Genomic variation in 3,010 diverse accessions of Asian cultivated rice

Wensheng Wang, Ramil Mauleon, Zhiqiang Hu, Dmytro Chebotarov, Shuaishuai Tai, Zhichao Wu, Min Li, Tianqing Zheng, Roven Rommel Fuentes, Fan Zhang, Locedie Mansueto, Dario Copetti, Millicent Sanciangco, Kevin Christian Palis, Jianlong Xu, Chen Sun, Binying Fu, Hongliang Zhang, Yongming Gao, Xiuqin Zhao, Fei Shen, Xiao Cui, Hong Yu, Zichao Li, Miaolin Chen, Jeffrey Detras, Yongli Zhou, Xinyuan Zhang, Yue Zhao, Dave Kudrna, Chunchao Wang, Rui Li, Ben Jia, Jinyuan Lu, Xianchang He, Zhaotong Dong, Jiabao Xu, Yanhong Li, Miao Wang, Jianxin Shi, Jing Li, Dabing Zhang, Seunghee Lee, Wushu Hu, Alexander Poliakov, Inna Dubchak, Victor Jun Ulat, Frances Nikki Borja, John Robert Mendoza, Jauhar Ali, Jing Li, Qiang Gao, Yongchao Niu, Zhen Yue, Ma. Elizabeth B. Naredo, Jayson Talag, Xueqiang Wang, Jinjie Li, Xiaodong Fang, Ye Yin, Jean-Christophe Glaszmann, Jianwei Zhang, Jiayang Li, Ruaraidh Sackville Hamilton, Rod A. Wing (), Jue Ruan (), Gengyun Zhang (), Chaochun Wei (), Nickolai Alexandrov (), Kenneth L. McNally (), Zhikang Li () and Hei Leung
Additional contact information
Wensheng Wang: Chinese Academy of Agricultural Sciences
Ramil Mauleon: International Rice Research Institute
Zhiqiang Hu: Chinese Academy of Agricultural Sciences
Dmytro Chebotarov: International Rice Research Institute
Shuaishuai Tai: BGI Genomics, BGI-Shenzhen
Zhichao Wu: Chinese Academy of Agricultural Sciences
Min Li: Chinese Academy of Agricultural Sciences
Tianqing Zheng: Chinese Academy of Agricultural Sciences
Roven Rommel Fuentes: International Rice Research Institute
Fan Zhang: Chinese Academy of Agricultural Sciences
Locedie Mansueto: International Rice Research Institute
Dario Copetti: International Rice Research Institute
Millicent Sanciangco: International Rice Research Institute
Kevin Christian Palis: International Rice Research Institute
Jianlong Xu: Chinese Academy of Agricultural Sciences
Chen Sun: Shanghai Jiao Tong University
Binying Fu: Chinese Academy of Agricultural Sciences
Hongliang Zhang: China Agricultural University
Yongming Gao: Chinese Academy of Agricultural Sciences
Xiuqin Zhao: Chinese Academy of Agricultural Sciences
Fei Shen: China Agricultural University
Xiao Cui: Shanghai Jiao Tong University
Hong Yu: Chinese Academy of Sciences
Zichao Li: China Agricultural University
Miaolin Chen: Shanghai Jiao Tong University
Jeffrey Detras: International Rice Research Institute
Yongli Zhou: Chinese Academy of Agricultural Sciences
Xinyuan Zhang: Chinese Academy of Agricultural Sciences
Yue Zhao: Shanghai Jiao Tong University
Dave Kudrna: University of Arizona
Chunchao Wang: Chinese Academy of Agricultural Sciences
Rui Li: Shanghai Jiao Tong University
Ben Jia: Shanghai Jiao Tong University
Jinyuan Lu: Shanghai Jiao Tong University
Xianchang He: Shanghai Jiao Tong University
Zhaotong Dong: Shanghai Jiao Tong University
Jiabao Xu: BGI Genomics, BGI-Shenzhen
Yanhong Li: BGI Genomics, BGI-Shenzhen
Miao Wang: BGI Genomics, BGI-Shenzhen
Jianxin Shi: Shanghai Jiao Tong University
Jing Li: Shanghai Jiao Tong University
Dabing Zhang: Shanghai Jiao Tong University
Seunghee Lee: University of Arizona
Wushu Hu: BGI Genomics, BGI-Shenzhen
Alexander Poliakov: DOE Joint Genome Institute
Inna Dubchak: DOE Joint Genome Institute
Victor Jun Ulat: International Rice Research Institute
Frances Nikki Borja: International Rice Research Institute
John Robert Mendoza: Advanced Science and Technology Institute, Department of Science and Technology
Jauhar Ali: International Rice Research Institute
Jing Li: Shanghai Jiao Tong University
Qiang Gao: BGI Genomics, BGI-Shenzhen
Yongchao Niu: BGI Genomics, BGI-Shenzhen
Zhen Yue: BGI Genomics, BGI-Shenzhen
Ma. Elizabeth B. Naredo: International Rice Research Institute
Jayson Talag: University of Arizona
Xueqiang Wang: China Agricultural University
Jinjie Li: China Agricultural University
Xiaodong Fang: BGI Genomics, BGI-Shenzhen
Ye Yin: BGI Genomics, BGI-Shenzhen
Jean-Christophe Glaszmann: UMR AGAP, CIRAD
Jianwei Zhang: University of Arizona
Jiayang Li: Chinese Academy of Agricultural Sciences
Ruaraidh Sackville Hamilton: International Rice Research Institute
Rod A. Wing: International Rice Research Institute
Jue Ruan: Chinese Academy of Agricultural Sciences
Gengyun Zhang: BGI Genomics, BGI-Shenzhen
Chaochun Wei: Shanghai Jiao Tong University
Nickolai Alexandrov: International Rice Research Institute
Kenneth L. McNally: International Rice Research Institute
Zhikang Li: Chinese Academy of Agricultural Sciences
Hei Leung: International Rice Research Institute

Nature, 2018, vol. 557, issue 7703, 43-49

Abstract: Abstract Here we analyse genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our results are consistent with the five major groups previously recognized, but also suggest several unreported subpopulations that correlate with geographic location. We identified 29 million single nucleotide polymorphisms, 2.4 million small indels and over 90,000 structural variations that contribute to within- and between-population variation. Using pan-genome analyses, we identified more than 10,000 novel full-length protein-coding genes and a high number of presence–absence variations. The complex patterns of introgression observed in domestication genes are consistent with multiple independent rice domestication events. The public availability of data from the 3,000 Rice Genomes Project provides a resource for rice genomics research and breeding.

Date: 2018
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DOI: 10.1038/s41586-018-0063-9

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