ABSTRACT
Naturally occurring functional genetic variation is often employed to identify genetic loci that regulate specific traits. Existing approaches to link functional genetic variation to quantitative phenotypic outcomes typically evaluate one or several traits at a time. Advances in high throughput phenotyping now enable datasets which include information on dozens or hundreds of traits scored across multiple environments. Here, we develop an approach to use data from many phenotypic traits simultaneously to identify causal genetic loci. Using data for 260 traits scored across a maize diversity panel, we demonstrate that a distinct set of genes are identified relative to conventional genome wide association. The genes identified using this many-trait approach are more likely to be independently validated than the genes identified by conventional analysis of the same dataset. Genes identified by the new many-trait approach share a number of molecular, population genetic, and evolutionary features with a gold standard set of genes characterized through forward genetics. These features, as well as substantially stronger functional enrichment and purification, separate them from both genes identified by conventional genome wide association and from the overall population of annotated gene models. These results are consistent with a large subset of annotated gene models in maize playing little or no role in determining organismal phenotypes.
