Genomic Selection for Milk Production Traits in Xinjiang Brown Cattle

SIMPLE SUMMARY: Milk production is an important trait in the breeding and genetic improvement of Xinjiang Brown cattle. To obtain the best strategy for improving the reliability of the breeding value estimation for each trait, we used single-trait and multitrait models based on the A-array pedigree-based best linear unbiased prediction (PBLUP) and H-array single-step genomic best linear unbiased prediction (ssGBLUP) to perform the genetic evaluation of different strategies using the restricted maximum likelihood (REML) and Bayesian methods. Upon comparison, the ssGBLUP calculation results of the multitrait models obtained using the REML and Bayesian methods were better than those of other strategies. Considering the calculation time, the multitrait model REML method is recommended for ssGBLUP calculation to accurately predict the breeding value of young animals; thus, this strategy should be used for the early breeding selection of Xinjiang Brown cattle. ABSTRACT: One-step genomic selection is a method for improving the reliability of the breeding value estimation. This study aimed to compare the reliability of pedigree-based best linear unbiased prediction (PBLUP) and single-step genomic best linear unbiased prediction (ssGBLUP), single-trait and multitrait models, and the restricted maximum likelihood (REML) and Bayesian methods. Data were collected from the production performance records of 2207 Xinjiang Brown cattle in Xinjiang from 1983 to 2018. A cross test was designed to calculate the genetic parameters and reliability of the breeding value of 305 daily milk yield (305 dMY), milk fat yield (MFY), milk protein yield (MPY), and somatic cell score (SCS) of Xinjiang Brown cattle. The heritability of 305 dMY, MFY, MPY, and SCS estimated using the REML and Bayesian multitrait models was approximately 0.39 (0.02), 0.40 (0.03), 0.49 (0.02), and 0.07 (0.02), respectively. The heritability and estimated breeding value (EBV) and the reliability of milk production traits of these cattle calculated based on PBLUP and ssGBLUP using the multitrait model REML and Bayesian methods were higher than those of the single-trait model REML method; the ssGBLUP method was significantly better than the PBLUP method. The reliability of the estimated breeding value can be improved from 0.9% to 3.6%, and the reliability of the genomic estimated breeding value (GEBV) for the genotyped population can reach 83%. Therefore, the genetic evaluation of the multitrait model is better than that of the single-trait model. Thus, genomic selection can be applied to small population varieties such as Xinjiang Brown cattle, in improving the reliability of the genomic estimated breeding value.