Genomic history and ecology of the geographic spread of rice

Abstract

Rice (Oryza sativa) is one of the worlds 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.\n\nOne sentence summaryWe reconstructed the ancient dispersal of rice in Asia and identified extrinsic factors that impact its genomic diversity.