Linking Genome Wide Association Studies (GWAS) and Plant Breeding

Understanding the relationship between genetic and phenotypic variation lies at the heart of the study of genetics and is also critically important to applications in plant and animal breeding. The development of high-resolution single nucleotide polymorphism (SNP) assays has made it possible to assess genotype-phenotype associations using genome wide association (GWA) studies in a wide range of species. Here we report on a GWA study based on genotyping a purified panel of diverse wild and cultivated rice accessions with 700K SNPs and the evaluation of those accessions for a wide range of agronomic and physiological traits in diverse environments. Using cross-population-based mapping strategies, we identified numerous common variants influencing complex traits.  Significant heterogeneity was observed in the genetic architecture associated with subpopulation structure and response to environment. This work establishes an open-source translational research platform for genome-wide association studies in rice that directly links molecular variation in genes and metabolic pathways with the germplasm resources needed to accelerate varietal development and crop improvement for diverse environments.