Including non-additive genetic effects in Bayesian methods for the prediction of genetic values based on genome-wide markers

We extended a fast Bayesian method (fBayesB), which was previously proposed for a purely additive model, to include non-additive effects. The fBayesB approach was used to estimate genetic effects on the basis of simulated datasets. Different scenarios were simulated to study the loss of accuracy of prediction, if epistatic effects were not simulated but modelled and vice versa.If 23 QTL were simulated to cause additive and dominance effects, both fBayesB and a conventional MCMC sampler BayesB yielded similar results in terms of accuracy of genetic value prediction and bias of variance component estimation based on a model including additive and dominance effects. Applying fBayesB to data with epistasis, accuracy could be improved by 5% when all pairwise interactions were modelled as well. The accuracy decreased more than 20% if genetic variation was spread over 230 QTL. In this scenario, accuracy based on modelling only additive and dominance effects was generally superior to that of the complex model including epistatic effects.This simulation study showed that the fBayesB approach is convenient for genetic value prediction. Jointly estimating additive and non-additive effects (especially dominance) has reasonable impact on the accuracy of prediction and the proportion of genetic variation assigned to the additive genetic source.Molecular marker information is commonly used to draw inferences about the relationship between genetic and phenotypic variation in various species, e.g. humans [1], dairy cattle [2] or mice [3]. Assuming linkage disequilibrium (LD) between quantitative trait loci (QTL) and markers, genetic effects can be estimated and explained as QTL effects captured by the neighbouring markers. If breeding values are the focal point, genetic effects are typically modelled as additively acting marker allele effects (e.g. [4,5]). The mode of biological action can, of course, be different from the assumption of pure additivity. One possibility to better und