The Impact of Variable Degrees of Freedom and Scale Parameters in Bayesian Methods for Genomic Prediction in Chinese Simmental Beef Cattle

Three conventional Bayesian approaches (BayesA, BayesB and BayesC(TT)) 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 BayesFC(TT)) 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 BayesFC(TT) noticeably outperformed BayesC(TT) with the highest increase (3.8%) for live weight using the cohort masking cross-validation.