hosts. In spite of observing clear differences between host egg phenotypes, we found no clear differences in cuckoo egg morphologies. Interestingly, although chromatically cuckoo eggs were more similar to reed warbler eggs, after taking into account achromatic differences, cuckoo eggs seemed to be equally similar to both host species. We hypothesize that such pattern may represent an initial stage of an averaging strategy of cuckoos, that – instead of specializing for specific hosts or exploiting only one host – adapt to multiple hosts. PMID:25180796

  11. Population size is weakly related to quantitative genetic variation and trait differentiation in a stream fish.

    PubMed

    Wood, Jacquelyn L A; Tezel, Defne; Joyal, Destin; Fraser, Dylan J

    2015-09-01

    How population size influences quantitative genetic variation and differentiation among natural, fragmented populations remains unresolved. Small, isolated populations might occupy poor quality habitats and lose genetic variation more rapidly due to genetic drift than large populations. Genetic drift might furthermore overcome selection as population size decreases. Collectively, this might result in directional changes in additive genetic variation (VA ) and trait differentiation (QST ) from small to large population size. Alternatively, small populations might exhibit larger variation in VA and QST if habitat fragmentation increases variability in habitat types. We explored these alternatives by investigating VA and QST using nine fragmented populations of brook trout varying 50-fold in census size N (179-8416) and 10-fold in effective number of breeders, Nb (18-135). Across 15 traits, no evidence was found for consistent differences in VA and QST with population size and almost no evidence for increased variability of VA or QST estimates at small population size. This suggests that (i) small populations of some species may retain adaptive potential according to commonly adopted quantitative genetic measures and (ii) populations of varying sizes experience a variety of environmental conditions in nature, however extremely large studies are likely required before any firm conclusions can be made. PMID:26207947

  12. Adrenocortical responses in zebra finches (Taeniopygia guttata): Individual variation, repeatability, and relationship to phenotypic quality

    E-print Network

    for natural selection, little is known about the magnitude and patterns of individual variation in endocrine systems or the functional significance of that variation. Here we describe (1) the extent response was seen in both sexes and ages, e.g., stress-induced corticosterone ranged from 2.2 to 62.5 ng

  13. Genetic and phenotypic variations of inherited retinal diseases in dogs: the power of within- and across-breed studies

    PubMed Central

    Acland, Gregory M.

    2014-01-01

    Considerable clinical and molecular variations have been known in retinal blinding diseases in man and also in dogs. Different forms of retinal diseases occur in specific breed(s) caused by mutations segregating within each isolated breeding population. While molecular studies to find genes and mutations underlying retinal diseases in dogs have benefited largely from the phenotypic and genetic uniformity within a breed, within- and across-breed variations have often played a key role in elucidating the molecular basis. The increasing knowledge of phenotypic, allelic, and genetic heterogeneities in canine retinal degeneration has shown that the overall picture is rather more complicated than initially thought. Over the past 20 years, various approaches have been developed and tested to search for genes and mutations underlying genetic traits in dogs, depending on the availability of genetic tools and sample resources. Candidate gene, linkage analysis, and genome-wide association studies have so far identified 24 mutations in 18 genes underlying retinal diseases in at least 58 dog breeds. Many of these genes have been associated with retinal diseases in humans, thus providing opportunities to study the role in pathogenesis and in normal vision. Application in therapeutic interventions such as gene therapy has proven successful initially in a naturally occurring dog model followed by trials in human patients. Other genes whose human homologs have not been associated with retinal diseases are potential candidates to explain equivalent human diseases and contribute to the understanding of their function in vision. PMID:22065099

  14. Contrasting the distribution of phenotypic and molecular variation in the freshwater snail Biomphalaria pfeifferi, the intermediate host of Schistosoma mansoni

    PubMed Central

    Tian-Bi, Y-NT; Jarne, P; Konan, J-NK; Utzinger, J; N'Goran, E K

    2013-01-01

    Population differentiation was investigated by confronting phenotypic and molecular variation in the highly selfing freshwater snail Biomphalaria pfeifferi, the intermediate host of Schistosoma mansoni. We sampled seven natural populations separated by a few kilometers, and characterized by different habitat regimes (permanent/temporary) and openness (open/closed). A genetic analysis based on five microsatellite markers confirms that B. pfeifferi is a selfer (s?0.9) and exhibits limited variation within populations. Most pairwise FST were significant indicating marked population structure, though no isolation by distance was detected. Families from the seven populations were monitored under laboratory conditions over two generations (G1 and G2), allowing to record several life-history traits, including growth, fecundity and survival, over 25 weeks. Marked differences were detected among populations for traits expressed early in the life cycle (up to sexual maturity). Age and size at first reproduction had high heritability values, but such a trend was not found for early reproductive traits. In most populations, G1 snails matured later and at a larger size than G2 individuals. Individuals from permanent habitats matured at a smaller size and were more fecund than those from temporary habitats. The mean phenotypic differentiation over all populations (QST) was lower than the mean genetic differentiation (FST), suggesting stabilizing selection. However, no difference was detected between QST and FST for both habitat regime and habitat openness. PMID:23321708

  15. Mutations Affecting Keratin 10 Surface-Exposed Residues Highlight the Structural Basis of Phenotypic Variation in Epidermolytic Ichthyosis.

    PubMed

    Mirza, Haris; Kumar, Anil; Craiglow, Brittany G; Zhou, Jing; Saraceni, Corey; Torbeck, Richard; Ragsdale, Bruce; Rehder, Paul; Ranki, Annamari; Choate, Keith A

    2015-12-01

    Epidermolytic ichthyosis (EI) due to KRT10 mutations is a rare, typically autosomal dominant, disorder characterized by generalized erythema and cutaneous blistering at birth followed by hyperkeratosis and less frequent blistering later in life. We identified two KRT10 mutations p.Q434del and p.R441P in subjects presenting with a mild EI phenotype. Both occur within the mutational "hot spot" of the keratin 10 (K10) 2B rod domain, adjacent to severe EI-associated mutations. p.Q434del and p.R441P formed collapsed K10 fibers rather than aggregates characteristic of severe EI KRT10 mutations such as p.R156C. Upon differentiation, keratinocytes from p.Q434del showed significantly lower apoptosis (P-value<0.01) compared with p.R156C as assessed by the TUNEL assay. Conversely, the mitotic index of the p.Q434del epidermis was significantly higher compared with that of p.R156C (P-value<0.01) as estimated by the Ki67 assay. Structural basis of EI phenotype variation was investigated by homology-based modeling of wild-type and mutant K1-K10 dimers. Both mild EI mutations were found to affect the surface-exposed residues of the K10 alpha helix coiled-coil and caused localized disorganization of the K1-K10 heterodimer. In contrast, adjacent severe EI mutations disrupt key intermolecular dimer interactions. Our findings provide structural insights into phenotypic variation in EI due to KRT10 mutations. PMID:26176760

  16. Conformation of polyelectrolytes in poor solvents: Variational approach and quantitative comparison with scaling predictions

    NASA Astrophysics Data System (ADS)

    Tang, Haozhe; Liao, Qi; Zhang, Pingwen

    2014-05-01

    We present the results of variational calculations of a polyelectrolyte solution with low salt in poor solvent conditions for a polymer backbone. By employing the variation method, we quantitatively determined the diagram of the state of the polyelectrolyte in poor solvents as a function of the charge density and the molecular weight. The exact structure and diagram of the polyelectrolyte were compared to the scaling predictions of the necklace model developed by Dobrynin and Rubinstein [Prog. Polym. Sci. 30, 1049-1118 (2005); Dobrynin and Rubinstein, Macromolecules 32, 915-922 (1999); Dobrynin and Rubinstein, Macromolecules 34, 1964-1972 (2001)]. We find that the scaling necklace model may be used as a rather good estimation and analytical approximation of the exact variational model. It is also pointed out that the molecular connection of polymer is crucial for ellipsoid and necklace conformation.

  17. Quantitative variation in obesity-related traits and insulin precursors linked to the OB gene region on human chromosome 7

    SciTech Connect

    Duggirala, R.; Stern, M.P.; Reinhart, L.J.

    1996-09-01

    Despite the evidence that human obesity has strong genetic determinants, efforts at identifying specific genes that influence human obesity have largely been unsuccessful. Using the sibship data obtained from 32 low-income Mexican American pedigrees ascertained on a type II diabetic proband and a multipoint variance-components method, we tested for linkage between various obesity-related traits plus associated metabolic traits and 15 markers on human chromosome 7. We found evidence for linkage between markers in the OB gene region and various traits, as follows: D7S514 and extremity skinfolds (LOD = 3.1), human carboxypeptidase A1 (HCPA1) and 32,33-split proinsulin level (LOD = 4.2), and HCPA1 and proinsulin level (LOD = 3.2). A putative susceptibility locus linked to the marker D7S514 explained 56% of the total phenotypic variation in extremity skinfolds. Variation at the HCPA1 locus explained 64% of phenotypic variation in proinsulin level and {approximately}73% of phenotypic variation in split proinsulin concentration, respectively. Weaker evidence for linkage to several other obesity-related traits (e.g., waist circumference, body-mass index, fat mass by bioimpedance, etc.) was observed for a genetic location, which is {approximately}15 cM telomeric to OB. In conclusion, our study reveals that the OB region plays a significant role in determining the phenotypic variation of both insulin precursors and obesity-related traits, at least in Mexican Americans. 66 refs., 3 figs., 4 tabs.

  18. Phenotypic variation and sexual dimorphism in anadromous threespine stickleback: implications for

    E-print Network

    Aguirre, Windsor E.

    ­ ancestral variation ­ evolutionary diversification ­ Gasterosteus aculeatus ­ geometric morphometrics stickleback fish, Gasterosteus aculeatus, are primitively oceanic, spending most or all of their lives repeatedly established resident popula- tions in postglacial lakes and streams throughout much

  19. Genetic and Phenotypic Variation of FMDV During Serial Passages in a Natural Host

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Foot-and-Mouth Disease Virus (FMDV) exhibits high mutation rates during replication that have been suggested to be of adaptive value. However, even though genetic variation in RNA viruses has been extensively examined during virus replication in a wide variety of in vitro cell cultures, very little ...

  20. Investigating genetic determinants of phenotypic variation in natural isolates of Saccharomyces cerevisiae

    E-print Network

    Lee, Hana

    2012-01-01

    evolutionary change. Our work in the wild yeast model makesIn this work, we set out to use wild yeast as a model systemwork, we undertook a proof of concept for hypothesis- driven genetic dissection of natural variation, using yeast

  1. RESEARCH PAPER Sex-specific phenotypic selection and geographic variation in

    E-print Network

    Herrera, Carlos M.

    differentiation in floral traits of a plant spe- cies requires the verification of several components of selection Biology, University of Texas at Austin, Austin, TX, USA Keywords Floral and phenological traits; gender traits, are expected. We tested for pollination-driven geographic variation in the gender divergence

  2. SNP signatures of selection on standing genetic variation and their association with adaptive phenotypes along

    E-print Network

    Bernatchez, Louis

    SNP signatures of selection on standing genetic variation and their association with adaptive. Using a data set of over 100 SNP markers, genome scans were performed to investigate the effect more intensively in dwarf whitefish. SNP associations in backcross hybrid progeny identified 16 genes

  3. Phenotypic Variation in Overwinter Environmental Transmission of a Baculovirus and the Cost of Virulence.

    PubMed

    Fleming-Davies, Arietta E; Dwyer, Greg

    2015-12-01

    A pathogen's ability to persist in the environment is an ecologically important trait, and variation in this trait may promote coexistence of different pathogen strains. We asked whether naturally occurring isolates of the baculovirus that infects gypsy moth larvae varied in their overwinter environmental transmission and whether this variation was consistent with a trade-off or an upper limit to virulence that might promote pathogen diversity. We used experimental manipulations to replicate the natural overwinter infection process, using 16 field-collected isolates. Virus isolates varied substantially in the fraction of larvae infected, leading to differences in overwinter transmission rates. Furthermore, isolates that killed more larvae also had higher rates of early larval death in which no infectious particles were produced, consistent with a cost of high virulence. Our results thus support the existence of a cost that could impose an upper limit to virulence even in a highly virulent pathogen. PMID:26655986

  4. Deficiencies in Jasmonate-Mediated Plant Defense Reveal Quantitative Variation in Botrytis cinerea Pathogenesis

    PubMed Central

    Rowe, Heather C.; Walley, Justin W.; Corwin, Jason; Chan, Eva K.-F.; Dehesh, Katayoon; Kliebenstein, Daniel J.

    2010-01-01

    Despite the described central role of jasmonate signaling in plant defense against necrotrophic pathogens, the existence of intraspecific variation in pathogen capacity to activate or evade plant jasmonate-mediated defenses is rarely considered. Experimental infection of jasmonate-deficient and jasmonate-insensitive Arabidopsis thaliana with diverse isolates of the necrotrophic fungal pathogen Botrytis cinerea revealed pathogen variation for virulence inhibition by jasmonate-mediated plant defenses and induction of plant defense metabolites. Comparison of the transcriptional effects of infection by two distinct B. cinerea isolates showed only minor differences in transcriptional responses of wild-type plants, but notable isolate-specific transcript differences in jasmonate-insensitive plants. These transcriptional differences suggest B. cinerea activation of plant defenses that require plant jasmonate signaling for activity in response to only one of the two B. cinerea isolates tested. Thus, similar infection phenotypes observed in wild-type plants result from different signaling interactions with the plant that are likely integrated by jasmonate signaling. PMID:20419157

  5. Quantitative Variation in Responses to Root Spatial Constraint within Arabidopsis thaliana[OPEN

    PubMed Central

    Joseph, Bindu; Lau, Lillian; Kliebenstein, Daniel J.

    2015-01-01

    Among the myriad of environmental stimuli that plants utilize to regulate growth and development to optimize fitness are signals obtained from various sources in the rhizosphere that give an indication of the nutrient status and volume of media available. These signals include chemical signals from other plants, nutrient signals, and thigmotropic interactions that reveal the presence of obstacles to growth. Little is known about the genetics underlying the response of plants to physical constraints present within the rhizosphere. In this study, we show that there is natural variation among Arabidopsis thaliana accessions in their growth response to physical rhizosphere constraints and competition. We mapped growth quantitative trait loci that regulate a positive response of foliar growth to short physical constraints surrounding the root. This is a highly polygenic trait and, using quantitative validation studies, we showed that natural variation in EARLY FLOWERING3 (ELF3) controls the link between root constraint and altered shoot growth. This provides an entry point to study how root and shoot growth are integrated to respond to environmental stimuli. PMID:26243313

  6. Genotypic and phenotypic variation in six patients with solitary median maxillary central incisor syndrome.

    PubMed

    Poelmans, Simon; Kawamoto, Tatsuro; Cristofoli, Francesca; Politis, Constantinus; Vermeesch, Joris; Bailleul-Forestier, Isabelle; Hens, Greet; Devriendt, Koenraad; Verdonck, Anna; Carels, Carine

    2015-10-01

    Solitary Median Maxillary Central Incisor occurs in 1 of 50,000 live births. It is the mildest manifestation of the holoprosencephaly spectrum and is genetically heterogeneous. Here we report six patients with solitary median maxillary central incisor, and a range of other phenotypic anomalies with different degrees of severity, varying from mild signs of holoprosencephaly to associated intellectual disability, and with different genetic background. Using array comparative genomic hybridization, pathogenic copy number variants were found in three of the six patients. Two patients had a deletion at the 18p11 chromosomal region that includes TGIF1 while the other patient had a deletion at 7q36, including the SHH gene. In one patient, a mutation in SIX3 was detected with exome sequencing, while in the two remaining patients all known holoprosencephaly genes were excluded using multiplex ligation-dependent probe amplification and sequencing, and remain unsolved. One of the two latter patients had isolated solitary median maxillary central incisor without other visible dentofacial anomalies, while the other had clinical features not part of the known holoprosencephaly spectrum. PMID:26080100

  7. Application of quantitative trait locus mapping and transcriptomics to studies of the senescence-accelerated phenotype in rats

    PubMed Central

    2014-01-01

    Background Etiology of complex disorders, such as cataract and neurodegenerative diseases including age-related macular degeneration (AMD), remains poorly understood due to the paucity of animal models, fully replicating the human disease. Previously, two quantitative trait loci (QTLs) associated with early cataract, AMD-like retinopathy, and some behavioral aberrations in senescence-accelerated OXYS rats were uncovered on chromosome 1 in a cross between OXYS and WAG rats. To confirm the findings, we generated interval-specific congenic strains, WAG/OXYS-1.1 and WAG/OXYS-1.2, carrying OXYS-derived loci of chromosome 1 in the WAG strain. Both congenic strains displayed early cataract and retinopathy but differed clinically from OXYS rats. Here we applied a high-throughput RNA sequencing (RNA-Seq) strategy to facilitate nomination of the candidate genes and functional pathways that may be responsible for these differences and can contribute to the development of the senescence-accelerated phenotype of OXYS rats. Results First, the size and map position of QTL-derived congenic segments were determined by comparative analysis of coding single-nucleotide polymorphisms (SNPs), which were identified for OXYS, WAG, and congenic retinal RNAs after sequencing. The transferred locus was not what we expected in WAG/OXYS-1.1 rats. In rat retina, 15442 genes were expressed. Coherent sets of differentially expressed genes were identified when we compared RNA-Seq retinal profiles of 20-day-old WAG/OXYS-1.1, WAG/OXYS-1.2, and OXYS rats. The genes most different in the average expression level between the congenic strains included those generally associated with the Wnt, integrin, and TGF-? signaling pathways, widely involved in neurodegenerative processes. Several candidate genes (including Arhgap33, Cebpg, Gtf3c1, Snurf, Tnfaip3, Yme1l1, Cbs, Car9 and Fn1) were found to be either polymorphic in the congenic loci or differentially expressed between the strains. These genes may contribute to the development of cataract and retinopathy. Conclusions This study is the first RNA-Seq analysis of the rat retinal transcriptome generated with 40 mln sequencing read depth. The integration of QTL and transcriptomic analyses in our study forms the basis of future research into the relationship between the candidate genes within the congenic regions and specific changes in the retinal transcriptome as possible causal mechanisms that underlie age-associated disorders. PMID:25563673

  8. Pharmacologically distinct phenotypes of ?1B-adrenoceptors: variation in binding and functional affinities for antagonists

    PubMed Central

    Yoshiki, Hatsumi; Uwada, Junsuke; Anisuzzaman, Abu Syed Md; Umada, Hidenori; Hayashi, Ryoji; Kainoh, Mie; Masuoka, Takayoshi; Nishio, Matomo; Muramatsu, Ikunobu

    2014-01-01

    Background and Purpose The pharmacological properties of particular receptors have recently been suggested to vary under different conditions. We compared the pharmacological properties of the ?1B-adrenoceptor subtype in various tissue preparations and under various conditions. Experimental Approach [3H]-prazosin binding to ?1B-adrenoceptors in rat liver (segments, dispersed hepatocytes and homogenates) was assessed and the pharmacological profiles were compared with the functional and binding profiles in rat carotid artery and recombinant ?1B-adrenoceptors. Key Results In association and saturation-binding experiments with rat liver, binding affinity for [3H]-prazosin varied significantly between preparations (KD value approximately ten times higher in segments than in homogenates). The binding profile for various drugs in liver segments also deviated from the representative ?1B-adrenoceptor profile observed in liver homogenates and recombinant receptors. L-765,314 and ALS-77, selective antagonists of ?1B-adrenoceptors, showed high binding and antagonist affinities in liver homogenates and recombinant ?1B-adrenoceptors. However, binding affinities for both ligands in the segments of rat liver and carotid artery were 10 times lower, and the antagonist potencies in ?1B-adrenoceptor-mediated contractions of carotid artery were more than 100 times lower than the representative ?1B-adrenoceptor profile. Conclusions and Implications In contrast to the consistent profile of recombinant ?1B-adrenoceptors, the pharmacological profile of native ?1B-adrenoceptors of rat liver and carotid artery varied markedly under various receptor environments, showing significantly different binding properties between intact tissues and homogenates, and dissociation between functional and binding affinities. In addition to conventional ‘subtype’ characterization, ‘phenotype’ pharmacology must be considered in native receptor evaluations in vivo and in future pharmacotherapy. PMID:24923551

  9. Quantitative NMR Metabolite Profiling of Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus Discriminates between Biofilm and Planktonic Phenotypes

    PubMed Central

    2015-01-01

    Wound bioburden in the form of colonizing biofilms is a major contributor to nonhealing wounds. Staphylococcus aureus is a Gram-positive, facultative anaerobe commonly found in chronic wounds; however, much remains unknown about the basic physiology of this opportunistic pathogen, especially with regard to the biofilm phenotype. Transcriptomic and proteomic analysis of S. aureus biofilms have suggested that S. aureus biofilms exhibit an altered metabolic state relative to the planktonic phenotype. Herein, comparisons of extracellular and intracellular metabolite profiles detected by 1H NMR were conducted for methicillin-resistant (MRSA) and methicillin-susceptible (MSSA) S. aureus strains grown as biofilm and planktonic cultures. Principal component analysis distinguished the biofilm phenotype from the planktonic phenotype, and factor loadings analysis identified metabolites that contributed to the statistical separation of the biofilm from the planktonic phenotype, suggesting that key features distinguishing biofilm from planktonic growth include selective amino acid uptake, lipid catabolism, butanediol fermentation, and a shift in metabolism from energy production to assembly of cell-wall components and matrix deposition. These metabolite profiles provide a basis for the development of metabolite biomarkers that distinguish between biofilm and planktonic phenotypes in S. aureus and have the potential for improved diagnostic and therapeutic use in chronic wounds. PMID:24809402

  10. Intraspecific Phenotypic Variation and Morphological Divergence of Strains of Folsomia candida (Willem) (Collembola: Isotomidae), the "Standard" Test Springtaill

    PubMed Central

    Tully, Thomas; Potapov, Mikhail

    2015-01-01

    We describe and compare the external morphology of eleven clonal strains and one sexual lineage of the globally distributed Folsomia candida, known as “standard” test Collembola. Of the 18 morphological characters studied, we measured 14 to have significant between-strains genetic variations, 9 of these had high heritabilities (>78%). The quantified morphological polymorphism was used to analyse the within-species relationships between strains by using both a parsimony analysis and a distance tree. These two detailed morphological phylogenies have revealed that the parthenogenetic strains grouped themselves into two major clades. However the exact position of the sexual strain remains unclear and further analysis is needed to confirm its exact relationship with the parthenogenetic ones. The two morphologically based clades were found to be the same as the ones previously described using molecular analysis. This shows that despite large within-strain variations, morphological characters can be used to differentiate some strains that have diverged within a single morphospecies. We discuss the potential evolutionary interpretations and consequences of these different levels of phenotypic variability. PMID:26355293

  11. Effect of trinucleotide repeat length and parental sex on phenotypic variation in spinocerebellar ataxia I

    SciTech Connect

    Jodice, C.; Malaspina, P.; Persichetti, F.; Novelletto, A.; Terrenato, L. ); Spadaro, M.; Morocutti, C. ); Giunti, P. Institute of Neurology, London ); Harding, A.E. ); Frontali, M. )

    1994-06-01

    Trinucleotide repeat expansion has been found in 64 subjects from 19 families: 57 patients with SCA1 and 7 subjects predicted, by haplotype analysis, to carry the mutation. Comparison with a large set of normal chromosomes shows two distinct distributions, with a much wider variation among expanded chromosomes. The sex of transmitting parent plays a major role in the size distribution of expanded alleles, those with >54 repeats being transmitted by affected fathers exclusively. The data suggest that alleles with >54 repeats have a reduced chance of survival; these appear to be replaced in each generation by further expansion of alleles in the low- to medium-expanded repeat range, preferentially in male transmission. Detailed clinical follow-up of a subset of patients demonstrates significant relationships between increasing repeat number on expanded chromosomes and earlier age at onset, faster progression of the disease, and earlier age at death.

  12. Geographic and phenotypic variation in heartwood and essential-oil characters in natural populations of Santalum austrocaledonicum in Vanuatu.

    PubMed

    Page, Tony; Southwell, Ian; Russell, Mike; Tate, Hanington; Tungon, Joseph; Sam, Chanel; Dickinson, Geoff; Robson, Ken; Leakey, Roger R B

    2010-08-01

    Phenotypic variation in heartwood and essential-oil characters of Santalum austrocaledonicum was assessed across eleven populations on seven islands of Vanuatu. Trees differed significantly in their percentage heartwood cross-sectional area and this varied independently of stem diameter. The concentrations of the four major essential-oil constituents (alpha-santalol, beta-santalol, (Z)-beta-curcumen-12-ol, and cis-nuciferol) of alcohol-extracted heartwood exhibited at least tenfold and continuous tree-to-tree variation. Commercially important components alpha- and beta-santalol found in individual trees ranged from 0.8-47% and 0-24.1%, respectively, across all populations, and significant (P<0.05) differences for each were found between individual populations. The Erromango population was unique in that the mean concentrations of its monocyclic ((Z)-beta-curcumen-12-ol and cis-nuciferol) sesquiterpenes exceeded those of its bi- and tricyclic (alpha- and beta-santalol) sesquiterpenes. Heartwood colour varied between trees and spanned 65 colour categories, but no identifiable relationships were found between heartwood colour and alpha- and beta-santalol, although a weak relationship was evident between colour saturation and total oil concentration. These results indicate that the heartwood colour is not a reliable predictive trait for oil quality. The results of this study highlight the knowledge gaps in fundamental understanding of heartwood biology in Santalum genus. The intraspecific variation in heartwood cross-sectional area, oil concentration, and oil quality traits is of considerable importance to the domestication of sandalwood and present opportunities for the development of highly superior S. austrocaledonicum cultivars that conform to the industry's International Standards used for S. album. PMID:20730962

  13. Association between allelic variation due to short tandem repeats in tRNA gene of Entamoeba histolytica and clinical phenotypes of amoebiasis.

    PubMed

    Jaiswal, Virendra; Ghoshal, Ujjala; Mittal, Balraj; Dhole, Tapan N; Ghoshal, Uday C

    2014-05-01

    Genotypes of Entamoeba histolytica (E. histolytica) may contribute clinical phenotypes of amoebiasis such as amoebic liver abscess (ALA), dysentery and asymptomatic cyst passers state. Hence, we evaluated allelic variation due to short tandem repeats (STRs) in tRNA gene of E. histolytica and clinical phenotypes of amoebiasis. Asymptomatic cyst passers (n=24), patients with dysentery (n=56) and ALA (n=107) were included. Extracted DNA from stool (dysentery, asymptomatic cyst passers) and liver aspirate was amplified using 6 E. histolytica specific tRNA-linked STRs (D-A, A-L, N-K2, R-R, S-Q, and S(TGA)-D) primers. PCR products were subjected to sequencing. Association between allelic variation and clinical phenotypes was analyzed. A total of 9 allelic variations were found in D-A, 8 in A-L, 4 in N-K2, 5 in R-R, 10 in S(TAG)-D and 7 in S-Q loci. A significant association was found between allelic variants and clinical phenotypes of amoebiasis. This study reveals that allelic variation due to short tandem repeats (STRs) in tRNA gene of E. histolytica is associated different clinical outcome of amoebiasis. PMID:24495629

  14. Associations of prodynorphin sequence variation with alcohol dependence and related traits are phenotype-specific and sex-dependent

    PubMed Central

    Winham, Stacey J.; Preuss, Ulrich W.; Geske, Jennifer R.; Zill, Peter; Heit, John A.; Bakalkin, Georgy; Biernacka, Joanna M.; Karpyak, Victor M.

    2015-01-01

    We previously demonstrated that prodynorphin (PDYN) haplotypes and single nucleotide polymorphism (SNP) rs2281285 are associated with alcohol dependence and the propensity to drink in negative emotional states, and recent studies suggest that PDYN gene effects on substance dependence risk may be sex-related. We examined sex-dependent associations of PDYN variation with alcohol dependence and related phenotypes, including negative craving, time until relapse after treatment and the length of sobriety episodes before seeking treatment, in discovery and validation cohorts of European ancestry. We found a significant haplotype-by-sex interaction (p??=??0.03), suggesting association with alcohol dependence in males (p?=?1E-4) but not females. The rs2281285?G allele increased risk for alcohol dependence in males in the discovery cohort (OR?=?1.49, p?=?0.002), with a similar trend in the validation cohort (OR?=?1.35, p?=?0.086). However, rs2281285 showed a trend towards association with increased negative craving in females in both the discovery (beta?=?10.16, p?=?0.045) and validation samples (OR?=?7.11, p?=?0.066). In the discovery cohort, rs2281285 was associated with time until relapse after treatment in females (HR?=?1.72, p?=?0.037); in the validation cohort, it was associated with increased length of sobriety episodes before treatment in males (beta?=?13.49, p?=?0.001). Our findings suggest that sex-dependent effects of PDYN variants in alcohol dependence are phenotype-specific. PMID:26502829

  15. Quantitative assessment of the importance of phenotypic plasticity in adaptation to climate change in wild bird populations.

    PubMed

    Vedder, Oscar; Bouwhuis, Sandra; Sheldon, Ben C

    2013-07-01

    Predictions about the fate of species or populations under climate change scenarios typically neglect adaptive evolution and phenotypic plasticity, the two major mechanisms by which organisms can adapt to changing local conditions. As a consequence, we have little understanding of the scope for organisms to track changing environments by in situ adaptation. Here, we use a detailed individual-specific long-term population study of great tits (Parus major) breeding in Wytham Woods, Oxford, UK to parameterise a mechanistic model and thus directly estimate the rate of environmental change to which in situ adaptation is possible. Using the effect of changes in early spring temperature on temporal synchrony between birds and a critical food resource, we focus in particular on the contribution of phenotypic plasticity to population persistence. Despite using conservative estimates for evolutionary and reproductive potential, our results suggest little risk of population extinction under projected local temperature change; however, this conclusion relies heavily on the extent to which phenotypic plasticity tracks the changing environment. Extrapolating the model to a broad range of life histories in birds suggests that the importance of phenotypic plasticity for adjustment to projected rates of temperature change increases with slower life histories, owing to lower evolutionary potential. Understanding the determinants and constraints on phenotypic plasticity in natural populations is thus crucial for characterising the risks that rapidly changing environments pose for the persistence of such populations. PMID:23874152

  16. EFFICIENCY OF RECURRENT SELECTION BY MARKER AND PHENOTYPE FOR MULTIPLE, QUANTITATIVE YIELD COMPONENTS IN FOUR CUCUMBER POPULATIONS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Four cucumber (Cucumus sativus L.) inbred lines were intermated then bulked maternally to create four base populations denoted as cycle 0 (i.e., Pop.1 C0, Pop.2 C0, Pop.3 C0, Pop.4 C0). Each of these populations underwent phenotypic selection (PHE; open-field evaluations), selection by marker (MAS; ...

  17. SU-E-T-635: Quantitative Study On Beam Flatness Variation with Beam Energy Change

    SciTech Connect

    Li, J S; Eldib, A; Ma, C; Lin, M

    2014-06-15

    Purpose: Beam flatness check has been proposed for beam energy check for photon beams with flattering filters. In this work, beam flatness change with beam energy was investigated quantitatively using the Monte Carlo method and its significance was compared with depth dose curve change. Methods: Monte Carlo simulations for a linear accelerator with flattering filter were performed with different initial electron energies for photon beams of 6MV and 10MV. Dose calculations in a water phantom were then perform with the phase space files obtained from the simulations. The beam flatness was calculated based on the dose profile at 10 cm depth for all the beams with different initial electron energies. The percentage depth dose (PDD) curves were also analyzed. The dose at 10cm depth (D10) and the ratio of the dose at 10cm and 20cm depth (D10/D20) and their change with the beam energy were calculated and compared with the beam flatness variation. Results: It was found that the beam flatness variation with beam energy change was more significant than the change of D10 and the ratio between D10 and D20 for both 6MV and 10MV beams. Half MeV difference on the initial electron beam energy brought in at least 20% variation on the beam flatness but only half percent change on the ratio of D10 and D20. The change of D10 or D20 alone is even less significant. Conclusion: The beam energy impact on PDD is less significant than that on the beam flatness. If the PDD is used for checking the beam energy, uncertainties of the measurement could possibly disguise its change. Beam flatness changes more significantly with beam energy and therefore it can be used for monitoring the energy change for photon beams with flattering filters. However, other factors which may affect the beam flatness should be watched as well.

  18. Genetic and phenotypic variation among four Nguni sheep breeds using random amplified polymorphic DNA (RAPD) and morphological features.

    PubMed

    Gwala, Phiwamandla Emanuel; Kunene, Nokuthula Winfred; Bezuidenhout, Cornelius Carlos; Mavule, Bafowethu Sibanda

    2015-10-01

    This study was conducted to investigate phenotypic and genetic differentiation among the four Nguni sheep breeds. Sheep with two permanent incisors and above were sampled from areas, namely KwaZulu-Natal (Zulu sheep), Limpopo (Pedi sheep), Mozambique (Landim sheep) and Swaziland (Swazi sheep). The Dorper was used as an out-group. Eight morphometric variables were measured from each animal, and blood samples were collected (n?=?50 per population) for genetic characterization. The mean body weights for sheep were 30.41?±?0.41, 35.34?±?0.43, 35.23?±?0.43, 37.63?±?0.42 and 52.84?±?0.30 for Swazi, Zulu, Landim, Pedi and Dorper, respectively. Morphometric cluster analysis showed the Landim, Swazi and Zulu breeds in one cluster. The Pedi sheep were closer to the Dorper than to the other Nguni sheep. Random amplified polymorphic DNA (RAPD) technique was used to assess genetic variation. Eight primers were selected for analysis based on band pattern quality, reproducibility and the presence of distinctive bands. The Swazi sheep formed a cluster with Zulu sheep, and the Pedi formed a cluster with the Dorper. These results confirm indications by other researchers that Pedi sheep are genetically distant from Zulu and Swazi sheep breeds. This could indicate the possibility of cross breeding Zulu and Swazi sheep as a possible conservation strategy to control inbreeding. The mtDNA should be analyzed to trace the relationships between Pedi and the three Nguni sheep breeds through maternal lines. PMID:26178370

  19. R2OBBIE-3D, a Fast Robotic High-Resolution System for Quantitative Phenotyping of Surface Geometry and Colour-Texture

    PubMed Central

    Manukyan, Liana; Milinkovitch, Michel C.

    2015-01-01

    While recent imaging techniques provide insights into biological processes from the molecular to the cellular scale, phenotypes at larger scales remain poorly amenable to quantitative analyses. For example, investigations of the biophysical mechanisms generating skin morphological complexity and diversity would greatly benefit from 3D geometry and colour-texture reconstructions. Here, we report on R2OBBIE-3D, an integrated system that combines a robotic arm, a high-resolution digital colour camera, an illumination basket of high-intensity light-emitting diodes and state-of-the-art 3D-reconstruction approaches. We demonstrate that R2OBBIE generates accurate 3D models of biological objects between 1 and 100 cm, makes multiview photometric stereo scanning possible in practical processing times, and enables the capture of colour-texture and geometric resolutions better than 15 ?m without the use of magnifying lenses. R2OBBIE has the potential to greatly improve quantitative analyses of phenotypes in addition to providing multiple new applications in, e.g., biomedical science. PMID:26039509

  20. R(2)OBBIE-3D, a Fast Robotic High-Resolution System for Quantitative Phenotyping of Surface Geometry and Colour-Texture.

    PubMed

    Martins, António F; Bessant, Michel; Manukyan, Liana; Milinkovitch, Michel C

    2015-01-01

    While recent imaging techniques provide insights into biological processes from the molecular to the cellular scale, phenotypes at larger scales remain poorly amenable to quantitative analyses. For example, investigations of the biophysical mechanisms generating skin morphological complexity and diversity would greatly benefit from 3D geometry and colour-texture reconstructions. Here, we report on R(2)OBBIE-3D, an integrated system that combines a robotic arm, a high-resolution digital colour camera, an illumination basket of high-intensity light-emitting diodes and state-of-the-art 3D-reconstruction approaches. We demonstrate that R(2)OBBIE generates accurate 3D models of biological objects between 1 and 100 cm, makes multiview photometric stereo scanning possible in practical processing times, and enables the capture of colour-texture and geometric resolutions better than 15 ?m without the use of magnifying lenses. R(2)OBBIE has the potential to greatly improve quantitative analyses of phenotypes in addition to providing multiple new applications in, e.g., biomedical science. PMID:26039509

  1. Quantitative genetic analysis of among-population variation in sperm and female sperm-storage organ length in

    E-print Network

    Pitnick, Scott

    Quantitative genetic analysis of among-population variation in sperm and female sperm-storage organ and in revised form 30 December 2002) Summary In Drosophila, sperm length and the length of the females' primary sperm-storage organ have rapidly coevolved through post-copulatory sexual selection. This pattern

  2. Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice

    PubMed Central

    Yang, Wanneng; Guo, Zilong; Huang, Chenglong; Duan, Lingfeng; Chen, Guoxing; Jiang, Ni; Fang, Wei; Feng, Hui; Xie, Weibo; Lian, Xingming; Wang, Gongwei; Luo, Qingming; Zhang, Qifa; Liu, Qian; Xiong, Lizhong

    2014-01-01

    Even as the study of plant genomics rapidly develops through the use of high-throughput sequencing techniques, traditional plant phenotyping lags far behind. Here we develop a high-throughput rice phenotyping facility (HRPF) to monitor 13 traditional agronomic traits and 2 newly defined traits during the rice growth period. Using genome-wide association studies (GWAS) of the 15 traits, we identify 141 associated loci, 25 of which contain known genes such as the Green Revolution semi-dwarf gene, SD1. Based on a performance evaluation of the HRPF and GWAS results, we demonstrate that high-throughput phenotyping has the potential to replace traditional phenotyping techniques and can provide valuable gene identification information. The combination of the multifunctional phenotyping tools HRPF and GWAS provides deep insights into the genetic architecture of important traits. PMID:25295980

  3. Flower color changes in three Japanese hibiscus species: further quantitative variation of anthocyanin and flavonols.

    PubMed

    Shimokawa, Satoshi; Iwashina, Tsukasa; Murakami, Noriaki

    2015-03-01

    One anthocyanin and four flavonols were detected from the petals of Hibiscus hamabo, H. tiliaceus and H. glaber. They were identified as cyanidin 3-0- sambubioside, gossypetin 3-O-glucuronide-8-O-glucoside, quercetin 7-O-rutinoside, gossypetin 3-O-glucoside and gossypetin 8-O-glucuronide by UV spectra, LC-MS, acid hydrolysis and HPLC. The flavonoid composition was essentially the same among the petals ofH. hamabo, H. tiliaceus and H. glaber, and there was little quantitative variation, except for cyanidin 3-O-sambubioside, the content of which in the petals ofH. tiliaceus and H. glaber was much higher than in that of H. hamabo. Flower colors of H. tiliaceus and H. glaber change from yellow to red, and that of H. hamabo changes from yellow to orange. These changes were caused by contents of anthocyanin and flavonols, which increased after flowering of H. hamabo, H. tiliaceus and H. glaber. PMID:25924527

  4. Quantitative Susceptibility Mapping of Human Brain Reflects Spatial Variation in Tissue Composition

    PubMed Central

    Li, Wei; Wu, Bing; Liu, Chunlei

    2011-01-01

    Image phase from gradient echo MRI provides a unique contrast that reflects brain tissue composition variations, such as iron and myelin distribution. Phase imaging is emerging as a powerful tool for the investigation of functional brain anatomy and disease diagnosis. However, the quantitative value of phase is compromised by its nonlocal and orientation dependent properties. There is an increasing need for reliable quantification of magnetic susceptibility, the intrinsic property of tissue. In this study, we developed a novel and accurate susceptibility mapping method that is also phase-wrap insensitive. The proposed susceptibility mapping method utilized two complementary equations: (1) the Fourier relationship of phase and magnetic susceptibility; and (2) the first-order partial derivative of the first equation in the spatial frequency domain. In numerical simulation, this method reconstructed the susceptibility map almost free of streaking artifact. Further, the iterative implementation of this method allowed for high quality reconstruction of susceptibility maps of human brain in vivo. The reconstructed susceptibility map provided excellent contrast of iron-rich deep nuclei and white matter bundles from surrounding tissues. Further, it also revealed anisotropic magnetic susceptibility in brain white matter. Hence, the proposed susceptibility mapping method may provide a powerful tool for the study of brain physiology and pathophysiology. Further elucidation of anisotropic magnetic susceptibility in vivo may allow us to gain more insight into the white matter microarchitectures. PMID:21224002

  5. Genes and quantitative genetic variation involved with senescence in cells, organs, and the whole plant

    PubMed Central

    Pujol, Benoit

    2015-01-01

    Senescence, the deterioration of morphological, physiological, and reproductive functions with age that ends with the death of the organism, was widely studied in plants. Genes were identified that are linked to the deterioration of cells, organs and the whole plant. It is, however, unclear whether those genes are the source of age dependent deterioration or get activated to regulate such deterioration. Furthermore, it is also unclear whether such genes are active as a direct consequence of age or because they are specifically involved in some developmental stages. At the individual level, it is the relationship between quantitative genetic variation, and age that can be used to detect the genetic signature of senescence. Surprisingly, the latter approach was only scarcely applied to plants. This may be the consequence of the demanding requirements for such approaches and/or the fact that most research interest was directed toward plants that avoid senescence. Here, I review those aspects in turn and call for an integrative genetic theory of senescence in plants. Such conceptual development would have implications for the management of plant genetic resources and generate progress on fundamental questions raised by aging research. PMID:25755664

  6. Quantitative measurements of localized density variations in cylindrical tablets using X-ray microtomography.

    PubMed

    Busignies, Virginie; Leclerc, Bernard; Porion, Patrice; Evesque, Pierre; Couarraze, Guy; Tchoreloff, Pierre

    2006-08-01

    Direct compaction is a complex process that results in a density distribution inside the tablets which is often heterogeneous. Therefore, the density variations may affect the compact properties. A quantitative analysis of this phenomenon is still lacking. Recently, X-ray microtomography has been successfully used in pharmaceutical development to study qualitatively the impact of tablet shape and break-line in the density of pharmaceutical tablets. In this study, we evaluate the density profile in microcrystalline cellulose (Vivapur 12) compacts obtained at different mean porosity (ranging from 7.7% to 33.5%) using X-ray tomography technique. First, the validity of the Beer-Lambert law is studied. Then, density calibration is performed and density maps of cylindrical tablets are obtained and visualized using a process with colour-scale calibration plot which is explained. As expected, important heterogeneity in density is observed and quantified. The higher densities in peripheral region were particularly investigated and appraised in regard to the lower densities observed in the middle of the tablet. The results also underlined that in the case of pharmaceutical tablets, it is important to differentiate the mechanical properties representative of the total volume tablet and the mechanical properties that only characterize the tablet surface like the Brinell hardness measurements. PMID:16621489

  7. High genetic and epigenetic stability in Coffea arabica plants derived from embryogenic suspensions and secondary embryogenesis as revealed by AFLP, MSAP and the phenotypic variation rate.

    PubMed

    Bobadilla Landey, Roberto; Cenci, Alberto; Georget, Frédéric; Bertrand, Benoît; Camayo, Gloria; Dechamp, Eveline; Herrera, Juan Carlos; Santoni, Sylvain; Lashermes, Philippe; Simpson, June; Etienne, Hervé

    2013-01-01

    Embryogenic suspensions that involve extensive cell division are risky in respect to genome and epigenome instability. Elevated frequencies of somaclonal variation in embryogenic suspension-derived plants were reported in many species, including coffee. This problem could be overcome by using culture conditions that allow moderate cell proliferation. In view of true-to-type large-scale propagation of C. arabica hybrids, suspension protocols based on low 2,4-D concentrations and short proliferation periods were developed. As mechanisms leading to somaclonal variation are often complex, the phenotypic, genetic and epigenetic changes were jointly assessed so as to accurately evaluate the conformity of suspension-derived plants. The effects of embryogenic suspensions and secondary embryogenesis, used as proliferation systems, on the genetic conformity of somatic embryogenesis-derived plants (emblings) were assessed in two hybrids. When applied over a 6 month period, both systems ensured very low somaclonal variation rates, as observed through massive phenotypic observations in field plots (0.74% from 200,000 plant). Molecular AFLP and MSAP analyses performed on 145 three year-old emblings showed that polymorphism between mother plants and emblings was extremely low, i.e. ranges of 0-0.003% and 0.07-0.18% respectively, with no significant difference between the proliferation systems for the two hybrids. No embling was found to cumulate more than three methylation polymorphisms. No relation was established between the variant phenotype (27 variants studied) and a particular MSAP pattern. Chromosome counting showed that 7 of the 11 variant emblings analyzed were characterized by the loss of 1-3 chromosomes. This work showed that both embryogenic suspensions and secondary embryogenesis are reliable for true-to-type propagation of elite material. Molecular analyses revealed that genetic and epigenetic alterations are particularly limited during coffee somatic embryogenesis. The main change in most of the rare phenotypic variants was aneuploidy, indicating that mitotic aberrations play a major role in somaclonal variation in coffee. PMID:23418563

  8. Associating Multivariate Quantitative Phenotypes with Genetic Variants in Family Samples with a Novel Kernel Machine Regression Method.

    PubMed

    Yan, Qi; Weeks, Daniel E; Celedón, Juan C; Tiwari, Hemant K; Li, Bingshan; Wang, Xiaojing; Lin, Wan-Yu; Lou, Xiang-Yang; Gao, Guimin; Chen, Wei; Liu, Nianjun

    2015-12-01

    The recent development of sequencing technology allows identification of association between the whole spectrum of genetic variants and complex diseases. Over the past few years, a number of association tests for rare variants have been developed. Jointly testing for association between genetic variants and multiple correlated phenotypes may increase the power to detect causal genes in family-based studies, but familial correlation needs to be appropriately handled to avoid an inflated type I error rate. Here we propose a novel approach for multivariate family data using kernel machine regression (denoted as MF-KM) that is based on a linear mixed-model framework and can be applied to a large range of studies with different types of traits. In our simulation studies, the usual kernel machine test has inflated type I error rates when applied directly to familial data, while our proposed MF-KM method preserves the expected type I error rates. Moreover, the MF-KM method has increased power compared to methods that either analyze each phenotype separately while considering family structure or use only unrelated founders from the families. Finally, we illustrate our proposed methodology by analyzing whole-genome genotyping data from a lung function study. PMID:26482791

  9. Exploring the quantitative relationship between metabolism and enzymatic phenotype by physiological modeling of glucose metabolism and lactate oxidation in solid tumors

    NASA Astrophysics Data System (ADS)

    Wang, Qian; Vaupel, Peter; Ziegler, Sibylle I.; Shi, Kuangyu

    2015-03-01

    Molecular imaging using PET or hyperpolarized MRI can characterize tumor phenotypes by assessing the related metabolism of certain substrates. However, the interpretation of the substrate turnover in terms of a pathophysiological understanding is not straightforward and only semiquantitative. The metabolism of imaging probes is influenced by a number of factors, such as the microvascular structure or the expression of key enzymes. This study aims to use computational simulation to investigate the relationship between the metabolism behind molecular imaging and the underlying tumor phenotype. The study focused on the pathways of glucose metabolism and lactate oxidation in order to establish the quantitative relationship between the expression of several transporters (GLUT, MCT1 and MCT4), expression of the enzyme hexokinase (HK), microvasculature and the metabolism of glucose or lactate and the extracellular pH distribution. A computational model for a 2D tumor tissue phantom was constructed and the spatio-temporal evolution of related species (e.g. oxygen, glucose, lactate, protons, bicarbonate ions) was estimated by solving reaction-diffusion equations. The proposed model was tested by the verification of the simulation results using in vivo and in vitro literature data. The influences of different expression levels of GLUT, MCT1, MCT4, HK and microvessel distribution on substrate concentrations were analyzed. The major results are consistent with experimental data (e.g. GLUT is more influential to glycolytic flux than HK; extracellular pH is not correlated with MCT expressions) and provide theoretical interpretation of the co-influence of multiple factors of the tumor microenvironment. This computational simulation may assist the generation of hypotheses to bridge the discrepancy between tumor metabolism and the functions of transporters and enzymes. It has the potential to accelerate the development of multi-modal imaging strategies for assessment of tumor phenotypes.

  10. The development of quick, robust, quantitative phenotypic assays for describing the host–nonhost landscape to stripe rust

    PubMed Central

    Dawson, Andrew M.; Bettgenhaeuser, Jan; Gardiner, Matthew; Green, Phon; Hernández-Pinzón, Inmaculada; Hubbard, Amelia; Moscou, Matthew J.

    2015-01-01

    Nonhost resistance is often conceptualized as a qualitative separation from host resistance. Classification into these two states is generally facile, as they fail to fully describe the range of states that exist in the transition from host to nonhost. This poses a problem when studying pathosystems that cannot be classified as either host or nonhost due to their intermediate status relative to these two extremes. In this study, we investigate the efficacy of the Poaceae-stripe rust (Puccinia striiformis Westend.) interaction for describing the host–nonhost landscape. First, using barley (Hordeum vulgare L.) and Brachypodium distachyon (L.) P. Beauv. We observed that macroscopic symptoms of chlorosis and leaf browning were associated with hyphal colonization by P. striiformis f. sp. tritici, respectively. This prompted us to adapt a protocol for visualizing fungal structures into a phenotypic assay that estimates the percent of leaf colonized. Use of this assay in intermediate host and intermediate nonhost systems found the frequency of infection decreases with evolutionary divergence from the host species. Similarly, we observed that the pathogen’s ability to complete its life cycle decreased faster than its ability to colonize leaf tissue, with no incidence of pustules observed in the intermediate nonhost system and significantly reduced pustule formation in the intermediate host system as compared to the host system, barley-P. striiformis f. sp. hordei. By leveraging the stripe rust pathosystem in conjunction with macroscopic and microscopic phenotypic assays, we now hope to dissect the genetic architecture of intermediate host and intermediate nonhost resistance using structured populations in barley and B. distachyon. PMID:26579142

  11. Phenotypic variation of Val1589Met mutation in a four-generation Chinese pedigree with mild paramyotonia congenitia: case report

    PubMed Central

    Xu, Changshui; Qi, Junjia; Shi, Yingying; Feng, Yan; Zang, Weizhou; Zhang, Jiewen

    2015-01-01

    Four generations of a Chinese family with a mild form of paramyotonia congenital was characterized in phenotype and genotype. For each member, clinical history, physical examination, laboratory tests, electrophysiological and gene analyses were recorded and carried out. A potassium loading, exercise and cold provocation were further tested to diagnose the clinical differentiation. All members shared the characteristics of mild muscle cramp and stiffness induced by exercise or exposed to cold. The symptoms were relieved after rest and warming. A Val1589Met mutation at exon 24 of the SCN4A gene appears in affected subjects, while healthy members had a point mutation at position 1513 at exon 24 of the SCN4A gene. The mild phenotype of the paramyotonia congenital in the family had a Val1589Met mutation in the SCN4A gene. Various phenotypes can exist among different families, indicating that family, individual, genetic or environmental factors influence symptoms. PMID:25755818

  12. Phenotypic variation of Val1589Met mutation in a four-generation Chinese pedigree with mild paramyotonia congenitia: case report.

    PubMed

    Xu, Changshui; Qi, Junjia; Shi, Yingying; Feng, Yan; Zang, Weizhou; Zhang, Jiewen

    2015-01-01

    Four generations of a Chinese family with a mild form of paramyotonia congenital was characterized in phenotype and genotype. For each member, clinical history, physical examination, laboratory tests, electrophysiological and gene analyses were recorded and carried out. A potassium loading, exercise and cold provocation were further tested to diagnose the clinical differentiation. All members shared the characteristics of mild muscle cramp and stiffness induced by exercise or exposed to cold. The symptoms were relieved after rest and warming. A Val1589Met mutation at exon 24 of the SCN4A gene appears in affected subjects, while healthy members had a point mutation at position 1513 at exon 24 of the SCN4A gene. The mild phenotype of the paramyotonia congenital in the family had a Val1589Met mutation in the SCN4A gene. Various phenotypes can exist among different families, indicating that family, individual, genetic or environmental factors influence symptoms. PMID:25755818

  13. Opposite risk patterns for autism and schizophrenia are associated with normal variation in birth size: phenotypic support for hypothesized diametric gene-dosage effects

    PubMed Central

    Byars, Sean G.; Stearns, Stephen C.; Boomsma, Jacobus J.

    2014-01-01

    Opposite phenotypic and behavioural traits associated with copy number variation and disruptions to imprinted genes with parent-of-origin effects have led to the hypothesis that autism and schizophrenia share molecular risk factors and pathogenic mechanisms, but a direct phenotypic comparison of how their risks covary has not been attempted. Here, we use health registry data collected on Denmark's roughly 5 million residents between 1978 and 2009 to detect opposing risks of autism and schizophrenia depending on normal variation (mean ± 1 s.d.) in adjusted birth size, which we use as a proxy for diametric gene-dosage variation in utero. Above-average-sized babies (weight, 3691–4090 g; length, 52.8–54.3 cm) had significantly higher risk for autism spectrum (AS) and significantly lower risk for schizophrenia spectrum (SS) disorders. By contrast, below-average-sized babies (2891–3290 g; 49.7–51.2 cm) had significantly lower risk for AS and significantly higher risk for SS disorders. This is the first study directly comparing autism and schizophrenia risks in the same population, and provides the first large-scale empirical support for the hypothesis that diametric gene-dosage effects contribute to these disorders. Only the kinship theory of genomic imprinting predicts the opposing risk patterns that we discovered, suggesting that molecular research on mental disease risk would benefit from considering evolutionary theory. PMID:25232142

  14. Genetic Variation, Heritability, and Diversity Analysis of Upland Rice (Oryza sativa L.) Genotypes Based on Quantitative Traits

    PubMed Central

    Tuhina-Khatun, Mst.; Hanafi, Mohamed M.; Rafii Yusop, Mohd; Wong, M. Y.; Salleh, Faezah M.; Ferdous, Jannatul

    2015-01-01

    Upland rice is important for sustainable crop production to meet future food demands. The expansion in area of irrigated rice faces limitations due to water scarcity resulting from climate change. Therefore, this research aimed to identify potential genotypes and suitable traits of upland rice germplasm for breeding programmes. Forty-three genotypes were evaluated in a randomised complete block design with three replications. All genotypes exhibited a wide and significant variation for 22 traits. The highest phenotypic and genotypic coefficient of variation was recorded for the number of filled grains/panicle and yields/plant (g). The highest heritability was found for photosynthetic rate, transpiration rate, stomatal conductance, intercellular CO2, and number of filled grains/panicle and yields/plant (g). Cluster analysis based on 22 traits grouped the 43 rice genotypes into five clusters. Cluster II was the largest and consisted of 20 genotypes mostly originating from the Philippines. The first four principle components of 22 traits accounted for about 72% of the total variation and indicated a wide variation among the genotypes. The selected best trait of the number of filled grains/panicle and yields/plant (g), which showed high heritability and high genetic advance, could be used as a selection criterion for hybridisation programmes in the future. PMID:26258135

  15. Genetic Variation, Heritability, and Diversity Analysis of Upland Rice (Oryza sativa L.) Genotypes Based on Quantitative Traits.

    PubMed

    Tuhina-Khatun, Mst; Hanafi, Mohamed M; Rafii Yusop, Mohd; Wong, M Y; Salleh, Faezah M; Ferdous, Jannatul

    2015-01-01

    Upland rice is important for sustainable crop production to meet future food demands. The expansion in area of irrigated rice faces limitations due to water scarcity resulting from climate change. Therefore, this research aimed to identify potential genotypes and suitable traits of upland rice germplasm for breeding programmes. Forty-three genotypes were evaluated in a randomised complete block design with three replications. All genotypes exhibited a wide and significant variation for 22 traits. The highest phenotypic and genotypic coefficient of variation was recorded for the number of filled grains/panicle and yields/plant (g). The highest heritability was found for photosynthetic rate, transpiration rate, stomatal conductance, intercellular CO?, and number of filled grains/panicle and yields/plant (g). Cluster analysis based on 22 traits grouped the 43 rice genotypes into five clusters. Cluster II was the largest and consisted of 20 genotypes mostly originating from the Philippines. The first four principle components of 22 traits accounted for about 72% of the total variation and indicated a wide variation among the genotypes. The selected best trait of the number of filled grains/panicle and yields/plant (g), which showed high heritability and high genetic advance, could be used as a selection criterion for hybridisation programmes in the future. PMID:26258135

  16. Geographical variation of genetic and phenotypic traits in the Mexican sailfin mollies, Poecilia velifera and P. petenensis.

    PubMed

    Hankison, S J; Ptacek, M B

    2008-05-01

    Comparing the patterns of population divergence using both neutral genetic and phenotypic traits provides an opportunity to examine the relative importance of evolutionary mechanisms in shaping population differences. We used microsatellite markers to examine population genetic structure in the Mexican sailfin mollies Poecilia velifera and P. petenensis. We compared patterns of genetic structure and divergence to that in two types of phenotypic traits: morphological characters and mating behaviours. Populations within each species were genetically distinct, and conformed to a model of isolation by distance, with populations within different geographical regions being more genetically similar to one another than were populations from different regions. Bayesian clustering and barrier analyses provided additional support for population separation, especially between geographical regions. In contrast, none of the phenotypic traits showed any type of geographical pattern, and population divergence in these traits was uncorrelated with that found in neutral markers. There was also a weaker pattern of regional differences among geographical regions compared to neutral genetic divergence. These results suggest that while divergence in neutral traits is likely a product of population history and genetic drift, phenotypic divergence is governed by different mechanisms, such as natural and sexual selection, and arises at spatial scales independent from those of neutral markers. PMID:18410289

  17. Worm variation made accessible

    PubMed Central

    Snoek, L Basten; Joeri van der Velde, K; Li, Yang; Jansen, Ritsert C; Swertz, Morris A; Kammenga, Jan E

    2014-01-01

    In Caenorhabditis elegans, the recent advances in high-throughput quantitative analyses of natural genetic and phenotypic variation have led to a wealth of data on genotype phenotype relations. This data has resulted in the discovery of genes with major allelic effects and insights in the effect of natural genetic variation on a whole range of complex traits as well as how this variation is distributed across the genome. Regardless of the advances presented in specific studies, the majority of the data generated in these studies had yet to be made easily accessible, allowing for meta-analysis. Not only data in figures or tables but meta-data should be accessible for further investigation and comparison between studies. A platform was created where all the data, phenotypic measurements, genotypes, and mappings can be stored, compared, and new linkages within and between published studies can be discovered. WormQTL focuses on quantitative genetics in Caenorhabditis and other nematode species, whereas WormQTLHD quantitatively links gene expression quantitative trait loci (eQTL) in C. elegans to gene–disease associations in humans. PMID:24843834

  18. The effects of qualitative and quantitative variation of aristolochic acids on preference and performance of a

    E-print Network

    Fordyce, James

    might ignore qualitative variation in activity. Aristolochic acids are alkaloids characteristic broadly be defined as alkaloids. Alkaloids can further be divided into classes of compounds with similar

  19. Population Substructure and Patterns of Quantitative Variation among the Gollas of Southern Andhra Pradesh, India

    E-print Network

    Reddy, B. Mohan; Pfeffer, Alexa; Crawford, Michael H.; Langstieh, Banrida T.

    2001-04-01

    Population substructure and biological differentiation was studied among the Golla, a pastoral caste living in the southern areas of Andhra Pradesh (AP) in India, using 11 anthropometric measurements and 20 quantitative dermatoglyphic variables...

  20. An experimental method for evaluating the contribution of deleterious mutations to quantitative trait variation

    E-print Network

    Kelly, John K.

    1999-06-01

    alleles occur at high frequencies (greater than 0?5). All these quantities can be estimated from phenotypic comparisons among relatives if inbred individuals are included in the pedigree (Cockerham & Weir, 1984; Cornelius, 1988; Mutations and quantitati e...-allele definition for C ad (Cockerham & Weir, 1984), we obtain DBfl 0 S V p 1 C ad .(A5) Linkage disequilibrium will develop among quan- titative trait loci if selection is sustained (Bulmer, 1985). This violates the assumptions of the preceding analysis. However...

  1. A synthetic framework for modeling the genetic basis of phenotypic plasticity and its costs.

    PubMed

    Zhai, Yi; Lv, Yafei; Li, Xin; Wu, Weimiao; Bo, Wenhao; Shen, Dengfeng; Xu, Fang; Pang, Xiaoming; Zheng, Bingsong; Wu, Rongling

    2014-01-01

    The phenotype of an individual is controlled not only by its genes, but also by the environment in which it grows. A growing body of evidence shows that the extent to which phenotypic changes are driven by the environment, known as phenotypic plasticity, is also under genetic control, but an overall picture of genetic variation for phenotypic plasticity remains elusive. Here, we develop a model for mapping quantitative trait loci (QTLs) that regulate environment-induced plastic response. This model enables geneticists to test whether there exist actual QTLs that determine phenotypic plasticity and, if there are, further test how plasticity QTLs control the costs of plastic response by dissecting the genetic correlation of phenotypic plasticity and trait value. The model was used to analyze real data for grain yield of winter wheat (Triticum aestivum), leading to the detection of pleiotropic QTLs and epistatic QTLs that affect phenotypic plasticity and its cost in this crop. PMID:24032980

  2. Validation and Estimation of Additive Genetic Variation Associated with DNA Tests for Quantitative Beef Cattle Traits

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The U.S. National Beef Cattle Evaluation Consortium (NBCEC) has been involved in the validation of commercial DNA tests for quantitative beef quality traits since their first appearance on the U.S. market in the early 2000s. The NBCEC Advisory Council initially requested that the NBCEC set up a syst...

  3. Quantitative mapping of pore fraction variations in silicon nitride using an ultrasonic contact scan technique

    NASA Technical Reports Server (NTRS)

    Roth, Don J.; Kiser, James D.; Swickard, Suzanne M.; Szatmary, Steven A.; Kerwin, David P.

    1993-01-01

    An ultrasonic scan procedure using the pulse-echo contact configuration was employed to obtain maps of pore fraction variations in sintered silicon nitride samples in terms of ultrasonic material properties. Ultrasonic velocity, attenuation coefficient, and reflection coefficient images were obtained simultaneously over a broad band of frequencies (e.g., 30 to 110 MHz) by using spectroscopic analysis. Liquid and membrane (dry) coupling techniques and longitudinal and shear-wave energies were used. The major results include the following: Ultrasonic velocity (longitudinal and shear wave) images revealed and correlated with the extent of average through-thickness pore fraction variations in the silicon nitride disks. Attenuation coefficient images revealed pore fraction nonuniformity due to the scattering that occurred at boundaries between regions of high and low pore fraction. Velocity and attenuation coefficient images were each nearly identical for machined and polished disks, making the method readily applicable to machined materials. Velocity images were similar for wet and membrane coupling. Maps of apparent Poisson's ratio constructed from longitudinal and shear-wave velocities quantified Poisson's ratio variations across a silicon nitride disk. Thermal wave images of a disk indicated transient thermal behavior variations that correlated with observed variations in pore fraction and velocity and attenuation coefficients.

  4. A quantitative evaluation of microstructure by electron back-scattered diffraction pattern quality variations.

    PubMed

    Kang, Suk Hoon; Jin, Hyung-Ha; Jang, Jinsung; Choi, Yong Seok; Oh, Kyu Hwan; Foley, David C; Zhang, Xinghang

    2013-08-01

    Band contrast (BC) is a qualitative measure of electron back-scattered diffraction (EBSD), which is derived from the intensity of the Kikuchi bands. The BC is dependent upon several factors including scanning electron microscope measurement parameters, EBSD camera setup, and the specimen itself (lattice defect and grain orientation). In this study, the effective factors for BC variations and the feasibility of using BC variations for the quantification of microstructure evolutions have been investigated. In addition, the effects of the lattice defect and the grain orientation on the BC variations are studied. Next, a shear-deformed microstructure of 316L stainless steel, which contains nanosized grains and a large portion of twin boundaries, is revealed by BC map and histogram. Recovery and recrystallization of shear-deformed 316L stainless steel are displayed by BC variations during isothermal annealing at 700 and 800°C, respectively. It is observed that the BC turns bright as the shear-deformed crystal structure is recovered or recrystallized. PMID:23920181

  5. Rainfall can explain adaptive phenotypic variation with high gene flow in the New Holland Honeyeater (Phylidonyris novaehollandiae)

    PubMed Central

    Myers, Steven A; Donnellan, Stephen; Kleindorfer, Sonia

    2012-01-01

    Identifying environmentally driven changes in traits that serve an ecological function is essential for predicting evolutionary outcomes of climate change. We examined population genetic structure, sex-specific dispersal patterns, and morphology in relation to rainfall patterns across an island and three peninsulas in South Australia. The study system was the New Holland Honeyeater (Phylidonyris novaehollandiae), a nectarivorous passerine that is a key pollinator species. We predicted that rainfall-related mechanisms would be driving local adaptation of morphological traits, such that in areas of lower rainfall, where nectar is less available, more insectivorous traits – shorter, deeper bills, longer tarsi, and longer wings – would be favored. The study populations differed in phenotype across the Eyre, Yorke, and Fleurieu Peninsulas and Kangaroo Island despite high gene flow (single continuous population) and sex-biased dispersal (males were philopatric and females dispersed). We tested the role of rainfall in shaping the observed phenotypic differences, and found strong support for our predicted relationships: birds in areas of higher rainfall had higher condition indices, as well as longer bill-head length, deeper bills, and shorter tarsi. Bill depth in males in high-rainfall sites showed signals of stabilizing selection, suggesting local adaptation. In addition to these local indications of selection, a global pattern of directional selection toward larger size for bill-head length, bill-nostril length, and wing length was also observed. We suggest this pattern may reflect an adaptive response to the relatively dry conditions that South Australia has experienced over the last decade. We conclude that rainfall has shaped aspects of phenology in P. novaehollandiae, both locally, with different patterns of stabilizing and directional selection, and globally, with evidence of adaptive divergence at a landscape scale. PMID:23145327

  6. Phenotypic variation as an indicator of pesticide stress in gudgeon: Accounting for confounding factors in the wild.

    PubMed

    Shinn, Cândida; Blanchet, Simon; Loot, Géraldine; Lek, Sovan; Grenouillet, Gaël

    2015-12-15

    The response of organisms to environmental stress is currently used in the assessment of ecosystem health. Morphological changes integrate the multiple effects of one or several stress factors upon the development of the exposed organisms. In a natural environment, many factors determine the patterns of morphological differentiation between individuals. However, few studies have sought to distinguish and measure the independent effect of these factors (genetic diversity and structure, spatial structuring of populations, physical-chemical conditions, etc.). Here we investigated the relationship between pesticide levels measured at 11 sites sampled in rivers of the Garonne river basin (SW France) and morphological changes of a freshwater fish species, the gudgeon (Gobio gobio). Each individual sampled was genotyped using 8 microsatellite markers and their phenotype characterized via 17 morphological traits. Our analysis detected a link between population genetic structure (revealed by a Bayesian method) and morphometry (linear discriminant analysis) of the studied populations. We then developed an original method based on general linear models using distance matrices, an extension of the partial Mantel test beyond 3 matrices. This method was used to test the relationship between contamination (toxicity index) and morphometry (PST of morphometric traits), taking into account (1) genetic differentiation between populations (FST), (2) geographical distances between sites, (3) site catchment area, and (4) various physical-chemical parameters for each sampling site. Upon removal of confounding effects, 3 of the 17 morphological traits studied were significantly correlated with pesticide toxicity, suggesting a response of these traits to the anthropogenic stress. These results underline the importance of taking into account the different sources of phenotypic variability between organisms when identifying the stress factors involved. The separation and quantification of the independent effect of such factors provides an interesting outlook regarding the use of these evaluation metrics as indicators of ecosystem health. PMID:26327641

  7. Conflicting selection from fire and seed predation drives fine-scaled phenotypic variation in a widespread North American conifer.

    PubMed

    Talluto, Matthew V; Benkman, Craig W

    2014-07-01

    Recent work has demonstrated that evolutionary processes shape ecological dynamics on relatively short timescales (eco-evolutionary dynamics), but demonstrating these effects at large spatial scales in natural landscapes has proven difficult. We used empirical studies and modeling to investigate how selective pressures from fire and predispersal seed predation affect the evolution of serotiny, an ecologically important trait. Serotiny is a highly heritable key reproductive trait in Rocky Mountain lodgepole pine (Pinus contorta subsp. latifolia), a conifer that dominates millions of hectares in western North America. In these forests, the frequency of serotiny determines postfire seedling density with corresponding community- and ecosystem-level effects. We found that serotinous individuals have a selective advantage at high fire frequencies and low predation pressure; however, very high seed predation shifted the selective advantage to nonserotinous individuals even at high fire frequencies. Simulation modeling suggests that spatial variation in the frequency of serotiny results from heterogeneity in these two selective agents. These results, combined with previous findings showing a negative association between the density of seed predators and the frequency of serotiny at both landscape and continental scales, demonstrate that contemporary patterns in serotiny reflect an evolutionary response to conflicting selection pressures from fire and seed predation. Thus, we show that variation in the frequency of a heritable polygenic trait depends on spatial variation in two dominant selective agents, and, importantly, the effects of the local trait variation propagate with profound consequences to the structure and function of communities and ecosystems across a large landscape. PMID:24979772

  8. Conflicting selection from fire and seed predation drives fine-scaled phenotypic variation in a widespread North American conifer

    PubMed Central

    Talluto, Matthew V.; Benkman, Craig W.

    2014-01-01

    Recent work has demonstrated that evolutionary processes shape ecological dynamics on relatively short timescales (eco-evolutionary dynamics), but demonstrating these effects at large spatial scales in natural landscapes has proven difficult. We used empirical studies and modeling to investigate how selective pressures from fire and predispersal seed predation affect the evolution of serotiny, an ecologically important trait. Serotiny is a highly heritable key reproductive trait in Rocky Mountain lodgepole pine (Pinus contorta subsp. latifolia), a conifer that dominates millions of hectares in western North America. In these forests, the frequency of serotiny determines postfire seedling density with corresponding community- and ecosystem-level effects. We found that serotinous individuals have a selective advantage at high fire frequencies and low predation pressure; however, very high seed predation shifted the selective advantage to nonserotinous individuals even at high fire frequencies. Simulation modeling suggests that spatial variation in the frequency of serotiny results from heterogeneity in these two selective agents. These results, combined with previous findings showing a negative association between the density of seed predators and the frequency of serotiny at both landscape and continental scales, demonstrate that contemporary patterns in serotiny reflect an evolutionary response to conflicting selection pressures from fire and seed predation. Thus, we show that variation in the frequency of a heritable polygenic trait depends on spatial variation in two dominant selective agents, and, importantly, the effects of the local trait variation propagate with profound consequences to the structure and function of communities and ecosystems across a large landscape. PMID:24979772

  9. Quantitation of fixative-induced morphologic and antigenic variation in mouse and human breast cancers

    PubMed Central

    Cardiff, Robert D; Hubbard, Neil E; Engelberg, Jesse A; Munn, Robert J; Miller, Claramae H; Walls, Judith E; Chen, Jane Q; Velásquez-García, Héctor A; Galvez, Jose J; Bell, Katie J; Beckett, Laurel A; Li, Yue-Ju; Borowsky, Alexander D

    2013-01-01

    Quantitative Image Analysis (QIA) of digitized whole slide images for morphometric parameters and immunohistochemistry of breast cancer antigens was used to evaluate the technical reproducibility, biological variability, and intratumoral heterogeneity in three transplantable mouse mammary tumor models of human breast cancer. The relative preservation of structure and immunogenicity of the three mouse models and three human breast cancers was also compared when fixed with representatives of four distinct classes of fixatives. The three mouse mammary tumor cell models were an ER + /PR + model (SSM2), a Her2 + model (NDL), and a triple negative model (MET1). The four breast cancer antigens were ER, PR, Her2, and Ki67. The fixatives included examples of (1) strong cross-linkers, (2) weak cross-linkers, (3) coagulants, and (4) combination fixatives. Each parameter was quantitatively analyzed using modified Aperio Technologies ImageScope algorithms. Careful pre-analytical adjustments to the algorithms were required to provide accurate results. The QIA permitted rigorous statistical analysis of results and grading by rank order. The analyses suggested excellent technical reproducibility and confirmed biological heterogeneity within each tumor. The strong cross-linker fixatives, such as formalin, consistently ranked higher than weak cross-linker, coagulant and combination fixatives in both the morphometric and immunohistochemical parameters. PMID:23399853

  10. The effect of variation in physical properties of porous bioactive glass on the expression and maintenance of the osteoblastic phenotype

    NASA Astrophysics Data System (ADS)

    Effah Kaufmann, Elsie Akosua Biraa

    Revision surgery to replace failed hip implants is a significant health care issue that is expected to escalate as life expectancy increases. A major goal of revision surgery is to reconstruct femoral intramedullary bone-stock loss. To address this problem of bone loss, grafting techniques are widely used. Although fresh autografts remain the optimal material for all forms of surgery seeking to restore structural integrity to the skeleton, it is evident that the supply of such tissue is limited. In recent years, calcium phosphate ceramics have been studied as alternatives to autografts and allografts. The significant limitations associated with the use of biological and synthetic grafts have led to a growing interest in the in vitro synthesis of bone tissue. The approach is to synthesize bone tissue in vitro with the patient's own cells, and use this tissue for the repair of bony defects. Various substrates including metals, polymers, calcium phosphate ceramics and bioactive glasses, have been seeded with osteogenic cells. The selection of bioactive glass in this study is based on the fact that this material has shown an intense beneficial biological effect which has not been reproduced by other biomaterials. Even though the literature provides extensive data on the effect of pore size and porosity on in vivo bone tissue ingrowth into porous materials for joint prosthesis fixation, the data from past studies cannot be applied to the use of bioactive glass as a substrate for the in vitro synthesis of bone tissue. First, unlike the in vivo studies in the literature, this research deals with the growth of bone tissue in vitro. Second, unlike the implants used in past studies, bioactive glass is a degradable and resorbable material. Thus, in order to establish optimal substrate characteristics (porosity and pore size) for bioactive glass, it was important to study these parameters in an in vitro model. We synthesized porous bioactive glass substrates (BG) with varying pore sizes and porosity and determined the effect of substrate properties on the expression and maintenance of the osteoblastic phenotype, using an in vitro culture of osteoblast-like cells. Our data showed that porous bioactive glass substrates support the proliferation and maturation of osteoblast-like cells. Within the conditions of the experiment, we also found that at a given porosity of 44% the pore size of bioactive glass neither directs nor modulates the in vitro expression of the osteoblastic phenotype. On the other hand, at an average pore size of 92 mum, when cultures are maintained for 14 days, cell activity is greatly affected by the substrate porosity. As the porosity increases from 35% to 59%, osteoblast activity is adversely affected. (Abstract shortened by UMI.)

  11. Variations in dysfunction of sister chromatid cohesion in esco2 mutant zebrafish reflect the phenotypic diversity of Roberts syndrome

    PubMed Central

    Percival, Stefanie M.; Thomas, Holly R.; Amsterdam, Adam; Carroll, Andrew J.; Lees, Jacqueline A.; Yost, H. Joseph; Parant, John M.

    2015-01-01

    ABSTRACT Mutations in ESCO2, one of two establishment of cohesion factors necessary for proper sister chromatid cohesion (SCC), cause a spectrum of developmental defects in the autosomal-recessive disorder Roberts syndrome (RBS), warranting in vivo analysis of the consequence of cohesion dysfunction. Through a genetic screen in zebrafish targeting embryonic-lethal mutants that have increased genomic instability, we have identified an esco2 mutant zebrafish. Utilizing the natural transparency of zebrafish embryos, we have developed a novel technique to observe chromosome dynamics within a single cell during mitosis in a live vertebrate embryo. Within esco2 mutant embryos, we observed premature chromatid separation, a unique chromosome scattering, prolonged mitotic delay, and genomic instability in the form of anaphase bridges and micronuclei formation. Cytogenetic studies indicated complete chromatid separation and high levels of aneuploidy within mutant embryos. Amongst aneuploid spreads, we predominantly observed decreases in chromosome number, suggesting that either cells with micronuclei or micronuclei themselves are eliminated. We also demonstrated that the genomic instability leads to p53-dependent neural tube apoptosis. Surprisingly, although many cells required Esco2 to establish cohesion, 10-20% of cells had only weakened cohesion in the absence of Esco2, suggesting that compensatory cohesion mechanisms exist in these cells that undergo a normal mitotic division. These studies provide a unique in vivo vertebrate view of the mitotic defects and consequences of cohesion establishment loss, and they provide a compensation-based model to explain the RBS phenotypes. PMID:26044958

  12. Copy Number Variation in Intron 1 of SOX5 Causes the Pea-comb Phenotype in Chickens

    PubMed Central

    Wright, Dominic; Boije, Henrik; Meadows, Jennifer R. S.; Bed'hom, Bertrand; Gourichon, David; Vieaud, Agathe; Tixier-Boichard, Michèle; Rubin, Carl-Johan; Imsland, Freyja; Hallböök, Finn; Andersson, Leif

    2009-01-01

    Pea-comb is a dominant mutation in chickens that drastically reduces the size of the comb and wattles. It is an adaptive trait in cold climates as it reduces heat loss and makes the chicken less susceptible to frost lesions. Here we report that Pea-comb is caused by a massive amplification of a duplicated sequence located near evolutionary conserved non-coding sequences in intron 1 of the gene encoding the SOX5 transcription factor. This must be the causative mutation since all other polymorphisms associated with the Pea-comb allele were excluded by genetic analysis. SOX5 controls cell fate and differentiation and is essential for skeletal development, chondrocyte differentiation, and extracellular matrix production. Immunostaining in early embryos demonstrated that Pea-comb is associated with ectopic expression of SOX5 in mesenchymal cells located just beneath the surface ectoderm where the comb and wattles will subsequently develop. The results imply that the duplication expansion interferes with the regulation of SOX5 expression during the differentiation of cells crucial for the development of comb and wattles. The study provides novel insight into the nature of mutations that contribute to phenotypic evolution and is the first description of a spontaneous and fully viable mutation in this developmentally important gene. PMID:19521496

  13. Quantitative mapping of a digenic behavioral trait implicates globin variation in C. elegans sensory behaviors.

    PubMed

    McGrath, Patrick T; Rockman, Matthew V; Zimmer, Manuel; Jang, Heeun; Macosko, Evan Z; Kruglyak, Leonid; Bargmann, Cornelia I

    2009-03-12

    Most heritable behavioral traits have a complex genetic basis, but few multigenic traits are understood at a molecular level. Here we show that the C. elegans strains N2 and CB4856 have opposite behavioral responses to simultaneous changes in environmental O(2) and CO(2). We identify two quantitative trait loci (QTL) that affect this trait and map each QTL to a single-gene polymorphism. One gene, npr-1, encodes a previously described neuropeptide receptor whose high activity in N2 promotes CO(2) avoidance. The second gene, glb-5, encodes a neuronal globin domain protein whose high activity in CB4856 modifies behavioral responses to O(2) and combined O(2)/CO(2) stimuli. glb-5 acts in O(2)-sensing neurons to increase O(2)-evoked calcium signals, implicating globins in sensory signaling. An analysis of wild C. elegans strains indicates that the N2 alleles of npr-1 and glb-5 arose recently in the same strain background, possibly as an adaptation to laboratory conditions. PMID:19285466

  14. Minimizing technical variation during sample preparation prior to label-free quantitative mass spectrometry.

    PubMed

    Scheerlinck, E; Dhaenens, M; Van Soom, A; Peelman, L; De Sutter, P; Van Steendam, K; Deforce, D

    2015-12-01

    Sample preparation is the crucial starting point to obtain high-quality mass spectrometry data and can be divided into two main steps in a bottom-up proteomics approach: cell/tissue lysis with or without detergents and a(n) (in-solution) digest comprising denaturation, reduction, alkylation, and digesting of the proteins. Here, some important considerations, among others, are that the reagents used for sample preparation can inhibit the digestion enzyme (e.g., 0.1% sodium dodecyl sulfate [SDS] and 0.5 M guanidine HCl), give rise to ion suppression (e.g., polyethylene glycol [PEG]), be incompatible with liquid chromatography-tandem mass spectrometry (LC-MS/MS) (e.g., SDS), and can induce additional modifications (e.g., urea). Taken together, all of these irreproducible effects are gradually becoming a problem when label-free quantitation of the samples is envisioned such as during the increasingly popular high-definition mass spectrometry (HDMS(E)) and sequential window acquisition of all theoretical fragment ion spectra (SWATH) data-independent acquisition strategies. Here, we describe the detailed validation of a reproducible method with sufficient protein yield for sample preparation without any known LC-MS/MS interfering substances by using 1% sodium deoxycholate (SDC) during both cell lysis and in-solution digest. PMID:26302362

  15. A comparison of isozyme and quantitative genetic variation in Pinus contorta ssp. latifolia by F{sub ST}

    SciTech Connect

    Yang, Rong-Cai; Yeh, F.C.; Yanchuk, A.D.

    1996-03-01

    We employed F-statistics to analyze quantitative and isozyme variation among five populations of Pinus contorta ssp. latifolia, a wind-pollinated outcrossing conifer with wide and continuous distribution in west North America. Estimates of population differentiation (F{sub ST}) for six quantitative traits were compared with the overall estimate of the differentiation (F*{sub ST}) from 19 isozymes that tested neutral to examine whether similar evolutionary processes were involved in morphological and isozyme differentiation. While the F{sub ST} estimates for specific gravity, stem diameter, stem height and branch length were significantly greater than the F*{sub ST} estimate, as judged from the 95% confidence intervals by bootstrapping, the F{sub ST} estimates for branch angle and branch diameter were indistinguishable from the F*{sub ST} estimate. Differentiation in stem height and stem diameter might reflect the inherent adaptation of the populations for rapid growth to escape suppression by neighboring plants during establishment and to regional differences in photoperiod, precipitation and temperature. In contrast, divergences in wood specific gravity and branch length might be correlated responses to population differentiation in stem growth. Possible bias in the estimation of F{sub ST} due to Hardy-Weinberg disequilibrium (F{sub IS} {ne} 0), linkage disequilibrium, maternal effects and nonadditive genetic effects was discussed with special reference to P. contorta ssp. latifolia. 48 refs., 1 fig., 3 tabs.

  16. A Comparison of Isozyme and Quantitative Genetic Variation in Pinus Contorta Ssp. Latifolia by F(st)

    PubMed Central

    Yang, R. C.; Yeh, F. C.; Yanchuk, A. D.

    1996-01-01

    We employed F-statistics to analyze quantitative and isozyme variation among five populations of Pinus contorta ssp. latifolia, a wind-pollinated outcrossing conifer with wide and continuous distribution in west North America. Estimates of population differentiation (F(ST)) for six quantitative traits were compared with the overall estimate of the differentiation (F*(ST)) from 19 isozymes that tested neutral to examine whether similar evolutionary processes were involved in morphological and isozyme differentiation. While the F(ST) estimates for specific gravity, stem diameter, stem height and branch length were significantly greater than the F*(ST) estimate, as judged from the 95% confidence intervals by bootstrapping, the F(ST) estimates for branch angle and branch diameter were indistinguishable from the F*(ST) estimate. Differentiation in stem height and stem diameter might reflect the inherent adaptation of the populations for rapid growth to escape suppression by neighboring plants during establishment and to regional differences in photoperiod, precipitation and temperature. In contrast, divergences in wood specific gravity and branch length might be correlated responses to population differentiation in stem growth. Possible bias in the estimation of F(ST) due to Hardy-Weinberg disequilibrium (F(IS) & 0), linkage disequilibrium, maternal effects and nonadditive genetic effects was discussed with special reference to P. contorta ssp. latifolia. PMID:8849910

  17. Genetic and environmental components of phenotypic variation in immune response and body size of a colonial bird, Delichon urbica (the house martin).

    PubMed

    Christe, P; Moller, A P; Saino, N; De Lope, F

    2000-07-01

    Directional selection for parasite resistance is often intense in highly social host species. Using a partial cross-fostering experiment we studied environmental and genetic variation in immune response and morphology in a highly colonial bird species, the house martin (Delichon urbica). We manipulated intensity of infestation of house martin nests by the haematophagous parasitic house martin bug Oeciacus hirundinis either by spraying nests with a weak pesticide or by inoculating them with 50 bugs. Parasitism significantly affected tarsus length, T cell response, immunoglobulin and leucocyte concentrations. We found evidence of strong environmental effects on nestling body mass, body condition, wing length and tarsus length, and evidence of significant additive genetic variance for wing length and haematocrit. We found significant environmental variance, but no significant additive genetic variance in immune response parameters such as T cell response to the antigenic phytohemagglutinin, immunoglobulins, and relative and absolute numbers of leucocytes. Environmental variances were generally greater than additive genetic variances, and the low heritabilities of phenotypic traits were mainly a consequence of large environmental variances and small additive genetic variances. Hence, highly social bird species such as the house martin, which are subject to intense selection by parasites, have a limited scope for immediate microevolutionary response to selection because of low heritabilities, but also a limited scope for long-term response to selection because evolvability as indicated by small additive genetic coefficients of variation is weak. PMID:10971693

  18. Are we Genomic Mosaics? Variations of the Genome of Somatic Cells can Contribute to Diversify our Phenotypes.

    PubMed

    Astolfi, P A; Salamini, F; Sgaramella, V

    2010-09-01

    Theoretical and experimental evidences support the hypothesis that the genomes and the epigenomes may be different in the somatic cells of complex organisms. In the genome, the differences range from single base substitutions to chromosome number; in the epigenome, they entail multiple postsynthetic modifications of the chromatin. Somatic genome variations (SGV) may accumulate during development in response both to genetic programs, which may differ from tissue to tissue, and to environmental stimuli, which are often undetected and generally irreproducible. SGV may jeopardize physiological cellular functions, but also create novel coding and regulatory sequences, to be exposed to intraorganismal Darwinian selection. Genomes acknowledged as comparatively poor in genes, such as humans', could thus increase their pristine informational endowment. A better understanding of SGV will contribute to basic issues such as the "nature vs nurture" dualism and the inheritance of acquired characters. On the applied side, they may explain the low yield of cloning via somatic cell nuclear transfer, provide clues to some of the problems associated with transdifferentiation, and interfere with individual DNA analysis. SGV may be unique in the different cells types and in the different developmental stages, and thus explain the several hundred gaps persisting in the human genomes "completed" so far. They may compound the variations associated to our epigenomes and make of each of us an "(epi)genomic" mosaic. An ensuing paradigm is the possibility that a single genome (the ephemeral one assembled at fertilization) has the capacity to generate several different brains in response to different environments. PMID:21358981

  19. Quantitative estimation of Holocene surface salinity variation in the Black Sea using dinoflagellate cyst process length

    NASA Astrophysics Data System (ADS)

    Mertens, Kenneth Neil; Bradley, Lee R.; Takano, Yoshihito; Mudie, Petra J.; Marret, Fabienne; Aksu, Ali E.; Hiscott, Richard N.; Verleye, Thomas J.; Mousing, Erik A.; Smyrnova, Ludmila L.; Bagheri, Siamak; Mansor, Mashhor; Pospelova, Vera; Matsuoka, Kazumi

    2012-04-01

    Reconstruction of salinity in the Holocene Black Sea has been an ongoing debate over the past four decades. Here we calibrate summer surface water salinity in the Black Sea, Sea of Azov and Caspian Sea with the process length of the dinoflagellate cyst Lingulodinium machaerophorum. We then apply this calibration to make a regional reconstruction of paleosalinity in the Black Sea, calculated by averaging out process length variation observed at four core sites from the Black Sea with high sedimentation rates and dated by multiple mollusk shell ages. Results show a very gradual change of salinity from ˜14 ± 0.91 psu around 9.9 cal ka BP to a minimum ˜12.3 ± 0.91 psu around 8.5 cal ka BP, reaching current salinities of ˜17.1 ± 0.91 psu around 4.1 cal ka BP. The resolution of our sampling is about 250 years, and it fails to reveal a catastrophic salinization event at ˜9.14 cal ka BP advocated by other researchers. The dinoflagellate cyst salinity-proxy does not record large Holocene salinity fluctuations, and after early Holocene freshening, it shows correspondence to the regional sea-level curve of Brückner et al. (2010) derived from Balabanov (2007).

  20. Genome-wide quantitative assessment of variation in DNA methylation patterns

    PubMed Central

    Xie, Hehuang; Wang, Min; de Andrade, Alexandre; de F. Bonaldo, Maria; Galat, Vasil; Arndt, Kelly; Rajaram, Veena; Goldman, Stewart; Tomita, Tadanori; Soares, Marcelo B.

    2011-01-01

    Genomic DNA methylation contributes substantively to transcriptional regulations that underlie mammalian development and cellular differentiation. Much effort has been made to decipher the molecular mechanisms governing the establishment and maintenance of DNA methylation patterns. However, little is known about genome-wide variation of DNA methylation patterns. In this study, we introduced the concept of methylation entropy, a measure of the randomness of DNA methylation patterns in a cell population, and exploited it to assess the variability in DNA methylation patterns of Alu repeats and promoters. A few interesting observations were made: (i) within a cell population, methylation entropy varies among genomic loci; (ii) among cell populations, the methylation entropies of most genomic loci remain constant; (iii) compared to normal tissue controls, some tumors exhibit greater methylation entropies; (iv) Alu elements with high methylation entropy are associated with high GC content but depletion of CpG dinucleotides and (v) Alu elements in the intronic regions or far from CpG islands are associated with low methylation entropy. We further identified 12 putative allelic-specific methylated genomic loci, including four Alu elements and eight promoters. Lastly, using subcloned normal fibroblast cells, we demonstrated the highly variable methylation patterns are resulted from low fidelity of DNA methylation inheritance. PMID:21278160

  1. Quantitative Monitoring for Enhanced Geothermal Systems Using Double-Difference Waveform Inversion with Spatially-Variant Total-Variation Regularization

    SciTech Connect

    Lin, Youzuo; Huang, Lianjie; Zhang, Zhigang

    2011-01-01

    Double-difference waveform inversion is a promising tool for quantitative monitoring for enhanced geothermal systems (EGS). The method uses time-lapse seismic data to jointly inverts for reservoir changes. Due to the ill-posedness of waveform inversion, it is a great challenge to obtain reservoir changes accurately and efficiently, particularly when using timelapse seismic reflection data. To improve reconstruction, we develop a spatially-variant total-variation regularization scheme into double-difference waveform inversion to improve the inversion accuracy and robustness. The new regularization scheme employs different regularization parameters in different regions of the model to obtain an optimal regularization in each area. We compare the results obtained using a spatially-variant parameter with those obtained using a constant regularization parameter. Utilizing a spatially-variant regularization scheme, the target monitoring regions are well reconstructed and the image noise is significantly reduced outside the monitoring regions. Our numerical examples demonstrate that the spatially-variant total-variation regularization scheme provides the flexibility to regularize local regions based on the a priori spatial information without increasing computational costs and the computer memory requirement.

  2. Genetic and phenotypic traits of streptomycetes used to characterize antibiotic activities of

    E-print Network

    Thomas, David D.

    Genetic and phenotypic traits of streptomycetes used to characterize antibiotic activities of field-collected microbes Anita L. Davelos, Kun Xiao, Jennifer M. Flor, and Linda L. Kinkel Abstract: Although antibiotic of antibiotic-producing microbial populations in soil. Indeed, quantitative information on the variation

  3. Mapping phenotypic, expression and transmission ratio distortion QTL using RAD markers in the Lake

    E-print Network

    Bernatchez, Louis

    benthic relative by numerous life history, behavioural, morphological and gene expression traits selection may operate. These include variation in quantitative phenotypic traits, regulation of gene-Sequencing method to a hybrid backcross family to reconstruct a high-density genetic linkage map and perform QTL

  4. The genetic and molecular origin of natural variation for the fragrance trait in an elite Malaysian aromatic rice through quantitative trait loci mapping using SSR and gene-based markers.

    PubMed

    Golestan Hashemi, Farahnaz Sadat; Rafii, Mohd Y; Ismail, Mohd Razi; Mohamed, Mahmud Tengku Muda; Rahim, Harun A; Latif, Mohammad Abdul; Aslani, Farzad

    2015-01-25

    MRQ74, a popular aromatic Malaysian landrace, allows for charging considerably higher prices than non-aromatic landraces. Thus, breeding this profitable trait has become a priority for Malaysian rice breeding. Despite many studies on aroma genetics, ambiguities considering its genetic basis remain. It has been observed that identifying quantitative trait loci (QTLs) based on anchor markers, particularly candidate genes controlling a trait of interest, can increase the power of QTL detection. Hence, this study aimed to locate QTLs that influence natural variations in rice scent using microsatellites and candidate gene-based sequence polymorphisms. For this purpose, an F2 mapping population including 189 individual plants was developed by MRQ74 crosses with 'MR84', a non-scented Malaysian accession. Additionally, qualitative and quantitative approaches were applied to obtain a phenotype data framework. Consequently, we identified two QTLs on chromosomes 4 and 8. These QTLs explained from 3.2% to 39.3% of the total fragrance phenotypic variance. In addition, we could resolve linkage group 8 by adding six gene-based primers in the interval harboring the most robust QTL. Hence, we could locate a putative fgr allele in the QTL found on chromosome 8 in the interval RM223-SCU015RM (1.63cM). The identified QTLs represent an important step toward recognition of the rice flavor genetic control mechanism. In addition, this identification will likely accelerate the progress of the use of molecular markers for gene isolation, gene-based cloning, and marker-assisted selection breeding programs aimed at improving rice cultivars. PMID:25445269

  5. Phenotypic switching in bacteria

    NASA Astrophysics Data System (ADS)

    Merrin, Jack

    Living matter is a non-equilibrium system in which many components work in parallel to perpetuate themselves through a fluctuating environment. Physiological states or functionalities revealed by a particular environment are called phenotypes. Transitions between phenotypes may occur either spontaneously or via interaction with the environment. Even in the same environment, genetically identical bacteria can exhibit different phenotypes of a continuous or discrete nature. In this thesis, we pursued three lines of investigation into discrete phenotypic heterogeneity in bacterial populations: the quantitative characterization of the so-called bacterial persistence, a theoretical model of phenotypic switching based on those measurements, and the design of artificial genetic networks which implement this model. Persistence is the phenotype of a subpopulation of bacteria with a reduced sensitivity to antibiotics. We developed a microfluidic apparatus, which allowed us to monitor the growth rates of individual cells while applying repeated cycles of antibiotic treatments. We were able to identify distinct phenotypes (normal and persistent) and characterize the stochastic transitions between them. We also found that phenotypic heterogeneity was present prior to any environmental cue such as antibiotic exposure. Motivated by the experiments with persisters, we formulated a theoretical model describing the dynamic behavior of several discrete phenotypes in a periodically varying environment. This theoretical framework allowed us to quantitatively predict the fitness of dynamic populations and to compare survival strategies according to environmental time-symmetries. These calculations suggested that persistence is a strategy used by bacterial populations to adapt to fluctuating environments. Knowledge of the phenotypic transition rates for persistence may provide statistical information about the typical environments of bacteria. We also describe a design of artificial genetic networks that would implement a more general theoretical model of phenotypic switching. We will use a new cloning strategy in order to systematically assemble a large number of genetic features, such as site-specific recombination components from the R64 plasmid, which invert several coexisting DNA segments. The inversion of these segments would lead to discrete phenotypic transitions inside a living cell. These artificial phenotypic switches can be controlled precisely in experiments and may serve as a benchmark for their natural counterparts.

  6. Quantitative flavonoid variation accompanied by change of flower colors in Edgeworthia chrysantha, Pittosporum tobira and Wisteria floribunda.

    PubMed

    Ono, Megumi; Iwashina, Tsukasa

    2015-03-01

    The flavonoids in the flowers of Edgeworthia chrysantha, Pittosporum tobira and Wisteria floribunda were isolated and identified. Quercetin and kaempferol 3-O-glucosides and 3-O-rutinosides were found in E. chrysantha, and quercetin 3-O-rutinoside, 3-O-glucoside and 3-O-pentosylrhamnosylglucoside, kaempferol 3-O-robinobioside, 3-O-rutinoside, 3-O-glucoside and 3-O-pentosylrhamnosylglucoside, and isorhamnetin 3-O-rutinoside were isolated from P. tobira. Ten flavonoids, quercetin 3-O-sophoroside, 3-O-rutinoside, 3-O-glucoside, kaempferol 3-O-sophoroside and 3-O-glucoside, luteolin 5-O-glucoside, 7- O-glucoside and 7-O-hexoside, and apigenin 7-O-glucoside and 4'-O-hexoside were isolated from W floribunda. The major pigments of E. chrysantha were carotenoids. Their content decreased with the change in flower color to white from yellow via cream, and total flavonoid content also slightly decreased by ca. 0.8 in cream and ca. 0.9 fold in white flowers. In contrast with E. chrysantha, white flowers of P. tobira turn to cream and then yellow in which the major pigments are also carotenoids. In this species, both carotenoid and flavonoid contents are gradually increased from white to yellow flowers. Though the petal color of Wisteria floribunda is mauve, due to anthocyanin pigments, the yellow areas are due to carotenoids; these turn to white in the late flowering stage. However, their flavonoid contents were essentially the same among the yellow, cream and white spots of flags. Thus, it was shown by HPLC analysis of the flower flavonoids of E. chrysantha, P. tobira and W. floribunda, although the visible pigments such as carotenoids and anthocyanins are quantitatively varied, the quantitative variation in UV-absorbing substances, such as flavones and flavonols, differs with plant species. PMID:25924517

  7. Molecular dissection of phenotypic variation between Gossypium hirsutum and Gossypium barbadense (cotton) by a backcross-self approach: III. Fiber length.

    PubMed

    Chee, Peng W; Draye, Xavier; Jiang, Chun-Xiao; Decanini, Laura; Delmonte, Terrie A; Bredhauer, Robert; Smith, C Wayne; Paterson, Andrew H

    2005-08-01

    A backcross-self population from a cross between Gossypium hirsutum and G. barbadense was used to dissect the molecular basis of genetic variation governing 15 parameters that reflect fiber length. Applying a detailed restriction fragment length polymorphism (RFLP) map to 3,662 BC(3)F(2) plants from 24 independently derived BC(3) families, we detected 28, nine, and eight quantitative trait loci (QTLs) for fiber length, length uniformity, and short fiber content, respectively. For eight, six, and two chromosomal regions containing quantitative trait loci (QTLs) for fiber length, length uniformity, and short fiber content (respectively), two-way analysis of variance showed a significant (P<0.001) among-family genotypic effect. A total of 13, two, and four loci showed genotype x family interaction, illustrating some of the complexities that are likely to be faced in introgression of exotic germplasm into the gene pool of cultivated cotton. Co-location of many QTLs for fiber length, length uniformity, and short fiber content accounted for correlations among these traits, while the discovery of many QTLs unique to each trait suggests that maximum genetic gain will require breeding efforts that target each trait (or an index including all three). The availability of DNA markers linked to G. barbadense QTLs identified in this and other studies promise to assist breeders in transferring and maintaining valuable traits from exotic sources during cultivar development. PMID:15983757

  8. Dissecting quantitative trait variation in the resequencing era: complementarity of bi-parental, multi-parental and association panels.

    PubMed

    Pascual, Laura; Albert, Elise; Sauvage, Christopher; Duangjit, Janejira; Bouchet, Jean-Paul; Bitton, Frédérique; Desplat, Nelly; Brunel, Dominique; Le Paslier, Marie-Christine; Ranc, Nicolas; Bruguier, Laure; Chauchard, Betty; Verschave, Philippe; Causse, Mathilde

    2016-01-01

    Quantitative trait loci (QTL) have been identified using traditional linkage mapping and positional cloning identified several QTLs. However linkage mapping is limited to the analysis of traits differing between two lines and the impact of the genetic background on QTL effect has been underlined. Genome-wide association studies (GWAs) were proposed to circumvent these limitations. In tomato, we have shown that GWAs is possible, using the admixed nature of cherry tomato genomes that reduces the impact of population structure. Nevertheless, GWAs success might be limited due to the low decay of linkage disequilibrium, which varies along the genome in this species. Multi-parent advanced generation intercross (MAGIC) populations offer an alternative to traditional linkage and GWAs by increasing the precision of QTL mapping. We have developed a MAGIC population by crossing eight tomato lines whose genomes were resequenced. We showed the potential of the MAGIC population when coupled with whole genome sequencing to detect candidate single nucleotide polymorphisms (SNPs) underlying the QTLs. QTLs for fruit quality traits were mapped and related to the variations detected at the genome sequence and expression levels. The advantages and limitations of the three types of population, in the context of the available genome sequence and resequencing facilities, are discussed. PMID:26566830

  9. Quantitative estimation of density variation in high-speed flows through inversion of the measured wavefront distortion

    NASA Astrophysics Data System (ADS)

    Medhi, Biswajit; Hegde, Gopalkrishna Mahadeva; Reddy, Kalidevapura Polareddy Jagannath; Roy, Debasish; Vasu, Ram Mohan

    2014-12-01

    A simple method employing an optical probe is presented to measure density variations in a hypersonic flow obstructed by a test model in a typical shock tunnel. The probe has a plane light wave trans-illuminating the flow and casting a shadow of a random dot pattern. Local slopes of the distorted wavefront are obtained from shifts of the dots in the pattern. Local shifts in the dots are accurately measured by cross-correlating local shifted shadows with the corresponding unshifted originals. The measured slopes are suitably unwrapped by using a discrete cosine transform based phase unwrapping procedure and also through iterative procedures. The unwrapped phase information is used in an iterative scheme for a full quantitative recovery of density distribution in the shock around the model through refraction tomographic inversion. Hypersonic flow field parameters around a missile shaped body at a free-stream Mach number of 5.8 measured using this technique are compared with the numerically estimated values.

  10. Association analysis of the ACTN3 R577X polymorphism and complex quantitative body composition and performance phenotypes in adolescent Greeks.

    PubMed

    Moran, Colin N; Yang, Nan; Bailey, Mark E S; Tsiokanos, Athanasios; Jamurtas, Athanasios; MacArthur, Daniel G; North, Kathryn; Pitsiladis, Yannis P; Wilson, Richard H

    2007-01-01

    The functional allele (577R) of ACTN3, which encodes human alpha-actinin-3, has been reported to be associated with elite athletic status and with response to resistance training, while the nonfunctional allele (577X) has been proposed as a candidate metabolically thrifty allele. In a study of 992 adolescent Greeks, we show that there is a significant association (P=0.003) between the ACTN3 R577X polymorphism and 40 m sprint time in males that accounts for 2.3% of phenotypic variance, with the 577R allele contributing to faster times in an additive manner. The R577X polymorphism is not associated with other power phenotypes related to 40 m sprint, nor with an endurance phenotype. Furthermore, the polymorphism is not associated with obesity-related phenotypes in our population, suggesting that the 577X allele is not a thrifty allele, and thus the persistence of this null allele must be explained in other terms. PMID:17033684

  11. Pseudohyphal variations of yeasts exposed to specific space flight parameters.

    PubMed

    Volz, P A; Hunter, R L

    1998-01-01

    Phenotypes of Saccharomyces cerevisiae and Rhodotorula rubra exposed to specific parameters of space flight, which were measured both quantitatively and qualitatively, produced variations in pseudohyphal formation. Both the length of the parent and branch psuedohyphal filaments varied according to specific wavelengths and energy levels of UV light exposures when phenotypic isolates were compared with the parent or ground control isolate of each yeast species. PMID:9881461

  12. Phenotypic and Genetic Characterization of Avian Influenza H5N2 Viruses with Intra- and Inter-Duck Variations in Taiwan

    PubMed Central

    Li, Yao-Tsun; Lai, Ching-Yu; Kao, Chuan-Liang; Yang, Chinglai; Wang, Won-Bo; King, Chwan-Chuen

    2015-01-01

    Background Human infections with avian influenza viruses (AIVs) have frequently raised global concerns of emerging, interspecies-transmissible viruses with pandemic potential. Waterfowl, the predominant reservoir of influenza viruses in nature, harbor precursors of different genetic lineages that have contributed to novel pandemic influenza viruses in the past. Methods Two duck influenza H5N2 viruses, DV518 and DV413, isolated through virological surveillance at a live-poultry market in Taiwan, showed phylogenetic relatedness but exhibited different replication capabilities in mammalian Madin-Darby Canine Kidney (MDCK) cells. This study characterizes the replication properties of the two duck H5N2 viruses and the determinants involved. Results The DV518 virus replicated more efficiently than DV413 in both MDCK and chicken DF1 cells. Interestingly, the infection of MDCK cells by DV518 formed heterogeneous plaques with great differences in size [large (L) and small (S)], and the two viral strains (p518-L and p518-S) obtained from plaque purification exhibited distinguishable replication kinetics in MDCK cells. Nonetheless, both plaque-purified DV518 strains still maintained their growth advantages over the plaque-purified p413 strain. Moreover, three amino acid substitutions in PA (P224S), PB2 (E72D), and M1 (A128T) were identified in intra-duck variations (p518-L vs p518-S), whereas other changes in HA (N170D), NA (I56T), and NP (Y289H) were present in inter-duck variations (DV518 vs DV413). Both p518-L and p518-S strains had the N170D substitution in HA, which might be related to their greater binding to MDCK cells. Additionally, polymerase activity assays on 293T cells demonstrated the role of vRNP in modulating the replication capability of the duck p518-L viruses in mammalian cells. Conclusion These results demonstrate that intra-host phenotypic variation occurs even within an individual duck. In view of recent human infections by low pathogenic AIVs, this study suggests possible determinants involved in the stepwise selection of virus variants from the duck influenza virus population which may facilitate inter-species transmission. PMID:26263554

  13. Comparison of quantitative and molecular variation in agroforestry populations of the shea tree (Vitellaria paradoxa C.F. Gaertn) in Mali.

    PubMed

    Sanou, H; Lovett, P N; Bouvet, J-M

    2005-07-01

    In this study we investigated the within- and between-population genetic variation using microsatellite markers and quantitative traits of the shea tree, Vitellaria paradoxa, an important agroforestry tree species of the Sudano-Sahelian region in Africa. Eleven populations were sampled across Mali and in northern Côte d'Ivoire. Leaf size and form and growth traits were measured in a progeny test at the nursery stage. Eight microsatellites were used to assess neutral genetic variation. Low levels of heterozygosity were recorded (1.6-3.0 alleles/locus; H(E) = 0.25-0.42) and the fixation index (F(IS) = -0.227-0.186) was not significantly different from zero suggesting that Hardy-Weinberg equilibrium is encountered in all populations sampled. Quantitative traits exhibited a strong genetic variation between populations and between families within populations. The degree of population differentiation of the quantitative traits (Q(ST) = 0.055-0.283, Q(STmean) = 0.189) strongly exceeds that in eight microsatellite loci (F(ST) = -0.011-0.142, F(STmean) = 0.047). Global and pairwise F(ST) values were very low and not significantly different from zero suggesting agroforestry practices are amplifying gene flow (Nm = 5.07). The population means for quantitative traits and the rainfall variable were not correlated, showing variation was not linked with this climatic cline. It is suggested that this marked differentiation for quantitative traits, independent of environmental clines and despite a high gene flow, is a result of local adaptation and human selection of shea trees. This process has induced high linkage disequilibrium between underlying loci of polygenic characters. PMID:15969738

  14. Quantitative trait loci in hop (Humulus lupulus L.) reveal complex genetic architecture underlying variation in sex, yield and cone chemistry

    PubMed Central

    2013-01-01

    Background Hop (Humulus lupulus L.) is cultivated for its cones, the secondary metabolites of which contribute bitterness, flavour and aroma to beer. Molecular breeding methods, such as marker assisted selection (MAS), have great potential for improving the efficiency of hop breeding. The success of MAS is reliant on the identification of reliable marker-trait associations. This study used quantitative trait loci (QTL) analysis to identify marker-trait associations for hop, focusing on traits related to expediting plant sex identification, increasing yield capacity and improving bittering, flavour and aroma chemistry. Results QTL analysis was performed on two new linkage maps incorporating transferable Diversity Arrays Technology (DArT) markers. Sixty-three QTL were identified, influencing 36 of the 50 traits examined. A putative sex-linked marker was validated in a different pedigree, confirming the potential of this marker as a screening tool in hop breeding programs. An ontogenetically stable QTL was identified for the yield trait dry cone weight; and a QTL was identified for essential oil content, which verified the genetic basis for variation in secondary metabolite accumulation in hop cones. A total of 60 QTL were identified for 33 secondary metabolite traits. Of these, 51 were pleiotropic/linked, affecting a substantial number of secondary metabolites; nine were specific to individual secondary metabolites. Conclusions Pleiotropy and linkage, found for the first time to influence multiple hop secondary metabolites, have important implications for molecular selection methods. The selection of particular secondary metabolite profiles using pleiotropic/linked QTL will be challenging because of the difficulty of selecting for specific traits without adversely changing others. QTL specific to individual secondary metabolites, however, offer unequalled value to selection programs. In addition to their potential for selection, the QTL identified in this study advance our understanding of the genetic control of traits of current economic and breeding significance in hop and demonstrate the complex genetic architecture underlying variation in these traits. The linkage information obtained in this study, based on transferable markers, can be used to facilitate the validation of QTL, crucial to the success of MAS. PMID:23718194

  15. Phenotypic integration between antipredator behavior and camouflage pattern in juvenile sticklebacks.

    PubMed

    Kim, Sin-Yeon; Velando, Alberto

    2015-03-01

    Predation is a strong selective force that promotes the evolution of antipredator behaviors and camouflage in prey animals. However, the independent evolution of single traits cannot explain how observed phenotypic variations of these traits are maintained within populations. We studied genetic and phenotypic correlations between antipredator behaviors (shoaling and risk-taking) and morphology traits (pigmentation and size) in juvenile three-spined sticklebacks by using pedigree-based quantitative genetic analysis to test phenotypic integration (or complex phenotype) as an evolutionary response to predation risk. Individuals with strongly melanized (i.e., camouflaged) phenotype and genotype were less sociable to conspecifics, but bolder during foraging under predation risk. Individuals with faster growing phenotype and genotype were bolder, and those with lager eyes were more fearful. These phenotypic integrations were not confounded with correlated plastic responses to predation risk because the phenotypes were measured in naïve fish born in the laboratory, but originated from a natural population with predation pressure. Consistent selection for particular combinations of traits under predation pressure or pleiotropic genes might influence the maintenance of the genetic (co)variations and polymorphism in melanin color, growth trajectory, and behavior patterns. PMID:25572122

  16. Expression Quantitative Trait Loci Information Improves Predictive Modeling of Disease Relevance of Non-Coding Genetic Variation

    PubMed Central

    Raj, Towfique; McGeachie, Michael J.; Qiu, Weiliang; Ziniti, John P.; Stubbs, Benjamin J.; Liang, Liming; Martinez, Fernando D.; Strunk, Robert C.; Lemanske, Robert F.; Liu, Andrew H.; Stranger, Barbara E.; Carey, Vincent J.; Raby, Benjamin A.

    2015-01-01

    Disease-associated loci identified through genome-wide association studies (GWAS) frequently localize to non-coding sequence. We and others have demonstrated strong enrichment of such single nucleotide polymorphisms (SNPs) for expression quantitative trait loci (eQTLs), supporting an important role for regulatory genetic variation in complex disease pathogenesis. Herein we describe our initial efforts to develop a predictive model of disease-associated variants leveraging eQTL information. We first catalogued cis-acting eQTLs (SNPs within 100kb of target gene transcripts) by meta-analyzing four studies of three blood-derived tissues (n = 586). At a false discovery rate < 5%, we mapped eQTLs for 6,535 genes; these were enriched for disease-associated genes (P < 10?04), particularly those related to immune diseases and metabolic traits. Based on eQTL information and other variant annotations (distance from target gene transcript, minor allele frequency, and chromatin state), we created multivariate logistic regression models to predict SNP membership in reported GWAS. The complete model revealed independent contributions of specific annotations as strong predictors, including evidence for an eQTL (odds ratio (OR) = 1.2–2.0, P < 10?11) and the chromatin states of active promoters, different classes of strong or weak enhancers, or transcriptionally active regions (OR = 1.5–2.3, P < 10?11). This complete prediction model including eQTL association information ultimately allowed for better discrimination of SNPs with higher probabilities of GWAS membership (6.3–10.0%, compared to 3.5% for a random SNP) than the other two models excluding eQTL information. This eQTL-based prediction model of disease relevance can help systematically prioritize non-coding GWAS SNPs for further functional characterization. PMID:26474488

  17. Variation in Adult Plant Phenotypes and Partitioning among Seed and Stem-Borne Roots across Brachypodium distachyon Accessions to Exploit in Breeding Cereals for Well-Watered and Drought Environments.

    PubMed

    Chochois, Vincent; Vogel, John P; Rebetzke, Gregory J; Watt, Michelle

    2015-07-01

    Seedling roots enable plant establishment. Their small phenotypes are measured routinely. Adult root systems are relevant to yield and efficiency, but phenotyping is challenging. Root length exceeds the volume of most pots. Field studies measure partial adult root systems through coring or use seedling roots as adult surrogates. Here, we phenotyped 79 diverse lines of the small grass model Brachypodium distachyon to adults in 50-cm-long tubes of soil with irrigation; a subset of 16 lines was droughted. Variation was large (total biomass, ×8; total root length [TRL], ×10; and root mass ratio, ×6), repeatable, and attributable to genetic factors (heritabilities ranged from approximately 50% for root growth to 82% for partitioning phenotypes). Lines were dissected into seed-borne tissues (stem and primary seminal axile roots) and stem-borne tissues (tillers and coleoptile and leaf node axile roots) plus branch roots. All lines developed one seminal root that varied, with branch roots, from 31% to 90% of TRL in the well-watered condition. With drought, 100% of TRL was seminal, regardless of line because nodal roots were almost always inhibited in drying topsoil. Irrigation stimulated nodal roots depending on genotype. Shoot size and tillers correlated positively with roots with irrigation, but partitioning depended on genotype and was plastic with drought. Adult root systems of B. distachyon have genetic variation to exploit to increase cereal yields through genes associated with partitioning among roots and their responsiveness to irrigation. Whole-plant phenotypes could enhance gain for droughted environments because root and shoot traits are coselected. PMID:25975834

  18. Rapid evolution of quantitative traits: theoretical perspectives

    PubMed Central

    Kopp, Michael; Matuszewski, Sebastian

    2014-01-01

    An increasing number of studies demonstrate phenotypic and genetic changes in natural populations that are subject to climate change, and there is hope that some of these changes will contribute to avoiding species extinctions (‘evolutionary rescue’). Here, we review theoretical models of rapid evolution in quantitative traits that can shed light on the potential for adaptation to a changing climate. Our focus is on quantitative-genetic models with selection for a moving phenotypic optimum. We point out that there is no one-to-one relationship between the rate of adaptation and population survival, because the former depends on relative fitness and the latter on absolute fitness. Nevertheless, previous estimates that sustainable rates of genetically based change usually do not exceed 0.1 haldanes (i.e., phenotypic standard deviations per generation) are probably correct. Survival can be greatly facilitated by phenotypic plasticity, and heritable variation in plasticity can further speed up genetic evolution. Multivariate selection and genetic correlations are frequently assumed to constrain adaptation, but this is not necessarily the case and depends on the geometric relationship between the fitness landscape and the structure of genetic variation. Similar conclusions hold for adaptation to shifting spatial gradients. Recent models of adaptation in multispecies communities indicate that the potential for rapid evolution is strongly influenced by interspecific competition. PMID:24454555

  19. Identifying the loci that influence quantitative trait variation in oats: Lessons from human population-based GWAS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In recent years, the resources have become available to enable genome-wide genotype-phenotype association analyses in cereal crops using thousands of genetic markers measured on hundreds of lines. One open question is whether these resources are sufficient to identify the loci influencing quantitati...

  20. Quantitative Autism Traits in First Degree Relatives: Evidence for the Broader Autism Phenotype in Fathers, but Not in Mothers and Siblings

    ERIC Educational Resources Information Center

    De la Marche, Wouter; Noens, Ilse; Luts, Jan; Scholte, Evert; Van Huffel, Sabine; Steyaert, Jean

    2012-01-01

    Autism spectrum disorder (ASD) symptoms are present in unaffected relatives and individuals from the general population. Results are inconclusive, however, on whether unaffected relatives have higher levels of quantitative autism traits (QAT) or not. This might be due to differences in research populations, because behavioral data and molecular…

  1. Behavioral idiosyncrasy reveals genetic control of phenotypic variability.

    PubMed

    Ayroles, Julien F; Buchanan, Sean M; O'Leary, Chelsea; Skutt-Kakaria, Kyobi; Grenier, Jennifer K; Clark, Andrew G; Hartl, Daniel L; de Bivort, Benjamin L

    2015-05-26

    Quantitative genetics has primarily focused on describing genetic effects on trait means and largely ignored the effect of alternative alleles on trait variability, potentially missing an important axis of genetic variation contributing to phenotypic differences among individuals. To study the genetic effects on individual-to-individual phenotypic variability (or intragenotypic variability), we used Drosophila inbred lines and measured the spontaneous locomotor behavior of flies walking individually in Y-shaped mazes, focusing on variability in locomotor handedness, an assay optimized to measure variability. We discovered that some lines had consistently high levels of intragenotypic variability among individuals, whereas lines with low variability behaved as although they tossed a coin at each left/right turn decision. We demonstrate that the degree of variability is itself heritable. Using a genome-wide association study (GWAS) for the degree of intragenotypic variability as the phenotype across lines, we identified several genes expressed in the brain that affect variability in handedness without affecting the mean. One of these genes, Ten-a, implicates a neuropil in the central complex of the fly brain as influencing the magnitude of behavioral variability, a brain region involved in sensory integration and locomotor coordination. We validated these results using genetic deficiencies, null alleles, and inducible RNAi transgenes. Our study reveals the constellation of phenotypes that can arise from a single genotype and shows that different genetic backgrounds differ dramatically in their propensity for phenotypic variabililty. Because traditional mean-focused GWASs ignore the contribution of variability to overall phenotypic variation, current methods may miss important links between genotype and phenotype. PMID:25953335

  2. Population sub-structure and patterns of quantitative variation among the Gollas of Southern Andhra Pradesh, India

    E-print Network

    Reddy, B. Mohan; Pfeffer, Alexa; Crawford, Michael H.; Langstieh, Banrida T.

    2001-08-01

    Population substructure and biological differentiation was studied among the Golla, a pastoral caste living in the southern areas of Andhra Pradesh (AP) in India, using 11 anthropometric measurements and 20 quantitative dermatoglyphic variables...

  3. Dissecting Genetic Networks Underlying Complex Phenotypes: The Theoretical Framework

    PubMed Central

    Zhang, Fan; Zhai, Hu-Qu; Paterson, Andrew H.; Xu, Jian-Long; Gao, Yong-Ming; Zheng, Tian-Qing; Wu, Rong-Ling; Fu, Bin-Ying; Ali, Jauhar; Li, Zhi-Kang

    2011-01-01

    Great progress has been made in genetic dissection of quantitative trait variation during the past two decades, but many studies still reveal only a small fraction of quantitative trait loci (QTLs), and epistasis remains elusive. We integrate contemporary knowledge of signal transduction pathways with principles of quantitative and population genetics to characterize genetic networks underlying complex traits, using a model founded upon one-way functional dependency of downstream genes on upstream regulators (the principle of hierarchy) and mutual functional dependency among related genes (functional genetic units, FGU). Both simulated and real data suggest that complementary epistasis contributes greatly to quantitative trait variation, and obscures the phenotypic effects of many ‘downstream’ loci in pathways. The mathematical relationships between the main effects and epistatic effects of genes acting at different levels of signaling pathways were established using the quantitative and population genetic parameters. Both loss of function and “co-adapted” gene complexes formed by multiple alleles with differentiated functions (effects) are predicted to be frequent types of allelic diversity at loci that contribute to the genetic variation of complex traits in populations. Downstream FGUs appear to be more vulnerable to loss of function than their upstream regulators, but this vulnerability is apparently compensated by different FGUs of similar functions. Other predictions from the model may account for puzzling results regarding responses to selection, genotype by environment interaction, and the genetic basis of heterosis. PMID:21283795

  4. Topological Phenotypes in Complex Leaf Venation Networks

    NASA Astrophysics Data System (ADS)

    Ronellenfitsch, Henrik; Lasser, Jana; Daly, Douglas; Katifori, Eleni

    2015-03-01

    The leaves of vascular plants contain highly complex venation networks consisting of recursively nested, hierarchically organized loops. We analyze the topology of the venation of leaves from ca. 200 species belonging to ca. 10 families, defining topological metrics that quantify the hierarchical nestedness of the network cycles. We find that most of the venation variability can be described by a two dimensional phenotypic space, where one dimension consists of a linear combination of geometrical metrics and the other dimension of topological, previously uncharacterized metrics. We show how this new topological dimension in the phenotypic space significantly improves identification of leaves from fragments, by calculating a ``leaf fingerprint'' from the topology and geometry of the higher order veins. Further, we present a simple model suggesting that the topological phenotypic traits can be explained by noise effects and variations in the timing of higher order vein developmental events. This work opens the path to (a) new quantitative identification techniques for leaves which go beyond simple geometric traits such as vein density and (b) topological quantification of other planar or almost planar networks such as arterial vaculature in the neocortex and lung tissue.

  5. Explaining Quantitative Variation in the Rate of Optional Infinitive Errors across Languages: A Comparison of MOSAIC and the Variational Learning Model

    ERIC Educational Resources Information Center

    Freudenthal, Daniel: Pine, Julian; Gobet, Fernando

    2010-01-01

    In this study, we use corpus analysis and computational modelling techniques to compare two recent accounts of the OI stage: Legate & Yang's (2007) Variational Learning Model and Freudenthal, Pine & Gobet's (2006) Model of Syntax Acquisition in Children. We first assess the extent to which each of these accounts can explain the level of OI errors…

  6. Precision phenotyping of biomass accumulation in triticale reveals temporal genetic patterns of regulation

    NASA Astrophysics Data System (ADS)

    Busemeyer, Lucas; Ruckelshausen, Arno; Möller, Kim; Melchinger, Albrecht E.; Alheit, Katharina V.; Maurer, Hans Peter; Hahn, Volker; Weissmann, Elmar A.; Reif, Jochen C.; Würschum, Tobias

    2013-08-01

    To extend agricultural productivity by knowledge-based breeding and tailor varieties adapted to specific environmental conditions, it is imperative to improve our ability to assess the dynamic changes of the phenome of crops under field conditions. To this end, we have developed a precision phenotyping platform that combines various sensors for a non-invasive, high-throughput and high-dimensional phenotyping of small grain cereals. This platform yielded high prediction accuracies and heritabilities for biomass of triticale. Genetic variation for biomass accumulation was dissected with 647 doubled haploid lines derived from four families. Employing a genome-wide association mapping approach, two major quantitative trait loci (QTL) for biomass were identified and the genetic architecture of biomass accumulation was found to be characterized by dynamic temporal patterns. Our findings highlight the potential of precision phenotyping to assess the dynamic genetics of complex traits, especially those not amenable to traditional phenotyping.

  7. Neurochemical phenotype of corticocortical connections in the macaque monkey: quantitative analysis of a subset of neurofilament protein-immunoreactive projection neurons in frontal, parietal, temporal, and cingulate cortices

    NASA Technical Reports Server (NTRS)

    Hof, P. R.; Nimchinsky, E. A.; Morrison, J. H.; Bloom, F. E. (Principal Investigator)

    1995-01-01

    The neurochemical characteristics of the neuronal subsets that furnish different types of corticocortical connections have been only partially determined. In recent years, several cytoskeletal proteins have emerged as reliable markers to distinguish subsets of pyramidal neurons in the cerebral cortex of primates. In particular, previous studies using an antibody to nonphosphorylated neurofilament protein (SMI-32) have revealed a consistent degree of regional and laminar specificity in the distribution of a subpopulation of pyramidal cells in the primate cerebral cortex. The density of neurofilament protein-immunoreactive neurons was shown to vary across corticocortical pathways in macaque monkeys. In the present study, we have used the antibody SMI-32 to examine further and to quantify the distribution of a subset of corticocortically projecting neurons in a series of long ipsilateral corticocortical pathways in comparison to short corticocortical, commissural, and limbic connections. The results demonstrate that the long association pathways interconnecting the frontal, parietal, and temporal neocortex have a high representation of neurofilament protein-enriched pyramidal neurons (45-90%), whereas short corticocortical, callosal, and limbic pathways are characterized by much lower numbers of such neurons (4-35%). These data suggest that different types of corticocortical connections have differential representation of highly specific neuronal subsets that share common neurochemical characteristics, thereby determining regional and laminar cortical patterns of morphological and molecular heterogeneity. These differences in neuronal neurochemical phenotype among corticocortical circuits may have considerable influence on cortical processing and may be directly related to the type of integrative function subserved by each cortical pathway. Finally, it is worth noting that neurofilament protein-immunoreactive neurons are dramatically affected in the course of Alzheimer's disease. The present results support the hypothesis that neurofilament protein may be crucially linked to the development of selective neuronal vulnerability and subsequent disruption of corticocortical pathways that lead to the severe impairment of cognitive function commonly observed in age-related dementing disorders.

  8. Quantitative genetic analysis of brain size variation in sticklebacks: support for the mosaic model of brain evolution.

    PubMed

    Noreikiene, Kristina; Herczeg, Gábor; Gonda, Abigél; Balázs, Gergely; Husby, Arild; Merilä, Juha

    2015-07-01

    The mosaic model of brain evolution postulates that different brain regions are relatively free to evolve independently from each other. Such independent evolution is possible only if genetic correlations among the different brain regions are less than unity. We estimated heritabilities, evolvabilities and genetic correlations of relative size of the brain, and its different regions in the three-spined stickleback (Gasterosteus aculeatus). We found that heritabilities were low (average h(2) = 0.24), suggesting a large plastic component to brain architecture. However, evolvabilities of different brain parts were moderate, suggesting the presence of additive genetic variance to sustain a response to selection in the long term. Genetic correlations among different brain regions were low (average rG = 0.40) and significantly less than unity. These results, along with those from analyses of phenotypic and genetic integration, indicate a high degree of independence between different brain regions, suggesting that responses to selection are unlikely to be severely constrained by genetic and phenotypic correlations. Hence, the results give strong support for the mosaic model of brain evolution. However, the genetic correlation between brain and body size was high (rG = 0.89), suggesting a constraint for independent evolution of brain and body size in sticklebacks. PMID:26108633

  9. Understanding Variation in Treatment Effects in Education Impact Evaluations: An Overview of Quantitative Methods. NCEE 2014-4017

    ERIC Educational Resources Information Center

    Schochet, Peter Z.; Puma, Mike; Deke, John

    2014-01-01

    This report summarizes the complex research literature on quantitative methods for assessing how impacts of educational interventions on instructional practices and student learning differ across students, educators, and schools. It also provides technical guidance about the use and interpretation of these methods. The research topics addressed…

  10. Exploiting Gene Expression Variation to Capture Gene-Environment Interactions for Disease

    PubMed Central

    Idaghdour, Youssef; Awadalla, Philip

    2013-01-01

    Gene-environment interactions have long been recognized as a fundamental concept in evolutionary, quantitative, and medical genetics. In the genomics era, study of how environment and genome interact to shape gene expression variation is relevant to understanding the genetic architecture of complex phenotypes. While genetic analysis of gene expression variation focused on main effects, little is known about the extent of interaction effects implicating regulatory variants and their consequences on transcriptional variation. Here we survey the current state of the concept of transcriptional gene-environment interactions and discuss its utility for mapping disease phenotypes in light of the insights gained from genome-wide association studies of gene expression. PMID:23755064

  11. Detection and quantitation of single nucleotide polymorphisms, DNA sequence variations, DNA mutations, DNA damage and DNA mismatches

    DOEpatents

    McCutchen-Maloney, Sandra L. (Pleasanton, CA)

    2002-01-01

    DNA mutation binding proteins alone and as chimeric proteins with nucleases are used with solid supports to detect DNA sequence variations, DNA mutations and single nucleotide polymorphisms. The solid supports may be flow cytometry beads, DNA chips, glass slides or DNA dips sticks. DNA molecules are coupled to solid supports to form DNA-support complexes. Labeled DNA is used with unlabeled DNA mutation binding proteins such at TthMutS to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by binding which gives an increase in signal. Unlabeled DNA is utilized with labeled chimeras to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by nuclease activity of the chimera which gives a decrease in signal.

  12. Shift in phenotypic variation coupled with rapid loss of genetic diversity in captive populations of Eristalis tenax (Diptera: Syrphidae): consequences for rearing and potential commercial use.

    PubMed

    Francuski, Ljubinka; Djurakic, Marko; Ludoski, Jasmina; Hurtado, Pilar; Pérez-Bañón, Celeste; Ståhls, Gunilla; Rojo, Santos; Milankov, Vesna

    2014-04-01

    Because of its importance as a pollinator and its potential economic usefulness for the biodegradation of organic animal waste, the genetic and phenotypic diversity of the drone fly, Eristalis tenax L. (Diptera: Syrphidae), was studied in both wild and captive populations from southeastern Europe. Wild specimens from a natural protected habitat (with low human impact), field crop habitat (semisynanthropic condition), and intensive pig farming habitat (synanthropic condition) were compared with a laboratory colony reared on artificial media An integrative approach was applied based on allozyme loci, cytochrome c oxidase I mitochondrial DNA, wing traits (size and shape), and abdominal color patterns. Our results indicate that the fourth and eighth generations of the laboratory colony show a severe lack of genetic diversity compared with natural populations. Reduced genetic diversity in subsequent generations (F4 and F8) of the laboratory colony was found to be linked with phenotypic divergence. Loss of genetic variability associated with phenotypic differentiation in laboratory samples suggests a founder effect, followed by stochastic genetic processes and inbreeding. Hence, our results have implications for captive bred Eristalis flies, which have been used in crop pollination and biodegradation of organic waste under synanthropic conditions. PMID:24772566

  13. General quantitative analysis of stress partitioning and boundary conditions in undrained biphasic porous media via a purely macroscopic and purely variational approach

    NASA Astrophysics Data System (ADS)

    Serpieri, Roberto; Travascio, Francesco

    2015-03-01

    In poroelasticity, the effective stress law relates the external stress applied to the medium to the macroscopic strain of the solid phase and the interstitial pressure of the fluid saturating the mixture. Such relationship has been formerly introduced by Terzaghi in form of a principle. To date, no poroelastic theory is capable of recovering a stress partitioning law in agreement with Terzaghi's postulated one in the absence of ad hoc constitutive assumptions on the medium. We recently proposed a variational macroscopic continuum description of two-phase poroelasticity to derive a general biphasic formulation at finite deformations, termed variational macroscopic theory of porous media (VMTPM). Such approach proceeds from the inclusion of the intrinsic volumetric strain among the kinematic descriptors aside to macroscopic displacements, and as a variational theory, uses the Hamilton least-action principle as the unique primitive concept of mechanics invoked to derive momentum balance equations. In a previous related work it was shown that, for the subclass of undrained problems, VMTPM predicts that stress is partitioned in the two phases in strict compliance with Terzaghi's law, irrespective of the microstructural and constitutive features of a given medium. In the present contribution, we further develop the linearized framework of VMTPM to arrive at a general operative formula that allows the quantitative determination of stress partitioning in a jacketed test over a generic isotropic biphasic specimen. This formula is quantitative and general, in that it relates the partial phase stresses to the externally applied stress as function of partitioning coefficients that are all derived by strictly following a purely variational and purely macroscopic approach, and in the absence of any specific hypothesis on the microstructural or constitutive features of a given medium. To achieve this result, the stiffness coefficients of the theory are derived by using exclusively variational arguments. We derive the boundary conditions attained across the boundary of a poroelastic saturated medium in contact with an impermeable surface also based on purely variational arguments. A technique to retrieve bounds for the resulting elastic moduli, based on Hashin's composite spheres assemblage method, is also reported. Notably, in spite of the minimal mechanical hypotheses introduced, a rich mechanical behavior is observed.

  14. Experimental studies of adaptation in Clarkia xantiana. III. Phenotypic selection across a subspecies border.

    PubMed

    Anderson, Jill T; Eckhart, Vincent M; Geber, Monica A

    2015-09-01

    Sister taxa with distinct phenotypes often occupy contrasting environments in parapatric ranges, yet we generally do not know whether trait divergence reflects spatially varying selection. We conducted a reciprocal transplant experiment to test whether selection favors "native phenotypes" in two subspecies of Clarkia xantiana (Onagraceae), an annual plant in California. For four quantitative traits that differ between subspecies, we estimated phenotypic selection in subspecies' exclusive ranges and their contact zone in two consecutive years. We predicted that in the arid, pollinator-scarce eastern region, selection favors phenotypes of the native subspecies parviflora: small leaves, slow leaf growth, early flowering, and diminutive flowers. In the wetter, pollinator-rich, western range of subspecies xantiana, we expected selection for opposite phenotypes. We investigated pollinator contributions to selection by comparing naturally pollinated and pollen-supplemented individuals. For reproductive traits and for subspecies xantiana, selection generally matched expectations. The contact zone sometimes showed distinctive selection, and in ssp. parviflora selection sometimes favored nonnative phenotypes. Pollinators influenced selection on flowering time but not on flower size. Little temporal variation in selection occurred, possibly because of plastic trait responses across years. Though there were exceptions and some causes of selection remain obscure, phenotypic differentiation between subspecies appears to reflect spatially variable selection. PMID:26257193

  15. Genome-wide Association Study of N370S Homozygous Gaucher Disease Reveals the Candidacy of CLN8 gene as a Genetic Modifier Contributing to Extreme Phenotypic Variation

    PubMed Central

    Zhang, Clarence K.; Stein, Philip B.; Liu, Jun; Pastores, Gregory M.; Wang, Zuoheng; Yang, Ruhua; Cho, Judy H.; Gregersen, Peter K.; Aerts, Johannes M. F. G.; Zhao, Hongyu; Mistry, Pramod K.

    2013-01-01

    Mutations in GBA1 gene result in defective acid ?-glucosidase and the complex phenotype of Gaucher disease (GD) related to the accumulation of glucosylceramide-laden macrophages. The phenotype is highly variable even among patients harboring identical GBA1 mutations. We hypothesized that modifier gene(s) underlie phenotypic diversity in GD and performed a GWAS study in Ashkenazi Jewish patients with type 1 GD (GD1), homozygous for N370S mutation. Patients were assigned to mild, moderate or severe disease category using composite disease severity scoring systems. Whole-genome genotyping for >500,000 SNPs was performed to search for associations using OQLS algorithm in 139 eligible patients. Several SNPs in linkage disequilibrium within the CLN8 gene locus were associated with the GD1 severity: SNP rs11986414 was associated with GD1 severity at p value 1.26 × 10?6. Compared to mild disease, risk allele A at rs11986414 conferred an odds ratio of 3.72 for moderate/severe disease. Loss of function mutations in CLN8 causes neuronal ceroid-lipofuscinosis but our results indicate that its increased expression may protect against severe GD1. In cultured skin fibroblasts, the relative expression of CLN8 was higher in mild GD compared to severely affected patients in whom CLN8 risk alleles were over-represented. In an in vitro cell model of GD, CLN8 expression was increased which was further enhanced in the presence of bioactive substrate, glucosylsphingosine. Taken together, CLN8 is a candidate modifier gene for GD1 that may function as a protective sphingolipid sensor and/or in glycosphingolipid trafficking. Future studies should explore the role of CLN8 in pathophysiology of GD. PMID:22388998

  16. Phylogenetic Classification at Generic Level in the Absence of Distinct Phylogenetic Patterns of Phenotypical Variation: A Case Study in Graphidaceae (Ascomycota)

    PubMed Central

    Parnmen, Sittiporn; Lücking, Robert; Lumbsch, H. Thorsten

    2012-01-01

    Molecular phylogenies often reveal that taxa circumscribed by phenotypical characters are not monophyletic. While re-examination of phenotypical characters often identifies the presence of characters characterizing clades, there is a growing number of studies that fail to identify diagnostic characters, especially in organismal groups lacking complex morphologies. Taxonomists then can either merge the groups or split taxa into smaller entities. Due to the nature of binomial nomenclature, this decision is of special importance at the generic level. Here we propose a new approach to choose among classification alternatives using a combination of morphology-based phylogenetic binning and a multiresponse permutation procedure to test for morphological differences among clades. We illustrate the use of this method in the tribe Thelotremateae focusing on the genus Chapsa, a group of lichenized fungi in which our phylogenetic estimate is in conflict with traditional classification and the morphological and chemical characters do not show a clear phylogenetic pattern. We generated 75 new DNA sequences of mitochondrial SSU rDNA, nuclear LSU rDNA and the protein-coding RPB2. This data set was used to infer phylogenetic estimates using maximum likelihood and Bayesian approaches. The genus Chapsa was found to be polyphyletic, forming four well-supported clades, three of which clustering into one unsupported clade, and the other, supported clade forming two supported subclades. While these clades cannot be readily separated morphologically, the combined binning/multiresponse permutation procedure showed that accepting the four clades as different genera each reflects the phenotypical pattern significantly better than accepting two genera (or five genera if splitting the first clade). Another species within the Thelotremateae, Thelotrema petractoides, a unique taxon with carbonized excipulum resembling Schizotrema, was shown to fall outside Thelotrema. Consequently, the new genera Astrochapsa, Crutarndina, Pseudochapsa, and Pseudotopeliopsis are described here and 39 new combinations are proposed. PMID:23251515

  17. Genome-wide association studies of quantitatively measured skin, hair, and eye pigmentation in four European populations.

    PubMed

    Candille, Sophie I; Absher, Devin M; Beleza, Sandra; Bauchet, Marc; McEvoy, Brian; Garrison, Nanibaa' A; Li, Jun Z; Myers, Richard M; Barsh, Gregory S; Tang, Hua; Shriver, Mark D

    2012-01-01

    Pigmentation of the skin, hair, and eyes varies both within and between human populations. Identifying the genes and alleles underlying this variation has been the goal of many candidate gene and several genome-wide association studies (GWAS). Most GWAS for pigmentary traits to date have been based on subjective phenotypes using categorical scales. But skin, hair, and eye pigmentation vary continuously. Here, we seek to characterize quantitative variation in these traits objectively and accurately and to determine their genetic basis. Objective and quantitative measures of skin, hair, and eye color were made using reflectance or digital spectroscopy in Europeans from Ireland, Poland, Italy, and Portugal. A GWAS was conducted for the three quantitative pigmentation phenotypes in 176 women across 313,763 SNP loci, and replication of the most significant associations was attempted in a sample of 294 European men and women from the same countries. We find that the pigmentation phenotypes are highly stratified along axes of European genetic differentiation. The country of sampling explains approximately 35% of the variation in skin pigmentation, 31% of the variation in hair pigmentation, and 40% of the variation in eye pigmentation. All three quantitative phenotypes are correlated with each other. In our two-stage association study, we reproduce the association of rs1667394 at the OCA2/HERC2 locus with eye color but we do not identify new genetic determinants of skin and hair pigmentation supporting the lack of major genes affecting skin and hair color variation within Europe and suggesting that not only careful phenotyping but also larger cohorts are required to understand the genetic architecture of these complex quantitative traits. Interestingly, we also see that in each of these four populations, men are more lightly pigmented in the unexposed skin of the inner arm than women, a fact that is underappreciated and may vary across the world. PMID:23118974

  18. A Quantitative-Trait Genome-Wide Association Study of Alcoholism Risk in the Community: Findings and

    E-print Network

    Nyholt, Dale R.

    A Quantitative-Trait Genome-Wide Association Study of Alcoholism Risk in the Community: Findings contributions to variation in alcoholism and heaviness of drinking (50% to 60% heritability) with high) for phenotypes related to alcohol use and dependence. Methods: Diagnostic interview and blood/buccal samples were

  19. Genome wide search for variation associated with micronutrient density of developing rice grains

    Technology Transfer Automated Retrieval System (TEKTRAN)

    “Omic” tools are rapidly being employed to delineate the biological framework controlling phenotypes of interest in crop species. An advanced understanding of the genetic basis for quantitative trait variation has been made possible through genome wide association studies (GWAS) that make use of ge...

  20. Genome wide search for variation associated with micronutrient density of developing rice grains

    Technology Transfer Automated Retrieval System (TEKTRAN)

    "Omic" tools are rapidly being employed to delineate the biological framework controlling phenotypes of interest in crop species. An advanced understanding of the genetic basis for quantitative trait variation has been made possible through genome wide association studies (GWAS) that make use of gen...

  1. Chimeric proteins for detection and quantitation of DNA mutations, DNA sequence variations, DNA damage and DNA mismatches

    DOEpatents

    McCutchen-Maloney, Sandra L. (Pleasanton, CA)

    2002-01-01

    Chimeric proteins having both DNA mutation binding activity and nuclease activity are synthesized by recombinant technology. The proteins are of the general formula A-L-B and B-L-A where A is a peptide having DNA mutation binding activity, L is a linker and B is a peptide having nuclease activity. The chimeric proteins are useful for detection and identification of DNA sequence variations including DNA mutations (including DNA damage and mismatches) by binding to the DNA mutation and cutting the DNA once the DNA mutation is detected.

  2. Effects of geomagnetic activity and atmospheric power variations on quantitative measures of brain activity: Replication of the Azerbaijani studies

    NASA Astrophysics Data System (ADS)

    Mulligan, Bryce P.; Hunter, Mathew D.; Persinger, Michael A.

    2010-04-01

    This study replicates and extends the observations by Babayev and Allahveriyeva that changes in right hemispheric electroencephalographic activity are correlated with increases in geomagnetic activity. During the geomagnetically quiet interface between solar cycle 23 and 24 quantitative electroencephalographic (QEEG) measurements were completed for normal young adults in three separate experiments involving about 120 samples over 1.5 years. The most consistent, moderate strength correlations occurred for the changes in power within the gamma and theta ranges over the right frontal lobe. Real-time measures of atmospheric power obtained from polar orbiting satellites showed similar effects. The preferential involvement of the right frontal lobe and the regions subject to its inhibition with environmental energetic changes are consistent with the behavioural correlations historically associated with these conditions. They include increased incidence of emotional lability, erroneous reconstruction of experiences, social confrontations, and unusual perceptions.

  3. A colony multiplex quantitative PCR-Based 3S3DBC method and variations of it for screening DNA libraries.

    PubMed

    An, Yang; Toyoda, Atsushi; Zhao, Chen; Fujiyama, Asao; Agata, Kiyokazu

    2015-01-01

    A DNA library is a collection of DNA fragments cloned into vectors and stored individually in host cells, and is a valuable resource for molecular cloning, gene physical mapping, and genome sequencing projects. To take the best advantage of a DNA library, a good screening method is needed. After describing pooling strategies and issues that should be considered in DNA library screening, here we report an efficient colony multiplex quantitative PCR-based 3-step, 3-dimension, and binary-code (3S3DBC) method we used to screen genes from a planarian genomic DNA fosmid library. This method requires only 3 rounds of PCR reactions and only around 6 hours to distinguish one or more desired clones from a large DNA library. According to the particular situations in different research labs, this method can be further modified and simplified to suit their requirements. PMID:25646755

  4. A Colony Multiplex Quantitative PCR-Based 3S3DBC Method and Variations of It for Screening DNA Libraries

    PubMed Central

    An, Yang; Toyoda, Atsushi; Zhao, Chen; Fujiyama, Asao; Agata, Kiyokazu

    2015-01-01

    A DNA library is a collection of DNA fragments cloned into vectors and stored individually in host cells, and is a valuable resource for molecular cloning, gene physical mapping, and genome sequencing projects. To take the best advantage of a DNA library, a good screening method is needed. After describing pooling strategies and issues that should be considered in DNA library screening, here we report an efficient colony multiplex quantitative PCR-based 3-step, 3-dimension, and binary-code (3S3DBC) method we used to screen genes from a planarian genomic DNA fosmid library. This method requires only 3 rounds of PCR reactions and only around 6 hours to distinguish one or more desired clones from a large DNA library. According to the particular situations in different research labs, this method can be further modified and simplified to suit their requirements. PMID:25646755

  5. A Quantitative Model of Motility Reveals Low-Dimensional Variation in Exploratory Behavior Across Multiple Nematode Species

    NASA Astrophysics Data System (ADS)

    Helms, Stephen; Avery, Leon; Stephens, Greg; Shimizu, Tom

    2014-03-01

    Animal behavior emerges from many layers of biological organization--from molecular signaling pathways and neuronal networks to mechanical outputs of muscles. In principle, the large number of interconnected variables at each of these layers could imply dynamics that are complex and hard to control or even tinker with. Yet, for organisms to survive in a competitive, ever-changing environment, behavior must readily adapt. We applied quantitative modeling to identify important aspects of behavior in chromadorean nematodes ranging from the lab strain C. elegans N2 to wild strains and distant species. We revealed subtle yet important features such as speed control and heavy-tailed directional changes. We found that the parameters describing this behavioral model varied among individuals and across species in a correlated way that is consistent with a trade-off between exploratory and exploitative behavior.

  6. Quantitative variation in plasma angiotensin-I converting enzyme activity shows allelic heterogeneity in the ABO blood group locus.

    PubMed

    Terao, Chikashi; Bayoumi, Nervana; McKenzie, Colin A; Zelenika, Diana; Muro, Shigeo; Mishima, Michiaki; Connell, John M C; Vickers, Mark A; Lathrop, G Mark; Farrall, Martin; Matsuda, Fumihiko; Keavney, Bernard D

    2013-11-01

    Angiotensin-I converting enzyme (ACE) occupies a pivotal role in cardiovascular homeostasis. Major loci for plasma ACE have been identified at ACE on Chromosome 17 and at ABO on Chromosome 9. We sought to characterise the genetic architecture of plasma ACE at finer resolution in two populations. We carried out a GWAS in 1810 individuals of Japanese ethnicity; this identified signals at ACE and ABO that together accounted for nearly half of the population variability of the trait. We conducted measured haplotype analysis at the ABO locus in 1425 members of 248 British families using haplotypes of three SNPs, which together tagged the alleles responsible for the principal blood group antigens A1, A2, B and O. Type O alleles were associated with intermediate plasma ACE activity compared to Type A1 alleles (in whom plasma ACE activity was ?36% lower) and Type B alleles (in whom plasma ACE activity was ?36% higher). We demonstrated heterogeneity among A alleles: A2 alleles were associated with plasma ACE activity that was very similar to the O alleles. Variation at ACE accounted for 35% of the trait variance, and variation at ABO accounted for 15%. A further 10% could be ascribed to polygenic effects. PMID:23937567

  7. Relaxed selection is a precursor to the evolution of phenotypic plasticity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phenotypic plasticity represents one of the most important ways that organisms adaptively respond to environmental variation. Alternate phenotypes produced through phenotypic plasiticity generally arise through conditional gene expression, which is predicted to result in relaxed selective constrain...

  8. On the capability of Swarm for surface mass variation monitoring: Quantitative assessment based on orbit information from CHAMP, GRACE and GOCE

    NASA Astrophysics Data System (ADS)

    Baur, Oliver; Weigelt, Matthias; Zehentner, Norbert; Mayer-Gürr, Torsten; Jäggi, Adrian

    2014-05-01

    In the last decade, temporal variations of the gravity field from GRACE observations have become one of the most ubiquitous and valuable sources of information for geophysical and environmental studies. In the context of global climate change, mass balance of the Arctic and Antarctic ice sheets gained particular attention. Because GRACE has outlived its predicted lifetime by several years already, it is very likely that a gap between GRACE and its successor GRACE follow-on (supposed to be launched in 2017, at the earliest) occurs. The Swarm mission - launched on November 22, 2013 - is the most promising candidate to bridge this potential gap, i.e., to directly acquire large-scale mass variation information on the Earth's surface in case of a gap between the present GRACE and the upcoming GRACE follow-on projects. Although the magnetometry mission Swarm has not been designed for gravity field purposes, its three satellites have the characteristics for such an endeavor: (i) low, near-circular and near-polar orbits, (ii) precise positioning with high-quality GNSS receivers, (iii) on-board accelerometers to measure the influence of non-gravitational forces. Hence, from an orbit analysis point of view the Swarm satellites are comparable to the CHAMP, GRACE and GOCE spacecraft. Indeed and as data analysis from CHAMP has been shown, the detection of annual signals and trends from orbit analysis is possible for long-wavelength features of the gravity field, although the accuracy associated with the inter-satellite GRACE measurements cannot be reached. We assess the capability of the (non-dedicated) mission Swarm for mass variation detection in a real-case environment (opposed to simulation studies). For this purpose, we "approximate" the Swarm scenario by the GRACE+CHAMP and GRACE+GOCE constellations. In a first step, kinematic orbits of the individual satellites are derived from GNSS observations. From these orbits, we compute monthly combined GRACE+CHAMP and GRACE+GOCE time-variable gravity fields; sophisticated techniques based on Kalman filtering are applied to reduce noise in the time series. Finally, we infer mass variation in selected areas from to gravity signal. These results are compared to the findings obtained from mass variation detection exploiting CSR-RL05 gravity fields; due to their superior quality (which is due to the fact that they are derived from inter-satellite GRACE measurements), the CSR-RL05 solutions serve as benchmark. Our quantitative assessment shows the potential and limitations of what can be expected from Swarm with regard to surface mass variation monitoring.

  9. Quantitative assessment of single-cell whole genome amplification methods for detecting copy number variation using hippocampal neurons

    PubMed Central

    Ning, Luwen; Li, Zhoufang; Wang, Guan; Hu, Wen; Hou, Qingming; Tong, Yin; Zhang, Meng; Chen, Yao; Qin, Li; Chen, Xiaoping; Man, Heng-Ye; Liu, Pinghua; He, Jiankui

    2015-01-01

    Single-cell genomic analysis has grown rapidly in recent years and finds widespread applications in various fields of biology, including cancer biology, development, immunology, pre-implantation genetic diagnosis, and neurobiology. To date, the amplification bias, amplification uniformity and reproducibility of the three major single cell whole genome amplification methods (GenomePlex WGA4, MDA and MALBAC) have not been systematically investigated using mammalian cells. In this study, we amplified genomic DNA from individual hippocampal neurons using three single-cell DNA amplification methods, and sequenced them at shallow depth. We then systematically evaluated the GC-bias, reproducibility, and copy number variations among individual neurons. Our results showed that single-cell genome sequencing results obtained from the MALBAC and WGA4 methods are highly reproducible and have a high success rate. The MALBAC displays significant biases towards high GC content. We then attempted to correct the GC bias issue by developing a bioinformatics pipeline, which allows us to call CNVs in single cell sequencing data, and chromosome level and sub-chromosomal level CNVs among individual neurons can be detected. We also proposed a metric to determine the CNV detection limits. Overall, MALBAC and WGA4 have better performance than MDA in detecting CNVs. PMID:26091148

  10. The phenotypic variance gradient – a novel concept

    PubMed Central

    Pertoldi, Cino; Bundgaard, Jørgen; Loeschcke, Volker; Barker, James Stuart Flinton

    2014-01-01

    Evolutionary ecologists commonly use reaction norms, which show the range of phenotypes produced by a set of genotypes exposed to different environments, to quantify the degree of phenotypic variance and the magnitude of plasticity of morphometric and life-history traits. Significant differences among the values of the slopes of the reaction norms are interpreted as significant differences in phenotypic plasticity, whereas significant differences among phenotypic variances (variance or coefficient of variation) are interpreted as differences in the degree of developmental instability or canalization. We highlight some potential problems with this approach to quantifying phenotypic variance and suggest a novel and more informative way to plot reaction norms: namely “a plot of log (variance) on the y-axis versus log (mean) on the x-axis, with a reference line added”. This approach gives an immediate impression of how the degree of phenotypic variance varies across an environmental gradient, taking into account the consequences of the scaling effect of the variance with the mean. The evolutionary implications of the variation in the degree of phenotypic variance, which we call a “phenotypic variance gradient”, are discussed together with its potential interactions with variation in the degree of phenotypic plasticity and canalization. PMID:25540685

  11. Quantitative Estimation of the Impact of European Teleconnections on Interannual Variation of East Asian Winter Temperature and Monsoon

    NASA Technical Reports Server (NTRS)

    Lim, Young-Kwon; Kim, Hae-Dong

    2014-01-01

    The impact of European teleconnections including the East AtlanticWest Russia (EA-WR), the Scandinavia (SCA), and the East Atlantic (EA) on East Asian winter temperature variability was quantified and compared with the combined effect of the Arctic Oscillation (AO), the Western Pacific (WP), and the El-Nino Southern Oscillation (ENSO), which are originated in the Northern Hemispheric high-latitudes or the Pacific. Three European teleconnections explained 22-25 percent of the total monthly upper-tropospheric height variance over Eurasia. Regression analysis revealed warming by EA-WR and EA and cooling by SCA over mid-latitude East Asia during their positive phase and vice versa. Temperature anomalies were largely explained by the advective temperature change process at the lower troposphere. The average spatial correlation over East Asia (90-180E, 10-80N) for the last 34 winters between observed and reconstructed temperature comprised of AO, WP and ENSO effect (AWE) was approximately 0.55, and adding the European teleconnection components (ESE) to the reconstructed temperature improved the correlation up to approximately 0.64. Lower level atmospheric structure demonstrated that approximately five of the last 34 winters were significantly better explained by ESE than AWE to determine East Asian seasonal winter temperatures. We also compared the impact between EA-WR and AO on the 1) East Asian winter monsoon, 2) cold surge, and 3) the Siberian high. These three were strongly coupled, and their spatial features and interannual variation were somewhat better explained by EA-WR than AO. Results suggest that the EA-WR impact must be treated more importantly than previously thought for a better understanding of East Asian winter temperature and monsoon variability.

  12. Quantitative variations of individual carotenoids in relationship with the leaflet development of six species of the genus Ceratozamia (Cycads).

    PubMed

    Cardini, Franco; Pucci, Susanna; Calamassi, Roberto

    2006-02-01

    The content and relative variations of individual carotenoids during the leaflet development stages (I, II, III, A and P) of six species of Ceratozamia (Cycads) were investigated. There is an unusual, transitory and marked presence of six red stroma keto-carotenoids in the first development stages, while the thylakoidal carotenoids showed a low concentration during the same period. As no official A1cm1% coefficients were available, it was necessary to calculate these for the following stroma carotenoids: semi-beta-carotenone (major component), triphasiaxanthin, ceratoxanthin, ceratozamiaxanthin, kuesteriaxanthin and ceratoxanthone. The stroma keto-carotenoids, which reached the highest content in the first development stage (average of 78% of total carotenoids), were always present in the five species: C. fuscoviridis, C. robusta, C. spinosa, C. kuesteriana and C. hildae, but never in C. mexicana. From stage II, the stroma keto-carotenoids decreased and finally disappeared in the green adult leaflets. The thylakoidal carotenoids showed a minimum at stage III, and then increased to a maximum in the perennial leaflets. Among these, beta-carotene showed an anomalous and characteristic behaviour, being a minor component during leaflet development (from stage I to A). In stage P it was markedly exceeded not only by lutein but also by alpha-carotene, neoxanthin and violaxanthin, and in C. robusta also by lutein-5,6-epoxide. Additionally, the alpha/beta ratio in these species is unusual: it increased from 0.3-0.5 to 1.5-3.0 during leaflet development. Moreover, antheraxanthin amounts are very small, while zeaxanthin was present only in the evergreen leaflets of C. mexicana in small quantities. Lutein-5,6-epoxide represented more than 5% of thylakoidal carotenoids in the leaflets of all the species. A revision of the taxonomic rank of C. fuscoviridis is recommended. PMID:16399003

  13. Extensive intrafamilial and interfamilial phenotypic variation among patients with autosomal dominant retinal dystrophy and mutations in the human RDS/peripherin gene.

    PubMed

    Apfelstedt-Sylla, E; Theischen, M; Rüther, K; Wedemann, H; Gal, A; Zrenner, E

    1995-01-01

    Clinical phenotypes of patients with mutations in the human RDS/peripherin gene are described. A 67-year-old woman, who carried a 1 base pair deletion in codon 307, presented with typical late onset autosomal dominant retinitis pigmentosa (RP). In another autosomal dominant pedigree, a nonsense mutation at codon 46 caused 'inverse' retinitis pigmentosa-like fundus changes associated with progressive cone-rod degeneration in a 58-year-old man, whereas his 40-year-old son presented with yellow deposits in the retinal pigment epithelial layer resembling a pattern dystrophy, and with moderately reduced rod and cone function, as determined by two colour dark adapted threshold perimetry and electroretinography. It is suggested that both clinical pictures within this latter family may represent manifestations of fundus flavimaculatus. The clinical data of the three patients provide further evidence for the remarkable variety of disease expression within and between families with mutations in the RDS/peripherin gene. Currently, the most comprehensive statement could be that RDS/peripherin mutations are associated either with typical RP or with various forms of flecked retinal disease. PMID:7880786

  14. HORTSCIENCE 44(3):725729. 2009. Phenotypic Characteristics

    E-print Network

    Marler, Thomas E.

    , cycads, Guam, phenotypic plasticity, size, sterol, steryl glucoside Abstract. The relationship between and steryl glucoside concentration and seed content in relation to whole plant and organ size variation

  15. Experimental Crossing of Two Distinct Species of Leopard Geckos, Eublepharis angramainyu and E. macularius: Viability, Fertility and Phenotypic Variation of the Hybrids

    PubMed Central

    Jan?úchová-Lásková, Jitka; Landová, Eva; Frynta, Daniel

    2015-01-01

    Hybridization between distinct species of animals and subsequent genetic introgression plays a considerable role in the speciation process and the emergence of adaptive characters. Fitness of between-species hybrids usually sharply decreases with the divergence time of the concerned species and the divergence depth, which still allows for a successful crossing differs among principal clades of vertebrates. Recently, a review of hybridization events among distinct lizard species revealed that lizards belong to vertebrates with a highly developed ability to hybridize. In spite of this, reliable reports of experimental hybridizations between genetically fairly divergent species are only exceptional. Here, we show the results of the crossing of two distinct allopatric species of eyelid geckos possessing temperature sex determination and lacking sex chromosomes: Eublepharis macularius distributed in Pakistan/Afghanistan area and E. angramainyu, which inhabits Mesopotamia and adjacent areas. We demonstrated that F1 hybrids were viable and fertile, and the introgression of E. angramainyu genes into the E. macularius genome can be enabled via a backcrossing. The examined hybrids (except those of the F2 generation) displayed neither malformations nor a reduced survival. Analyses of morphometric and coloration traits confirmed phenotypic distinctness of both parental species and their F1 hybrids. These findings contrast with long-term geographic and an evolutionary separation of the studied species. Thus, the occurrence of fertile hybrids of comparably divergent species, such as E. angramainyu and E. macularius, may also be expected in other taxa of squamates. This would violate the current estimates of species diversity in lizards. PMID:26633648

  16. The genetic architecture of psychophysiological phenotypes

    PubMed Central

    Munafò, Marcus R; Flint, Jonathan

    2014-01-01

    It is now clear that almost all complex traits have a highly polygenic component; that is, their genetic basis consists of relatively frequent risk alleles at a very large number of loci, each making a small contribution to variation, or disease susceptibility. This general conclusion appears to hold for intermediate phenotypes. Therefore, we should not expect these phenotypes to be associated with substantially larger effect sizes than conventional phenotypes. Instead, their usefulness is likely to lie in understanding the mechanism underpinning associations identified via genome-wide association studies of conventional phenotypes. PMID:25387716

  17. Optofluidic Detection for Cellular Phenotyping

    PubMed Central

    Tung, Yi-Chung; Huang, Nien-Tsu; Oh, Bo-Ram; Patra, Bishnubrata; Pan, Chi-Chun; Qiu, Teng; Paul, K. Chu; Zhang, Wenjun; Kurabayashi, Katsuo

    2012-01-01

    Quantitative analysis of the output of processes and molecular interactions within a single cell is highly critical to the advancement of accurate disease screening and personalized medicine. Optical detection is one of the most broadly adapted measurement methods in biological and clinical assays and serves cellular phenotyping. Recently, microfluidics has obtained increasing attention due to several advantages, such as small sample and reagent volumes, very high throughput, and accurate flow control in the spatial and temporal domains. Optofluidics, which is the attempt to integrate optics with microfluidic, shows great promise to enable on-chip phenotypic measurements with high precision, sensitivity, specificity, and simplicity. This paper reviews the most recent developments of optofluidic technologies for cellular phenotyping optical detection. PMID:22854915

  18. Ectodysplasin signalling genes and phenotypic evolution in sculpins (Cottus).

    PubMed

    Cheng, Jie; Sedlazek, Fritz; Altmüller, Janine; Nolte, Arne W

    2015-09-22

    Despite their deeply conserved function among vertebrates, ectodysplasin (Eda) signalling genes are involved in microevolutionary change in humans and sticklebacks. If such a dual role is common, Eda signalling genes constitute hotspots for morphological evolution. Variation in sculpin (Cottus) skin prickling and body shape resembles patterns caused by variation in Eda signalling in sticklebacks. We mapped Eda signalling genes and performed quantitative trait locus mapping in crosses between Cottus rhenanus and Cottus perifretum. A genomic region containing the Eda receptor (Edar) was strongly associated with prickling and contributed to shape. The expression of Edar in developing prickles and skeletal elements in Cottus was confirmed by in situ hybridization. Coding sequence changes between Edar alleles in C. rhenanus and C. perifretum exceeded sequence differentiation in other vertebrates. However, it is likely that additional genetic elements besides coding changes affect the phenotypic variation. Although the phenotype in a natural hybrid lineage between C. rhenanus and C. perifretum resembles C. perifretum, the respective coding Edar alleles are not fully fixed (88.6%). Hence, our results support an involvement of Eda signalling in microevolutionary changes, but imply that the Edar gene is affected by multiple evolutionary processes that vary among freshwater sculpins. PMID:26354934

  19. Phenotypic Heterogeneity in Mycobacterial Stringent Response

    E-print Network

    Sayantari Ghosh; Kamakshi Sureka; Bhaswar Ghosh; Indrani Bose; Joyoti Basu; Manikuntala Kundu

    2011-02-03

    A common survival strategy of microorganisms subjected to stress involves the generation of phenotypic heterogeneity in the isogenic microbial population enabling a subset of the population to survive under stress. In a recent study, a mycobacterial population of M. smegmatis was shown to develop phenotypic heterogeneity under nutrient depletion. The observed heterogeneity is in the form of a bimodal distribution of the expression levels of the Green Fluorescent Protein (GFP) as reporter with the gfp fused to the promoter of the rel gene. The stringent response pathway is initiated in the subpopulation with high rel activity.In the present study, we characterize quantitatively the single cell promoter activity of the three key genes, namely, mprA, sigE and rel, in the stringent response pathway with gfp as the reporter. The origin of bimodality in the GFP distribution lies in two stable expression states, i.e., bistability. We develop a theoretical model to study the dynamics of the stringent response pathway. The model incorporates a recently proposed mechanism of bistability based on positive feedback and cell growth retardation due to protein synthesis. Based on flow cytometry data, we establish that the distribution of GFP levels in the mycobacterial population at any point of time is a linear superposition of two invariant distributions, one Gaussian and the other lognormal, with only the coefficients in the linear combination depending on time. This allows us to use a binning algorithm and determine the time variation of the mean protein level, the fraction of cells in a subpopulation and also the coefficient of variation, a measure of gene expression noise.The results of the theoretical model along with a comprehensive analysis of the flow cytometry data provide definitive evidence for the coexistence of two subpopulations with overlapping protein distributions.

  20. Phenotypic variation resulting from a deficiency of epidermal growth factor receptor in mice is caused by extensive genetic heterogeneity that can be genetically and molecularly partitioned.

    PubMed Central

    Strunk, Karen E; Amann, Vicky; Threadgill, David W

    2004-01-01

    The timing of lethality caused by homozygosity for a null allele of the epidermal growth factor receptor (Egfrtm1Mag) in mice is strongly dependent on genetic background. Initial attempts to genetically map background modifiers using Swiss-derived, outbred CD-1 mice were unsuccessful. To investigate the genetic architecture contributing to survival of Egfrtm1Mag homozygous embryos, the genetic variability segregating within the outbred population was partitioned by surveying viability of Egfrtm1Mag mutants using intercrosses between 129S6/SvEvTAC-Egfrtm1Mag and nine Swiss-derived, inbred strains: ALR/LtJ, ALS/LtJ, APN, APS, ICR/HaRos, NOD/LtJ, NON/LtJ, SJL/J, and SWR/J. The observations showed that these strains support varying levels of survival of Egfrtm1Mag homozygous embryos, suggesting that genetic heterogeneity within the CD-1 stock contributed to the original lack of Egfrtm1Mag modifier detection. Similar to the Swiss-derived intercrosses, nine congenic strains, derived from 129S6/SvEvTAC, AKR/J, APN, BALB/cJ, BTBR-T+ tf/tf, C3H/HeJ, C57BL/6J, DBA/2J, and FVB/NJ inbred backgrounds, also supported varying levels of survival of Egfrtm1Mag mutants. By intercrossing the congenic lines to create hybrid F1 embryos, different genetic backgrounds were found to have complementary modifiers. Analysis of the congenic lines argues against heterosis of outbred backgrounds contributing to Egfrtm1Mag phenotypic variability. A detailed analysis of the crosses suggests that modifiers function at three distinct stages of development. One class of modifiers supports survival of Egfrtm1Mag homozygous embryos to mid-gestation, another class supports development through the mid-gestation transition from yolk-sac to placental-derived nutrient sources, and a third class supports survival through later stages of gestation. Data from microarray analysis using RNA from wild-type and Egfrtm1Mag mutant placentas support the existence of extensive genetic heterogeneity and suggest that it can be molecularly partitioned. This method should be generally useful to partition heterogeneity contributing to other complex traits. PMID:15342520

  1. A Simple Genetic Architecture Underlies Morphological Variation in Dogs

    PubMed Central

    Schoenebeck, Jeffrey J.; Degenhardt, Jeremiah D.; Lohmueller, Kirk E.; Zhao, Keyan; Brisbin, Abra; Parker, Heidi G.; vonHoldt, Bridgett M.; Cargill, Michele; Auton, Adam; Reynolds, Andy; Elkahloun, Abdel G.; Castelhano, Marta; Mosher, Dana S.; Sutter, Nathan B.; Johnson, Gary S.; Novembre, John; Hubisz, Melissa J.; Siepel, Adam; Wayne, Robert K.; Bustamante, Carlos D.; Ostrander, Elaine A.

    2010-01-01

    Domestic dogs exhibit tremendous phenotypic diversity, including a greater variation in body size than any other terrestrial mammal. Here, we generate a high density map of canine genetic variation by genotyping 915 dogs from 80 domestic dog breeds, 83 wild canids, and 10 outbred African shelter dogs across 60,968 single-nucleotide polymorphisms (SNPs). Coupling this genomic resource with external measurements from breed standards and individuals as well as skeletal measurements from museum specimens, we identify 51 regions of the dog genome associated with phenotypic variation among breeds in 57 traits. The complex traits include average breed body size and external body dimensions and cranial, dental, and long bone shape and size with and without allometric scaling. In contrast to the results from association mapping of quantitative traits in humans and domesticated plants, we find that across dog breeds, a small number of quantitative trait loci (?3) explain the majority of phenotypic variation for most of the traits we studied. In addition, many genomic regions show signatures of recent selection, with most of the highly differentiated regions being associated with breed-defining traits such as body size, coat characteristics, and ear floppiness. Our results demonstrate the efficacy of mapping multiple traits in the domestic dog using a database of genotyped individuals and highlight the important role human-directed selection has played in altering the genetic architecture of key traits in this important species. PMID:20711490

  2. Pharmacometabonomic characterization of xenobiotic and endogenous metabolic phenotypes that account for inter-individual variation in isoniazid-induced toxicological response.

    PubMed

    Cunningham, Katharine; Claus, Sandrine P; Lindon, John C; Holmes, Elaine; Everett, Jeremy R; Nicholson, Jeremy K; Coen, Muireann

    2012-09-01

    An NMR-based pharmacometabonomic approach was applied to investigate inter-animal variation in response to isoniazid (INH; 200 and 400 mg/kg) in male Sprague-Dawley rats, alongside complementary clinical chemistry and histopathological analysis. Marked inter-animal variability in central nervous system (CNS) toxicity was identified following administration of a high dose of INH, which enabled characterization of CNS responders and CNS non-responders. High-resolution post-dose urinary ¹H NMR spectra were modeled both by their xenobiotic and endogenous metabolic information sets, enabling simultaneous identification of the differential metabolic fate of INH and its associated endogenous metabolic consequences in CNS responders and CNS non-responders. A characteristic xenobiotic metabolic profile was observed for CNS responders, which revealed higher urinary levels of pyruvate isonicotinylhydrazone and ?-glucosyl isonicotinylhydrazide and lower levels of acetylisoniazid compared to CNS non-responders. This suggested that the capacity for acetylation of INH was lower in CNS responders, leading to increased metabolism via conjugation with pyruvate and glucose. In addition, the endogenous metabolic profile of CNS responders revealed higher urinary levels of lactate and glucose, in comparison to CNS non-responders. Pharmacometabonomic analysis of the pre-dose ¹H NMR urinary spectra identified a metabolic signature that correlated with the development of INH-induced adverse CNS effects and may represent a means of predicting adverse events and acetylation capacity when challenged with high dose INH. Given the widespread use of INH for the treatment of tuberculosis, this pharmacometabonomic screening approach may have translational potential for patient stratification to minimize adverse events. PMID:22873827

  3. Implications of the apportionment of human genetic diversity for the apportionment of human phenotypic diversity.

    PubMed

    Edge, Michael D; Rosenberg, Noah A

    2015-08-01

    Researchers in many fields have considered the meaning of two results about genetic variation for concepts of "race." First, at most genetic loci, apportionments of human genetic diversity find that worldwide populations are genetically similar. Second, when multiple genetic loci are examined, it is possible to distinguish people with ancestry from different geographical regions. These two results raise an important question about human phenotypic diversity: To what extent do populations typically differ on phenotypes determined by multiple genetic loci? It might be expected that such phenotypes follow the pattern of similarity observed at individual loci. Alternatively, because they have a multilocus genetic architecture, they might follow the pattern of greater differentiation suggested by multilocus ancestry inference. To address the question, we extend a well-known classification model of Edwards (2003) by adding a selectively neutral quantitative trait. Using the extended model, we show, in line with previous work in quantitative genetics, that regardless of how many genetic loci influence the trait, one neutral trait is approximately as informative about ancestry as a single genetic locus. The results support the relevance of single-locus genetic-diversity partitioning for predictions about phenotypic diversity. PMID:25677859

  4. Evolution of molecular phenotypes under stabilizing selection

    NASA Astrophysics Data System (ADS)

    Nourmohammad, Armita; Schiffels, Stephan; Lässig, Michael

    2013-01-01

    Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution builds on genome evolution in a complicated way, which involves selection, genetic drift, mutations and recombination. Here we develop a coarse-grained evolutionary statistics for phenotypes, which decouples from details of the underlying genotypes. We derive approximate evolution equations for the distribution of phenotype values within and across populations. This dynamics covers evolutionary processes at high and low recombination rates, that is, it applies to sexual and asexual populations. In a fitness landscape with a single optimal phenotype value, the phenotypic diversity within populations and the divergence between populations reach evolutionary equilibria, which describe stabilizing selection. We compute the equilibrium distributions of both quantities analytically and we show that the ratio of mean divergence and diversity depends on the strength of selection in a universal way: it is largely independent of the phenotype’s genomic encoding and of the recombination rate. This establishes a new method for the inference of selection on molecular phenotypes beyond the genome level. We discuss the implications of our findings for the predictability of evolutionary processes.

  5. The Genetic Basis of Natural Variation in Oenological Traits in Saccharomyces cerevisiae

    PubMed Central

    Salinas, Francisco; Cubillos, Francisco A.; Soto, Daniela; Garcia, Verónica; Bergström, Anders; Warringer, Jonas; Ganga, M. Angélica; Louis, Edward J.

    2012-01-01

    Saccharomyces cerevisiae is the main microorganism responsible for wine alcoholic fermentation. The oenological phenotypes resulting from fermentation, such as the production of acetic acid, glycerol, and residual sugar concentration are regulated by multiple genes and vary quantitatively between different strain backgrounds. With the aim of identifying the quantitative trait loci (QTLs) that regulate oenological phenotypes, we performed linkage analysis using three crosses between highly diverged S. cerevisiae strains. Segregants from each cross were used as starter cultures for 20-day fermentations, in synthetic wine must, to simulate actual winemaking conditions. Linkage analysis on phenotypes of primary industrial importance resulted in the mapping of 18 QTLs. We tested 18 candidate genes, by reciprocal hemizygosity, for their contribution to the observed phenotypic variation, and validated five genes and the chromosome II right subtelomeric region. We observed that genes involved in mitochondrial metabolism, sugar transport, nitrogen metabolism, and the uncharacterized ORF YJR030W explained most of the phenotypic variation in oenological traits. Furthermore, we experimentally validated an exceptionally strong epistatic interaction resulting in high level of succinic acid between the Sake FLX1 allele and the Wine/European MDH2 allele. Overall, our work demonstrates the complex genetic basis underlying wine traits, including natural allelic variation, antagonistic linked QTLs and complex epistatic interactions between alleles from strains with different evolutionary histories. PMID:23185390

  6. Modeling causality for pairs of phenotypes in system genetics

    E-print Network

    Yandell, Brian S.

    for causal inference in systems genetics are genetic variation preceding phenotypic variation and MendelianModeling causality for pairs of phenotypes in system genetics Elias Chaibub Neto1 Aimee T. Broman2 mechanisms under- lying complex disease traits. Integration of genetic information with genomic, proteomic

  7. Advanced phenotyping and phenotype data analysis for the study of plant growth and development

    PubMed Central

    Rahaman, Md. Matiur; Chen, Dijun; Gillani, Zeeshan; Klukas, Christian; Chen, Ming

    2015-01-01

    Due to an increase in the consumption of food, feed, fuel and to meet global food security needs for the rapidly growing human population, there is a necessity to breed high yielding crops that can adapt to the future climate changes, particularly in developing countries. To solve these global challenges, novel approaches are required to identify quantitative phenotypes and to explain the genetic basis of agriculturally important traits. These advances will facilitate the screening of germplasm with high performance characteristics in resource-limited environments. Recently, plant phenomics has offered and integrated a suite of new technologies, and we are on a path to improve the description of complex plant phenotypes. High-throughput phenotyping platforms have also been developed that capture phenotype data from plants in a non-destructive manner. In this review, we discuss recent developments of high-throughput plant phenotyping infrastructure including imaging techniques and corresponding principles for phenotype data analysis. PMID:26322060

  8. Quantitative radiography

    SciTech Connect

    Logan, C.M.; Hernandez, J.M.; Devine, G.J.

    1991-02-01

    We have developed a system of quantitative radiography in order to produce quantitative images displaying homogeneity of parts. The materials that we characterize are synthetic composites and may contain important subtle density variations not discernable by examining a raw film x-radiograph. In order to quantitatively interpret film radiographs, it is necessary to digitize, interpret, and display the images. Our integrated system of quantitative radiography displays accurate, high-resolution pseudocolor images in units of density. We characterize approximately 10,000 parts per year in hundreds of different configurations and compositions with this system. Images are captured using DuPont NDT55 industrial x-ray film in Daypack{trademark} packages. X-ray cabinets are of custom design, with helium flight path and a filter wheel for positioning filters if desired. The cabinets contain baffles to reduce scattered radiation and are equipped with drawer for rapid load/unload of parts. Separate units with tungsten-anode or copper-anode tubes are available. The usual operating voltage is 15 to 35 kVp. Fixturing provides for rough part positioning and precise alignment with respect to the x-ray source. Areal density standards are placed at several locations on each film. In interpreting the image, we use the standards nearest the image of the part being quantified. Because of this, small variations in x-ray flux uniformity (heel effects) are unimportant. The usual standard is a step wedge of aluminum containing 13 steps. Films are permanently labeled by imaging a perforated metal numbering strip. Data such as part number, step wedge identification, etc. are read from barcode labels and transferred to a data base for later retrieval and use in quantifying the image.

  9. The Nature of Stable Insomnia Phenotypes

    PubMed Central

    Pillai, Vivek; Roth, Thomas; Drake, Christopher L.

    2015-01-01

    Study Objectives: We examined the 1-y stability of four insomnia symptom profiles: sleep onset insomnia; sleep maintenance insomnia; combined onset and maintenance insomnia; and neither criterion (i.e., insomnia cases that do not meet quantitative thresholds for onset or maintenance problems). Insomnia cases that exhibited the same symptom profile over a 1-y period were considered to be phenotypes, and were compared in terms of clinical and demographic characteristics. Design: Longitudinal. Setting: Urban, community-based. Participants: Nine hundred fifty-four adults with Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition based current insomnia (46.6 ± 12.6 y; 69.4% female). Interventions: None. Measurements and results: At baseline, participants were divided into four symptom profile groups based on quantitative criteria. Follow-up assessment 1 y later revealed that approximately 60% of participants retained the same symptom profile, and were hence judged to be phenotypes. Stability varied significantly by phenotype, such that sleep onset insomnia (SOI) was the least stable (42%), whereas combined insomnia (CI) was the most stable (69%). Baseline symptom groups (cross-sectionally defined) differed significantly across various clinical indices, including daytime impairment, depression, and anxiety. Importantly, however, a comparison of stable phenotypes (longitudinally defined) did not reveal any differences in impairment or comorbid psychopathology. Another interesting finding was that whereas all other insomnia phenotypes showed evidence of an elevated wake drive both at night and during the day, the “neither criterion” phenotype did not; this latter phenotype exhibited significantly higher daytime sleepiness despite subthreshold onset and maintenance difficulties. Conclusions: By adopting a stringent, stability-based definition, this study offers timely and important data on the longitudinal trajectory of specific insomnia phenotypes. With the exception of daytime sleepiness, few clinical differences are apparent across stable phenotypes. Citation: Pillai V, Roth T, Drake CL. The nature of stable insomnia phenotypes. SLEEP 2015;38(1):127–138. PMID:25325468

  10. Quantitative PCR Reveals Strong Spatial and Temporal Variation of the Wasting Disease Pathogen, Labyrinthula zosterae in Northern European Eelgrass (Zostera marina) Beds

    PubMed Central

    Bockelmann, Anna-Christina; Tams, Verena; Ploog, Jana; Schubert, Philipp R.; Reusch, Thorsten B. H.

    2013-01-01

    Seagrass beds are the foundation species of functionally important coastal ecosystems worldwide. The world’s largest losses of the widespread seagrass Zostera marina (eelgrass) have been reported as a consequence of wasting disease, an infection with the endophytic protist Labyrinthula zosterae. During one of the most extended epidemics in the marine realm, ?90% of East and Western Atlantic eelgrass beds died-off between 1932 and 1934. Today, small outbreaks continue to be reported, but the current extent of L. zosterae in European meadows is completely unknown. In this study we quantify the abundance and prevalence of the wasting disease pathogen among 19 Z. marina populations in northern European coastal waters, using quantitative PCR (QPCR) with primers targeting a species specific portion of the internally transcribed spacer (ITS1) of L. zosterae. Spatially, we found marked variation among sites with abundances varying between 0 and 126 cells mg?1 Z. marina dry weight (mean: 5.7 L. zosterae cells mg?1 Z. marina dry weight ±1.9 SE) and prevalences ranged from 0–88.9%. Temporarily, abundances varied between 0 and 271 cells mg?1 Z. marina dry weight (mean: 8.5±2.6 SE), while prevalences ranged from zero in winter and early spring to 96% in summer. Field concentrations accessed via bulk DNA extraction and subsequent QPCR correlated well with prevalence data estimated via isolation and cultivation from live plant tissue. L. zosterae was not only detectable in black lesions, a sign of Labyrinthula-induced necrosis, but also occurred in green, apparently healthy tissue. We conclude that L. zosterae infection is common (84% infected populations) in (northern) European eelgrass populations with highest abundances during the summer months. In the light of global climate change and increasing rate of marine diseases our data provide a baseline for further studies on the causes of pathogenic outbreaks of L. zosterae. PMID:23658711

  11. Male fertility versus sterility, cytotype, and DNA quantitative variation in seed production in diploid and tetraploid sea lavenders (Limonium sp., Plumbaginaceae) reveal diversity in reproduction modes.

    PubMed

    Róis, Ana Sofia; Teixeira, Generosa; Sharbel, Timothy F; Fuchs, Jörg; Martins, Sérgio; Espírito-Santo, Dalila; Caperta, Ana D

    2012-12-01

    The genus Limonium Miller, a complex taxonomic group, comprises annuals and perennials that can produce sexual and/or asexual seeds (apomixis). In this study, we used diverse cytogenetic and cytometric approaches to analyze male sporogenesis and gametogenesis for characterizing male reproductive output on seed production in Limonium ovalifolium and Limonium multiflorum. We showed here that the first species is mostly composed of diploid cytotypes with 2n = 16 chromosomes and the latter species by tetraploid cytotypes with 2n = 32, 34, 35, 36 chromosomes and had a genome roughly twice as big as the former one. In both species, euploid and aneuploid cytotypes with large metacentric chromosomes having decondensed interstitial sites were found within and among populations, possibly involved in chromosomal reconstructions. L. ovalifolium diploids showed regular meiosis resulting in normal tetrads, while diverse chromosome pairing and segregation irregularities leading to the formation of abnormal meiotic products are found in balanced and non-balanced L. multiflorum tetraploids. Before anther dehiscence, the characteristic unicellular, bicellular, or tricellular pollen grains showing the typical Limonium micro- or macro-reticulate exine ornamentation patterns were observed in L. ovalifolium using scanning electron microscopy. Most of these grains were viable and able to produce pollen tubes in vitro. In both balanced and unbalanced L. multiflorum tetraploids, microspores only developed until the "ring-vacuolate stage" with a collapsed morphology without the typical exine patterns, pointing to a sporophytic defect. These microspores were unviable and therefore never germinated in vitro. L. ovalifolium individuals presented larger pollen grains than those of L. multiflorum, indicating that pollen size and ploidy levels are not correlated in the Limonium system. Cytohistological studies in mature seeds from both species revealed that an embryo and a residual endosperm were present in each seed. Flow cytometric seed screens using such mature seeds showed quantitative variations in seeds ploidy level. It is concluded that male function seems to play an important role in the reproduction modes of Limonium diploids and tetraploids. PMID:23086613

  12. Building mouse phenotype ontologies.

    PubMed

    Gkoutos, G V; Green, E C J; Mallon, A M; Hancock, J M; Davidson, D

    2004-01-01

    The structured description of mutant phenotypes presents a major conceptual and practical problem. A general model for generating mouse phenotype ontologies that involves combing a variety of different ontologies to better link and describe phenotypes is presented. This model is based on the Phenotype and Trait Ontology schema proposal and incorporates practical limitations and designing solutions in an attempt to model a testbed for the first phenotype ontology constructed in this manner, namely the mouse behavior phenotype ontology. We propose the application of such a model could provide curators with a powerful mechanism of annotation, mining and knowledge representation as well as achieving some level of free text disassociation. PMID:14992502

  13. Endothelial cell phenotypic behaviors cluster into dynamic state transition programs modulated by angiogenic and angiostatic cytokines.

    PubMed

    Rimchala, Tharathorn; Kamm, Roger D; Lauffenburger, Douglas A

    2013-03-01

    Angiogenesis requires coordinated dynamic regulation of multiple phenotypic behaviors of endothelial cells in response to environmental cues. Multi-scale computational models of angiogenesis can be useful for analyzing effects of cell behaviors on the tissue level outcome, but these models require more intensive experimental studies dedicated to determining the required quantitative "rules" for cell-level phenotypic responses across a landscape of pro- and anti-angiogenic stimuli in order to ascertain how changes in these single cell responses lead to emerging multi-cellular behavior such as sprout formation. Here we employ single-cell microscopy to ascertain phenotypic behaviors of more than 800 human microvascular endothelial cells under various combinational angiogenic (VEGF) and angiostatic (PF4) cytokine treatments, analyzing their dynamic behavioral transitions among sessile, migratory, proliferative, and apoptotic states. We find that an endothelial cell population clusters into an identifiable set of a few distinct phenotypic state transition patterns (clusters) that is consistent across all cytokine conditions. Varying the cytokine conditions, such as VEGF and PF4 combinations here, modulates the proportion of the population following a particular pattern (referred to as phenotypic cluster weights) without altering the transition dynamics within the patterns. We then map the phenotypic cluster weights to quantified population level sprout densities using a multi-variate regression approach, and identify linear combinations of the phenotypic cluster weights that associate with greater or lesser sprout density across the various treatment conditions. VEGF-dominant cytokine combinations yielding high sprout densities are characterized by high proliferative and low apoptotic cluster weights, whereas PF4-dominant conditions yielding low sprout densities are characterized by low proliferative and high apoptotic cluster weights. Migratory cluster weights show only mild association with sprout density outcomes under the VEGF/PF4 conditions and the sprout formation characteristics explored here. PMID:23303249

  14. Endothelial cell phenotypic behaviors cluster into dynamic state transition programs modulated by angiogenic and angiostatic cytokines

    PubMed Central

    Rimchala, Tharathorn; Kamm, Roger D.; Lauffenburger, Douglas A.

    2013-01-01

    Angiogenesis requires coordinated dynamic regulation of multiple phenotypic behaviors of endothelial cells in response to environmental cues. Multi-scale computational models of angiogenesis can be useful for analyzing effects of cell behaviors on the tissue level outcome, but these models require more intensive experimental studies dedicated to determining the required quantitative “rules” for cell-level phenotypic responses across a landscape of pro- and anti-angiogenic stimuli in order to ascertain how changes in these single cell responses lead to emerging multi-cellular behavior such as sprout formation. Here we employ single-cell microscopy to ascertain phenotypic behaviors of more than 800 human microvascular endothelial cells under various combinational angiogenic (VEGF) and angiostatic (PF4) cytokine treatments, analyzing their dynamic behavioral transitions among sessile, migratory, proliferative, and apoptotic states. We find that an endothelial cell population clusters into an identifiable set of a few distinct phenotypic state transition patterns (clusters) that is consistent across all cytokine conditions. Varying the cytokine conditions, such as VEGF and PF4 combinations here, modulates the proportion of the population following a particular pattern (referred to as phenotypic cluster weights) without altering the transition dynamics within the patterns. We then map the phenotypic cluster weights to quantified population level sprout densities using a multi-variate regression approach, and identify linear combinations of the phenotypic cluster weights that associate with greater or lesser sprout density across the various treatment conditions. VEGF-dominant cytokine combinations yielding high sprout densities are characterized by high proliferative and low apoptotic cluster weights, whereas PF4-dominant conditions yielding low sprout densities are characterized by low proliferative and high apoptotic cluster weights. Migratory cluster weights show only mild association with sprout density outcomes under the VEGF/PF4 conditions and the sprout formation characteristics explored here. PMID:23303249

  15. Genetic and Environmental Contributions to Variation in Baboon Cranial Morphology

    PubMed Central

    Roseman, Charles C.; Willmore, Katherine E.; Rogers, Jeffrey; Hildebolt, Charles; Sadler, Brooke E.; Richtsmeier, Joan T.; Cheverud, James M.

    2011-01-01

    The development, function, and integration of morphological characteristics are all hypothesized to influence the utility of traits for phylogenetic reconstruction by affecting the way in which morphological characteristics evolve. We use a baboon model to test the hypotheses about phenotypic and quantitative genetic variation of traits in the cranium that bear on a phenotype’s propensity to evolve. We test the hypotheses that: 1) individual traits in different functionally and developmentally defined regions of the cranium are differentially environmentally, genetically, and phenotypically variable; 2) genetic covariance with other traits constrains traits in one region of the cranium more than those in others; 3) and regions of the cranium subject to different levels of mechanical strain differ in the magnitude of variation in individual traits. We find that the levels of environmental and genetic variation in individual traits are randomly distributed across regions of the cranium rather than being structured by developmental origin or degree of exposure to strain. Individual traits in the cranial vault tend to be more constrained by covariance with other traits than those in other regions. Traits in regions subject to high degrees of strain during mastication are not any more variable at any level than other traits. If these results are generalizable to other populations, they indicate that there is no reason to suppose that individual traits from any one part of the cranium are intrinsically less useful for reconstructing patterns of evolution than those from any other part. PMID:20623673

  16. Gene Networks Underlying Convergent and Pleiotropic Phenotypes in a Large and Systematically-Phenotyped Cohort with Heterogeneous Developmental Disorders

    PubMed Central

    Vulto-van Silfhout, Anneke; Taylor, Avigail; Steinberg, Julia; Hehir-Kwa, Jayne; Pfundt, Rolph; de Leeuw, Nicole; de Vries, Bert B. A.; Webber, Caleb

    2015-01-01

    Readily-accessible and standardised capture of genotypic variation has revolutionised our understanding of the genetic contribution to disease. Unfortunately, the corresponding systematic capture of patient phenotypic variation needed to fully interpret the impact of genetic variation has lagged far behind. Exploiting deep and systematic phenotyping of a cohort of 197 patients presenting with heterogeneous developmental disorders and whose genomes harbour de novo CNVs, we systematically applied a range of commonly-used functional genomics approaches to identify the underlying molecular perturbations and their phenotypic impact. Grouping patients into 408 non-exclusive patient-phenotype groups, we identified a functional association amongst the genes disrupted in 209 (51%) groups. We find evidence for a significant number of molecular interactions amongst the association-contributing genes, including a single highly-interconnected network disrupted in 20% of patients with intellectual disability, and show using microcephaly how these molecular networks can be used as baits to identify additional members whose genes are variant in other patients with the same phenotype. Exploiting the systematic phenotyping of this cohort, we observe phenotypic concordance amongst patients whose variant genes contribute to the same functional association but note that (i) this relationship shows significant variation across the different approaches used to infer a commonly perturbed molecular pathway, and (ii) that the phenotypic similarities detected amongst patients who share the same inferred pathway perturbation result from these patients sharing many distinct phenotypes, rather than sharing a more specific phenotype, inferring that these pathways are best characterized by their pleiotropic effects. PMID:25781962

  17. A common, non-optimal phenotypic endpoint in experimental adaptations of bacteriophage lysis time

    E-print Network

    Heineman, Richard H.

    Background: Optimality models of evolution, which ignore genetic details and focus on natural selection, are widely used but sometimes criticized as oversimplifications. Their utility for quantitatively predicting phenotypic ...

  18. Multitrait mixed modeling and categorical data analyses of phenotypic variances

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Quantitative and categorical data were digitally recorded, measured or scored on whole canopies; single plants, leaves, and siliques; and on random seed samples of 224 genotypes in a phenotyping nursery of Brassica napus. They were used to (1) develop a pyramiding phenotyping model based on multitra...

  19. Elucidating the evolution of hominid dentition in the age of phenomics, modularity, and quantitative genetics.

    PubMed

    Hlusko, Leslea J

    2016-01-01

    An organism's anatomy is the result of millions of years of interplay between DNA sequence, developmental processes, the environment, and evolutionary forces. The anatomical sciences are consequently highly integrative and interdisciplinary. That said, reaching across all of the relevant disciplines can be a daunting task because scientific publications are produced today at an astounding rate. This manuscript brings together insights from the quantitative genetic analysis of dental variation into the study of human evolutionary odontology within the context of genomics, genetic modularity, and phenomics. It primarily advocates the use of quantitative genetics to not only identify QTLs, but also to assess the patterns of genetic covariance that underlie phenotypic covariance, thereby enabling us to conceptualize phenotypic variation as a reflection of the underlying genetic mechanisms. By highlighting three phenotypes of importance within the study of human evolution (patterning of the dental arcade, enamel thickness, and taurodontism), it is demonstrated how an integrated consideration of quantitative genetics, genomic analyses, and paleontology can bring us to more detailed hypotheses about the evolution of the hominid clade. PMID:26100767

  20. Epigenetic correlates of plant phenotypic plasticity: DNA methylation differs between prickly and

    E-print Network

    Herrera, Carlos M.

    Epigenetic correlates of plant phenotypic plasticity: DNA methylation differs between prickly that epigenetic variation caused by changes in DNA methylation are related to phenotypic plasticity plasticity and epigenetic changes in plants, and also contribute to the crystallization of the consensus

  1. Phenotypic plasticity in nematodes

    PubMed Central

    Viney, Mark; Diaz, Anaid

    2012-01-01

    Model systems, including C. elegans, have been successfully studied to understand the genetic control of development. A genotype’s phenotype determines its evolutionary fitness in natural environments, which are typically harsh, heterogeneous and dynamic. Phenotypic plasticity, the process by which one genome can produce different phenotypes in response to the environment, allows genotypes to better match their phenotype to their environment. Phenotypic plasticity is rife among nematodes, seen both as differences among life-cycles stages, perhaps best exemplified by parasitic nematodes, as well as developmental choices, such as shown by the C. elegans dauer/non-dauer developmental choice. Understanding the genetic basis of phenotypically plastic traits will probably explain the function of many genes whose function still remains unclear. Understanding the adaptive benefits of phenotypically plastic traits requires that we understand how plasticity differs among genotypes, and the effects of this in diverse, different environments. PMID:24058831

  2. Statistical models for trisomic phenotypes

    SciTech Connect

    Lamb, N.E.; Sherman, S.L.; Feingold, E.

    1996-01-01

    Certain genetic disorders are rare in the general population but more common in individuals with specific trisomies, which suggests that the genes involved in the etiology of these disorders may be located on the trisomic chromosome. As with all aneuploid syndromes, however, a considerable degree of variation exists within each phenotype so that any given trait is present only among a subset of the trisomic population. We have previously presented a simple gene-dosage model to explain this phenotypic variation and developed a strategy to map genes for such traits. The mapping strategy does not depend on the simple model but works in theory under any model that predicts that affected individuals have an increased likelihood of disomic homozygosity at the trait locus. This paper explores the robustness of our mapping method by investigating what kinds of models give an expected increase in disomic homozygosity. We describe a number of basic statistical models for trisomic phenotypes. Some of these are logical extensions of standard models for disomic phenotypes, and some are more specific to trisomy. Where possible, we discuss genetic mechanisms applicable to each model. We investigate which models and which parameter values give an expected increase in disomic homozygosity in individuals with the trait. Finally, we determine the sample sizes required to identify the increased disomic homozygosity under each model. Most of the models we explore yield detectable increases in disomic homozygosity for some reasonable range of parameter values, usually corresponding to smaller trait frequencies. It therefore appears that our mapping method should be effective for a wide variety of moderately infrequent traits, even though the exact mode of inheritance is unlikely to be known. 21 refs., 8 figs., 1 tab.

  3. IL10 Gene Polymorphisms Are Associated With Asthma Phenotypes in Children

    PubMed Central

    Lyon, Helen; Lange, Christoph; Lake, Stephen; Silverman, Edwin K.; Randolph, Adrienne G.; Kwiatkowski, David; Raby, Benjamin A.; Lazarus, Ross; Weiland, Katy M.; Laird, Nan; Weiss, Scott T.

    2013-01-01

    IL10 is an anti-inflammatory cytokine that has been found to have lower production in macrophages and mononuclear cells from asthmatics. Since reduced IL10 levels may influence the severity of asthma phenotypes, we examined IL10 single-nucleotide polymorphisms (SNPs) for association with asthma severity and allergy phenotypes as quantitative traits. Utilizing DNA samples from 518 Caucasian asthmatic children from the Childhood Asthma Management Program (CAMP) and their parents, we genotyped six IL10 SNPs: 3 in the promoter, 2 in introns, and one in the 3? UTR. Using family-based association tests, each SNP was tested for association with asthma and allergy phenotypes individually. Population-based association analysis was performed with each SNP locus, the promoter haplotypes and the 6-loci haplotypes. The 3? UTR SNP was significantly associated with FEV1 as a percent of predicted (FEV1PP) (P=0.0002) in both the family and population analyses. The promoter haplotype GCC was positively associated with IgE levels and FEV1PP (P=0.007 and 0.012, respectively). The promoter haplotype ATA was negatively associated with lnPC20 and FEV1PP (P=0.008 and 0.043, respectively). Polymorphisms in IL10 are associated with asthma phenotypes in this cohort. Further studies of variation in the IL10 gene may help elucidate the mechanism of asthma development in children. PMID:14748015

  4. Genetic Architecture of Natural Variation in Thermal Responses of Arabidopsis.

    PubMed

    Sanchez-Bermejo, Eduardo; Zhu, Wangsheng; Tasset, Celine; Eimer, Hannes; Sureshkumar, Sridevi; Singh, Rupali; Sundaramoorthi, Vignesh; Colling, Luana; Balasubramanian, Sureshkumar

    2015-09-01

    Wild strains of Arabidopsis (Arabidopsis thaliana) exhibit extensive natural variation in a wide variety of traits, including response to environmental changes. Ambient temperature is one of the major external factors that modulates plant growth and development. Here, we analyze the genetic architecture of natural variation in thermal responses of Arabidopsis. Exploiting wild accessions and recombinant inbred lines, we reveal extensive phenotypic variation in response to ambient temperature in distinct developmental traits such as hypocotyl elongation, root elongation, and flowering time. We show that variation in thermal response differs between traits, suggesting that the individual phenotypes do not capture all the variation associated with thermal response. Genome-wide association studies and quantitative trait locus analyses reveal that multiple rare alleles contribute to the genetic architecture of variation in thermal response. We identify at least 20 genomic regions that are associated with variation in thermal response. Further characterizations of temperature sensitivity quantitative trait loci that are shared between traits reveal a role for the blue-light receptor CRYPTOCHROME2 (CRY2) in thermosensory growth responses. We show the accession Cape Verde Islands is less sensitive to changes in ambient temperature, and through transgenic analysis, we demonstrate that allelic variation at CRY2 underlies this temperature insensitivity across several traits. Transgenic analyses suggest that the allelic effects of CRY2 on thermal response are dependent on genetic background suggestive of the presence of modifiers. In addition, our results indicate that complex light and temperature interactions, in a background-dependent manner, govern growth responses in Arabidopsis. PMID:26195568

  5. First insights into the genotype–phenotype map of phenotypic stability in rye

    PubMed Central

    Wang, Yu; Mette, Michael Florian; Miedaner, Thomas; Wilde, Peer; Reif, Jochen C.; Zhao, Yusheng

    2015-01-01

    Improving phenotypic stability of crops is pivotal for coping with the detrimental impacts of climate change. The goal of this study was to gain first insights into the genetic architecture of phenotypic stability in cereals. To this end, we determined grain yield, thousand kernel weight, test weight, falling number, and both protein and soluble pentosan content for two large bi-parental rye populations connected through one common parent and grown in multi-environmental field trials involving more than 15 000 yield plots. Based on these extensive phenotypic data, we calculated parameters for static and dynamic phenotypic stability of the different traits and applied linkage mapping using whole-genome molecular marker profiles. While we observed an absence of large-effect quantitative trait loci (QTLs) underlying yield stability, large and stable QTLs were found for phenotypic stability of test weight, soluble pentosan content, and falling number. Applying genome-wide selection, which in contrast to marker-assisted selection also takes into account loci with small-effect sizes, considerably increased the accuracy of prediction of phenotypic stability for all traits by exploiting both genetic relatedness and linkage between single-nucleotide polymorphisms and QTLs. We conclude that breeding for crop phenotypic stability can be improved in related populations using genomic selection approaches established upon extensive phenotypic data. PMID:25873667

  6. Dominance Genetic Variation Contributes Little to the Missing Heritability for Human Complex Traits

    PubMed Central

    Zhu, Zhihong; Bakshi, Andrew; Vinkhuyzen, Anna A.E.; Hemani, Gibran; Lee, Sang Hong; Nolte, Ilja M.; van Vliet-Ostaptchouk, Jana V.; Snieder, Harold; Esko, Tonu; Milani, Lili; Mägi, Reedik; Metspalu, Andres; Hill, William G.; Weir, Bruce S.; Goddard, Michael E.; Visscher, Peter M.; Yang, Jian

    2015-01-01

    For human complex traits, non-additive genetic variation has been invoked to explain “missing heritability,” but its discovery is often neglected in genome-wide association studies. Here we propose a method of using SNP data to partition and estimate the proportion of phenotypic variance attributed to additive and dominance genetic variation at all SNPs (hSNP2 and ?SNP2) in unrelated individuals based on an orthogonal model where the estimate of hSNP2 is independent of that of ?SNP2. With this method, we analyzed 79 quantitative traits in 6,715 unrelated European Americans. The estimate of ?SNP2 averaged across all the 79 quantitative traits was 0.03, approximately a fifth of that for additive variation (average hSNP2 = 0.15). There were a few traits that showed substantial estimates of ?SNP2, none of which were replicated in a larger sample of 11,965 individuals. We further performed genome-wide association analyses of the 79 quantitative traits and detected SNPs with genome-wide significant dominance effects only at the ABO locus for factor VIII and von Willebrand factor. All these results suggest that dominance variation at common SNPs explains only a small fraction of phenotypic variation for human complex traits and contributes little to the missing narrow-sense heritability problem. PMID:25683123

  7. The genetics of phenotypic plasticity in plant defense: trichome production in Mimulus guttatus.

    PubMed

    Holeski, Liza M; Chase-Alone, Ronnette; Kelly, John K

    2010-04-01

    Insect herbivory is a major driving force of plant evolution. Phenotypic plasticity and developmental variation provide a means for plants to cope with variable herbivory. We characterized the genetics of developmental variation and phenotypic plasticity in trichome density, a putative defensive trait of Mimulus guttatus (yellow monkeyflower). Our results are evaluated in relation to the optimal defense theory, which provides testable predictions for plastic and developmental patterns in defense traits. We found that both developmental stage and simulated insect damage affected trichome production, but in different ways. Plants were more likely to produce at least some trichomes on later leaves than on earlier leaves, regardless of damage. Damage did not affect the average probability of producing trichomes, but it did increase the density of hairs on trichome-positive plants. We mapped trichome quantitative trait loci (QTL) by selectively genotyping a large panel of recombinant inbred lines derived from two highly divergent populations. Several highly pleiotropic QTL influenced multiple aspects of the trichome phenotype (constitutive, developmental, and/or plastic responses). Only one of the QTL influenced trichome induction following damage. In a result that is consistent with a central prediction of optimal defense theory, the high allele at this location was from the ancestral population with low constitutive trichome production. PMID:20180699

  8. A Review of Imaging Techniques for Plant Phenotyping

    PubMed Central

    Li, Lei; Zhang, Qin; Huang, Danfeng

    2014-01-01

    Given the rapid development of plant genomic technologies, a lack of access to plant phenotyping capabilities limits our ability to dissect the genetics of quantitative traits. Effective, high-throughput phenotyping platforms have recently been developed to solve this problem. In high-throughput phenotyping platforms, a variety of imaging methodologies are being used to collect data for quantitative studies of complex traits related to the growth, yield and adaptation to biotic or abiotic stress (disease, insects, drought and salinity). These imaging techniques include visible imaging (machine vision), imaging spectroscopy (multispectral and hyperspectral remote sensing), thermal infrared imaging, fluorescence imaging, 3D imaging and tomographic imaging (MRT, PET and CT). This paper presents a brief review on these imaging techniques and their applications in plant phenotyping. The features used to apply these imaging techniques to plant phenotyping are described and discussed in this review. PMID:25347588

  9. A review of imaging techniques for plant phenotyping.

    PubMed

    Li, Lei; Zhang, Qin; Huang, Danfeng

    2014-01-01

    Given the rapid development of plant genomic technologies, a lack of access to plant phenotyping capabilities limits our ability to dissect the genetics of quantitative traits. Effective, high-throughput phenotyping platforms have recently been developed to solve this problem. In high-throughput phenotyping platforms, a variety of imaging methodologies are being used to collect data for quantitative studies of complex traits related to the growth, yield and adaptation to biotic or abiotic stress (disease, insects, drought and salinity). These imaging techniques include visible imaging (machine vision), imaging spectroscopy (multispectral and hyperspectral remote sensing), thermal infrared imaging, fluorescence imaging, 3D imaging and tomographic imaging (MRT, PET and CT). This paper presents a brief review on these imaging techniques and their applications in plant phenotyping. The features used to apply these imaging techniques to plant phenotyping are described and discussed in this review. PMID:25347588

  10. Quantitative Trait Loci for the Circadian Clock in Neurospora crassa

    PubMed Central

    Kim, Tae-Sung; Logsdon, Benjamin A.; Park, Sohyun; Mezey, Jason G.; Lee, Kwangwon

    2007-01-01

    Neurospora crassa has been a model organism for the study of circadian clocks for the past four decades. Among natural accessions of Neurospora crassa, there is significant variation in clock phenotypes. In an attempt to investigate natural allelic variants contributing to quantitative variation, we used a quantitative trait loci mapping approach to analyze three independent mapping populations whose progenitors were collected from geographically isolated locations. Two circadian clock phenotypes, free-running period and entrained phase, were evaluated in the 188 F1 progeny of each mapping population. To identify the clock QTL, we applied two QTL mapping analyses: composite interval mapping (CIM) and Bayesian multiple QTL analysis (BMQ). When controlling false positive rates ?0.05, BMQ appears to be the more sensitive of the two approaches. BMQ confirmed most of the QTL from CIM (18 QTL) and identified 23 additional QTL. While 13 QTL colocalize with previously identified clock genes, we identified 30 QTL that were not linked with any previously characterized clock genes. These are candidate regions where clock genes may be located and are expected to lead to new insights in clock regulation. PMID:17947430

  11. Factors That Contribute to Assay Variation in Quantitative Analysis of Sex Steroid Hormones Using Liquid and Gas Chromatography-Mass Spectrometry

    ERIC Educational Resources Information Center

    Xu, Xia; Veenstra, Timothy D.

    2012-01-01

    The list of physiological events in which sex steroids play a role continues to increase. To decipher the roles that sex steroids play in any condition requires high quality cohorts of samples and assays that provide highly accurate quantitative measures. Liquid and gas chromatography coupled with mass spectrometry (LC-MS and GC-MS) have…

  12. mQTL.NMR: an integrated suite for genetic mapping of quantitative variations of (1)H NMR-based metabolic profiles.

    PubMed

    Hedjazi, Lyamine; Gauguier, Dominique; Zalloua, Pierre A; Nicholson, Jeremy K; Dumas, Marc-Emmanuel; Cazier, Jean-Baptiste

    2015-04-21

    High-throughput (1)H nuclear magnetic resonance (NMR) is an increasingly popular robust approach for qualitative and quantitative metabolic profiling, which can be used in conjunction with genomic techniques to discover novel genetic associations through metabotype quantitative trait locus (mQTL) mapping. There is therefore a crucial necessity to develop specialized tools for an accurate detection and unbiased interpretability of the genetically determined metabolic signals. Here we introduce and implement a combined chemoinformatic approach for objective and systematic analysis of untargeted (1)H NMR-based metabolic profiles in quantitative genetic contexts. The R/Bioconductor mQTL.NMR package was designed to (i) perform a series of preprocessing steps restoring spectral dependency in collinear NMR data sets to reduce the multiple testing burden, (ii) carry out robust and accurate mQTL mapping in human cohorts as well as in rodent models, (iii) statistically enhance structural assignment of genetically determined metabolites, and (iv) illustrate results with a series of visualization tools. Built-in flexibility and implementation in the powerful R/Bioconductor framework allow key preprocessing steps such as peak alignment, normalization, or dimensionality reduction to be tailored to specific problems. The mQTL.NMR package is freely available with its source code through the Comprehensive R/Bioconductor repository and its own website ( http://www.ican-institute.org/tools/ ). It represents a significant advance to facilitate untargeted metabolomic data processing and quantitative analysis and their genetic mapping. PMID:25803548

  13. Exploiting Regulatory Variation to Identify Genes Underlying Quantitative Resistance to the Wheat Stem Rust Pathogen Puccinia graminis f. sp. tritici in Barley

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We previously mapped mRNA transcript abundance traits 1 eQTL (expression- quantitative trait loci) using the Barley1 Affymetrix array and "whole plant" tissue from 139 progeny of the Steptoe x Morex (St/Mx) reference barley mapping population. Of the 22,840 probesets (genes) on the array, 15,987 rep...

  14. [Research progress on the phenotype informative SNP in forensic science].

    PubMed

    Liu, Yu-Xuan; Hu, Qing-Qing; Ma, Hong-Du; Huang, Dai-Xin

    2014-10-01

    Single nucleotide polymorphism (SNP) refers to the single base sequence variation in specific location of the human genome. Phenotype informative SNP has gradually become one of the research hot spots in forensic science. In this paper, the forensic research situation and application prospect of phenotype informative SNP in the characteristics of hair, eye and skin color, height, and facial feature are reviewed. PMID:25735077

  15. Phenotypic heterogeneity and evolutionary games in microbial populations

    E-print Network

    Healey, David W. (David Wendell)

    2015-01-01

    One of the most interesting discoveries of the last decade is the surprising degree of phenotypic variability between individual cells in clonal microbial populations, even in identical environments. While some variation ...

  16. Widespread phenotypic and genetic divergence along altitudinal gradients in animals

    E-print Network

    on phenotypic variation assessed under common garden or reciprocal transplant designs and (ii) studies looking-population differences are common and taxo- nomically widespread, involving traits such as mass, wing size, tolerance

  17. The contribution of pleiotropy of blood pressure and body-mass index variation: The Gubbio study

    SciTech Connect

    Schork, N.J.; Weder, A.B. ); Trevisan, M. Univ. of Naples Northwestern Univ., Chicago, IL ); Laurenzi, M. Center for Epidemiological Research, Merck, Sharp and Dohme Center for Preventive Medicine, Gubbio )

    1994-02-01

    Blood pressure (BP), body-mass index (BMI), and quantitative phenotypes thought to influence BP (e.g., lithium-sodium countertransport activity) were studied in 2,184 households comprising 5,376 people in Gubbio, Italy. Variance-components models were used to partition the variation of these phenotypes into components characterizing the effects of age-related, measured environmental, additive genetic, pleiotropic, unmeasured shared-household, and individual-specific (or random) factors. The goal of the investigation was to estimate the contribution of pleiotropy to variation in BP and BMI in population-based samples. Although the results suggest that numerous significant bivariate genetic correlations exist between BP and some of the traits investigated, they ultimately lead to rejection of a prominent role for any individual bivariate pleiotropic system influencing the natural variation of BP. However, because the authors found evidence that many traits enter into small-impact pleiotropic relationships with BP, they cannot rule out the possibility that pleiotropic genes, when considered collectively, may contribute to BP variation at the population level. Similar results were obtained when BMI was taken as the primary variable of interest. The authors argue that the small but significant portion of BP variation explained by individual genes displaying bivariate pleiotropic effects is intuitive, in light of the relatively low heritabilities associated with quantitative cardiovascular phenotypes and the low phenotypic correlations between BP, BMI, and many other physiologically linked measures of cardiovascular function. The results not only bear directly on both the nature of the multifactorial determinants of BP and the maintenance of BP variation in the population genetics research. 37 refs., 5 tabs.

  18. Copy number variations among silkworms

    PubMed Central

    2014-01-01

    Background Copy number variations (CNVs), which are important source for genetic and phenotypic variation, have been shown to be associated with disease as well as important QTLs, especially in domesticated animals. However, little is known about the CNVs in silkworm. Results In this study, we have constructed the first CNVs map based on genome-wide analysis of CNVs in domesticated silkworm. Using next-generation sequencing as well as quantitative PCR (qPCR), we identified ~319 CNVs in total and almost half of them (~ 49%) were distributed on uncharacterized chromosome. The CNVs covered 10.8 Mb, which is about 2.3% of the entire silkworm genome. Furthermore, approximately 61% of CNVs directly overlapped with SDs in silkworm. The genes in CNVs are mainly related to reproduction, immunity, detoxification and signal recognition, which is consistent with the observations in mammals. Conclusions An initial CNVs map for silkworm has been described in this study. And this map provides new information for genetic variations in silkworm. Furthermore, the silkworm CNVs may play important roles in reproduction, immunity, detoxification and signal recognition. This study provided insight into the evolution of the silkworm genome and an invaluable resource for insect genomics research. PMID:24684762

  19. The fossil record of phenotypic integration and modularity: A deep-time perspective on developmental and evolutionary dynamics

    PubMed Central

    Goswami, Anjali; Binder, Wendy J.; Meachen, Julie; O’Keefe, F. Robin

    2015-01-01

    Variation is the raw material for natural selection, but the factors shaping variation are still poorly understood. Genetic and developmental interactions can direct variation, but there has been little synthesis of these effects with the extrinsic factors that can shape biodiversity over large scales. The study of phenotypic integration and modularity has the capacity to unify these aspects of evolutionary study by estimating genetic and developmental interactions through the quantitative analysis of morphology, allowing for combined assessment of intrinsic and extrinsic effects. Data from the fossil record in particular are central to our understanding of phenotypic integration and modularity because they provide the only information on deep-time developmental and evolutionary dynamics, including trends in trait relationships and their role in shaping organismal diversity. Here, we demonstrate the important perspective on phenotypic integration provided by the fossil record with a study of Smilodon fatalis (saber-toothed cats) and Canis dirus (dire wolves). We quantified temporal trends in size, variance, phenotypic integration, and direct developmental integration (fluctuating asymmetry) through 27,000 y of Late Pleistocene climate change. Both S. fatalis and C. dirus showed a gradual decrease in magnitude of phenotypic integration and an increase in variance and the correlation between fluctuating asymmetry and overall integration through time, suggesting that developmental integration mediated morphological response to environmental change in the later populations of these species. These results are consistent with experimental studies and represent, to our knowledge, the first deep-time validation of the importance of developmental integration in stabilizing morphological evolution through periods of environmental change. PMID:25901310

  20. The fossil record of phenotypic integration and modularity: A deep-time perspective on developmental and evolutionary dynamics.

    PubMed

    Goswami, Anjali; Binder, Wendy J; Meachen, Julie; O'Keefe, F Robin

    2015-04-21

    Variation is the raw material for natural selection, but the factors shaping variation are still poorly understood. Genetic and developmental interactions can direct variation, but there has been little synthesis of these effects with the extrinsic factors that can shape biodiversity over large scales. The study of phenotypic integration and modularity has the capacity to unify these aspects of evolutionary study by estimating genetic and developmental interactions through the quantitative analysis of morphology, allowing for combined assessment of intrinsic and extrinsic effects. Data from the fossil record in particular are central to our understanding of phenotypic integration and modularity because they provide the only information on deep-time developmental and evolutionary dynamics, including trends in trait relationships and their role in shaping organismal diversity. Here, we demonstrate the important perspective on phenotypic integration provided by the fossil record with a study of Smilodon fatalis (saber-toothed cats) and Canis dirus (dire wolves). We quantified temporal trends in size, variance, phenotypic integration, and direct developmental integration (fluctuating asymmetry) through 27,000 y of Late Pleistocene climate change. Both S. fatalis and C. dirus showed a gradual decrease in magnitude of phenotypic integration and an increase in variance and the correlation between fluctuating asymmetry and overall integration through time, suggesting that developmental integration mediated morphological response to environmental change in the later populations of these species. These results are consistent with experimental studies and represent, to our knowledge, the first deep-time validation of the importance of developmental integration in stabilizing morphological evolution through periods of environmental change. PMID:25901310

  1. Vertical Profile and Temporal Variation of Chlorophyll in Maize Canopy: Quantitative "Crop Vigor" Indicator by Means of Reflectance-Based Techniques

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Chlorophyll (Chl) content is among the most important crop biophysical characteristics. Chlorophyll can be related to photosynthetic capacity, thus, productivity, developmental stage, and canopy stresses. The objective of this study was to quantify and characterize the temporal variation of Chl cont...

  2. A New Method to Infer Causal Phenotype Networks Using QTL and Phenotypic Information

    PubMed Central

    Wang, Huange; van Eeuwijk, Fred A.

    2014-01-01

    In the context of genetics and breeding research on multiple phenotypic traits, reconstructing the directional or causal structure between phenotypic traits is a prerequisite for quantifying the effects of genetic interventions on the traits. Current approaches mainly exploit the genetic effects at quantitative trait loci (QTLs) to learn about causal relationships among phenotypic traits. A requirement for using these approaches is that at least one unique QTL has been identified for each trait studied. However, in practice, especially for molecular phenotypes such as metabolites, this prerequisite is often not met due to limited sample sizes, high noise levels and small QTL effects. Here, we present a novel heuristic search algorithm called the QTL+phenotype supervised orientation (QPSO) algorithm to infer causal directions for edges in undirected phenotype networks. The two main advantages of this algorithm are: first, it does not require QTLs for each and every trait; second, it takes into account associated phenotypic interactions in addition to detected QTLs when orienting undirected edges between traits. We evaluate and compare the performance of QPSO with another state-of-the-art approach, the QTL-directed dependency graph (QDG) algorithm. Simulation results show that our method has broader applicability and leads to more accurate overall orientations. We also illustrate our method with a real-life example involving 24 metabolites and a few major QTLs measured on an association panel of 93 tomato cultivars. Matlab source code implementing the proposed algorithm is freely available upon request. PMID:25144184

  3. Phenotypic and genomic plasticity of alternative male reproductive tactics in sailfin mollies.

    PubMed

    Fraser, Bonnie A; Janowitz, Ilana; Thairu, Margaret; Travis, Joseph; Hughes, Kimberly A

    2014-04-22

    A major goal of modern evolutionary biology is to understand the causes and consequences of phenotypic plasticity, the ability of a single genotype to produce multiple phenotypes in response to variable environments. While ecological and quantitative genetic studies have evaluated models of the evolution of adaptive plasticity, some long-standing questions about plasticity require more mechanistic approaches. Here, we address two of those questions: does plasticity facilitate adaptive evolution? And do physiological costs place limits on plasticity? We examine these questions by comparing genetically and plastically regulated behavioural variation in sailfin mollies (Poecilia latipinna), which exhibit striking variation in plasticity for male mating behaviour. In this species, some genotypes respond plastically to a change in the social environment by switching between primarily courting and primarily sneaking behaviour. In contrast, other genotypes have fixed mating strategies (either courting or sneaking) and do not display plasticity. We found that genetic and plastic variation in behaviour were accompanied by partially, but not completely overlapping changes in brain gene expression, in partial support of models that predict that plasticity can facilitate adaptive evolution. We also found that behavioural plasticity was accompanied by broader and more robust changes in brain gene expression, suggesting a substantial physiological cost to plasticity. We also observed that sneaking behaviour, but not courting, was associated with upregulation of genes involved in learning and memory, suggesting that sneaking is more cognitively demanding than courtship. PMID:24573842

  4. Gain-of-Function Phenotypes of Many CLAVATA3/ESR Genes, Including Four New Family Members, Correlate with Tandem Variations in the Conserved CLAVATA3/ESR Domain1[W

    PubMed Central

    Strabala, Timothy J.; O'Donnell, Philip J.; Smit, Anne-Marie; Ampomah-Dwamena, Charles; Martin, E. Jane; Netzler, Natalie; Nieuwenhuizen, Niels J.; Quinn, Brian D.; Foote, Humphrey C.C.; Hudson, Keith R.

    2006-01-01

    Secreted peptide ligands are known to play key roles in the regulation of plant growth, development, and environmental responses. However, phenotypes for surprisingly few such genes have been identified via loss-of-function mutant screens. To begin to understand the processes regulated by the CLAVATA3 (CLV3)/ESR (CLE) ligand gene family, we took a systems approach to gene identification and gain-of-function phenotype screens in transgenic plants. We identified four new CLE family members in the Arabidopsis (Arabidopsis thaliana) genome sequence and determined their relative transcript levels in various organs. Overexpression of CLV3 and the 17 CLE genes we tested resulted in premature mortality and/or developmental timing delays in transgenic Arabidopsis plants. Overexpression of 10 CLE genes and the CLV3 positive control resulted in arrest of growth from the shoot apical meristem (SAM). Overexpression of nearly all the CLE genes and CLV3 resulted in either inhibition or stimulation of root growth. CLE4 expression reversed the SAM proliferation phenotype of a clv3 mutant to one of SAM arrest. Dwarf plants resulted from overexpression of five CLE genes. Overexpression of new family members CLE42 and CLE44 resulted in distinctive shrub-like dwarf plants lacking apical dominance. Our results indicate the capacity for functional redundancy of many of the CLE ligands. Additionally, overexpression phenotypes of various CLE family members suggest roles in organ size regulation, apical dominance, and root growth. Similarities among overexpression phenotypes of many CLE genes correlate with similarities in their CLE domain sequences, suggesting that the CLE domain is responsible for interaction with cognate receptors. PMID:16489133

  5. Geographically multifarious phenotypic divergence during speciation

    PubMed Central

    Gompert, Zachariah; Lucas, Lauren K; Nice, Chris C; Fordyce, James A; Alex Buerkle, C; Forister, Matthew L

    2013-01-01

    Speciation is an important evolutionary process that occurs when barriers to gene flow evolve between previously panmictic populations. Although individual barriers to gene flow have been studied extensively, we know relatively little regarding the number of barriers that isolate species or whether these barriers are polymorphic within species. Herein, we use a series of field and lab experiments to quantify phenotypic divergence and identify possible barriers to gene flow between the butterfly species Lycaeides idas and Lycaeides melissa. We found evidence that L. idas and L. melissa have diverged along multiple phenotypic axes. Specifically, we identified major phenotypic differences in female oviposition preference and diapause initiation, and more moderate divergence in mate preference. Multiple phenotypic differences might operate as barriers to gene flow, as shown by correlations between genetic distance and phenotypic divergence and patterns of phenotypic variation in admixed Lycaeides populations. Although some of these traits differed primarily between species (e.g., diapause initiation), several traits also varied among conspecific populations (e.g., male mate preference and oviposition preference). PMID:23532669

  6. Quantitative Assessment of Intra-Patient Variation in CD4+ T Cell Counts in Stable, Virologically-Suppressed, HIV-Infected Subjects

    PubMed Central

    Gordon, Claire L.; Cheng, Allen C.; Cameron, Paul U.; Bailey, Michael; Crowe, Suzanne M.; Mills, John

    2015-01-01

    Objectives Counts of absolute CD4+ T lymphocytes (CD4+ T cells) are known to be highly variable in untreated HIV-infected individuals, but there are no data in virologically-suppressed individuals. We investigated CD4+ T cell variability in stable, virologically-suppressed, HIV-1 infected adults on combination antiretroviral therapy (cART). Methods From a large hospital database we selected patients with stable virological suppression on cART for >3 years with >10 CD4+ T cell measurements performed over a further >2 years; and a control group of 95 patients not on cART. Results We identified 161 HIV-infected patients on cART without active HCV or HBV infection, with stable virological suppression for a median of 6.4 years. Over the study period 88 patients had reached a plateau in their absolute CD4+ T cell counts, while 65 patients had increasing and 8 patients had decreasing absolute CD4+ T cell counts. In patients with plateaued CD4+ T cell counts, variability in absolute CD4+ T cell counts was greater than in percent CD4+ T cells (median coefficient of variation (CV) 16.6% [IQR 13.8-20.1%] and CV 9.6% [IQR 7.4-13.0%], respectively). Patients with increasing CD4+ T cell counts had greater variability in absolute CD4+ T cell counts than those with plateaued CD4 T cell counts (CV 19.5% [IQR 16.1-23.8%], p<0.001) while there was no difference in percent CD4+ T cell variability between the two groups. As previously reported, untreated patients had CVs significantly higher than patients on cART (CVs of 21.1% [IQR 17.2-32.0%], p<0.001 and 15.2% (IQR 10.7-20.0%), p<0.001, respectively). Age or sex did not affect the degree of CD4+ variation. Conclusions Adults with stable, virologically-suppressed HIV infection continue to have significant variations in individual absolute CD4+ T cell and percent CD4+ T cell counts; this variation can be of clinical relevance especially around CD4+ thresholds. However, the variation seen in individuals on cART is substantially less than in untreated subjects. PMID:26110761

  7. Genetic basis for systems of skeletal quantitative traits: Principal component analysis of the canid skeleton

    PubMed Central

    Chase, Kevin; Carrier, David R.; Adler, Frederick R.; Jarvik, Tyler; Ostrander, Elaine A.; Lorentzen, Travis D.; Lark, Karl G.

    2002-01-01

    Evolution of mammalian skeletal structure can be rapid and the changes profound, as illustrated by the morphological diversity of the domestic dog. Here we use principal component analysis of skeletal variation in a population of Portuguese Water Dogs to reveal systems of traits defining skeletal structures. This analysis classifies phenotypic variation into independent components that can be used to dissect genetic networks regulating complex biological systems. We show that unlinked quantitative trait loci associated with these principal components individually promote both correlations within structures (e.g., within the skull or among the limb bones) and inverse correlations between structures (e.g., skull vs. limb bones). These quantitative trait loci are consistent with regulatory genes that inhibit growth of some bones while enhancing growth of others. These systems of traits could explain the skeletal differences between divergent breeds such as Greyhounds and Pit Bulls, and even some of the skeletal transformations that characterize the evolution of hominids. PMID:12114542

  8. Cross-cultural variation in blood pressure: a quantitative analysis of the relationships of blood pressure to cultural characteristics, salt consumption and body weight.

    PubMed

    Waldron, I; Nowotarski, M; Freimer, M; Henry, J P; Post, N; Witten, C

    1982-01-01

    This study has analyzed the relationships of cross-cultural variation in blood pressure to cultural characteristics, salt consumption and body weight. The data used were blood pressures for adults in 84 groups, ratings of cultural characteristics (based on anthropological data and made by raters who had no knowledge of the blood pressure data) and, where available, salt consumption and body mass index (weight/height2). Blood pressures were higher and the slopes of blood pressure with age were greater in groups which had greater involvement in a money economy, more economic competition, more contact with people of different culture or beliefs, and more unfulfilled aspirations for a return to traditional beliefs and values. Blood pressures were also higher in groups for which the predominant family type was a nuclear or father-absent family, as opposed to an extended family. For Negroes, groups who were descended from slaves had higher blood pressures than other groups. The correlations between blood pressures and involvement in a money economy were substantial and significant even after controlling for level of salt consumption and, for men, also after controlling for body mass index. For men there were also significant partial correlations between blood pressure and salt consumption, controlling for type of economy. For women there were significant partial correlations between blood pressure and body mass index, controlling for type of economy. In conclusion, cross-cultural variation in blood pressure appears to be due to multiple factors. One contributory factor appears to be psychosocial stress due to cultural disruption, including the disruption of cooperative relationships and traditional cultural patterns which frequently occurs during economic modernization. In addition, both the protective effects of very low salt consumption in some groups and differences in body weight appear to contribute to cross-cultural variation in blood pressure. PMID:7079796

  9. A Quantitative Analysis of Growth and Size Regulation in Manduca sexta: The Physiological Basis of Variation in Size and Age at Metamorphosis

    PubMed Central

    Grunert, Laura W.; Clarke, Jameson W.; Ahuja, Chaarushi; Eswaran, Harish; Nijhout, H. Frederik

    2015-01-01

    Body size and development time are important life history traits because they are often highly correlated with fitness. Although the developmental mechanisms that control growth have been well studied, the mechanisms that control how a species-characteristic body size is achieved remain poorly understood. In insects adult body size is determined by the number of larval molts, the size increment at each molt, and the mechanism that determines during which instar larval growth will stop. Adult insects do not grow, so the size at which a larva stops growing determines adult body size. Here we develop a quantitative understanding of the kinetics of growth throughout larval life of Manduca sexta, under different conditions of nutrition and temperature, and for genetic strains with different adult body sizes. We show that the generally accepted view that the size increment at each molt is constant (Dyar’s Rule) is systematically violated: there is actually a progressive increase in the size increment from instar to instar that is independent of temperature. In addition, the mass-specific growth rate declines throughout the growth phase in a temperature-dependent manner. We show that growth within an instar follows a truncated Gompertz trajectory. The critical weight, which determines when in an instar a molt will occur, and the threshold size, which determines which instar is the last, are different in genetic strains with different adult body sizes. Under nutrient and temperature stress Manduca has a variable number of larval instars and we show that this is due to the fact that more molts at smaller increments are taken before threshold size is reached. We test whether the new insight into the kinetics of growth and size determination are sufficient to explain body size and development time through a mathematical model that incorporates our quantitative findings. PMID:26011714

  10. Forging links between population and quantitative genetics.

    PubMed

    Frankham, R; Nurthen, R K

    1981-07-01

    An initially rare allele with a large effect on a quantitative character is expected to exhibit the following behaviour in artificial selection lines: 1. It should change in frequency, or be lost by chance, at rates predictable from the effects of the allele on the quantitative character and the selection regime imposed. 2. At the phenotypic level the behaviour of the allele should cause (a) asymmetrical responses to bidirectional selection, (b) variation among replicate lines in response to selection corresponding to the behaviour of the allele in individual lines, (c) changes in heritability in lines in which the allele increases in frequency and (d) selection response compatible with the effects of the allele. This paper reports an experimental evaluation of these predictions utilizing a rare allele of large effect (sm (lab) ) detected in a sample of the Canberra outbred population of Drosophila melanogaster at a frequency of 1/120. Homosygosity for this allele reduced abdominal bristle number by more than 50%, altered the abdominal bristle pattern and reversed the sexual dimorphism for abdominal bristle number. Experiments were done to characterise sm (lab) and all evidence indicates that it is a single allele with a very large effect.Bidirectional selection for abdominal bristle number was carried out in three high and three low lines from this sample of the Canberra population. The sm (lab) allele rose in frequency and went to fixation in two of the low lines (in 10 generations) but was lost from the third. These times to fixation were slower than the expectations derived from computer simulations of the behaviour of such an allele but this can be attributed to the lower fitness of sm (lab) homozygotes. The proportions of lines with the allele fixed or lost were compatible with expectations. At the phenotypic level, the behavior of sm (lab) had the expected consequences, namely, (i) asymmetrical responses to bidirectional selection, (ii) variation in response among replicate low lines corresponding to the behaviour of sm (lab) , (iii) changes in heritabilities in the lines in which sm (lab) went to fixation, and (iv) selection responses compatible with the effects of the allele.A test for rare alleles of large effect was proposed, based on the expected pattern of change in heritability under artificial selection. This test was applied to the high selection lines but no evidence was found for important effects due to rare alleles of large effect increasing abdominal bristle number, a conclusion consistent with other independent evidence.This work provides experimental corroboration of the links between population genetics and quantitative genetics. PMID:24276487

  11. Spatiotemporal variation of leaf epidermal cell growth: a quantitative analysis of Arabidopsis thaliana wild-type and triple cyclinD3 mutant plants

    PubMed Central

    Elsner, Joanna; Michalski, Marek; Kwiatkowska, Dorota

    2012-01-01

    Background and Aims The epidermis of an expanding dicot leaf is a mosaic of cells differing in identity, size and differentiation stage. Here hypotheses are tested that in such a cell mosaic growth is heterogeneous and changes with time, and that this heterogeneity is not dependent on the cell cycle regulation per se. Methods Shape, size and growth of individual cells were followed with the aid of sequential replicas in expanding leaves of wild-type Arabidopsis thaliana and triple cyclinD3 mutant plants, and combined with ploidy estimation using epi-fluorescence microscopy. Key Results Relative growth rates in area of individual epidermal cells or small cell groups differ several fold from those of adjacent cells, and change in time. This spatial and temporal variation is not related to the size of either the cell or the nucleus. Shape changes and growth within an individual cell are also heterogeneous: anticlinal wall waviness appears at different times in different wall portions; portions of the cell periphery in contact with different neighbours grow with different rates. This variation is not related to cell growth anisotropy. The heterogeneity is typical for both the wild type and cycD3. Conclusions Growth of leaf epidermis exhibits spatiotemporal variability. PMID:22307569

  12. Human lymphocyte polymorphisms detected by quantitative two-dimensional electrophoresis.

    PubMed Central

    Goldman, D; Merril, C R

    1983-01-01

    A survey of 186 soluble lymphocyte proteins for genetic polymorphism was carried out utilizing two-dimensional electrophoresis of 14C-labeled phytohemagglutinin (PHA)-stimulated human lymphocyte proteins. Nineteen of these proteins exhibited positional variation consistent with independent genetic polymorphism in a primary sample of 28 individuals. Each of these polymorphisms was characterized by quantitative gene-dosage dependence insofar as the heterozygous phenotype expressed approximately 50% of each allelic gene product as was seen in homozygotes. Patterns observed were also identical in monozygotic twins, replicate samples, and replicate gels. The three expected phenotypes (two homozygotes and a heterozygote) were observed in each of 10 of these polymorphisms while the remaining nine had one of the homozygous classes absent. The presence of the three phenotypes, the demonstration of gene-dosage dependence, and our own and previous pedigree analysis of certain of these polymorphisms supports the genetic basis of these variants. Based on this data, the frequency of polymorphic loci for man is: P = 19/186 = .102, and the average heterozygosity is .024. This estimate is approximately 1/3 to 1/2 the rate of polymorphism previously estimated for man in other studies using one-dimensional electrophoresis of isozyme loci. The newly described polymorphisms and others which should be detectable in larger protein surveys with two-dimensional electrophoresis hold promise as genetic markers of the human genome for use in gene mapping and pedigree analyses. Images Fig. 1 Fig. 3 PMID:6577787

  13. Structural mapping: how to study the genetic architecture of a phenotypic trait through its formation mechanism.

    PubMed

    Tong, Chunfa; Shen, Lianying; Lv, Yafei; Wang, Zhong; Wang, Xiaoling; Feng, Sisi; Li, Xin; Sui, Yihan; Pang, Xiaoming; Wu, Rongling

    2014-01-01

    Traditional approaches for genetic mapping are to simply associate the genotypes of a quantitative trait locus (QTL) with the phenotypic variation of a complex trait. A more mechanistic strategy has emerged to dissect the trait phenotype into its structural components and map specific QTLs that control the mechanistic and structural formation of a complex trait. We describe and assess such a strategy, called structural mapping, by integrating the internal structural basis of trait formation into a QTL mapping framework. Electrical impedance spectroscopy (EIS) has been instrumental for describing the structural components of a phenotypic trait and their interactions. By building robust mathematical models on circuit EIS data and embedding these models within a mixture model-based likelihood for QTL mapping, structural mapping implements the EM algorithm to obtain maximum likelihood estimates of QTL genotype-specific EIS parameters. The uniqueness of structural mapping is to make it possible to test a number of hypotheses about the pattern of the genetic control of structural components. We validated structural mapping by analyzing an EIS data collected for QTL mapping of frost hardiness in a controlled cross of jujube trees. The statistical properties of parameter estimates were examined by simulation studies. Structural mapping can be a powerful alternative for genetic mapping of complex traits by taking account into the biological and physical mechanisms underlying their formation. PMID:23104859

  14. Lect 13: Quantitative genetics II Evolution at multiple loci

    E-print Network

    Lect 13: Quantitative genetics II · Evolution at multiple loci · Quantitative genetics ­ Selection gradients ­ 3 generalization · Constraints on evolutionary responses ­ Genetic variation ­ Genetic Multiple loci: quantitative genetics Fig. 8.1 Xb Measuring Directional Selection Xa Selection differential

  15. Plant phenotyping: from bean weighing to image analysis.

    PubMed

    Walter, Achim; Liebisch, Frank; Hund, Andreas

    2015-01-01

    Plant phenotyping refers to a quantitative description of the plant's anatomical, ontogenetical, physiological and biochemical properties. Today, rapid developments are taking place in the field of non-destructive, image-analysis -based phenotyping that allow for a characterization of plant traits in high-throughput. During the last decade, 'the field of image-based phenotyping has broadened its focus from the initial characterization of single-plant traits in controlled conditions towards 'real-life' applications of robust field techniques in plant plots and canopies. An important component of successful phenotyping approaches is the holistic characterization of plant performance that can be achieved with several methodologies, ranging from multispectral image analyses via thermographical analyses to growth measurements, also taking root phenotypes into account. PMID:25767559

  16. Quantitative film radiography

    SciTech Connect

    Devine, G.; Dobie, D.; Fugina, J.; Hernandez, J.; Logan, C.; Mohr, P.; Moss, R.; Schumacher, B.; Updike, E.; Weirup, D.

    1991-02-26

    We have developed a system of quantitative radiography in order to produce quantitative images displaying homogeneity of parts. The materials that we characterize are synthetic composites and may contain important subtle density variations not discernible by examining a raw film x-radiograph. In order to quantitatively interpret film radiographs, it is necessary to digitize, interpret, and display the images. Our integrated system of quantitative radiography displays accurate, high-resolution pseudo-color images in units of density. We characterize approximately 10,000 parts per year in hundreds of different configurations and compositions with this system. This report discusses: the method; film processor monitoring and control; verifying film and processor performance; and correction of scatter effects.

  17. Heritable Variation in Garter Snake Color Patterns in Postglacial Populations

    PubMed Central

    Westphal, Michael F.; Massie, Jodi L.; Bronkema, Joanna M.; Smith, Brian E.; Morgan, Theodore J.

    2011-01-01

    Global climate change is expected to trigger northward shifts in the ranges of natural populations of plants and animals, with subsequent effects on intraspecific genetic diversity. Investigating how genetic diversity is patterned among populations that arose following the last Ice Age is a promising method for understanding the potential future effects of climate change. Theoretical and empirical work has suggested that overall genetic diversity can decrease in colonial populations following rapid expansion into postglacial landscapes, with potential negative effects on the ability of populations to adapt to new environmental regimes. The crucial measure of this genetic variation and a population's overall adaptability is the heritable variation in phenotypic traits, as it is this variation that mediates the rate and direction of a population's multigenerational response to selection. Using two large full-sib quantitative genetic studies (NManitoba?=?144; NSouth Dakota?=?653) and a smaller phenotypic analysis from Kansas (NKansas?=?44), we compared mean levels of pigmentation, genetic variation and heritability in three pigmentation traits among populations of the common garter snake, Thamnophis sirtalis, along a north-south gradient, including a postglacial northern population and a putative southern refuge population. Counter to our expectations, we found that genetic variance and heritability for the three pigmentation traits were the same or higher in the postglacial population than in the southern population. PMID:21935386

  18. Skin, hair, and iris pigmentation are phenotypic traits that exhibit

    E-print Network

    Schieber, Juergen

    Skin, hair, and iris pigmentation are phenotypic traits that exhibit extensive variation across the human species. The strong relationship between skin pigmentation and ultra- violet radiation (UVR) suggests a model in which global patterns of human skin pigmentation variation reflect localized adaptation

  19. Male and female secondary sexual traits show different patterns of quantitative genetic and environmental variation in the horned beetle Onthophagus sagittarius.

    PubMed

    Watson, N L; Simmons, L W

    2010-11-01

    The expression of secondary sexual traits in females has often been attributed to a correlated response to selection on male traits. In rare cases, females have secondary sexual traits that are not homologous structures to secondary sexual traits in males and are thus less likely to have evolved in females because of correlated selection. In this study, we used the dung beetle Onthophagus sagittarius, a species with sex-specific horns, to examine the environmental and quantitative genetic control of horn expression in males and females. Offspring subjected to different brood mass manipulations (dung addition/removal) were found to differ significantly in body size. Brood mass manipulation also had a significant effect on the length of male horns; however, female horn length was found to be relatively impervious to the treatment, showing stronger patterns of additive genetic variance than males. We found no correlations between horn expression in males and females. We therefore conclude that the horns of O. sagittarius females are unlikely to result from genetic correlations between males and females. Rather, our data suggest that they may be under independent genetic control. PMID:20831732

  20. High-Resolution Inflorescence Phenotyping Using a Novel Image-Analysis Pipeline, PANorama1[W][OPEN

    PubMed Central

    Crowell, Samuel; Falcão, Alexandre X.; Shah, Ankur; Wilson, Zachary; Greenberg, Anthony J.; McCouch, Susan R.

    2014-01-01

    Variation in inflorescence development is an important target of selection for numerous crop species, including many members of the Poaceae (grasses). In Asian rice (Oryza sativa), inflorescence (panicle) architecture is correlated with yield and grain-quality traits. However, many rice breeders continue to use composite phenotypes in selection pipelines, because measuring complex, branched panicles requires a significant investment of resources. We developed an open-source phenotyping platform, PANorama, which measures multiple architectural and branching phenotypes from images simultaneously. PANorama automatically extracts skeletons from images, allows users to subdivide axes into individual internodes, and thresholds away structures, such as awns, that normally interfere with accurate panicle phenotyping. PANorama represents an improvement in both efficiency and accuracy over existing panicle imaging platforms, and flexible implementation makes PANorama capable of measuring a range of organs from other plant species. Using high-resolution phenotypes, a mapping population of recombinant inbred lines, and a dense single-nucleotide polymorphism data set, we identify, to our knowledge, the largest number of quantitative trait loci (QTLs) for panicle traits ever reported in a single study. Several areas of the genome show pleiotropic clusters of panicle QTLs, including a region near the rice Green Revolution gene SEMIDWARF1. We also confirm that multiple panicle phenotypes are distinctly different among a small collection of diverse rice varieties. Taken together, these results suggest that clusters of small-effect QTLs may be responsible for varietal or subpopulation-specific panicle traits, representing a significant opportunity for rice breeders selecting for yield performance across different genetic backgrounds. PMID:24696519

  1. Multiparameter Phenotyping of Human PBMCs Using Mass Cytometry.

    PubMed

    Leipold, Michael D; Newell, Evan W; Maecker, Holden T

    2015-01-01

    The standard for single-cell analysis of phenotype and function in recent decades has been fluorescence flow cytometry. Mass cytometry is a newer technology that uses heavy metal ions, rather than fluorochromes, as labels for probes such as antibodies. The binding of these ion-labeled probes to cells is quantitated by mass spectrometry. This greatly increases the number of phenotypic and functional markers that can be probed simultaneously. Here, we review topics that must be considered when adapting existing flow cytometry panels to mass cytometry analysis. We present a protocol and representative panels for surface phenotyping and intracellular cytokine staining (ICS) assays. PMID:26420710

  2. Phenotypic Models of Evolution and Development: Geometry as Destiny

    PubMed Central

    Francois, Paul; Siggia, Eric D.

    2012-01-01

    Quantitative models of development that consider all relevant genes typically are difficult to fit to embryonic data alone and have many redundant parameters. Computational evolution supplies models of phenotype with relatively few variables and parameters that allows the patterning dynamics to be reduced to a geometrical picture for how the state of a cell moves. The clock and wavefront model, that defines the phenotype of somitogenesis, can be represented as a sequence of two discrete dynamical transitions (bifurcations). The expression-time to space map for Hox genes and the posterior dominance rule are phenotypes that naturally follow from computational evolution without considering the genetics of Hox regulation. PMID:23026724

  3. Quantitative Effect of a CNV on a Morphological Trait in Chickens

    PubMed Central

    Moro, Céline; Cornette, Raphaël; Vieaud, Agathe; Bruneau, Nicolas; Gourichon, David; Bed’hom, Bertrand; Tixier-Boichard, Michèle

    2015-01-01

    Copy Number Variation has been associated with morphological traits, developmental defects or disease susceptibility. The autosomal dominant Pea-comb mutation in chickens is due to the massive amplification of a CNV in intron 1 of SOX5 and provides a unique opportunity to assess the effect of variation in the number of repeats on quantitative traits such as comb size and comb mass in Pea-comb chickens. The quantitative variation of comb size was estimated by 2D morphometry and the number of repeats (RQ) was estimated by qPCR, in a total of 178 chickens from 3 experimental lines, two of them showing segregation for the Pea-comb mutation. This study included only Pea-comb chickens. Analysis of variance showed highly significant effects of line and sex on comb measurements. Adult body weight (BW) and RQ were handled as covariates. BW significantly influenced comb mass but not comb size. RQ values significantly influenced comb size, and the linear regression coefficient was highest for heterozygous carriers: the higher the number of repeats, the smaller the comb size. A similar trend was observed for comb mass. The CNV contributed to 3.4% of the phenotypic variance of comb size in heterozygous carriers of the CNV, an order of magnitude frequently encountered for QTLs. Surprisingly, there was no such relationship between RQ values and comb size in the homozygous line. It may be concluded that heterozygosity for a CNV in a non-coding region may contribute to phenotypic plasticity. PMID:25768125

  4. Quantitative effect of a CNV on a morphological trait in chickens.

    PubMed

    Moro, Céline; Cornette, Raphaël; Vieaud, Agathe; Bruneau, Nicolas; Gourichon, David; Bed'hom, Bertrand; Tixier-Boichard, Michèle

    2015-01-01

    Copy Number Variation has been associated with morphological traits, developmental defects or disease susceptibility. The autosomal dominant Pea-comb mutation in chickens is due to the massive amplification of a CNV in intron 1 of SOX5 and provides a unique opportunity to assess the effect of variation in the number of repeats on quantitative traits such as comb size and comb mass in Pea-comb chickens. The quantitative variation of comb size was estimated by 2D morphometry and the number of repeats (RQ) was estimated by qPCR, in a total of 178 chickens from 3 experimental lines, two of them showing segregation for the Pea-comb mutation. This study included only Pea-comb chickens. Analysis of variance showed highly significant effects of line and sex on comb measurements. Adult body weight (BW) and RQ were handled as covariates. BW significantly influenced comb mass but not comb size. RQ values significantly influenced comb size, and the linear regression coefficient was highest for heterozygous carriers: the higher the number of repeats, the smaller the comb size. A similar trend was observed for comb mass. The CNV contributed to 3.4% of the phenotypic variance of comb size in heterozygous carriers of the CNV, an order of magnitude frequently encountered for QTLs. Surprisingly, there was no such relationship between RQ values and comb size in the homozygous line. It may be concluded that heterozygosity for a CNV in a non-coding region may contribute to phenotypic plasticity. PMID:25768125

  5. Quantitative analysis of intraspecific variations in the carbon and oxygen isotope compositions of the modern cool-temperate brachiopod Terebratulina crossei

    NASA Astrophysics Data System (ADS)

    Takayanagi, Hideko; Asami, Ryuji; Otake, Tsuguo; Abe, Osamu; Miyajima, Toshihiro; Kitagawa, Hiroyuki; Iryu, Yasufumi

    2015-12-01

    This study unravels intraspecific variations in the carbon isotope (?13C) and oxygen isotope (?18O) compositions of shells of the modern cool-temperate brachiopod Terebratulina crossei collected at a water depth of 70 m in Otsuchi Bay, northeastern Honshu, Japan. Brachiopod shells have been used as proxies of the ?13C values of dissolved inorganic carbon (DIC) (?13CDIC) and seawater temperature/?18O (?18OSW) values to reconstruct the evolution of Phanerozoic oceans. To identify more reliable shell portions as the proxies, we conducted a rigorous time-series comparison of ?13C and ?18O values between the brachiopod shells and calcite precipitated in isotopic equilibrium with ambient seawater (equilibrium calcite) (?13CEC and ?18OEC values, respectively). Samples were collected from the outer and inner surfaces of the secondary shell layer along the maximum growth axis (ontogenetic-series and inner-series samples, respectively). The ontogenetic-series ?13C values, which showed regular annual and irregular non-annual cycles, partly fell in but were mostly less than the range of the ?13CEC values. The ?13C cycles were often associated with one or two minor negative peaks. The peaks were likely resulted from an increased incorporation of respiration-derived 12C due to elevated metabolic activity during spawning. The ontogenetic-series ?18O values showed distinct seasonal variations and were mostly within the range of ?18OEC values. The amplitude of the ?18O profiles was relatively large during the younger fast-growth stage, and decreased during the senescent slow-growth stage. The inner-series ?13C and ?18O values of individual shells varied within narrow ranges. The inner-series ?13C values were close to the minimum ?13CEC values. The inner-series ?18O values were in the upper range of the ?18OEC values. Kinetic isotope fractionation effects were evident, but its degree varied among different shells. We identified the shell portions reliably recording past ocean environments. The best estimates of annual average ?13CDIC values were obtained from ontogenetic-series ?13C values near the anterior shell edge and from inner-series ?13C values; those of the annual average seawater temperature were obtained from ontogenetic-series ?18O values from the entire transect and from the fast-growth stage.

  6. Variation in Quantitative Requirements for Na+ for Transport of Metabolizable Compounds by the Marine Bacteria Alteromonas haloplanktis 214 and Vibrio fischeri

    PubMed Central

    Droniuk, Randal; Wong, P. T. S.; Wisse, Gesine; MacLeod, Robert A.

    1987-01-01

    The rates of uptake by Alteromonas haloplanktis of 19 metabolizable compounds and by V. fischeri of 16 of 17 metabolizable compounds were negligible in the absence of added alkali-metal cations but rapid in the presence of Na+. Only d-glucose uptake by V. fischeri occurred at a reasonable rate in the absence of alkali-metal cations, although the rate was further increased by added Na+, K+, or Li+. Quantitative requirements for Na+ for the uptake of 11 metabolites by A. haloplanktis and of 6 metabolites by V. fischeri and the characteristics of the Na+ response at constant osmotic pressure varied with each metabolite and were different from the Na+ effects on the energy sources used. Li+ stimulated transport of some metabolites in the presence of suboptimal Na+ concentrations and for a few replaced Na+ for transport but functioned less effectively. K+ had a small capacity to stimulate lysine transport. The rate of transport of most of the compounds increased to a maximum at 50 to 300 mM Na+, depending on the metabolite, and then decreased as the Na+ concentration was further increased. For a few metabolites, the rate of transport continued to increase in a biphasic manner as the Na+ concentration was increased to 500 mM. Concentrations of choline chloride equimolar to inhibitory concentrations of NaCl were either not inhibitory or appreciably less inhibitory than those of NaCl. All metabolites examined accumulated inside the cells against a gradient of unchanged metabolite in the presence of Na+, even though some were very rapidly metabolized. The transport of l-alanine, succinate, and d-galactose into A. haloplanktis and of l-alanine and succinate into V. fischeri was inhibited essentially completely by the uncoupler 3,5,3?,4?-tetrachlorosalicylanilide. Glucose uptake by V. fischeri was inhibited partially by 3,5,3?,4?-tetrachlorosalicylanilide and also by arsenate and iodoacetate. PMID:16347378

  7. Phenotypic approaches to drought in cassava: review

    PubMed Central

    Okogbenin, Emmanuel; Setter, Tim L.; Ferguson, Morag; Mutegi, Rose; Ceballos, Hernan; Olasanmi, Bunmi; Fregene, Martin

    2012-01-01

    Cassava is an important crop in Africa, Asia, Latin America, and the Caribbean. Cassava can be produced adequately in drought conditions making it the ideal food security crop in marginal environments. Although cassava can tolerate drought stress, it can be genetically improved to enhance productivity in such environments. Drought adaptation studies in over three decades in cassava have identified relevant mechanisms which have been explored in conventional breeding. Drought is a quantitative trait and its multigenic nature makes it very challenging to effectively manipulate and combine genes in breeding for rapid genetic gain and selection process. Cassava has a long growth cycle of 12–18 months which invariably contributes to a long breeding scheme for the crop. Modern breeding using advances in genomics and improved genotyping, is facilitating the dissection and genetic analysis of complex traits including drought tolerance, thus helping to better elucidate and understand the genetic basis of such traits. A beneficial goal of new innovative breeding strategies is to shorten the breeding cycle using minimized, efficient or fast phenotyping protocols. While high throughput genotyping have been achieved, this is rarely the case for phenotyping for drought adaptation. Some of the storage root phenotyping in cassava are often done very late in the evaluation cycle making selection process very slow. This paper highlights some modified traits suitable for early-growth phase phenotyping that may be used to reduce drought phenotyping cycle in cassava. Such modified traits can significantly complement the high throughput genotyping procedures to fast track breeding of improved drought tolerant varieties. The need for metabolite profiling, improved phenomics to take advantage of next generation sequencing technologies and high throughput phenotyping are basic steps for future direction to improve genetic gain and maximize speed for drought tolerance breeding. PMID:23717282

  8. Quantitative assessment of atmospheric emissions of toxic heavy metals from anthropogenic sources in China: historical trend, spatial variation distribution, uncertainties and control policies

    NASA Astrophysics Data System (ADS)

    Tian, H. Z.; Zhu, C. Y.; Gao, J. J.; Cheng, K.; Hao, J. M.; Wang, K.; Hua, S. B.; Wang, Y.; Zhou, J. R.

    2015-04-01

    Anthropogenic atmospheric emissions of typical toxic heavy metals have received worldwide concerns due to their adverse effects on human health and the ecosystem. By determining the best available representation of time-varying emission factors with S-shape curves, we established the multiyear comprehensive atmospheric emission inventories of 12 typical toxic heavy metals (Hg, As, Se, Pb, Cd, Cr, Ni, Sb, Mn, Co, Cu and Zn) from primary anthropogenic activities in China for the period of 1949-2012 for the first time. Further, we allocated the annual emissions of these heavy metals in 2010 at a high spatial resolution of 0.5° × 0.5° grid with ArcGIS methodology and surrogate indexes, such as regional population and gross domestic product (GDP). Our results show that the historical emissions of Hg, As, Se, Cd, Cr, Ni, Sb, Mn, Co, Cu and Zn during the period of 1949-2012, have been increased by about 22-128 times at an annual average growth rate of 5.1-8.0%, amounting to about 79 570 t in 2012. Nonferrous metal smelting, coal combustion of industrial boilers, brake and tyre wear, and ferrous metals smelting represent the dominant sources for Hg / Cd, As / Se / Pb / Cr / Ni / Mn / Co, Sb / Cu, and Zn, respectively. In terms of spatial variation, the majority of emissions were concentrated in relatively developed regions, especially for the northern, eastern and southern coastal regions. In addition, because of the flourishing nonferrous metals smelting industry, several southwestern and central-southern provinces play a prominent role in some specific toxic heavy metals emissions, like Hg in Guizhou and As in Yunnan. Finally, integrated countermeasures are proposed to minimize the final toxic heavy metals discharge on accounting of the current and future demand of energy-saving and pollution reduction in China.

  9. Resolving within- and between-population variation in feeding ecology with a biomechanical model.

    PubMed

    Osenberg, Craig W; Huckins, Casey J F; Kaltenberg, Anthony; Martinez, Ari

    2004-09-01

    Studies of phenotypic plasticity have emphasized the effect of the environment on the phenotype, but plasticity can also be used as a tool to study the functional significance of key traits. By inducing variation in phenotypes and testing quantitative models that predict performance based on biological mechanisms, we can develop functionally general models of performance. Pumpkinseed sunfish from lakes with high snail availability have large levator posterior muscles (which are used to crush snail shells), whereas fish from lakes with few snails have relatively small muscles. Here we: (1) quantify differences in the feeding ability of an ontogenetic series of pumpkinseed from two populations; and (2) evaluate whether a biomechanical model can resolve the observed ontogenetic and between-population variation in feeding ecology. Mass, but not length, of the levator posterior muscle in fish from Three Lakes (a lake rich in snails) was greater than for comparably sized fish from Wintergreen Lake (a lake with few snails). Handling times were shorter, crushing strengths were 71% greater, and foraging rate (snail tissue mass consumed per time) and the fraction of thick-shelled snails in the diet were approximately 100% greater for fish from Three Lakes compared to comparably sized fish from Wintergreen. These between-lake differences were not significant after adjusting for variation in pharyngeal morphology, suggesting that the biomechanical model of snail crushing resolved observed ontogenetic and population-level variation in the feeding ecology of pumpkinseed. PMID:15338265

  10. Quantitative Phylogenomics of Within-Species Mitogenome Variation: Monte Carlo and Non-Parametric Analysis of Phylogeographic Structure among Discrete Transatlantic Breeding Areas of Harp Seals (Pagophilus groenlandicus)

    PubMed Central

    Carr, Steven M.; Duggan, Ana T.; Stenson, Garry B.; Marshall, H. Dawn

    2015-01-01

    Phylogenomic analysis of highly-resolved intraspecific phylogenies obtained from complete mitochondrial DNA genomes has had great success in clarifying relationships within and among human populations, but has found limited application in other wild species. Analytical challenges include assessment of random versus non-random phylogeographic distributions, and quantification of differences in tree topologies among populations. Harp Seals (Pagophilus groenlandicus Erxleben, 1777) have a biogeographic distribution based on four discrete trans-Atlantic breeding and whelping populations located on “fast ice” attached to land in the White Sea, Greenland Sea, the Labrador ice Front, and Southern Gulf of St Lawrence. This East to West distribution provides a set of a priori phylogeographic hypotheses. Outstanding biogeographic questions include the degree of genetic distinctiveness among these populations, in particular between the Greenland Sea and White Sea grounds. We obtained complete coding-region DNA sequences (15,825 bp) for 53 seals. Each seal has a unique mtDNA genome sequence, which differ by 6 ~ 107 substitutions. Six major clades / groups are detectable by parsimony, neighbor-joining, and Bayesian methods, all of which are found in breeding populations on either side of the Atlantic. The species coalescent is at 180 KYA; the most recent clade, which accounts for 66% of the diversity, reflects an expansion during the mid-Wisconsinan glaciation 40 ~ 60 KYA. FST is significant only between the White Sea and Greenland Sea or Ice Front populations. Hierarchal AMOVA of 2-, 3-, or 4-island models identifies small but significant ?SC among populations within groups, but not among groups. A novel Monte-Carlo simulation indicates that the observed distribution of individuals within breeding populations over the phylogenetic tree requires significantly fewer dispersal events than random expectation, consistent with island or a priori East to West 2- or 3-stepping-stone biogeographic models, but not a simple 1-step trans-Atlantic model. Plots of the cumulative pairwise sequence difference curves among seals in each of the four populations provide continuous proxies for phylogenetic diversification within each. Non-parametric Kolmogorov-Smirnov (K-S) tests of maximum pairwise differences between these curves indicates that the Greenland Sea population has a markedly younger phylogenetic structure than either the White Sea population or the two Northwest Atlantic populations, which are of intermediate age and homogeneous structure. The Monte Carlo and K-S assessments provide sensitive quantitative tests of within-species mitogenomic phylogeography. This is the first study to indicate that the White Sea and Greenland Sea populations have different population genetic histories. The analysis supports the hypothesis that Harp Seals comprises three genetically distinguishable breeding populations, in the White Sea, Greenland Sea, and Northwest Atlantic. Implications for an ice-dependent species during ongoing climate change are discussed. PMID:26301872

  11. Using Extended Genealogy to Estimate Components of Heritability for 23 Quantitative and Dichotomous Traits

    E-print Network

    Zaitlen, Noah

    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, ...

  12. Genetic resources for phenotyping

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phenotyping of structured populations, along with molecular genotyping, will be essential for marker development in peanut. This research is essential for making the peanut genome sequence and genomic tools useful to breeders because it makes the connection between genes, gene markers, genetic maps...

  13. Down Syndrome: Cognitive Phenotype

    ERIC Educational Resources Information Center

    Silverman, Wayne

    2007-01-01

    Down syndrome is the most prevalent cause of intellectual impairment associated with a genetic anomaly, in this case, trisomy of chromosome 21. It affects both physical and cognitive development and produces a characteristic phenotype, although affected individuals vary considerably with respect to severity of specific impairments. Studies…

  14. Genetic Architecture of Natural Variation in Thermal Responses of Arabidopsis1[OPEN

    PubMed Central

    Sanchez-Bermejo, Eduardo; Zhu, Wangsheng; Tasset, Celine; Eimer, Hannes; Sureshkumar, Sridevi; Singh, Rupali; Sundaramoorthi, Vignesh; Colling, Luana; Balasubramanian, Sureshkumar

    2015-01-01

    Wild strains of Arabidopsis (Arabidopsis thaliana) exhibit extensive natural variation in a wide variety of traits, including response to environmental changes. Ambient temperature is one of the major external factors that modulates plant growth and development. Here, we analyze the genetic architecture of natural variation in thermal responses of Arabidopsis. Exploiting wild accessions and recombinant inbred lines, we reveal extensive phenotypic variation in response to ambient temperature in distinct developmental traits such as hypocotyl elongation, root elongation, and flowering time. We show that variation in thermal response differs between traits, suggesting that the individual phenotypes do not capture all the variation associated with thermal response. Genome-wide association studies and quantitative trait locus analyses reveal that multiple rare alleles contribute to the genetic architecture of variation in thermal response. We identify at least 20 genomic regions that are associated with variation in thermal response. Further characterizations of temperature sensitivity quantitative trait loci that are shared between traits reveal a role for the blue-light receptor CRYPTOCHROME2 (CRY2) in thermosensory growth responses. We show the accession Cape Verde Islands is less sensitive to changes in ambient temperature, and through transgenic analysis, we demonstrate that allelic variation at CRY2 underlies this temperature insensitivity across several traits. Transgenic analyses suggest that the allelic effects of CRY2 on thermal response are dependent on genetic background suggestive of the presence of modifiers. In addition, our results indicate that complex light and temperature interactions, in a background-dependent manner, govern growth responses in Arabidopsis. PMID:26195568

  15. Associations Between KCNJ6 (GIRK2) Gene Polymorphisms and Pain-Related Phenotypes

    PubMed Central

    Bruehl, Stephen; Denton, Jerod S.; Lonergan, Daniel; Koran, Mary Ellen; Chont, Melissa; Sobey, Christopher; Fernando, Shanik; Bush, William S.; Mishra, Puneet; Thornton-Wells, Tricia A.

    2013-01-01

    Summary Variations in the KCNJ6 gene appear to influence both acute and chronic pain phenotypes. G-protein coupled inwardly rectifying potassium (GIRK) channels are effectors determining degree of analgesia experienced upon opioid receptor activation by endogenous and exogenous opioids. The impact of GIRK-related genetic variation on human pain responses has received little research attention. We used a tag SNP approach to comprehensively examine pain-related effects of KCNJ3 (GIRK1) and KCNJ6 (GIRK2) gene variation. Forty-one KCNJ3 and 69 KCNJ6 tag SNPs were selected, capturing the known variability in each gene. The primary sample included 311 Caucasian patients undergoing total knee arthroplasty in whom post-surgical oral opioid analgesic medication order data were available. Primary sample findings were then replicated in an independent Caucasian sample of 63 healthy pain-free individuals and 75 individuals with chronic low back pain (CLBP) who provided data regarding laboratory acute pain responsiveness (ischemic task) and chronic pain intensity and unpleasantness (CLBP Only). Univariate quantitative trait analyses in the primary sample revealed that 8 KCNJ6 SNPs were significantly associated with the medication order phenotype (p < 0.05); overall effects of the KCNJ6 gene (gene set-based analysis) just failed to reach significance (p=.054). No significant KCNJ3 effects were observed. A continuous GIRK Related Risk Score (GRRS) was derived in the primary sample to summarize each individual's number of KCNJ6 “pain risk” alleles. This GRRS was applied to the replication sample, which revealed significant associations (p<.05) between higher GRRS values and lower acute pain tolerance and higher CLBP intensity and unpleasantness. Results suggest further exploration of the impact of KCNJ6 genetic variation on pain outcomes is warranted. PMID:23994450

  16. Mouse embryonic fibroblasts exhibit extensive developmental and phenotypic diversity.

    PubMed

    Singhal, Prabhat K; Sassi, Slim; Lan, Lan; Au, Patrick; Halvorsen, Stefan C; Fukumura, Dai; Jain, Rakesh K; Seed, Brian

    2016-01-01

    Analysis of embryonic fibroblasts from GFP reporter mice indicates that the fibroblast cell type harbors a large collection of developmentally and phenotypically heterogeneous subtypes. Some of these cells exhibit multipotency, whereas others do not. Multiparameter flow cytometry analysis shows that a large number of distinct populations of fibroblast-like cells can be found in cultures initiated from different embryonic organs, and cells sorted according to their surface phenotype typically retain their characteristics on continued propagation in culture. Similarly, surface phenotypes of individual cloned fibroblast-like cells exhibit significant variation. The fibroblast cell class appears to contain a very large number of denumerable subtypes. PMID:26699463

  17. Phenotype Ontologies and Cross-Species Analysis for Translational Research

    PubMed Central

    Robinson, Peter N.; Webber, Caleb

    2014-01-01

    The use of model organisms as tools for the investigation of human genetic variation has significantly and rapidly advanced our understanding of the aetiologies underlying hereditary traits. However, while equivalences in the DNA sequence of two species may be readily inferred through evolutionary models, the identification of equivalence in the phenotypic consequences resulting from comparable genetic variation is far from straightforward, limiting the value of the modelling paradigm. In this review, we provide an overview of the emerging statistical and computational approaches to objectively identify phenotypic equivalence between human and model organisms with examples from the vertebrate models, mouse and zebrafish. Firstly, we discuss enrichment approaches, which deem the most frequent phenotype among the orthologues of a set of genes associated with a common human phenotype as the orthologous phenotype, or phenolog, in the model species. Secondly, we introduce and discuss computational reasoning approaches to identify phenotypic equivalences made possible through the development of intra- and interspecies ontologies. Finally, we consider the particular challenges involved in modelling neuropsychiatric disorders, which illustrate many of the remaining difficulties in developing comprehensive and unequivocal interspecies phenotype mappings. PMID:24699242

  18. Protein change in plant evolution: tracing one thread connecting molecular and phenotypic diversity

    PubMed Central

    Bartlett, Madelaine E.; Whipple, Clinton J.

    2013-01-01

    Proteins change over the course of evolutionary time. New protein-coding genes and gene families emerge and diversify, ultimately affecting an organism’s phenotype and interactions with its environment. Here we survey the range of structural protein change observed in plants and review the role these changes have had in the evolution of plant form and function. Verified examples tying evolutionary change in protein structure to phenotypic change remain scarce. We will review the existing examples, as well as draw from investigations into domestication, and quantitative trait locus (QTL) cloning studies searching for the molecular underpinnings of natural variation. The evolutionary significance of many cloned QTL has not been assessed, but all the examples identified so far have begun to reveal the extent of protein structural diversity tolerated in natural systems. This molecular (and phenotypic) diversity could come to represent part of natural selection’s source material in the adaptive evolution of novel traits. Protein structure and function can change in many distinct ways, but the changes we identified in studies of natural diversity and protein evolution were predicted to fall primarily into one of six categories: altered active and binding sites; altered protein–protein interactions; altered domain content; altered activity as an activator or repressor; altered protein stability; and hypomorphic and hypermorphic alleles. There was also variability in the evolutionary scale at which particular changes were observed. Some changes were detected at both micro- and macroevolutionary timescales, while others were observed primarily at deep or shallow phylogenetic levels. This variation might be used to determine the trajectory of future investigations in structural molecular evolution. PMID:24124420

  19. Irritable bowel syndrome-diarrhea: characterization of genotype by exome sequencing, and phenotypes of bile acid synthesis and colonic transit.

    PubMed

    Camilleri, Michael; Klee, Eric W; Shin, Andrea; Carlson, Paula; Li, Ying; Grover, Madhusudan; Zinsmeister, Alan R

    2014-01-01

    The study objectives were: to mine the complete exome to identify putative rare single nucleotide variants (SNVs) associated with irritable bowel syndrome (IBS)-diarrhea (IBS-D) phenotype, to assess genes that regulate bile acids in IBS-D, and to explore univariate associations of SNVs with symptom phenotype and quantitative traits in an independent IBS cohort. Using principal components analysis, we identified two groups of IBS-D (n = 16) with increased fecal bile acids: rapid colonic transit or high bile acids synthesis. DNA was sequenced in depth, analyzing SNVs in bile acid genes (ASBT, FXR, OST?/?, FGF19, FGFR4, KLB, SHP, CYP7A1, LRH-1, and FABP6). Exome findings were compared with those of 50 similar ethnicity controls. We assessed univariate associations of each SNV with quantitative traits and a principal components analysis and associations between SNVs in KLB and FGFR4 and symptom phenotype in 405 IBS, 228 controls and colonic transit in 70 IBS-D, 71 IBS-constipation. Mining the complete exome did not reveal significant associations with IBS-D over controls. There were 54 SNVs in 10 of 11 bile acid-regulating genes, with no SNVs in FGF19; 15 nonsynonymous SNVs were identified in similar proportions of IBS-D and controls. Variations in KLB (rs1015450, downstream) and FGFR4 [rs434434 (intronic), rs1966265, and rs351855 (nonsynonymous)] were associated with colonic transit (rs1966265; P = 0.043), fecal bile acids (rs1015450; P = 0.064), and principal components analysis groups (all 3 FGFR4 SNVs; P < 0.05). In the 633-person cohort, FGFR4 rs434434 was associated with symptom phenotype (P = 0.027) and rs1966265 with 24-h colonic transit (P = 0.066). Thus exome sequencing identified additional variants in KLB and FGFR4 associated with bile acids or colonic transit in IBS-D. PMID:24200957

  20. Precision phenotyping of imidazolinone-induced chlorosis in sunflower

    PubMed Central

    Ochogavía, Ana Claudia; Gil, Mercedes; Picardi, Liliana; Nestares, Graciela

    2014-01-01

    Chlorosis level is a useful parameter to assess imidazolinone resistance in sunflower (Helianthus annuus L.). The aim of this study was to quantify chlorosis through two different methods in sunflower plantlets treated with imazapyr. The genotypes used in this study were two inbred lines reported to be different in their resistance to imidazolinones. Chlorosis was evaluated by spectrophotometrical quantification of photosynthetic leaf pigments and by a bioinformatics-based color analysis. A protocol for pigment extraction was presented which improved pigment stability. Chlorophyll amount decreased significantly when both genotypes were treated with 10 ?M of imazapyr. Leaf color was characterized using Tomato Analyzer® color test software. A significant positive correlation between color reduction and chlorophyll concentration was found. It suggests that leaf color measurement could be an accurate method to estimate chlorosis and infer chlorophyll levels in sunflower plants. These results highlight a strong relationship between imidazolinone-induced chlorosis and variations in leaf color and in chlorophyll concentration. Both methods are quantitative, rapid, simple, and reproducible. Thus, they could be useful tools for phenotyping and screening large number of plants when breeding for imidazolinone resistance in this species. PMID:25914598

  1. Phenotyping for drought tolerance of crops in the genomics era

    PubMed Central

    Tuberosa, Roberto

    2012-01-01

    Improving crops yield under water-limited conditions is the most daunting challenge faced by breeders. To this end, accurate, relevant phenotyping plays an increasingly pivotal role for the selection of drought-resilient genotypes and, more in general, for a meaningful dissection of the quantitative genetic landscape that underscores the adaptive response of crops to drought. A major and universally recognized obstacle to a more effective translation of the results produced by drought-related studies into improved cultivars is the difficulty in properly phenotyping in a high-throughput fashion in order to identify the quantitative trait loci that govern yield and related traits across different water regimes. This review provides basic principles and a broad set of references useful for the management of phenotyping practices for the study and genetic dissection of drought tolerance and, ultimately, for the release of drought-tolerant cultivars. PMID:23049510

  2. Estimation of Genetic Effects and Genotype-Phenotype Maps

    PubMed Central

    Le Rouzic, Arnaud; Álvarez-Castro, José M.

    2008-01-01

    Determining the genetic architecture of complex traits is a necessary step to understand phenotypic changes in natural, experimental and domestic populations. However, this is still a major challenge for modern genetics, since the estimation of genetic effects tends to be complicated by genetic interactions, which lead to changes in the effect of allelic substitutions depending on the genetic background. Recent progress in statistical tools aiming to describe and quantify genetic effects meaningfully improves the efficiency and the availability of genotype-to-phenotype mapping methods. In this contribution, we facilitate the practical use of the recently published ‘NOIA’ quantitative framework by providing an implementation of linear and multilinear regressions, change of reference operation and genotype-to-phenotype mapping in a package (‘noia’) for the software R, and we discuss theoretical and practical benefits evolutionary and quantitative geneticists may find in using proper modeling strategies to quantify the effects of genes. PMID:19204820

  3. Estimation of genetic effects and genotype-phenotype maps.

    PubMed

    Le Rouzic, Arnaud; Alvarez-Castro, José M

    2008-01-01

    Determining the genetic architecture of complex traits is a necessary step to understand phenotypic changes in natural, experimental and domestic populations. However, this is still a major challenge for modern genetics, since the estimation of genetic effects tends to be complicated by genetic interactions, which lead to changes in the effect of allelic substitutions depending on the genetic background. Recent progress in statistical tools aiming to describe and quantify genetic effects meaningfully improves the efficiency and the availability of genotype-to-phenotype mapping methods. In this contribution, we facilitate the practical use of the recently published 'NOIA' quantitative framework by providing an implementation of linear and multilinear regressions, change of reference operation and genotype-to-phenotype mapping in a package ('noia') for the software R, and we discuss theoretical and practical benefits evolutionary and quantitative geneticists may find in using proper modeling strategies to quantify the effects of genes. PMID:19204820

  4. [Phenotype specific therapy of COPD].

    PubMed

    Rothe, Thomas

    2014-12-10

    COPD is not a homogenous disease but consists of at least four different phenotypes: Emphysema, COPD with chronic bronchitis, asthma-COPD overlap syndrome (ACOS), and COPD with recurrent exacerbations. With differentiation, treatment can be designed phenotype-specific. Some modern drugs are not indicated in all phenotypes. PMID:25491053

  5. Generating Phenotypic Diversity in a Fungal Biocatalyst to Investigate Alcohol Stress Tolerance Encountered during Microbial Cellulosic Biofuel Production

    PubMed Central

    Hennessy, Rosanna C.; Doohan, Fiona; Mullins, Ewen

    2013-01-01

    Consolidated bioprocessing (CBP) of lignocellulosic biomass offers an alternative route to renewable energy. The crop pathogen Fusarium oxysporum is a promising fungal biocatalyst because of its broad host range and innate ability to co-saccharify and ferment lignocellulose to bioethanol. A major challenge for cellulolytic CBP-enabling microbes is alcohol inhibition. This research tested the hypothesis that Agrobacterium tumefaciens - mediated transformation (ATMT) could be exploited as a tool to generate phenotypic diversity in F. oxysporum to investigate alcohol stress tolerance encountered during CBP. A random mutagenesis library of gene disruption transformants (n=1,563) was constructed and screened for alcohol tolerance in order to isolate alcohol sensitive or tolerant phenotypes. Following three rounds of screening, exposure of select transformants to 6% ethanol and 0.75% n-butanol resulted respectively in increased (?11.74%) and decreased (?43.01%) growth compared to the wild –type (WT). Principal component analysis (PCA) quantified the level of phenotypic diversity across the population of genetically transformed individuals and isolated candidate strains for analysis. Characterisation of one strain, Tr. 259, ascertained a reduced growth phenotype under alcohol stress relative to WT and indicated the disruption of a coding region homologous to a putative sugar transporter (FOXG_09625). Quantitative PCR (RT-PCR) showed FOXG_09625 was differentially expressed in Tr. 259 compared to WT during alcohol-induced stress (P<0.05). Phylogenetic analysis of putative sugar transporters suggests diverse functional roles in F. oxysporum and other filamentous fungi compared to yeast for which sugar transporters form part of a relatively conserved family. This study has confirmed the potential of ATMT coupled with a phenotypic screening program to select for genetic variation induced in response to alcohol stress. This research represents a first step in the investigation of alcohol tolerance in F. oxysporum and has resulted in the identification of several novel strains, which will be of benefit to future biofuel research. PMID:24147009

  6. The phenotypic difference discards sib-pair QTL linkage information

    SciTech Connect

    Wright, F.A. |

    1997-03-01

    Kruglyak and Lander provide an important synthesis of methods for (IBD) sib-pair linkage mapping, with an emphasis on the use of complete multipoint inheritance information for each sib pair. These procedures are implemented in the computer program MAPMAKER/SIBS, which performs interval mapping for dichotomous and quantitative traits. The authors present three methods for mapping quantitative trait loci (QTLs): a variant of the commonly used Haseman-Elston regression approach, a maximum-likelihood procedure involving variance components, and a rank-based nonparametric procedure. These approaches and related work use the magnitude of the difference in the sibling phenotype values for each sib pair as the observation for analysis. Linkage is detected if siblings sharing more alleles IBD have similar phenotypes (i.e., a small difference in the phenotype values), while siblings sharing fewer alleles IBD have less similar phenotypes. Such techniques have been used to detect linkage for a number of quantitative traits. However, the exclusive reliance on the phenotypic differences may be due in large part to historical inertia. A likelihood argument is presented here to show that, under certain classical assumptions, the phenotypic differences do not contain the full likelihood information for QTL mapping. Furthermore, considerable gains in power to detect linkage can be achieved with an expanded likelihood model. The development here is related to previous work, which incorporates the full set of phenotypic data using likelihood and robust quasi-likelihood methods. The purpose of this letter is not to endorse a particular approach but to spur research in alternative and perhaps more powerful linkage tests. 17 refs.

  7. Association Between a High-Risk Autism Locus on 5p14 and Social Communication Spectrum Phenotypes in the General Population

    PubMed Central

    St. Pourcain, Beate; Wang, Kai; Glessner, Joseph T.; Golding, Jean; Steer, Colin; Ring, Susan M.; Skuse, David H.; Grant, Struan F.A.; Hakonarson, Hakon; Davey Smith, George

    2010-01-01

    Objective Recent genome-wide analysis identified a genetic variant on 5p14.1 (rs4307059), which is associated with risk for autism spectrum disorder. This study investigated whether rs4307059 also operates as a quantitative trait locus underlying a broader autism phenotype in the general population, focusing specifically on the social communication aspect of the spectrum. Method Study participants were 7,313 children from the Avon Longitudinal Study of Parents and Children. Single-trait and joint-trait genotype associations were investigated for 29 measures related to language and communication, verbal intelligence, social interaction, and behavioral adjustment, assessed between ages 3 and 12 years. Analyses were performed in one-sided or directed mode and adjusted for multiple testing, trait interrelatedness, and random genotype dropout. Results Single phenotype analyses showed that an increased load of rs4307059 risk allele is associated with stereotyped conversation and lower pragmatic communication skills, as measured by the Children's Communication Checklist (at a mean age of 9.7 years). In addition a trend toward a higher frequency of identification of special educational needs (at a mean age of 11.8 years) was observed. Variation at rs4307059 was also associated with the phenotypic profile of studied traits. This joint signal was fully explained neither by single-trait associations nor by overall behavioral adjustment problems but suggested a combined effect, which manifested through multiple subthreshold social, communicative, and cognitive impairments. Conclusions Our results suggest that common variation at 5p14.1 is associated with social communication spectrum phenotypes in the general population and support the role of rs4307059 as a quantitative trait locus for autism spectrum disorder. PMID:20634369

  8. Hormones and phenotypic plasticity in an ecological context: linking physiological mechanisms to evolutionary processes.

    PubMed

    Lema, Sean C

    2014-11-01

    Hormones are chemical signaling molecules that regulate patterns of cellular physiology and gene expression underlying phenotypic traits. Hormone-signaling pathways respond to an organism's external environment to mediate developmental stage-specific malleability in phenotypes, so that environmental variation experienced at different stages of development has distinct effects on an organism's phenotype. Studies of hormone-signaling are therefore playing a central role in efforts to understand how plastic phenotypic responses to environmental variation are generated during development. But, how do adaptive, hormonally mediated phenotypes evolve if the individual signaling components (hormones, conversion enzymes, membrane transporters, and receptors) that comprise any hormone-signaling pathway show expressional flexibility in response to environmental variation? What relevance do these components hold as molecular targets for selection to couple or decouple correlated hormonally mediated traits? This article explores how studying the endocrine underpinnings of phenotypic plasticity in an ecologically relevant context can provide insights into these, and other, crucial questions into the role of phenotypic plasticity in evolution, including how plasticity itself evolves. These issues are discussed in the light of investigations into how thyroid hormones mediate morphological plasticity in Death Valley's clade of pupfishes (Cyprinodon spp.). Findings from this work with pupfish illustrate that the study of hormone-signaling from an ecological perspective can reveal how phenotypic plasticity contributes to the generation of phenotypic novelty, as well as how physiological mechanisms developmentally link an organism's phenotype to its environmental experiences. PMID:24752548

  9. Linkage and association mapping for quantitative phenotypes in isolated populations 

    E-print Network

    Franklin, Christopher Steven

    2011-11-25

    Many complex diseases are known to have a substantial genetically heritable component. Elucidation of these genetic risk factors provides increased knowledge of the biological mechanisms that result in the diseases while ...

  10. Fluctuation and noise propagation in phenotypic transition cascades of clonal populations

    NASA Astrophysics Data System (ADS)

    Pei, Qi-ming; Zhan, Xuan; Yang, Li-jian; Shen, Jian; Wang, Li-fang; Qui, Kang; Liu, Ting; Kirunda, J. B.; Yousif, A. A. M.; Li, An-bang; Jia, Ya

    2015-07-01

    Quantitative modeling of fluctuations of each phenotype is a crucial step towards a fundamental understanding of noise propagation through various phenotypic transition cascades. The theoretical formulas for noise propagation in various phenotypic transition cascades are derived by using the linear noise approximation of master equation and the logarithmic gain. By virtue of the theoretical formulas, we study the noise propagation in bidirectional and unidirectional phenotypic transition cascades, respectively. It is found that noise propagation in these two phenotypic transition cascades evidently differs: In the bidirectional cascade, a systemic random environment is provided by a correlated global component. The total noise of each phenotype is mainly determined by the intrinsic noise and the transmitted noise from other phenotypes. The intrinsic noise enlarged by interconversion through an added part shows a novel noise propagation mechanism. However, in the unidirectional cascade, the random environment of each downstream phenotype is provided by upstream phenotypes. The total noise of each downstream phenotype is mainly determined by the transmitted noises from upstream phenotypes. The intrinsic noise and the conversion noise can propagate in both bidirectional and unidirectional phenotypic transition cascades.

  11. New Insights into Genotype and Phenotype of VWD

    PubMed Central

    Flood, Veronica H.

    2015-01-01

    Recent advances in VWD research have improved our understanding of the genotype and phenotype of VWD. The VWF gene is highly polymorphic, with a large number of sequence variations reported in healthy individuals. This can lead to some difficulty when attempting to discern genotype-phenotype correlations, as sequence variations may not represent disease. In type 1 VWD, mutations can be found throughout the VWF gene, but likely pathogenic sequence variations are found in only about 2/3 of type 1 VWD patients. Sequence variations in type 2 VWD are located in the region corresponding to the defect in the VWF protein found in each type 2 variant. In type 3 VWD, sequence variations are not confined to a specific region of the VWF gene, and also include large deletions which may not be picked up using conventional sequencing techniques. Use of genetic testing may be most helpful in diagnosis of type 2 VWD, where a larger number of known, well characterized mutations are present and demonstration of one of these may help confirm the diagnosis. Bleeding symptoms in general are more severe with decreasing VWF levels, and more severe in type 2 and type 3 VWD as compared to type 1 VWD. Prediction of phenotype for an individual patient, however, is still difficult, and the addition of genetic data most helpful in ascertaining the correct diagnosis for VWD patients. Learner objective: to understand the relationship of genotype and phenotype as currently understood for VWD variants PMID:25696906

  12. Natural Variation of Plant Metabolism: Genetic Mechanisms, Interpretive Caveats, and Evolutionary and Mechanistic Insights.

    PubMed

    Soltis, Nicole E; Kliebenstein, Daniel J

    2015-11-01

    Combining quantitative genetics studies with metabolomics/metabolic profiling platforms, genomics, and transcriptomics is creating significant progress in identifying the causal genes controlling natural variation in metabolite accumulations and profiles. In this review, we discuss key mechanistic and evolutionary insights that are arising from these studies. This includes the potential role of transport and other processes in leading to a separation of the site of mechanistic causation and metabolic consequence. A reilluminated observation is the potential for genomic variation in the organelle to alter phenotypic variation alone and in epistatic interaction with the nuclear genetic variation. These studies are also highlighting new aspects of metabolic pleiotropy both in terms of the breadth of loci altering metabolic variation as well as the potential for broader effects on plant defense regulation of the metabolic variation than has previously been predicted. We also illustrate caveats that can be overlooked when translating quantitative genetics descriptors such as heritability and per-locus r(2) to mechanistic or evolutionary interpretations. PMID:26272883

  13. Phenotypic plasticity and divergence in gene expression.

    PubMed

    Healy, Timothy M; Schulte, Patricia M

    2015-07-01

    The extent to which phenotypic plasticity, or the ability of a single genotype to produce different phenotypes in different environments, impedes or promotes genetic divergence has been a matter of debate within evolutionary biology for many decades (see, for example, Ghalambor et al. ; Pfennig et al. ). Similarly, the role of evolution in shaping phenotypic plasticity remains poorly understood (Pigliucci ). In this issue of Molecular Ecology, Dayan et al. () provide empirical data relevant to these questions by assessing the extent of plasticity and divergence in the expression levels of 2272 genes in muscle tissue from killifish (genus Fundulus) exposed to different temperatures. F. heteroclitus (Fig. A) and F. grandis are minnows that inhabit estuarine marshes (Fig. B) along the coasts of the Atlantic Ocean and Gulf of Mexico in North America. These habitats undergo large variations in temperature both daily and seasonally, and these fish are known to demonstrate substantial phenotypic plasticity in response to temperature change (e.g. Fangue et al. ). Furthermore, the range of F. heteroclitus spans a large latitudinal gradient of temperatures, such that northern populations experience temperatures that are on average ~10°C colder than do southern populations (Schulte ). By comparing gene expression patterns between populations of these fish from different thermal habitats held in the laboratory at three different temperatures, Dayan et al. () address two important questions regarding the interacting effects of plasticity and evolution: (i) How does phenotypic plasticity affect adaptive divergence? and (ii) How does adaptive divergence affect plasticity? PMID:26096949

  14. Genetic analysis of natural variations in the architecture of Arabidopsis thaliana vegetative leaves.

    PubMed Central

    Pérez-Pérez, José Manuel; Serrano-Cartagena, José; Micol, José Luis

    2002-01-01

    To ascertain whether intraspecific variability might be a source of information as regards the genetic controls underlying plant leaf morphogenesis, we analyzed variations in the architecture of vegetative leaves in a large sample of Arabidopsis thaliana natural races. A total of 188 accessions from the Arabidopsis Information Service collection were grown and qualitatively classified into 14 phenotypic classes, which were defined according to petiole length, marginal configuration, and overall lamina shape. Accessions displaying extreme and opposite variations in the above-mentioned leaf architectural traits were crossed and their F(2) progeny was found to be not classifiable into discrete phenotypic classes. Furthermore, the leaf trait-based classification was not correlated with estimates on the genetic distances between the accessions being crossed, calculated after determining variations in repeat number at 22 microsatellite loci. Since these results suggested that intraspecific variability in A. thaliana leaf morphology arises from an accumulation of mutations at quantitative trait loci (QTL), we studied a mapping population of recombinant inbred lines (RILs) derived from a Landsberg erecta-0 x Columbia-4 cross. A total of 100 RILs were grown and the third and seventh leaves of 15 individuals from each RIL were collected and morphometrically analyzed. We identified a total of 16 and 13 QTL harboring naturally occurring alleles that contribute to natural variations in the architecture of juvenile and adult leaves, respectively. Our QTL mapping results confirmed the multifactorial nature of the observed natural variations in leaf architecture. PMID:12399398

  15. Genome-Wide Transcription Analysis of Clinal Genetic Variation in Drosophila

    PubMed Central

    Chen, Ying; Lee, Siu F.; Blanc, Eric; Reuter, Caroline; Wertheim, Bregje; Martinez-Diaz, Pedro; Hoffmann, Ary A.; Partridge, Linda

    2012-01-01

    Clinal variation in quantitative traits is widespread, but its genetic basis awaits identification. Drosophila melanogaster shows adaptive, clinal variation in traits such as body size along latitudinal gradients on multiple continents. To investigate genome wide transcription differentiation between North and South that might contribute to the clinal phenotypic variation, we compared RNA expression patterns during development of D. melanogaster from tropical northern and temperate southern populations using whole genome tiling arrays. We found that genes that were differentially expressed between the cline ends were generally associated with metabolism and growth, and experimental alteration of expression of a sample of them generally resulted in altered body size in the predicted direction, sometimes significantly so. We further identified the serpent (srp) transcription factor binding sites to be enriched near genes up-regulated in expression in the south. Analysis of clinal populations revealed a significant cline in the expression level of srp. Experimental over-expression of srp increased body size, as predicted from its clinal expression pattern, suggesting that it may be involved in regulating adaptive clinal variation in Drosophila. This study identified a handful of genes that contributed to clinal phenotypic variation through altered gene expression level, yet misexpression of individual gene led to modest body size change. PMID:22514645

  16. Limited plasticity in the phenotypic variance-covariance matrix for male advertisement calls in the black field cricket, Teleogryllus commodus

    PubMed Central

    Pitchers, W. R.; Brooks, R.; Jennions, M. D.; Tregenza, T.; Dworkin, I.; Hunt, J.

    2013-01-01

    Phenotypic integration and plasticity are central to our understanding of how complex phenotypic traits evolve. Evolutionary change in complex quantitative traits can be predicted using the multivariate breeders’ equation, but such predictions are only accurate if the matrices involved are stable over evolutionary time. Recent work, however, suggests that these matrices are temporally plastic, spatially variable and themselves evolvable. The data available on phenotypic variance-covariance matrix (P) stability is sparse, and largely focused on morphological traits. Here we compared P for the structure of the complex sexual advertisement call of six divergent allopatric populations of the Australian black field cricket, Teleogryllus commodus. We measured a subset of calls from wild-caught crickets from each of the populations and then a second subset after rearing crickets under common-garden conditions for three generations. In a second experiment, crickets from each population were reared in the laboratory on high- and low-nutrient diets and their calls recorded. In both experiments, we estimated P for call traits and used multiple methods to compare them statistically (Flury hierarchy, geometric subspace comparisons and random skewers). Despite considerable variation in means and variances of individual call traits, the structure of P was largely conserved among populations, across generations and between our rearing diets. Our finding that P remains largely stable, among populations and between environmental conditions, suggests that selection has preserved the structure of call traits in order that they can function as an integrated unit. PMID:23530814

  17. Toward automatic phenotyping of retinal images from genetically determined mono- and dizygotic twins using amplitude modulation-frequency modulation methods

    NASA Astrophysics Data System (ADS)

    Soliz, P.; Davis, B.; Murray, V.; Pattichis, M.; Barriga, S.; Russell, S.

    2010-03-01

    This paper presents an image processing technique for automatically categorize age-related macular degeneration (AMD) phenotypes from retinal images. Ultimately, an automated approach will be much more precise and consistent in phenotyping of retinal diseases, such as AMD. We have applied the automated phenotyping to retina images from a cohort of mono- and dizygotic twins. The application of this technology will allow one to perform more quantitative studies that will lead to a better understanding of the genetic and environmental factors associated with diseases such as AMD. A method for classifying retinal images based on features derived from the application of amplitude-modulation frequency-modulation (AM-FM) methods is presented. Retinal images from identical and fraternal twins who presented with AMD were processed to determine whether AM-FM could be used to differentiate between the two types of twins. Results of the automatic classifier agreed with the findings of other researchers in explaining the variation of the disease between the related twins. AM-FM features classified 72% of the twins correctly. Visual grading found that genetics could explain between 46% and 71% of the variance.

  18. 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

  19. Learning probabilistic phenotypes from heterogeneous EHR data.

    PubMed

    Pivovarov, Rimma; Perotte, Adler J; Grave, Edouard; Angiolillo, John; Wiggins, Chris H; Elhadad, Noémie

    2015-12-01

    We present the Unsupervised Phenome Model (UPhenome), a probabilistic graphical model for large-scale discovery of computational models of disease, or phenotypes. We tackle this challenge through the joint modeling of a large set of diseases and a large set of clinical observations. The observations are drawn directly from heterogeneous patient record data (notes, laboratory tests, medications, and diagnosis codes), and the diseases are modeled in an unsupervised fashion. We apply UPhenome to two qualitatively different mixtures of patients and diseases: records of extremely sick patients in the intensive care unit with constant monitoring, and records of outpatients regularly followed by care providers over multiple years. We demonstrate that the UPhenome model can learn from these different care settings, without any additional adaptation. Our experiments show that (i) the learned phenotypes combine the heterogeneous data types more coherently than baseline LDA-based phenotypes; (ii) they each represent single diseases rather than a mix of diseases more often than the baseline ones; and (iii) when applied to unseen patient records, they are correlated with the patients' ground-truth disorders. Code for training, inference, and quantitative evaluation is made available to the research community. PMID:26464024

  20. Plasticity and heritability of morphological variation within and between parapatric stickleback demes

    E-print Network

    Bernatchez, Louis

    O L O G Y 1097 Keywords: Gasterosteus aculeatus; geometric morphometrics; phenotypic plasticity; quantitative genetics; sexual dimorphism. Abstract The threespine stickleback (Gasterosteus aculeatus) has

  1. Topological Phenotypes Constitute a New Dimension in the Phenotypic Space of Leaf Venation Networks.

    PubMed

    Ronellenfitsch, Henrik; Lasser, Jana; Daly, Douglas C; Katifori, Eleni

    2015-12-01

    The leaves of angiosperms contain highly complex venation networks consisting of recursively nested, hierarchically organized loops. We describe a new phenotypic trait of reticulate vascular networks based on the topology of the nested loops. This phenotypic trait encodes information orthogonal to widely used geometric phenotypic traits, and thus constitutes a new dimension in the leaf venation phenotypic space. We apply our metric to a database of 186 leaves and leaflets representing 137 species, predominantly from the Burseraceae family, revealing diverse topological network traits even within this single family. We show that topological information significantly improves identification of leaves from fragments by calculating a "leaf venation fingerprint" from topology and geometry. Further, we present a phenomenological model suggesting that the topological traits can be explained by noise effects unique to specimen during development of each leaf which leave their imprint on the final network. This work opens the path to new quantitative identification techniques for leaves which go beyond simple geometric traits such as vein density and is directly applicable to other planar or sub-planar networks such as blood vessels in the brain. PMID:26700471

  2. Sample size calculation in metabolic phenotyping studies.

    PubMed

    Billoir, Elise; Navratil, Vincent; Blaise, Benjamin J

    2015-09-01

    The number of samples needed to identify significant effects is a key question in biomedical studies, with consequences on experimental designs, costs and potential discoveries. In metabolic phenotyping studies, sample size determination remains a complex step. This is due particularly to the multiple hypothesis-testing framework and the top-down hypothesis-free approach, with no a priori known metabolic target. Until now, there was no standard procedure available to address this purpose. In this review, we discuss sample size estimation procedures for metabolic phenotyping studies. We release an automated implementation of the Data-driven Sample size Determination (DSD) algorithm for MATLAB and GNU Octave. Original research concerning DSD was published elsewhere. DSD allows the determination of an optimized sample size in metabolic phenotyping studies. The procedure uses analytical data only from a small pilot cohort to generate an expanded data set. The statistical recoupling of variables procedure is used to identify metabolic variables, and their intensity distributions are estimated by Kernel smoothing or log-normal density fitting. Statistically significant metabolic variations are evaluated using the Benjamini-Yekutieli correction and processed for data sets of various sizes. Optimal sample size determination is achieved in a context of biomarker discovery (at least one statistically significant variation) or metabolic exploration (a maximum of statistically significant variations). DSD toolbox is encoded in MATLAB R2008A (Mathworks, Natick, MA) for Kernel and log-normal estimates, and in GNU Octave for log-normal estimates (Kernel density estimates are not robust enough in GNU octave). It is available at http://www.prabi.fr/redmine/projects/dsd/repository, with a tutorial at http://www.prabi.fr/redmine/projects/dsd/wiki. PMID:25600654

  3. Kernel methods for phenotyping complex plant architecture.

    PubMed

    Kawamura, Koji; Hibrand-Saint Oyant, Laurence; Foucher, Fabrice; Thouroude, Tatiana; Loustau, Sébastien

    2014-02-01

    The Quantitative Trait Loci (QTL) mapping of plant architecture is a critical step for understanding the genetic determinism of plant architecture. Previous studies adopted simple measurements, such as plant-height, stem-diameter and branching-intensity for QTL mapping of plant architecture. Many of these quantitative traits were generally correlated to each other, which give rise to statistical problem in the detection of QTL. We aim to test the applicability of kernel methods to phenotyping inflorescence architecture and its QTL mapping. We first test Kernel Principal Component Analysis (KPCA) and Support Vector Machines (SVM) over an artificial dataset of simulated inflorescences with different types of flower distribution, which is coded as a sequence of flower-number per node along a shoot. The ability of discriminating the different inflorescence types by SVM and KPCA is illustrated. We then apply the KPCA representation to the real dataset of rose inflorescence shoots (n=1460) obtained from a 98 F1 hybrid mapping population. We find kernel principal components with high heritability (>0.7), and the QTL analysis identifies a new QTL, which was not detected by a trait-by-trait analysis of simple architectural measurements. The main tools developed in this paper could be use to tackle the general problem of QTL mapping of complex (sequences, 3D structure, graphs) phenotypic traits. PMID:24211258

  4. Phenotypic plasticity in gene expression contributes to divergence of locally adapted populations of Fundulus heteroclitus.

    PubMed

    Dayan, David I; Crawford, Douglas L; Oleksiak, Marjorie F

    2015-07-01

    We examine the interaction between phenotypic plasticity and evolutionary adaptation using muscle gene expression levels among populations of the fish Fundulus heteroclitus acclimated to three temperatures. Our analysis reveals shared patterns of phenotypic plasticity due to thermal acclimation as well as non-neutral patterns of variation among populations adapted to different thermal environments. For the majority of significant differences in gene expression levels, phenotypic plasticity and adaptation operate on different suites of genes. The subset of genes that demonstrate both adaptive differences and phenotypic plasticity, however, exhibit countergradient variation of expression. Thus, expression differences among populations counteract environmental effects, reducing the phenotypic differentiation between populations. Finally, gene-by-environment interactions among genes with non-neutral patterns of expression suggest that the penetrance of adaptive variation depends on the environmental conditions experienced by the individual. PMID:25847331

  5. Modeling phenotypic plasticity in growth trajectories: a statistical framework.

    PubMed

    Wang, Zhong; Pang, Xiaoming; Wu, Weimiao; Wang, Jianxin; Wang, Zuoheng; Wu, Rongling

    2014-01-01

    Phenotypic plasticity, that is multiple phenotypes produced by a single genotype in response to environmental change, has been thought to play an important role in evolution and speciation. Historically, knowledge about phenotypic plasticity has resulted from the analysis of static traits measured at a single time point. New insight into the adaptive nature of plasticity can be gained by an understanding of how organisms alter their developmental processes in a range of environments. Recent advances in statistical modeling of functional data and developmental genetics allow us to construct a dynamic framework of plastic response in developmental form and pattern. Under this framework, development, genetics, and evolution can be synthesized through statistical bridges to better address how evolution results from phenotypic variation in the process of development via genetic alterations. PMID:24111588

  6. On Quantitizing

    ERIC Educational Resources Information Center

    Sandelowski, Margarete; Voils, Corrine I.; Knafl, George

    2009-01-01

    "Quantitizing", commonly understood to refer to the numerical translation, transformation, or conversion of qualitative data, has become a staple of mixed methods research. Typically glossed are the foundational assumptions, judgments, and compromises involved in converting disparate data sets into each other and whether such conversions advance…

  7. The Genomic and Phenotypic Diversity of Schizosaccharomyces pombe

    PubMed Central

    Jeffares, Daniel C.; Rallis, Charalampos; Rieux, Adrien; Speed, Doug; P?evorovský, Martin; Mourier, Tobias; Marsellach, Francesc X.; Iqbal, Zamin; Lau, Winston; Cheng, Tammy M.K.; Pracana, Rodrigo; Mülleder, Michael; Lawson, Jonathan L.D.; Chessel, Anatole; Bala, Sendu; Hellenthal, Garrett; O’Fallon, Brendan; Keane, Thomas; Simpson, Jared T.; Bischof, Leanne; Tomiczek, Bartlomiej; Bitton, Danny A.; Sideri, Theodora; Codlin, Sandra; Hellberg, Josephine E.E.U.; van Trigt, Laurent; Jeffery, Linda; Li, Juan-Juan; Atkinson, Sophie; Thodberg, Malte; Febrer, Melanie; McLay, Kirsten; Drou, Nizar; Brown, William; Hayles, Jacqueline; Carazo Salas, Rafael E.; Ralser, Markus; Maniatis, Nikolas; Balding, David J.; Balloux, Francois; Durbin, Richard; Bähler, Jürg

    2015-01-01

    Natural variation within species reveals aspects of genome evolution and function. The fission yeast Schizosaccharomyces pombe is an important model for eukaryotic biology, but researchers typically use one standard laboratory strain. To extend the utility of this model, we surveyed the genomic and phenotypic variation in 161 natural isolates. We sequenced the genomes of all strains, revealing moderate genetic diversity (? = 3 ×10?3) and weak global population structure. We estimate that dispersal of S. pombe began within human antiquity (~340 BCE), and ancestors of these strains reached the Americas at ~1623 CE. We quantified 74 traits, revealing substantial heritable phenotypic diversity. We conducted 223 genome-wide association studies, with 89 traits showing at least one association. The most significant variant for each trait explained 22% of variance on average, with indels having higher effects than SNPs. This analysis presents a rich resource to examine genotype-phenotype relationships in a tractable model. PMID:25665008

  8. The nutritional phenotype in the age of metabolomics.

    PubMed

    Zeisel, S H; Freake, H C; Bauman, D E; Bier, D M; Burrin, D G; German, J B; Klein, S; Marquis, G S; Milner, J A; Pelto, G H; Rasmussen, K M

    2005-07-01

    The concept of the nutritional phenotype is proposed as a defined and integrated set of genetic, proteomic, metabolomic, functional, and behavioral factors that, when measured, form the basis for assessment of human nutritional status. The nutritional phenotype integrates the effects of diet on disease/wellness and is the quantitative indication of the paths by which genes and environment exert their effects on health. Advances in technology and in fundamental biological knowledge make it possible to define and measure the nutritional phenotype accurately in a cross section of individuals with various states of health and disease. This growing base of data and knowledge could serve as a resource for all scientific disciplines involved in human health. Nutritional sciences should be a prime mover in making key decisions that include: what environmental inputs (in addition to diet) are needed; what genes/proteins/metabolites should be measured; what end-point phenotypes should be included; and what informatics tools are available to ask nutritionally relevant questions. Nutrition should be the major discipline establishing how the elements of the nutritional phenotype vary as a function of diet. Nutritional sciences should also be instrumental in linking the elements that are responsive to diet with the functional outcomes in organisms that derive from them. As the first step in this initiative, a prioritized list of genomic, proteomic, and metabolomic as well as functional and behavioral measures that defines a practically useful subset of the nutritional phenotype for use in clinical and epidemiological investigations must be developed. From this list, analytic platforms must then be identified that are capable of delivering highly quantitative data on these endpoints. This conceptualization of a nutritional phenotype provides a concrete form and substance to the recognized future of nutritional sciences as a field addressing diet, integrated metabolism, and health. PMID:15987837

  9. Molecular population genetics and phenotypic sensitivity to ethanol for a globally diverse sample of the

    E-print Network

    Cutter, Asher D.

    Molecular population genetics and phenotypic sensitivity to ethanol for a globally diverse sample cedex 13, France Abstract New genomic resources and genetic tools of the past few years have advanced genetic variation at molecular and phenotypic levels remains rudimentary for most species in this genus

  10. EHR Big Data Deep Phenotyping

    PubMed Central

    Lenert, L.; Lopez-Campos, G.

    2014-01-01

    Summary Objectives Given the quickening speed of discovery of variant disease drivers from combined patient genotype and phenotype data, the objective is to provide methodology using big data technology to support the definition of deep phenotypes in medical records. Methods As the vast stores of genomic information increase with next generation sequencing, the importance of deep phenotyping increases. The growth of genomic data and adoption of Electronic Health Records (EHR) in medicine provides a unique opportunity to integrate phenotype and genotype data into medical records. The method by which collections of clinical findings and other health related data are leveraged to form meaningful phenotypes is an active area of research. Longitudinal data stored in EHRs provide a wealth of information that can be used to construct phenotypes of patients. We focus on a practical problem around data integration for deep phenotype identification within EHR data. The use of big data approaches are described that enable scalable markup of EHR events that can be used for semantic and temporal similarity analysis to support the identification of phenotype and genotype relationships. Conclusions Stead and colleagues’ 2005 concept of using light standards to increase the productivity of software systems by riding on the wave of hardware/processing power is described as a harbinger for designing future healthcare systems. The big data solution, using flexible markup, provides a route to improved utilization of processing power for organizing patient records in genotype and phenotype research. PMID:25123744

  11. Countergradient variation in body shape between two populations of Atlantic cod (Gadus morhua)

    E-print Network

    Hutchings, Jeffrey A.

    environments involves both genetic differentiation and adaptive phenotypic plasticity. Mor- phological traits, Moncton, New Brunswick E1C 9B6, Canada Variation in morphological traits is generally thought differences between popu- lations, inflating the phenotypic differentiation between populations

  12. Variation in Fetal Outcome, Viral Load and ORF5 Sequence Mutations in a Large Scale Study of Phenotypic Responses to Late Gestation Exposure to Type 2 Porcine Reproductive and Respiratory Syndrome Virus

    PubMed Central

    Ladinig, Andrea; Wilkinson, Jamie; Ashley, Carolyn; Detmer, Susan E.; Lunney, Joan K.; Plastow, Graham; Harding, John C. S.

    2014-01-01

    In spite of extensive research, the mechanisms of reproductive disease associated with Porcine Reproductive and Respiratory Syndrome virus (PRRSv) are still poorly understood. The objectives of this large scale study were to evaluate associations between viral load and fetal preservation, determine the impact of type 2 PRRSv on fetal weights, and investigate changes in ORF5 PRRSv genome in dams and fetuses during a 21-day period following challenge. At gestation day 85 (±1), 114 gilts were experimentally infected with type 2 PRRSv, while 19 gilts served as reference controls. At necropsy, fetuses were categorized according to their preservation status and tissue samples were collected. PRRSv RNA concentrations were measured in gilt serum collected on days 0, 2, 6, and 21 post-infection, as well as in gilt and fetal tissues collected at termination. Fetal mortality was 41±22.8% in PRRS infected litters. Dead fetuses appeared to cluster in some litters but appeared solitary or random in others. Nine percent of surviving piglets were meconium-stained. PRRSv RNA concentration in fetal thymus, fetal serum and endometrium differed significantly across preservation category and was greatest in tissues of meconium-stained fetuses. This, together with the virtual absence of meconium staining in non-infected litters indicates it is an early pathological condition of reproductive PRRS. Viral load in fetal thymus and in fetal serum was positively associated with viral load in endometrium, suggesting the virus exploits dynamic linkages between individual maternal-fetal compartments. Point mutations in ORF5 sequences from gilts and fetuses were randomly located in 20 positions in ORF5, but neither nucleotide nor amino acid substitutions were associated with fetal preservation. PRRSv infection decreased the weights of viable fetuses by approximately 17%. The considerable variation in gilt and fetal outcomes provides tremendous opportunity for more detailed investigations of potential mechanisms and single nucleotide polymorphisms associated with fetal death. PMID:24756023

  13. Phenotypic and genomic analysis of a fast neutron mutant population resource in soybean

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mutagenized populations have become indispensable resources for introducing variation and studying gene function in plant genomics research. We utilized fast neutron radiation to induce deletion mutations in the soybean genome and phenotypically screened the resulting population. We exposed approxim...

  14. Patterns of genetic variation and covariation in ejaculate traits reveal potential evolutionary constraints in guppies.

    PubMed

    Evans, J P

    2011-05-01

    Ejaculates comprise multiple and potentially interacting traits that determine male fertility and sperm competitiveness. Consequently, selection on these traits is likely to be intense, but the efficacy of selection will depend critically on patterns of genetic variation and covariation underlying their expression. In this study, I provide a prospective quantitative genetic analysis of ejaculate traits in the guppy Poecilia reticulata, a highly promiscuous live-bearing fish. I used a standard paternal half-sibling breeding design to characterize patterns of genetic (co)variation in components of sperm length and in vitro sperm performance. All traits exhibited high levels of phenotypic and additive genetic variation, and in several cases, patterns of genetic variation was consistent with Y-linkage. There were also highly significant negative genetic correlations between the various measures of sperm length and sperm performance. In particular, the length of the sperm's midpiece was strongly, negatively and genetically correlated with sperm's swimming velocity-an important determinant of sperm competitiveness in this and other species. Other components of sperm length, including the flagellum and head, were independently and negatively genetically correlated with the proportion of live sperm in the ejaculate (sperm viability). Whether these relationships represent evolutionary trade-offs depends on the precise relationships between these traits and competitive fertilization rates, which have yet to be fully resolved in this (and indeed most) species. Nevertheless, these prospective analyses point to potential constraints on ejaculate evolution and may explain the high level of phenotypic variability in ejaculate traits in this species. PMID:20959863

  15. Analysis of Microsatellite Variation in Drosophila melanogaster with Population-Scale Genome Sequencing

    PubMed Central

    Fondon, John W.; Martin, Andy; Richards, Stephen; Gibbs, Richard A.; Mittelman, David

    2012-01-01

    Genome sequencing technologies promise to revolutionize our understanding of genetics, evolution, and disease by making it feasible to survey a broad spectrum of sequence variation on a population scale. However, this potential can only be realized to the extent that methods for extracting and interpreting distinct forms of variation can be established. The error profiles and read length limitations of early versions of next-generation sequencing technologies rendered them ineffective for some sequence variant types, particularly microsatellites and other tandem repeats, and fostered the general misconception that such variants are inherently inaccessible to these platforms. At the same time, tandem repeats have emerged as important sources of functional variation. Tandem repeats are often located in and around genes, and frequent mutations in their lengths exert quantitative effects on gene function and phenotype, rapidly degrading linkage disequilibrium between markers and traits. Sensitive identification of these variants in large-scale next-gen sequencing efforts will enable more comprehensive association studies capable of revealing previously invisible associations. We present a population-scale analysis of microsatellite repeats using whole-genome data from 158 inbred isolates from the Drosophila Genetics Reference Panel, a collection of over 200 extensively phenotypically characterized isolates from a single natural population, to uncover processes underlying repeat mutation and to enable associations with behavioral, morphological, and life-history traits. Analysis of repeat variation from next-generation sequence data will also enhance studies of genome stability and neurodegenerative diseases. PMID:22427938

  16. Quantitative analysis of colony morphology in yeast

    PubMed Central

    Ruusuvuori, Pekka; Lin, Jake; Scott, Adrian C.; Tan, Zhihao; Sorsa, Saija; Kallio, Aleksi; Nykter, Matti; Yli-Harja, Olli; Shmulevich, Ilya; Dudley, Aimée M.

    2014-01-01

    Microorganisms often form multicellular structures such as biofilms and structured colonies that can influence the organism’s virulence, drug resistance, and adherence to medical devices. Phenotypic classification of these structures has traditionally relied on qualitative scoring systems that limit detailed phenotypic comparisons between strains. Automated imaging and quantitative analysis have the potential to improve the speed and accuracy of experiments designed to study the genetic and molecular networks underlying different morphological traits. For this reason, we have developed a platform that uses automated image analysis and pattern recognition to quantify phenotypic signatures of yeast colonies. Our strategy enables quantitative analysis of individual colonies, measured at a single time point or over a series of time-lapse images, as well as the classification of distinct colony shapes based on image-derived features. Phenotypic changes in colony morphology can be expressed as changes in feature space trajectories over time, thereby enabling the visualization and quantitative analysis of morphological development. To facilitate data exploration, results are plotted dynamically through an interactive Yeast Image Analysis web application (YIMAA; http://yimaa.cs.tut.fi) that integrates the raw and processed images across all time points, allowing exploration of the image-based features and principal components associated with morphological development. PMID:24447135

  17. Studying Developmental Variation with Geometric Morphometric Image Analysis (GMIA)

    PubMed Central

    Mayer, Christine; Metscher, Brian D.; Müller, Gerd B.; Mitteroecker, Philipp

    2014-01-01

    The ways in which embryo development can vary across individuals of a population determine how genetic variation translates into adult phenotypic variation. The study of developmental variation has been hampered by the lack of quantitative methods for the joint analysis of embryo shape and the spatial distribution of cellular activity within the developing embryo geometry. By drawing from the strength of geometric morphometrics and pixel/voxel-based image analysis, we present a new approach for the biometric analysis of two-dimensional and three-dimensional embryonic images. Well-differentiated structures are described in terms of their shape, whereas structures with diffuse boundaries, such as emerging cell condensations or molecular gradients, are described as spatial patterns of intensities. We applied this approach to microscopic images of the tail fins of larval and juvenile rainbow trout. Inter-individual variation of shape and cell density was found highly spatially structured across the tail fin and temporally dynamic throughout the investigated period. PMID:25500820

  18. Genetic variation in bacterial kidney disease (BKD) susceptibility in Lake Michigan Chinook Salmon and its progenitor population from the Puget Sound

    USGS Publications Warehouse

    Purcell, Maureen K.; Hard, Jeffrey J.; Neely, Kathleen G.; Park, Linda K.; Winton, James R.; Elliott, Diane G.

    2014-01-01

    Mass mortality events in wild fish due to infectious diseases are troubling, especially given the potential for long-term, population-level consequences. Evolutionary theory predicts that populations with sufficient genetic variation will adapt in response to pathogen pressure. Chinook Salmon Oncorhynchus tshawytscha were introduced into Lake Michigan in the late 1960s from a Washington State hatchery population. In the late 1980s, collapse of the forage base and nutritional stress in Lake Michigan were thought to contribute to die-offs of Chinook Salmon due to bacterial kidney disease (BKD). Previously, we demonstrated that Lake Michigan Chinook Salmon from a Wisconsin hatchery have greater survival following BKD challenge relative to their progenitor population. Here, we evaluated whether the phenotypic divergence of these populations in BKD susceptibility was due to selection rather than genetic drift. Comparison of the overall magnitude of quantitative trait to neutral marker divergence between the populations suggested selection had occurred but a direct test of quantitative trait divergence was not significant, preventing the rejection of the null hypothesis of differentiation through genetic drift. Estimates of phenotypic variation (VP), additive genetic variation (VA) and narrow-sense heritability (h2) were consistently higher in the Wisconsin relative to the Washington population. If selection had acted on the Wisconsin population there was no evidence of a concomitant loss of genetic variation in BKD susceptibility. The Renibacterium salmoninarum exposures were conducted at both 14°C and 9°C; the warmer temperature accelerated time to death in both populations and there was no evidence of phenotypic plasticity or a genotype-by-environment (G × E) interaction. High h2 estimates for BKD susceptibility in the Wisconsin population, combined with a lack of phenotypic plasticity, predicts that future adaptive gains in BKD resistance are still possible and that these adaptive gains would be stable under the temperature range evaluated here.

  19. Effect of Surface Modification and Macrophage Phenotype on Particle Internalization

    SciTech Connect

    Wang, Daniel; Phan, Ngoc; Isely, Christopher; Bruene, Lucas; Bratlie, Kaitlin M

    2014-11-10

    Material properties play a key role in the cellular internalization of polymeric particles. In the present study, we have investigated the effects of material characteristics such as water contact angle, zeta potential, melting temperature, and alternative activation of complement on particle internalization for pro-inflammatory, pro-angiogenic, and naïve macrophages by using biopolymers (?600 nm), functionalized with 13 different molecules. Understanding how material parameters influence particle internalization for different macrophage phenotypes is important for targeted delivery to specific cell populations. Here, we demonstrate that material parameters affect the alternative pathway of complement activation as well as particle internalization for different macrophage phenotypes. Here, we show that the quantitative structure–activity relationship method (QSAR) previously used to predict physiochemical properties of materials can be applied to targeting different macrophage phenotypes. These findings demonstrated that targeted drug delivery to macrophages could be achieved by exploiting material parameters.

  20. The Genetic Basis of Variation in Clean Lineages of Saccharomyces cerevisiae in Response to Stresses Encountered during Bioethanol Fermentations

    PubMed Central

    Leung, Kay; Marvin, Marcus E.; Chandelia, Yogeshwar; Hart, Andrew J.; Phister, Trevor G.; Tucker, Gregory A.; Louis, Edward J.; Smart, Katherine A.

    2014-01-01

    Saccharomyces cerevisiae is the micro-organism of choice for the conversion of monomeric sugars into bioethanol. Industrial bioethanol fermentations are intrinsically stressful environments for yeast and the adaptive protective response varies between strain backgrounds. With the aim of identifying quantitative trait loci (QTL's) that regulate phenotypic variation, linkage analysis on six F1 crosses from four highly divergent clean lineages of S. cerevisiae was performed. Segregants from each cross were assessed for tolerance to a range of stresses encountered during industrial bioethanol fermentations. Tolerance levels within populations of F1 segregants to stress conditions differed and displayed transgressive variation. Linkage analysis resulted in the identification of QTL's for tolerance to weak acid and osmotic stress. We tested candidate genes within loci identified by QTL using reciprocal hemizygosity analysis to ascertain their contribution to the observed phenotypic variation; this approach validated a gene (COX20) for weak acid stress and a gene (RCK2) for osmotic stress. Hemizygous transformants with a sensitive phenotype carried a COX20 allele from a weak acid sensitive parent with an alteration in its protein coding compared with other S. cerevisiae strains. RCK2 alleles reveal peptide differences between parental strains and the importance of these changes is currently being ascertained. PMID:25116161

  1. Switching behaviour of two-phenotype bacteria in varying environment

    NASA Astrophysics Data System (ADS)

    Friedman, G.; Gurevich, P.; McCarthy, S.; Rachinskii, D.

    2015-02-01

    An increasing interest in multi-phenotype species has stimulated both experimental and mathematical research. One example is bacteria which have two phenotypes and can make transitions from one phenotype to the other in response to variations in environmental conditions. We model a population of such bacteria subjected to a stochastic environmental input, which fluctuates between two conditions preferred by the phenotypes. Our interest in this model is how the average growth rate of the total population is affected by alterations to the environmental thresholds at which the transitions between phenotypes are allowed. Under certain conditions, we find that the bacteria achieve a maximum growth rate by adjusting their behavior to act in a similar manner to a non-ideal relay. In this scenario, memory helps to increase fitness. We then extend the model to include multiple competing species with different thresholds and examine the limit of distribution of population among these species and phenotypes as time increases. For this purpose, we formulate a reaction-diffusion model which involves non-ideal relays describing the evolution of the state of different species; and, a Preisach operator with time-dependent density function to account for the integral effect of the species on the environment. Formation of patterns and multiple stationary limits are shown numerically in the multi-species model.

  2. Virulence attributes and hyphal growth of C. neoformans are quantitative traits and the MATalpha allele enhances filamentation.

    PubMed

    Lin, Xiaorong; Huang, Johnny C; Mitchell, Thomas G; Heitman, Joseph

    2006-11-17

    Cryptococcus neoformans is a fungal human pathogen with a bipolar mating system. It undergoes a dimorphic transition from a unicellular yeast to hyphal filamentous growth during mating and monokaryotic fruiting. The traditional sexual cycle that leads to the production of infectious basidiospores involves cells of both alpha and a mating type. Monokaryotic fruiting is a modified form of sexual reproduction that involves cells of the same mating type, most commonly alpha, which is the predominant mating type in both the environment and clinical isolates. However, some a isolates can also undergo monokaryotic fruiting. To determine whether mating type and other genetic loci contribute to the differences in fruiting observed between alpha and a cells, we applied quantitative trait loci (QTL) mapping to an inbred population of F2 progeny. We discovered that variation in hyphal length produced during fruiting is a quantitative trait resulting from the combined effects of multiple genetic loci, including the mating type (MAT) locus. Importantly, the alpha allele of the MAT locus enhanced hyphal growth compared with the a allele. Other virulence traits, including melanization and growth at 39 degrees C, also are quantitative traits that share a common QTL with hyphal growth. The Mac1 transcription factor, encoded in this common QTL, regulates copper homeostasis. MAC1 allelic differences contribute to phenotypic variation, and mac1Delta mutants exhibit defects in filamentation, melanin production, and high temperature growth. Further characterization of these QTL regions will reveal additional quantitative trait genes controlling biological processes central to fungal development and pathogenicity. PMID:17112316

  3. The contribution of genetic and environmental factors to quantitative variability of erythrocyte membrane proteins in primary hypotension.

    PubMed

    Ivanov, V P; Polonikov, A V; Solodilova, M A

    2005-01-01

    Our previous studies have shown that, compared with healthy individuals, patients with primary arterial hypotension (PAH) have significant quantitative changes in erythrocyte membrane proteins. The purpose of the present study was to evaluate the contribution made by genetic and environmental factors to quantitative variation of erythrocyte membrane proteins in PAH. We studied 109 hypotensive patients, 124 normotensive subjects, 222 of their first-degree relatives and 24 twin pairs by sodium dodecyl sulphate (SDS) polyacrylamide gel electrophoresis. The decomposition of total phenotypic variance of erythrocyte membrane proteins to genetic and environmental components was performed on the basis of correlations among first-degree relatives by the least squares method. The genetic dominance and shared environmental factors were found to influence the variability of cytoskeletal membrane proteins whose contents were changed in PAH. Furthermore, variations in alpha-spectrin, actin and anion exchanger in hypotensives were substantially influenced by major gene and maternal effects. Ankyrin 2.1 and actin content was under the control of common underlying genes. Variations in membrane-associated glutathione-S-transferase and tropomyosin were predominantly affected by polygenes. These findings suggest that the putative major genes with pleiotropic effects appear to be involved in the control of quantitative disorders of erythrocyte membrane proteins in primary hypotension. PMID:15638825

  4. Wild worm embryogenesis harbors ubiquitous polygenic modifier variation.

    PubMed

    Paaby, Annalise B; White, Amelia G; Riccardi, David D; Gunsalus, Kristin C; Piano, Fabio; Rockman, Matthew V

    2015-01-01

    Embryogenesis is an essential and stereotypic process that nevertheless evolves among species. Its essentiality may favor the accumulation of cryptic genetic variation (CGV) that has no effect in the wild-type but that enhances or suppresses the effects of rare disruptions to gene function. Here, we adapted a classical modifier screen to interrogate the alleles segregating in natural populations of Caenorhabditis elegans: we induced gene knockdowns and used quantitative genetic methodology to examine how segregating variants modify the penetrance of embryonic lethality. Each perturbation revealed CGV, indicating that wild-type genomes harbor myriad genetic modifiers that may have little effect individually but which in aggregate can dramatically influence penetrance. Phenotypes were mediated by many modifiers, indicating high polygenicity, but the alleles tend to act very specifically, indicating low pleiotropy. Our findings demonstrate the extent of conditional functionality in complex trait architecture. PMID:26297805

  5. Wild worm embryogenesis harbors ubiquitous polygenic modifier variation

    PubMed Central

    Paaby, Annalise B; White, Amelia G; Riccardi, David D; Gunsalus, Kristin C; Piano, Fabio; Rockman, Matthew V

    2015-01-01

    Embryogenesis is an essential and stereotypic process that nevertheless evolves among species. Its essentiality may favor the accumulation of cryptic genetic variation (CGV) that has no effect in the wild-type but that enhances or suppresses the effects of rare disruptions to gene function. Here, we adapted a classical modifier screen to interrogate the alleles segregating in natural populations of Caenorhabditis elegans: we induced gene knockdowns and used quantitative genetic methodology to examine how segregating variants modify the penetrance of embryonic lethality. Each perturbation revealed CGV, indicating that wild-type genomes harbor myriad genetic modifiers that may have little effect individually but which in aggregate can dramatically influence penetrance. Phenotypes were mediated by many modifiers, indicating high polygenicity, but the alleles tend to act very specifically, indicating low pleiotropy. Our findings demonstrate the extent of conditional functionality in complex trait architecture. DOI: http://dx.doi.org/10.7554/eLife.09178.001 PMID:26297805

  6. QUANTITATIVE TRAIT LOCUS ANALYSIS AND METABOLIC PATHWAYS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The development of molecular markers for crop plants has enabled research on the genetic basis of quantitative traits. However, despite more than a decade of these studies, called quantitative trait locus (QTL) analyses, the molecular basis for variation in most agronomic traits is still largely unk...

  7. Body size phenotypes are heritable and mediate fecundity but not fitness in the lepidopteran frugivore, Cydia pomonella

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The inheritance and functional roles of quantitative traits are central concerns of evolutionary ecology. We report two sets of experiments that investigated the heritability and reproductive consequences of body size phenotypes in a globally distributed lepidopteran frugivore, Cydia pomonella (L.)....

  8. Human genotype-phenotype databases: aims, challenges and opportunities.

    PubMed

    Brookes, Anthony J; Robinson, Peter N

    2015-12-01

    Genotype-phenotype databases provide information about genetic variation, its consequences and its mechanisms of action for research and health care purposes. Existing databases vary greatly in type, areas of focus and modes of operation. Despite ever larger and more intricate datasets - made possible by advances in DNA sequencing, omics methods and phenotyping technologies - steady progress is being made towards integrating these databases rather than using them as separate entities. The consequential shift in focus from single-gene variants towards large gene panels, exomes, whole genomes and myriad observable characteristics creates new challenges and opportunities in database design, interpretation of variant pathogenicity and modes of data representation and use. PMID:26553330

  9. Plant Phenotype Characterization System

    SciTech Connect

    Daniel W McDonald; Ronald B Michaels

    2005-09-09

    This report is the final scientific report for the DOE Inventions and Innovations Project: Plant Phenotype Characterization System, DE-FG36-04GO14334. The period of performance was September 30, 2004 through July 15, 2005. The project objective is to demonstrate the viability of a new scientific instrument concept for the study of plant root systems. The root systems of plants are thought to be important in plant yield and thus important to DOE goals in renewable energy sources. The scientific study and understanding of plant root systems is hampered by the difficulty in observing root activity and the inadequacy of existing root study instrumentation options. We have demonstrated a high throughput, non-invasive, high resolution technique for visualizing plant root systems in-situ. Our approach is based upon low-energy x-ray radiography and the use of containers and substrates (artificial soil) which are virtually transparent to x-rays. The system allows us to germinate and grow plant specimens in our containers and substrates and to generate x-ray images of the developing root system over time. The same plant can be imaged at different times in its development. The system can be used for root studies in plant physiology, plant morphology, plant breeding, plant functional genomics and plant genotype screening.

  10. Phenotypic profiling of ABC transporter coding genes in Myxococcus xanthus.

    PubMed

    Yan, Jinyuan; Bradley, Michael D; Friedman, Jannice; Welch, Roy D

    2014-01-01

    Information about a gene sometimes can be deduced by examining the impact of its mutation on phenotype. However, the genome-scale utility of the method is limited because, for nearly all model organisms, the majority of mutations result in little or no observable phenotypic impact. The cause of this is often attributed to robustness or redundancy within the genome, but that is only one plausible hypothesis. We examined a standard set of phenotypic traits, and applied statistical methods commonly used in the study of natural variants to an engineered mutant strain collection representing disruptions in 180 of the 192 ABC transporters within the bacterium Myxococcus xanthus. These strains display continuous variation in their phenotypic distributions, with a small number of "outlier" strains at both phenotypic extremes, and the majority within a confidence interval about the mean that always includes wild type. Correlation analysis reveals substantial pleiotropy, indicating that the traits do not represent independent variables. The traits measured in this study co-cluster with expression profiles, thereby demonstrating that these changes in phenotype correspond to changes at the molecular level, and therefore can be indirectly connected to changes in the genome. However, the continuous distributions, the pleiotropy, and the placement of wild type always within the confidence interval all indicate that this standard set of M. xanthus phenotypic assays is measuring a narrow range of partially overlapping traits that do not directly reflect fitness. This is likely a significant cause of the observed small phenotypic impact from mutation, and is unrelated to robustness and redundancy. PMID:25101061

  11. Simulation of avascular tumor growth by agent-based game model involving phenotype-phenotype interactions

    PubMed Central

    Chen, Yong; Wang, Hengtong; Zhang, Jiangang; Chen, Ke; Li, Yumin

    2015-01-01

    All tumors, both benign and metastatic, undergo an avascular growth stage with nutrients supplied by the surrounding tissue. This avascular growth process is much easier to carry out in more qualitative and quantitative experiments starting from tumor spheroids in vitro with reliable reproducibility. Essentially, this tumor progression would be described as a sequence of phenotypes. Using agent-based simulation in a two-dimensional spatial lattice, we constructed a composite growth model in which the phenotypic behavior of tumor cells depends on not only the local nutrient concentration and cell count but also the game among cells. Our simulation results demonstrated that in silico tumors are qualitatively similar to those observed in tumor spheroid experiments. We also found that the payoffs in the game between two living cell phenotypes can influence the growth velocity and surface roughness of tumors at the same time. Finally, this current model is flexible and can be easily extended to discuss other situations, such as environmental heterogeneity and mutation. PMID:26648395

  12. Darwin's finches: population variation and natural selection.

    PubMed Central

    Grant, P R; Grant, B R; Smith, J N; Abbott, I J; Abbott, L K

    1976-01-01

    Van Valen's model, which relates morphological variation to ecological variation in an adaptive scheme, was investigated with individually marked and measured Darwin's finches on two adjacent Galápagos islands, Santa Cruz and Daphne Major. Results show that environmental heterogeneity is correlated with large continuous, morphological variation: variation in bill dimensions of Geospiza fortis is greater on Santa Cruz than on Daphne, as is environmental heterogeneity. Within populations of this species, different phenotypes distribute themselves in different habitat patches, select foods of different sizes and hardness, and exploit them with efficiencies that are phenotype- (bill size) dependent. These data constitute indirect evidence that natural selection has a controlling influence over the level of phenotypic variation exhibited by a population. Further evidence is that phenotypes did not survive equally well during the study period; on Daphne island G. fortis was apparently subjected to directional selection on bill tip length and G. scandens to normalizing selection on body weight and bill depth. Other factors which may have contributed to the establishment of a difference in variation between Santa Cruz and Daphne populations are the founder effect, genetic drift, and assortative mating. Annual climatic unpredictability is considered a source of environmental heterogeneity which, through its effect upon food supply, favors large morphological variation. It is predicted that species of large individual size are more influenced by this than are small species, and consequently exhibit greater size-corrected variation. The prediction is tested with data from six Geospiza species, and found to be correct. PMID:1061123

  13. Phenotypic mapping and clinical ideology

    SciTech Connect

    Lurie, I.W.; Opitz, J.M.

    1995-07-17

    Scientists have been trying to determine whether the main clinical findings in the 4p deletion syndrome are due to a deletion of one small critical segment, or whether deletions of some particular segments of 4p are responsible for different phenotypic manifestations. This is the basic issue for the whole group of autosomal deletion syndromes, as well as for our understanding of mechanisms of the origin of the abnormal phenotype. All circumstances need to be taken into consideration when trying to apply molecular methods for the mapping of phenotypic findings in the 4p deletion or in any other autosomal deletion syndrome. 8 refs.

  14. From Individuals to Groups and Back: The Evolutionary Implications of Group Phenotypic Composition

    PubMed Central

    Farine, Damien R.; Montiglio, Pierre-Olivier; Spiegel, Orr

    2015-01-01

    There is increasing interest in understanding the processes that maintain phenotypic variation in groups, populations, or communities. Recent studies have investigated how the phenotypic composition of groups or aggregations (e.g., its average phenotype or phenotypic variance) affects ecological and social processes, and how multi-level selection can drive phenotypic covariance among interacting individuals. However, we argue that these questions are rarely studied together. We present a unified framework to address this gap, and discuss how group phenotypic composition (GPC) can impact on processes ranging from individual fitness to population demography. By emphasising the breadth of topics affected, we hope to motivate more integrated empirical studies of the ecological and evolutionary implications of GPC. PMID:26411618

  15. Analysis of two-state multivariate phenotypic change in ecological studies.

    PubMed

    Collyer, Michael L; Adams, Dean C

    2007-03-01

    Analyses of two-state phenotypic change are common in ecological research. Some examples include phenotypic changes due to phenotypic plasticity between two environments, changes due to predator/non-predator character shifts, character displacement via competitive interactions, and patterns of sexual dimorphism. However, methods for analyzing phenotypic change for multivariate data have not been rigorously developed. Here we outline a method for testing vectors of phenotypic change in terms of two important attributes: the magnitude of change (vector length) and the direction of change described by trait covariation (angular difference between vectors). We describe a permutation procedure for testing these attributes, which allows non-targeted sources of variation to be held constant. We provide examples that illustrate the importance of considering vector attributes of phenotypic change in biological studies, and we demonstrate how greater inference can be made than by evaluating variance components with MANOVA alone. Finally, we consider how our method may be extended to more complex data. PMID:17503596

  16. From Individuals to Groups and Back: The Evolutionary Implications of Group Phenotypic Composition.

    PubMed

    Farine, Damien R; Montiglio, Pierre-Olivier; Spiegel, Orr

    2015-10-01

    There is increasing interest in understanding the processes that maintain phenotypic variation in groups, populations, or communities. Recent studies have investigated how the phenotypic composition of groups or aggregations (e.g., its average phenotype or phenotypic variance) affects ecological and social processes, and how multi-level selection can drive phenotypic covariance among interacting individuals. However, we argue that these questions are rarely studied together. We present a unified framework to address this gap, and discuss how group phenotypic composition (GPC) can impact on processes ranging from individual fitness to population demography. By emphasising the breadth of topics affected, we hope to motivate more integrated empirical studies of the ecological and evolutionary implications of GPC. PMID:26411618

  17. Epigenetic and epigenomic variation in Arabidopsis thaliana

    PubMed Central

    Schmitz, Robert J.; Ecker, Joseph R.

    2013-01-01

    Arabidopsis thaliana (Arabidopsis) is ideally suited for studies of natural phenotypic variation. This species has also provided an unparalleled experimental system to explore the mechanistic link between genetic and epigenetic variation, especially with regard to cytosine methylation. Using high-throughput sequencing methods, genotype to epigenotype to phenotype observations can now be extended to plant populations. We review the evidence for induced and spontaneous epigenetic variants that have been identified in Arabidopsis in the laboratory and discuss how these experimental observations could explain existing variation in the wild. PMID:22342533

  18. More than the sum of its parts: a complex epistatic network underlies natural variation in thermal preference behavior in Caenorhabditis elegans.

    PubMed

    Gaertner, Bryn E; Parmenter, Michelle D; Rockman, Matthew V; Kruglyak, Leonid; Phillips, Patrick C

    2012-12-01

    Behavior is a complex trait that results from interactions among multiple genes and the environment. Both additive and nonadditive effects are expected to contribute to broad-sense heritability of complex phenotypes, although the relative contribution of each of these mechanisms is unknown. Here, we mapped genetic variation in the correlated phenotypes of thermal preference and isothermal dispersion in the nematode Caenorhabditis elegans. Genetic variation underlying these traits is characterized by a set of linked quantitative trait loci (QTL) that interact in a complex epistatic network. In particular, two loci located on the X chromosome interact with one another to generate extreme thermophilic behavior and are responsible for ?50% of the total variation observed in a cross between two parental lines, even though these loci individually explain very little of the among-line variation. Our results demonstrate that simultaneously considering the influence of a quantitative trait locus (QTL) on multiple scales of behavior can inform the physiological mechanism of the QTL and show that epistasis can explain significant proportions of otherwise unattributed variance within populations. PMID:23086219

  19. More Than the Sum of Its Parts: A Complex Epistatic Network Underlies Natural Variation in Thermal Preference Behavior in Caenorhabditis elegans

    PubMed Central

    Gaertner, Bryn E.; Parmenter, Michelle D.; Rockman, Matthew V.; Kruglyak, Leonid; Phillips, Patrick C.

    2012-01-01

    Behavior is a complex trait that results from interactions among multiple genes and the environment. Both additive and nonadditive effects are expected to contribute to broad-sense heritability of complex phenotypes, although the relative contribution of each of these mechanisms is unknown. Here, we mapped genetic variation in the correlated phenotypes of thermal preference and isothermal dispersion in the nematode Caenorhabditis elegans. Genetic variation underlying these traits is characterized by a set of linked quantitative trait loci (QTL) that interact in a complex epistatic network. In particular, two loci located on the X chromosome interact with one another to generate extreme thermophilic behavior and are responsible for ?50% of the total variation observed in a cross between two parental lines, even though these loci individually explain very little of the among-line variation. Our results demonstrate that simultaneously considering the influence of a quantitative trait locus (QTL) on multiple scales of behavior can inform the physiological mechanism of the QTL and show that epistasis can explain significant proportions of otherwise unattributed variance within populations. PMID:23086219

  20. Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

    PubMed Central

    Huang, Wen; Massouras, Andreas; Inoue, Yutaka; Peiffer, Jason; Ràmia, Miquel; Tarone, Aaron M.; Turlapati, Lavanya; Zichner, Thomas; Zhu, Dianhui; Lyman, Richard F.; Magwire, Michael M.; Blankenburg, Kerstin; Carbone, Mary Anna; Chang, Kyle; Ellis, Lisa L.; Fernandez, Sonia; Han, Yi; Highnam, Gareth; Hjelmen, Carl E.; Jack, John R.; Javaid, Mehwish; Jayaseelan, Joy; Kalra, Divya; Lee, Sandy; Lewis, Lora; Munidasa, Mala; Ongeri, Fiona; Patel, Shohba; Perales, Lora; Perez, Agapito; Pu, LingLing; Rollmann, Stephanie M.; Ruth, Robert; Saada, Nehad; Warner, Crystal; Williams, Aneisa; Wu, Yuan-Qing; Yamamoto, Akihiko; Zhang, Yiqing; Zhu, Yiming; Anholt, Robert R.H.; Korbel, Jan O.; Mittelman, David; Muzny, Donna M.; Gibbs, Richard A.; Barbadilla, Antonio; Johnston, J. Spencer; Stone, Eric A.; Richards, Stephen; Deplancke, Bart; Mackay, Trudy F.C.

    2014-01-01

    The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenced inbred lines, derived to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used an integrated genotyping strategy to identify 4,853,802 single nucleotide polymorphisms (SNPs) and 1,296,080 non-SNP variants. Our molecular population genomic analyses show higher deletion than insertion mutation rates and stronger purifying selection on deletions. Weaker selection on insertions than deletions is consistent with our observed distribution of genome size determined by flow cytometry, which is skewed toward larger genomes. Insertion/deletion and single nucleotide polymorphisms are positively correlated with each other and with local recombination, suggesting that their nonrandom distributions are due to hitchhiking and background selection. Our cytogenetic analysis identified 16 polymorphic inversions in the DGRP. Common inverted and standard karyotypes are genetically divergent and account for most of the variation in relatedness among the DGRP lines. Intriguingly, variation in genome size and many quantitative traits are significantly associated with inversions. Approximately 50% of the DGRP lines are infected with Wolbachia, and four lines have germline insertions of Wolbachia sequences, but effects of Wolbachia infection on quantitative traits are rarely significant. The DGRP complements ongoing efforts to functionally annotate the Drosophila genome. Indeed, 15% of all D. melanogaster genes segregate for potentially damaged proteins in the DGRP, and genome-wide analyses of quantitative traits identify novel candidate genes. The DGRP lines, sequence data, genotypes, quality scores, phenotypes, and analysis and visualization tools are publicly available. PMID:24714809

  1. Population genetic variation in gene expression is associated withphenotypic variation in Saccharomyces cerevisiae

    SciTech Connect

    Fay, Justin C.; McCullough, Heather L.; Sniegowski, Paul D.; Eisen, Michael B.

    2004-02-25

    The relationship between genetic variation in gene expression and phenotypic variation observable in nature is not well understood. Identifying how many phenotypes are associated with differences in gene expression and how many gene-expression differences are associated with a phenotype is important to understanding the molecular basis and evolution of complex traits. Results: We compared levels of gene expression among nine natural isolates of Saccharomyces cerevisiae grown either in the presence or absence of copper sulfate. Of the nine strains, two show a reduced growth rate and two others are rust colored in the presence of copper sulfate. We identified 633 genes that show significant differences in expression among strains. Of these genes,20 were correlated with resistance to copper sulfate and 24 were correlated with rust coloration. The function of these genes in combination with their expression pattern suggests the presence of both correlative and causative expression differences. But the majority of differentially expressed genes were not correlated with either phenotype and showed the same expression pattern both in the presence and absence of copper sulfate. To determine whether these expression differences may contribute to phenotypic variation under other environmental conditions, we examined one phenotype, freeze tolerance, predicted by the differential expression of the aquaporin gene AQY2. We found freeze tolerance is associated with the expression of AQY2. Conclusions: Gene expression differences provide substantial insight into the molecular basis of naturally occurring traits and can be used to predict environment dependent phenotypic variation.

  2. Finding Our Way through Phenotypes

    PubMed Central

    Deans, Andrew R.; Lewis, Suzanna E.; Huala, Eva; Anzaldo, Salvatore S.; Ashburner, Michael; Balhoff, James P.; Blackburn, David C.; Blake, Judith A.; Burleigh, J. Gordon; Chanet, Bruno; Cooper, Laurel D.; Courtot, Mélanie; Csösz, Sándor; Cui, Hong; Dahdul, Wasila; Das, Sandip; Dececchi, T. Alexander; Dettai, Agnes; Diogo, Rui; Druzinsky, Robert E.; Dumontier, Michel; Franz, Nico M.; Friedrich, Frank; Gkoutos, George V.; Haendel, Melissa; Harmon, Luke J.; Hayamizu, Terry F.; He, Yongqun; Hines, Heather M.; Ibrahim, Nizar; Jackson, Laura M.; Jaiswal, Pankaj; James-Zorn, Christina; Köhler, Sebastian; Lecointre, Guillaume; Lapp, Hilmar; Lawrence, Carolyn J.; Le Novère, Nicolas; Lundberg, John G.; Macklin, James; Mast, Austin R.; Midford, Peter E.; Mikó, István; Mungall, Christopher J.; Oellrich, Anika; Osumi-Sutherland, David; Parkinson, Helen; Ramírez, Martín J.; Richter, Stefan; Robinson, Peter N.; Ruttenberg, Alan; Schulz, Katja S.; Segerdell, Erik; Seltmann, Katja C.; Sharkey, Michael J.; Smith, Aaron D.; Smith, Barry; Specht, Chelsea D.; Squires, R. Burke; Thacker, Robert W.; Thessen, Anne; Fernandez-Triana, Jose; Vihinen, Mauno; Vize, Peter D.; Vogt, Lars; Wall, Christine E.; Walls, Ramona L.; Westerfeld, Monte; Wharton, Robert A.; Wirkner, Christian S.; Woolley, James B.; Yoder, Matthew J.; Zorn, Aaron M.; Mabee, Paula

    2015-01-01

    Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. PMID:25562316

  3. Finding our way through phenotypes.

    PubMed

    Deans, Andrew R; Lewis, Suzanna E; Huala, Eva; Anzaldo, Salvatore S; Ashburner, Michael; Balhoff, James P; Blackburn, David C; Blake, Judith A; Burleigh, J Gordon; Chanet, Bruno; Cooper, Laurel D; Courtot, Mélanie; Csösz, Sándor; Cui, Hong; Dahdul, Wasila; Das, Sandip; Dececchi, T Alexander; Dettai, Agnes; Diogo, Rui; Druzinsky, Robert E; Dumontier, Michel; Franz, Nico M; Friedrich, Frank; Gkoutos, George V; Haendel, Melissa; Harmon, Luke J; Hayamizu, Terry F; He, Yongqun; Hines, Heather M; Ibrahim, Nizar; Jackson, Laura M; Jaiswal, Pankaj; James-Zorn, Christina; Köhler, Sebastian; Lecointre, Guillaume; Lapp, Hilmar; Lawrence, Carolyn J; Le Novère, Nicolas; Lundberg, John G; Macklin, James; Mast, Austin R; Midford, Peter E; Mikó, István; Mungall, Christopher J; Oellrich, Anika; Osumi-Sutherland, David; Parkinson, Helen; Ramírez, Martín J; Richter, Stefan; Robinson, Peter N; Ruttenberg, Alan; Schulz, Katja S; Segerdell, Erik; Seltmann, Katja C; Sharkey, Michael J; Smith, Aaron D; Smith, Barry; Specht, Chelsea D; Squires, R Burke; Thacker, Robert W; Thessen, Anne; Fernandez-Triana, Jose; Vihinen, Mauno; Vize, Peter D; Vogt, Lars; Wall, Christine E; Walls, Ramona L; Westerfeld, Monte; Wharton, Robert A; Wirkner, Christian S; Woolley, James B; Yoder, Matthew J; Zorn, Aaron M; Mabee, Paula

    2015-01-01

    Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. PMID:25562316

  4. INTRODUCTION Variation in physiological phenotype between animal populations

    E-print Network

    Burggren, Warren

    populations. Part of the appeal of the model is that the poultry industry rigorously promotes two chicken, and the broiler chicken is selected for rapid growth for meat production. As an unfortunate consequence capacity than that of the layer chicken to deliver sufficient oxygen to relatively under-perfused muscle

  5. Phenotypic and genetic variation among soybean rust isolates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phakopsora pachyrhizi, the causal agent of soybean rust, is an aggressive foliar disease that is found in all major soybean growing regions. The discovery of soybean rust in production fields in the southeastern U. S. in 2004 and its spread to other areas in subsequent years has heightened concerns ...

  6. Resource variation and the evolution of phenotypic plasticity in fishes 

    E-print Network

    Ruehl, Clifton Benjamin

    2004-09-30

    it played during the modern evolutionary synthesis. T. Dobzhansky, G. G. Simpson, B. Rensch, J. Huxley, J. B. S. Haldane, R. A. Fisher, E. Mayr, and many others brought 7 together disparate aspects of biological research between the years of nineteen... during the early part of the twentieth century. Schmalhausen expands earlier work on reaction norms by applying the concept to the theory of stabilizing selection, initially proposed by W. Bateson, J. B. S Haldane, and R. A. Fisher (Schlichting...

  7. Quantitative interactome analysis reveals a chemoresistant edgotype

    PubMed Central

    Chavez, Juan D.; Schweppe, Devin K.; Eng, Jimmy K.; Zheng, Chunxiang; Taipale, Alex; Zhang, Yiyi; Takara, Kohji; Bruce, James E.

    2015-01-01

    Chemoresistance is a common mode of therapy failure for many cancers. Tumours develop resistance to chemotherapeutics through a variety of mechanisms, with proteins serving pivotal roles. Changes in protein conformations and interactions affect the cellular response to environmental conditions contributing to the development of new phenotypes. The ability to understand how protein interaction networks adapt to yield new function or alter phenotype is limited by the inability to determine structural and protein interaction changes on a proteomic scale. Here, chemical crosslinking and mass spectrometry were employed to quantify changes in protein structures and interactions in multidrug-resistant human carcinoma cells. Quantitative analysis of the largest crosslinking-derived, protein interaction network comprising 1,391 crosslinked peptides allows for ‘edgotype' analysis in a cell model of chemoresistance. We detect consistent changes to protein interactions and structures, including those involving cytokeratins, topoisomerase-2-alpha, and post-translationally modified histones, which correlate with a chemoresistant phenotype. PMID:26235782

  8. Molecular Mechanisms of Epigenetic Variation in Plants

    PubMed Central

    Fujimoto, Ryo; Sasaki, Taku; Ishikawa, Ryo; Osabe, Kenji; Kawanabe, Takahiro; Dennis, Elizabeth S.

    2012-01-01

    Natural variation is defined as the phenotypic variation caused by spontaneous mutations. In general, mutations are associated with changes of nucleotide sequence, and many mutations in genes that can cause changes in plant development have been identified. Epigenetic change, which does not involve alteration to the nucleotide sequence, can also cause changes in gene activity by changing the structure of chromatin through DNA methylation or histone modifications. Now there is evidence based on induced or spontaneous mutants that epigenetic changes can cause altering plant phenotypes. Epigenetic changes have occurred frequently in plants, and some are heritable or metastable causing variation in epigenetic status within or between species. Therefore, heritable epigenetic variation as well as genetic variation has the potential to drive natural variation. PMID:22949838

  9. Single Cell Quantification of Reporter Gene Expression in Live Adult Caenorhabditis elegans Reveals Reproducible Cell-Specific Expression Patterns and Underlying Biological Variation

    PubMed Central

    Mendenhall, Alexander R.; Tedesco, Patricia M.; Sands, Bryan; Johnson, Thomas E.; Brent, Roger

    2015-01-01

    In multicellular organisms such as Caenorhabditis elegans, differences in complex phenotypes such as lifespan correlate with the level of expression of particular engineered reporter genes. In single celled organisms, quantitative understanding of responses to extracellular signals and of cell-to-cell variation in responses has depended on precise measurement of reporter gene expression. Here, we developed microscope-based methods to quantify reporter gene expression in cells of Caenorhabditis elegans with low measurement error. We then quantified expression in strains that carried different configurations of Phsp-16.2-fluorescent-protein reporters, in whole animals, and in all 20 cells of the intestine tissue, which is responsible for most of the fluorescent signal. Some animals bore more recently developed single copy Phsp-16.2 reporters integrated at defined chromosomal sites, others, “classical” multicopy reporter gene arrays integrated at random sites. At the level of whole animals, variation in gene expression was similar: strains with single copy reporters showed the same amount of animal-to-animal variation as strains with multicopy reporters. At the level of cells, in animals with single copy reporters, the pattern of expression in cells within the tissue was highly stereotyped. In animals with multicopy reporters, the cell-specific expression pattern was also stereotyped, but distinct, and somewhat more variable. Our methods are rapid and gentle enough to allow quantification of expression in the same cells of an animal at different times during adult life. They should allow investigators to use changes in reporter expression in single cells in tissues as quantitative phenotypes, and link those to molecular differences. Moreover, by diminishing measurement error, they should make possible dissection of the causes of the remaining, real, variation in expression. Understanding such variation should help reveal its contribution to differences in complex phenotypic outcomes in multicellular organisms. PMID:25946008

  10. 1 Phenotypic Fluctuation (Plasticity) vs Evolution 2 Phenotypic Fluctuation vs Genetic Variation

    E-print Network

    Kaneko, Kunihiko

    and Fluctuation Gene regulation network Molecule Cell Multicelluarity Ecosystem Stochsatic dynamics Complex-Systems between cell growth and gene expression dynamics Consistency between Multicelluar development and cell be discussed informally) (1) Cooperative Adaptation Dynamics by high- dimensional gene regulation dynamics

  11. Quantitative Genetics Bruce Walsh, University of Arizona, Tucson, Arizona, USA

    E-print Network

    Walsh, Bruce

    Quantitative Genetics Bruce Walsh, University of Arizona, Tucson, Arizona, USA Almost any trait that can be defined shows variation, both within and between populations. Quantitative genetics is concerned with the analysis of the genetic and environmental basis of this variation. Classical genetics

  12. Natural selection on quantitative immune defence traits: a comparison between theory and data.

    PubMed

    Seppälä, O

    2015-01-01

    Parasites present a threat for free-living species and affect several ecological and evolutionary processes. Immune defence is the main physiological barrier against infections, and understanding its evolution is central for predicting disease dynamics. I review theoretical predictions and empirical data on natural selection on quantitative immune defence traits in the wild. Evolutionary theory predicts immune traits to be under stabilizing selection owing to trade-offs between immune function and life-history traits. Empirical data, however, support mainly positive directional selection, but also show variation in the form of selection among study systems, immune traits and fitness components. I argue that the differences between theory and empirical data may at least partly arise from methodological difficulties in testing stabilizing selection as well as measuring fitness. I also argue that the commonness of positive directional selection and the variation in selection may be caused by several biological factors. First, selection on immune function may show spatial and temporal variation as epidemics are often local/seasonal. Second, factors affecting the range of phenotypic variation in immune traits could alter potential for selection. Third, different parasites may impose different selective pressures depending on their characteristics. Fourth, condition dependence of immune defence can obscure trade-offs related to it, thus possibly modifying observed selection gradients. Fifth, nonimmunological defences could affect the form of selection by reducing the benefits of strong immune function. To comprehensively understand the evolution of immune defence, the role of above factors should be considered in future studies. PMID:25400248

  13. Inferring causal phenotype networks using structural equation models.

    PubMed

    Rosa, Guilherme J M; Valente, Bruno D; de los Campos, Gustavo; Wu, Xiao-Lin; Gianola, Daniel; Silva, Martinho A

    2011-01-01

    Phenotypic traits may exert causal effects between them. For example, on the one hand, high yield in dairy cows may increase the liability to certain diseases and, on the other hand, the incidence of a disease may affect yield negatively. Likewise, the transcriptome may be a function of the reproductive status in mammals and the latter may depend on other physiological variables. Knowledge of phenotype networks describing such interrelationships can be used to predict the behavior of complex systems, e.g. biological pathways underlying complex traits such as diseases, growth and reproduction. Structural Equation Models (SEM) can be used to study recursive and simultaneous relationships among phenotypes in multivariate systems such as genetical genomics, system biology, and multiple trait models in quantitative genetics. Hence, SEM can produce an interpretation of relationships among traits which differs from that obtained with traditional multiple trait models, in which all relationships are represented by symmetric linear associations among random variables, such as covariances and correlations. In this review, we discuss the application of SEM and related techniques for the study of multiple phenotypes. Two basic scenarios are considered, one pertaining to genetical genomics studies, in which QTL or molecular marker information is used to facilitate causal inference, and another related to quantitative genetic analysis in livestock, in which only phenotypic and pedigree information is available. Advantages and limitations of SEM compared to traditional approaches commonly used for the analysis of multiple traits, as well as some indication of future research in this area are presented in a concluding section. PMID:21310061

  14. Emergence of phenotype switching through continuous and discontinuous evolutionary transitions

    NASA Astrophysics Data System (ADS)

    Patra, Pintu; Klumpp, Stefan

    2015-07-01

    Bacterial persistence (phenotypic tolerance to antibiotics) provides a prime example of bet-hedging, where normally growing cells generate slow-growing but antibiotic-tolerant persister cells to survive through periods of exposure to antibiotics. The population dynamics of persistence is explained by a phenotype switching mechanism that allows individual cells to switch between these different cellular states with different environmental sensitivities. Here, we perform a theoretical study based on an exact solution for the case of a periodic variation of the environment to address how phenotype switching emerges and under what conditions switching is or is not beneficial for long-time growth. Specifically we report a bifurcation through which a fitness maximum and minimum emerge above a threshold in the duration of exposure to the antibiotic. Only above this threshold, the optimal phenotype switching rates are adjusted to the time scales of the environment, as emphasized by previous theoretical studies, while below the threshold a non-switching population is fitter than a switching one. The bifurcation can be of different type, depending on how the phenotype switching rates are allowed to vary. If the switching rates for both directions of the switch are coupled, the transition is discontinuous and results in evolutionary hysteresis, which we confirm with a stochastic simulation. If the switching rates vary individually, a continuous transition is obtained and no hysteresis is found. We discuss how both scenarios can be linked to changes in the underlying molecular networks.

  15. Quantitative DNA Methylation Profiling in Cancer.

    PubMed

    Ammerpohl, Ole; Haake, Andrea; Kolarova, Julia; Siebert, Reiner

    2016-01-01

    Epigenetic mechanisms including DNA methylation are fundamental for the regulation of gene expression. Epigenetic alterations can lead to the development and the evolution of malignant tumors as well as the emergence of phenotypically different cancer cells or metastasis from one single tumor cell. Here we describe bisulfite pyrosequencing, a technology to perform quantitative DNA methylation analyses, to detect aberrant DNA methylation in malignant tumors. PMID:26667456

  16. The Arrival of the Frequent: How Bias in Genotype-Phenotype Maps Can Steer Populations to Local Optima

    PubMed Central

    Schaper, Steffen; Louis, Ard A.

    2014-01-01

    Genotype-phenotype (GP) maps specify how the random mutations that change genotypes generate variation by altering phenotypes, which, in turn, can trigger selection. Many GP maps share the following general properties: 1) The total number of genotypes is much larger than the number of selectable phenotypes; 2) Neutral exploration changes the variation that is accessible to the population; 3) The distribution of phenotype frequencies , with the number of genotypes mapping onto phenotype , is highly biased: the majority of genotypes map to only a small minority of the phenotypes. Here we explore how these properties affect the evolutionary dynamics of haploid Wright-Fisher models that are coupled to a random GP map or to a more complex RNA sequence to secondary structure map. For both maps the probability of a mutation leading to a phenotype scales to first order as , although for the RNA map there are further correlations as well. By using mean-field theory, supported by computer simulations, we show that the discovery time of a phenotype similarly scales to first order as for a wide range of population sizes and mutation rates in both the monomorphic and polymorphic regimes. These differences in the rate at which variation arises can vary over many orders of magnitude. Phenotypic variation with a larger is therefore be much more likely to arise than variation with a small . We show, using the RNA model, that frequent phenotypes (with larger ) can fix in a population even when alternative, but less frequent, phenotypes with much higher fitness are potentially accessible. In other words, if the fittest never ‘arrive’ on the timescales of evolutionary change, then they can't fix. We call this highly non-ergodic effect the ‘arrival of the frequent’. PMID:24505262

  17. Quantitative trait locus analysis for kernel width using maize recombinant inbred lines.

    PubMed

    Hui, G Q; Wen, G Q; Liu, X H; Yang, H P; Luo, Q; Song, H X; Wen, L; Sun, Y; Zhang, H M

    2015-01-01

    Maize (Zea mays L.) kernel width is one of the most important traits that is related to yield and appearance. To understand its genetic mechanisms more clearly, a recombinant inbred line (RIL) segregation population consisting of 239 RILs was used for quantitative trait locus (QTL) mapping for kernel width. We found four QTLs on chromosomes 3 (one), 5 (two), and 10 (one). The QTLs were close to their adjacent markers, with a range of 0-23.8 cM, and explained 6.2-19.7% of the phenotypic variation. The three QTLs on chromosomes 3 and 5 had positive additive effects, and to a certain extent increased kernel width, whereas the one on chromosome 10 exhibited negative additive effects and decreased kernel width. These results can be used for gene cloning and marker-assisted selection in maize-breeding programs. PMID:26600508

  18. Phenotypic integration in the feeding system of the eastern diamondback rattlesnake (Crotalus adamanteus).

    PubMed

    Margres, Mark J; Wray, Kenneth P; Seavy, Margaret; McGivern, James J; Sanader, Dragana; Rokyta, Darin R

    2015-07-01

    Selection can vary geographically across environments and temporally over the lifetime of an individual. Unlike geographic contexts, where different selective regimes can act on different alleles, age-specific selection is constrained to act on the same genome by altering age-specific expression. Snake venoms are exceptional traits for studying ontogeny because toxin expression variation directly changes the phenotype; relative amounts of venom components determine, in part, venom efficacy. Phenotypic integration is the dependent relationship between different traits that collectively produce a complex phenotype and, in venomous snakes, may include traits as diverse as venom, head shape and fang length. We examined the feeding system of the eastern diamondback rattlesnake (Crotalus adamanteus) across environments and over the lifetime of individuals and used a genotype-phenotype map approach, protein expression data and morphological data to demonstrate that: (i) ontogenetic effects explained more of the variation in toxin expression variation than geographic effects, (ii) both juveniles and adults varied geographically, (iii) toxin expression variation was a result of directional selection and (iv) different venom phenotypes covaried with morphological traits also associated with feeding in temporal (ontogenetic) and geographic (functional) contexts. These data are the first to demonstrate, to our knowledge, phenotypic integration between multiple morphological characters and a biochemical phenotype across populations and age classes. We identified copy number variation as the mechanism driving the difference in the venom phenotype associated with these morphological differences, and the parallel mitochondrial, venom and morphological divergence between northern and southern clades suggests that each clade may warrant classification as a separate evolutionarily significant unit. PMID:25988233

  19. Genetic mapping of quantitative trait loci controlling growth and wood quality traits in Eucalyptus grandis using a maternal half-sib family and RAPD markers.

    PubMed

    Grattapaglia, D; Bertolucci, F L; Penchel, R; Sederoff, R R

    1996-11-01

    Quantitative trait loci (QTL) mapping of forest productivity traits was performed using an open pollinated half-sib family of Eucalyptus grandis. For volume growth, a sequential QTL mapping approach was applied using bulk segregant analysis (BSA), selective genotyping (SG) and cosegregation analysis (CSA). Despite the low heritability of this trait and the heterogeneous genetic background employed for mapping, BSA detected one putative QTL and SG two out of the three later found by CSA. The three putative QTL for volume growth were found to control 13.7% of the phenotypic variation, corresponding to an estimated 43.7% of the genetic variation. For wood specific gravity five QTL were identified controlling 24.7% of the phenotypic variation corresponding to 49% of the genetic variation. Overlapping QTL for CBH, WSG and percentage dry weight of bark were observed. A significant case of digenic epistasis was found, involving unlinked QTL for volume. Our results demonstrate the applicability of the within half-sib design for QTL mapping in forest trees and indicate the existence of major genes involved in the expression of economically important traits related to forest productivity in Eucalyptus grandis. These findings have important implications for marker-assisted tree breeding. PMID:8913761

  20. Phenomics: The systematic study of phenotypes on a genome-wide scale

    PubMed Central

    Bilder, Robert M.; Sabb, Fred w.; Cannon, Tyrone D.; London, Edythe D.; Jentsch, J. David; Parker, D. Stott; Poldrack, Russell A.; Evans, Chris; Freimer, Nelson B.

    2009-01-01

    Phenomics is an emerging transdiscipline dedicated to the systematic study of phenotypes on a genome-wide scale. New methods for high-throughput genotyping have changed the priority for biomedical research to phenotyping, but the human phenome is vast and its dimensionality remains unknown. Phenomics research strategies capable of linking genetic variation to public health concerns need to prioritize development of mechanistic frameworks that relate neural systems functioning to human behavior. New approaches to phenotype definition will benefit from crossing neuropsychiatric syndromal boundaries, and defining phenotypic features across multiple levels of expression from proteome to syndrome. The demand for high throughput phenotyping may stimulate a migration from conventional laboratory to web-based assessment of behavior, and this offers the promise of dynamic phenotyping –the iterative refinement of phenotype assays based on prior genotype-phenotype associations. Phenotypes that can be studied across species may provide greatest traction, particularly given rapid development in transgenic modeling. Phenomics research demands vertically integrated research teams, novel analytic strategies and informatics infrastructure to help manage complexity. The Consortium for Neuropsychiatric Phenomics at UCLA has been supported by the NIH Roadmap Initiative to illustrate these principles, and is developing applications that may help investigators assemble, visualize, and ultimately test multi-level phenomics hypotheses. As the transdiscipline of phenomics matures, and work is extended to large-scale international collaborations, there is promise that systematic new knowledgebases will help fulfill the promise of personalized medicine and the rational diagnosis and treatment of neuropsychiatric syndromes. PMID:19344640

  1. FROG - Fingerprinting Genomic Variation Ontology.

    PubMed

    Abinaya, E; Narang, Pankaj; Bhardwaj, Anshu

    2015-01-01

    Genetic variations play a crucial role in differential phenotypic outcomes. Given the complexity in establishing this correlation and the enormous data available today, it is imperative to design machine-readable, efficient methods to store, label, search and analyze this data. A semantic approach, FROG: "FingeRprinting Ontology of Genomic variations" is implemented to label variation data, based on its location, function and interactions. FROG has six levels to describe the variation annotation, namely, chromosome, DNA, RNA, protein, variations and interactions. Each level is a conceptual aggregation of logically connected attributes each of which comprises of various properties for the variant. For example, in chromosome level, one of the attributes is location of variation and which has two properties, allosomes or autosomes. Another attribute is variation kind which has four properties, namely, indel, deletion, insertion, substitution. Likewise, there are 48 attributes and 278 properties to capture the variation annotation across six levels. Each property is then assigned a bit score which in turn leads to generation of a binary fingerprint based on the combination of these properties (mostly taken from existing variation ontologies). FROG is a novel and unique method designed for the purpose of labeling the entire variation data generated till date for efficient storage, search and analysis. A web-based platform is designed as a test case for users to navigate sample datasets and generate fingerprints. The platform is available at http://ab-openlab.csir.res.in/frog. PMID:26244889

  2. FROG - Fingerprinting Genomic Variation Ontology

    PubMed Central

    Bhardwaj, Anshu

    2015-01-01

    Genetic variations play a crucial role in differential phenotypic outcomes. Given the complexity in establishing this correlation and the enormous data available today, it is imperative to design machine-readable, efficient methods to store, label, search and analyze this data. A semantic approach, FROG: “FingeRprinting Ontology of Genomic variations” is implemented to label variation data, based on its location, function and interactions. FROG has six levels to describe the variation annotation, namely, chromosome, DNA, RNA, protein, variations and interactions. Each level is a conceptual aggregation of logically connected attributes each of which comprises of various properties for the variant. For example, in chromosome level, one of the attributes is location of variation and which has two properties, allosomes or autosomes. Another attribute is variation kind which has four properties, namely, indel, deletion, insertion, substitution. Likewise, there are 48 attributes and 278 properties to capture the variation annotation across six levels. Each property is then assigned a bit score which in turn leads to generation of a binary fingerprint based on the combination of these properties (mostly taken from existing variation ontologies). FROG is a novel and unique method designed for the purpose of labeling the entire variation data generated till date for efficient storage, search and analysis. A web-based platform is designed as a test case for users to navigate sample datasets and generate fingerprints. The platform is available at http://ab-openlab.csir.res.in/frog. PMID:26244889

  3. Identifying the genes underlying quantitative traits: a rationale for the QTN programme

    PubMed Central

    Lee, Young Wha; Gould, Billie A.; Stinchcombe, John R.

    2014-01-01

    The goal of identifying the genes or even nucleotides underlying quantitative and adaptive traits has been characterized as the ‘QTN programme’ and has recently come under severe criticism. Part of the reason for this criticism is that much of the QTN programme has asserted that finding the genes and nucleotides for adaptive and quantitative traits is a fundamental goal, without explaining why it is such a hallowed goal. Here we outline motivations for the QTN programme that offer general insight, regardless of whether QTNs are of large or small effect, and that aid our understanding of the mechanistic dynamics of adaptive evolution. We focus on five areas: (i) vertical integration of insight across different levels of biological organization, (ii) genetic parallelism and the role of pleiotropy in shaping evolutionary dynamics, (iii) understanding the forces maintaining genetic variation in populations, (iv) distinguishing between adaptation from standing variation and new mutation, and (v) the role of genomic architecture in facilitating adaptation. We argue that rather than abandoning the QTN programme, we should refocus our efforts on topics where molecular data will be the most effective for testing hypotheses about phenotypic evolution. PMID:24790125

  4. Associations between KCNJ6 (GIRK2) gene polymorphisms and pain-related phenotypes.

    PubMed

    Bruehl, Stephen; Denton, Jerod S; Lonergan, Daniel; Koran, Mary Ellen; Chont, Melissa; Sobey, Christopher; Fernando, Shanik; Bush, William S; Mishra, Puneet; Thornton-Wells, Tricia A

    2013-12-01

    G-protein coupled inwardly rectifying potassium (GIRK) channels are effectors determining degree of analgesia experienced upon opioid receptor activation by endogenous and exogenous opioids. The impact of GIRK-related genetic variation on human pain responses has received little research attention. We used a tag single nucleotide polymorphism (SNP) approach to comprehensively examine pain-related effects of KCNJ3 (GIRK1) and KCNJ6 (GIRK2) gene variation. Forty-one KCNJ3 and 69 KCNJ6 tag SNPs were selected, capturing the known variability in each gene. The primary sample included 311 white patients undergoing total knee arthroplasty in whom postsurgical oral opioid analgesic medication order data were available. Primary sample findings were then replicated in an independent white sample of 63 healthy pain-free individuals and 75 individuals with chronic low back pain (CLBP) who provided data regarding laboratory acute pain responsiveness (ischemic task) and chronic pain intensity and unpleasantness (CLBP only). Univariate quantitative trait analyses in the primary sample revealed that 8 KCNJ6 SNPs were significantly associated with the medication order phenotype (P < .05); overall effects of the KCNJ6 gene (gene set-based analysis) just failed to reach significance (P = .054). No significant KCNJ3 effects were observed. A continuous GIRK Related Risk Score (GRRS) was derived in the primary sample to summarize each individual's number of KCNJ6 "pain risk" alleles. This GRRS was applied to the replication sample, which revealed significant associations (P < .05) between higher GRRS values and lower acute pain tolerance and higher CLBP intensity and unpleasantness. Results suggest further exploration of the impact of KCNJ6 genetic variation on pain outcomes is warranted. PMID:23994450

  5. Hsp90 and Environmental Stress Transform the Adaptive Value of Natural Genetic Variation

    E-print Network

    Jarosz, Daniel F.

    How can species remain unaltered for long periods yet also undergo rapid diversification? By linking genetic variation to phenotypic variation via environmental stress, the Hsp90 protein-folding reservoir might promote ...

  6. Individual variation in endocrine systems: moving beyond the `tyranny of the Golden Mean'

    E-print Network

    Review Individual variation in endocrine systems: moving beyond the `tyranny of the Golden Mean and functional significance of phenotypic variation, plasticity and flexibility in endocrine systems, and argue interest to evolutionary biologists (cf. behavioural endocrinology). Keywords: endocrine systems; inter

  7. Copy-Number Variation: The Balance between Gene Dosage and Expression in Drosophila melanogaster

    E-print Network

    Dopman, Erik B.

    . melanogaster genome. Key words: copy-number variation, gene expression, gene dosage sensitivity, recessive CNVCopy-Number Variation: The Balance between Gene Dosage and Expression in Drosophila melanogaster (CNVs) reshape gene structure, modulate gene expression, and contribute to significant phenotypic

  8. Interpopulation Variation in Developmental Titers of Vitellogenin, but Not Storage Proteins, in Lubber Grasshoppers

    E-print Network

    Juliano, Steven A.

    is produced (Travis et al. 1999; Hodin 2000). Such phenotypic variation can arise either by developmental and interpopulation variation in the time courses of hemo- lymph protein titers during oocyte development. The Eastern

  9. Screening of candidate genes and fine mapping of drought tolerance quantitative trait loci on chromosome 4 in rice (Oryza sativa L.) under drought stress.

    PubMed

    Nie, Yuan-Yuan; Zhang, Lin; Wu, Yun-Hua; Liu, Hao-Jie; Mao, Wei-Wei; Du, Juan; Xiu, Hai-Lin; Wu, Xiao-Yu; Li, Xia; Yan, Yu-Wei; Liu, Guo-Lan; Liu, Hong-Yan; Hu, Song-Ping

    2015-11-01

    Due to severe water resource shortage, genetics of and breeding for DT (drought tolerance) in rice (Oryza sativa L.) have become one of the hot research topics. Identification of grain yield QTLs (quantitative trait loci) directly related to the DT trait of rice can provide useful information for breeding new drought-resistant and water-saving rice varieties via marker-assisted selection. A population of 105 advanced BILs (backcross introgression lines) derived from a cross between Zhenshan97B and IRAT109 in Zhenshan97B background were grown under drought stress in a field experiment and phenotypic traits were investigated. The results showed that in the target interval of RM273-RM255 on chromosome 4, three main-effect QTLs related to panicle length, panicle number, and spikelet number per panicle were identified (LOD [logarithm of the odds] > 2.0). The panicle length-related QTL had two loci located in the neighboring intervals of RM17308-RM17305 and RM17349-RM17190, which explained 18.80% and 20.42%, respectively, of the phenotypic variation, while the panicle number-related QTL was identified in the interval of RM1354-RM17308, explaining 11.47% of the phenotypic variation. As far as the spikelet number per panicle-related QTL was concerned, it was found to be located in the interval of RM17308-RM17305, which explained 28.08% of the phenotypic variation. Using the online Plant-GE query system, a total of 13 matched ESTs (expressed sequence tags) were found in the target region, and of the 13 ESTs, 12 had corresponding predicted genes. For instance, the two ESTs CB096766 and CA765747 were corresponded to the same predicted gene LOC_Os04g46370, while the other four ESTs, CA754286, CB000011, CX056247, and CX056240, were corresponded to the same predicted gene LOC_Os04g46390. PMID:26640678

  10. Phenotypic integration in style dimorphic daffodils (Narcissus, Amaryllidaceae) with different pollinators

    PubMed Central

    Pérez-Barrales, Rocío; Simón-Porcar, Violeta I.; Santos-Gally, Rocío; Arroyo, Juan

    2014-01-01

    Different pollinators can exert different selective pressures on floral traits, depending on how they fit with flowers, which should be reflected in the patterns of variation and covariation of traits. Surprisingly, empirical evidence in support of this view is scarce. Here, we have studied whether the variation observed in floral phenotypic integration and covariation of traits in Narcissus species is associated with different groups of pollinators. Phenotypic integration was studied in two style dimorphic species, both with dimorphic populations mostly visited by long-tongued pollinators (close fit with flowers), and monomorphic populations visited by short-tongued insects (loose fit). For N. papyraceus, the patterns of variation and correlation among traits involved in different functions (attraction and fit with pollinators, transfer of pollen) were compared within and between population types. The genetic diversity of populations was also studied to control for possible effects on phenotypic variation. In both species, populations with long-tongued pollinators displayed greater phenotypic integration than those with short-tongued pollinators. Also, the correlations among traits involved in the same function were stronger than across functions. Furthermore, traits involved in the transfer of pollen were consistently more correlated and less variable than traits involved in the attraction of insects, and these differences were larger in dimorphic than monomorphic populations. In addition, population genetic parameters did not correlate with phenotypic integration or variation. Altogether, our results support current views of the role of pollinators in the evolution of floral integration. PMID:25002703

  11. High-throughput behavioral phenotyping in the expanded panel of BXD recombinant inbred strains

    PubMed Central

    Philip, V M; Duvvuru, S; Gomero, B; Ansah, T A; Blaha, C D; Cook, M N; Hamre, K M; Lariviere, W R; Matthews, D B; Mittleman, G; Goldowitz, D; Chesler, E J

    2010-01-01

    Genetic reference populations, particularly the BXD recombinant inbred (BXD RI) strains derived from C57BL/6J and DBA/2J mice, are a valuable resource for the discovery of the bio-molecular substrates and genetic drivers responsible for trait variation and covariation. This approach can be profitably applied in the analysis of susceptibility and mechanisms of drug and alcohol use disorders for which many predisposing behaviors may predict the occurrence and manifestation of increased preference for these substances. Many of these traits are modeled by common mouse behavioral assays, facilitating the detection of patterns and sources of genetic coregulation of predisposing phenotypes and substance consumption. Members of the Tennessee Mouse Genome Consortium (TMGC) have obtained phenotype data from over 250 measures related to multiple behavioral assays across several batteries: response to, and withdrawal from cocaine, 3,4-methylenedioxymethamphetamine; “ecstasy” (MDMA), morphine and alcohol; novelty seeking; behavioral despair and related neurological phenomena; pain sensitivity; stress sensitivity; anxiety; hyperactivity and sleep/wake cycles. All traits have been measured in both sexes in approximately 70 strains of the recently expanded panel of BXD RI strains. Sex differences and heritability estimates were obtained for each trait, and a comparison of early (N = 32) and recent (N = 37) BXD RI lines was performed. Primary data are publicly available for heritability, sex difference and genetic analyses using the MouseTrack database, and are also available in GeneNetwork.org for quantitative trait locus (QTL) detection and genetic analysis of gene expression. Together with the results of related studies, these data form a public resource for integrative systems genetic analysis of neurobehavioral traits. PMID:19958391

  12. Pleiotropy Can Be Effectively Estimated Without Counting Phenotypes Through the Rank of a Genotype–Phenotype Map

    PubMed Central

    Gu, Xun

    2014-01-01

    Although pleiotropy, the capability of a gene to affect multiple phenotypes, has been well known as one of the common gene properties, a quantitative estimation remains a great challenge, simply because of the phenotype complexity. Not surprisingly, it is hard for general readers to understand how, without counting phenotypes, gene pleiotropy can be effectively estimated from the genetics data. In this article we extensively discuss the Gu-2007 method that estimated pleiotropy from the protein sequence analysis. We show that this method is actually to estimate the rank (K) of genotype–phenotype mapping that can be concisely written as K = min(r, Pmin), where Pmin is the minimum pleiotropy among all legitimate measures including the fitness components, and r is the rank of mutational effects of an amino acid site. Together, the effective gene pleiotropy (Ke) estimated by the Gu-2007 method has the following meanings: (i) Ke is an estimate of K = min(r, Pmin), the rank of a genotype–phenotype map; (ii) Ke is an estimate for the minimum pleiotropy Pmin only if Pmin < r; (iii) the Gu-2007 method attempted to estimate the pleiotropy of amino acid sites, a conserved proxy to the true gene pleiotropy; (iv) with a sufficiently large phylogeny such that the rank of mutational effects at an amino acid site is r ? 19, one can estimate Pmin between 1 and 19; and (v) Ke is a conserved estimate of K because those slightly affected components in fitness have been effectively removed by the estimation procedure. In addition, we conclude that mutational pleiotropy (number of traits affected by a single mutation) cannot be estimated without knowing the phenotypes. PMID:24899162

  13. High-Throughput Quantification of Phenotype Heterogeneity Using Statistical Features

    PubMed Central

    Chaddad, Ahmad; Tanougast, Camel

    2015-01-01

    Statistical features are widely used in radiology for tumor heterogeneity assessment using magnetic resonance (MR) imaging technique. In this paper, feature selection based on decision tree is examined to determine the relevant subset of glioblastoma (GBM) phenotypes in the statistical domain. To discriminate between active tumor (vAT) and edema/invasion (vE) phenotype, we selected the significant features using analysis of variance (ANOVA) with p value < 0.01. Then, we implemented the decision tree to define the optimal subset features of phenotype classifier. Naïve Bayes (NB), support vector machine (SVM), and decision tree (DT) classifier were considered to evaluate the performance of the feature based scheme in terms of its capability to discriminate vAT from vE. Whole nine features were statistically significant to classify the vAT from vE with p value < 0.01. Feature selection based on decision tree showed the best performance by the comparative study using full feature set. The feature selected showed that the two features Kurtosis and Skewness achieved a highest range value of 58.33–75.00% accuracy classifier and 73.88–92.50% AUC. This study demonstrated the ability of statistical features to provide a quantitative, individualized measurement of glioblastoma patient and assess the phenotype progression. PMID:26640485

  14. Mechanisms by Which Phenotypic Plasticity Affects Adaptive Divergence and Ecological Speciation.

    PubMed

    Nonaka, Etsuko; Svanbäck, Richard; Thibert-Plante, Xavier; Englund, Göran; Brännström, Åke

    2015-11-01

    Phenotypic plasticity is the ability of one genotype to produce different phenotypes depending on environmental conditions. Several conceptual models emphasize the role of plasticity in promoting reproductive isolation and, ultimately, speciation in populations that forage on two or more resources. These models predict that plasticity plays a critical role in the early stages of speciation, prior to genetic divergence, by facilitating fast phenotypic divergence. The ability to plastically express alternative phenotypes may, however, interfere with the early phase of the formation of reproductive barriers, especially in the absence of geographic barriers. Here, we quantitatively investigate mechanisms under which plasticity can influence progress toward adaptive genetic diversification and ecological speciation. We use a stochastic, individual-based model of a predator-prey system incorporating sexual reproduction and mate choice in the predator. Our results show that evolving plasticity promotes the evolution of reproductive isolation under diversifying environments when individuals are able to correctly select a more profitable habitat with respect to their phenotypes (i.e., adaptive habitat choice) and to assortatively mate with relatively similar phenotypes. On the other hand, plasticity facilitates the evolution of plastic generalists when individuals have a limited capacity for adaptive habitat choice. We conclude that plasticity can accelerate the evolution of a reproductive barrier toward adaptive diversification and ecological speciation through enhanced phenotypic differentiation between diverging phenotypes. PMID:26655782

  15. A testable genotype-phenotype map: modeling evolution of RNA molecules

    NASA Astrophysics Data System (ADS)

    Schuster, Peter

    Recent experiments and progress in modelling evolution in silico converge towards a coherent view of Darwinian evolution in molecular systems. Conventional population genetics and quasi-species theory model evolution in genotype space and properties of phenotypes enter evolutionary dynamics as parameters only. RNA evolution in vitro is an appropriate basis for the development of a new and comprehensive model of evolution, which is focussed on the phenotype and its fit ness relevant properties. Relation between genotypes and phenotypes are described by mappings from genotype space onto a space of phenotypes. These mappings are many-to-one and thus give ample room for neutrality. The RNA model reduces genotype-phenotype relations to a mapping from sequences into secondary structures with minimal free energies and allows to derive otherwise inaccessible quantitative results. RNA sequences that fold into the same structure form neutral networks in genotype space, which deter mine the course of evolution. Neutral networks are embedded in sets of compatible sequences. Intersections of these sets represent regions in sequence space where single molecules can form two or more structures. Continuity and discontinuity in evolution are defined through straightforward interpretation of computer simulations of RNA optimization. In silico evolution provides insight into the accessibility of phenotypes and demonstrate the constructive role of random genetic drift in the search fo r phenotypes of higher fitness. New experimental data, among them the results of genome research, will present a solid basis for test and further development of the model for phenotype evolution.

  16. Linking genotypes database with locus-specific database and genotype-phenotype correlation in phenylketonuria.

    PubMed

    Wettstein, Sarah; Underhaug, Jarl; Perez, Belen; Marsden, Brian D; Yue, Wyatt W; Martinez, Aurora; Blau, Nenad

    2015-03-01

    The wide range of metabolic phenotypes in phenylketonuria is due to a large number of variants causing variable impairment in phenylalanine hydroxylase function. A total of 834 phenylalanine hydroxylase gene variants from the locus-specific database PAHvdb and genotypes of 4181 phenylketonuria patients from the BIOPKU database were characterized using FoldX, SIFT Blink, Polyphen-2 and SNPs3D algorithms. Obtained data was correlated with residual enzyme activity, patients' phenotype and tetrahydrobiopterin responsiveness. A descriptive analysis of both databases was compiled and an interactive viewer in PAHvdb database was implemented for structure visualization of missense variants. We found a quantitative relationship between phenylalanine hydroxylase protein stability and enzyme activity (r(s) = 0.479), between protein stability and allelic phenotype (r(s) = -0.458), as well as between enzyme activity and allelic phenotype (r(s) = 0.799). Enzyme stability algorithms (FoldX and SNPs3D), allelic phenotype and enzyme activity were most powerful to predict patients' phenotype and tetrahydrobiopterin response. Phenotype prediction was most accurate in deleterious genotypes (? 100%), followed by homozygous (92.9%), hemizygous (94.8%), and compound heterozygous genotypes (77.9%), while tetrahydrobiopterin response was correctly predicted in 71.0% of all cases. To our knowledge this is the largest study using algorithms for the prediction of patients' phenotype and tetrahydrobiopterin responsiveness in phenylketonuria patients, using data from the locus-specific and genotypes database. PMID:24939588

  17. Quantification of Facial Skeletal Shape Variation in Fibroblast Growth Factor Receptor-Related Craniosynostosis Syndromes

    PubMed Central

    Heuzé, Yann; Martínez-Abadías, Neus; Stella, Jennifer M.; Arnaud, Eric; Collet, Corinne; Fructuoso, Gemma García; Alamar, Mariana; Lo, Lun-Jou; Boyadjiev, Simeon A.; Di Rocco, Federico; Richtsmeier, Joan T.

    2014-01-01

    Background fibroblast growth factor receptor (FGFR) -related craniosynostosis syndromes are caused by many different mutations within FGFR-1, 2, 3, and certain FGFR mutations are associated with more than one clinical syndrome. These syndromes share coronal craniosynostosis and characteristic facial skeletal features, although Apert syndrome (AS) is characterized by a more dysmorphic facial skeleton relative to Crouzon (CS), Muenke (MS), or Pfeiffer syndromes. Methods Here we perform a detailed three-dimensional evaluation of facial skeletal shape in a retrospective sample of cases clinically and/or genetically diagnosed as AS, CS, MS, and Pfeiffer syndrome to quantify variation in facial dysmorphology, precisely identify specific facial features pertaining to these four syndromes, and further elucidate what knowledge of the causative FGFR mutation brings to our understanding of these syndromes. Results Our results confirm a strong correspondence between genotype and facial phenotype for AS and MS with severity of facial dysmorphology diminishing from Apert FGFR2S252W to Apert FGFR2P253R to MS. We show that AS facial shape variation is increased relative to CS, although CS has been shown to be caused by numerous distinct mutations within FGFRs and reduced dosage in ERF. Conclusion Our quantitative analysis of facial phenotypes demonstrate subtle variation within and among craniosynostosis syndromes that might, with further research, provide information about the impact of the mutation on facial skeletal and nonskeletal development. We suggest that precise studies of the phenotypic consequences of genetic mutations at many levels of analysis should accompany next-generation genetic research and that these approaches should proceed cooperatively. PMID:24578066

  18. Natural variations in Os?TMT contribute to diversity of the ?-tocopherol content in rice.

    PubMed

    Wang, Xiao-Qiang; Yoon, Min-Young; He, Qiang; Kim, Tae-Sung; Tong, Wei; Choi, Bu-Woong; Lee, Young-Sang; Park, Yong-Jin

    2015-12-01

    Tocopherols and tocotrienols, collectively known as tocochromanols, are lipid-soluble molecules that belong to the group of vitamin E compounds. Among them, ?-tocopherol (??) is one of the antioxidants with diverse functions and benefits for humans and animals. Thus, understanding the genetic basis of these traits would be valuable to improve nutritional quality by breeding in rice. Genome-wide association study (GWAS) has emerged as a powerful strategy for identifying genes or quantitative trait loci (QTL) underlying complex traits in plants. To discover the genes or QTLs underlying the naturally occurring variations of ?? content in rice, we performed GWAS using 1.44 million high-quality single-nucleotide polymorphisms acquired from re-sequencing of 137 accessions from a diverse rice core collection. Thirteen candidate genes were found across 2-year phenotypic data, among which gamma-tocopherol methyltransferase (Os?TMT) was identified as the major factor responsible for the ?? content among rice accessions. Nucleotide variations in the coding region of Os?TMT were significantly associated with the ?? content variations, while nucleotide polymorphisms in the promoter region of Os?TMT also could partly demonstrate the correlation with ?? content variations, according to our RNA expression analyses. This study provides useful information for genetic factors underlying ?? content variations in rice, which will significantly contribute the research on ?? biosynthesis mechanisms and ?? improvement of rice. PMID:25990214

  19. Quantitative differences in adhesiveness of type 1 fimbriated Escherichia coli due to structural differences in fimH genes.

    PubMed Central

    Sokurenko, E V; Courtney, H S; Maslow, J; Siitonen, A; Hasty, D L

    1995-01-01

    Type 1 fimbriae are heteropolymeric surface organelles responsible for the D-mannose-sensitive (MS) adhesion of Escherichia coli. We recently reported that variation of receptor specificity of type 1 fimbriae can result solely from minor alterations in the structure of the gene for the FimH adhesin subunit. To further study the relationship between allelic variation of the fimH gene and adhesive properties of type 1 fimbriae, the fimH genes from five additional strains were cloned and used to complement the FimH deletion in E. coli KB18. When the parental and recombinant strains were tested for adhesion to immobilized mannan, a wide quantitative range in the ability of bacteria to adhere was noted. The differences in adhesion do not appear to be due to differences in the levels of fimbriation or relative levels of incorporation of FimH, because these parameters were similar in low-adhesion and high-adhesion strains. The nucleotide sequence for each of the fimH genes was determined. Analysis of deduced FimH sequences allowed identification of two sequence homology groups, based on the presence of Asn-70 and Ser-78 or Ser-70 and Asn-78 residues. The consensus sequences for each group conferred very low adhesion activity, and this low-adhesion phenotype predominated among a group of 43 fecal isolates. Strains isolated from a different host niche, the urinary tract, expressed type 1 fimbriae that conferred an increased level of adhesion. The results presented here strongly suggest that the quantitative variations in MS adhesion are due primarily to structural differences in the FimH adhesin. The observed differences in MS adhesion among populations of E. coli isolated from different host niches call attention to the possibility that phenotypic variants of FimH may play a functional role in populations dynamics. PMID:7601831

  20. Quantitative Genetic Analysis of Thermal Dissipation in Arabidopsis1[W][OA

    PubMed Central

    Jung, Hou-Sung; Niyogi, Krishna K.

    2009-01-01

    Feedback deexcitation is a photosynthetic regulatory mechanism that can protect plants from high light stress by harmlessly dissipating excess absorbed light energy as heat. To understand the genetic basis for intraspecies differences in thermal dissipation capacity, we investigated natural variation in Arabidopsis (Arabidopsis thaliana). We determined the variation in the amount of thermal dissipation by measuring nonphotochemical quenching (NPQ) of chlorophyll fluorescence in Arabidopsis accessions of diverse origins. Ll-1 and Sf-2 were selected as high NPQ Arabidopsis accessions, and Columbia-0 (Col-0) and Wassilewskija-2 were selected as relatively low NPQ accessions. In spite of significant differences in NPQ, previously identified NPQ factors were indistinguishable between the high and the low NPQ accessions. Intermediate levels of NPQ in Ll-1 × Col-0 F1 and Sf-2 × Col-0 F1 compared to NPQ levels in their parental lines and continuous distribution of NPQ in F2 indicated that the variation in NPQ is under the control of multiple nuclear factors. To identify genetic factors responsible for the NPQ variation, we developed a polymorphic molecular marker set for Sf-2 × Col-0 at approximately 10-centimorgan intervals. From quantitative trait locus (QTL) mapping with undistorted genotype data and NPQ measurements in an F2 mapping population, we identified two high NPQ QTLs, HQE1 (high qE 1, for high energy-dependent quenching 1) and HQE2, on chromosomes 1 and 2, and the phenotype of HQE2 was validated by analysis of near isogenic lines. Neither QTL maps to a gene that had been identified previously in extensive forward genetics screens using induced mutants, suggesting that quantitative genetics can be used to find new genes affecting thermal dissipation. PMID:19339502

  1. MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals

    PubMed Central

    Carlson, Keisha D.; Sudmant, Peter H.; Press, Maximilian O.; Eichler, Evan E.; Shendure, Jay; Queitsch, Christine

    2015-01-01

    Short tandem repeats (STRs) are highly mutable genetic elements that often reside in regulatory and coding DNA. The cumulative evidence of genetic studies on individual STRs suggests that STR variation profoundly affects phenotype and contributes to trait heritability. Despite recent advances in sequencing technology, STR variation has remained largely inaccessible across many individuals compared to single nucleotide variation or copy number variation. STR genotyping with short-read sequence data is confounded by (1) the difficulty of uniquely mapping short, low-complexity reads; and (2) the high rate of STR amplification stutter. Here, we present MIPSTR, a robust, scalable, and affordable method that addresses these challenges. MIPSTR uses targeted capture of STR loci by single-molecule Molecular Inversion Probes (smMIPs) and a unique mapping strategy. Targeted capture and our mapping strategy resolve the first challenge; the use of single molecule information resolves the second challenge. Unlike previous methods, MIPSTR is capable of distinguishing technical error due to amplification stutter from somatic STR mutations. In proof-of-principle experiments, we use MIPSTR to determine germline STR genotypes for 102 STR loci with high accuracy across diverse populations of the plant A. thaliana. We show that putatively functional STRs may be identified by deviation from predicted STR variation and by association with quantitative phenotypes. Using DNA mixing experiments and a mutant deficient in DNA repair, we demonstrate that MIPSTR can detect low-frequency somatic STR variants. MIPSTR is applicable to any organism with a high-quality reference genome and is scalable to genotyping many thousands of STR loci in thousands of individuals. PMID:25659649

  2. Trans-eQTLs Reveal That Independent Genetic Variants Associated with a Complex Phenotype Converge on Intermediate Genes, with a Major Role for the HLA

    PubMed Central

    Fehrmann, Rudolf S. N.; Arends, Danny; Bonder, Marc Jan; Fu, Jingyuan; Deelen, Patrick; Groen, Harry J. M.; Smolonska, Asia; Weersma, Rinse K.; Hofstra, Robert M. W.; Buurman, Wim A.; Rensen, Sander; Wolfs, Marcel G. M.; Platteel, Mathieu; Zhernakova, Alexandra; Elbers, Clara C.; Festen, Eleanora M.; Trynka, Gosia; Hofker, Marten H.; Saris, Christiaan G. J.; Ophoff, Roel A.; van den Berg, Leonard H.; van Heel, David A.; Wijmenga, Cisca; te Meerman, Gerard J.; Franke, Lude

    2011-01-01

    For many complex traits, genetic variants have been found associated. However, it is still mostly unclear through which downstream mechanism these variants cause these phenotypes. Knowledge of these intermediate steps is crucial to understand pathogenesis, while also providing leads for potential pharmacological intervention. Here we relied upon natural human genetic variation to identify effects of these variants on trans-gene expression (expression quantitative trait locus mapping, eQTL) in whole peripheral blood from 1,469 unrelated individuals. We looked at 1,167 published trait- or disease-associated SNPs and observed trans-eQTL effects on 113 different genes, of which we replicated 46 in monocytes of 1,490 different individuals and 18 in a smaller dataset that comprised subcutaneous adipose, visceral adipose, liver tissue, and muscle tissue. HLA single-nucleotide polymorphisms (SNPs) were 10-fold enriched for trans-eQTLs: 48% of the trans-acting SNPs map within the HLA, including ulcerative colitis susceptibility variants that affect plausible candidate genes AOAH and TRBV18 in trans. We identified 18 pairs of unlinked SNPs associated with the same phenotype and affecting expression of the same trans-gene (21 times more than expected, P<10?16). This was particularly pronounced for mean platelet volume (MPV): Two independent SNPs significantly affect the well-known blood coagulation genes GP9 and F13A1 but also C19orf33, SAMD14, VCL, and GNG11. Several of these SNPs have a substantially higher effect on the downstream trans-genes than on the eventual phenotypes, supporting the concept that the effects of these SNPs on expression seems to be much less multifactorial. Therefore, these trans-eQTLs could well represent some of the intermediate genes that connect genetic variants with their eventual complex phenotypic outcomes. PMID:21829388

  3. Phenotypic variance explained by local ancestry in admixed African Americans

    PubMed Central

    Shriner, Daniel; Bentley, Amy R.; Doumatey, Ayo P.; Chen, Guanjie; Zhou, Jie; Adeyemo, Adebowale; Rotimi, Charles N.

    2015-01-01

    We surveyed 26 quantitative traits and disease outcomes to understand the proportion of phenotypic variance explained by local ancestry in admixed African Americans. After inferring local ancestry as the number of African-ancestry chromosomes at hundreds of thousands of genotyped loci across all autosomes, we used a linear mixed effects model to estimate the variance explained by local ancestry in two large independent samples of unrelated African Americans. We found that local ancestry at major and polygenic effect genes can explain up to 20 and 8% of phenotypic variance, respectively. These findings provide evidence that most but not all additive genetic variance is explained by genetic markers undifferentiated by ancestry. These results also inform the proportion of health disparities due to genetic risk factors and the magnitude of error in association studies not controlling for local ancestry. PMID:26579196

  4. Journal of Theoretical Biology 240 (2006) 7886 An evolutionary relationship between genetic variation and

    E-print Network

    Kaneko, Kunihiko

    2006-01-01

    of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 2; Phenotype­genotype correspondence 1. Introduction The importance of genetic variation to evolution has been variation and phenotypic fluctuation Kunihiko Kanekoa,b,Ã, Chikara Furusawab,c a Department of Pure

  5. Partial Complementarity of the Mimetic Yellow Bar Phenotype in Heliconius Butterflies

    PubMed Central

    Maroja, Luana S.; Alschuler, Rebecca; McMillan, W. Owen; Jiggins, Chris D.

    2012-01-01

    Heliconius butterflies are an excellent system for understanding the genetic basis of phenotypic change. Here we document surprising diversity in the genetic control of a common phenotype. Two disjunct H. erato populations have each recruited the Cr and/or Sd loci that control similar yellow hindwing patterns, but the alleles involved partially complement one another indicating either multiple origins for the patterning alleles or developmental drift in genetic control of similar patterns. We show that in these H. erato populations cr and sd are epistatically interacting and that the parental origin of alleles can explain phenotypes of backcross individuals. In contrast, mimetic H. melpomene populations with identical phenotypes (H. m. rosina and H. m. amaryllis) do not show genetic complementation (F1s and F2s are phenotypically identical to parentals). Finally, we report hybrid female inviability in H. m. melpomene × H. m. rosina crosses (previously only female infertility had been reported) and presence of standing genetic variation for alternative color alleles at the Yb locus in true breeding H. melpomene melpomene populations (expressed when in a different genomic background) that could be an important source of variation for the evolution of novel phenotypes or a result of developmental drift. Although recent work has emphasized the simple genetic control of wing pattern in Heliconius, we show there is underlying complexity in the allelic variation and epistatic interactions between major patterning loci. PMID:23119074

  6. Partial complementarity of the mimetic yellow bar phenotype in Heliconius butterflies.

    PubMed

    Maroja, Luana S; Alschuler, Rebecca; McMillan, W Owen; Jiggins, Chris D

    2012-01-01

    Heliconius butterflies are an excellent system for understanding the genetic basis of phenotypic change. Here we document surprising diversity in the genetic control of a common phenotype. Two disjunct H. erato populations have each recruited the Cr and/or Sd loci that control similar yellow hindwing patterns, but the alleles involved partially complement one another indicating either multiple origins for the patterning alleles or developmental drift in genetic control of similar patterns. We show that in these H. erato populations cr and sd are epistatically interacting and that the parental origin of alleles can explain phenotypes of backcross individuals. In contrast, mimetic H. melpomene populations with identical phenotypes (H. m. rosina and H. m. amaryllis) do not show genetic complementation (F(1)s and F(2)s are phenotypically identical to parentals). Finally, we report hybrid female inviability in H. m. melpomene × H. m. rosina crosses (previously only female infertility had been reported) and presence of standing genetic variation for alternative color alleles at the Yb locus in true breeding H. melpomene melpomene populations (expressed when in a different genomic background) that could be an important source of variation for the evolution of novel phenotypes or a result of developmental drift. Although recent work has emphasized the simple genetic control of wing pattern in Heliconius, we show there is underlying complexity in the allelic variation and epistatic interactions between major patterning loci. PMID:23119074

  7. Quantitative trait loci for maternal performance for offspring survival in mice.

    PubMed Central

    Peripato, Andréa C; De Brito, Reinaldo A; Vaughn, Ty T; Pletscher, L Susan; Matioli, Sergio R; Cheverud, James M

    2002-01-01

    Maternal performance refers to the effect that the environment provided by mothers has on their offspring's phenotypes, such as offspring survival and growth. Variations in maternal behavior and physiology are responsible for variations in maternal performance, which in turn affects offspring survival. In our study we found females that failed to nurture their offspring and showed abnormal maternal behaviors. The genetic architecture of maternal performance for offspring survival was investigated in 241 females of an F(2) intercross of the SM/J and LG/J inbred mouse strains. Using interval-mapping methods we found two quantitative trait loci (QTL) affecting maternal performance at D2Mit17 + 6 cM and D7Mit21 + 2 cM on chromosomes 2 and 7, respectively. In a two-way genome-wide epistasis scan we found 15 epistatic interactions involving 23 QTL distributed across all chromosomes except 12, 16, and 17. These loci form several small sets of interacting QTL, suggesting a complex set of mechanisms operating to determine maternal performance for offspring survival. Taken all together and correcting for the large number of significant factors, QTL and their interactions explain almost 35% of the phenotypic variation for maternal performance for offspring survival in this cross. This study allowed the identification of many possible candidate genes, as well as the relative size of gene effects and patterns of gene action affecting maternal performance in mice. Detailed behavior observation of mothers from later generations suggests that offspring survival in the first week is related to maternal success in building nests, grooming their pups, providing milk, and/or manifesting aggressive behavior against intruders. PMID:12454078

  8. Rethinking inheritance, yet again: inheritomes, contextomes and dynamic phenotypes.

    PubMed

    Prasad, N G; Dey, Sutirth; Joshi, Amitabh; Vidya, T N C

    2015-09-01

    In recent years, there have been many calls for an extended evolutionary synthesis, based in part upon growing evidence for nongenetic mechanisms of inheritance, i.e., similarities in phenotype between parents and offspring that are not due to shared genes. While there has been an impressive marshalling of evidence for diverse forms of nongenetic inheritance (epigenetic, ecological, behavioural and symbolic), there have been relatively few studies trying to integrate the different forms of inheritance into a common conceptual structure, a development that would be important to formalize elements of the extended evolutionary synthesis. Here, we propose a framework for an extended view of inheritance and introduce some conceptual distinctions that we believe, are important to this issue. In this framework, the phenotype is conceived of as a dynamic entity, its state, at any point in time resulting from intertwined effects of previous phenotypic state, and of hereditary materials (DNA and otherwise) and environment. We contrast our framework with the standard gene-based view of inheritance, and also discuss our framework in the specific context of recent attempts to accommodate nongenetic inheritance within the framework of classical quantitative genetics and the Price equation. In particular, we believe that the extended view of inheritance and effects on the phenotype developed here is particularly well-suited to individual-based simulation studies of evolutionary dynamics. The results of such simulations, in turn, could be useful for assessing, how well extended models based on quantitative genetics or the Price equation perform at capturing complex evolutionary dynamics. PMID:26440075

  9. Natural variation and genetic covariance in adult hippocampal neurogenesis

    SciTech Connect

    Kempermann, Gerd; Chesler, Elissa J; Lu, Lu; Williams, Robert; Gage, Fred

    2006-01-01

    Adult hippocampal neurogenesis is highly variable and heritable among laboratory strains of mice. Adult neurogenesis is also remarkably plastic and can be modulated by environment and activity. Here, we provide a systematic quantitative analysis of adult hippocampal neurogenesis in two large genetic reference panels of recombinant inbred strains (BXD and AXB?BXA, n ? 52 strains). We combined data on variation in neurogenesis with a new transcriptome database to extract a set of 190 genes with expression patterns that are also highly variable and that covary with rates of (i) cell proliferation, (ii) cell survival, or the numbers of surviving (iii) new neurons, and (iv) astrocytes. Expression of a subset of these neurogenesis-associated transcripts was controlled in cis across the BXD set. These self-modulating genes are particularly interesting candidates to control neurogenesis. Among these were musashi (Msi1h) and prominin1?CD133 (Prom1), both of which are linked to stem-cell maintenance and division. Twelve neurogenesis-associated transcripts had significant cis-acting quantitative trait loci, and, of these, six had plausible biological association with adult neurogenesis (Prom1, Ssbp2, Kcnq2, Ndufs2, Camk4, and Kcnj9). Only one cis- cting candidate was linked to both neurogenesis and gliogenesis, Rapgef6, a downstream target of ras signaling. The use of genetic reference panels coupled with phenotyping and global transcriptome profiling thus allowed insight into the complexity of the genetic control of adult neurogenesis.

  10. Application of an Effective Statistical Technique for an Accurate and Powerful Mining of Quantitative Trait Loci for Rice Aroma Trait

    PubMed Central

    Golestan Hashemi, Farahnaz Sadat; Rafii, Mohd Y.; Ismail, Mohd Razi; Mohamed, Mahmud Tengku Muda; Rahim, Harun A.; Latif, Mohammad Abdul; Aslani, Farzad

    2015-01-01

    When a phenotype of interest is associated with an external/internal covariate, covariate inclusion in quantitative trait loci (QTL) analyses can diminish residual variation and subsequently enhance the ability of QTL detection. In the in vitro synthesis of 2-acetyl-1-pyrroline (2AP), the main fragrance compound in rice, the thermal processing during the Maillard-type reaction between proline and carbohydrate reduction produces a roasted, popcorn-like aroma. Hence, for the first time, we included the proline amino acid, an important precursor of 2AP, as a covariate in our QTL mapping analyses to precisely explore the genetic factors affecting natural variation for rice scent. Consequently, two QTLs were traced on chromosomes 4 and 8. They explained from 20% to 49% of the total aroma phenotypic variance. Additionally, by saturating the interval harboring the major QTL using gene-based primers, a putative allele of fgr (major genetic determinant of fragrance) was mapped in the QTL on the 8th chromosome in the interval RM223-SCU015RM (1.63 cM). These loci supported previous studies of different accessions. Such QTLs can be widely used by breeders in crop improvement programs and for further fine mapping. Moreover, no previous studies and findings were found on simultaneous assessment of the relationship among 2AP, proline and fragrance QTLs. Therefore, our findings can help further our understanding of the metabolomic and genetic basis of 2AP biosynthesis in aromatic rice. PMID:26061689

  11. The colour of an avifauna: A quantitative analysis of the colour of Australian birds

    PubMed Central

    Delhey, Kaspar

    2015-01-01

    Animal coloration is a poorly-understood aspect of phenotypic variability. Here I expand initial studies of the colour gamut of birds by providing the first quantitative description of the colour variation of an entire avifauna: Australian landbirds (555 species). The colour of Australian birds occupies a small fraction (19%) of the entire possible colour space and colour variation is extremely uneven. Most colours are unsaturated, concentrated in the centre of colour space and based on the deposition of melanins. Other mechanisms of colour production are less common but account for larger portions of colour space and for most saturated colours. Male colours occupy 45–25% more colour space than female colours, indicating that sexual dichromatism translates into a broader range of male colours. Male-exclusive colours are often saturated, at the edge of chromatic space, and have most likely evolved for signalling. While most clades of birds occupy expected or lower-than-expected colour volumes, parrots and cockatoos (Order Psittaciformes) occupy a much larger volume than expected. This uneven distribution of colour variation across mechanisms of colour production, sexes and clades is probably shared by avifaunas in other parts of the world, but this remains to be tested with comparable data. PMID:26679370

  12. The colour of an avifauna: A quantitative analysis of the colour of Australian birds.

    PubMed

    Delhey, Kaspar

    2015-01-01

    Animal coloration is a poorly-understood aspect of phenotypic variability. Here I expand initial studies of the colour gamut of birds by providing the first quantitative description of the colour variation of an entire avifauna: Australian landbirds (555 species). The colour of Australian birds occupies a small fraction (19%) of the entire possible colour space and colour variation is extremely uneven. Most colours are unsaturated, concentrated in the centre of colour space and based on the deposition of melanins. Other mechanisms of colour production are less common but account for larger portions of colour space and for most saturated colours. Male colours occupy 45-25% more colour space than female colours, indicating that sexual dichromatism translates into a broader range of male colours. Male-exclusive colours are often saturated, at the edge of chromatic space, and have most likely evolved for signalling. While most clades of birds occupy expected or lower-than-expected colour volumes, parrots and cockatoos (Order Psittaciformes) occupy a much larger volume than expected. This uneven distribution of colour variation across mechanisms of colour production, sexes and clades is probably shared by avifaunas in other parts of the world, but this remains to be tested with comparable data. PMID:26679370

  13. Quantitative genetic variance and multivariate clines in the Ivyleaf morning glory, Ipomoea hederacea

    PubMed Central

    Stock, Amanda J.; Campitelli, Brandon E.; Stinchcombe, John R.

    2014-01-01

    Clinal variation is commonly interpreted as evidence of adaptive differentiation, although clines can also be produced by stochastic forces. Understanding whether clines are adaptive therefore requires comparing clinal variation to background patterns of genetic differentiation at presumably neutral markers. Although this approach has frequently been applied to single traits at a time, we have comparatively fewer examples of how multiple correlated traits vary clinally. Here, we characterize multivariate clines in the Ivyleaf morning glory, examining how suites of traits vary with latitude, with the goal of testing for divergence in trait means that would indicate past evolutionary responses. We couple this with analysis of genetic variance in clinally varying traits in 20 populations to test whether past evolutionary responses have depleted genetic variance, or whether genetic variance declines approaching the range margin. We find evidence of clinal differentiation in five quantitative traits, with little evidence of isolation by distance at neutral loci that would suggest non-adaptive or stochastic mechanisms. Within and across populations, the traits that contribute most to population differentiation and clinal trends in the multivariate phenotype are genetically variable as well, suggesting that a lack of genetic variance will not cause absolute evolutionary constraints. Our data are broadly consistent theoretical predictions of polygenic clines in response to shallow environmental gradients. Ecologically, our results are consistent with past findings of natural selection on flowering phenology, presumably due to season-length variation across the range. PMID:25002704

  14. Towards improving phenotype representation in OWL

    E-print Network

    Loebe, Frank; Stumpf, Frank; Hoehndorf, Robert; Herre, Heinrich

    2012-09-21

    known [3]. To standardize the terminology used in describing phenotypes, multiple species- specific phenotype ontologies were developed. For example, the Mammalian Phenotype Ontology (MP) [4,5] is used to characterize phenotypes in mice and other mammals... by verbs, participles can be used as role names in many cases. Admittedly, that approach likely requires manual care and checking, e.g. remembering the remarks on misinterpret- ing the roles of concentration of (PATO:0000033) in the section Ontological...

  15. Strong and parallel salinity-induced phenotypic plasticity in one generation of threespine stickleback.

    PubMed

    Mazzarella, A B; Voje, K L; Hansson, T H; Taugbøl, A; Fischer, B

    2015-03-01

    Phenotypic plasticity is a major factor contributing to variation of organisms in nature, yet its evolutionary significance is insufficiently understood. One example system where plasticity might have played an important role in an adaptive radiation is the threespine stickleback (Gasterosteus aculeatus), a fish that has diversified after invading freshwater lakes repeatedly from the marine habitat. The parallel phenotypic changes that occurred in this radiation were extremely rapid. This study evaluates phenotypic plasticity in stickleback body shape in response to salinity in fish stemming from a wild freshwater population. Using a split-clutch design, we detected surprisingly large phenotypically plastic changes in body shape after one generation. Fish raised in salt water developed shallower bodies and longer jaws, and these changes were consistent and parallel across families. Although this work highlights the effect of phenotypic plasticity, we also find indications that constraints may play a role in biasing the direction of possible phenotypic change. The slopes of the allometric relationship of individual linear traits did not change across treatments, indicating that plastic change does not affect the covariation of traits with overall size. We conclude that stickleback have a large capacity for plastic phenotypic change in response to salinity and that plasticity and evolutionary constraints have likely contributed to the phenotypic diversification of these fish. PMID:25656304

  16. Does plasticity enhance or dampen phenotypic parallelism? A test with three lake-stream stickleback pairs.

    PubMed

    Oke, K B; Bukhari, M; Kaeuffer, R; Rolshausen, G; Räsänen, K; Bolnick, D I; Peichel, C L; Hendry, A P

    2016-01-01

    Parallel (and convergent) phenotypic variation is most often studied in the wild, where it is difficult to disentangle genetic vs. environmentally induced effects. As a result, the potential contributions of phenotypic plasticity to parallelism (and nonparallelism) are rarely evaluated in a formal sense. Phenotypic parallelism could be enhanced by plasticity that causes stronger parallelism across populations in the wild than would be expected from genetic differences alone. Phenotypic parallelism could be dampened if site-specific plasticity induced differences between otherwise genetically parallel populations. We used a common-garden study of three independent lake-stream stickleback population pairs to evaluate the extent to which adaptive divergence has a genetic or plastic basis, and to investigate the enhancing vs. dampening effects of plasticity on phenotypic parallelism. We found that lake-stream differences in most traits had a genetic basis, but that several traits also showed contributions from plasticity. Moreover, plasticity was much more prevalent in one watershed than in the other two. In most cases, plasticity enhanced phenotypic parallelism, whereas in a few cases, plasticity had a dampening effect. Genetic and plastic contributions to divergence seem to play a complimentary, likely adaptive, role in phenotypic parallelism of lake-stream stickleback. These findings highlight the value of formally comparing wild-caught and laboratory-reared individuals in the study of phenotypic parallelism. PMID:26411538

  17. The topology of robustness and evolvability in evolutionary systems with genotype-phenotype map.

    PubMed

    Ibáñez-Marcelo, Esther; Alarcón, Tomás

    2014-09-01

    In this paper we formulate a topological definition of the concepts of robustness and evolvability. We start our investigation by formulating a multiscale model of the evolutionary dynamics of a population of cells. Our cells are characterised by a genotype-phenotype map: their chances of survival under selective pressure are determined by their phenotypes, whereas the latter are determined their genotypes. According to our multiscale dynamics, the population dynamics generates the evolution of a genotype-phenotype network. Our representation of the genotype-phenotype network is similar to previously described ones, but has a novel element, namely, our network contains two types of nodes: genotype and phenotype nodes. This network representation allows us to characterise robustness and evolvability in terms of its topological properties: phenotypic robustness by means of the clustering coefficient of the phenotype nodes, and evolvability as the emergence of giant connected component which allows navigation between phenotypes. This topological definition of evolvability allows us to characterise the so-called robustness of evolvability, which is defined in terms of the robustness against attack (i.e. edge removal) of the giant connected component. An investigation of the factors that affect the robustness of evolvability shows that phenotypic robustness and the cryptic genetic variation are key to the integrity of the ability to innovate. These results fit within the framework of a number of models which point out that robustness favours rather than hindering evolvability. We further show that the corresponding phenotype network, defined as the one-component projection of the whole genotype-phenotype network, exhibits the small-world phenomenon, which implies that in this type of evolutionary system the rate of adaptability is enhanced. PMID:24793533

  18. Bayesian model determination for quantitative trait Jaya M. Satagopan

    E-print Network

    Yandell, Brian S.

    -maker genetic distances. Given such molecular marker information, the probability distribution of the unobserved Markov chain Monte Carlo (MCMC) algorithm is illustrated to infer the number of quantitative trait loci (QTL) a ecting a phenotypic trait, their chromosomallocations, and their e ects. A multi

  19. Quantitative trait locus mapping of gravitaxis behaviour in Drosophila melanogaster

    E-print Network

    Sokolowski, Marla

    . Drosophila melanogaster is an excellent model organism to study the genetic basis of behavioural response by Erlenmeyer-Kimling & Hirsch (1961) to demonstrate that a behavioural phenotype can be analysed geneticallyQuantitative trait locus mapping of gravitaxis behaviour in Drosophila melanogaster CHRISTIE E

  20. Natural variation in epigenetic pathways affects the specification of female gamete precursors in Arabidopsis.

    PubMed

    Rodríguez-Leal, Daniel; León-Martínez, Gloria; Abad-Vivero, Ursula; Vielle-Calzada, Jean-Philippe

    2015-04-01

    In angiosperms, the transition to the female gametophytic phase relies on the specification of premeiotic gamete precursors from sporophytic cells in the ovule. In Arabidopsis thaliana, a single diploid cell is specified as the premeiotic female gamete precursor. Here, we show that ecotypes of Arabidopsis exhibit differences in megasporogenesis leading to phenotypes reminiscent of defects in dominant mutations that epigenetically affect the specification of female gamete precursors. Intraspecific hybridization and polyploidy exacerbate these defects, which segregate quantitatively in F2 populations derived from ecotypic hybrids, suggesting that multiple loci control cell specification at the onset of female meiosis. This variation in cell differentiation is influenced by the activity of ARGONAUTE9 (AGO9) and RNA-DEPENDENT RNA POLYMERASE6 (RDR6), two genes involved in epigenetic silencing that control the specification of female gamete precursors. The pattern of transcriptional regulation and localization of AGO9 varies among ecotypes, and abnormal gamete precursors in ovules defective for RDR6 share identity with ectopic gamete precursors found in selected ecotypes. Our results indicate that differences in the epigenetic control of cell specification lead to natural phenotypic variation during megasporogenesis. We propose that this mechanism could be implicated in the emergence and evolution of the reproductive alternatives that prevail in flowering plants. PMID:25829442

  1. Natural Variation in Epigenetic Pathways Affects the Specification of Female Gamete Precursors in Arabidopsis[OPEN

    PubMed Central

    Rodríguez-Leal, Daniel; León-Martínez, Gloria; Abad-Vivero, Ursula; Vielle-Calzada, Jean-Philippe

    2015-01-01

    In angiosperms, the transition to the female gametophytic phase relies on the specification of premeiotic gamete precursors from sporophytic cells in the ovule. In Arabidopsis thaliana, a single diploid cell is specified as the premeiotic female gamete precursor. Here, we show that ecotypes of Arabidopsis exhibit differences in megasporogenesis leading to phenotypes reminiscent of defects in dominant mutations that epigenetically affect the specification of female gamete precursors. Intraspecific hybridization and polyploidy exacerbate these defects, which segregate quantitatively in F2 populations derived from ecotypic hybrids, suggesting that multiple loci control cell specification at the onset of female meiosis. This variation in cell differentiation is influenced by the activity of ARGONAUTE9 (AGO9) and RNA-DEPENDENT RNA POLYMERASE6 (RDR6), two genes involved in epigenetic silencing that control the specification of female gamete precursors. The pattern of transcriptional regulation and localization of AGO9 varies among ecotypes, and abnormal gamete precursors in ovules defective for RDR6 share identity with ectopic gamete precursors found in selected ecotypes. Our results indicate that differences in the epigenetic control of cell specification lead to natural phenotypic variation during megasporogenesis. We propose that this mechanism could be implicated in the emergence and evolution of the reproductive alternatives that prevail in flowering plants. PMID:25829442

  2. Comparative analysis of marker-assisted and phenotypic selection in cucumber

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Previously developed marker-trait associations in cucumber (Cucumus sativus L.) were employed to compare the effectiveness of marker-assisted selection (MAS; genotyping with 20 molecular markers) to phenotypic selection (PHE; open-field evaluations) for multiple, quantitative traits. Four inbred li...

  3. Phosphate uptake in Saccharomyces cerevisiae Hansen wild type and phenotypes exposed to space flight irradiation.

    PubMed

    Berry, D; Volz, P A

    1979-10-01

    Rates of phosphate uptake were approximately twice as great for Saccharomyces cerevisiae single-cell phenotypic isolates exposed to space parameters as for the wild-type ground control. Quantitative determination of 32P was performed by liquid scintillation spectrometry utilizing Cerenkov radiation counting techniques. PMID:395899

  4. The G-Matrix as One Piece of the Phenotypic Evolution Puzzle Sean H. Rice

    E-print Network

    Rice, Sean

    COMMENTARY The G-Matrix as One Piece of the Phenotypic Evolution Puzzle Sean H. Rice Received: 5, a single term, the genetic covari- ance matrix (G-matrix), is used to encompass all important associations quantitative geneticists have argued that the G-matrix is a sufficient descriptor of the ways in which

  5. From cellular characteristics to disease diagnosis: uncovering phenotypes with supercells.

    PubMed

    Candia, Julián; Maunu, Ryan; Driscoll, Meghan; Biancotto, Angélique; Dagur, Pradeep; McCoy, J Philip; Sen, H Nida; Wei, Lai; Maritan, Amos; Cao, Kan; Nussenblatt, Robert B; Banavar, Jayanth R; Losert, Wolfgang

    2013-01-01

    Cell heterogeneity and the inherent complexity due to the interplay of multiple molecular processes within the cell pose difficult challenges for current single-cell biology. We introduce an approach that identifies a disease phenotype from multiparameter single-cell measurements, which is based on the concept of "supercell statistics", a single-cell-based averaging procedure followed by a machine learning classification scheme. We are able to assess the optimal tradeoff between the number of single cells averaged and the number of measurements needed to capture phenotypic differences between healthy and diseased patients, as well as between different diseases that are difficult to diagnose otherwise. We apply our approach to two kinds of single-cell datasets, addressing the diagnosis of a premature aging disorder using images of cell nuclei, as well as the phenotypes of two non-infectious uveitides (the ocular manifestations of Behçet's disease and sarcoidosis) based on multicolor flow cytometry. In the former case, one nuclear shape measurement taken over a group of 30 cells is sufficient to classify samples as healthy or diseased, in agreement with usual laboratory practice. In the latter, our method is able to identify a minimal set of 5 markers that accurately predict Behçet's disease and sarcoidosis. This is the first time that a quantitative phenotypic distinction between these two diseases has been achieved. To obtain this clear phenotypic signature, about one hundred CD8(+) T cells need to be measured. Although the molecular markers identified have been reported to be important players in autoimmune disorders, this is the first report pointing out that CD8(+) T cells can be used to distinguish two systemic inflammatory diseases. Beyond these specific cases, the approach proposed here is applicable to datasets generated by other kinds of state-of-the-art and forthcoming single-cell technologies, such as multidimensional mass cytometry, single-cell gene expression, and single-cell full genome sequencing techniques. PMID:24039568

  6. Comparative quantitative trait loci for silique length and seed weight in Brassica napus.

    PubMed

    Fu, Ying; Wei, Dayong; Dong, Hongli; He, Yajun; Cui, Yixin; Mei, Jiaqin; Wan, Huafang; Li, Jiana; Snowdon, Rod; Friedt, Wolfgang; Li, Xiaorong; Qian, Wei

    2015-01-01

    Silique length (SL) and seed weight (SW) are important yield-associated traits in rapeseed (Brassica napus). Although many quantitative trait loci (QTL) for SL and SW have been identified in B. napus, comparative analysis for those QTL is seldom performed. In the present study, 20 and 21 QTL for SL and SW were identified in doubled haploid (DH) and DH-derived reconstructed F2 populations in rapeseed, explaining 55.1-74.3% and 24.4-62.9% of the phenotypic variation across three years, respectively. Of which, 17 QTL with partially or completely overlapped confidence interval on chromosome A09, were homologous with two overlapped QTL on chromosome C08 by aligning QTL confidence intervals with the reference genomes of Brassica crops. By high density selective genotyping of DH lines with extreme phenotypes, using a Brassica single-nucleotide polymorphism (SNP) array, the QTL on chromosome A09 was narrowed, and aligned into 1.14-Mb region from 30.84 to 31.98?Mb on chromosome R09 of B. rapa and 1.05-Mb region from 27.21 to 28.26?Mb on chromosome A09 of B. napus. The alignment of QTL with Brassica reference genomes revealed homologous QTL on A09 and C08 for SL. The narrowed QTL region provides clues for gene cloning and breeding cultivars by marker-assisted selection. PMID:26394547

  7. Comparative quantitative trait loci for silique length and seed weight in Brassica napus

    PubMed Central

    Fu, Ying; Wei, Dayong; Dong, Hongli; He, Yajun; Cui, Yixin; Mei, Jiaqin; Wan, Huafang; Li, Jiana; Snowdon, Rod; Friedt, Wolfgang; Li, Xiaorong; Qian, Wei

    2015-01-01

    Silique length (SL) and seed weight (SW) are important yield-associated traits in rapeseed (Brassica napus). Although many quantitative trait loci (QTL) for SL and SW have been identified in B. napus, comparative analysis for those QTL is seldom performed. In the present study, 20 and 21 QTL for SL and SW were identified in doubled haploid (DH) and DH-derived reconstructed F2 populations in rapeseed, explaining 55.1–74.3% and 24.4–62.9% of the phenotypic variation across three years, respectively. Of which, 17 QTL with partially or completely overlapped confidence interval on chromosome A09, were homologous with two overlapped QTL on chromosome C08 by aligning QTL confidence intervals with the reference genomes of Brassica crops. By high density selective genotyping of DH lines with extreme phenotypes, using a Brassica single-nucleotide polymorphism (SNP) array, the QTL on chromosome A09 was narrowed, and aligned into 1.14-Mb region from 30.84 to 31.98?Mb on chromosome R09 of B. rapa and 1.05-Mb region from 27.21 to 28.26?Mb on chromosome A09 of B. napus. The alignment of QTL with Brassica reference genomes revealed homologous QTL on A09 and C08 for SL. The narrowed QTL region provides clues for gene cloning and breeding cultivars by marker-assisted selection. PMID:26394547

  8. Integrating the genotype and phenotype in hominid paleontology

    PubMed Central

    Hlusko, Leslea J.

    2004-01-01

    Competing interpretations of human origins and evolution have recently proliferated despite the accelerated pace of fossil discovery. These controversies parallel those involving other vertebrate families and result from the difficulty of studying evolution among closely related species. Recent advances in developmental and quantitative genetics show that some conventions routinely used by hominid and other mammalian paleontologists are unwarranted. These same advances provide ways to integrate knowledge of the genotype into the study of the phenotype. The result is an approach that promises to yield a fuller understanding of evolution below the family level. PMID:14967810

  9. Perception Viewed as a Phenotypic Expression Perception Viewed as a Phenotypic Expression

    E-print Network

    Perception Viewed as a Phenotypic Expression 1 Perception Viewed as a Phenotypic Expression Dennis Cybernetics Proffitt, D.R. and Linkenauger, S.A. (in press). Perception viewed as a phenotypic expression: Perception Viewed as a Phenotypic Expression Correspondence: Dennis Proffitt Department of Psychology

  10. Neurocognitive Phenotypes and Genetic Dissection of Disorders of Brain and Behavior

    PubMed Central

    Congdon, Eliza; Poldrack, Russell A.; Freimer, Nelson B.

    2014-01-01

    Summary Elucidating the molecular mechanisms underlying quantitative neurocognitive phenotypes will further our understanding of the brain’s structural and functional architecture and advance the diagnosis and treatment of the psychiatric disorders that these traits underlie. Although many neurocognitive traits are highly heritable, little progress has been made in identifying genetic variants unequivocally associated with these phenotypes. A major obstacle to such progress is the difficulty in identifying heritable neurocognitive measures which are precisely defined, systematically assessed and represent unambiguous mental constructs, yet are amenable to the high-throughput phenotyping necessary to obtain adequate power for genetic association studies. In this perspective we compare the current status of genetic investigations of neurocognitive phenotypes to that of other categories of biomedically relevant traits and suggest strategies for genetically dissecting traits that may underlie disorders of brain and behavior. PMID:20955930

  11. Have studies of the developmental regulation of behavioral phenotypes revealed the mechanisms of gene-environment interactions?

    PubMed Central

    Hall, F. Scott; Perona, Maria T. G.

    2012-01-01

    This review addresses the recent convergence of our long-standing knowledge of the regulation of behavioral phenotypes by developmental experience with recent advances in our understanding of mechanisms regulating gene expression. This review supports a particular perspective on the developmental regulation of behavioral phenotypes: That the role of common developmental experiences (e.g. maternal interactions, peer interactions, exposure to a complex environment, etc.) is to fit individuals to the circumstances of their lives within bounds determined by long-standing (evolutionary) mechanisms that have shaped responses to critical and fundamental types of experience via those aspects of gene structure that regulate gene expression. The phenotype of a given species is not absolute for a given genotype but rather variable within bounds that are determined by mechanisms regulated by experience (e.g. epigenetic mechanisms). This phenotypic variation is not necessarily random, or evenly distributed along a continuum of description or measurement, but often highly disjointed, producing distinct, even opposing, phenotypes. The potentiality for these varying phenotypes is itself the product of evolution, the potential for alternative phenotypes itself conveying evolutionary advantage. Examples of such phenotypic variation, resulting from environmental or experiential influences, have a long history of study in neurobiology, and a number of these will be discussed in this review: neurodevelopmental experiences that produce phenotypic variation in visual perception, cognitive function, and emotional behavior. Although other examples will be discussed, particular emphasis will be made on the role of social behavior on neurodevelopment and phenotypic determination. It will be argued that an important purpose of some aspects of social behavior is regulation of neurobehavioral phenotypes by experience via genetic regulatory mechanisms. PMID:22643448

  12. Quantitative Trait Locus Mapping of Yield-Related Components and Oligogenic Control of the Cap Color of the Button Mushroom, Agaricus bisporus

    PubMed Central

    Rodier, Anne; Rousseau, Thierry; Savoie, Jean-Michel

    2012-01-01

    As in other crops, yield is an important trait to be selected for in edible mushrooms, but its inheritance is poorly understood. Therefore, we have investigated the complex genetic architecture of yield-related traits in Agaricus bisporus through the mapping of quantitative trait loci (QTL), using second-generation hybrid progeny derived from a cross between a wild strain and a commercial cultivar. Yield, average weight per mushroom, number of fruiting bodies per m2, earliness, and cap color were evaluated in two independent experiments. A total of 23 QTL were detected for 7 yield-related traits. These QTL together explained between 21% (two-flushes yield) and 59% (earliness) of the phenotypic variation. Fifteen QTL (65%) were consistent between the two experiments. Four regions underlying significant QTL controlling yield, average weight, and number were detected on linkage groups II, III, IV, and X, suggesting a pleiotropic effect or tight linkage. Up to six QTL were identified for earliness. The PPC1 locus, together with two additional genomic regions, explained up to 90% of the phenotypic variation of the cap color. Alleles from the wild parent showed beneficial effects for some yield traits, suggesting that the wild germ plasm is a valuable source of variation for several agronomic traits. Our results constitute a key step toward marker-assisted selection and provide a solid foundation to go further into the biological mechanisms controlling productive traits in the button mushroom. PMID:22267676

  13. [Plasticity of the cellular phenotype].

    PubMed

    Chneiweiss, Hervé

    2011-01-01

    The tragical consequences of the Hiroshima and Nagasaki atomic bombs in 1945 were to lead to the discovery of hematopoietic stem cells and their phenotypic plasticity, in response to environmental factors. These concepts were much later extended to the founding cells of other tissues. In the following collection of articles, the mechanisms underlying this plasticity, at the frontiers of developmental biology and oncology, are illustrated in the case of various cell types of neural origin and of some tumours. PMID:21501574

  14. Phenotypic plasticity in evolutionary rescue experiments

    PubMed Central

    Chevin, Luis-Miguel; Gallet, Romain; Gomulkiewicz, Richard; Holt, Robert D.; Fellous, Simon

    2013-01-01

    Population persistence in a new and stressful environment can be influenced by the plastic phenotypic responses of individuals to this environment, and by the genetic evolution of plasticity itself. This process has recently been investigated theoretically, but testing the quantitative predictions in the wild is challenging because (i) there are usually not enough population replicates to deal with the stochasticity of the evolutionary process, (ii) environmental conditions are not controlled, and (iii) measuring selection and the inheritance of traits affecting fitness is difficult in natural populations. As an alternative, predictions from theory can be tested in the laboratory with controlled experiments. To illustrate the feasibility of this approach, we briefly review the literature on the experimental evolution of plasticity, and on evolutionary rescue in the laboratory, paying particular attention to differences and similarities between microbes and multicellular eukaryotes. We then highlight a set of questions that could be addressed using this framework, which would enable testing the robustness of theoretical predictions, and provide new insights into areas that have received little theoretical attention to date. PMID:23209170

  15. Molecular-Marker-Facilitated Investigations of Quantitative-Trait Loci in Maize. I. Numbers, Genomic Distribution and Types of Gene Action

    PubMed Central

    Edwards, M. D.; Stuber, C. W.; Wendel, J. F.

    1987-01-01

    Individual genetic factors which underlie variation in quantitative traits of maize were investigated in each of two F2 populations by examining the mean trait expressions of genotypic classes at each of 17–20 segregating marker loci. It was demonstrated that the trait expression of marker locus classes could be interpreted in terms of genetic behavior at linked quantitative trait loci (QTLs). For each of 82 traits evaluated, QTLs were detected and located to genomic sites. The numbers of detected factors varied according to trait, with the average trait significantly influenced by almost two-thirds of the marked genomic sites. Most of the detected associations between marker loci and quantitative traits were highly significant, and could have been detected with fewer than the 1800–1900 plants evaluated in each population. The cumulative, simple effects of marker-linked regions of the genome explained between 8 and 40% of the phenotypic variation for a subset of 25 traits evaluated. Single marker loci accounted for between 0.3% and 16% of the phenotypic variation of traits. Individual plant heterozygosity, as measured by marker loci, was significantly associated with variation in many traits. The apparent types of gene action at the QTLs varied both among traits and between loci for given traits, although overdominance appeared frequently, especially for yield-related traits. The prevalence of apparent overdominance may reflect the effects of multiple QTLs within individual marker-linked regions, a situation which would tend to result in overestimation of dominance. Digenic epistasis did not appear to be important in determining the expression of the quantitative traits evaluated. Examination of the effects of marked regions on the expression of pairs of traits suggests that genomic regions vary in the direction and magnitudes of their effects on trait correlations, perhaps providing a means of selecting to dissociate some correlated traits. Marker-facilitated investigations appear to provide a powerful means of examining aspects of the genetic control of quantitative traits. Modifications of the methods employed herein will allow examination of the stability of individual gene effects in varying genetic backgrounds and environments. PMID:3596228

  16. Extent of QTL Reuse During Repeated Phenotypic Divergence of Sympatric Threespine Stickleback.

    PubMed

    Conte, Gina L; Arnegard, Matthew E; Best, Jacob; Chan, Yingguang Frank; Jones, Felicity C; Kingsley, David M; Schluter, Dolph; Peichel, Catherine L

    2015-11-01

    How predictable is the genetic basis of phenotypic adaptation? Answering this question begins by estimating the repeatability of adaptation at the genetic level. Here, we provide a comprehensive estimate of the repeatability of the genetic basis of adaptive phenotypic evolution in a natural system. We used quantitative trait locus (QTL) mapping to discover genomic regions controlling a large number of morphological traits that have diverged in parallel between pairs of threespine stickleback (Gasterosteus aculeatus species complex) in Paxton and Priest lakes, British Columbia. We found that nearly half of QTL affected the same traits in the same direction in both species pairs. Another 40% influenced a parallel phenotypic trait in one lake but not the other. The remaining 10% of QTL had phenotypic effects in opposite directions in the two species pairs. Similarity in the proportional contributions of all QTL to parallel trait differences was about 0.4. Surprisingly, QTL reuse was unrelated to phenotypic effect size. Our results indicate that repeated use of the same genomic regions is a pervasive feature of parallel phenotypic adaptation, at least in sticklebacks. Identifying the causes of this pattern would aid prediction of the genetic basis of phenotypic evolution. PMID:26384359

  17. Transcriptomic Analysis of Phenotypic Changes in Birch (Betula platyphylla) Autotetraploids

    PubMed Central

    Mu, Huai-Zhi; Liu, Zi-Jia; Lin, Lin; Li, Hui-Yu; Jiang, Jing; Liu, Gui-Feng

    2012-01-01

    Plant breeders have focused much attention on polyploid trees because of their importance to forestry. To evaluate the impact of intraspecies genome duplication on the transcriptome, a series of Betula platyphylla autotetraploids and diploids were generated from four full-sib families. The phenotypes and transcriptomes of these autotetraploid individuals were compared with those of diploid trees. Autotetraploids were generally superior in breast-height diameter, volume, leaf, fruit and stoma and were generally inferior in height compared to diploids. Transcriptome data revealed numerous changes in gene expression attributable to autotetraploidization, which resulted in the upregulation of 7052 unigenes and the downregulation of 3658 unigenes. Pathway analysis revealed that the biosynthesis and signal transduction of indoleacetate (IAA) and ethylene were altered after genome duplication, which may have contributed to phenotypic changes. These results shed light on variations in birch autotetraploidization and help identify important genes for the genetic engineering of birch trees. PMID:23202935

  18. Neural phenotypes of common and rare genetic variants

    PubMed Central

    Bearden, Carrie E.; Glahn, David C.; Lee, Agatha D.; Chiang, Ming-Chang; van Erp, Theo G.M.; Cannon, Tyrone D.; Reiss, Allan L.; Toga, Arthur W.; Thompson, Paul M.

    2008-01-01

    Neuroimaging methods offer a powerful way to bridge the gaps between genes, neurobiology and behavior. Such investigations may be further empowered by complementary strategies involving chromosomal abnormalities associated with particular neurobehavioral phenotypes, which can help to localize causative genes and better understand the genetics of complex traits in the general population. Here we review the evidence from studies using these convergent approaches to investigate genetic influences on brain structure: 1) Studies of common genetic variation associated with particular neuroanatomic phenotypes, and 2) Studies of possible ‘genetic subtypes’ of neuropsychiatric disorders with very high penetrance, with a focus on neuroimaging studies using novel computational brain mapping algorithms. Finally, we discuss the contribution of behavioral neurogenetics research to our understanding of the genetic basis of neuropsychiatric disorders in the broader population. PMID:18395317

  19. Towards quantitative assessment of calciphylaxis

    NASA Astrophysics Data System (ADS)

    Deserno, Thomas M.; Sárándi, István.; Jose, Abin; Haak, Daniel; Jonas, Stephan; Specht, Paula; Brandenburg, Vincent

    2014-03-01

    Calciphylaxis is a rare disease that has devastating conditions associated with high morbidity and mortality. Calciphylaxis is characterized by systemic medial calcification of the arteries yielding necrotic skin ulcerations. In this paper, we aim at supporting the installation of multi-center registries for calciphylaxis, which includes a photographic documentation of skin necrosis. However, photographs acquired in different centers under different conditions using different equipment and photographers cannot be compared quantitatively. For normalization, we use a simple color pad that is placed into the field of view, segmented from the image, and its color fields are analyzed. In total, 24 colors are printed on that scale. A least-squares approach is used to determine the affine color transform. Furthermore, the card allows scale normalization. We provide a case study for qualitative assessment. In addition, the method is evaluated quantitatively using 10 images of two sets of different captures of the same necrosis. The variability of quantitative measurements based on free hand photography is assessed reg