scholarly journals The Multi-allelic Genetic Architecture of a Variance-Heterogeneity Locus for Molybdenum Concentration in Leaves Acts as a Source of Unexplained Additive Genetic Variance

PLoS Genetics ◽  
2015 ◽  
Vol 11 (11) ◽  
pp. e1005648 ◽  
Author(s):  
Simon K. G. Forsberg ◽  
Matthew E. Andreatta ◽  
Xin-Yuan Huang ◽  
John Danku ◽  
David E. Salt ◽  
...  
Keyword(s):  
Genetic Architecture ◽  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Variance Heterogeneity ◽  
Molybdenum Concentration

scholarly journals The Multi-allelic Genetic Architecture of a Variance-heterogeneity Locus for Molybdenum Accumulation Acts as a Source of Unexplained Additive Genetic Variance

2015 ◽  
Author(s):  
Simon K G Forsberg ◽  
Matthew E Andreatta ◽  
Xin-Yuan Huang ◽  
John Danku ◽  
David E Salt ◽  
...  
Keyword(s):  
Genetic Architecture ◽  
Genetic Variance ◽  
Phenotypic Diversity ◽  
Additive Genetic Variance ◽  
Genetic Regulation ◽  
Ion Homeostasis ◽  
Natural Populations ◽  
Biological Traits ◽  
Variance Heterogeneity ◽  
Copper Transporter

Most biological traits are regulated by both genetic and environmental factors. Individual loci contributing to the phenotypic diversity in a population are generally identified by their contributions to the trait mean. Genome-wide association (GWA) analyses can also detect loci based on variance differences between genotypes and several hypotheses have been proposed regarding the possible genetic mechanisms leading to such signals. Little is, however, known about what causes them and whether this genetic variance-heterogeneity reflects mechanisms of importance in natural populations. Previously, we identified a variance-heterogeneity GWA (vGWA) signal for leaf molybdenum concentrations in Arabidopsis thaliana. Here, fine-mapping of this association to a ~78 kb Linkage Disequilibrium (LD)-block reveals that it emerges from the independent effects of three genetic polymorphisms on the high-variance associated version of this LD-block. By revealing the genetic architecture underlying this vGWA signal, we uncovered the molecular source of a significant amount of hidden additive genetic variation (“missing heritability”). Two of the three polymorphisms on the high-variance LD-block are promoter variants for Molybdate transporter 1 (MOT1), and the third a variant located ~25 kb downstream of this gene. A fourth independent association was also detected ~600 kb upstream of the LD-block. Testing of T-DNA knockout alleles for genes in the associated regions suggest AT2G25660 (unknown function) and AT2G26975 (Copper Transporter 6; COPT6) as the strongest candidates for the associations outside MOT1. Our results show that multi-allelic genetic architectures within a single LD-block can lead to a variance-heterogeneity between genotypes in natural populations. Further they provide novel insights into the genetic regulation of ion homeostasis in A. thaliana, and empirically confirm that variance-heterogeneity based GWA methods are a valuable tool to detect novel associations of biological importance in natural populations.

scholarly journals Introduced populations of ragweed show as much evolutionary potential as native populations

2018 ◽  
Author(s):  
Brechann V. McGoey ◽  
John R. Stinchcombe
Keyword(s):  
Genetic Architecture ◽  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Ambrosia Artemisiifolia ◽  
Empirical Literature ◽  
Ecological Problem ◽  
Adaptive Potential ◽  
Evolutionary Potential ◽  
Introduced Populations ◽  
Native Populations

AbstractInvasive species are a global economic and ecological problem. They also offer an opportunity to understand evolutionary processes in a colonizing context. The impacts of evolutionary factors, such as genetic variation, on the invasion process are increasingly appreciated but there remain gaps in the empirical literature. The adaptive potential of populations can be quantified using genetic variance-covariance matrices (G), which encapsulate the heritable genetic variance in a population. Here, we use a multivariate, Bayesian approach to assess the adaptive potential of introduced populations of ragweed, Ambrosia artemisiifolia, a serious allergen and agricultural weed. We compared several aspects of genetic architecture and the structure of G matrices between three native and three introduced populations, based on data collected in the field in a common garden experiment. We find moderate differences in the quantitative genetic architecture among populations, but we do not find that introduced populations suffer from a limited adaptive potential compared to native populations. Ragweed has an annual life history, is an obligate outcrosser, and produces billions of seeds and pollen grains per. These characteristics, combined with the significant additive genetic variance documented here, suggest ragweed will be able to respond quickly to selection pressures in both its native and introduced ranges.

scholarly journals The genetic architecture of teosinte catalyzed and constrained maize domestication

2019 ◽  
Vol 116 (12) ◽  
pp. 5643-5652 ◽  
Author(s):  
Chin Jian Yang ◽  
Luis Fernando Samayoa ◽  
Peter J. Bradbury ◽  
Bode A. Olukolu ◽  
Wei Xue ◽  
...  
Keyword(s):  
Genetic Architecture ◽  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Genetic Correlations ◽  
Reproductive Traits ◽  
Maize Landrace ◽  
Dominance Genetic Variance ◽  
Trait Locus ◽  
Maize Domestication ◽  
Selection Intensities

The process of evolution under domestication has been studied using phylogenetics, population genetics–genomics, quantitative trait locus (QTL) mapping, gene expression assays, and archaeology. Here, we apply an evolutionary quantitative genetic approach to understand the constraints imposed by the genetic architecture of trait variation in teosinte, the wild ancestor of maize, and the consequences of domestication on genetic architecture. Using modern teosinte and maize landrace populations as proxies for the ancestor and domesticate, respectively, we estimated heritabilities, additive and dominance genetic variances, genetic-by-environment variances, genetic correlations, and genetic covariances for 18 domestication-related traits using realized genomic relationships estimated from genome-wide markers. We found a reduction in heritabilities across most traits, and the reduction is stronger in reproductive traits (size and numbers of grains and ears) than vegetative traits. We observed larger depletion in additive genetic variance than dominance genetic variance. Selection intensities during domestication were weak for all traits, with reproductive traits showing the highest values. For 17 of 18 traits, neutral divergence is rejected, suggesting they were targets of selection during domestication. Yield (total grain weight) per plant is the sole trait that selection does not appear to have improved in maize relative to teosinte. From a multivariate evolution perspective, we identified a strong, nonneutral divergence between teosinte and maize landrace genetic variance–covariance matrices (G-matrices). While the structure of G-matrix in teosinte posed considerable genetic constraint on early domestication, the maize landrace G-matrix indicates that the degree of constraint is more unfavorable for further evolution along the same trajectory.

scholarly journals Genomic and phenomic insights from an atlas of genetic effects on DNA methylation

2020 ◽  
Author(s):  
Josine L Min ◽  
Gibran Hemani ◽  
Eilis Hannon ◽  
Koen F Dekkers ◽  
Juan Castillo-Fernandez ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Genetic Variants ◽  
Complex Traits ◽  
Genetic Architecture ◽  
Genetic Variance ◽  
Genetic Factors ◽  
Additive Genetic Variance ◽  
Genetic Influences ◽  
Methylation Quantitative Trait Loci ◽  
Shared Genetic

Characterizing genetic influences on DNA methylation (DNAm) provides an opportunity to understand mechanisms underpinning gene regulation and disease. Here we describe results of DNA methylation-quantitative trait loci (mQTL) analyses on 32,851 participants, identifying genetic variants associated with DNAm at 420,509 DNAm sites in blood. We present a database of >270,000 independent mQTL of which 8.5% comprise long-range (trans) associations. Identified mQTL associations explain 15-17% of the additive genetic variance of DNAm. We reveal that the genetic architecture of DNAm levels is highly polygenic and DNAm exhibits signatures of negative and positive natural selection. Using shared genetic control between distal DNAm sites we construct networks, identifying 405 discrete genomic communities enriched for genomic annotations and complex traits. Shared genetic factors are associated with both blood DNAm levels and complex diseases but in most cases these associations do not reflect causal relationships from DNAm to trait or vice versa indicating a more complex genotype-phenotype map than has previously been hypothesised.

scholarly journals SELECTION FOR BLOOD PRESSURE LEVELS IN MICE

Genetics ◽  
1974 ◽  
Vol 76 (3) ◽  
pp. 537-549
Author(s):  
Gunther Schlager
Keyword(s):  
Blood Pressure ◽  
Systolic Blood Pressure ◽  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Population Bottleneck ◽  
Control Line ◽  
Selected Lines ◽  
High Line ◽  
Selection For ◽  
Random Control

ABSTRACT Response to two-way selection for systolic blood pressure was immediate and continuous for about eight generations. In the twelfth generation, the High males differed from the Low males by 38 mmHG; the females differed by 39 mmHg. There was little overlap between the two lines and they were statistically significant from each other and from the Random control line. There appeared to be no more additive genetic variance in the eleventh and twelfth generations. Causes for the cessation of response are explored. This is probably due to a combination of natural selection acting to reduce litter sizes in the Low line, a higher incidence of sudden deaths in the High line, and loss of favorable alleles as both selection lines went through a population bottleneck in the ninth generation.—In the eleventh generation, the selected lines were used to produce F1, F2, and backcross generations. A genetic analysis yielded significant additive and dominance components in the inheritance of systolic blood pressure.

scholarly journals Sapling and coppice biomass heritabilities and potential gains from Eucalyptus polybractea progeny trials

2021 ◽  
Vol 17 (2) ◽  
Author(s):  
Beren Spencer ◽  
Richard Mazanec ◽  
Mark Gibberd ◽  
Ayalsew Zerihun
Keyword(s):  
Western Australia ◽  
Growth Rates ◽  
Genetic Parameters ◽  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Short Rotation ◽  
Sapling Growth ◽  
Genetic And Phenotypic Correlations ◽  
Breeding Selections ◽  
Cross Site

AbstractEucalyptus polybractea has been planted as a short-rotation coppice crop for bioenergy in Western Australia. Historical breeding selections were based on sapling biomass and despite a long history as a coppice crop, the genetic parameters of coppicing are unknown. Here, we assessed sapling biomass at ages 3 and 6 from three progeny trials across southern Australia. After the second sapling assessment, all trees were harvested. Coppice biomass was assessed 3.5 years later. Mortality following harvest was between 1 and 2%. Additive genetic variance for the 6-sapling estimate at one site was not significant. Sapling heritabilities were between 0.06 and 0.36 at 3 years, and 0.18 and 0.20 at 6 years. The heritability for the coppice biomass was between 0.07 and 0.17. Within-site genetic and phenotypic correlations were strong between all biomass assessments. Cross-site correlations were not different from unity. Selections based on net breeding values revealed positive gains in sapling and coppice biomass. Lower or negative gains were estimated if 3-year sapling selections were applied to the coppice assessments (−7.1% to 3.4%) with useful families culled. Positive gains were obtained if 6-year sapling selections were applied to the coppice assessment (6.4% to 9.3%) but these were lower than those obtained by applying coppice selections to the coppice assessment (8.4% to 14.8%). Removal of poor performing families and families that displayed fast sapling growth rates but under-performed as coppice will benefit potential coppice production. These results indicate that selections should be made using coppice data.

scholarly journals Estimation of non-additive genetic variance in human complex traits from a large sample of unrelated individuals

2021 ◽  
Author(s):  
Valentin Hivert ◽  
Julia Sidorenko ◽  
Florian Rohart ◽  
Michael E. Goddard ◽  
Jian Yang ◽  
...  
Keyword(s):  
Complex Traits ◽  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Large Sample ◽  
Human Complex

scholarly journals Heritability of DNA methylation in threespine stickleback (Gasterosteus aculeatus)

Genetics ◽  
2021 ◽  
Vol 217 (1) ◽  
Author(s):  
Juntao Hu ◽  
Sara J S Wuitchik ◽  
Tegan N Barry ◽  
Heather A Jamniczky ◽  
Sean M Rogers ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Genetic Architecture ◽  
Gasterosteus Aculeatus ◽  
Additive Genetic Variance ◽  
Natural Populations ◽  
Threespine Stickleback ◽  
Phenotypic Change ◽  
Cpg Sites ◽  
Cis And Trans ◽  
Methylation Variation

Abstract Epigenetic mechanisms underlying phenotypic change are hypothesized to contribute to population persistence and adaptation in the face of environmental change. To date, few studies have explored the heritability of intergenerationally stable methylation levels in natural populations, and little is known about the relative contribution of cis- and trans-regulatory changes to methylation variation. Here, we explore the heritability of DNA methylation, and conduct methylation quantitative trait loci (meQTLs) analysis to investigate the genetic architecture underlying methylation variation between marine and freshwater ecotypes of threespine stickleback (Gasterosteus aculeatus). We quantitatively measured genome-wide DNA methylation in fin tissue using reduced representation bisulfite sequencing of F1 and F2 crosses, and their marine and freshwater source populations. We identified cytosines (CpG sites) that exhibited stable methylation levels across generations. We found that additive genetic variance explained an average of 24–35% of the methylation variance, with a number of CpG sites possibly autonomous from genetic control. We also detected both cis- and trans-meQTLs, with only trans-meQTLs overlapping with previously identified genomic regions of high differentiation between marine and freshwater ecotypes. Finally, we identified the genetic architecture underlying two key CpG sites that were differentially methylated between ecotypes. These findings demonstrate a potential role for DNA methylation in facilitating adaptation to divergent environments and improve our understanding of the heritable basis of population epigenomic variation.

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