title: The Impact of Variable Degrees of Freedom and Scale Parameters in Bayesian Methods for Genomic Prediction in Chinese Simmental Beef Cattle.
abstract: Three conventional Bayesian approaches (BayesA, BayesB and BayesCπ) have been demonstrated to be powerful in predicting genomic merit for complex traits in livestock. A priori, these Bayesian models assume that the non-zero SNP effects (marginally) follow a t-distribution depending on two fixed hyperparameters, degrees of freedom and scale parameters. In this study, we performed genomic prediction in Chinese Simmental beef cattle and treated degrees of freedom and scale parameters as unknown with inappropriate priors. Furthermore, we compared the modified methods (BayesFA, BayesFB and BayesFCπ) with their corresponding counterparts using simulation datasets. We found that the modified methods with distribution assumed to the two hyperparameters were beneficial for improving the predictive accuracy. Our results showed that the predictive accuracies of the modified methods were slightly higher than those of their counterparts especially for traits with low heritability and a small number of QTLs. Moreover, cross-validation analysis for three traits, namely carcass weight, live weight and tenderloin weight, in 1136 Simmental beef cattle suggested that predictive accuracy of BayesFCπ noticeably outperformed BayesCπ with the highest increase (3.8%) for live weight using the cohort masking cross-validation.
authors.affiliation: Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Zhu
authors.affiliation: Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Miao
authors.initials: M
authors.lastname: Zhu
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, China Agricultural University, Beijing, China.
authors.forename: Jicai
authors.initials: J
authors.lastname: Jiang
authors.affiliation: Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Niu
authors.affiliation: Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Yanhui
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Wu
authors.affiliation: Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Lingyang
authors.initials: L
authors.lastname: Xu
authors.affiliation: Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Lupei
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Xue
authors.initials: X
authors.lastname: Gao
authors.affiliation: Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Huijiang
authors.initials: H
authors.lastname: Gao
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, China Agricultural University, Beijing, China.
authors.forename: Jianfeng
authors.initials: J
authors.lastname: Liu
authors.affiliation: Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Junya
authors.initials: J
authors.lastname: Li
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D002417:Cattle / Q000235:genetics*; D005260:Female; D023281:Genomics / Q000379:methods*; D008297:Male; D015233:Models, Statistical; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics