Hitchhiking of bactericidal/permeability-increasing protein-like gene with the fibromelanosis locus in Kadaknath black-bone-chicken

Abstract

AbstractBlack-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 expression of the endothelin-3 (EDN3) gene 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 theFmlocus spanning both Dup1 and Dup2 regions and establish that theFm_2scenario 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 establishes that all BBC breeds, including Kadaknath, share the complex chromosomal rearrangement junctions at the fibromelanosis (Fm) locus. We also identify twoFmlocus proximal regions (∼70Kb 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 (BPIL) gene having two Kadaknath-specific changes within protein domains. Our results indicate that protein-coding changes in theBPILgene hitchhiked with theFmlocus in Kadaknath due to close physical linkage. Identifying thisFmlocus proximal selective sweep sheds light on the genetic distinctiveness of Kadaknath compared to other BBC.