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Common Ancestry of the Id Locus: Chromosomal Rearrangement and Polygenic Possibilities
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Common Ancestry of the Id Locus: Chromosomal Rearrangement and Polygenic Possibilities
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Journal Article
Common Ancestry of the Id Locus: Chromosomal Rearrangement and Polygenic Possibilities
2025
Overview
The diversity in dermal pigmentation and plumage color among domestic chickens is striking, with Black Bone Chickens (BBC) particularly notable for their intense melanin hyperpigmentation. This unique trait is driven by a complex chromosomal rearrangement on chromosome 20 at the
Fm
locus, resulting in the overexpression of the
EDN3
(a gene central to melanocyte regulation). In contrast, the inhibition of dermal pigmentation is regulated by the
Id
locus. Although prior studies using genetic crosses, GWAS, and gene expression analysis have investigated the genetic underpinnings of the
Id
locus, its precise location and functional details remain elusive. Our study aims to precisely locate the
Id
locus, identify associated chromosomal rearrangements and candidate genes influencing dermal pigmentation, and examine the ancestral status of the
Id
locus in BBC breeds. Using public genomic data from BBC and non-BBC breeds, we refined the
Id
locus to a ~1.6 Mb region that co-localizes with Z amplicon repeat units at the distal end of the q-arm of chromosome Z within a 10.36 Mb inversion in Silkie BBC. Phylogenetic and population structure analyses reveal that the
Id
locus shares a common ancestry across all BBC breeds, much like the
Fm
locus. Selection signatures and highly differentiated BBC-specific SNPs within the
MTAP
gene position it as the prime candidate for the
Id
locus with
CCDC112
and additional genes, suggesting a possible polygenic nature. Our results suggest that the
Id
locus is shared among BBC breeds and may function as a supergene cluster in shank and dermal pigmentation variation.
Publisher
Springer US,Springer Nature B.V
