Genetic Mapping And Functional Analysis Of The Muffs And Beard Trait In Chickens

For several thousand years, domesticated animals have been subjected to a combination of natural and artificial selections, and during this process accumulated numerous phenotypic variations. The resulting genetic and phenotypic diversity in domesticated animals provides an excellent basis for improving our understanding of the role of genes in development and disease resistance. The feather, a complex integumentary appendage, exists in multiple variants on different body parts. The derived feathering phenotypes in domestic birds are perfect resources to decipher the mechanisms regulating feather development and differentiation. In the present study, we explored the Muffs and beard (Mb) trait in chickens, which is a phenotype where groups of elongated feathers gather from both sides of the cheek (Muffs) and below the beak (Beard). It is an autosomal, incomplete dominant phenotype encoded by the Muffs and beard (Mb) locus. In order to dissect the genetic basis and molecular processes of the trait, we designed an intercross line using Huiyang Bearded chicken (HB) and High Quality of Chicken Line A (HQLA). Huiyang Bearded chicken is a kind of native breeds in China. It is characterized by the Muffs and beard trait, which makes it an excellent model to study tissue specificity and feather regional diversification. HQLA is a kind of a non-Mb broiler line that generated by Guangdong Academy of Agricultural Sciences.Here we used genome-wide association study (GWAS), linkage analysis, Identity by Descent (IBD) mapping, array comparative genomic hybridization (array CGH), genome re-sequencing and expression analysis to show that the Mb allele causing the Mb phenotype is a derived allele where a complex structural variation (SV) on GGA27 leads to an altered expression of the HOXB8. This Mb allele was shown to be completely associated with the Mb phenotype in nine other independent Mb chicken breeds. The Mb allele differs from the wild-type mb allele by duplications located on 1.7 Mb,3.5 Mb and 4.4 Mb, one in tandem and two that are translocated to that of the tandem repeat around 1.7 Mb on GGA27. The duplications contain in total seven annotated genes and their expressions were tested during distinct stages of Mb morphogenesis. A continuous high ectopic expression of HOXB8 was found in the facial skin of Mb chickens, strongly suggesting that HOXB8 directs this regional feather-development.In conclusion, we studied the genetics of the Muffs and beard trait, a feather variant that alters the feather development in the facial area of chickens. We show that the phenotype is associated with a genomic structural variant that leads to an ectopic expression of HOXB8 in the facial skin during feather development. Our results provide an interesting example of how genomic structural rearrangements alters the regulation of genes leading to novel phenotypes. Further, it again illustrates the value of utilizing derived phenotypes in domestic animals to dissect the genetic basis of developmental traits, and provides novel insights into the likely role of HOXB8 in feather development and differentiation.