ArticleNature2018
Genomic variation in 3,010 diverse accessions of Asian cultivated rice.
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822 citing papers in PubMed, 1 synthesis or guideline pooled it.
- GWAS meta-analysis using a graph-based pan-genome enhanced gene mining efficiency for agronomic traits in rice.Nature communications · 2025Pooled it
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- Two telomere-to-telomere Nelumbo genome assemblies reveal domestication history and empower precision breeding.Nature communications · 2026Article
- Haplotype Analysis of the Wx and SSIIa Genes and Their Association with Starch Physicochemical Properties in Diverse Rice Germplasm.Molecular biotechnology · 2026Review
- Different genomic footprint of small insertion-deletion and structural variants determines the genetic divergence of indica and japonica rice.BMC genomics · 2026Article
- Phylogeny-driven pangenome analysis uncovers the genomic landscape of domesticated and wild Armeniaca species.Horticulture research · 2026Article
- PanGraphRNA: An efficient and flexible bioinformatics platform for graph pangenome-based RNA-seq data analysis.Journal of integrative plant biology · 2026Article
- The Pan-Genome of 1107 Spotted Sea Bass Accessions Reveals Gene Evolution Patterns During Domestication Selection.Molecular ecology resources · 2026Article
762 more citing papers are in PubMed but not listed here.
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Authors and funding
72 authors.
Wensheng WangInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
Ramil MauleonInternational Rice Research Institute, Manila, Philippines.
Zhiqiang HuInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
Dmytro ChebotarovInternational Rice Research Institute, Manila, Philippines.
Shuaishuai TaiBGI Genomics, BGI-Shenzhen, Shenzhen, China.
Zhichao WuInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
Min LiShenzhen Institute for Innovative Breeding, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Tianqing ZhengInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
Roven Rommel FuentesInternational Rice Research Institute, Manila, Philippines.
Fan ZhangInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
Locedie MansuetoInternational Rice Research Institute, Manila, Philippines.
Dario CopettiInternational Rice Research Institute, Manila, Philippines.
Millicent SanciangcoInternational Rice Research Institute, Manila, Philippines.
Kevin Christian PalisInternational Rice Research Institute, Manila, Philippines.
Jianlong XuInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
Chen SunSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
Binying FuInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
Hongliang ZhangChina Agricultural University, Beijing, China.
Yongming GaoInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
Xiuqin ZhaoInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
Fei ShenChina Agricultural University, Beijing, China.
Xiao CuiSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
Hong YuInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
Zichao LiChina Agricultural University, Beijing, China.
Miaolin ChenSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
Jeffrey DetrasInternational Rice Research Institute, Manila, Philippines.
Yongli ZhouInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
Xinyuan ZhangAgricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Yue ZhaoSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
Dave KudrnaArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
Chunchao WangInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
Rui LiSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
Ben JiaSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
Jinyuan LuSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
Xianchang HeSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
Zhaotong DongSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
Jiabao XuBGI Genomics, BGI-Shenzhen, Shenzhen, China.
Yanhong LiBGI Genomics, BGI-Shenzhen, Shenzhen, China.
Miao WangBGI Genomics, BGI-Shenzhen, Shenzhen, China.
Jianxin ShiSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
Jing LiSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
Dabing ZhangSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
Seunghee LeeArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
Wushu HuBGI Genomics, BGI-Shenzhen, Shenzhen, China.
Alexander PoliakovDOE Joint Genome Institute, Walnut Creek, CA, USA.
Inna DubchakDOE Joint Genome Institute, Walnut Creek, CA, USA.
Victor Jun UlatInternational Rice Research Institute, Manila, Philippines.
Frances Nikki BorjaInternational Rice Research Institute, Manila, Philippines.
John Robert MendozaAdvanced Science and Technology Institute, Department of Science and Technology, Quezon City, Philippines.
Jauhar AliInternational Rice Research Institute, Manila, Philippines.
Jing LiSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
Qiang GaoBGI Genomics, BGI-Shenzhen, Shenzhen, China.
Yongchao NiuBGI Genomics, BGI-Shenzhen, Shenzhen, China.
Zhen YueBGI Genomics, BGI-Shenzhen, Shenzhen, China.
Ma Elizabeth B NaredoInternational Rice Research Institute, Manila, Philippines.
Jayson TalagArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
Xueqiang WangChina Agricultural University, Beijing, China.
Jinjie LiChina Agricultural University, Beijing, China.
Xiaodong FangBGI Genomics, BGI-Shenzhen, Shenzhen, China.
Ye YinBGI Genomics, BGI-Shenzhen, Shenzhen, China.
Jean-Christophe GlaszmannUMR AGAP, CIRAD, Montpellier, France.
Jianwei ZhangArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
Jiayang LiInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
Ruaraidh Sackville HamiltonInternational Rice Research Institute, Manila, Philippines.
Rod A WingInternational Rice Research Institute, Manila, Philippines. rwing@ag.arizona.edu.
Jue RuanAgricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China. ruanjue@caas.cn.
Gengyun ZhangBGI Genomics, BGI-Shenzhen, Shenzhen, China. zhanggengyun@genomics.cn.
Chaochun WeiSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China. ccwei@sjtu.edu.cn.
Nickolai AlexandrovInternational Rice Research Institute, Manila, Philippines. nalexandrov@inariag.com.
Kenneth L McNallyInternational Rice Research Institute, Manila, Philippines. k.mcnally@irri.org.
Zhikang LiInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China. lizhikang@caas.cn.
Hei LeungInternational Rice Research Institute, Manila, Philippines.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Here we analyse genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our results are consistent with the five major groups previously recognized, but also suggest several unreported subpopulations that correlate with geographic location. We identified 29 million single nucleotide polymorphisms, 2.4 million small indels and over 90,000 structural variations that contribute to within- and between-population variation. Using pan-genome analyses, we identified more than 10,000 novel full-length protein-coding genes and a high number of presence-absence variations. The complex patterns of introgression observed in domestication genes are consistent with multiple independent rice domestication events. The public availability of data from the 3,000 Rice Genomes Project provides a resource for rice genomics research and breeding.
Indexed as
Genetic VariationAsiaCrops, AgriculturalEvolution, MolecularGenes, PlantGenetics, PopulationGenome, PlantGenomicsHaplotypesINDEL MutationOryzaPhylogenyPlant BreedingPolymorphism, Single Nucleotide
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