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

Wensheng Wang; Ramil Mauleon; Zhiqiang Hu; Dmytro Chebotarov; Shuaishuai Tai; Zhichao Wu; Min Li; Tianqing Zheng; Roven Rommel Fuentes; Fan Zhang; Locedie Mansueto; Dario Copetti; Millicent Sanciangco; Kevin Christian Palis; Jianlong Xu; Chen Sun; Binying Fu; Hongliang Zhang; Yongming Gao; Xiuqin Zhao; Fei Shen; Xiao Cui; Hong Yu; Zichao Li; Miaolin Chen; Jeffrey Detras; Yongli Zhou; Xinyuan Zhang; Yue Zhao; Dave Kudrna; Chunchao Wang; Rui Li; Ben Jia; Jinyuan Lu; Xianchang He; Zhaotong Dong; Jiabao Xu; Yanhong Li; Miao Wang; Jianxin Shi; Jing Li; Dabing Zhang; Seunghee Lee; Wushu Hu; Alexander Poliakov; Inna Dubchak; Victor Jun Ulat; Frances Nikki Borja; John Robert Mendoza; Jauhar Ali; Qiang Gao; Yongchao Niu; Zhen Yue; Ma Elizabeth B. Naredo; Jayson Talag; Xueqiang Wang; Jinjie Li; Xiaodong Fang; Ye Yin; Jean Christophe Glaszmann; Jianwei Zhang; Jiayang Li; Ruaraidh Sackville Hamilton; Rod A. Wing; Jue Ruan; Gengyun Zhang; Chaochun Wei; Nickolai Alexandrov; Kenneth L. McNally; Zhikang Li; Hei Leung

doi:10.1038/s41586-018-0063-9

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

Wensheng Wang, Ramil Mauleon, Zhiqiang Hu, Dmytro Chebotarov, Shuaishuai Tai, Zhichao Wu, Min Li, Tianqing Zheng, Roven Rommel Fuentes, Fan Zhang, Locedie Mansueto, Dario Copetti, Millicent Sanciangco, Kevin Christian Palis, Jianlong Xu, Chen Sun, Binying Fu, Hongliang Zhang, Yongming Gao, Xiuqin ZhaoFei Shen, Xiao Cui, Hong Yu, Zichao Li, Miaolin Chen, Jeffrey Detras, Yongli Zhou, Xinyuan Zhang, Yue Zhao, Dave Kudrna, Chunchao Wang, Rui Li, Ben Jia, Jinyuan Lu, Xianchang He, Zhaotong Dong, Jiabao Xu, Yanhong Li, Miao Wang, Jianxin Shi, Jing Li, Dabing Zhang, Seunghee Lee, Wushu Hu, Alexander Poliakov, Inna Dubchak, Victor Jun Ulat, Frances Nikki Borja, John Robert Mendoza, Jauhar Ali, Qiang Gao, Yongchao Niu, Zhen Yue, Ma Elizabeth B. Naredo, Jayson Talag, Xueqiang Wang, Jinjie Li, Xiaodong Fang, Ye Yin, Jean Christophe Glaszmann, Jianwei Zhang, Jiayang Li, Ruaraidh Sackville Hamilton, Rod A. Wing, Jue Ruan, Gengyun Zhang, Chaochun Wei, Nickolai Alexandrov, Kenneth L. McNally, Zhikang Li, Hei Leung

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1044 Scopus citations

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.

Original language	English (US)
Journal	Nature
Volume	557
Issue number	7703
DOIs	https://doi.org/10.1038/s41586-018-0063-9
State	Published - May 3 2018
Externally published	Yes

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Generated from Scopus record by KAUST IRTS on 2019-11-20

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@article{e65be071cbc54429b8d41261d1eaf008,

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.",

author = "Wensheng Wang and Ramil Mauleon and Zhiqiang Hu and Dmytro Chebotarov and Shuaishuai Tai and Zhichao Wu and Min Li and Tianqing Zheng and Fuentes, {Roven Rommel} and Fan Zhang and Locedie Mansueto and Dario Copetti and Millicent Sanciangco and Palis, {Kevin Christian} and Jianlong Xu and Chen Sun and Binying Fu and Hongliang Zhang and Yongming Gao and Xiuqin Zhao and Fei Shen and Xiao Cui and Hong Yu and Zichao Li and Miaolin Chen and Jeffrey Detras and Yongli Zhou and Xinyuan Zhang and Yue Zhao and Dave Kudrna and Chunchao Wang and Rui Li and Ben Jia and Jinyuan Lu and Xianchang He and Zhaotong Dong and Jiabao Xu and Yanhong Li and Miao Wang and Jianxin Shi and Jing Li and Dabing Zhang and Seunghee Lee and Wushu Hu and Alexander Poliakov and Inna Dubchak and Ulat, {Victor Jun} and Borja, {Frances Nikki} and Mendoza, {John Robert} and Jauhar Ali and Qiang Gao and Yongchao Niu and Zhen Yue and Naredo, {Ma Elizabeth B.} and Jayson Talag and Xueqiang Wang and Jinjie Li and Xiaodong Fang and Ye Yin and Glaszmann, {Jean Christophe} and Jianwei Zhang and Jiayang Li and Hamilton, {Ruaraidh Sackville} and Wing, {Rod A.} and Jue Ruan and Gengyun Zhang and Chaochun Wei and Nickolai Alexandrov and McNally, {Kenneth L.} and Zhikang Li and Hei Leung",

note = "Generated from Scopus record by KAUST IRTS on 2019-11-20",

year = "2018",

month = may,

day = "3",

doi = "10.1038/s41586-018-0063-9",

language = "English (US)",

volume = "557",

journal = "Nature",

issn = "1476-4687",

publisher = "Nature Research",

number = "7703",

}

Wang, W, Mauleon, R, Hu, Z, Chebotarov, D, Tai, S, Wu, Z, Li, M, Zheng, T, Fuentes, RR, Zhang, F, Mansueto, L, Copetti, D, Sanciangco, M, Palis, KC, Xu, J, Sun, C, Fu, B, Zhang, H, Gao, Y, Zhao, X, Shen, F, Cui, X, Yu, H, Li, Z, Chen, M, Detras, J, Zhou, Y, Zhang, X, Zhao, Y, Kudrna, D, Wang, C, Li, R, Jia, B, Lu, J, He, X, Dong, Z, Xu, J, Li, Y, Wang, M, Shi, J, Li, J, Zhang, D, Lee, S, Hu, W, Poliakov, A, Dubchak, I, Ulat, VJ, Borja, FN, Mendoza, JR, Ali, J, Gao, Q, Niu, Y, Yue, Z, Naredo, MEB, Talag, J, Wang, X, Li, J, Fang, X, Yin, Y, Glaszmann, JC, Zhang, J, Li, J, Hamilton, RS, Wing, RA, Ruan, J, Zhang, G, Wei, C, Alexandrov, N, McNally, KL, Li, Z & Leung, H 2018, 'Genomic variation in 3,010 diverse accessions of Asian cultivated rice', Nature, vol. 557, no. 7703. https://doi.org/10.1038/s41586-018-0063-9

TY - JOUR

T1 - Genomic variation in 3,010 diverse accessions of Asian cultivated rice

AU - Wang, Wensheng

AU - Mauleon, Ramil

AU - Hu, Zhiqiang

AU - Chebotarov, Dmytro

AU - Tai, Shuaishuai

AU - Wu, Zhichao

AU - Li, Min

AU - Zheng, Tianqing

AU - Fuentes, Roven Rommel

AU - Zhang, Fan

AU - Mansueto, Locedie

AU - Copetti, Dario

AU - Sanciangco, Millicent

AU - Palis, Kevin Christian

AU - Xu, Jianlong

AU - Sun, Chen

AU - Fu, Binying

AU - Zhang, Hongliang

AU - Gao, Yongming

AU - Zhao, Xiuqin

AU - Shen, Fei

AU - Cui, Xiao

AU - Yu, Hong

AU - Li, Zichao

AU - Chen, Miaolin

AU - Detras, Jeffrey

AU - Zhou, Yongli

AU - Zhang, Xinyuan

AU - Zhao, Yue

AU - Kudrna, Dave

AU - Wang, Chunchao

AU - Li, Rui

AU - Jia, Ben

AU - Lu, Jinyuan

AU - He, Xianchang

AU - Dong, Zhaotong

AU - Xu, Jiabao

AU - Li, Yanhong

AU - Wang, Miao

AU - Shi, Jianxin

AU - Li, Jing

AU - Zhang, Dabing

AU - Lee, Seunghee

AU - Hu, Wushu

AU - Poliakov, Alexander

AU - Dubchak, Inna

AU - Ulat, Victor Jun

AU - Borja, Frances Nikki

AU - Mendoza, John Robert

AU - Ali, Jauhar

AU - Gao, Qiang

AU - Niu, Yongchao

AU - Yue, Zhen

AU - Naredo, Ma Elizabeth B.

AU - Talag, Jayson

AU - Wang, Xueqiang

AU - Li, Jinjie

AU - Fang, Xiaodong

AU - Yin, Ye

AU - Glaszmann, Jean Christophe

AU - Zhang, Jianwei

AU - Li, Jiayang

AU - Hamilton, Ruaraidh Sackville

AU - Wing, Rod A.

AU - Ruan, Jue

AU - Zhang, Gengyun

AU - Wei, Chaochun

AU - Alexandrov, Nickolai

AU - McNally, Kenneth L.

AU - Li, Zhikang

AU - Leung, Hei

N1 - Generated from Scopus record by KAUST IRTS on 2019-11-20

PY - 2018/5/3

Y1 - 2018/5/3

N2 - 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.

AB - 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.

UR - http://www.nature.com/articles/s41586-018-0063-9

UR - http://www.scopus.com/inward/record.url?scp=85046452038&partnerID=8YFLogxK

U2 - 10.1038/s41586-018-0063-9

DO - 10.1038/s41586-018-0063-9

M3 - Article

C2 - 29695866

SN - 1476-4687

VL - 557

JO - Nature

JF - Nature

IS - 7703

ER -

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

Abstract

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