Comparison of a single-step with a multistep single nucleotide polymorphism best linear unbiased predictor model for genomic evaluation of conformation traits in German Holsteins

Abstract

Genomic evaluation based on a single-step model uses all available data of phenotype, genotype, and pedigree; therefore, it should provide unbiased genomic breeding values with a higher correlation of prediction than the current multistep genomic model. Since 2019, a mixed reference population of cows and bulls has been applied to the routine multistep genomic evaluation in German Holsteins. For a fair comparison between the single-step and multistep genomic models, the same phenotype, genotype, and pedigree data were used. Because of its simple structure of the standard multitrait 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 for the large, genotyped population of German Holsteins. 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 multiple across-country evaluation for the conformation traits, deregressed multiple across-country evaluation estimated breeding value (EBV) of foreign bulls were treated as a new source of data for the same trait in the genomic evaluations. Due to a short history of female genotyping in Germany, the last 3 yr of youngest cows and bulls were deleted, instead of 4 yr, to perform a genomic validation. In comparison to the multistep genomic model, the single-step SNP BLUP model resulted in a higher correlation and greater variance of genomic EBV 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 multistep model. For the validation bulls or youngest genomic artificial insemination bulls, correlation of genomic EBV between the 2 models was, on average, 0.95 across all the conformation traits. We did not find overprediction of young animals by the single-step SNP BLUP model for the conformation traits in German Holsteins.