Genome-wide egg hunt: Unhiding candidate genes for egg component traits in layers of an F2 resource population

Simple Summary

Certain features in eggs (including the weight of the yolk, albumen, and eggshell) are important economically for poultry breeding and production. This study aimed to establish if there are genes (and, more specifically, variants of genes) that are associated with these traits. To this end, we scanned the genomes of 142 hens phenotyped in different periods of laying; these hens had previously been obtained by crossing breeds with contrasting characteristics. We found a total of 33 gene variants that were associated with yolk weight at 18–28 weeks of age (we called these “YW1”). We found 87 that were associated with thick albumen weight at 18–28 weeks of age (TAW1) and 29–42 weeks of age (TAW2). Finally, four variants were associated with eggshell weight at 18–28 weeks of age (ESW1).These 124 variants were in 53 genes, of which we prioritized 7 genes on the basis that at least 2 variants were found in them. These genes, and the variants that they contain, are potential genetic markers for describing egg weight parameters and their components for the breeding of chickens and possibly other poultry. Using these molecular tools, egg production can be improved significantly through genetic selection.

Abstract

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 (n = 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: SYTL5 (YW1, TAW1), FRY (TAW1), GABRG3 (YW1, TAW1), ALDH1A3 (YW1), VCL (YW1), HYDIN (YW1), and TIMP4 (TAW1). Allelic variants at the ALDH1A3, VCL, HYDIN, FRY, and TIMP4 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.