{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T17:23:16Z","timestamp":1792516996757,"version":"4.5.0"},"reference-count":69,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T00:00:00Z","timestamp":1786924800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/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":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["acsess.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["The Plant Genome"],"published-print":{"date-parts":[[2026,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    The emergence of rice (\n                    <jats:italic>Oryza sativa<\/jats:italic>\n                    ) as a cultivated crop has represented a landmark in the history of agriculture in Kashmir Valley. Unlike winter cereals, such as wheat and barley, which exhibit clear West\u2010Asian origins, rice attained a different domestication trajectory linked to East\u2010Asian Neolithic cultures. However, evidence of such origins and adaptive history of Kashmir's rice landraces have relied on limited archaeo\u2010botanical data, tool typologies, and information pertaining regional cultural exchange. We present the first comprehensive genomics\u2010resource for the region produced through whole genome re\u2010sequencing of 142 rice germplasm lines. By leveraging on the 3000 Rice Genomes Project (3K RGP) database, we analyzed fine\u2010scale population structures and evolutionary relationships. Our findings reveal that local landraces possess\n                    <jats:italic>temperate japonica<\/jats:italic>\n                    (\n                    <jats:italic>Tej<\/jats:italic>\n                    ) genetic signatures with the origins having been traced to North\u2010East Asia, while the modern bred varieties in the region often align with\n                    <jats:italic>indica<\/jats:italic>\n                    (derivative) lineages from subtropical India. The sequence data were generated with a mean depth of 13.6x, and 3.94 million high\u2010confidence single nucleotide polymorphisms (SNPs) after stringent filtering. Populations resolved into a bipartite genetic structure (\n                    <jats:italic>K<\/jats:italic>\n                    \u00a0=\u00a02) comprising two major sub\u2010populations with an admixed group, with the help of high\u2010polymorphism information content SNP panels. Genome\u2010wide diversity analyses revealed the positive Tajima's\n                    <jats:italic>D<\/jats:italic>\n                    values, indicating extensive population structure and balancing selection, with localized signatures of directional selection. The allelic characterization explained the rich diversity at the functionally polymorphic loci linked to domestication, quality, and adaptive traits, particularly those associated with cold tolerance. The gene repository shall provide for development of better quality and climate resilient cultivars.\n                  <\/jats:p>","DOI":"10.1002\/tpg2.70289","type":"journal-article","created":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T06:47:56Z","timestamp":1787035676000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Re\u2010sequencing 142 rice genomes reveals the fine\u2010scale population structure and phylogenetic affinities of landraces of Kashmir Valley: Evidence from domestication and adaptive signatures"],"prefix":"10.1002","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2911-5536","authenticated-orcid":false,"given":"Asif Bashir","family":"Shikari","sequence":"first","affiliation":[{"name":"Division of Genetics &amp; Plant Breeding Sher\u2010e\u2010Kashmir University of Agricultural Sciences and Technology of Kashmir, Wadura Campus  Sopore Jammu and Kashmir India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-4863-2117","authenticated-orcid":false,"given":"V. Shasi Kiran","family":"Reddy","sequence":"additional","affiliation":[{"name":"Division of Genetics &amp; Plant Breeding Sher\u2010e\u2010Kashmir University of Agricultural Sciences and Technology of Kashmir, Wadura Campus  Sopore Jammu and Kashmir India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9115-3966","authenticated-orcid":false,"given":"Raheel Shafeeq","family":"Khan","sequence":"additional","affiliation":[{"name":"Division of Genetics &amp; Plant Breeding Sher\u2010e\u2010Kashmir University of Agricultural Sciences and Technology of Kashmir, Wadura Campus  Sopore Jammu and Kashmir India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-4764-2965","authenticated-orcid":false,"given":"Noor","family":"ul\u2010Ain","sequence":"additional","affiliation":[{"name":"Division of Genetics &amp; Plant Breeding Sher\u2010e\u2010Kashmir University of Agricultural Sciences and Technology of Kashmir, Wadura Campus  Sopore Jammu and Kashmir India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3850-5592","authenticated-orcid":false,"given":"Gazala H.","family":"Khan","sequence":"additional","affiliation":[{"name":"Mountain Research Centre for Field Crops Sher\u2010e\u2010Kashmir University of Agricultural Sciences and Technology of Kashmir, Khudwani Campus  Anantnag Jammu and Kashmir India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8934-3936","authenticated-orcid":false,"given":"Najeeb\u2010ul\u2010Rehman","family":"Sofi","sequence":"additional","affiliation":[{"name":"Mountain Research Centre for Field Crops Sher\u2010e\u2010Kashmir University of Agricultural Sciences and Technology of Kashmir, Khudwani Campus  Anantnag Jammu and Kashmir India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7584-8477","authenticated-orcid":false,"given":"Zahoor A.","family":"Dar","sequence":"additional","affiliation":[{"name":"Dryland Agricultural Research Station Sher\u2010e\u2010Kashmir University of Agricultural Sciences and Technology of Kashmir  Srinagar Jammu and Kashmir India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2500-537X","authenticated-orcid":false,"given":"Nazir A.","family":"Ganai","sequence":"additional","affiliation":[{"name":"Division of ABG Sher\u2010e\u2010Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar Campus  Srinagar Jammu and Kashmir India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7605-0926","authenticated-orcid":false,"given":"R. K.","family":"Salgotra","sequence":"additional","affiliation":[{"name":"School of Biotechnology Sher\u2010e\u2010Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha Campus  Jammu Jammu and Kashmir India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0793-0185","authenticated-orcid":false,"given":"Manmohan","family":"Sharma","sequence":"additional","affiliation":[{"name":"School of Biotechnology Sher\u2010e\u2010Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha Campus  Jammu Jammu and Kashmir India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"G. A.","family":"Parray","sequence":"additional","affiliation":[{"name":"Mountain Research Centre for Field Crops Sher\u2010e\u2010Kashmir University of Agricultural Sciences and Technology of Kashmir, Khudwani Campus  Anantnag Jammu and Kashmir India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9777-8163","authenticated-orcid":false,"given":"A. 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