Evolutionary histories of functional mutations during the domestication and spread of japonica rice in Asia.

Rice (Oryza sativa) was first domesticated beginning ~9,000 y ago in China as the japonica variety group/subspecies. Using genomic data from 456 japonica landraces, including data for 47 herbarium specimens collected over the last 167 y, we reconstruct how japonica rice moved from its center of origin to other parts of Asia beginning ~4,000 to 5,500 y ago. We observe an enrichment of pathogen resistance loci in selective sweeps associated with distinct geographic populations, suggesting that biotic interactions may be a key driver of local adaptation. We also find that the majority of 76 known functional mutations present in our japonica landraces—many of them associated with japonica rice domestication and diversification and important for modern breeding—had their origins in the Pleistocene >11,700 y ago and increased in allele frequency during key events in the evolution of rice.