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Peer-reviewedCC BY-NC-NDPoultry science

Genome-wide association study identifies candidate loci and a functional regulatory variant associated with egg-production traits in Wenchang chickens

  • Lingzhi Fan1
  • Xing Hong1
  • Mingze Li1
  • Jiao Li1
  • Xiuping Wang2
  • Xiaomei Wang3
  • Shijun Li1
  1. 1College of Animal Science & Technology, Hainan Research Institute, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
  2. 2Hainan (Tan Niu) Wenchang Chicken Co., LTD, Haikou, 570100, China
  3. 3Yazhouwan National Laboratory, Sanya, 572024, China
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Abstract

Egg-production traits are economically important in the poultry industry but genetically complex, and their molecular basis in indigenous chicken breeds remains poorly characterized. The Wenchang chicken, an indigenous meat-type breed from Hainan, China, retains abundant genetic variation but has been less extensively studied at the genomic level. In this study, we performed a genome-wide association study (GWAS) for six egg-production traits—average egg weight (AEW), age at first egg (AFE), total egg number to 43 and 56 weeks of age (TEN43W and TEN56W), average clutch size (ACS), and maximum clutch size (MCS)—in 361 Wenchang hens using whole-genome resequencing data. We identified 104 significant SNPs (5 genome-wide significant and 99 suggestive associations) across 10 chromosomes, corresponding to 47 candidate genes. The strongest association was identified at the ELMO1 locus on chromosome 2 for MCS (peak P = 1.3 × 10–9), and chr2:46,273,794T>C within this locus was further prioritized as a candidate regulatory variant based on enhancer annotation, transcription factor binding prediction, and allele-specific reporter assays. Additional candidate genes included CCDC85C for MCS, SPSB4 for TEN56W, CALM2 for ACS, FRMPD4 for AFE, and SLC12A7 for TEN43W. These findings provide new insights into the genetic architecture of egg-production traits in Wenchang chickens and identify candidate loci for marker-assisted selection and functional genomic studies in indigenous chicken breeds.

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Cite

BibTeXRIS
BibTeX
@article{fan2026genomewide,
  title = {{Genome-wide association study identifies candidate loci and a functional regulatory variant associated with egg-production traits in Wenchang chickens}},
  author = {Lingzhi Fan and Xing Hong and Mingze Li and Jiao Li and Xiuping Wang and Xiaomei Wang and Shijun Li},
  journal = {Poultry science},
  year = {2026},
  month = oct,
  doi = {10.1016/j.psj.2026.107890},
  url = {https://europepmc.org/article/PMC/PMC13718810},
  note = {CC BY-NC-ND},
}
RIS
TY  - JOUR
TI  - Genome-wide association study identifies candidate loci and a functional regulatory variant associated with egg-production traits in Wenchang chickens
AU  - Lingzhi Fan
AU  - Xing Hong
AU  - Mingze Li
AU  - Jiao Li
AU  - Xiuping Wang
AU  - Xiaomei Wang
AU  - Shijun Li
PY  - 2026
DA  - 2026/10/05
JO  - Poultry science
DO  - 10.1016/j.psj.2026.107890
UR  - https://europepmc.org/article/PMC/PMC13718810
AB  - Egg-production traits are economically important in the poultry industry but genetically complex, and their molecular basis in indigenous chicken breeds remains poorly characterized. The Wenchang chicken, an indigenous meat-type breed from Hainan, China, retains abundant genetic variation but has been less extensively studied at the genomic level. In this study, we performed a genome-wide association study (GWAS) for six egg-production traits—average egg weight (AEW), age at first egg (AFE), total egg number to 43 and 56 weeks of age (TEN43W and TEN56W), average clutch size (ACS), and maximum clutch size (MCS)—in 361 Wenchang hens using whole-genome resequencing data. We identified 104 significant SNPs (5 genome-wide significant and 99 suggestive associations) across 10 chromosomes, corresponding to 47 candidate genes. The strongest association was identified at the ELMO1 locus on chromosome 2 for MCS (peak P = 1.3 × 10–9), and chr2:46,273,794T>C within this locus was further prioritized as a candidate regulatory variant based on enhancer annotation, transcription factor binding prediction, and allele-specific reporter assays. Additional candidate genes included CCDC85C for MCS, SPSB4 for TEN56W, CALM2 for ACS, FRMPD4 for AFE, and SLC12A7 for TEN43W. These findings provide new insights into the genetic architecture of egg-production traits in Wenchang chickens and identify candidate loci for marker-assisted selection and functional genomic studies in indigenous chicken breeds.
SN  - 0032-5791
SN  - 1525-3171
ER  -