Recent geographic dispersal and environmental adaptation of indica rice

Rice (Oryza sativa), one of the key domesticated cereal crops, is comprised of several subspecies or variety groups. A major variety group, O. sativa var. indica was domesticated in the Indian subcontinent ∼4500 years ago via introgression of domestication alleles from var. japonica and today represents the predominant rice that is grown worldwide, particularly in tropical and subtropical regions in Asia. Using genome data from 957 indica landraces, including 194 newly re-sequenced cultivars and 38 herbarium specimens collected over the last 167 years, we reconstruct how indica rice moved from the Indian subcontinent to other parts of Asia. Unlike japonica rice, indica rice seems to have dispersed relatively recently (within the last 2,000 years) to China, mainland and island Southeast (SE) Asia. Interestingly, we find that the island SE Asia indica rice landraces show gene flow with island SE Asian japonica landraces. We also find significant gene-environment associations of indica rice with local climatic and edaphic variables that may be associated with local adaptation, and possible cultural selection for grain quality traits, associated with indica dispersal.