Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations

Peng Qin; Hongwei Lu; Huilong Du; Hao Wang; Weilan Chen; Zhuo Chen; Qiang He; Shujun Ou; Hongyu Zhang; Xuanzhao Li; Xiuxiu Li; Yan Li; Yi Liao; Qiang Gao; Bin Tu; Hua Yuan; Bingtian Ma; Yuping Wang; Yangwen Qian; Shijun Fan; Weitao Li; Jing Wang; Min He; Junjie Yin; Ting Li; Ning Jiang; Xuewei Chen; Chengzhi Liang; Shigui Li

doi:10.1016/j.cell.2021.04.046

Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations

Cell. 2021 Jun 24;184(13):3542-3558.e16. doi: 10.1016/j.cell.2021.04.046. Epub 2021 May 28.

Authors

Peng Qin¹, Hongwei Lu², Huilong Du³, Hao Wang⁴, Weilan Chen⁴, Zhuo Chen², Qiang He⁵, Shujun Ou⁶, Hongyu Zhang⁵, Xuanzhao Li⁵, Xiuxiu Li², Yan Li⁷, Yi Liao⁸, Qiang Gao⁷, Bin Tu⁴, Hua Yuan⁴, Bingtian Ma⁴, Yuping Wang⁴, Yangwen Qian⁹, Shijun Fan⁴, Weitao Li⁴, Jing Wang⁴, Min He⁴, Junjie Yin⁴, Ting Li⁴, Ning Jiang¹⁰, Xuewei Chen⁴, Chengzhi Liang¹¹, Shigui Li¹²

Affiliations

¹ State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China. Electronic address: qinpeng@sicau.edu.cn.
² State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
³ State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China; School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China.
⁴ State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.
⁵ School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China.
⁶ Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.
⁷ State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.
⁸ Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA.
⁹ Biogle Genome Editing Center, Changzhou, Jiangsu, China.
¹⁰ Department of Horticulture, Michigan State University, East Lansing, MI, USA.
¹¹ State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China. Electronic address: cliang@genetics.ac.cn.
¹² State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China. Electronic address: lishigui@sicau.edu.cn.

PMID: 34051138
DOI: 10.1016/j.cell.2021.04.046

Abstract

Structural variations (SVs) and gene copy number variations (gCNVs) have contributed to crop evolution, domestication, and improvement. Here, we assembled 31 high-quality genomes of genetically diverse rice accessions. Coupling with two existing assemblies, we developed pan-genome-scale genomic resources including a graph-based genome, providing access to rice genomic variations. Specifically, we discovered 171,072 SVs and 25,549 gCNVs and used an Oryza glaberrima assembly to infer the derived states of SVs in the Oryza sativa population. Our analyses of SV formation mechanisms, impacts on gene expression, and distributions among subpopulations illustrate the utility of these resources for understanding how SVs and gCNVs shaped rice environmental adaptation and domestication. Our graph-based genome enabled genome-wide association study (GWAS)-based identification of phenotype-associated genetic variations undetectable when using only SNPs and a single reference assembly. Our work provides rich population-scale resources paired with easy-to-access tools to facilitate rice breeding as well as plant functional genomics and evolutionary biology research.

Keywords: Gene copy number variation; Graph-based genome; High-quality assembly; Pan-genome; Rice; Structural variation.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adaptation, Physiological / genetics
Agriculture
Domestication
Ecotype*
Gene Expression Profiling
Gene Expression Regulation, Plant
Genes, Plant
Genetic Variation*
Genome, Plant*
Genomic Structural Variation
Molecular Sequence Annotation
Oryza / genetics*
Phenotype