{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T04:55:17Z","timestamp":1790571317273,"version":"4.1.0"},"reference-count":25,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T00:00:00Z","timestamp":1787529600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"},{"start":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T00:00:00Z","timestamp":1787529600000},"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                    Rice (\n                    <jats:italic>Oryza sativa<\/jats:italic>\n                    \u00a0L.) genomics has made significant progress, with over 13000 genome sequences available and more than 4500 genes functionally characterized. However, limited haplotype\u2010level information has constrained the effective deployment of these genes in breeding programs. Here, we investigated haplotype variation of 1644 functionally characterized genes representing six major trait categories using the 3000 Rice Genome panel. High haplotypic diversity was observed, with more than 300 haplotypes, which clustered into 2\u201315 major haplogroups. Several haplotypes showed subpopulation or region\u2010specific distributions, whereas others were broadly distributed across the panel. To identify rare haplotypes (frequency\u00a0&lt;\u00a00.1) with potential breeding value, we prioritized 180 genes relevant to defined product concepts and identified 210 rare haplotypes across 51 genes. Notably, a rare haplotype of\n                    <jats:italic>DEP1<\/jats:italic>\n                    (\n                    <jats:italic>DEP1<\/jats:italic>\n                    \u2010H2: frequency 0.07) associated with increased panicle length was introgressed into the mega rice variety Swarna through haplotype\u2010based backcross breeding. The resulting introgression lines showed a 29%\u201334% increase in panicle length compared to the recurrent parent, confirming the functional advantage of the rare haplotype.\n                  <\/jats:p>","DOI":"10.1002\/tpg2.70292","type":"journal-article","created":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T05:27:16Z","timestamp":1787635636000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Mining rare haplotypes to accelerate precision breeding in rice"],"prefix":"10.1002","volume":"19","author":[{"given":"Swati","family":"Tyagi","sequence":"first","affiliation":[{"name":"International Rice Research Institute  Los Banos Philippines"},{"name":"International Rice Research Institute South Asia Research Centre  Varanasi India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anoop Kishor Singh","family":"Gurjar","sequence":"additional","affiliation":[{"name":"International Rice Research Institute  Los Banos Philippines"},{"name":"International Rice Research Institute South Asia Research Centre  Varanasi India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sonali Vijay","family":"Habde","sequence":"additional","affiliation":[{"name":"International Rice Research Institute  Los Banos Philippines"},{"name":"International Rice Research Institute South Asia Research Centre  Varanasi India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Krishna Tesman","family":"Sundaram","sequence":"additional","affiliation":[{"name":"International Rice Research Institute  Los Banos Philippines"},{"name":"International Rice Research Institute South Asia Hub  Hyderabad India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Namrata Devidas","family":"Patil","sequence":"additional","affiliation":[{"name":"International Rice Research Institute  Los Banos Philippines"},{"name":"International Rice Research Institute South Asia Research Centre  Varanasi India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diksha","family":"Rai","sequence":"additional","affiliation":[{"name":"International Rice Research Institute  Los Banos Philippines"},{"name":"International Rice Research Institute South Asia Research Centre  Varanasi India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ajay","family":"Bogati","sequence":"additional","affiliation":[{"name":"International Rice Research Institute  Los Banos Philippines"},{"name":"International Rice Research Institute South Asia Hub  Hyderabad India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pronob J.","family":"Paul","sequence":"additional","affiliation":[{"name":"International Rice Research Institute  Los Banos Philippines"},{"name":"International Rice Research Institute South Asia Hub  Hyderabad India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ankur Kumar","family":"Singh","sequence":"additional","affiliation":[{"name":"International Rice Research Institute  Los Banos Philippines"},{"name":"International Rice Research Institute South Asia Research Centre  Varanasi India"},{"name":"Acharya Narendra Deva University of Agriculture and Technology  Ayodhya India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ajay","family":"Tripathi","sequence":"additional","affiliation":[{"name":"International Rice Research Institute  Los Banos Philippines"},{"name":"International Rice Research Institute South Asia Research Centre  Varanasi India"},{"name":"Acharya Narendra Deva University of Agriculture and Technology  Ayodhya India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sanjay","family":"Kalia","sequence":"additional","affiliation":[{"name":"Department of Biotechnology (DBT) CGO Complex  New Delhi India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ajay","family":"Kohli","sequence":"additional","affiliation":[{"name":"International Rice Research Institute  Los Banos Philippines"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arvind","family":"Kumar","sequence":"additional","affiliation":[{"name":"International Rice Research Institute  Los Banos Philippines"},{"name":"International Rice Research Institute South Asia Hub  Hyderabad India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0810-0711","authenticated-orcid":false,"given":"Pallavi","family":"Sinha","sequence":"additional","affiliation":[{"name":"International Rice Research Institute  Los Banos Philippines"},{"name":"International Rice Research Institute South Asia Hub  Hyderabad India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Uma Maheshwar","family":"Singh","sequence":"additional","affiliation":[{"name":"International Rice Research Institute  Los Banos Philippines"},{"name":"International Rice Research Institute South Asia Research Centre  Varanasi India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1560-1648","authenticated-orcid":false,"given":"Vikas Kumar","family":"Singh","sequence":"additional","affiliation":[{"name":"International Rice Research Institute  Los Banos Philippines"},{"name":"International Rice Research Institute South Asia Hub  Hyderabad India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,8,24]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.1111\/pbi.13087"},{"key":"e_1_2_11_3_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1039"},{"key":"e_1_2_11_4_1","doi-asserted-by":"publisher","DOI":"10.1038\/s42003\u2010021\u201002782\u2010y"},{"key":"e_1_2_11_5_1","doi-asserted-by":"crossref","unstructured":"Felipe de Mendiburu. 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