Genome-wide association study of egg numbers across different laying phases in a large-scale layer population

1. Egg production is a primary economic driver in the poultry industry, determining the total yield of commercial layers. However, the complex polygenic mechanism remains largely elusive. This study investigated the phase-specific genetic mechanisms of egg production using a high-precision genomic approach.2. A genome-wide association study (GWAS) was conducted on a layer population (n = 3,587). Egg numbers were recorded across four distinct production phases: onset to 300 days, 301 to 560 days, 561 to 651 days and the cumulative onset to 651 days period. Following whole-genome SNP genotyping, GWAS signals were integrated with functional enrichment analyses to prioritise key loci and candidate genes associated with egg‑number traits.3. A total of 425 significant SNP were identified across the evaluated phases. Functional annotation revealed significant enrichment in 47 GO terms and four KEGG pathways, primarily involved in cell cycle regulation, cytoskeleton assembly and reproductive development. MAP2K3, TRIM37 and ACTR3were highlighted as compelling candidate genes. Potential genetic markers were identified, including rs14072717 within MAP2K3, a cluster of nine SNP within the ACTR3 locus and three variants within TRIM37.4. These findings elucidated the dynamic genetic regulation of egg production throughout the laying cycle and highlight MAP2K3, TRIM37 and ACTR3 as genomic targets. These markers provide a foundation for marker-assisted selection to enhance egg yield and production persistency in poultry.