Genomic history and ecology of the geographic spread of rice

ABSTRACT Rice ( Oryza sativa ) is one of the world’s most important food crops. We reconstruct the history of rice dispersal in Asia using whole-genome sequences of >1,400 landraces, coupled with geographic, environmental, archaeobotanical and paleoclimate data. We also identify extrinsic factors that impact genome diversity, with temperature a leading abiotic factor. Originating ∼9,000 years ago in the Yangtze Valley, rice diversified into temperate and tropical japonica during a global cooling event ∼4,200 years ago. Soon after, tropical rice reached Southeast Asia, where it rapidly diversified starting ∼2,500 yBP. The history of indica rice dispersal appears more complicated, moving into China ∼2,000 yBP. Reconstructing the dispersal history of rice and its climatic correlates may help identify genetic adaptation associated with the spread of a key domesticated species. One sentence summary We reconstructed the ancient dispersal of rice in Asia and identified extrinsic factors that impact its genomic diversity.