Genomic history and ecology of the geographic spread of rice

Rafal M. Gutaker; Simon C. Groen; Emily S. Bellis; Jae Y. Choi; Inês S. Pires; R. Kyle Bocinsky; Emma R. Slayton; Olivia Wilkins; Cristina C. Castillo; Sónia Negrão; M. Margarida Oliveira; Dorian Q. Fuller; Jade A.d’Alpoim Guedes; Jesse R. Lasky; Michael D. Purugganan

doi:10.1038/s41477-020-0659-6

Genomic history and ecology of the geographic spread of rice

Rafal M. Gutaker, Simon C. Groen, Emily S. Bellis, Jae Y. Choi, Inês S. Pires, R. Kyle Bocinsky, Emma R. Slayton, Olivia Wilkins, Cristina C. Castillo, Sónia Negrão, M. Margarida Oliveira, Dorian Q. Fuller, Jade A.d’Alpoim Guedes, Jesse R. Lasky, Michael D. Purugganan

Research output: Contribution to journal › Article › peer-review

Abstract

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.

Original language	English (US)
Pages (from-to)	492-502
Number of pages	11
Journal	Nature Plants
Volume	6
Issue number	5
DOIs	https://doi.org/10.1038/s41477-020-0659-6
State	Published - May 1 2020

ASJC Scopus subject areas

Plant Science

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10.1038/s41477-020-0659-6

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Gutaker, R. M., Groen, S. C., Bellis, E. S., Choi, J. Y., Pires, I. S., Bocinsky, R. K., Slayton, E. R., Wilkins, O., Castillo, C. C., Negrão, S., Oliveira, M. M., Fuller, D. Q., Guedes, J. A. DA., Lasky, J. R., & Purugganan, M. D. (2020). Genomic history and ecology of the geographic spread of rice. Nature Plants, 6(5), 492-502. https://doi.org/10.1038/s41477-020-0659-6

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abstract = "Rice (Oryza sativa) is one of the world{\textquoteright}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.",

author = "Gutaker, {Rafal M.} and Groen, {Simon C.} and Bellis, {Emily S.} and Choi, {Jae Y.} and Pires, {In{\^e}s S.} and Bocinsky, {R. Kyle} and Slayton, {Emma R.} and Olivia Wilkins and Castillo, {Cristina C.} and S{\'o}nia Negr{\~a}o and Oliveira, {M. Margarida} and Fuller, {Dorian Q.} and Guedes, {Jade A.d{\textquoteright}Alpoim} and Lasky, {Jesse R.} and Purugganan, {Michael D.}",

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AU - Bocinsky, R. Kyle

AU - Slayton, Emma R.

AU - Wilkins, Olivia

AU - Castillo, Cristina C.

AU - Negrão, Sónia

AU - Oliveira, M. Margarida

AU - Fuller, Dorian Q.

AU - Guedes, Jade A.d’Alpoim

AU - Lasky, Jesse R.

AU - Purugganan, Michael D.

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N2 - 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.

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Genomic history and ecology of the geographic spread of rice

Abstract

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