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

机译：水稻基因组变异图揭示了栽培水稻的起源

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摘要

栽培水稻(Oryza sativa)被认为是几千年前从野生水稻(Oryza rufipogon)驯化的。这一中日合作研究项目报告了来自亚洲和大洋洲的446种野生水稻隔离种和来自1000个indica和]1apont。ca栽培水稻亚种的完整基因组序列。由此获得的“基因组变异图”对于水稻育种和作物驯化研究来说将是一个重要资源。%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.
机译：栽培水稻(Oryza sativa)被认为是几千年前从野生水稻(Oryza rufipogon)驯化的。这一中日合作研究项目报告了来自亚洲和大洋洲的446种野生水稻隔离种和来自1000个indica和]1apont。ca栽培水稻亚种的完整基因组序列。由此获得的“基因组变异图”对于水稻育种和作物驯化研究来说将是一个重要资源。%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.

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  • 来源
    《Nature》 |2012年第7421期|p.497-501A3|共6页
  • 作者

    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; Chuanrang Zhu; Tao Huang; Lei Zhang; Yongchun Wang; Lei Feng; Hiroyasu Furuumi; Takahiko Kubo; Toshie Miyabayashi; Xiaoping Yuan; Qun Xu; Guojun Dong; Qilin Zhan; Canyang Li; Asao Fujiyama; Atsushi Toyoda; Tingting Lu; Qi Feng; Qian Qian; Jiayang Li; Bin Han;

  • 作者单位

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

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

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

    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, Mishima, Shizuoka 411-8540, Japan;

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    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, Mishima, Shizuoka 411-8540, Japan;

    Plant Genetics Laboratory and Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan;

    Plant Genetics Laboratory and Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan;

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

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

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

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

    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, Mishima, Shizuoka 411-8540, Japan;

    Plant Genetics Laboratory and Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan;

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

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

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

    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;

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

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