Application of a single-step SNP BLUP model to conformation traits of German Holsteins

Abstract

Genomic evaluation based on a single-step model utilizes all available data of phenotype, genotype and pedigree and therefore provides unbiased genomic prediction with a higher accuracy than the current multi-step genomic model. Until today, a mixed reference population of cows and bulls has been applied to the routine multi-step genomic evaluation in German Holsteins. For a fair comparison between the single-step and multi-step genomic models, the same phenotype, genotype and pedigree data were used. Because of the standard multi-trait animal model used for German Holstein conventional evaluation, conformation traits were chosen as the first trait group to test a single-step SNP BLUP model (Liu-Goddard) for the large, genotyped population of German Holstein. Genotype, phenotype and pedigree data were taken from the official August 2020 conventional and genomic evaluation. Because of the same trait definition in national and MACE evaluation for the conformation traits, deregressed MACE EBV of foreign bulls were treated as a new source of data for the same trait in the single-step evaluation. Due to a short history of female genotyping, last three years of youngest cows and bulls were deleted, instead of four years, for performing a genomic validation. In comparison to the multi-step genomic model, the single-step SNP BLUP model resulted in a higher prediction accuracy and greater GEBV variance according to 798 national validation bulls. The regression of genomic prediction of the current, full evaluation on the earlier, truncated evaluation was slightly closer to 1 than the multi-step model. For the validation bulls or youngest genomic AI bulls, correlation of GEBV between the two models was, on average, 0.95 across all the conformation traits. We found no major concern about a possible over-prediction of young animals by the single-step SNP BLUP model for the conformation traits in German Holsteins.