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

被引：1110

作者：

Wang, Wensheng ^{[1
]}

Mauleon, Ramil ^{[2
]}

Hu, Zhiqiang ^{[1
,3
]}

Chebotarov, Dmytro ^{[2
]}

Tai, Shuaishuai ^{[4
]}

Wu, Zhichao ^{[1
,5
]}

Li, Min ^{[6
,7
]}

Zheng, Tianqing ^{[1
]}

Fuentes, Roven Rommel ^{[2
]}

Zhang, Fan ^{[1
]}

Mansueto, Locedie ^{[2
]}

Copetti, Dario ^{[2
,8
]}

Sanciangco, Millicent ^{[2
]}

Palis, Kevin Christian ^{[2
]}

Xu, Jianlong ^{[1
,5
]}

Sun, Chen ^{[3
]}

Fu, Binying ^{[1
]}

Zhang, Hongliang ^{[9
]}

Gao, Yongming ^{[1
]}

Zhao, Xiuqin ^{[1
]}

Shen, Fei ^{[9
]}

Cui, Xiao ^{[3
]}

Yu, Hong ^{[10
]}

Li, Zichao ^{[9
]}

Chen, Miaolin ^{[3
]}

Detras, Jeffrey ^{[2
]}

Zhou, Yongli ^{[1
]}

Zhang, Xinyuan ^{[5
]}

Zhao, Yue ^{[3
]}

Kudrna, Dave ^{[8
]}

Wang, Chunchao ^{[1
]}

Li, Rui ^{[3
]}

Jia, Ben ^{[3
]}

Lu, Jinyuan ^{[3
]}

He, Xianchang ^{[3
]}

Dong, Zhaotong ^{[3
]}

Xu, Jiabao ^{[4
]}

Li, Yanhong ^{[4
]}

Wang, Miao ^{[4
]}

Shi, Jianxin ^{[3
]}

Li, Jing ^{[2
,3
]}

Zhang, Dabing ^{[3
]}

Lee, Seunghee ^{[8
]}

Hu, Wushu ^{[4
]}

Poliakov, Alexander ^{[11
]}

Dubchak, Inna ^{[11
,12
]}

Ulat, Victor Jun ^{[2
]}

Borja, Frances Nikki ^{[2
]}

Mendoza, John Robert ^{[13
]}

Ali, Jauhar ^{[2
]}

机构：

[1] Chinese Acad Agr Sci, Inst Crop Sci, Beijing, Peoples R China

[2] Int Rice Res Inst, Manila, Philippines

[3] Shanghai Jiao Tong Univ, Sch Life Sci & Biotechnol, Shanghai, Peoples R China

[4] BGI Shenzhen, BGI Genom, Shenzhen, Peoples R China

[5] Chinese Acad Agr Sci, Agr Genom Inst, Shenzhen, Peoples R China

[6] Chinese Acad Agr Sci, Shenzhen Inst Innovat Breeding, Shenzhen, Peoples R China

[7] Anhui Agr Univ, Hefei, Anhui, Peoples R China

[8] Univ Arizona, Arizona Genom Inst, Sch Plant Sci, Tucson, AZ 85721 USA

[9] China Agr Univ, Beijing, Peoples R China

[10] Chinese Acad Sci, Inst Genet & Dev Biol, Beijing, Peoples R China

[11] DOE Joint Genome Inst, Walnut Creek, CA USA

[12] Lawrence Berkeley Natl Lab, Berkeley, CA USA

[13] Adv Sci & Technol Inst, Dept Sci & Technol, Quezon City, Philippines

[14] CIRAD, UMR AGAP, Montpellier, France

[15] Univ Montpellier, UMR AGAP, Montpellier, France

[16] Shanghai Ctr Bioinformat Technol, Shanghai, Peoples R China

来源：

NATURE | 2018年 / 557卷 / 7703期

基金：

比尔及梅琳达.盖茨基金会; 中国国家自然科学基金;

关键词：

GRAIN WIDTH; WEB SERVER; MAJOR QTL; GENE; DOMESTICATION; ENCODES; DIVERSIFICATION; IDENTIFICATION; ASSOCIATION; TRANSITION;

D O I：

10.1038/s41586-018-0063-9

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页码：43 / +

页数：21

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