A Complex Structural Variation on Chromosome 27 Leads to the Ectopic Expression of HOXB8 and the Muffs and Beard Phenotype in Chickens

Abstract

Muffs and beard (Mb) is a phenotype in chickens where groups of elongated feathers gather from both sides of the face (muffs) and below the beak (beard). It is an autosomal, incomplete dominant phenotype encoded by the Muffs and beard (Mb) locus. Here we use genome-wide association (GWA) analysis, linkage analysis, Identity-by-Descent (IBD) mapping, 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 gene 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 three duplications, one in tandem and two that are translocated to that of the tandem repeat around 1.70 Mb on GGA27. The duplications contain total seven annotated genes and their expression was 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, our results provide an interesting example of how genomic structural rearrangements alter 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, herein providing novel insights into the likely role of HOXB8 in feather development and differentiation.

Enhancer evolution and the origins of morphological novelty

“…Although the evolution of enhancers de novo from mutations in non-functional sequences represents an obvious null hypothesis (Figure 1B), this mechanism has been difficult to study, and it more often turns out that new regulatory sequences have evolved from pre-existing ancestral ones. Studies of the domesticated chicken have shown how large-scale chromosome rearrangements and structural variations have contributed to diverse phenotypes by rearranging or duplicating regulatory elements and placing them in association with new genes (“promoter switching” in Figure 1B) [12–14]. Multiple studies have shown how novel expression domains can evolve from pre-existing enhancers that derive additional tissue specificities (“co-option” in Figure 1B) [15–18].…”

Genomic determinants of epidermal appendage patterning and structure in domestic birds

“…Consistent with these findings, genetic crosses and genomic mapping approaches implicate the mesodermally-expressed transcription factors PITX1 and TBX5 in feather-footed domestic pigeons and chickens (Domyan et al, 2016). The head crests of certain chicken breeds probably result from a re-specification of cranial to dorsal body skin identity, and this phenotype is linked to ectopic expression of HOXC8 , a mesodermally-expressed transcription factor (Kanzler et al, 1997; Wang et al, 2012) ( HOXB8 , which is linked to the muffs and beard phenotype in chickens, is expressed in both mesodermal and ectodermal skin derivatives; Guo et al, 2016; Hughes et al, 2011). However, the pigeon head crest maps to EPHB2 , which is expressed throughout the skin mesenchyme and at the mesenchymal-epithelial interface (Suksaweang et al, 2012).…”

“…The Muffs and beard (Mb) trait is found in a variety of chicken breeds and is characterized by small tufts of elongated feathers that surround the face and beak (Bartels, 2003; Guo et al, 2016). By combining genetic mapping, genomic association tests, and IBD analyses, Guo et al (2016) identified a 48-kb region as the Mb candidate locus.…”

“…By combining genetic mapping, genomic association tests, and IBD analyses, Guo et al (2016) identified a 48-kb region as the Mb candidate locus. Within this genomic interval, Guo et al discovered and characterized a complex genomic structural variant (SV) composed of three unique copy number variants (CNVs), which they predicted was the underlying cause of the Mb phenotype.…”

“…Some degree of differential expression was observed for five of the genes within the Mb SV. However, differential expression of HOXB8 was the most pronounced at all developmental stages and correlated best with Mb genotype, suggesting that ectopic HOXB8 expression in facial skin causes elongated feathers near the face and beak of Mb chickens (Guo et al, 2016). Although further work is required to determine the specific functional consequence of ectopic HOXB8 expression in neck skin, this study demonstrates that complex genomic SVs can contribute to epidermal appendage variation.…”