Title: “What are we learning from genome-wide association studies (GWAS) in rice?”


Understanding the relationship between genotypic and phenotypic variation lies at the heart of the study of genetics and is also critically important to applications in plant breeding. Here, we present a genome-wide association study (GWAS) based on genotyping a rice (O. sativa) diversity panel with a high-density SNP array and systematically phenotyping the panel for a range of agronomic, physiological and morphological traits.  Deep population structure punctuated by significant cross-population introgression was documented in the diversity panel, which consisted of both landraces and modern elite cultivars.  Using Principle Components as fixed variables in the mixed model, we identified numerous G->P associations and demonstrate significant heterogeneity of genetic architecture across subpopulations. The heterogeneity provides insight into a wide range of natural genetic variation that remains underutilized in rice genetics and breeding. This work establishes an open-source research platform for genome-wide association studies in rice that directly links molecular variation in genes and metabolic/regulatory pathways directly with the germplasm resources needed to accelerate varietal development and crop improvement.