Accuracy of genomic prediction for milk production traits in the Chinese Holstein population using a reference population consisting of cows

Abstract

Genomic selection using dense markers covering the whole genome is a tool for the genetic improvement of livestock and is revolutionizing the breeding system in dairy cattle. Progeny-tested bulls have been used to form reference populations in almost all countries where genomic selection has been implemented. In this study, the accuracy of genomic prediction when cows are used to form the reference population was investigated. The reference population consisted of 3,087 cows. All individuals were genotyped with Illumina BovineSNP50. After genotype imputation and editing, 48,676 single nucleotide polymorphisms were available for analysis. Two methods, genomic BLUP (GBLUP) and BayesB, were used to render genomic estimated breeding values (GEBV) for 5 milk production traits. Accuracies of GEBV were assessed in 3 ways: r(GEBV,EBV) (the correlation between GEBV and conventional EBV) in 67 progeny-tested bulls, rGEBV,EBV from a 5-fold cross validation in the 3,087 cow reference population, and the theoretical accuracy (for GBLUP) calculated in the same way as for conventional BLUP. The results showed that using GBLUP, the r(GEBV,EBV) and theoretical accuracy of genomic prediction in Chinese Holstein ranged from 0.59 to 0.76 and 0.70 to 0.80, respectively, which was 0.13 to 0.30 and 0.23 to 0.33 higher than the accuracies of conventional pedigree index, respectively. The results indicate that, as an alternative, genomic selection using cows in the reference population is feasible.

Keywords: Chinese Holstein; cow; cross validation; genomic selection.