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

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
Nature 2012 October 25, 490 (7421): 497-501
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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