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A map of rice genome variation reveals the origin of cultivated rice

Author

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  • Xuehui Huang

    (National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China)

  • Nori Kurata

    (Plant Genetics Laboratory and Comparative Genomics Laboratory, National Institute of Genetics)

  • Xinghua Wei

    (State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China)

  • Zi-Xuan Wang

    (National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
    Plant Genetics Laboratory and Comparative Genomics Laboratory, National Institute of Genetics)

  • Ahong Wang

    (National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China)

  • Qiang Zhao

    (National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China)

  • Yan Zhao

    (National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China)

  • Kunyan Liu

    (National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China)

  • Hengyun Lu

    (National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China)

  • Wenjun Li

    (National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China)

  • Yunli Guo

    (National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China)

  • Yiqi Lu

    (National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China)

  • Congcong Zhou

    (National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China)

  • Danlin Fan

    (National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China)

  • Qijun Weng

    (National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China)

  • Chuanrang Zhu

    (National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China)

  • Tao Huang

    (National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China)

  • Lei Zhang

    (National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China)

  • Yongchun Wang

    (National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China)

  • Lei Feng

    (National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China)

  • Hiroyasu Furuumi

    (Plant Genetics Laboratory and Comparative Genomics Laboratory, National Institute of Genetics)

  • Takahiko Kubo

    (Plant Genetics Laboratory and Comparative Genomics Laboratory, National Institute of Genetics)

  • Toshie Miyabayashi

    (Plant Genetics Laboratory and Comparative Genomics Laboratory, National Institute of Genetics)

  • Xiaoping Yuan

    (State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China)

  • Qun Xu

    (State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China)

  • Guojun Dong

    (State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China)

  • Qilin Zhan

    (National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China)

  • Canyang Li

    (National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China)

  • Asao Fujiyama

    (Plant Genetics Laboratory and Comparative Genomics Laboratory, National Institute of Genetics)

  • Atsushi Toyoda

    (Plant Genetics Laboratory and Comparative Genomics Laboratory, National Institute of Genetics)

  • Tingting Lu

    (National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China)

  • Qi Feng

    (National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China)

  • Qian Qian

    (State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China)

  • Jiayang Li

    (National Center for Plant Gene Research, State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China)

  • Bin Han

    (National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
    Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China)

Abstract

Crop domestications are long-term selection experiments that have greatly advanced human civilization. The domestication of cultivated rice (Oryza sativa L.) ranks as one of the most important developments in history. However, its origins and domestication processes are controversial and have long been debated. Here we generate genome sequences from 446 geographically diverse accessions of the wild rice species Oryza rufipogon, the immediate ancestral progenitor of cultivated rice, and from 1,083 cultivated indica and japonica varieties to construct a comprehensive map of rice genome variation. In the search for signatures of selection, we identify 55 selective sweeps that have occurred during domestication. In-depth analyses of the domestication sweeps and genome-wide patterns reveal that Oryza sativa japonica rice was first domesticated from a specific population of O. rufipogon around the middle area of the Pearl River in southern China, and that Oryza sativa indica rice was subsequently developed from crosses between japonica rice and local wild rice as the initial cultivars spread into South East and South Asia. The domestication-associated traits are analysed through high-resolution genetic mapping. This study provides an important resource for rice breeding and an effective genomics approach for crop domestication research.

Suggested Citation

  • Xuehui Huang & Nori Kurata & Xinghua Wei & Zi-Xuan Wang & Ahong Wang & Qiang Zhao & Yan Zhao & Kunyan Liu & Hengyun Lu & Wenjun Li & Yunli Guo & Yiqi Lu & Congcong Zhou & Danlin Fan & Qijun Weng & Chu, 2012. "A map of rice genome variation reveals the origin of cultivated rice," Nature, Nature, vol. 490(7421), pages 497-501, October.
  • Handle: RePEc:nat:nature:v:490:y:2012:i:7421:d:10.1038_nature11532
    DOI: 10.1038/nature11532
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    5. Bin Yang & Jiali Zeng & Shaona Chen & Shengyu Li & Longmei Wu & Xiaorong Wan, 2022. "Genome-Wide Association Study Reveals the Genetic Basis of Seed Germination in Japonica Rice," Agriculture, MDPI, vol. 13(1), pages 1-14, December.
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    10. Seung Young Lee & Hyun-Sook Lee & Chang-Min Lee & Su-Kyung Ha & Hyang-Mi Park & So-Myeong Lee & Youngho Kwon & Ji-Ung Jeung & Youngjun Mo, 2023. "Multi-Environment Trials and Stability Analysis for Yield-Related Traits of Commercial Rice Cultivars," Agriculture, MDPI, vol. 13(2), pages 1-13, January.
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    13. Xiaofeng Cai & Xuepeng Sun & Chenxi Xu & Honghe Sun & Xiaoli Wang & Chenhui Ge & Zhonghua Zhang & Quanxi Wang & Zhangjun Fei & Chen Jiao & Quanhua Wang, 2021. "Genomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    14. Zihao Wang & Wenxi Wang & Xiaoming Xie & Yongfa Wang & Zhengzhao Yang & Huiru Peng & Mingming Xin & Yingyin Yao & Zhaorong Hu & Jie Liu & Zhenqi Su & Chaojie Xie & Baoyun Li & Zhongfu Ni & Qixin Sun &, 2022. "Dispersed emergence and protracted domestication of polyploid wheat uncovered by mosaic ancestral haploblock inference," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    15. Naihui Guo & Shengjia Tang & Yakun Wang & Wei Chen & Ruihu An & Zongliang Ren & Shikai Hu & Shaoqing Tang & Xiangjin Wei & Gaoneng Shao & Guiai Jiao & Lihong Xie & Ling Wang & Ying Chen & Fengli Zhao , 2024. "A mediator of OsbZIP46 deactivation and degradation negatively regulates seed dormancy in rice," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    16. Elisa Zampieri & Michele Pesenti & Fabio Francesco Nocito & Gian Attilio Sacchi & Giampiero Valè, 2023. "Rice Responses to Water Limiting Conditions: Improving Stress Management by Exploiting Genetics and Physiological Processes," Agriculture, MDPI, vol. 13(2), pages 1-23, February.
    17. Chew, Soo Hong & Ebstein, Richard P. & Lu, Yunfeng, 2023. "Rice culture and the cushion hypothesis: Experimental evidence from incentivized risk taking tasks," Economics Letters, Elsevier, vol. 223(C).
    18. Yongqi He & Shan Sun & Jia Zhao & Zhibo Huang & Liling Peng & Chengwei Huang & Zhengbin Tang & Qianqian Huang & Zhoufei Wang, 2023. "UDP-glucosyltransferase OsUGT75A promotes submergence tolerance during rice seed germination," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    19. Luchang Ming & Debao Fu & Zhaona Wu & Hu Zhao & Xingbing Xu & Tingting Xu & Xiaohu Xiong & Mu Li & Yi Zheng & Ge Li & Ling Yang & Chunjiao Xia & Rongfang Zhou & Keyan Liao & Qian Yu & Wenqi Chai & Sij, 2023. "Transcriptome-wide association analyses reveal the impact of regulatory variants on rice panicle architecture and causal gene regulatory networks," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    20. Dunpin Xiong & Juan Wang & Ruci Wang & Yueming Wang & Yi Li & Ge Sun & Shanguo Yao, 2024. "A point mutation in VIG1 boosts development and chilling tolerance in rice," Nature Communications, Nature, vol. 15(1), pages 1-16, December.

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