The diversity of dermal pigmentation and plumage color in domestic chickens is intriguing. Black bone chickens (BBC) stand out with their intense melanin hyperpigmentation, driven by a complex chromosomal rearrangement on chromosome 20, specifically the Fm locus, causing overexpression of the EDN3 gene. In contrast, dermal pigmentation inhibition is regulated by the sex-linked Id locus. Previous studies have used crosses, GWAS and gene expression analysis to identify the genetic basis of the Id locus, but the puzzle remains unsolved. Our study seeks to precisely locate the Id locus, identify gene(s) inhibiting dermal pigmentation, and explore its ancestral state in BBC breeds. We analyzed public data from 270 chickens (42 BBC and 228 non-BBC) to refine the position of the Id locus to a ~1.6 Mb region between Z amplicon repeats on the distal end of q-arm and found that it shares a common ancestry among all BBC breeds, much like the Fm locus. The selection signatures and high fixation levels within MTAP, CCDC112 and a few other genes within this region support multiple candidates. Our results suggest that the Id locus is shared among BBC breeds and may have a polygenic nature, explaining the shank and dermal pigmentation variation.

Common Ancestry of the Id Locus: Genetic Clues and Polygenic Possibilities