{
  "abstract": "Rice (Oryza sativa L.) improvement increasingly uses genome-scale variation, but breeding decisions remain trait-oriented and depend on genetic architecture, recipient background, target environment, and selection resources. This review assesses when phased haplotype information adds value beyond causal-gene markers, single-nucleotide polymorphism assays, phenotypic selection, and genomic prediction. Reported configurations for yield, grain quality, nutrition, biotic resistance, and abiotic-stress adaptation are evaluated according to population structure, carrier frequency, effect uncertainty, haplotype-by-background interaction, haplotype-by-environment interaction, linkage drag, transferability, assay availability, and current breeding use. A three-tier hierarchy classifies configurations as Candidate, Validated, or Breeder-Ready. Most reported favorable haplotypes remain Candidate targets, fewer have controlled genetic validation, and few sequence-defined multi-variant haplotypes have documented use in active breeding programs. Practical deployment requires stable sequence nomenclature, accessible donors, diagnostic assays, elite-background and multi-environment evaluation, cost analysis, and donor-segment recovery. Graph pangenomes, phased long-read assemblies, causal reconstruction, and prospective comparisons with current selection methods can improve future assessment. Haplotype information has greatest value when phase improves a defined breeding decision and increases target-environment performance, annual genetic gain, selection efficiency, or cultivar delivery.",
  "abstract_shown": true,
  "affiliations": [
    "Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi City 100000, Vietnam",
    "Faculty of Agricultural Technology, University of Engineering and Technology, Vietnam National University Hanoi, Hanoi City 100000, Vietnam",
    "VinUni Bigdata Research Institute, VinUniversity, Hanoi City 100000, Vietnam",
    "Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA",
    "Department of Integrative Agriculture, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain P.O. Box 15551, Abu Dhabi, United Arab Emirates",
    "Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Hanoi City 100000, Vietnam",
    "Department of Environmental Science, Central University of Kerala, Kasaragod 671316, India",
    "Institute of Scientific Research and Applications, Hanoi Pedagogical University 2, Phuc Yen City 35000, Vietnam"
  ],
  "article_type": "review article",
  "arxiv": null,
  "author_total": 11,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Trung Quoc Nguyen",
      "orcid": "0000-0003-1123-3419"
    },
    {
      "affs": [
        0
      ],
      "name": "Anh Quynh Ho",
      "orcid": "0009-0007-6973-6621"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "Ha Duc Chu",
      "orcid": "0000-0003-0087-9994"
    },
    {
      "affs": [
        3
      ],
      "name": "Nguyen Nguyen Chuong",
      "orcid": "0000-0001-9631-9953"
    },
    {
      "affs": [
        3
      ],
      "name": "Touhidur Rahman Anik",
      "orcid": "0000-0003-1995-494X"
    },
    {
      "affs": [
        0
      ],
      "name": "Gioi Huy Dong",
      "orcid": "0000-0003-4977-3576"
    },
    {
      "affs": [
        4
      ],
      "name": "Saad Sulieman",
      "orcid": "0000-0003-2070-6660"
    },
    {
      "affs": [
        5
      ],
      "name": "Nguyet Thi Minh Nguyen",
      "orcid": "0009-0003-0978-3996"
    },
    {
      "affs": [
        6
      ],
      "name": "Sudisha Jogaiah",
      "orcid": "0000-0003-2831-651X"
    },
    {
      "affs": [
        7
      ],
      "name": "Hong Viet La",
      "orcid": "0000-0002-6016-5857"
    },
    {
      "affs": [
        3
      ],
      "name": "Lam-Son Phan Tran",
      "orcid": "0000-0001-9883-9768"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/3fmw0s0962pz2.bib",
  "cited_by": 0,
  "doi": "10.3390/ijms27208972",
  "fulltext_url": "https://europepmc.org/articles/PMC13704196",
  "id": "3fmw0s0962pz2",
  "issns": [
    "1422-0067"
  ],
  "landing_url": "https://www.mdpi.com/1422-0067/27/20/8972",
  "language": "eng",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1311|Genetic Mapping and Diversity in Plants and Animals"
    ]
  ],
  "openalex": "W7221120326",
  "pdf_url": "https://europepmc.org/articles/PMC13704196?pdf=render",
  "pmcid": "PMC13704196",
  "pmid": "42941748",
  "published": "2026-10-10",
  "publisher": "MDPI AG",
  "ris": "https://research.draconitic.com/paper/3fmw0s0962pz2.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:55Z",
      "native_id": "10.3390/ijms27208972",
      "source": "crossref",
      "url": "https://www.mdpi.com/1422-0067/27/20/8972"
    },
    {
      "first_seen": "2026-10-30T12:22:24Z",
      "native_id": "MED:42941748",
      "source": "europepmc",
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  "subjects": [
    {
      "field": "biology",
      "origin": "openalex:1311|Genetic Mapping and Diversity in Plants and Animals",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "From Gene-Based Breeding to Haplotype-Based Breeding for Rice (Oryza sativa) Improvement in the Genomics Era",
  "title_text": "From Gene-Based Breeding to Haplotype-Based Breeding for Rice (Oryza sativa) Improvement in the Genomics Era",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:22:24Z",
  "url": "https://research.draconitic.com/paper/3fmw0s0962pz2",
  "venue": "International Journal of Molecular Sciences",
  "versions": []
}