Genome-Wide Association Study Reveals Candidate Genes Associated With the Intensity of Green Eggshell Color in Chickens.

Abstract

Eggshell color is an important economic trait in poultry. In green-eggshell chickens, eggshell color intensity is primarily determined by the amount of biliverdin deposited in the shell, but its genetic basis remains unclear. In this study, 230 Dongxiang green-eggshell chickens at 29 weeks of age were genotyped for the green-shell locus. Homozygous green-shell individuals were identified and subjected to a genome-wide association study (GWAS) using eggshell biliverdin concentration as the phenotype. The results showed that all 230 individuals were homozygous for the green-shell genotype, and eggshell biliverdin concentration was approximately normally distributed in the population. GWAS identified seven SNPs that exceeded the genome-wide significance threshold within a 110-kb region (3035804-3143838 bp) on chromosome 12. Functional annotation of the significant loci identified ALAS1 as a candidate gene. ALAS1 encodes the rate-limiting enzyme in heme biosynthesis and is therefore biologically linked to biliverdin production. Haplotype analysis further revealed a strong linkage block encompassing the ALAS1 region, supporting its potential role in regulating green eggshell color intensity. These findings provide candidate genetic markers for improving green eggshell color intensity in breeding programs.