A super pan-genomic landscape of rice
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Published:2022-07-12
Issue:10
Volume:32
Page:878-896
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ISSN:1748-7838
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Container-title:Cell Research
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language:en
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Short-container-title:Cell Res
Author:
Shang LianguangORCID, Li XiaoxiaORCID, He HuiyingORCID, Yuan QiaolingORCID, Song YanniORCID, Wei ZhaoranORCID, Lin Hai, Hu Min, Zhao FengliORCID, Zhang Chao, Li YuhuaORCID, Gao Hongsheng, Wang Tianyi, Liu XiangpeiORCID, Zhang Hong, Zhang Ya, Cao Shuaimin, Yu XiaomanORCID, Zhang BintaoORCID, Zhang YongORCID, Tan Yiqing, Qin Mao, Ai Cheng, Yang YingxueORCID, Zhang Bin, Hu ZhiqiangORCID, Wang HongruORCID, Lv YangORCID, Wang YuexingORCID, Ma Jie, Wang QuanORCID, Lu Hongwei, Wu ZheORCID, Liu ShanlinORCID, Sun Zongyi, Zhang Hongliang, Guo LongbiaoORCID, Li Zichao, Zhou YongfengORCID, Li JiayangORCID, Zhu ZuofengORCID, Xiong GuoshengORCID, Ruan JueORCID, Qian QianORCID
Abstract
AbstractPan-genomes from large natural populations can capture genetic diversity and reveal genomic complexity. Using de novo long-read assembly, we generated a graph-based super pan-genome of rice consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice. Our pan-genome reveals extensive structural variations (SVs) and gene presence/absence variations. Additionally, our pan-genome enables the accurate identification of nucleotide-binding leucine-rich repeat genes and characterization of their inter- and intraspecific diversity. Moreover, we uncovered grain weight-associated SVs which specify traits by affecting the expression of their nearby genes. We characterized genetic variants associated with submergence tolerance, seed shattering and plant architecture and found independent selection for a common set of genes that drove adaptation and domestication in Asian and African rice. This super pan-genome facilitates pinpointing of lineage-specific haplotypes for trait-associated genes and provides insights into the evolutionary events that have shaped the genomic architecture of various rice species.
Funder
China Postdoctoral Science Foundation Guangdong Basic and Applied Basic Research Foundation
Publisher
Springer Science and Business Media LLC
Subject
Cell Biology,Molecular Biology
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