Genomic variation in 3,010 diverse accessions of Asian cultivated rice
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 subpopulatio...
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2018
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/164883 |
| _version_ | 1855515057023090688 |
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| author | 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 |
| author_browse | Alexandrov, Nickolai Ali, Jauhar Borja, Frances Nikki Chebotarov, Dmytro Chen, Miaolin Copetti, Dario Cui, Xiao Detras, Jeffrey Dong, Zhaotong Dubchak, Inna Fang, Xiaodong Fu, Binying Fuentes, Roven Rommel Gao, Qiang Gao, Yongming Glaszmann, Jean-Christophe Hamilton, Ruaraidh Sackville He, Xianchang Hu, Wushu Hu, Zhiqiang Jia, Ben Kudrna, Dave Lee, Seunghee Leung, Hei Li, Jiayang Li, Jing Li, Jinjie Li, Min Li, Rui Li, Yanhong Li, Zhikang Li, Zichao Lu, Jinyuan Mansueto, Locedie Mauleon, Ramil McNally, Kenneth L. Mendoza, John Robert Naredo, Ma.Elizabeth B. Niu, Yongchao Palis, Kevin Christian Poliakov, Alexander Ruan, Jue Sanciangco, Millicent Shen, Fei Shi, Jianxin Sun, Chen Tai, Shuaishuai Talag, Jayson Ulat, Victor Jun Wang, Chunchao Wang, Miao Wang, Wensheng Wang, Xueqiang Wei, Chaochun Wing, Rod A. Wu, Zhichao Xu, Jiabao Xu, Jianlong Yin, Ye Yu, Hong Yue, Zhen Zhang, Dabing Zhang, Fan Zhang, Gengyun Zhang, Hongliang Zhang, Jianwei Zhang, Xinyuan Zhao, Xiuqin Zhao, Yue Zheng, Tianqing Zhou, Yongli |
| author_facet | 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 |
| author_sort | Wang, Wensheng |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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 |
| format | Journal Article |
| id | CGSpace164883 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2018 |
| publishDateRange | 2018 |
| publishDateSort | 2018 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1648832026-01-06T12:03:44Z Genomic variation in 3,010 diverse accessions of Asian cultivated rice 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 cultivation genetic variation genomics indels introgression single nucleotide polymorphism varieties 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 2018-05 2024-12-19T12:54:26Z 2024-12-19T12:54:26Z Journal Article https://hdl.handle.net/10568/164883 en Open Access Springer 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. 2018. Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature, Volume 557 no. 7703 p. 43-49 |
| spellingShingle | cultivation genetic variation genomics indels introgression single nucleotide polymorphism varieties 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 |
| title | Genomic variation in 3,010 diverse accessions of Asian cultivated rice |
| title_full | Genomic variation in 3,010 diverse accessions of Asian cultivated rice |
| title_fullStr | Genomic variation in 3,010 diverse accessions of Asian cultivated rice |
| title_full_unstemmed | Genomic variation in 3,010 diverse accessions of Asian cultivated rice |
| title_short | Genomic variation in 3,010 diverse accessions of Asian cultivated rice |
| title_sort | genomic variation in 3 010 diverse accessions of asian cultivated rice |
| topic | cultivation genetic variation genomics indels introgression single nucleotide polymorphism varieties |
| url | https://hdl.handle.net/10568/164883 |
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