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A Catalog of Structural and Gene Copy Number Variations of Cultivated Rice

52 Pages Posted: 27 Jan 2020 Publication Status: Published

See all articles by Peng Qin

Peng Qin

Sichuan Agricultural University - Rice Research Institute

Hongwei Lu

Chinese Academy of Sciences (CAS) - State Key Laboratory of Plant Genomics

Huilong Du

Chinese Academy of Sciences (CAS) - State Key Laboratory of Plant Genomics

Weilan Chen

Sichuan Agricultural University - Rice Research Institute

Hao Wang

Sichuan Agricultural University - Rice Research Institute

Shujun Ou

Iowa State University - Department of Ecology, Evolution, and Organismal Biology

Zhuo Chen

Chinese Academy of Sciences (CAS) - State Key Laboratory of Plant Genomics

Xiuxiu Li

Chinese Academy of Sciences (CAS) - State Key Laboratory of Plant Genomics

Yan Li

Chinese Academy of Sciences (CAS) - State Key Laboratory of Plant Genomics

Yi Liao

University of California, Irvine - Department of Ecology and Evolutionary Biology

Qiang Gao

Chinese Academy of Sciences (CAS) - State Key Laboratory of Plant Genomics; Chinese Academy of Sciences (CAS) - Innovation Academy of Seed Design

Bin Tu

Sichuan Agricultural University - Rice Research Institute

Hua Yuan

Sichuan Agricultural University - Rice Research Institute

Bingtian Ma

Sichuan Agricultural University - Rice Research Institute

Yuping Wang

Sichuan Agricultural University - Rice Research Institute

Yangwen Qiang

Biogle Genome Editing Center

Shijun Fan

Sichuan Agricultural University - Rice Research Institute

Weitao Li

Sichuan Agricultural University - Rice Research Institute

Jiang Wang

Sichuan Agricultural University - Rice Research Institute

Min He

Sichuan Agricultural University - Rice Research Institute

Junjie Yin

Sichuan Agricultural University - Rice Research Institute

Ning Jiang

Michigan State University - Department of Horticulture

Xuewei Chen

Sichuan Agricultural University - Rice Research Institute

Chengzhi Liang

Chinese Academy of Sciences (CAS) - State Key Laboratory of Plant Genomics

Shigui Li

Sichuan Agricultural University - Rice Research Institute

More...

Abstract

The extent of structural variants (SVs), in particular copy number variations (CNVs) in plant and animal genomes remains unknown, mainly due to the lack of population-scale truly high-quality genomes. Here, we de novo assembled and annotated 31 gold-standard reference genomes from varieties representing all major cultivated rice subtypes, and accurately detected 107,251 non-redundant SVs affecting 644.91Mbp. A position-resolved pan-genome comprising 66,636 genes enabled our discovery that more than 38% of protein-coding genes in cultivated rice harbor CNVs, a far greater proportion than previous estimate. Illustrating functional consequences of these variations, CNVs of Awn3-1, OsVIL1 and OsMADS18, as well as a 345kb inversion likely contributed to major events in rice evolution, domestication and environmental adaptation. Beyond fully resolving the SVs of cultivated rice and comprehensively cataloguing CNVs among protein-coding genes, our study suggests that SVs-affected genes likely contribute to many mechanisms underlying domestication and phenotypic variation in rice.

Suggested Citation

Qin, Peng and Lu, Hongwei and Du, Huilong and Chen, Weilan and Wang, Hao and Ou, Shujun and Chen, Zhuo and Li, Xiuxiu and Li, Yan and Liao, Yi and Gao, Qiang and Tu, Bin and Yuan, Hua and Ma, Bingtian and Wang, Yuping and Qiang, Yangwen and Fan, Shijun and Li, Weitao and Wang, Jiang and He, Min and Yin, Junjie and Jiang, Ning and Chen, Xuewei and Liang, Chengzhi and Li, Shigui, A Catalog of Structural and Gene Copy Number Variations of Cultivated Rice. Available at SSRN: https://ssrn.com/abstract=3525548 or http://dx.doi.org/10.2139/ssrn.3525548
This version of the paper has not been formally peer reviewed.

Peng Qin (Contact Author)

Sichuan Agricultural University - Rice Research Institute ( email )

China

Hongwei Lu

Chinese Academy of Sciences (CAS) - State Key Laboratory of Plant Genomics

China

Huilong Du

Chinese Academy of Sciences (CAS) - State Key Laboratory of Plant Genomics

China

Weilan Chen

Sichuan Agricultural University - Rice Research Institute

China

Hao Wang

Sichuan Agricultural University - Rice Research Institute

China

Shujun Ou

Iowa State University - Department of Ecology, Evolution, and Organismal Biology

United States

Zhuo Chen

Chinese Academy of Sciences (CAS) - State Key Laboratory of Plant Genomics

China

Xiuxiu Li

Chinese Academy of Sciences (CAS) - State Key Laboratory of Plant Genomics

China

Yan Li

Chinese Academy of Sciences (CAS) - State Key Laboratory of Plant Genomics

China

Yi Liao

University of California, Irvine - Department of Ecology and Evolutionary Biology

321 Steinhaus Hall
Irvine, CA 92697-2525
United States

Qiang Gao

Chinese Academy of Sciences (CAS) - State Key Laboratory of Plant Genomics

China

Chinese Academy of Sciences (CAS) - Innovation Academy of Seed Design

Beijing
China

Bin Tu

Sichuan Agricultural University - Rice Research Institute

China

Hua Yuan

Sichuan Agricultural University - Rice Research Institute

China

Bingtian Ma

Sichuan Agricultural University - Rice Research Institute

China

Yuping Wang

Sichuan Agricultural University - Rice Research Institute

China

Yangwen Qiang

Biogle Genome Editing Center

China

Shijun Fan

Sichuan Agricultural University - Rice Research Institute

China

Weitao Li

Sichuan Agricultural University - Rice Research Institute

China

Jiang Wang

Sichuan Agricultural University - Rice Research Institute

China

Min He

Sichuan Agricultural University - Rice Research Institute

China

Junjie Yin

Sichuan Agricultural University - Rice Research Institute

China

Ning Jiang

Michigan State University - Department of Horticulture

United States

Xuewei Chen

Sichuan Agricultural University - Rice Research Institute

China

Chengzhi Liang

Chinese Academy of Sciences (CAS) - State Key Laboratory of Plant Genomics

China

Shigui Li

Sichuan Agricultural University - Rice Research Institute ( email )

China

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