Genomic prediction with parallel computing for slaughter traits in Chinese Simmental beef cattle using high-density genotypes

PLoS One. 2017 Jul 19;12(7):e0179885. doi: 10.1371/journal.pone.0179885. eCollection 2017.

Abstract

Genomic selection has been widely used for complex quantitative trait in farm animals. Estimations of breeding values for slaughter traits are most important to beef cattle industry, and it is worthwhile to investigate prediction accuracies of genomic selection for these traits. In this study, we assessed genomic predictive abilities for average daily gain weight (ADG), live weight (LW), carcass weight (CW), dressing percentage (DP), lean meat percentage (LMP) and retail meat weight (RMW) using Illumina Bovine 770K SNP Beadchip in Chinese Simmental cattle. To evaluate the abilities of prediction, marker effects were estimated using genomic BLUP (GBLUP) and three parallel Bayesian models, including multiple chains parallel BayesA, BayesB and BayesCπ (PBayesA, PBayesB and PBayesCπ). Training set and validation set were divided by random allocation, and the predictive accuracies were evaluated using 5-fold cross validations. We found the accuracies of genomic predictions ranged from 0.195±0.084 (GBLUP for LMP) to 0.424±0.147 (PBayesB for CW). The average accuracies across traits were 0.327±0.085 (GBLUP), 0.335±0.063 (PBayesA), 0.347±0.093 (PBayesB) and 0.334±0.077 (PBayesCπ), respectively. Notably, parallel Bayesian models were more accurate than GBLUP across six traits. Our study suggested that genomic selections with multiple chains parallel Bayesian models are feasible for slaughter traits in Chinese Simmental cattle. The estimations of direct genomic breeding values using parallel Bayesian methods can offer important insights into improving prediction accuracy at young ages and may also help to identify superior candidates in breeding programs.

MeSH terms

  • Animals
  • Breeding*
  • Cattle
  • Genome*
  • Genomics
  • Genotype*
  • Quantitative Trait, Heritable*
  • Red Meat*

Grants and funding

This work was supported by the National High Technology Research and Development Program of China (863 Program 2013AA102505-4), National Natural Science Foundation of China (31201782, 31672384 and 31372294), the Agricultural Science and Technology Innovation Program (ASTIP- IAS03 and ASTIP-IAS-TS-9), Cattle Breeding Innovative Research Team of Chinese Academy of Agricultural Sciences (cxgc-ias-03), Beijing Natural Science Foundation (6154032). L.Y.X was supported by the Elite Youth Program in Chinese Academy of Agricultural Sciences. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.