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Structural Variation Gives Rise to Chicken Beards, Muffs

NEW YORK (GenomeWeb) – Researchers have tied a complex structural variation to the development of beards and muff in chickens.

Some chicken breeds are known for having fluffy feathers on their faces and near their beaks that give them the appearance of being bearded. Through a combination of genome-wide association, linkage, and additional analyses, first author Ying Guo from China Agricultural University and her colleagues homed in on a structural variation consisting of three duplications that are associated with muffs and beards in chickens, as they reported today in PLOS Genetics. While this region contains a handful of genes, the researchers found that HOXB8 expression was higher in the facial tissues of chickens with muffs and beards, suggesting it has a role in their formation.

"Muffs and beard in chicken is caused by a structural variation that consists of three duplicated regions on GGA27 and results in the ectopic expression of HOXB8 in facial skin," Guo said in a statement. "Our findings show the significance for structural variations on phenotypic diversity and a novel role for HOXB8 in feather formation."

In their study, Guo and her colleagues focused on an F2 intercross between the Huiyang bearded chicken and the non-bearded High Quality of Chicken Line A breeds. Through identity-by-descent mapping, Guo and her colleagues homed in on a 48-kilobase region, and by genotyping some 585 birds, the researchers found a 2.5Mb region on GGA27 that was associated with having a muff and beard. They then validated that finding in a second bearded chicken population.

By further exploring this region, the researchers found that it contains three copy-number variations: a likely tandem duplication at 1.70 Mb on GGA27 and duplications at 3.58 Mb and 4.47 Mb on GGA27 that have been translocated with that first tandem duplication. This, they noted, suggests that a highly complex event led to this polymorphism.

Through linkage and association analysis, the researchers found that this complex structural variant is completely associated with beards and muffs in chickens.

Further, these duplicated regions house seven annotated genes, including HOX-family genes. HOX genes, according to the authors, are likely candidates as members of that family have been linked to alopecia in mice as well as to skin wound healing.

Guo and her colleagues examined the expression of these seven genes in skin samples from chickens at various developmental ages — embryos, two-week-old chicks, and adults. Wild-type chickens, they found, didn't express HOXB8 in their facial skin and only lowly expressed it in their dorsal skin. However, expression was high in chickens homozygous for the muff and beard phenotype. This difference in expression levels was apparent at each of the developmental stages, the researchers added.

This high ectopic expression of HOXB8 in muff and beard chickens could be due to a loss of repression through the structural variation from repressive elements typically present in the HOX cluster. This, then, could extend the growth phase of facial feathers.

"Our results … strongly suggest that this allele leads to an altered ectopic expression of a homeotic gene HOXB8, to suggest a novel role for HOXB8 in modulating the regional development of the feather," Guo and her colleagues wrote. "These results are another example of how striking phenotypes in domestic animals have facilitated the discovery of genomic structural variants that alter developmental phenotypes."