An Improved Bayesian Shrinkage Regression Algorithm for Genomic Selection

Abstract

Currently a hot topic, genomic selection (GS) has consistently provided powerful support for breeding studies and achieved more comprehensive and reliable selection in animal and plant breeding. GS estimates the effects of all single nucleotide polymorphisms (SNPs) and thereby predicts the genomic estimation of breeding value (GEBV), accelerating breeding progress and overcoming the limitations of conventional breeding. The successful application of GS primarily depends on the accuracy of the GEBV. Adopting appropriate advanced algorithms to improve the accuracy of the GEBV is time-saving and efficient for breeders, and the available algorithms can be further improved in the big data era. In this study, we develop a new algorithm under the Bayesian Shrinkage Regression (BSR, which is called BayesA) framework, an improved expectation-maximization algorithm for BayesA (emBAI). The emBAI algorithm first corrects the polygenic and environmental noise and then calculates the GEBV by emBayesA. We conduct two simulation experiments and a real dataset analysis for flowering time-related Arabidopsis phenotypes to validate the new algorithm. Compared to established methods, emBAI is more powerful in terms of prediction accuracy, mean square error (MSE), mean absolute error (MAE), the area under the receiver operating characteristic curve (AUC) and correlation of prediction in simulation studies. In addition, emBAI performs well under the increasing genetic background. The analysis of the Arabidopsis real dataset further illustrates the benefits of emBAI for genomic prediction according to prediction accuracy, MSE, MAE and correlation of prediction. Furthermore, the new method shows the advantages of significant loci detection and effect coefficient estimation, which are confirmed by The Arabidopsis Information Resource (TAIR) gene bank. In conclusion, the emBAI algorithm provides powerful support for GS in high-dimensional genomic datasets.