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Response of Polygenic Traits Under Stabilizing Selection and Mutation When Loci Have Unequal Effects.

ABSTRACT: We consider an infinitely large population under stabilizing selection and mutation in which the allelic effects determining a polygenic trait vary between loci. We obtain analytical expressions for the stationary genetic variance as a function of the distribution of effects, mutation rate, and selection coefficient. We also study the dynamics of the allele frequencies, focusing on short-term evolution of the phenotypic mean as it approaches the optimum after an environmental change. We find that when most effects are small, the genetic variance does not change appreciably during adaptation, and the time until the phenotypic mean reaches the optimum is short if the number of loci is large. However, when most effects are large, the change of the variance during the adaptive process cannot be neglected. In this case, the short-term dynamics may be described by those of a few loci of large effect. Our results may be used to understand polygenic selection driving rapid adaptation.

SUBMITTER: Jain K

PROVIDER: S-EPMC4478537 | biostudies-literature | 2015 Mar

REPOSITORIES: biostudies-literature

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Response of Polygenic Traits Under Stabilizing Selection and Mutation When Loci Have Unequal Effects.

Jain Kavita K Stephan Wolfgang W

G3 (Bethesda, Md.) 20150331 6

We consider an infinitely large population under stabilizing selection and mutation in which the allelic effects determining a polygenic trait vary between loci. We obtain analytical expressions for the stationary genetic variance as a function of the distribution of effects, mutation rate, and selection coefficient. We also study the dynamics of the allele frequencies, focusing on short-term evolution of the phenotypic mean as it approaches the optimum after an environmental change. We find tha ...[more]

PMID: 25834214

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Project description:A new mixed-model method was developed for mapping quantitative trait loci (QTL) by incorporating multiple polygenic covariance structures. First, we used genome-wide markers to calculate six different kinship matrices. We then partitioned the total genetic variance into six variance components, one corresponding to each kinship matrix, including the additive, dominance, additive × additive, dominance × dominance, additive × dominance, and dominance × additive variances. The six different kinship matrices along with the six estimated polygenic variances were used to control the genetic background of a QTL mapping model. Simulation studies showed that incorporating epistatic polygenic covariance structure can improve QTL mapping resolution. The method was applied to yield component traits of rice. We analyzed four traits (yield, tiller number, grain number, and grain weight) using 278 immortal F2 crosses (crosses between recombinant inbred lines) and 1619 markers. We found that the relative importance of each type of genetic variance varies across different traits. The total genetic variance of yield is contributed by additive × additive (18%), dominance × dominance (14%), additive × dominance (48%), and dominance × additive (15%) variances. Tiller number is contributed by additive (17%), additive × additive (22%), and dominance × additive (43%) variances. Grain number is mainly contributed by additive (42%), additive × additive (19%), and additive × dominance (31%) variances. Grain weight is almost exclusively contributed by the additive (73%) variance plus a small contribution from the additive × additive (10%) variance. Using the estimated genetic variance components to capture the polygenic covariance structure, we detected 39 effects for yield, 39 effects for tiller number, 24 for grain number, and 15 for grain weight. The new method can be directly applied to polygenic-effect-adjusted genome-wide association studies (GWAS) in human and other species.

Dataset Information

Response of Polygenic Traits Under Stabilizing Selection and Mutation When Loci Have Unequal Effects.

Publications

Response of Polygenic Traits Under Stabilizing Selection and Mutation When Loci Have Unequal Effects.

Similar Datasets

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