{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T04:38:29Z","timestamp":1792816709537,"version":"4.5.0"},"reference-count":42,"publisher":"Wiley","issue":"4","license":[{"start":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T00:00:00Z","timestamp":1792713600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"},{"start":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T00:00:00Z","timestamp":1792713600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100003627","name":"Rural Development Administration","doi-asserted-by":"publisher","award":["RS\u20102025\u201002214096"],"award-info":[{"award-number":["RS\u20102025\u201002214096"]}],"id":[{"id":"10.13039\/501100003627","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["RS\u20102024\u201000343462"],"award-info":[{"award-number":["RS\u20102024\u201000343462"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["acsess.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["The Plant Genome"],"published-print":{"date-parts":[[2026,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Drought\u2010yield quantitative trait loci (QTLs)\n                    <jats:italic>qDTY<\/jats:italic>\n                    <jats:sub>2.2<\/jats:sub>\n                    and\n                    <jats:italic>qDTY<\/jats:italic>\n                    <jats:sub>4.1<\/jats:sub>\n                    improve grain yield under reproductive\u2010stage drought in rice (\n                    <jats:italic>Oryza sativa<\/jats:italic>\n                    L.), yet their genomic architecture remains poorly resolved in elite\n                    <jats:italic>indica<\/jats:italic>\n                    breeding backgrounds. We generated a chromosome\u2010level assembly of IR87707\u2010446\u2010B\u2010B\u2010B (IR64\u2010qDTY\n                    <jats:sub>2.2<\/jats:sub>\n                    + qDTY\n                    <jats:sub>4.1<\/jats:sub>\n                    ), which carries both QTLs in the IR64 background, and delineated donor\u2010derived introgressions using informative parental single\u2010nucleotide polymorphisms (SNPs). The 395.5\u2010Mb assembly comprised 12 chromosomes, showed 99.2% BUSCO completeness, and contained 40,189 predicted protein\u2010coding genes. Informative\u2010SNP analysis, supported by read\u2010depth assessment of low\u2010information regions, resolved\n                    <jats:italic>qDTY<\/jats:italic>\n                    <jats:sub>2.2<\/jats:sub>\n                    and\n                    <jats:italic>qDTY<\/jats:italic>\n                    <jats:sub>4.1<\/jats:sub>\n                    as continuous donor\u2010derived introgressions containing 194 and 97 genes, respectively. Comparative genome analysis showed that\n                    <jats:italic>qDTY<\/jats:italic>\n                    <jats:sub>2.2<\/jats:sub>\n                    was largely macrostructurally collinear with IRGSP\u20101.0, whereas\n                    <jats:italic>qDTY<\/jats:italic>\n                    <jats:sub>4.1<\/jats:sub>\n                    showed pronounced structural divergence and contained a 15.6\u2010kb inversion relative to IR64sj. Comparative gene\u2010content analysis further showed that 37.1% and 55.7% of genes in\n                    <jats:italic>qDTY<\/jats:italic>\n                    <jats:sub>2.2<\/jats:sub>\n                    and\n                    <jats:italic>qDTY<\/jats:italic>\n                    <jats:sub>4.1<\/jats:sub>\n                    , respectively, lacked collinear orthologs in IRGSP\u20101.0. Multi\u2010accession allele analysis revealed contrasting candidate\u2010gene profiles between the two loci. Six of eight\n                    <jats:italic>qDTY<\/jats:italic>\n                    <jats:sub>2.2<\/jats:sub>\n                    candidates had coding sequences identical to IR64sj, whereas all four\n                    <jats:italic>qDTY<\/jats:italic>\n                    <jats:sub>4.1<\/jats:sub>\n                    candidates showed coding differences from IR64sj. Coordinate\u2010based SNP markers were also developed for donor\u2010haplotype tracking across both QTL intervals. These results provide a genome\u2010resolved framework for characterizing drought\u2010yield QTLs and developing breeding\u2010background\u2010specific markers for recombination\u2010aware rice breeding.\n                  <\/jats:p>","DOI":"10.1002\/tpg2.70330","type":"journal-article","created":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T04:13:07Z","timestamp":1792815187000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A chromosome\u2010level genome assembly of an elite\n                    <i>indica<\/i>\n                    breeding line resolves the genomic architecture of drought\u2010yield QTLs\n                    <i>qDTY<\/i>\n                    <sub>2.2<\/sub>\n                    and\n                    <i>qDTY<\/i>\n                    <sub>4.1<\/sub>\n                    in rice"],"prefix":"10.1002","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9343-7257","authenticated-orcid":false,"given":"Jae\u2010Hyuk","family":"Han","sequence":"first","affiliation":[{"name":"Department of Integrative Biological Sciences and Industry Sejong University  Seoul Republic of Korea"},{"name":"IRRI\u2010Korea Office, International Rice Research Institute  Wanju Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Na\u2010Hyun","family":"Shin","sequence":"additional","affiliation":[{"name":"Life and Industry Convergence Research Institute Pusan National University  Miryang Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keunpyo","family":"Lee","sequence":"additional","affiliation":[{"name":"Supercomputing Center, Agricultural Biotechnology Department, National Institute of Agricultural Sciences Rural Development Administration  Jeonju Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yohei","family":"Koide","sequence":"additional","affiliation":[{"name":"Research Faculty of Agriculture Hokkaido University  Sapporo Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yeisoo","family":"Yu","sequence":"additional","affiliation":[{"name":"Department of Research and Development DNACARE Co. Ltd.  Seoul Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Il\u2010Ryong","family":"Choi","sequence":"additional","affiliation":[{"name":"IRRI\u2010Korea Office, International Rice Research Institute  Wanju Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3932-8639","authenticated-orcid":false,"given":"Joong Hyoun","family":"Chin","sequence":"additional","affiliation":[{"name":"Department of Integrative Biological Sciences and Industry Sejong University  Seoul Republic of Korea"},{"name":"Institute for Advanced Plant Breeding and Phytochemicals (IAPBP) Sejong University  Seoul Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,10,23]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cj.2024.06.011"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1002\/fes3.79"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.3390\/plants10091804"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cj.2021.03.005"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/srep15183"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00122\u2010012\u20101823\u20109"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature11346"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms27073020"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.1093\/jxb\/eru506"},{"key":"e_1_2_10_11_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1467\u20107652.2009.00415.x"},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2016.00004"},{"key":"e_1_2_10_13_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0604882103"},{"key":"e_1_2_10_14_1","doi-asserted-by":"publisher","DOI":"10.1111\/pbi.14224"},{"key":"e_1_2_10_15_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2018.00162"},{"key":"e_1_2_10_16_1","doi-asserted-by":"publisher","DOI":"10.1111\/tpj.12352"},{"key":"e_1_2_10_17_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12284\u2010022\u201000559\u20103"},{"key":"e_1_2_10_18_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2022.995634"},{"key":"e_1_2_10_19_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molp.2021.06.017"},{"key":"e_1_2_10_20_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2016.00047"},{"key":"e_1_2_10_21_1","doi-asserted-by":"publisher","DOI":"10.1111\/jipb.13414"},{"key":"e_1_2_10_22_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059\u2010025\u201003761\u2010w"},{"key":"e_1_2_10_23_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2017.00772"},{"key":"e_1_2_10_24_1","doi-asserted-by":"publisher","DOI":"10.1093\/hr\/uhab081"},{"key":"e_1_2_10_25_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059\u2010014\u20100506\u2010z"},{"key":"e_1_2_10_26_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molp.2021.06.018"},{"key":"e_1_2_10_27_1","doi-asserted-by":"publisher","DOI":"10.1093\/jxb\/ery332"},{"key":"e_1_2_10_28_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0062795"},{"key":"e_1_2_10_29_1","doi-asserted-by":"publisher","DOI":"10.1104\/pp.111.190389"},{"key":"e_1_2_10_30_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms25179728"},{"key":"e_1_2_10_31_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12711\u2010021\u201000619\u20100"},{"key":"e_1_2_10_32_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586\u2010018\u20100063\u20109"},{"key":"e_1_2_10_33_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrg2165"},{"key":"e_1_2_10_34_1","doi-asserted-by":"publisher","DOI":"10.1104\/pp.107.101295"},{"key":"e_1_2_10_35_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature04920"},{"key":"e_1_2_10_36_1","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2022.1041078"},{"key":"e_1_2_10_37_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12870\u2010019\u20101872\u20101"},{"key":"e_1_2_10_38_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1611012113"},{"key":"e_1_2_10_39_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2022.1092630"},{"key":"e_1_2_10_40_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41588\u2010018\u20100041\u2010z"},{"key":"e_1_2_10_41_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.plaphy.2023.108138"},{"key":"e_1_2_10_42_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059\u2010024\u201003166\u20101"},{"key":"e_1_2_10_43_1","doi-asserted-by":"publisher","DOI":"10.3390\/agronomy14091954"}],"container-title":["The 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