A super pan-genomic landscape of rice

Shang, Lianguang1; Li, Xiaoxia1; He, Huiying1; Yuan, Qiaoling1; Song, Yanni1; Wei, Zhaoran1; Lin, Hai1; Hu, Min2; Zhao, Fengli1; Zhang, Chao1; Li, Yuhua1; Gao, Hongsheng1; Wang, Tianyi1; Liu, Xiangpei1; Zhang, Hong1; Zhang, Ya1; Cao, Shuaimin1; Yu, Xiaoman1; Zhang, Bintao1; Zhang, Yong1; Tan, Yiqing3; Qin, Mao1; Ai, Cheng1; Yang, Yingxue1; Zhang, Bin1; Hu, Zhiqiang4; Wang, Hongru5; Lv, Yang1,6; Wang, Yuexing6; Ma, Jie6; Wang, Quan1; Lu, Hongwei7; Wu, Zhe7; Liu, Shanlin8; Sun, Zongyi9; Zhang, Hongliang10; Guo, Longbiao6; Li, Zichao10; Zhou, Yongfeng1; Li, Jiayang11; Zhu, Zuofeng2; Xiong, Guosheng3; Ruan, Jue1; Qian, Qian1,6

2022-07-01

10.1038/s41422-022-00685-z

CELL RESEARCH   Impact Factor & Quartile

1001-0602

1748-7838

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.

SCI

English

Others

National Natural Science Foundation of China["32188102","32101718","31925029","31822029","31961143015","91735304"] ; Agricultural Science and Technology Innovation Program, Shenzhen Science and Technology Program[KQTD2016113010482651] ; Science Technology Innovation and Industrial Development of Shenzhen Dapeng New District[RC201901-05] ; Guangdong Basic and Applied Basic Research Foundation["2019A1515110557","2020B1515120086"] ; China Postdoctoral Science Foundation["BX201600151","2020M672903","BX2020372"] ; National Key RD Program[2019YFA0707003]

Cell Biology

Cell Biology

WOS:000823361200001

SPRINGERNATURE

MOLECULAR BIOLOGY & GENETICS

Web of Science

1.Chinese Acad Agr Sci, Guangdong Lab Lingnan Modern Agr, Agr Genom Inst Shenzhen,Shenzhen Branch, Genome Anal Lab,Minist Agr & Rural Affairs, Shenzhen, Guangdong, Peoples R China
2.China Agr Univ, Dept Plant Genet & Breeding, Natl Ctr Evaluat Agr Wild Plants Rice, State Key Lab Agrobiotechnol, Beijing, Peoples R China
3.Nanjing Agr Univ, Plant Phen Res Ctr, Acad Adv Interdisciplinary Studies, Nanjing, Jiangsu, Peoples R China
4.Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA
5.Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA
6.China Natl Rice Res Inst, State Key Lab Rice Biol, Hangzhou, Zhejiang, Peoples R China
7.Southern Univ Sci & Technol, Key Lab Mol Design Plant Cell Factory, Guangdong Higher Educ Inst, Dept Biol,Sch Life Sci,Inst Plant & Food Sci, Shenzhen, Guangdong, Peoples R China
8.China Agr Univ, Coll Plant Protect, Dept Entomol, Beijing, Peoples R China
9.Grand Biosci, Beijing, Peoples R China
10.China Agr Univ, Coll Agron & Biotechnol, Beijing Key Lab Crop Genet Improvement, State Key Lab Agrobiotechnol, Beijing, Peoples R China
11.Chinese Acad Sci, Inst Genet & Dev Biol, State Key Lab Plant Gen, Beijing, Peoples R China

Shang, Lianguang,Li, Xiaoxia,He, Huiying,et al. A super pan-genomic landscape of rice[J]. CELL RESEARCH,2022.

Shang, Lianguang.,Li, Xiaoxia.,He, Huiying.,Yuan, Qiaoling.,Song, Yanni.,...&Qian, Qian.(2022).A super pan-genomic landscape of rice.CELL RESEARCH.

Shang, Lianguang,et al."A super pan-genomic landscape of rice".CELL RESEARCH (2022).