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

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.

Authors:
 [1];  [2];  [3];  [2];  [4];  [5];  [6];  [1];  [2];  [1];  [2];  [7];  [2];  [2];  [5];  [8];  [5];  [9];  [5];  [1] more »;  [9];  [8];  [1];  [9];  [8];  [2];  [5];  [10];  [5];  [11];  [1];  [8];  [8];  [8];  [8];  [8];  [4];  [4];  [4];  [8];  [8];  [8];  [11];  [4];  [12];  [13];  [2];  [2];  [14];  [2];  [8];  [4];  [4];  [4];  [2];  [11];  [9];  [9];  [4];  [4];  [15];  [11];  [1];  [2];  [7];  [10];  [16];  [17];  [2];  [2];  [5];  [2] « less
  1. Chinese Academy of Sciences (CAS), Beijing (China)
  2. International Rice Research Inst., Manila (Philippines)
  3. Chinese Academy of Sciences (CAS), Beijing (China); Shanghai Jiao Tong Univ. (China)
  4. BGI-Shenzhen (China)
  5. Chinese Academy of Sciences (CAS), Beijing (China); Chinese Academy of Agricultural Sciences, Shenzhen (China)
  6. Chinese Academy of Agricultural Sciences, Shenzhen (China); Anhui Agricultural Univ., Hefei (China)
  7. International Rice Research Inst., Manila (Philippines); Univ. of Arizona, Tucson, AZ (United States)
  8. Shanghai Jiao Tong Univ. (China)
  9. China Agricultural Univ., Beijing (China)
  10. Chinese Academy of Agricultural Sciences, Shenzhen (China)
  11. Univ. of Arizona, Tucson, AZ (United States)
  12. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  13. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  14. Advanced Science and Technology Inst., Quezon City (Philippines)
  15. French Agricultural Research Centre for International Development (CIRAD), Montpellier (France); Univ. of Montpellier (France)
  16. BGI-Shenzhen (China); Chinese Academy of Agricultural Sciences, Shenzhen (China)
  17. Shanghai Jiao Tong Univ. (China); Shanghai Center for Bioinformation Technology (China)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Sponsoring Org.:
USDOE; National Key R&D Program; Chinese Ministry of Science & Technology; Bill & Melinda Gates Foundation Project; Agricultural Science and Technology Innovation Program Cooperation and Innovation Mission; CAAS Innovative Team Award; International S&T Cooperation Program of China; Shenzhen Peacock Plan; National Key Technology Support Program; Fundamental Research Funds for Central Non-Profit of CAAS; National Natural Science Foundation of China (NNSFC)
OSTI Identifier:
1543768
Resource Type:
Accepted Manuscript
Journal Name:
Nature (London)
Additional Journal Information:
Journal Name: Nature (London); Journal Volume: 557; Journal Issue: 7703; Journal ID: ISSN 0028-0836
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Wang, Wensheng, Mauleon, Ramil, Hu, Zhiqiang, Chebotarov, Dmytro, Tai, Shuaishuai, Wu, Zhichao, Li, Min, Zheng, Tianqing, Fuentes, Roven Rommel, Zhang, Fan, Mansueto, Locedie, Copetti, Dario, Sanciangco, Millicent, Palis, Kevin Christian, Xu, Jianlong, Sun, Chen, Fu, Binying, Zhang, Hongliang, Gao, Yongming, Zhao, Xiuqin, Shen, Fei, Cui, Xiao, Yu, Hong, Li, Zichao, Chen, Miaolin, Detras, Jeffrey, Zhou, Yongli, Zhang, Xinyuan, Zhao, Yue, Kudrna, Dave, Wang, Chunchao, Li, Rui, Jia, Ben, Lu, Jinyuan, He, Xianchang, Dong, Zhaotong, Xu, Jiabao, Li, Yanhong, Wang, Miao, Shi, Jianxin, Li, Jing, Zhang, Dabing, Lee, Seunghee, Hu, Wushu, Poliakov, Alexander, Dubchak, Inna, Ulat, Victor Jun, Borja, Frances Nikki, Mendoza, John Robert, Ali, Jauhar, Li, Jing, Gao, Qiang, Niu, Yongchao, Yue, Zhen, Naredo, Ma. Elizabeth B., Talag, Jayson, Wang, Xueqiang, Li, Jinjie, Fang, Xiaodong, Yin, Ye, Glaszmann, Jean-Christophe, Zhang, Jianwei, Li, Jiayang, Hamilton, Ruaraidh Sackville, Wing, Rod A., Ruan, Jue, Zhang, Gengyun, Wei, Chaochun, Alexandrov, Nickolai, McNally, Kenneth L., Li, Zhikang, and Leung, Hei. Genomic variation in 3,010 diverse accessions of Asian cultivated rice. United States: N. p., 2018. Web. doi:10.1038/s41586-018-0063-9.
Wang, Wensheng, Mauleon, Ramil, Hu, Zhiqiang, Chebotarov, Dmytro, Tai, Shuaishuai, Wu, Zhichao, Li, Min, Zheng, Tianqing, Fuentes, Roven Rommel, Zhang, Fan, Mansueto, Locedie, Copetti, Dario, Sanciangco, Millicent, Palis, Kevin Christian, Xu, Jianlong, Sun, Chen, Fu, Binying, Zhang, Hongliang, Gao, Yongming, Zhao, Xiuqin, Shen, Fei, Cui, Xiao, Yu, Hong, Li, Zichao, Chen, Miaolin, Detras, Jeffrey, Zhou, Yongli, Zhang, Xinyuan, Zhao, Yue, Kudrna, Dave, Wang, Chunchao, Li, Rui, Jia, Ben, Lu, Jinyuan, He, Xianchang, Dong, Zhaotong, Xu, Jiabao, Li, Yanhong, Wang, Miao, Shi, Jianxin, Li, Jing, Zhang, Dabing, Lee, Seunghee, Hu, Wushu, Poliakov, Alexander, Dubchak, Inna, Ulat, Victor Jun, Borja, Frances Nikki, Mendoza, John Robert, Ali, Jauhar, Li, Jing, Gao, Qiang, Niu, Yongchao, Yue, Zhen, Naredo, Ma. Elizabeth B., Talag, Jayson, Wang, Xueqiang, Li, Jinjie, Fang, Xiaodong, Yin, Ye, Glaszmann, Jean-Christophe, Zhang, Jianwei, Li, Jiayang, Hamilton, Ruaraidh Sackville, Wing, Rod A., Ruan, Jue, Zhang, Gengyun, Wei, Chaochun, Alexandrov, Nickolai, McNally, Kenneth L., Li, Zhikang, & Leung, Hei. Genomic variation in 3,010 diverse accessions of Asian cultivated rice. United States. doi:https://doi.org/10.1038/s41586-018-0063-9
Wang, Wensheng, Mauleon, Ramil, Hu, Zhiqiang, Chebotarov, Dmytro, Tai, Shuaishuai, Wu, Zhichao, Li, Min, Zheng, Tianqing, Fuentes, Roven Rommel, Zhang, Fan, Mansueto, Locedie, Copetti, Dario, Sanciangco, Millicent, Palis, Kevin Christian, Xu, Jianlong, Sun, Chen, Fu, Binying, Zhang, Hongliang, Gao, Yongming, Zhao, Xiuqin, Shen, Fei, Cui, Xiao, Yu, Hong, Li, Zichao, Chen, Miaolin, Detras, Jeffrey, Zhou, Yongli, Zhang, Xinyuan, Zhao, Yue, Kudrna, Dave, Wang, Chunchao, Li, Rui, Jia, Ben, Lu, Jinyuan, He, Xianchang, Dong, Zhaotong, Xu, Jiabao, Li, Yanhong, Wang, Miao, Shi, Jianxin, Li, Jing, Zhang, Dabing, Lee, Seunghee, Hu, Wushu, Poliakov, Alexander, Dubchak, Inna, Ulat, Victor Jun, Borja, Frances Nikki, Mendoza, John Robert, Ali, Jauhar, Li, Jing, Gao, Qiang, Niu, Yongchao, Yue, Zhen, Naredo, Ma. Elizabeth B., Talag, Jayson, Wang, Xueqiang, Li, Jinjie, Fang, Xiaodong, Yin, Ye, Glaszmann, Jean-Christophe, Zhang, Jianwei, Li, Jiayang, Hamilton, Ruaraidh Sackville, Wing, Rod A., Ruan, Jue, Zhang, Gengyun, Wei, Chaochun, Alexandrov, Nickolai, McNally, Kenneth L., Li, Zhikang, and Leung, Hei. Wed . "Genomic variation in 3,010 diverse accessions of Asian cultivated rice". United States. doi:https://doi.org/10.1038/s41586-018-0063-9. https://www.osti.gov/servlets/purl/1543768.
@article{osti_1543768,
title = {Genomic variation in 3,010 diverse accessions of Asian cultivated rice},
author = {Wang, Wensheng and Mauleon, Ramil and Hu, Zhiqiang and Chebotarov, Dmytro and Tai, Shuaishuai and Wu, Zhichao and Li, Min and Zheng, Tianqing and Fuentes, Roven Rommel and Zhang, Fan and Mansueto, Locedie and Copetti, Dario and Sanciangco, Millicent and Palis, Kevin Christian and Xu, Jianlong and Sun, Chen and Fu, Binying and Zhang, Hongliang and Gao, Yongming and Zhao, Xiuqin and Shen, Fei and Cui, Xiao and Yu, Hong and Li, Zichao and Chen, Miaolin and Detras, Jeffrey and Zhou, Yongli and Zhang, Xinyuan and Zhao, Yue and Kudrna, Dave and Wang, Chunchao and Li, Rui and Jia, Ben and Lu, Jinyuan and He, Xianchang and Dong, Zhaotong and Xu, Jiabao and Li, Yanhong and Wang, Miao and Shi, Jianxin and Li, Jing and Zhang, Dabing and Lee, Seunghee and Hu, Wushu and Poliakov, Alexander and Dubchak, Inna and Ulat, Victor Jun and Borja, Frances Nikki and Mendoza, John Robert and Ali, Jauhar and Li, Jing and Gao, Qiang and Niu, Yongchao and Yue, Zhen and Naredo, Ma. Elizabeth B. and Talag, Jayson and Wang, Xueqiang and Li, Jinjie and Fang, Xiaodong and Yin, Ye and Glaszmann, Jean-Christophe and Zhang, Jianwei and Li, Jiayang and Hamilton, Ruaraidh Sackville and Wing, Rod A. and Ruan, Jue and Zhang, Gengyun and Wei, Chaochun and Alexandrov, Nickolai and McNally, Kenneth L. and Li, Zhikang and Leung, Hei},
abstractNote = {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.},
doi = {10.1038/s41586-018-0063-9},
journal = {Nature (London)},
number = 7703,
volume = 557,
place = {United States},
year = {2018},
month = {4}
}

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    • DOI: 10.1007/s00122-018-3234-z

    Genome-wide dissection of segregation distortion using multiple inter-subspecific crosses in rice
    journal, March 2019


    Genetic analysis of roots and shoots in rice seedling by association mapping
    journal, September 2018

    • Zhao, Yan; Jiang, Cong-hui; Rehman, Rashid Muhammad Abdul
    • Genes & Genomics, Vol. 41, Issue 1
    • DOI: 10.1007/s13258-018-0741-x

    The Green Revolution shaped the population structure of the rice pathogen Xanthomonas oryzae pv. oryzae
    journal, October 2019

    • Quibod, Ian Lorenzo; Atieza-Grande, Genelou; Oreiro, Eula Gems
    • The ISME Journal, Vol. 14, Issue 2
    • DOI: 10.1038/s41396-019-0545-2

    In the name of the rose: a roadmap for rose research in the genome era
    journal, May 2019

    • Smulders, Marinus J. M.; Arens, Paul; Bourke, Peter M.
    • Horticulture Research, Vol. 6, Issue 1
    • DOI: 10.1038/s41438-019-0156-0

    Early selection of bZIP73 facilitated adaptation of japonica rice to cold climates
    journal, August 2018


    Tracking the origin of two genetic components associated with transposable element bursts in domesticated rice
    journal, February 2019


    The indica nitrate reductase gene OsNR2 allele enhances rice yield potential and nitrogen use efficiency
    journal, November 2019


    Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus
    journal, January 2020


    Genomic evidence of human selection on Vavilovian mimicry
    journal, September 2019


    NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice
    journal, April 2019


    A SWEET solution to rice blight
    journal, October 2019

    • Varshney, Rajeev K.; Godwin, Ian D.; Mohapatra, Trilochan
    • Nature Biotechnology, Vol. 37, Issue 11
    • DOI: 10.1038/s41587-019-0302-0

    Prime genome editing in rice and wheat
    journal, March 2020


    Genebank genomics highlights the diversity of a global barley collection
    journal, November 2018


    New alleles for chlorophyll content and stay-green traits revealed by a genome wide association study in rice (Oryza sativa)
    journal, February 2019


    Natural variation in the HAN1 gene confers chilling tolerance in rice and allowed adaptation to a temperate climate
    journal, February 2019

    • Mao, Donghai; Xin, Yeyun; Tan, Yongjun
    • Proceedings of the National Academy of Sciences, Vol. 116, Issue 9
    • DOI: 10.1073/pnas.1819769116

    ppsPCP: a plant presence/absence variants scanner and pan-genome construction pipeline
    journal, March 2019


    TASUKE+: a web-based platform for exploring GWAS results and large-scale resequencing data
    journal, September 2019

    • Kumagai, Masahiko; Nishikawa, Daiki; Kawahara, Yoshihiro
    • DNA Research, Vol. 26, Issue 6
    • DOI: 10.1093/dnares/dsz022

    Origin of the Aromatic Group of Cultivated Rice ( Oryza sativa L.) Traced to the Indian Subcontinent
    journal, February 2019

    • Civáň, Peter; Ali, Sajid; Batista-Navarro, Riza
    • Genome Biology and Evolution, Vol. 11, Issue 3
    • DOI: 10.1093/gbe/evz039

    Structural variants in 3000 rice genomes
    journal, April 2019

    • Fuentes, Roven Rommel; Chebotarov, Dmytro; Duitama, Jorge
    • Genome Research, Vol. 29, Issue 5
    • DOI: 10.1101/gr.241240.118

    Natural variation in the promoter of OsHMA3 contributes to differential grain cadmium accumulation between Indica and Japonica rice
    journal, March 2020

    • Liu, Chao‐Lei; Gao, Zhen‐Yu; Shang, Lian‐Guang
    • Journal of Integrative Plant Biology, Vol. 62, Issue 3
    • DOI: 10.1111/jipb.12794

    Blurring the boundaries between cereal crops and model plants
    journal, November 2019


    Towards a deeper haplotype mining of complex traits in rice with RFGB v2.0
    journal, June 2019

    • Wang, Chun‐Chao; Yu, Hong; Huang, Ji
    • Plant Biotechnology Journal, Vol. 18, Issue 1
    • DOI: 10.1111/pbi.13215

    Transcriptional landscape of pathogen‐responsive lnc RNA s in rice unveils the role of ALEX 1 in jasmonate pathway and disease resistance
    journal, September 2019

    • Yu, Yang; Zhou, Yan‐Fei; Feng, Yan‐Zhao
    • Plant Biotechnology Journal, Vol. 18, Issue 3
    • DOI: 10.1111/pbi.13234

    Genome‐wide association study identifies an NLR gene that confers partial resistance to Magnaporthe oryzae in rice
    journal, December 2019

    • Liu, Ming‐Hao; Kang, Houxiang; Xu, Yucheng
    • Plant Biotechnology Journal, Vol. 18, Issue 6
    • DOI: 10.1111/pbi.13300

    Selection and mutation of the avirulence gene AVR‐Pii of the rice blast fungus Magnaporthe oryzae
    journal, August 2018


    Enhanced sustainable green revolution yield via nitrogen-responsive chromatin modulation in rice
    journal, February 2020


    Genome-Wide Association Analysis of the Genetic Basis for Sheath Blight Resistance in Rice
    journal, December 2019


    Natural Sequence Variations and Combinations of GNP1 and NAL1 Determine the Grain Number per Panicle in Rice
    journal, February 2020


    Characterization of Haplotype Diversity in the BADH2 Aroma Gene and Development of a KASP SNP Assay for Predicting Aroma in U.S. Rice
    journal, July 2020


    MINI SEED 2 (MIS2) Encodes a Receptor-like Kinase that Controls Grain Size and Shape in Rice
    journal, January 2020


    Genome sequence of the model rice variety KitaakeX
    journal, November 2019


    Comparison of multiple algorithms to reliably detect structural variants in pears
    journal, January 2020


    HUPAN: a pan-genome analysis pipeline for human genomes
    journal, July 2019


    Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice
    journal, February 2020


    Identification and Analysis of Micro-Exon Genes in the Rice Genome
    journal, May 2019

    • Song, Qi; Lv, Fang; Tahir ul Qamar, Muhammad
    • International Journal of Molecular Sciences, Vol. 20, Issue 11
    • DOI: 10.3390/ijms20112685

    Relationships between Iraqi Rice Varieties at the Nuclear and Plastid Genome Levels
    journal, November 2019


    Hidden Rice Diversity in the Guianas
    text, January 2019