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Nature. 2018 May;557(7703):43-49. doi: 10.1038/s41586-018-0063-9. Epub 2018 Apr 25.

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

Author information

1
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
2
International Rice Research Institute, Manila, Philippines.
3
School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
4
BGI Genomics, BGI-Shenzhen, Shenzhen, China.
5
Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China.
6
Shenzhen Institute for Innovative Breeding, Chinese Academy of Agricultural Sciences, Shenzhen, China.
7
Anhui Agricultural University, Hefei, China.
8
Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
9
China Agricultural University, Beijing, China.
10
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
11
DOE Joint Genome Institute, Walnut Creek, CA, USA.
12
Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
13
Advanced Science and Technology Institute, Department of Science and Technology, Quezon City, Philippines.
14
UMR AGAP, CIRAD, Montpellier, France.
15
UMR AGAP, Université de Montpellier, Montpellier, France.
16
International Rice Research Institute, Manila, Philippines. rwing@ag.arizona.edu.
17
Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA. rwing@ag.arizona.edu.
18
Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China. ruanjue@caas.cn.
19
BGI Genomics, BGI-Shenzhen, Shenzhen, China. zhanggengyun@genomics.cn.
20
Shenzhen Institute for Innovative Breeding, Chinese Academy of Agricultural Sciences, Shenzhen, China. zhanggengyun@genomics.cn.
21
School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China. ccwei@sjtu.edu.cn.
22
Shanghai Center for Bioinformation Technology, Shanghai, China. ccwei@sjtu.edu.cn.
23
International Rice Research Institute, Manila, Philippines. nalexandrov@inariag.com.
24
International Rice Research Institute, Manila, Philippines. k.mcnally@irri.org.
25
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China. lizhikang@caas.cn.
26
Shenzhen Institute for Innovative Breeding, Chinese Academy of Agricultural Sciences, Shenzhen, China. lizhikang@caas.cn.

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.

PMID:
29695866
DOI:
10.1038/s41586-018-0063-9
[Indexed for MEDLINE]

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