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Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations.
Qin, Peng; Lu, Hongwei; Du, Huilong; Wang, Hao; Chen, Weilan; Chen, Zhuo; He, Qiang; Ou, Shujun; Zhang, Hongyu; Li, Xuanzhao; Li, Xiuxiu; Li, Yan; Liao, Yi; Gao, Qiang; Tu, Bin; Yuan, Hua; Ma, Bingtian; Wang, Yuping; Qian, Yangwen; Fan, Shijun; Li, Weitao; Wang, Jing; He, Min; Yin, Junjie; Li, Ting; Jiang, Ning; Chen, Xuewei; Liang, Chengzhi; Li, Shigui.
Afiliación
  • Qin P; 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.
  • Lu H; 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.
  • Du H; 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 Developme
  • Wang H; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.
  • Chen W; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.
  • Chen Z; 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.
  • He Q; School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China.
  • Ou S; Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.
  • Zhang H; School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China.
  • Li X; School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China.
  • Li X; 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.
  • Li Y; State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.
  • Liao Y; Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA.
  • Gao Q; State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.
  • Tu B; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.
  • Yuan H; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.
  • Ma B; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.
  • Wang Y; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.
  • Qian Y; Biogle Genome Editing Center, Changzhou, Jiangsu, China.
  • Fan S; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.
  • Li W; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.
  • Wang J; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.
  • He M; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.
  • Yin J; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.
  • Li T; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.
  • Jiang N; Department of Horticulture, Michigan State University, East Lansing, MI, USA.
  • Chen X; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.
  • Liang C; 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.
  • Li S; 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.
Cell ; 184(13): 3542-3558.e16, 2021 06 24.
Article en En | MEDLINE | ID: mdl-34051138
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.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Oryza / Variación Genética / Genoma de Planta / Ecotipo Idioma: En Revista: Cell Año: 2021 Tipo del documento: Article
Texto completo
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PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Oryza / Variación Genética / Genoma de Planta / Ecotipo Idioma: En Revista: Cell Año: 2021 Tipo del documento: Article