Multibreed genomic evaluation for production traits of dairy cattle in the United States using single-step genomic best linear unbiased predictor

Abstract

Official multibreed genomic evaluations for dairy cattle in the United States are based on multibreed BLUP evaluation followed by single-breed estimation of SNP effects. Single-step genomic BLUP (ssGBLUP) allows the straight computation of genomic (G)EBV in a multibreed context. This work aimed to develop ssGBLUP multibreed genomic predictions for US dairy cattle using the algorithm for proven and young (APY) to compute the inverse of the genomic relationship matrix. Only purebred Ayrshire (AY), Brown Swiss (BS), Guernsey (GU), Holstein (HO), and Jersey (JE) animals were considered. A 3-trait model with milk (MY), fat (FY), and protein (PY) yields was applied using about 45 million phenotypes recorded from January 2000 to June 2020. The whole data set included about 29.5 million animals, of which almost 4 million were genotyped. All the effects in the model were breed specific, and breed was also considered as fixed unknown parent groups. Evaluations were done for (1) each single breed separately (single); (2) HO and JE together (HO_JE); (3) AY, BS, and GU together (AY_BS_GU); (4) all the 5 breeds together (5_BREEDS). Initially, 15k core animals were used in APY for AY_BS_GU and 5_BREEDS, but larger core sets with more animals from the least represented breeds were also tested. The HO_JE evaluation had a fixed set of 30k core animals, with an equal representation of the 2 breeds, whereas HO and JE single-breed analysis involved 15k core animals. Validation for cows was based on correlations between adjusted phenotypes and (G)EBV, whereas for bulls on the regression of daughter yield deviations on (G)EBV. Because breed was correctly considered in the model, BLUP results for single and multibreed analyses were the same. Under ssGBLUP, predictability and reliability for AY, BS, and GU were on average 7% and 2% lower in 5_BREEDS compared with single-breed evaluations, respectively. However, validation parameters for these 3 breeds became better than in the single-breed evaluations when 45k animals were included in the core set for 5_BREEDS. Evaluations for Holsteins were more stable across scenarios because of the greatest number of genotyped animals and amount of data. Combining AY, BS, and GU into one evaluation resulted in predictions similar to the ones from single breed, especially when using about 30k core animals in APY. The results showed that single-step large-scale multibreed evaluations are computationally feasible, but fine tuning is needed to avoid a reduction in reliability when numerically dominant breeds are combined. Having evaluations for AY, BS, and GU separated from HO and JE may reduce inflation of GEBV for the first 3 breeds.