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

Author

Listed:
  • Wensheng Wang

    (Chinese Academy of Agricultural Sciences)

  • Ramil Mauleon

    (International Rice Research Institute)

  • Zhiqiang Hu

    (Chinese Academy of Agricultural Sciences
    Shanghai Jiao Tong University)

  • Dmytro Chebotarov

    (International Rice Research Institute)

  • Shuaishuai Tai

    (BGI Genomics, BGI-Shenzhen)

  • Zhichao Wu

    (Chinese Academy of Agricultural Sciences
    Chinese Academy of Agricultural Sciences)

  • Min Li

    (Chinese Academy of Agricultural Sciences
    Anhui Agricultural University)

  • 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
    University of Arizona)

  • Millicent Sanciangco

    (International Rice Research Institute)

  • Kevin Christian Palis

    (International Rice Research Institute)

  • Jianlong Xu

    (Chinese Academy of Agricultural Sciences
    Chinese Academy of Agricultural Sciences
    Chinese Academy of Agricultural Sciences)

  • Chen Sun

    (Shanghai Jiao Tong University)

  • Binying Fu

    (Chinese Academy of Agricultural Sciences
    Chinese Academy of Agricultural Sciences)

  • Hongliang Zhang

    (China Agricultural University)

  • Yongming Gao

    (Chinese Academy of Agricultural Sciences
    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
    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
    Lawrence Berkeley National Laboratory)

  • 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
    UMR AGAP, Université de Montpellier)

  • Jianwei Zhang

    (University of Arizona)

  • Jiayang Li

    (Chinese Academy of Agricultural Sciences
    Chinese Academy of Sciences)

  • Ruaraidh Sackville Hamilton

    (International Rice Research Institute)

  • Rod A. Wing

    (International Rice Research Institute
    University of Arizona)

  • Jue Ruan

    (Chinese Academy of Agricultural Sciences)

  • Gengyun Zhang

    (BGI Genomics, BGI-Shenzhen
    Chinese Academy of Agricultural Sciences)

  • Chaochun Wei

    (Shanghai Jiao Tong University
    Shanghai Center for Bioinformation Technology)

  • Nickolai Alexandrov

    (International Rice Research Institute)

  • Kenneth L. McNally

    (International Rice Research Institute)

  • Zhikang Li

    (Chinese Academy of Agricultural Sciences
    Chinese Academy of Agricultural Sciences)

  • Hei Leung

    (International Rice Research Institute)

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.

Suggested Citation

  • 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 & Millicen, 2018. "Genomic variation in 3,010 diverse accessions of Asian cultivated rice," Nature, Nature, vol. 557(7703), pages 43-49, May.
  • Handle: RePEc:nat:nature:v:557:y:2018:i:7703:d:10.1038_s41586-018-0063-9
    DOI: 10.1038/s41586-018-0063-9
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    Cited by:

    1. Xingming Sun & Haiyan Xiong & Conghui Jiang & Dongmei Zhang & Zengling Yang & Yuanping Huang & Wanbin Zhu & Shuaishuai Ma & Junzhi Duan & Xin Wang & Wei Liu & Haifeng Guo & Gangling Li & Jiawei Qi & C, 2022. "Natural variation of DROT1 confers drought adaptation in upland rice," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
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    4. Ting Wang & Shiyao Duan & Chen Xu & Yi Wang & Xinzhong Zhang & Xuefeng Xu & Liyang Chen & Zhenhai Han & Ting Wu, 2023. "Pan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    5. Muhammad Junaid Zaghum & Kashir Ali & Sheng Teng, 2022. "Integrated Genetic and Omics Approaches for the Regulation of Nutritional Activities in Rice ( Oryza sativa L.)," Agriculture, MDPI, vol. 12(11), pages 1-17, October.
    6. Changxuan Xia & Guohua Liang & Kang Chong & Yunyuan Xu, 2023. "The COG1-OsSERL2 complex senses cold to trigger signaling network for chilling tolerance in japonica rice," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    7. Tao Zhu & Chunjiao Xia & Ranran Yu & Xinkai Zhou & Xingbing Xu & Lin Wang & Zhanxiang Zong & Junjiao Yang & Yinmeng Liu & Luchang Ming & Yuxin You & Dijun Chen & Weibo Xie, 2024. "Comprehensive mapping and modelling of the rice regulome landscape unveils the regulatory architecture underlying complex traits," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    8. Yayu Wang & Xiaolin Wang & Shuai Sun & Canzhi Jin & Jianmu Su & Jinpu Wei & Xinyue Luo & Jiawen Wen & Tong Wei & Sunil Kumar Sahu & Hongfeng Zou & Hongyun Chen & Zhixin Mu & Gengyun Zhang & Xin Liu & , 2022. "GWAS, MWAS and mGWAS provide insights into precision agriculture based on genotype-dependent microbial effects in foxtail millet," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    9. Xiaojuan Fan & Yongtao Cui & Jian Song & Honghuan Fan & Liqun Tang & Jianjun Wang, 2024. "Preliminary Exploration of Physiology and Genetic Basis Underlying High Yield in Indica–Japonica Hybrid Rice," Agriculture, MDPI, vol. 14(4), pages 1-12, April.
    10. Sylvain Aubry, 2023. "Genebanking plant genetic resources in the postgenomic era," Agriculture and Human Values, Springer;The Agriculture, Food, & Human Values Society (AFHVS), vol. 40(3), pages 961-971, September.
    11. Yakun Wang & Shengjia Tang & Naihui Guo & Ruihu An & Zongliang Ren & Shikai Hu & Xiangjin Wei & Guiai Jiao & Lihong Xie & Ling Wang & Ying Chen & Fengli Zhao & Peisong Hu & Zhonghua Sheng & Shaoqing T, 2023. "Base Editing of EUI1 Improves the Elongation of the Uppermost Internode in Two-Line Male Sterile Rice Lines," Agriculture, MDPI, vol. 13(3), pages 1-13, March.
    12. Jian Sun & Guangchen Zhang & Zhibo Cui & Ximan Kong & Xiaoyu Yu & Rui Gui & Yuqing Han & Zhuan Li & Hong Lang & Yuchen Hua & Xuemin Zhang & Quan Xu & Liang Tang & Zhengjin Xu & Dianrong Ma & Wenfu Che, 2022. "Regain flood adaptation in rice through a 14-3-3 protein OsGF14h," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    13. Hideki Yoshida & Ko Hirano & Kenji Yano & Fanmiao Wang & Masaki Mori & Mayuko Kawamura & Eriko Koketsu & Masako Hattori & Reynante Lacsamana Ordonio & Peng Huang & Eiji Yamamoto & Makoto Matsuoka, 2022. "Genome-wide association study identifies a gene responsible for temperature-dependent rice germination," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    14. Yong Zhou & Zhichao Yu & Dmytro Chebotarov & Kapeel Chougule & Zhenyuan Lu & Luis F. Rivera & Nagarajan Kathiresan & Noor Al-Bader & Nahed Mohammed & Aseel Alsantely & Saule Mussurova & João Santos & , 2023. "Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    15. Yu Chen & Amy Y. Wang & Courtney A. Barkley & Yixin Zhang & Xinyang Zhao & Min Gao & Mick D. Edmonds & Zechen Chong, 2023. "Deciphering the exact breakpoints of structural variations using long sequencing reads with DeBreak," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    16. Yingyan Yu & Zhen Zhang & Xiaorui Dong & Ruixin Yang & Zhongqu Duan & Zhen Xiang & Jun Li & Guichao Li & Fazhe Yan & Hongzhang Xue & Du Jiao & Jinyuan Lu & Huimin Lu & Wenmin Zhang & Yangzhen Wei & Sh, 2022. "Pangenomic analysis of Chinese gastric cancer," Nature Communications, Nature, vol. 13(1), pages 1-13, December.

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