Abstract
Egg production traits are economically critical in poultry farming. However, the genetic mechanisms underlying these traits in indigenous chicken breeds remain largely unknown. In this study, we conducted a genome-wide association study (GWAS) using whole-genome sequencing data from 315 Wuhua yellow chickens, an indigenous breed characterized by low egg production but considerable genetic diversity. Phenotypic assessments included age at first egg (AFE), egg number (EN), and clutch size traits across three laying stages. The SNP-based heritability estimates ranged from 0.10 to 0.38, with AFE showing negative genetic correlations with EN and clutch-related traits. We identified 871 significant SNPs (51 genome-wide and 820 suggestive) associated with egg production traits and annotated 379 candidate genes. This study revealed that SCUBE1 and KRAS are important regulators of AFE through follicular development and metabolic pathways. Notably, IGF1 and PTK2 are associated with clutch size and EN, primarily through the mTOR and insulin signaling pathways. Additionally, 13 quantitative trait loci (QTLs) overlapped with known reproductive loci, including SOX5 and PPFIBP1. Functional enrichment analyses underscored the significant involvement of the identified genes in cell adhesion, hormone signaling, and oocyte maturation pathways. These findings improve our understanding of the genetic architecture of egg production traits in indigenous chickens and highlight potential molecular targets for marker-assisted selection to enhance egg yield while preserving genetic diversity.