{
  "abstract": "Three-dimensional (3D) genome folding shapes gene regulation, yet the genetic underpinnings linking 3D genome evolution to phenotypic innovation during domestication remain elusive. Using population-scale Hi-C profiling of 34 semi-wild and 267 cultivated allotetraploid cottons, we generated a pan-3D genome atlas capturing extensive diversity in topologically associating domains (TADs) and chromatin loops. Chromatin interactome-wide association studies identified 105 TAD reconfigurations and 58 loop rewirings that were established as the 3D chromatin basis of fiber quality, boosting heritability estimates for fiber strength by 16% and fiber length by 20%. We reveal that domestication selection within sequence-defined sweeps fixed 57% of 3D conformation signatures, thereby decoupling sequence-level from chromatin-level selection and shifting the subgenome expression balance of 39 homoeologs in cultivated cotton. Sequence-based modeling and mutational analyses identified the C2H2 zinc-finger protein YY1 as a conserved mediator of 3D genome organization. This study provides a resource for redefining precision-breeding paradigms by harnessing cryptic 3D chromatin targets.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": null,
  "author_total": 35,
  "authors": [
    {
      "name": "Xianhui Huang"
    },
    {
      "name": "Yabin Peng"
    },
    {
      "name": "Xiubao Hu"
    },
    {
      "name": "Yuejin Wang"
    },
    {
      "name": "Zeyu Zhang"
    },
    {
      "name": "Xianzhe Huang"
    },
    {
      "name": "Xuanxuan Luo"
    },
    {
      "name": "Sainan Zhang"
    },
    {
      "name": "Zengyuan Zhao"
    },
    {
      "name": "Erin Farmer"
    },
    {
      "name": "Sheng-Kai Hsu"
    },
    {
      "name": "Corrinne Grover"
    },
    {
      "name": "Zhengyang Qi"
    },
    {
      "name": "Lu Li"
    },
    {
      "name": "Jinglei Yang"
    },
    {
      "name": "Yinfang He"
    },
    {
      "name": "Zhiwei Chen"
    },
    {
      "name": "Yuanhang Zhang"
    },
    {
      "name": "Ye Mei"
    },
    {
      "name": "Pengcheng Deng"
    },
    {
      "name": "Yang Meng"
    },
    {
      "name": "Yufei Wang"
    },
    {
      "name": "Mengyuan Ji"
    },
    {
      "name": "Junyuan Lv"
    },
    {
      "name": "Liuling Pei"
    },
    {
      "name": "Fang Liu"
    },
    {
      "name": "Xinhui Nie"
    },
    {
      "name": "Lili Tu"
    },
    {
      "name": "Keith Lindsey"
    },
    {
      "name": "Adnane Boualem"
    },
    {
      "name": "Abdelhafid Bendahmane"
    },
    {
      "name": "Jonathan Wendel"
    },
    {
      "name": "Michael Gore"
    },
    {
      "name": "Xianlong Zhang"
    },
    {
      "name": "Maojun Wang"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/1b0jyrp443mk3.bib",
  "cited_by": 0,
  "doi": "10.1016/j.cell.2026.08.038",
  "fulltext_url": null,
  "id": "1b0jyrp443mk3",
  "issns": [
    "0092-8674",
    "1097-4172"
  ],
  "landing_url": "https://hal.science/hal-05780798v1",
  "language": "en",
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "hal",
      "0.sdv"
    ],
    [
      "openalex",
      "1110|Research in Cotton Cultivation"
    ]
  ],
  "openalex": "W7213439634",
  "pdf_url": "https://www.cell.com/cell/pdf/S0092-8674(26)01011-1.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-06",
  "publisher": "Elsevier",
  "ris": "https://research.draconitic.com/paper/1b0jyrp443mk3.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:49Z",
      "native_id": "hal-05780798",
      "source": "hal",
      "url": "https://hal.science/hal-05780798v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "openalex:1110|Research in Cotton Cultivation",
      "subfield": "plant-biology"
    }
  ],
  "title": "3D chromatin remodeling during domestication defines novel targets for crop improvement",
  "title_text": "3D chromatin remodeling during domestication defines novel targets for crop improvement",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:17:49Z",
  "url": "https://research.draconitic.com/paper/1b0jyrp443mk3",
  "venue": "Cell",
  "versions": []
}