Association mapping in the chicken: Loci affecting skin pigmentation, structural morphology and antibody response

The amount of morphological variation existing in domesticated poultry species is evident when considering the wide diversity in shape, size, color and structure of plumage and body patterning present across chicken breeds. Some of these traits have had a role in validating the principles of mendelian inheritance in animals and others demonstrate complex traits with polygenic effects. This research describes the generation of chicken populations designed for both single and polygenic trait mapping utilizing genetic marker trait-association analysis.;The Silkie chicken is notable for possessing many unusual characteristics, most principally the hyperpigmentation of dermal and connective tissues. This trait is controlled by two genes, Fibromelanosis (Fm) and Inhibitor of Dermal Melanin (Id), and is mediated by abnormal melanocyte precursor migration in the developing embryo. Development of segregating populations for these two classically described genes and association analysis of genetic markers with skin pigmentation traits has identified two genomic regions corresponding to Fm and Id on chromosome 20 and Z respectively. Other traits segregating in this population that have shown significant association to a restricted genomic region include rose comb, duplex comb, silkie feathering, feathered legs, vulture hock and polydactyly.;In a second study a 120-Kb region on chromosome Z was identified as harboring the causal mutation for the sex-linked barring gene (B) in the chicken. The B locus is primarily involved in regulating feather pigmentation but is also a strong inhibitor of skin pigmentation. Further work directed at identifying causal mutations of Id, Fm and B, representing unresolved mechanisms of neural crest cell migration, melanoblast proliferation and melanocyte differentiation, will undoubtedly yield a further understanding of these biological processes applicable across vertebrate species. Selection at these three loci for alleles that confer preferred pigmentation patterns in commercial poultry populations might be useful for tailoring products to meet consumer preferences in different global markets.;A third study focused on identification of genomic regions involved in regulating antibody response to the antigen sheep red blood cells (SRBCs) in a population of chickens having undergone divergent selection for 32 generations. The results from this study identify 11 loci in association with immune response including the major histocompatibility locus (MHC) and the presence of parent of origin or potentially epigenetic effects on immune response in the chicken. Very few loci were identified as having a significant association with body weight despite the dramatic difference in this trait between the selected lines. This suggests that the allocation of resources away from growth towards immune system related traits is responsible for the inverse relationship between growth and antibody response in the selected lines as opposed to selection for loci with a direct effect on growth. Fine mapping efforts are needed for all of these traits in order to identify causal mutations involved. These results show the utility of modern molecular and computational techniques to identify genetic elements controlling both single and polygenic traits that are important for understanding developmental and antibody response related systems in the chicken.