Genome-wide association study identifies candidate loci and a functional regulatory variant associated with...

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.