Population structure in O. sativa . A principal component analysis (PCA) based on 40,000 SNPs shows the deep subpopulation structure of a rice diversity panel (400 O. sativa accessions). The top two principal components (PC1 and PC2) explain 44.1% of the genetic variation. Accessions are color-coded based on subpopulation: red, indica; dark blue, temperate japonica; light blue, tropical japonica; yellow, aus; purple, aromatic; black, admixed. Figure reproduced with permission from .