A super pan-genomic landscape of rice

Lianguang Shang(Agricultural Genomics Institute at Shenzhen), Xiaoxia Li(Agricultural Genomics Institute at Shenzhen), Huiying He(Agricultural Genomics Institute at Shenzhen), Qiaoling Yuan(Agricultural Genomics Institute at Shenzhen), Yanni Song(Agricultural Genomics Institute at Shenzhen), Zhaoran Wei(Agricultural Genomics Institute at Shenzhen), Hai Lin(Agricultural Genomics Institute at Shenzhen), Min Hu(Agricultural Genomics Institute at Shenzhen), Fengli Zhao(Agricultural Genomics Institute at Shenzhen), Chao Zhang(Agricultural Genomics Institute at Shenzhen), Yuhua Li(Agricultural Genomics Institute at Shenzhen), Hongsheng Gao(Agricultural Genomics Institute at Shenzhen), Tianyi Wang(Agricultural Genomics Institute at Shenzhen), Xiangpei Liu(Agricultural Genomics Institute at Shenzhen), Hong Zhang(Agricultural Genomics Institute at Shenzhen), Ya Zhang(Agricultural Genomics Institute at Shenzhen), Shuaimin Cao(Agricultural Genomics Institute at Shenzhen), Xiaoman Yu(Agricultural Genomics Institute at Shenzhen), Bintao Zhang(Agricultural Genomics Institute at Shenzhen), Yong Zhang(Agricultural Genomics Institute at Shenzhen), Yiqing Tan(Nanjing Agricultural University), Qin Mao(Agricultural Genomics Institute at Shenzhen), Cheng Ai(Agricultural Genomics Institute at Shenzhen), Yingxue Yang(Agricultural Genomics Institute at Shenzhen), Bin Zhang(Agricultural Genomics Institute at Shenzhen), Zhiqiang Hu(University of California, Berkeley), Hongru Wang(University of California, Berkeley), Yang Lv(Agricultural Genomics Institute at Shenzhen), Yuexing Wang(China National Rice Research Institute), Jie Ma(China National Rice Research Institute), Quan Wang(Agricultural Genomics Institute at Shenzhen), Hongwei Lu(Southern University of Science and Technology), Zhe Wu(Southern University of Science and Technology), Shanlin Liu(China Agricultural University), Zongyi Sun(Bioscience (China)), Hongliang Zhang(Agricultural Genomics Institute at Shenzhen), Longbiao Guo(China National Rice Research Institute), Zichao Li(China Agricultural University), Yongfeng Zhou(Agricultural Genomics Institute at Shenzhen), Jiayang Li(Chinese Academy of Sciences), Zuofeng Zhu(China Agricultural University), Guosheng Xiong(Nanjing Agricultural University), Jue Ruan(Agricultural Genomics Institute at Shenzhen), Qian Qian(Agricultural Genomics Institute at Shenzhen)
Cell Research
July 12, 2022
10.1038/s41422-022-00685-z
Cited by 368Open Access
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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.

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