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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
+ Show Author Affiliations
  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 Laboratory (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 (NSFC)
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.
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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. https://doi.org/10.1038/s41586-018-0063-9
Copy to clipboard
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. https://doi.org/10.1038/s41586-018-0063-9. https://www.osti.gov/servlets/purl/1543768.
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@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 = {Wed Apr 25 00:00:00 EDT 2018},
month = {Wed Apr 25 00:00:00 EDT 2018}
}
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https://doi.org/10.1038/s41586-018-0063-9
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