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

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
Gene copy number variation Graph-based genome High-quality assembly Pan-genome Rice Structural variation

Journal

Cell
ISSN: 1097-4172
Titre abrégé: Cell
Pays: United States
ID NLM: 0413066

Informations de publication

Date de publication:
24 06 2021
Historique:
received: 10 01 2020
revised: 31 01 2021
accepted: 24 04 2021
pubmed: 30 5 2021
medline: 6 1 2022
entrez: 29 5 2021
Statut: ppublish

Résumé

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.

Identifiants

DOI: 10.1016/j.cell.2021.04.046 PMID: 34051138
pubmed: 34051138
pii: S0092-8674(21)00581-X
doi: 10.1016/j.cell.2021.04.046
pii:
doi:

Types de publication

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

Langues

eng

Sous-ensembles de citation

IM

Pagination

3542-3558.e16

Informations de copyright

Copyright © 2021 Elsevier Inc. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of interests The authors declare no competing interests.

Auteurs

Peng 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.

Hongwei 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.

Huilong 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 Development, Hebei University, Baoding, China.

Hao Wang (H)

State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.

Weilan Chen (W)

State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.

Zhuo 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.

Qiang He (Q)

School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China.

Shujun Ou (S)

Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.

Hongyu Zhang (H)

School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China.

Xuanzhao Li (X)

School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China.

Xiuxiu 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.

Yan 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.

Yi Liao (Y)

Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA.

Qiang 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.

Bin Tu (B)

State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.

Hua Yuan (H)

State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.

Bingtian Ma (B)

State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.

Yuping Wang (Y)

State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.

Yangwen Qian (Y)

Biogle Genome Editing Center, Changzhou, Jiangsu, China.

Shijun Fan (S)

State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.

Weitao Li (W)

State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.

Jing Wang (J)

State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.

Min He (M)

State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.

Junjie Yin (J)

State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.

Ting Li (T)

State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.

Ning Jiang (N)

Department of Horticulture, Michigan State University, East Lansing, MI, USA.

Xuewei Chen (X)

State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.

Chengzhi 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.

Shigui 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.

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Classifications MeSH

questionsmedicales.fr › Phénomènes biologiques › Adaptation biologique › Adaptation physiologique › Pan-genome analysis of 33 genetically diverse...
questionsmedicales.fr › Technologie, industrie et agriculture › Agriculture › Pan-genome analysis of 33 genetically diverse...
questionsmedicales.fr › Technologie, industrie et agriculture › Agriculture › Domestication › Pan-genome analysis of 33 genetically diverse...
questionsmedicales.fr › Environnement et santé publique › Environnement › Écosystème › Biodiversité › Écotype › Pan-genome analysis of 33 genetically diverse...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de profil d'expression de gènes › Pan-genome analysis of 33 genetically diverse...
questionsmedicales.fr › Phénomènes génétiques › Régulation de l'expression des gènes › Régulation de l'expression des gènes végétaux › Pan-genome analysis of 33 genetically diverse...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome végétal › Gènes de plante › Pan-genome analysis of 33 genetically diverse...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Pan-genome analysis of 33 genetically diverse...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome végétal › Pan-genome analysis of 33 genetically diverse...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Polymorphisme génétique › Variation structurale du génome › Pan-genome analysis of 33 genetically diverse...
questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Annotation de séquence moléculaire › Pan-genome analysis of 33 genetically diverse...
questionsmedicales.fr › Eucaryotes › Viridiplantae › Streptophyta › Embryophyta › Tracheobionta › Magnoliopsida › Poaceae › Oryza › Pan-genome analysis of 33 genetically diverse...
questionsmedicales.fr › Phénomènes génétiques › Phénotype › Pan-genome analysis of 33 genetically diverse...