Evaluation of GBLUP, BayesB and elastic net for genomic prediction in Chinese Simmental beef cattle

PLoS One. 2019 Feb 28;14(2):e0210442. doi: 10.1371/journal.pone.0210442. eCollection 2019.

Abstract

Chinese Simmental beef cattle are the most economically important cattle breed in China. Estimated breeding values for growth, carcass, and meat quality traits are commonly used as selection criteria in animal breeding. The objective of this study was to evaluate the accuracy of alternative statistical methods for the estimation of genomic breeding values. Analyses of the accuracy of genomic best linear unbiased prediction (GBLUP), BayesB, and elastic net (EN) were performed with an Illumina BovineHD BeadChip on 1,217 animals by applying 5-fold cross-validation. Overall, the accuracies ranged from 0.17 to 0.296 for ten traits, and the heritability estimates ranged from 0.36 to 0.63. The EN (alpha = 0.001) model provided the most accurate prediction, which was also slightly higher (0.2-2%) than that of GBLUP for most traits, such as average daily weight gain (ADG) and carcass weight (CW). BayesB was less accurate for each trait than were EN (alpha = 0.001) and GBLUP. These findings indicate the importance of using an appropriate variable selection method for the genomic selection of traits and suggest the influence of the genetic architecture of the traits we analyzed.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Breeding*
  • Cattle / genetics*
  • China
  • Genome
  • Genomics
  • Genotype
  • Models, Genetic
  • Phenotype
  • Quantitative Trait, Heritable*

Associated data

  • Dryad/10.5061/dryad.4qc06

Grants and funding

This work was supported by funds from the National Natural Science Foundation of China 31872975 for Huijiang Gao, National Natural Science Foundation of China 31672384 for Lupei Zhang, National Natural Science Foundation of China 31572376 for Xue Gao, and the Chinese Academy of Agricultural Sciences of Technology Innovation Project (CAAS-XTCX2016010, CAAS-ZDXT2018006 and ASTIP-IAS03) for Junya Li.