{
  "abstract": "Drought-yield quantitative trait loci (QTLs) qDTY2.2 and qDTY4.1 improve grain yield under reproductive-stage drought in rice (Oryza sativa L.), yet their genomic architecture remains poorly resolved in elite indica breeding backgrounds. We generated a chromosome-level assembly of IR87707-446-B-B-B (IR64-qDTY2.2 + qDTY4.1), which carries both QTLs in the IR64 background, and delineated donor-derived introgressions using informative parental single-nucleotide polymorphisms (SNPs). The 395.5-Mb assembly comprised 12 chromosomes, showed 99.2% BUSCO completeness, and contained 40,189 predicted protein-coding genes. Informative-SNP analysis, supported by read-depth assessment of low-information regions, resolved qDTY2.2 and qDTY4.1 as continuous donor-derived introgressions containing 194 and 97 genes, respectively. Comparative genome analysis showed that qDTY2.2 was largely macrostructurally collinear with IRGSP-1.0, whereas qDTY4.1 showed pronounced structural divergence and contained a 15.6-kb inversion relative to IR64sj. Comparative gene-content analysis further showed that 37.1% and 55.7% of genes in qDTY2.2 and qDTY4.1, respectively, lacked collinear orthologs in IRGSP-1.0. Multi-accession allele analysis revealed contrasting candidate-gene profiles between the two loci. Six of eight qDTY2.2 candidates had coding sequences identical to IR64sj, whereas all four qDTY4.1 candidates showed coding differences from IR64sj. Coordinate-based SNP markers were also developed for donor-haplotype tracking across both QTL intervals. These results provide a genome-resolved framework for characterizing drought-yield QTLs and developing breeding-background-specific markers for recombination-aware rice breeding.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, Republic of Korea.",
    "IRRI-Korea Office, International Rice Research Institute, Wanju, Republic of Korea.",
    "Life and Industry Convergence Research Institute, Pusan National University, Miryang, Republic of Korea.",
    "Supercomputing Center, Agricultural Biotechnology Department, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea.",
    "Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan.",
    "Department of Research and Development, DNACARE Co. Ltd., Seoul, Republic of Korea.",
    "Institute for Advanced Plant Breeding and Phytochemicals (IAPBP), Sejong University, Seoul, Republic of Korea."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 7,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Jae-Hyuk Han",
      "orcid": "0000-0002-9343-7257"
    },
    {
      "affs": [
        2
      ],
      "name": "Na-Hyun Shin"
    },
    {
      "affs": [
        3
      ],
      "name": "Keunpyo Lee"
    },
    {
      "affs": [
        4
      ],
      "name": "Yohei Koide"
    },
    {
      "affs": [
        5
      ],
      "name": "Yeisoo Yu"
    },
    {
      "affs": [
        1
      ],
      "name": "Il-Ryong Choi"
    },
    {
      "affs": [
        0,
        6
      ],
      "name": "Joong Hyoun Chin",
      "orcid": "0000-0003-3932-8639"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/ca52g6apefcv2.bib",
  "cited_by": 0,
  "doi": "10.1002/tpg2.70330",
  "fulltext_url": "https://europepmc.org/articles/PMC13694740",
  "id": "ca52g6apefcv2",
  "issns": [
    "1940-3372"
  ],
  "landing_url": "https://europepmc.org/article/MED/42920244",
  "language": "eng",
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1311|Genetic Mapping and Diversity in Plants and Animals"
    ]
  ],
  "openalex": "W7223468046",
  "pdf_url": "https://europepmc.org/articles/PMC13694740?pdf=render",
  "pmcid": "PMC13694740",
  "pmid": "42920244",
  "published": "2026-10-30",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/ca52g6apefcv2.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:20:32Z",
      "native_id": "MED:42920244",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42920244"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "openalex:1311|Genetic Mapping and Diversity in Plants and Animals",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "A chromosome-level genome assembly of an elite indica breeding line resolves the genomic architecture of drought-yield QTLs qDTY2.2 and qDTY4.1 in rice.",
  "title_text": "A chromosome-level genome assembly of an elite indica breeding line resolves the genomic architecture of drought-yield QTLs qDTY2.2 and qDTY4.1 in rice.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:20:32Z",
  "url": "https://research.draconitic.com/paper/ca52g6apefcv2",
  "venue": "The plant genome",
  "versions": []
}