Bayesian multi-trait kernel methods improve multi-environment genome based prediction.

When multi-trait data are available, the preferred models are those that are able to account for correlations between phenotypic traits because when the degree of correlation is moderate or large, this increases the genomic prediction accuracy. For this reason, in this paper we explore Bayesian multi-trait kernel methods for genomic prediction and we illustrate the power of these models with three real datasets. The kernels under study were the linear, Gaussian, polynomial and sigmoid kernels; they were compared with the conventional Ridge regression and GBLUP multi-trait models. The results show that, in general, the Gaussian kernel method outperformed conventional Bayesian Ridge and GBLUP multi-trait linear models by 2.2 to 17.45% (datasets 1 to 3) in terms of prediction performance based on the mean square error of prediction. This improvement in terms of prediction performance of the Bayesian multi-trait kernel method can be attributed to the fact that the proposed model is able to capture non-linear patterns more efficiently than linear multi-trait models. However, not all kernels perform well in the datasets used for evaluation, which is why more than one kernel should be evaluated to be able to choose the best kernel.