July 19, 2019  |  

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

Authors: 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

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.

Journal: Nature
DOI: 10.1038/s41586-018-0063-9
Year: 2018

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