{
  "abstract": "Indigenous chickens are an essential part of biodiversity and a vital protein resource to humans, yet global warming and environmental changes pose serious threats to their survival and productivity. Therefore, assessing population adaptive capacity under shifting environments is crucial for breeding resilient animals, and guiding conservation strategies. Here, we integrated ecological and whole-genome resequencing data from 1022 chickens from 44 Chinese indigenous populations to reveal genomic signatures of local adaptation. From 87 agroclimatic variables, we identified eight dominant environmental factors including solar radiation, precipitation, diurnal temperature range, and five landcover variables (cropland areas, water areas, trees coverage, bare ground and shrubs coverage) that shape ecological niches of indigenous chickens. Landscape and comparative genomics analyses revealed both known and novel candidate genes, such as UNC80, PTPRO, NCOR2, CSF2RB, NXT2 and PALLD for the solar radiation, precipitation, diurnal temperature range, cropland areas, trees coverage and bare ground, respectively. Particularly, adaptive non-coding variants harbored in these genes exhibited spatial allelic changes across populations and acted as regulatory elements via chromatin accessibility and DNA methylation, influencing adaptation in a tissue-specific manner. Our findings underscore the rich genetic diversity of Chinese indigenous chickens and provide new insights into genomic mechanisms of local adaptation, offering valuable references for domestic animal breeding, conservation, and climate resilience.",
  "abstract_shown": true,
  "affiliations": [
    "State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China",
    "Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu 225125, China",
    "Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China",
    "Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013, China",
    "Nujiang Promotion Station of Livestock Technology, Nujiang, Yunnan 673199, China",
    "Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 12,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Jing-Wei Yuan"
    },
    {
      "affs": [
        1
      ],
      "name": "Xiao-Xu Jia"
    },
    {
      "affs": [
        0
      ],
      "name": "Xiao-Long Huang"
    },
    {
      "affs": [
        0
      ],
      "name": "Yun-Lei Li"
    },
    {
      "affs": [
        0
      ],
      "name": "Ai-Xin Ni"
    },
    {
      "affs": [
        2
      ],
      "name": "Guo-Hong Chen"
    },
    {
      "affs": [
        3
      ],
      "name": "Nen-Zhu Zheng"
    },
    {
      "affs": [
        4
      ],
      "name": "Sheng He"
    },
    {
      "affs": [
        0
      ],
      "name": "Yan-Yan Sun"
    },
    {
      "affs": [
        5
      ],
      "name": "Guo-Qiang Yi"
    },
    {
      "affs": [
        1
      ],
      "name": "Wei Han"
    },
    {
      "affs": [
        0
      ],
      "name": "Ji-Lan Chen"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/ba2w2v3b8tk01.bib",
  "cited_by": 1,
  "doi": "10.24272/j.issn.2095-8137.2025.592",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13720413/",
  "id": "ba2w2v3b8tk01",
  "issns": [
    "2095-8137"
  ],
  "landing_url": "https://doi.org/10.24272/j.issn.2095-8137.2025.592",
  "language": "en",
  "licence": "CC-BY-NC-4.0",
  "licence_label": "CC BY-NC 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Article"
    ],
    [
      "openalex",
      "1311|Genetic and phenotypic traits in livestock"
    ]
  ],
  "openalex": "W7133556936",
  "pdf_url": null,
  "pmcid": "PMC13720413",
  "pmid": "42733044",
  "published": "2026-09-18",
  "publisher": "Editorial Office of Zoological Research, Kunming Institute of Zoology, The Chinese Academy of Sciences",
  "ris": "https://research.draconitic.com/paper/ba2w2v3b8tk01.ris",
  "sources": [
    {
      "first_seen": "2026-11-03T12:21:17Z",
      "native_id": "PMC13720413",
      "source": "pmc",
      "url": "https://doi.org/10.24272/j.issn.2095-8137.2025.592"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "openalex:1311|Genetic and phenotypic traits in livestock",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "Genomic insights into local adaptation of indigenous chickens",
  "title_text": "Genomic insights into local adaptation of indigenous chickens",
  "type": "peer-reviewed",
  "updated_at": "2026-11-03T12:21:17Z",
  "url": "https://research.draconitic.com/paper/ba2w2v3b8tk01",
  "venue": "Zoological Research",
  "versions": []
}