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.
Highlights
Genomic prediction (VanRaden, 2008) based on the genomic model (Meuwissen et al, 2001) has revolutionized animal breeding and selection, in Holstein dairy cattle
We demonstrated, based on the genomic breeding values (GEBV) of validation bulls, that the single-step model had a higher prediction correlation and a greater GEBV variance than the current multistep genomic model
Genetic trends of the single-step model were shown to be higher than the multistep model for the current multistep genomic model, based on the 7 conformation traits with an equal residual polygenic variance (RPV) between the 2 models
Summary
Genomic prediction (VanRaden, 2008) based on the genomic model (Meuwissen et al, 2001) has revolutionized animal breeding and selection, in Holstein dairy cattle. Single-step genomic models (Aguilar et al, 2010; Christensen and Lund 2010; Legarra and Ducrocq 2012; Liu et al, 2014; Mäntysaari and Strandén 2016; Gao et al, 2018; Misztal et al, 2020) use all available information on phenotype, genotype, and pedigree and should provide unbiased genomic prediction. For routine genomic evaluation in German Holsteins, a multistep SNP BLUP model including a residual polygenic model (RPG; Liu et al, 2011) has been applied to a mixed reference population of bulls and cows (Alkhoder et al, 2017). In comparison to the single-step genomic BLUP model (ssGBLUP; Aguilar et al, 2010; Gao et al, 2018), the single-step SNP BLUP model (ssSNPBLUP; Liu et al, 2014) does not need to set up the inverse of potentially huge genomic relationship matrix H−1, the ssSNPBLUP can analyze millions of genotyped animals without making approximation on the genomic relationships among animals. Vandenplas et al (2019, 2020) compared alternative ssSNPBLUP models and confirmed the single-step model
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