Dissecting the genetic architecture of quantitative traits using genome-wide identity-by-descent sharing among full-sibs

Abstract

ABSTRACTAdditive and dominance genetic variances underlying the expression of quantitative traits are important quantities for predicting short-term responses to selection, but they are notoriously challenging to estimate in most wild animal populations. Using estimates of genome-wide identity-by-descent (IBD) sharing from autosomal SNP loci, we estimated quantitative genetic parameters for traits known to be under directional natural selection in nine-spined sticklebacks (Pungitius pungitius) and compared these to traditional pedigree-based estimators. Using four different datasets, with varying sample sizes and pedigree complexity, we further assessed the performance of different Genomic Relationship Matrices (GRM) to estimate additive and dominance variance components. Large variance in IBD relationships allowed accurate estimation of genetic variance components, and revealed significant heritability for all measured traits, with negligible dominance contributions. Genome-partitioning analyses revealed that all traits have a polygenic basis and are controlled by genes at multiple chromosomes. The results demonstrate how large full-sib families of highly fecund vertebrates can be used to obtain accurate estimates quantitative genetic parameters to provide insights on genetic architecture of quantitative traits in non-model organisms from the wild. This approach should be particularly useful for studies requiring estimates of genetic variance components from multiple populations as for instance when aiming to infer the role of natural selection as a cause for population differentiation in quantitative traits.