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

PloS One
Xiaoqiao WangHuijiang Gao

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.

References

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Citations

Jul 16, 2020·Genes·Dennis N Lozada, Arron H Carter
Oct 23, 2020·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Mang LiangHuijiang Gao
Jan 21, 2021·Animals : an Open Access Journal From MDPI·Xinghai DuanHuijiang Gao
Mar 23, 2021·Frontiers in Genetics·Mang LiangHuijiang Gao
Apr 17, 2021·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Diego Rodrigues de SousaRaimundo Nonato Braga Lôbo
Jun 9, 2021·Tropical Animal Health and Production·Ana Paula Nascimento TerakadoLucia Galvão de Albuquerque

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Methods Mentioned

BETA
genotyping

Software Mentioned

GEBV
glmnet
LASSO
BayesB
ssGBLUP
EN
GBLUP
BGBLUP
BayesLasso
Beagle

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