Impacts of both reference population size and inclusion of a residual polygenic effect on the accuracy of genomic prediction

Direct genomic values were estimated for German Holstein cattle with a genomic BLUP model including a residual polygenic effect. A total of 17,429 genotyped Holstein bulls were evaluated using the phenotypes of 44 traits. The Interbull genomic validation test was implemented to investigate how the inclusion of a residual polygenic effect impacted genomic estimated breeding values.As the number of reference bulls increased, both the variance of the estimates of single nucleotide polymorphism effects and the reliability of the direct genomic values of selection candidates increased. Fitting a residual polygenic effect in the model resulted in less biased genome-enhanced breeding values and decreased the correlation between direct genomic values and estimated breeding values of sires in the reference population.Genetic evaluation of dairy cattle enhanced with genomic information is highly effective in increasing reliability, as well as using large genomic reference populations. We found that fitting a residual polygenic effect reduced the bias in genome-enhanced breeding values, decreased the correlation between direct genomic values and sire's estimated breeding values and made genome-enhanced breeding values more consistent in mean and variance as is the case for pedigree-based estimated breeding values.With the availability of the bovine genome sequence and the development of high-density arrays of single nucleotide polymorphism (SNP) markers, the accuracy of genetic predictions has improved compared to conventional breeding value estimations based on phenotypic data and pedigree [1-9]. In order to model genetic variation for quantitative traits, Meuwissen et al. [10] have proposed a genetic evaluation model that includes a large number of SNP markers simultaneously. This genomic model assumes that, all the loci that affect the trait are in linkage disequilibrium (LD) with at least one SNP marker and thus marker genotypes can be used as predictors for breeding value