Bayesian models with dominance effects for genomic evaluation of quantitative traits

Abstract

Genomic selection refers to the use of dense, genome-wide markers for the prediction of breeding values (BV) and subsequent selection of breeding individuals. It has become a standard tool in livestock and plant breeding for accelerating genetic gain. The core of genomic selection is the prediction of a large number of marker effects from a limited number of observations. Various Bayesian methods that successfully cope with this challenge are known. Until now, the main research emphasis has been on additive genetic effects. Dominance coefficients of quantitative trait loci (QTLs), however, can also be large, even if dominance variance and inbreeding depression are relatively small. Considering dominance might contribute to the accuracy of genomic selection and serve as a guide for choosing mating pairs with good combining abilities. A general hierarchical Bayesian model for genomic selection that can realistically account for dominance is introduced. Several submodels are proposed and compared with respect to their ability to predict genomic BV, dominance deviations and genotypic values (GV) by stochastic simulation. These submodels differ in the way the dependency between additive and dominance effects is modelled. Depending on the marker panel, the inclusion of dominance effects increased the accuracy of GV by about 17% and the accuracy of genomic BV by 2% in the offspring. Furthermore, it slowed down the decrease of the accuracies in subsequent generations. It was possible to obtain accurate estimates of GV, which enables mate selection programmes.