Application of single-step single nucleotide polymorphism best linear unbiased predictor model with unknown-parent groups for type traits in Japanese Holsteins

Abstract

The objectives of this study were to investigate the computational performance and the predictive ability and bias of a single-step SNP BLUP model (ssSNPBLUP) in genotyped young animals with unknown-parent groups (UPG) for type traits, using national genetic evaluation data from the Japanese Holstein population. The phenotype, genotype, and pedigree data were the same as those used in a national genetic evaluation of linear type traits classified between April 1984 and December 2020. In the current study, 2 data sets were prepared: the full data set containing all entries up to December 2020 and a truncated data set ending with December 2016. Genotyped animals were classified into 3 types: sires with classified daughters (S), cows with records (C), and young animals (Y). The computing performance and prediction accuracy of ssSNPBLUP were compared for the following 3 groups of genotyped animals: sires with classified daughters and young animals (SY); cows with records and young animals (CY); and sires with classified daughters, cows with records, and young animals (SCY). In addition, we tested 3 parameters of residual polygenic variance in ssSNPBLUP (0.1, 0.2, or 0.3). Daughter yield deviations (DYD) for the validation bulls and phenotypes adjusted for all fixed effects and random effects other than animal and residual (Y_adj) for the validation cows were obtained using the full data set from the pedigree-based BLUP model. The regression coefficients of DYD for bulls (or Y_adj for cows) on the genomic estimated breeding value (GEBV) using the truncated data set were used to measure the inflation of the predictions of young animals. The coefficient of determination of DYD on GEBV was used to measure the predictive ability of the predictions for the validation bulls. The reliability of the predictions for the validation cows was calculated as the square of the correlation between Y_adj and GEBV divided by heritability. The predictive ability was highest in the SCY group and lowest in the CY group. However, minimal difference was found in predictive abilities with or without UPG models using different parameters of residual polygenic variance. The regression coefficients approached 1.0 as the parameter of residual polygenic variance increased, but regression coefficients were mostly similar regardless of the use of UPG across the groups of genotyped animals. The ssSNPBLUP model, including UPG, was demonstrated as feasible for implementation in the national evaluation of type traits in Japanese Holsteins.

Keywords: Holstein; single nucleotide polymorphism best linear unbiased predictor; single-step genomic evaluation; type trait; unknown-parent groups.