Evaluation of the utility of gene expression and metabolic information for genomic prediction in maize

Predictive ability derived from gene expression and metabolic information was evaluated using genomic prediction methods based on datasets from a public maize panel. With the rapid development of high throughput biological technologies, information from gene expression and metabolites has received growing attention in plant genetics and breeding. In this study, we evaluated the utility of gene expression and metabolic information for genomic prediction using data obtained from a maize diversity panel. Our results show that, when used as predictor variables, gene expression levels and metabolite abundances provided reasonable predictive abilities relative to those based on genetic markers, although these values were not as large as those with genetic markers. Integrating gene expression levels and metabolite abundances with genetic markers significantly improved predictive abilities in comparison to the benchmark genomic best linear unbiased prediction model using genome-wide markers only. Predictive abilities based on gene expression and metabolites were trait-specific and were affected by the time of measurement and tissue samples as well as the number of genes and metabolites included in the model. In general, our results suggest that, rather than being conventionally used as intermediate phenotypes, gene expression and metabolic information can be used as predictors for genomic prediction and help improve genetic gains for complex traits in breeding programs.