Genome-wide association studies reveal key candidate genes for egg weight and quality components in an F2 Japanese quail resource population

Simple Summary

At the current stage of poultry breeding for egg production, the development and improvement of highly productive breeds and crosses increasingly depend on incorporating modern technologies involving genomics. These include using genetic markers established by integrating the whole genome data into breeding programs. The efficiency of these methods is largely determined by identifying markers that are reliable and enable targeted selection for enhanced egg production and quality traits. This study investigated DNA markers associated with the weight parameters of the egg and its primary components—albumen, yolk, and shell—in laying Japanese quails during active egg laying. We identified specific variations in the genome sequence of quails and candidate genes linked to these traits. We thereby determined the genetic variants that cause certain traits to be expressed. These findings expand our fundamental knowledge of the genetic architecture of egg production in quails. Furthermore, the identified genetic variants represent a baseline for future population-specific studies to explore their potential utility in marker-assisted and genomic selection.

Abstract

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.