Volume 32, No 10, Oct 2022

ISSN: 1001-0602 
EISSN: 1748-7838 2018 
impact factor 17.848* 
(Clarivate Analytics, 2019)

Volume 32 Issue 10, October 2022: 878-896   |  Open Access

ORIGINAL ARTICLES

A super pan-genomic landscape of rice

Lianguang Shang^1,†,* , Xiaoxia Li^1,† , Huiying He^1,† , Qiaoling Yuan^1,† , Yanni Song^1,† , Zhaoran Wei^1,† , Hai Lin^1,† , Min Hu^2,† , Fengli Zhao^1,† , Chao Zhang¹ , Yuhua Li¹ , Hongsheng Gao¹ , Tianyi Wang¹ , Xiangpei Liu¹ , Hong Zhang¹ , Ya Zhang¹ , Shuaimin Cao¹ , Xiaoman Yu¹ , Bintao Zhang¹ , Yong Zhang¹ , Yiqing Tan³ , Mao Qin¹ , Cheng Ai¹ , Yingxue Yang¹ , Bin Zhang¹ , Zhiqiang Hu⁴ , Hongru Wang⁵ , Yang Lv^1,6 , Yuexing Wang⁶ , Jie Ma⁶ , Quan Wang¹ , Hongwei Lu⁷ , Zhe Wu⁷ , Shanlin Liu⁸ , Zongyi Sun⁹ , Hongliang Zhang¹⁰ , Longbiao Guo⁶ , Zichao Li¹⁰ , Yongfeng Zhou¹ , Jiayang Li¹¹ , Zuofeng Zhu^2,* , Guosheng Xiong^3,* , Jue Ruan^1,* , Qian Qian^1,6

¹Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
²State Key Laboratory for Agrobiotechnology, National Center for Evaluation of Agricultural Wild Plants (Rice), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
³Academy for Advanced Interdisciplinary Studies, Plant Phenomics Research Center, Nanjing Agricultural University, Nanjing, Jiangsu, China
⁴Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
⁵Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
⁶State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China
⁷Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
⁸Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
⁹Grandomics Biosciences, Beijing, China
¹⁰State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
¹¹State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
^†These authors contributed equally: Lianguang Shang, Xiaoxia Li, Huiying He, Qiaoling Yuan, Yanni Song, Zhaoran Wei, Hai Lin, Min Hu, Fengli Zhao
Correspondence: Lianguang Shang(shanglianguang@caas.cn)Zuofeng Zhu(zhuzf@cau.edu.cn)Guosheng Xiong(gsxiong@njau.edu.cn)Jue Ruan(ruanjue@caas.cn)

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.

https://doi.org/10.1038/s41422-022-00685-z

FULL TEXT | PDF

Browse 762