Genome-Wide Association Studies Reveal Key Candidate Genes for Egg Weight and Quality Components in an F2 Japanese Quail Resource Population

Identifying genetic markers for economically important egg traits is essential for advancing marker-assisted and genomic selection in poultry breeding. Here, a genome-wide association study (GWAS) was performed using genotyping-by-sequencing data to identify single nucleotide polymorphisms (SNPs) and candidate genes associated with egg weight (EW) and its constituent components. We evaluated 102 laying Japanese quails from an F2 resource population generated by crossing divergent Japanese and Texas White breeds. Phenotypic traits included EW, eggshell weight (ESW), albumen weight (AW), thick albumen weight (TAW), yolk weight (YW), and albumen-to-yolk ratio (AYR). We identified 16 significant SNPs and 88 candidate genes. Notably, seven prioritized candidate genes (NTN4, CLDN10, AGAP3, DUSP19, STAB1, SFMBT1, and RNF130) overlapped with significant SNPs associated with EW, ESW, AW, YW, and AYR. Three pleiotropic SNPs (12:309207, 12:335220, and 12:470023) were associated with multiple traits, while the AGAP3 gene harbored two SNPs linked to AW. Our data offer insights into the polygenic regulation governing egg component development in quails. These newly detected genomic regions and candidate loci offer valuable targets for downstream replication studies aimed at enhancing avian breeding programs.