Genetic evaluation using single-step genomic BLUP in American Angus

Introduction Genomic selection in beef cattle has currently been performed with multistep methods, which uses deregressed EBV to estimate SNP effects and then direct genomic value (DGV) for selection candidates based on their genotypes (Meuwissen et al., 2001; Garrick et al., 2009). The main advantage of this approach is that the traditional BLUP evaluation is kept unchanged and genomic selection can be carried out by a separate entity owning genotypes but not phenotypes. Also new animals are easily evaluated if DGV is computed as a sum of marker effects, but not if selection indexes including DGV and parent average (PA) are used. When both phenotypes and genotypes are available jointly, single-step genomic BLUP (ssGBLUP) (Aguilar et al., 2010) is a simple alternative. This method does not rely on deregressed proofs, properly weighs information from genotyped sires and cows, thus avoiding double-counting of contributions due to relationships and records, and accounts for pre-selection bias of genomically selected parents without phenotypes (Legarra et al., 2014). In ssGBLUP it is also possible to quickly evaluate young genotyped animals without running a complete evaluation that requires several hours to converge. Quick predictions can be calculated indirectly, where genomic predictions for young animals are obtained from SNP effects. It was shown by Wang et al. (2012) that SNP effects can be derived from GEBV solutions from the main ssGBLUP evaluation.