ArticleCell research2022
A super pan-genomic landscape of rice.
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Article in Cell research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 190 papers, 1 of them a synthesis that pooled it.
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190citing papers in PubMed, 1 pooled it
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190 citing papers in PubMed, 1 synthesis or guideline pooled it, 350 citations in OpenAlex.
- GWAS meta-analysis using a graph-based pan-genome enhanced gene mining efficiency for agronomic traits in rice.Nature communications · 2025Pooled it
- An IRAT109 NAM population: Genetic characterization and mapping utility for trait dissection in japonica rice (Oryza sativa L.).The plant genome · 2026Article
- Uncovering structural variation in conifer gigagenomes: evolutionary insights and technical challenges.Molecular biology and evolution · 2026Article
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- Whole Genome Sequencing of the Moruga Hill Rice (Biotech (Basel (Switzerland)) · 2026Article
- Integrating deep learning and pangenomics to recover missing heritability from wild structural variations.BMC genomics · 2026Review
- Empowering Plant Biotechnology Research: Super-Pangenomes as a Novel Arsenal for Crop Breeding and Improvement.Molecular biotechnology · 2026Review
- Genomic analyses of weedy rice reveal historical connections between European and northwestern Chinese rice.Plant communications · 2026Article
- Pangenome-resolved structural variation drives adaptation and trait evolution in cucumber.Nature genetics · 2026Article
- A Rare Allele of ST5 From Wild Rice Enhances Salt Tolerance in Rice.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Genomic Insights into the Genetic Diversity, Selection Signals, and Agronomic Traits of Rice (Plants (Basel, Switzerland) · 2026Article
- Different genomic footprint of small insertion-deletion and structural variants determines the genetic divergence of indica and japonica rice.BMC genomics · 2026Article
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- Mapping structural variants in Populus tomentosa reveals adaptive signatures and improves prediction of wood properties.Nature communications · 2026Article
- Challenges in Bringing Pangenome Research Into Breeding: A Case Study in Rice.Plant biotechnology journal · 2026Review
- Pangenomics for Agricultural Breeding: Construction Strategies, Evidence Integration, and Translational Constraints.Biology · 2026Review
- QTL-Seq and pyramiding of yield-related loci from wild rice (Molecular breeding : new strategies in plant improvement · 2026Article
- Integrative multi-omics analysis reveals the domestication mechanism of black rice.National science review · 2026Article
- The receptor-like pseudokinase LENG stimulates chilling tolerance in rice by inhibiting the activity of the OsCRPK1-OsGF14d module.Journal of integrative plant biology · 2026Article
130 more citing papers are in PubMed but not listed here.
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Authors and funding
44 authors at 8 institutions in 2 countries.
Lianguang Shang *Shenzhen 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. shanglianguang@caas.cn.ORCID 0000-0002-4606-2800
Xiaoxia Li *Shenzhen 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.ORCID 0000-0001-8140-6712
Huiying He *Shenzhen 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.ORCID 0000-0003-4844-9870
Qiaoling Yuan *Shenzhen 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.ORCID 0000-0001-8547-2944
Yanni Song *Shenzhen 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.ORCID 0000-0002-9984-7476
Zhaoran Wei *Shenzhen 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.ORCID 0000-0001-8855-2608
Hai Lin *Shenzhen 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.
Min Hu *State Key Laboratory for Agrobiotechnology, National Center for Evaluation of Agricultural Wild Plants (Rice), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China.
Fengli Zhao *Shenzhen 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.ORCID 0000-0003-1335-445X
Chao ZhangShenzhen 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.
Yuhua LiShenzhen 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.ORCID 0000-0002-7902-080X
Hongsheng GaoShenzhen 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.
Tianyi WangShenzhen 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.
Xiangpei LiuShenzhen 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.ORCID 0000-0002-3567-1782
Hong ZhangShenzhen 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.
Ya ZhangShenzhen 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.
Shuaimin CaoShenzhen 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.
Xiaoman YuShenzhen 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.ORCID 0000-0002-6373-0145
Bintao ZhangShenzhen 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.ORCID 0000-0002-8499-1985
Yong ZhangShenzhen 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.ORCID 0000-0002-2078-1479
Yiqing TanAcademy for Advanced Interdisciplinary Studies, Plant Phenomics Research Center, Nanjing Agricultural University, Nanjing, Jiangsu, China.
Mao QinShenzhen 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.
Cheng AiShenzhen 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.
Yingxue YangShenzhen 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.ORCID 0000-0001-9785-3613
Bin ZhangShenzhen 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.
Zhiqiang HuDepartment of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.ORCID 0000-0001-8854-3410
Hongru WangDepartment of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA.ORCID 0000-0001-8305-5231
Yang LvShenzhen 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.ORCID 0000-0001-9664-6794
Yuexing WangState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China.ORCID 0000-0002-0646-5664
Jie MaState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China.
Quan WangShenzhen 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.ORCID 0000-0003-2912-1263
Hongwei LuKey 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.
Zhe WuKey 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.ORCID 0000-0001-9436-3299
Shanlin LiuDepartment of Entomology, College of Plant Protection, China Agricultural University, Beijing, China.ORCID 0000-0001-8118-8313
Zongyi SunGrandomics Biosciences, Beijing, China.
Hongliang ZhangState Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China.
Longbiao GuoState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China.ORCID 0000-0003-1016-049X
Zichao LiState Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China.
Yongfeng ZhouShenzhen 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.ORCID 0000-0003-0780-2973
Jiayang LiState Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.ORCID 0000-0002-0487-6574
Zuofeng ZhuState Key Laboratory for Agrobiotechnology, National Center for Evaluation of Agricultural Wild Plants (Rice), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China. zhuzf@cau.edu.cn.ORCID 0000-0003-2535-9725
Guosheng XiongAcademy for Advanced Interdisciplinary Studies, Plant Phenomics Research Center, Nanjing Agricultural University, Nanjing, Jiangsu, China. gsxiong@njau.edu.cn.ORCID 0000-0002-4312-1676
Jue RuanShenzhen 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. ruanjue@caas.cn.ORCID 0000-0003-3713-3192
Qian QianShenzhen 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. qianqian188@hotmail.com.ORCID 0000-0002-0349-4937
Agricultural Genomics Institute at Shenzhen · CNChina Agricultural University · CNChina National Rice Research Institute · CNNanjing Agricultural University · CNSouthern University of Science and Technology · CNUniversity of California, Berkeley · USBioscience (China) · CNChinese Academy of Sciences · CN
Funding
No grant is acknowledged in the PubMed record.
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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OryzaDomesticationGenome, PlantGenomicsLeucineNucleotidesLeucineNucleotides
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