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; Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)

doi:10.1038/s41586-018-0063-9

Back

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

Journal article

Open access

Peer reviewed

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, …

Nature (London), Vol.557(7703), pp.43-49

01/05/2018

DOI: https://doi.org/10.1038/s41586-018-0063-9

PMCID: PMC6784863

PMID: 29695866

Abstract

Agricultural genetics

Natural variation in plants

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. Analyses of genetic variation and population structure based on over 3,000 cultivated rice ( Oryza sativa ) genomes reveal subpopulations that correlate with geographic location and patterns of introgression consistent with multiple rice domestication events.

Files and links (1)

url

https://doi.org/10.1038/s41586-018-0063-9View

Published (Version of record) Open

Metrics

1 Record Views

See more details

Details

Title: Genomic variation in 3,010 diverse accessions of Asian cultivated rice
Creators - without role: Wensheng Wang - Beijing, China
Ramil Mauleon - Manila, Philippines
Zhiqiang Hu - Beijing, China Shanghai, China
Dmytro Chebotarov - Manila, Philippines
Shuaishuai Tai - Shenzhen, China
Zhichao Wu - Beijing, China Shenzhen, China
Min Li - Shenzhen, China Hefei, China
Tianqing Zheng - Beijing, China
Roven Rommel Fuentes - Manila, Philippines
Fan Zhang - Beijing, China
Locedie Mansueto - Manila, Philippines
Dario Copetti - Manila, Philippines Tucson, AZ USA
Millicent Sanciangco - Manila, Philippines
Kevin Christian Palis - Manila, Philippines
Jianlong Xu - Beijing, China Shenzhen, China Shenzhen, China
Chen Sun - Shanghai, China
Binying Fu - Beijing, China Shenzhen, China
Hongliang Zhang - Beijing, China
Yongming Gao - Beijing, China Shenzhen, China
Xiuqin Zhao - Beijing, China
Fei Shen - Beijing, China
Xiao Cui - Shanghai, China
Hong Yu - Beijing, China
Zichao Li - Beijing, China
Miaolin Chen - Shanghai, China
Jeffrey Detras - Manila, Philippines
Yongli Zhou - Beijing, China Shenzhen, China
Xinyuan Zhang - Shenzhen, China
Yue Zhao - Shanghai, China
Dave Kudrna - Tucson, AZ USA
Chunchao Wang - Beijing, China
Rui Li - Shanghai, China
Ben Jia - Shanghai, China
Jinyuan Lu - Shanghai, China
Xianchang He - Shanghai, China
Zhaotong Dong - Shanghai, China
Jiabao Xu - Shenzhen, China
Yanhong Li - Shenzhen, China
Miao Wang - Shenzhen, China
Jianxin Shi - Shanghai, China
Jing Li - Shanghai, China
Dabing Zhang - Shanghai, China
Seunghee Lee - Tucson, AZ USA
Wushu Hu - Shenzhen, China
Alexander Poliakov - Walnut Creek, CA USA
Inna Dubchak - Walnut Creek, CA USA Berkeley, CA USA
Victor Jun Ulat - Manila, Philippines
Frances Nikki Borja - Manila, Philippines
John Robert Mendoza - Quezon City, Philippines
Jauhar Ali - Manila, Philippines
Qiang Gao - Shenzhen, China
Yongchao Niu - Shenzhen, China
Zhen Yue - Shenzhen, China
Ma. Elizabeth B. Naredo - Manila, Philippines
Jayson Talag - Tucson, AZ USA
Xueqiang Wang - Beijing, China
Jinjie Li - Beijing, China
Xiaodong Fang - Shenzhen, China
Ye Yin - Shenzhen, China
Jean-Christophe Glaszmann - Montpellier, France Montpellier, France
Jianwei Zhang - Tucson, AZ USA
Jiayang Li - Beijing, China Beijing, China
Ruaraidh Sackville Hamilton - Manila, Philippines
Rod A. Wing - Manila, Philippines Tucson, AZ USA
Jue Ruan - Shenzhen, China
Gengyun Zhang - Shenzhen, China Shenzhen, China
Chaochun Wei - Shanghai, China Shanghai, China
Nickolai Alexandrov - Manila, Philippines
Kenneth L. McNally - Manila, Philippines
Zhikang Li - Beijing, China Shenzhen, China
Hei Leung - Manila, Philippines
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Publication Details: Nature (London), Vol.557(7703), pp.43-49
Publisher: Nature Publishing Group UK
Identifiers: 9943501508331
Academic Unit: King Abdullah University of Science & Technology
Language: English
Resource Type: Journal article