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Title: Chromosomal Mapping and Candidate Gene Discovery of Chicken Developmental Mutants and Genome-wide Variation Analysis of MHC-congenics

Author
item ROBB, ELIZABETH - University Of California
item GITTER, CYNTHIA - San Antonio Zoo
item Cheng, Hans
item DELANY, MARY - University Of California

Submitted to: Journal of Heredity
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/8/2010
Publication Date: 2/19/2011
Citation: Robb, E.A., Gitter, C.L., Cheng, H.H., Delany, M.E. 2011. Chromosomal mapping and candidate gene discovery of chicken developmental mutants and genome-wide variation analysis of MHC congenics. Journal of Heredity. 102(2):141-156.

Interpretive Summary: For over 100 years, chickens have been used as a model for human biology, especially with respect to development. In this paper, we use the chicken genome sequence and low (3K) and medium (60K) genetic marker termed single nucleotide polymorphism (SNP) DNA chips to map and identify candidate genes that are responsible for various developmental mutations in the chicken as well as characterize specialized lines. The identified genes provide important information for similar malformations found in humans and can serve as future biomedical models. Furthermore, these studies show the power of chicken genetics, which can and are being applied to agriculturally-relevant traits.

Technical Abstract: The chicken has been widely used in experimental research given its importance to agriculture and its utility as a model for vertebrate biology and biomedical pursuits for over 100 years. Herein we used recently developed advanced technologies to investigate the genomic characteristics of specialized chicken genetic resources. An Illumina 3K chicken single nucleotide polymorphism (SNP) array was utilized to study variation within and among MHC-congenic lines as well as investigate line-specific genomic diversity, inbreeding coefficients, and MHC B haplotype-specific GGA 16 SNP profiles. We also investigated developmental mutant- congenic lines to map a number of single gene mutations using both the Illumina 3K array and a recently-developed Illumina 60K chicken SNP array. In addition to identifying the chromosomes and specific subregions, the mapping results affirmed prior analyses indicating recessive or dominant and autosomal or sex-chromosome modes of inheritance. Priority candidate genes are described for each mutation based on association with similar phenotypes in other vertebrates. These single-gene mutations provide a means of studying vertebrate development serving as invaluable biomedical models for similar malformations found in human.