Genome-Wide Egg Hunt: Unhiding Candidate Genes for Egg Component Traits in Layers of an F2 Resource Population

Egg components, including weight of yolk, albumen, and eggshell, are economically important traits in poultry breeding and production, and we thus conducted a genome-wide association study (GWAS) for them. We used an F₂ resource population of hens (<i>n</i> = 142) in different periods of laying, obtained by crossing breeds with contrasting phenotypes, and then genotyped them using the Illumina Chicken 60K iSelect BeadChip. Significant associations were found between 33 single nucleotide polymorphisms (SNPs) and yolk weight at 18-28 weeks of age (YW1). Eighty-seven SNPs were associated with thick albumen weight at 18-28 (TAW1) and 29-42 (TAW2) weeks of age. Four SNPs were associated with eggshell weight at 18-28 weeks of age (ESW1). Fifty-three candidate genes were identified in the positions of these SNPs, and seven prioritized candidate genes (PGCs) were revealed in regions where 2-4 SNPs associated with the studied traits were localized. These were as follows: <i>SYTL5</i> (YW1, TAW1), <i>FRY</i> (TAW1), <i>GABRG3</i> (YW1, TAW1), <i>ALDH1A3</i> (YW1), <i>VCL</i> (YW1), <i>HYDIN</i> (YW1), and <i>TIMP4</i> (TAW1). Allelic variants at the <i>ALDH1A3</i>, <i>VCL</i>, <i>HYDIN</i>, <i>FRY,</i> and <i>TIMP4</i> loci were associated with higher YW1 and TAW1. These SNPs and PGCs are potential genetic markers for characterizing egg weight parameters and their components in chicken breeding to achieve egg production improvements.