Genomic history and ecology of the geographic spread of rice

• Published in: Nature plants Vol. 6; no. 5; pp. 492 - 502
• Main Authors: Gutaker, Rafal M., Groen, Simon C., Bellis, Emily S., Choi, Jae Y., Pires, Inês S., Bocinsky, R. Kyle, Slayton, Emma R., Wilkins, Olivia, Castillo, Cristina C., Negrão, Sónia, Oliveira, M. Margarida, Fuller, Dorian Q., Guedes, Jade A. d’Alpoim, Lasky, Jesse R., Purugganan, Michael D.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01-05-2020; Nature Publishing Group
• Subjects: 631/158/2456; 631/181/27; 631/181/457; 631/449/2669; Abiotic factors; Adaptation; Asia; Biological Evolution; Biomedical and Life Sciences; Climate; Dispersal; Dispersion; Domestication; Ecology; Gene sequencing; Genetic Variation - genetics; Genomes; Genomics; Global cooling; Life Sciences; Oryza - genetics; Paleoclimate; Paleoclimatology; Plant Sciences; Rice; Whole Genome Sequencing; Asia; New York; Southeast Asia; United States > US; China; Yangtze Valley
• ISSN: 2055-0278; 2055-0278
• DOI: 10.1038/s41477-020-0659-6

Rice (
Oryza sativa
) is one of the world’s most important food crops, and is comprised largely of
japonica
and
indica
subspecies. Here, we reconstruct the history of rice dispersal in Asia using whole-genome sequences of more than 1,400 landraces, coupled with geographic, environmental, archaeobotanical and paleoclimate data. Originating around 9,000 yr ago in the Yangtze Valley, rice diversified into temperate and tropical
japonica
rice during a global cooling event about 4,200 yr ago. Soon after, tropical
japonica
rice reached Southeast Asia, where it rapidly diversified, starting about 2,500 yr
bp
. The history of
indica
rice dispersal appears more complicated, moving into China around 2,000 yr
bp
. We also identify extrinsic factors that influence genome diversity, with temperature being a leading abiotic factor. Reconstructing the dispersal history of rice and its climatic correlates may help identify genetic adaptations associated with the spread of a key domesticated species.
A reconstruction of the genomic history of
japonica
and
indica
rice over 9,000 yr with geographic, environmental, archaeobotanical and paleoclimate data.