{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T17:04:35Z","timestamp":1788282275493,"version":"build-2803163510"},"reference-count":32,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T00:00:00Z","timestamp":1786924800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T00:00:00Z","timestamp":1786924800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/501100003093","name":"Ministry of Higher Education, Malaysia","doi-asserted-by":"publisher","award":["LRGS\/1\/2019\/UPM\/01\/2\/2"],"award-info":[{"award-number":["LRGS\/1\/2019\/UPM\/01\/2\/2"]}],"id":[{"id":"10.13039\/501100003093","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Data"],"DOI":"10.1038\/s41597-026-07727-w","type":"journal-article","created":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T07:58:50Z","timestamp":1786953530000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Whole-Genome Variants Resource of 144 Oryza rufipogon Accessions"],"prefix":"10.1038","volume":"13","author":[{"given":"Lihao","family":"Zheng","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohamad Iqbal Hakim","family":"Mohd Azhan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shairul Izan","family":"Ramlee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erneeza","family":"Mohd Hata","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dzarifah","family":"Zulperi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kumar","family":"Gaurav","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sanu","family":"Arora","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8952-5684","authenticated-orcid":false,"given":"Muhammad Asyraf","family":"Md Hatta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,8,17]]},"reference":[{"key":"7727_CR1","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1023\/A:1005810616885","volume":"35","author":"GS Khush","year":"1997","unstructured":"Khush, G. S. Origin, dispersal, cultivation and variation of rice. Plant Mol. Biol. 35, 25\u201334 (1997).","journal-title":"Plant Mol. Biol."},{"key":"7727_CR2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-025-08883-6","author":"D Guo","year":"2025","unstructured":"Guo, D. et al. A pangenome reference of wild and cultivated rice. Nature https:\/\/doi.org\/10.1038\/s41586-025-08883-6 (2025).","journal-title":"Nature"},{"key":"7727_CR3","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-48845-6","volume":"15","author":"J Huang","year":"2024","unstructured":"Huang, J. et al. Haplotype-resolved gapless genome and chromosome segment substitution lines facilitate gene identification in wild rice. Nat. Commun. 15, 4573, https:\/\/doi.org\/10.1038\/s41467-024-48845-6 (2024).","journal-title":"Nat. Commun."},{"key":"7727_CR4","doi-asserted-by":"publisher","unstructured":"Brar, D. S. & Khush, G. S. Wild relatives of rice: a valuable genetic resource for genomics and breeding research. in Compendium of Plant Genomes: The Wild Oryza Genomes (eds Mondal, T. K. & Henry, R. J.) 1\u201325 (Springer-Verlag, https:\/\/doi.org\/10.1007\/978-3-319-71997-9_1 2018).","DOI":"10.1007\/978-3-319-71997-9_1"},{"key":"7727_CR5","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-38726-9","volume":"14","author":"Y Li","year":"2023","unstructured":"Li, Y. et al. OsMADS17 simultaneously increases grain number and grain weight in rice. Nat. Commun. 14, 3098, https:\/\/doi.org\/10.1038\/s41467-023-38726-9 (2023).","journal-title":"Nat. Commun."},{"key":"7727_CR6","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1016\/s1369-5266(03)00009-8","volume":"6","author":"DA Vaughan","year":"2003","unstructured":"Vaughan, D. A., Morishima, H. & Kadowaki, K. Diversity in the Oryza genus. Curr. Opin. Plant Biol. 6, 139\u2013146, https:\/\/doi.org\/10.1016\/s1369-5266(03)00009-8 (2003).","journal-title":"Curr. Opin. Plant Biol."},{"key":"7727_CR7","doi-asserted-by":"publisher","first-page":"522","DOI":"10.1016\/j.tibtech.2009.05.006","volume":"27","author":"RK Varshney","year":"2009","unstructured":"Varshney, R. K. et al. Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol 27, 522\u2013530, https:\/\/doi.org\/10.1016\/j.tibtech.2009.05.006 (2009).","journal-title":"Trends Biotechnol"},{"key":"7727_CR8","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1038\/nrg.2016.49","volume":"17","author":"S Goodwin","year":"2016","unstructured":"Goodwin, S., McPherson, J. D. & McCombie, W. R. Coming of age: ten years of next-generation sequencing technologies. Nat. Rev. Genet. 17, 333\u2013351, https:\/\/doi.org\/10.1038\/nrg.2016.49 (2016).","journal-title":"Nat. Rev. Genet."},{"key":"7727_CR9","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-41669-w","volume":"14","author":"R Chen","year":"2023","unstructured":"Chen, R. et al. A de novo evolved gene contributes to rice grain shape difference between indica and japonica. Nat. Commun. 14, 5906, https:\/\/doi.org\/10.1038\/s41467-023-41669-w (2023).","journal-title":"Nat. Commun."},{"key":"7727_CR10","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-37004-y","volume":"14","author":"Y Zhou","year":"2023","unstructured":"Zhou, Y. et al. Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice. Nat. Commun. 14, 1567, https:\/\/doi.org\/10.1038\/s41467-023-37004-y (2023).","journal-title":"Nat. Commun."},{"key":"7727_CR11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.jare.2022.08.004","volume":"42","author":"X Wang","year":"2022","unstructured":"Wang, X. et al. Selective and comparative genome architecture of Asian cultivated rice (Oryza sativa L.) attributed to domestication and modern breeding. J. Adv. Res. 42, 1\u201316, https:\/\/doi.org\/10.1016\/j.jare.2022.08.004 (2022).","journal-title":"J. Adv. Res."},{"key":"7727_CR12","doi-asserted-by":"publisher","first-page":"3507","DOI":"10.1093\/molbev\/msaa185","volume":"37","author":"Y Kou","year":"2020","unstructured":"Kou, Y. et al. Evolutionary Genomics of Structural Variation in Asian Rice (Oryza sativa) Domestication. Mol. Biol. Evol. 37, 3507\u20133524, https:\/\/doi.org\/10.1093\/molbev\/msaa185 (2020).","journal-title":"Mol. Biol. Evol."},{"key":"7727_CR13","doi-asserted-by":"publisher","DOI":"10.1186\/s12284-021-00468-x","volume":"14","author":"H Kajiya-Kanegae","year":"2021","unstructured":"Kajiya-Kanegae, H. et al. OryzaGenome2.1: Database of Diverse Genotypes in Wild Oryza Species. Rice 14, 24, https:\/\/doi.org\/10.1186\/s12284-021-00468-x (2021).","journal-title":"Rice"},{"key":"7727_CR14","doi-asserted-by":"publisher","first-page":"497","DOI":"10.1038\/nature11532","volume":"490","author":"X Huang","year":"2012","unstructured":"Huang, X. et al. A map of rice genome variation reveals the origin of cultivated rice. Nature 490, 497\u2013501, https:\/\/doi.org\/10.1038\/nature11532 (2012).","journal-title":"Nature"},{"key":"7727_CR15","unstructured":"International Rice Research Institute (IRRI). International Rice Genebank Operations Manual (IRRI, Los Ba\u00f1os, Philippines, available at https:\/\/genebanks.cgiar.org\/resources\/publications\/international-rice-genebank-operations-manual\/ 2017) (accessed 21 November 2025)."},{"key":"7727_CR16","doi-asserted-by":"publisher","first-page":"4321","DOI":"10.1093\/nar\/8.19.4321","volume":"8","author":"MG Murray","year":"1980","unstructured":"Murray, M. G. & Thompson, W. F. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research 8, 4321\u20134325, https:\/\/doi.org\/10.1093\/nar\/8.19.4321 (1980).","journal-title":"Nucleic Acids Research"},{"key":"7727_CR17","unstructured":"Andrews, S. FastQC: A quality control tool for high throughput sequence data. Babraham Bioinformatics https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/ (2010)."},{"key":"7727_CR18","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114\u20132120, https:\/\/doi.org\/10.1093\/bioinformatics\/btu170 (2014).","journal-title":"Bioinformatics"},{"key":"7727_CR19","doi-asserted-by":"publisher","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","volume":"32","author":"P Ewels","year":"2016","unstructured":"Ewels, P., Magnusson, M., Lundin, S. & K\u00e4ller, M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32, 3047\u20133048, https:\/\/doi.org\/10.1093\/bioinformatics\/btw354 (2016).","journal-title":"Bioinformatics"},{"key":"7727_CR20","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754\u20131760, https:\/\/doi.org\/10.1093\/bioinformatics\/btp324 (2009).","journal-title":"Bioinformatics"},{"key":"7727_CR21","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. et al. The Sequence Alignment\/Map format and SAMtools. Bioinformatics 25, 2078\u20132079, https:\/\/doi.org\/10.1093\/bioinformatics\/btp352 (2009).","journal-title":"Bioinformatics"},{"key":"7727_CR22","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1038\/ng.806","volume":"43","author":"MA DePristo","year":"2011","unstructured":"DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491\u2013498, https:\/\/doi.org\/10.1038\/ng.806 (2011).","journal-title":"Nat. Genet."},{"key":"7727_CR23","doi-asserted-by":"publisher","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","volume":"27","author":"P Danecek","year":"2011","unstructured":"Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156\u20132158, https:\/\/doi.org\/10.1093\/bioinformatics\/btr330 (2011).","journal-title":"Bioinformatics"},{"key":"7727_CR24","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1086\/519795","volume":"81","author":"S Purcell","year":"2007","unstructured":"Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559\u2013575, https:\/\/doi.org\/10.1086\/519795 (2007).","journal-title":"Am. J. Hum. Genet."},{"key":"7727_CR25","year":"2026","unstructured":"NCBI Sequence Read Archive https:\/\/identifiers.org\/ncbi\/insdc.sra:SRP593153 (2026)."},{"key":"7727_CR26","author":"European Variation Archive","year":"2026","unstructured":"European Variation Archive. Variant detection of 144 Oryza rufipogon accessions https:\/\/www.ebi.ac.uk\/eva\/?eva-study=PRJEB111745 (2026)."},{"key":"7727_CR27","doi-asserted-by":"publisher","first-page":"132","DOI":"10.3390\/jcm9010132","volume":"9","author":"R Pereira","year":"2020","unstructured":"Pereira, R., Oliveira, J. & Sousa, M. Bioinformatics and Computational Tools for Next-Generation Sequencing Analysis in Clinical Genetics. J. Clin. Med. 9, 132, https:\/\/doi.org\/10.3390\/jcm9010132 (2020).","journal-title":"J. Clin. Med."},{"key":"7727_CR28","doi-asserted-by":"publisher","first-page":"879","DOI":"10.1093\/bib\/bbt069","volume":"15","author":"Y Guo","year":"2014","unstructured":"Guo, Y. et al. Three-stage quality control strategies for DNA re-sequencing data. Brief. Bioinform. 15, 879\u2013889, https:\/\/doi.org\/10.1093\/bib\/bbt069 (2014).","journal-title":"Brief. Bioinform."},{"key":"7727_CR29","doi-asserted-by":"publisher","DOI":"10.1038\/s41597-022-01129-4","volume":"9","author":"A Gheyas","year":"2022","unstructured":"Gheyas, A. et al. Whole genome sequences of 234 indigenous African chickens from Ethiopia. Sci. Data 9, 53, https:\/\/doi.org\/10.1038\/s41597-022-01129-4 (2022).","journal-title":"Sci. Data"},{"key":"7727_CR30","doi-asserted-by":"publisher","DOI":"10.1038\/s41597-024-02973-2","volume":"11","author":"S Belay","year":"2024","unstructured":"Belay, S. et al. Whole-genome resource sequences of 57 indigenous Ethiopian goats. Sci. Data 11, 139, https:\/\/doi.org\/10.1038\/s41597-024-02973-2 (2024).","journal-title":"Sci. Data"},{"key":"7727_CR31","doi-asserted-by":"publisher","DOI":"10.1186\/s12284-022-00582-4","volume":"15","author":"P Malik","year":"2022","unstructured":"Malik, P. et al. Genotyping-by-Sequencing Based Investigation of Population Structure and Genome Wide Association Studies for Seven Agronomically Important Traits in a Set of 346 Oryza rufipogon Accessions. Rice 15, 37, https:\/\/doi.org\/10.1186\/s12284-022-00582-4 (2022).","journal-title":"Rice"},{"key":"7727_CR32","doi-asserted-by":"publisher","first-page":"6519","DOI":"10.1016\/j.cell.2025.08.034","volume":"188","author":"M Akopyan","year":"2025","unstructured":"Akopyan, M. et al. Reference genome choice compromises population genetic analyses. Cell 188, 6519\u20136535, https:\/\/doi.org\/10.1016\/j.cell.2025.08.034 (2025).","journal-title":"Cell"}],"container-title":["Scientific Data"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41597-026-07727-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41597-026-07727-w","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41597-026-07727-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T07:58:57Z","timestamp":1786953537000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41597-026-07727-w"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,17]]},"references-count":32,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["7727"],"URL":"https:\/\/doi.org\/10.1038\/s41597-026-07727-w","relation":{"references":[{"id-type":"uri","id":"https:\/\/identifiers.org\/ncbi\/insdc.sra:SRP593153","asserted-by":"subject"},{"id-type":"uri","id":"https:\/\/www.ebi.ac.uk\/eva\/?eva-study=PRJEB111745Study PRJEB111745; analysis ERZ29297505","asserted-by":"subject"}]},"ISSN":["2052-4463"],"issn-type":[{"value":"2052-4463","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,17]]},"assertion":[{"value":"21 July 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 June 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 August 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"All authors have read and agreed to the published version of the manuscript.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Ethics"}}],"article-number":"1197"}}