Comparison of five methods for genomic breeding value estimation for the common dataset of the 15th QTL-MAS Workshop.
BACKGROUND
Genomic breeding value estimation is the key step in genomic selection. Among many approaches, BLUP methods and Bayesian methods are most commonly used for estimating genomic breeding values. Here, we applied two BLUP methods, TABLUP and GBLUP, and three Bayesian methods, BayesA, BayesB and BayesCπ, to the common dataset provided by the 15th QTL-MAS Workshop to evaluate and compare their predictive performances.


RESULTS
For the 1000 progenies without phenotypic values, the correlations between GEBVs by different methods ranged from 0.812 (GBLUP and BayesCπ) to 0.997 (TABLUP and BayesB). The accuracies of GEBVs (measured as correlations between true breeding values (TBVs) and GEBVs) were from 0.774 (GBLUP) to 0.938 (BayesCπ) and the biases of GEBVs (measure as regressions of TBVs on GEBVs) were from 1.033 (TABLUP) to 1.648 (GBLUP). The three Bayesian methods and TABLUP had similar accuracy and bias.


CONCLUSIONS
BayesA, BayesB, BayesCπ and TABLUP performed similarly and satisfactorily and remarkably outperformed GBLUP for genomic breeding value estimation in this dataset. TABLUP is a promising method for genomic breeding value estimation because of its easy computation of reliabilities of GEBVs and its easy extension to real life conditions such as multiple traits and consideration of individuals without genotypes.
Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.|Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China.
Chong-Long
CL
Wang
Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Pei-Pei
PP
Ma
Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Zhe
Z
Zhang
Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Xiang-Dong
XD
Ding
Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Jian-Feng
JF
Liu
Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Wei-Xuan
WX
Fu
Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Zi-Qing
ZQ
Weng
Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Qin
Q
Zhang