This study advances research aiming to understand the genetic basis of agriculturally important traits in Asian rice, Oryza sativa. The authors present a genome-wide association study (GWAS) including 413 rice varieties from 82 countries and provide a public resource of all of the genotypes and phenotypes and of the seed stocks. They found substantial genetic heterogeneity among varieties and suggest strategies for performing GWASs in species with extensive population structure, such as rice.