Persistence of accuracy of genome-wide breeding values over generations when including a polygenic effect

Genomic selection using the Bayesian method, 'BayesB' was evaluated for different marker densities when a polygenic effect is included (GWpEBV) and not included (GWEBV) in the model. Linkage disequilibrium and a mutation drift balance were obtained by simulating a population with a Ne of 100 over 1,000 generations.Accuracy of selection was slightly higher for the model including a polygenic effect than for the model not including a polygenic effect whatever the marker density. The accuracy decreased in later generations, and this reduction was stronger for lower marker densities. However, no significant difference in accuracy was observed between the two models. The linear regression of TBV on GWEBV and GWpEBV was used as a measure of bias. The regression coefficient was more stable over generations when a polygenic effect was included in the model, and was always between 0.98 and 1.00 for the highest marker density. The regression coefficient decreased more quickly with decreasing marker density.Including a polygenic effect had no impact on the selection accuracy, but showed reduced bias, which is especially important when estimates of genome-wide markers are used to estimate breeding values over more than one generation.High-throughput genotyping and availability of dense marker information have made prediction of breeding values based on dense marker genotyping possible resulting in so-called genome-wide breeding values (GWEBV). Several methods have been suggested to estimate marker effects in the prediction of GWEBV e.g. [1-4]. The advantage of selecting parents on GWEBV in genomic selection schemes is the potential to select candidates with high accuracy and low bias directly by using marker genotypes or haplotypes only. Several simulation studies in which markers were calibrated on a training set of phenotypes e.g. [5-8] have demonstrated these advantages. GWEBV may reduce the amount of phenotyping required for breeding schemes and hence constitute an attracti