Decoding the fibromelanosis locus complex chromosomal rearrangement of black-bone chicken: genetic differentiation, selective sweeps and protein-coding changes in Kadaknath chicken

Abstract

Black-bone chicken (BBC) meat is popular for its distinctive taste and texture. A complex chromosomal rearrangement at the fibromelanosis (Fm) locus on the 20th chromosome results in increased endothelin-3 (EDN3) gene expression and is responsible for melanin hyperpigmentation in BBC. We use public long-read sequencing data of the Silkie breed to resolve high-confidence haplotypes at the Fm locus spanning both Dup1 and Dup2 regions and establish that the Fm_2 scenario is correct of the three possible scenarios of the complex chromosomal rearrangement. The relationship between Chinese and Korean BBC breeds with Kadaknath native to India is underexplored. Our data from whole-genome re-sequencing establish that all BBC breeds, including Kadaknath, share the complex chromosomal rearrangement junctions at the fibromelanosis (Fm) locus. We also identify two Fm locus proximal regions (∼70 Kb and ∼300 Kb) with signatures of selection unique to Kadaknath. These regions harbor several genes with protein-coding changes, with the bactericidal/permeability-increasing-protein-like gene having two Kadaknath-specific changes within protein domains. Our results indicate that protein-coding changes in the bactericidal/permeability-increasing-protein-like gene hitchhiked with the Fm locus in Kadaknath due to close physical linkage. Identifying this Fm locus proximal selective sweep sheds light on the genetic distinctiveness of Kadaknath compared to other BBC.

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

“…The hyperpigmentation phenotype in the BBC breeds results from common complex chromosomal rearrangement at the Fm locus and distinguishes them from non-BBC breeds (Dharmayanthi et al, 2017;Shinde et al, 2023). The shared rearrangement in diverse BBC breeds supports a model of a common origin of BBC followed by dispersal globally.…”

“…Notably, various BBC breeds from different geographic regions across Asia exhibit this distinctive chromosomal rearrangement at the Fm locus. The shared rearrangement and the population genetic signature of this region suggest a common ancestral origin for all BBC breeds (Shinde et al, 2023).…”

“…The genetic basis of the Fm locus has been identified on chromosome 20 as a complex chromosomal rearrangement encompassing three different non-paralogous genomic regions, Dup1, Int, and Dup2, with the Dup1 and Dup2 regions being duplicated (Dharmayanthi et al, 2017;Dorshorst et al, 2011;Shinde et al, 2023;Shinomiya et al, 2012;Sohn et al, 2018). The most important region Dup1 contains five protein-coding genes: EDN3, ZNF831, SLMO2, ATP5E, and TUBB1.…”