Bayesian variable selection for genome-wide association study of grain traits in rice

Abstract

Rice (Oryza sativa) is a staple food crop for more than half of the world‘s population. Besides high gluten-free nutritional contents, it has high economic value supporting livelihood of millions of farmers. That is why a lot of research is being carried out to derive new varieties of rice and improve its yield, stress tolerance, and grain quality. It remains a central goal in agricultural research. Genome-wide association studies (GWAS) provide a powerful framework for linking genetic variation to complex phenotypic traits, but the high dimensionality of genomic data presents significant challenges for model selection and prediction. Using rice genotype and phenotype data, we compared the performance of several frequentist and Bayesian modeling approaches: multiple linear regression (OLS: Ordinary Least Squares), LASSO (Least Absolute Shrinkage and Selection Operator), Ridge, Bayesian LASSO, Bayesian Sparse Linear Mixed Model (BSLMM), and a Bayesian spike-and-slab prior model. Phenotypic traits were transformed where necessary to approximate normality, and predictive performance was evaluated through cross-validation using mean squared error and predictive correlation. The spike-and-slab prior model often outperformed the classical methods, yielding superior prediction and effective variable selection. Our findings demonstrate the value of Bayesian model selection frameworks for plant GWAS and trait prediction, and highlight the effectiveness of Bayesian methods in identifying informative markers in rice. Such approaches hold promise for accelerating genetic improvement and supporting marker-assisted selection in crop breeding programs. Rather than emphasizing biological interpretation of individual loci, our results highlight differences in predictive behavior, stability, and inferential characteristics across models.