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A super pan-genomic landscape of rice.

ABSTRACT: Pan-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.

SUBMITTER: Shang L

PROVIDER: S-EPMC9525306 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature

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A super pan-genomic landscape of rice.

Shang Lianguang L Li Xiaoxia X He Huiying H Yuan Qiaoling Q Song Yanni Y Wei Zhaoran Z Lin Hai H Hu Min M Zhao Fengli F Zhang Chao C Li Yuhua Y Gao Hongsheng H Wang Tianyi T Liu Xiangpei X Zhang Hong H Zhang Ya Y Cao Shuaimin S Yu Xiaoman X Zhang Bintao B Zhang Yong Y Tan Yiqing Y Qin Mao M Ai Cheng C Yang Yingxue Y Zhang Bin B Hu Zhiqiang Z Wang Hongru H Lv Yang Y Wang Yuexing Y Ma Jie J Wang Quan Q Lu Hongwei H Wu Zhe Z Liu Shanlin S Sun Zongyi Z Zhang Hongliang H Guo Longbiao L Li Zichao Z Zhou Yongfeng Y Li Jiayang J Zhu Zuofeng Z Xiong Guosheng G Ruan Jue J Qian Qian Q

Cell research 20220712 10

Pan-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 repe ...[more]

PMID: 35821092

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A super pan-genomic landscape of rice.

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A super pan-genomic landscape of rice.

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