Evolutionary histories of functional mutations during the domestication and spread of <i>japonica</i> rice in Asia

Rice (<i>Oryza sativa</i>) was first domesticated beginning ~9,000 y ago in China as the <i>japonica</i> variety group/subspecies. Using genomic data from 456 <i>japonica</i> landraces, including data for 47 herbarium specimens collected over the last 167 y, we reconstruct how <i>japonica</i> 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 <i>japonica</i> landraces-many of them associated with <i>japonica</i> 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.