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 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.

scholarly journals Quantitative genetics of response to competitors in Nemophila menziesii: a field experiment.

Genetics ◽  
1995 ◽  
Vol 139 (1) ◽  
pp. 397-406 ◽  
Author(s):  
R G Shaw ◽  
G A Platenkamp ◽  
F H Shaw ◽  
R H Podolsky
Keyword(s):  
Field Experiment ◽  
Genetic Variance ◽  
Plant Density ◽  
Additive Genetic Variance ◽  
Natural Populations ◽  
Plant Size ◽  
Heterogeneous Environments ◽  
Environmental Complexity ◽  
Sources Of Variation ◽  
Nemophila Menziesii

Abstract Recent investigations of evolution in heterogeneous environments have begun to accommodate genetic and environmental complexity typical of natural populations. Theoretical studies demonstrate that evolution of polygenic characters depends heavily on the genetic interdependence of the expression of traits in the different environments in which selection occurs, but information concerning this issue is scarce. We conducted a field experiment to assess the genetic variability of the annual plant Nemophila menziesii in five biotic regimes differing in plant density and composition. Significant, though modest, additive genetic variance in plant size was expressed in particular treatments. Evidence of additive genetic tradeoffs between interspecific and intraspecific competitive performance was found, but this result was not consistent throughout the experiment. Two aspects of experimental design may tend to obscure genetically based tradeoffs across environments in many previously published experiments: (1) inability to isolate additive genetic from other sources of variation and (2) use of novel (e.g., laboratory) environments.

scholarly journals The ‘algebra of evolution’: the Robertson–Price identity and viability selection for body mass in a wild bird population

2020 ◽  
Vol 375 (1797) ◽  
pp. 20190359 ◽  
Author(s):  
G. K. Hajduk ◽  
C. A. Walling ◽  
A. Cockburn ◽  
L. E. B. Kruuk
Keyword(s):  
Phenotypic Diversity ◽  
Additive Genetic Variance ◽  
Natural Populations ◽  
Phenotypic Selection ◽  
Relative Fitness ◽  
Price Equation ◽  
Genetic Covariance ◽  
Selection Gradient ◽  
Viability Selection ◽  
Temporal Correlations

By the Robertson–Price identity, the change in a quantitative trait owing to selection, is equal to the trait's covariance with relative fitness. In this study, we applied the identity to long-term data on superb fairy-wrens Malurus cyaneus , to estimate phenotypic and genetic change owing to juvenile viability selection. Mortality in the four-week period between fledging and independence was 40%, and heavier nestlings were more likely to survive, but why? There was additive genetic variance for both nestling mass and survival, and a positive phenotypic covariance between the traits, but no evidence of additive genetic covariance. Comparing standardized gradients, the phenotypic selection gradient was positive, β P = 0.108 (0.036, 0.187 95% CI), whereas the genetic gradient was not different from zero, β A = −0.025 (−0.19, 0.107 95% CI). This suggests that factors other than nestling mass were the cause of variation in survival. In particular, there were temporal correlations between mass and survival both within and between years. We suggest that use of the Price equation to describe cross-generational change in the wild may be challenging, but a more modest aim of estimating its first term, the Robertson–Price identity, to assess within-generation change can provide valuable insights into the processes shaping phenotypic diversity in natural populations. This article is part of the theme issue ‘Fifty years of the Price equation’.

scholarly journals Polygenic basis and biomedical consequences of telomere length variation

2021 ◽  
Vol 53 (10) ◽  
pp. 1425-1433
Author(s):  
Veryan Codd ◽  
Qingning Wang ◽  
Elias Allara ◽  
Crispin Musicha ◽  
Stephen Kaptoge ◽  
...  
Keyword(s):  
Telomere Length ◽  
Genetic Architecture ◽  
Cellular Proliferation ◽  
Genetic Regulation ◽  
Biological Traits ◽  
Length Variation ◽  
Leukocyte Telomere Length ◽  
Naturally Occurring ◽  
Bone Marrow Function ◽  
Genetically Determined

AbstractTelomeres, the end fragments of chromosomes, play key roles in cellular proliferation and senescence. Here we characterize the genetic architecture of naturally occurring variation in leukocyte telomere length (LTL) and identify causal links between LTL and biomedical phenotypes in 472,174 well-characterized UK Biobank participants. We identified 197 independent sentinel variants associated with LTL at 138 genomic loci (108 new). Genetically determined differences in LTL were associated with multiple biological traits, ranging from height to bone marrow function, as well as several diseases spanning neoplastic, vascular and inflammatory pathologies. Finally, we estimated that, at the age of 40 years, people with an LTL >1 s.d. shorter than the population mean had a 2.5-year-lower life expectancy compared with the group with ≥1 s.d. longer LDL. Overall, we furnish new insights into the genetic regulation of LTL, reveal wide-ranging influences of LTL on physiological traits, diseases and longevity, and provide a powerful resource available to the global research community.

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 structure of natural populations of Drosophila melanogaster. XXIV. Effects of hybrid dysgenesis on the components of genetic variance of variability.

Genetics ◽  
1991 ◽  
Vol 127 (3) ◽  
pp. 545-552
Author(s):  
D S Suh ◽  
T Mukai
Keyword(s):  
Drosophila Melanogaster ◽  
Population Genetic ◽  
Genetic Parameters ◽  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Natural Populations ◽  
Deleterious Mutations ◽  
Degree Of Dominance ◽  
Population Genetic Parameters ◽  
P Type

Abstract Eight hundred second chromosomes were extracted from the Ishigakijima population, one of the southernmost populations of Drosophila melanogaster in Japan. Half of them were extracted in Native cytoplasm (P-type), and half in Foreign cytoplasm (M-type). Various population-genetic parameters, including the frequency of lethal-carrying second chromosomes (Q = 0.235 for the Native; 0.218 for the Foreign), the allelism rate of lethal second chromosome (Ic = 0.0217 for the Native; 0.0134 for the Foreign), the homozygous detrimental and lethal loads (D = 0.179 for the Native; 0.270 for the Foreign; L = 0.262 for the Native; 0.240 for the Foreign), the average degree of dominance of mildly deleterious mutations (ĥE = 0.244 for the Native; 0.208 for the Foreign), and the components of genetic variance for viability [additive (sigma A2) and dominance (sigma D2)](ŝigma A2 = 0.0187 for the Native; 0.0172 for the Foreign; ŝigma D2 = 0.0005 for the Native; 0.0009 for the Foreign) were estimated. The data indicate that D was significantly larger and hE was significantly smaller in the Foreign cytoplasm. However, the estimates of additive and dominance variances were not significantly different between the two cytoplasms. The additive genetic variance for viability in the Ishigakijima population was greater than expected on the basis of mutation-selection balance confirming previous studies on papers of D. melanogaster in warm climates.

scholarly journals No additive genetic variance for tolerance to ethynylestradiol exposure in natural populations of brown trout ( Salmo trutta )

2019 ◽  
Vol 12 (5) ◽  
pp. 940-950 ◽  
Author(s):  
Lucas Marques da Cunha ◽  
Anshu Uppal ◽  
Emily Seddon ◽  
David Nusbaumer ◽  
Etienne L.M. Vermeirssen ◽  
...  
Keyword(s):  
Brown Trout ◽  
Salmo Trutta ◽  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Natural Populations ◽  
Brown Trout Salmo Trutta

scholarly journals Genetic variance and fixation probabilities at quantitative trait loci in mutation-selection balance

1991 ◽  
Vol 58 (2) ◽  
pp. 139-144 ◽  
Author(s):  
Peter D. Keightley
Keyword(s):  
Quantitative Trait Loci ◽  
Mutation Rate ◽  
Quantitative Trait ◽  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Natural Populations ◽  
Fixation Rate ◽  
Trait Loci ◽  
Fixation Probabilities

SummaryGenetic variance and fixation probabilities are evaluated for a model of a quantitative trait at a balance between mutation, selection and drift in which many alleles can segregate at each locus. If the distribution of effects of new mutant alleles is such that mutations are unconditionally deleterious, as might be the case in natural populations, genetic variance maintained is proportional to the number of mutations occurring in the genome per generation, but is independent of the number of loci at which they appear. If selectively advantageous alleles can occur these tend to interfere to a greater extent with each others' fixation and increasing mutation rate leads to a decrease in the genetic variance as a fraction of the variance maintained in the absence of selection. Fixation probabilities of new mutant alleles approach that for neutral alleles with increasing mutation rate at a locus irrespective of their effects on fitness. The additive genetic variance contributed by the locus may appear to be ‘decoupled’ from the fixation rate of mutant alleles.

scholarly journals Genotype-environment interactions and the maintenance of polygenic variation.

Genetics ◽  
1989 ◽  
Vol 121 (1) ◽  
pp. 129-138 ◽  
Author(s):  
J H Gillespie ◽  
M Turelli
Keyword(s):  
Genetic Variance ◽  
Balancing Selection ◽  
Additive Genetic Variance ◽  
Natural Populations ◽  
Extensive Literature ◽  
Multilocus Genotype ◽  
Polygenic Inheritance ◽  
Mean Fitness ◽  
The Mean ◽  
Polygenic Variation

Abstract Genotype-environment interactions may be a potent force maintaining genetic variation in quantitative traits in natural populations. This is shown by a simple model of additive polygenic inheritance in which the additive contributions of alleles vary with the environment. Under simplifying symmetry assumptions, the model implies that the variance of the phenotypes produced across environments by a multilocus genotype decreases as the number of heterozygous loci increases. In the region of an optimal phenotype, the mapping from the quantitative trait into fitness is concave, and the mean fitness of a genotype will increase with the number of heterozygous loci. This leads to balancing selection, polymorphism, and potentially high levels of additive genetic variance, even though all allelic effects remain additive within each specific environment. An important implication of the model is that the variation maintained by genotype-environment interactions is difficult to study with the restricted range of environments represented in typical experiments. In particular, if fluctuations in allelic effects are pervasive, as suggested by the extensive literature on genotype-environment interactions, efforts to estimate genetic parameters in a single environment may be of limited value.

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