Genomic Analysis of the Columbian Plumage Pattern in Various Chicken Breeds

Plumage coloration in birds is a complex genetic trait involving both direct pigmentation genes and their modifiers. The Columbian pattern, characterized by black feathers restricted to the neck, wing tips, and tail, remains poorly understood at the genetic level. This study aimed to conduct a genome-wide association study of the Columbian pattern across 29 chicken breeds of diverse origins. Blood samples were collected from breeds with (n = 11) and without (n = 18) the Columbian pattern. Genotyping was performed using the Illumina Chicken 60K SNP chip, and GWAS was conducted using EMMAX with Bonferroni correction. A total of 10 significant and nine suggestive SNPs on chromosomes GGA1, 2, 5, 7, 10, and 11 were identified. Eight significant SNPs mapped to a ~0.7 Mb region on GGA11 containing MC1R and multiple functionally diverse genes involved in melanocyte adhesion (CDH1), signaling (WWP2, NFAT5), transcription (ZFHX3, TCF25), protein degradation (PSMD7, ATXN1L), and vesicular trafficking (AP1G1). On GGA2, a significant SNP within a lncRNA gene was located in a QTL for yellow plumage, with positional candidates (ROCK1, GREB1L, CABLES1, TMEM241, ANKRD29) suggesting links to pheomelanin deposition. A suggestive locus near DLK1 on GGA5 was also identified. This study refines the genetic architecture of the Columbian pattern, implicating a core region on GGA11 modulating melanocyte function and a distinct locus on GGA2 involved in pheomelanin synthesis.