{
  "abstract": "Background\n\nDissecting the genetic basis of cell-type-specific gene regulation during gametogenesis remains a major challenge. Population-level studies mask cellular heterogeneity, while the extreme data sparsity of single-cell profiling precludes robust genetic mapping.Results\n\nWe present GAMETE (Genetic Architecture Mapping of Epigenetic Traits at single-nucleus resolution), an integrated framework combining MPS-ATAC-seq, a high-throughput single-nucleus ATAC-seq method, with robust computational approaches for genotype inference and genetic mapping from sparse single-nucleus data. Applying GAMETE to hybrid rice pollen, we simultaneously profile chromatin accessibility and infer the genotypes of 4,887 individual haploid nuclei, revealing distinct chromatin landscapes across pollen cell types. This uncovers an unexpected elevation of chromatin accessibility at gypsy retrotransposons in microspores preceding their silencing in sperm cells, exposing a surveillance gap that may contribute to genome expansion. The synchronized profiling enables us to construct a single-cell recombination map, map segregation distortion loci and trace their developmental origins, and identify 16,113 chromatin accessibility QTLs (caQTLs), 48.6% of which exhibit pronounced cell-type specificity. Analysis of introgression lines supports a cell-type-specific trans-acting caQTL regulating the pollen-essential gene DTM1.Conclusions\n\nThis work establishes GAMETE as a broadly applicable framework for dissecting the genetic architecture of chromatin accessibility during gametogenesis without the need for subsequent generations.",
  "abstract_shown": true,
  "affiliations": [
    "National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.",
    "Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430000, China.",
    "College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430000, China.",
    "National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China. weibo.xie@mail.hzau.edu.cn.",
    "Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430000, China. weibo.xie@mail.hzau.edu.cn."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 16,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Yinmeng Liu"
    },
    {
      "affs": [
        2
      ],
      "name": "Chunjiao Xia"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Junjie Li"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Jiacheng Li"
    },
    {
      "affs": [
        0,
        2
      ],
      "name": "Haichuan Yang"
    },
    {
      "affs": [
        0
      ],
      "name": "Zhanxiang Zong"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Luchang Ming"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Junjiao Yang"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Hantong Lian"
    },
    {
      "affs": [
        0
      ],
      "name": "Meng Luo"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Tao Zhu"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Xiaogang He"
    },
    {
      "affs": [
        0,
        2
      ],
      "name": "Yongzhong Xing"
    },
    {
      "affs": [
        0
      ],
      "name": "Sibin Yu"
    },
    {
      "affs": [
        0,
        2
      ],
      "name": "Yidan Ouyang"
    },
    {
      "affs": [
        3,
        4
      ],
      "name": "Weibo Xie"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/3fp4y7eeekctm.bib",
  "cited_by": 0,
  "doi": "10.1186/s13059-026-04226-4",
  "fulltext_url": "https://europepmc.org/articles/PMC13726271",
  "id": "3fp4y7eeekctm",
  "issns": [
    "1474-7596",
    "1474-760X"
  ],
  "landing_url": "https://europepmc.org/article/MED/42972586",
  "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": [
    [
      "heading",
      "Research"
    ],
    [
      "openalex",
      "1311|Genetic Mapping and Diversity in Plants and Animals"
    ]
  ],
  "openalex": "W7172377409",
  "pdf_url": "https://europepmc.org/articles/PMC13726271?pdf=render",
  "pmcid": "PMC13726271",
  "pmid": "42972586",
  "published": "2026-08-04",
  "publisher": "BMC",
  "ris": "https://research.draconitic.com/paper/3fp4y7eeekctm.ris",
  "sources": [
    {
      "first_seen": "2026-11-04T15:20:45Z",
      "native_id": "MED:42972586",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42972586"
    },
    {
      "first_seen": "2026-11-05T12:22:39Z",
      "native_id": "PMC13726271",
      "source": "pmc",
      "url": "https://doi.org/10.1186/s13059-026-04226-4"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "openalex:1311|Genetic Mapping and Diversity in Plants and Animals",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "GAMETE maps the genetic architecture of chromatin accessibility in rice pollen at single-nucleus resolution.",
  "title_text": "GAMETE maps the genetic architecture of chromatin accessibility in rice pollen at single-nucleus resolution.",
  "type": "peer-reviewed",
  "updated_at": "2026-11-05T12:22:39Z",
  "url": "https://research.draconitic.com/paper/3fp4y7eeekctm",
  "venue": "Genome biology",
  "versions": []
}