{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T07:41:29Z","timestamp":1792482089547,"version":"4.5.0"},"reference-count":55,"publisher":"Wiley","issue":"20","license":[{"start":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T00:00:00Z","timestamp":1792454400000},"content-version":"vor","delay-in-days":19,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Molecular Ecology"],"published-print":{"date-parts":[[2026,10]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    India is a major centre of rice diversity, where long\u2010term cultivation across contrasting environments has generated substantial genomic and phenotypic variation. We analysed genome\u2010wide SNP variation in 313 Indian rice accessions to resolve ancestry structure, regional diversity, spatial genetic processes, environmental associations and haplotype variation at key domestication and adaptation genes. Population structure analyses resolved eight ancestry groups corresponding to\n                    <jats:italic>indica<\/jats:italic>\n                    ,\n                    <jats:italic>aus<\/jats:italic>\n                    ,\n                    <jats:italic>aromatic<\/jats:italic>\n                    and\n                    <jats:italic>japonica<\/jats:italic>\n                    lineages. Ancestry explained substantially more genomic differentiation than biogeographic regionalization, while there is extensive historical connectivity among lineages and regions. Genetic diversity considerably varied across biogeographic zones. After balanced resampling, the Himalayan region showed the highest standardized allelic diversity and private\u2010allele richness, whereas the North\u2010East region retained high observed heterozygosity and broad ancestry representation. Isolation\u2010by\u2010distance was weak overall but strongly lineage\u2010 and region\u2010dependent. Spatial principal component analysis identified significant ancestry\u2010independent broad\u2010scale genetic gradients, demonstrating geography\u2010influenced structure beyond lineage composition. Redundancy analysis detected significant genome\u2013environment associations (\n                    <jats:italic>F<\/jats:italic>\n                    \u2009=\u20093.07,\n                    <jats:italic>p<\/jats:italic>\n                    \u2009=\u20090.001), with climate explaining more independent genomic variation (2.7%) than soil (0.9%). District\u2010level tribal population proportion showed only a weak negative association with individual heterozygosity (Spearman\n                    <jats:italic>\u03c1<\/jats:italic>\n                    \u2009=\u2009\u22120.155,\n                    <jats:italic>p<\/jats:italic>\n                    \u2009=\u20090.006), although PTP classes exhibited low\u2010to\u2010moderate genetic differentiation. Haplotype analysis revealed strong locus\u2010specific ancestry and geographic structuring at\n                    <jats:italic>sd1<\/jats:italic>\n                    ,\n                    <jats:italic>Wx<\/jats:italic>\n                    ,\n                    <jats:italic>GS3<\/jats:italic>\n                    and\n                    <jats:italic>DRO1<\/jats:italic>\n                    . Together, the results show that Indian rice diversity is a reticulate genomic mosaic shaped by ancestry, geography, historical gene flow and environmental heterogeneity. This study provides a landscape\u2010genomic framework for conservation and targeted germplasm utilization in breeding programmes.\n                  <\/jats:p>","DOI":"10.1111\/mec.70604","type":"journal-article","created":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T07:27:06Z","timestamp":1792481226000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genome\u2010Wide Analyses Reveal Spatially Structured Genetic Diversity in Indian Rice Shaped by Ancestry, Geography and Environment"],"prefix":"10.1111","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6590-9758","authenticated-orcid":false,"given":"Somnath","family":"Roy","sequence":"first","affiliation":[{"name":"Central Rainfed Upland Rice Research Station ICAR\u2010Central Rice Research Institute  Hazaribag Jharkhand India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2571-7169","authenticated-orcid":false,"given":"Puranjoy","family":"Sar","sequence":"additional","affiliation":[{"name":"Central Rainfed Upland Rice Research Station ICAR\u2010Central Rice Research Institute  Hazaribag Jharkhand India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4419-2345","authenticated-orcid":false,"given":"Sonal","family":"Gupta","sequence":"additional","affiliation":[{"name":"Trivedi School of Biosciences Ashoka University  Sonipat Haryana India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4929-2011","authenticated-orcid":false,"given":"Shreyasi Gupta","family":"Choudhury","sequence":"additional","affiliation":[{"name":"National Bureau of Soil Survey &amp; Land Use Planning, Regional Centre  Kolkata West Bengal India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7585-4006","authenticated-orcid":false,"given":"Amrita","family":"Banerjee","sequence":"additional","affiliation":[{"name":"Central Rainfed Upland Rice Research Station ICAR\u2010Central Rice Research Institute  Hazaribag Jharkhand India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9917-5403","authenticated-orcid":false,"given":"Nimai Prasad","family":"Mandal","sequence":"additional","affiliation":[{"name":"Central Rainfed Upland Rice Research Station ICAR\u2010Central Rice Research Institute  Hazaribag Jharkhand India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2498-5719","authenticated-orcid":false,"given":"Gautam","family":"Talukdar","sequence":"additional","affiliation":[{"name":"Wildlife Institute of India  Dehradun Uttarakhand India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8397-9466","authenticated-orcid":false,"given":"Arunava","family":"Pattanayak","sequence":"additional","affiliation":[{"name":"ICAR\u2010Indian Institute of Agricultural Biotechnology  Ranchi India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0302-7677","authenticated-orcid":false,"given":"Kailash Chander","family":"Bansal","sequence":"additional","affiliation":[{"name":"National Academy of Agricultural Sciences  New Delhi India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,10,20]]},"reference":[{"key":"e_1_2_12_2_1","doi-asserted-by":"publisher","DOI":"10.5958\/0976\u20101926.2022.00053.5"},{"key":"e_1_2_12_3_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.094052.109"},{"key":"e_1_2_12_4_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2023.1225445"},{"key":"e_1_2_12_5_1","doi-asserted-by":"publisher","DOI":"10.3389\/fevo.2022.924977"},{"key":"e_1_2_12_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jas.2016.04.018"},{"key":"e_1_2_12_7_1","doi-asserted-by":"publisher","DOI":"10.1093\/g3journal\/jkad194"},{"key":"e_1_2_12_8_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13742\u2010015\u20100047\u20108"},{"key":"e_1_2_12_9_1","doi-asserted-by":"publisher","DOI":"10.1002\/ppp3.10496"},{"key":"e_1_2_12_10_1","doi-asserted-by":"publisher","DOI":"10.1186\/2193\u20101801\u20102\u2010228"},{"key":"e_1_2_12_11_1","doi-asserted-by":"publisher","DOI":"10.3390\/agriculture13040823"},{"key":"e_1_2_12_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/nplants.2015.164"},{"key":"e_1_2_12_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evz039"},{"key":"e_1_2_12_14_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12862\u2010018\u20101180\u20107"},{"key":"e_1_2_12_15_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12284\u2010021\u201000497\u20106"},{"key":"e_1_2_12_16_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471\u20102156\u201014\u201071"},{"key":"e_1_2_12_17_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tplants.2015.10.012"},{"key":"e_1_2_12_18_1","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/131.2.479"},{"key":"e_1_2_12_19_1","doi-asserted-by":"publisher","DOI":"10.1007\/s12284\u2010011\u20109078\u20107"},{"key":"e_1_2_12_20_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1308942110"},{"key":"e_1_2_12_21_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41477\u2010020\u20100659\u20106"},{"key":"e_1_2_12_22_1","doi-asserted-by":"publisher","DOI":"10.1098\/rstb.1996.0112"},{"key":"e_1_2_12_23_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature11532"},{"issue":"6","key":"e_1_2_12_24_1","doi-asserted-by":"crossref","DOI":"10.1093\/molbev\/msaf117","article-title":"ShiNyP: Unlocking SNP\u2010Based Population Genetics\u2014AI\u2010Assisted Platform for Rapid and Interactive Visual Exploration","volume":"42","author":"Huang Y.\u2010H.","year":"2025","journal-title":"Molecular Biology and Evolution"},{"key":"e_1_2_12_25_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0800607105"},{"key":"e_1_2_12_26_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.281"},{"key":"e_1_2_12_27_1","doi-asserted-by":"publisher","DOI":"10.1111\/nph.17733"},{"key":"e_1_2_12_28_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.adq0018"},{"key":"e_1_2_12_29_1","volume-title":"Soil Series of India. 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