Unraveling the Genetic Basis of an Abnormal Gold Feather Phenotype in Auto-Sexing Chickens

The silver-gold (S/s) sex-linked locus is critically employed in chicken breeding for the auto-sexing of day-old layer chicks. However, the emergence of an abnormal gold feather phenotype, where females lack the characteristic dorsal stripes, leads to frequent misidentification and substantial economic loss. The genetic basis of this abnormality was unknown. To address this, we conducted a genome-wide association study (GWAS) using 9 445 763 high-quality SNPs obtained from whole genome resequencing of 103 female chicks (53 abnormal, 50 normal). Our analysis identified a single sharp peak on chromosome 2 (-log₁₀(P) = 34.7; 236 significant SNPs), which was refined to a 390-kb interval (102.62-103.01 Mb) by FST analysis. The top Absolute allele frequency difference (absAFD) variant, NC_006089.5:g.102638974T>C, located in intron 2 of the GATA6 gene, showed an allele frequency difference of 0.567 (p = 1.35 × 10^-12). This study identifies chromosome 2 as the major genomic region responsible for the abnormal gold feather phenotype, with a noncoding variant in GATA6 as the primary candidate causal mutation. This is the first study of the abnormal gold feather phenotype, and it provides a molecular target for developing a diagnostic assay to preserve auto-sexing accuracy in commercial layer breeding.