title: A locus-wide approach to assessing variation in the avian MHC: the B-locus of the wild turkey.
abstract: Studies of major histocompatibility complex (MHC) diversity in non-model vertebrates typically focus on structure and sequence variation in the antigen-presenting loci: the highly variable and polymorphic class I and class IIB genes. Although these studies provide estimates of the number of genes and alleles/locus, they often overlook variation in functionally related and co-inherited genes important in the immune response. This study utilizes the sequence of the MHC B-locus derived from a commercial turkey to investigate MHC variation in wild birds. Sequences were obtained for nine interspersed MHC amplicons (non-class I/II) from each of 40 birds representing 3 subspecies of wild turkey (Meleagris gallopavo). Analysis of aligned sequences identified 238 single-nucleotide variants approximately one-third of which had minor allele frequencies >0.2 in the sampled birds. PHASE analysis identified 70 prospective MHC haplotypes in the wild turkeys, whereas a combined analysis with commercial birds identified almost 100 haplotypes in the species. Denaturing gradient gel electrophoresis (DGGE) of the class IIB loci was used to test the efficacy of single-nucleotide polymorphism (SNP) haplotyping to capture locus-wide variation. Diversity in SNP haplotypes and haplotype sharing among individuals was directly reflected in the DGGE patterns. Utilization of a reference haplotype to sequence interspersed regions of the MHC has significant advantages over other methods of surveying diversity while identifying high-frequency SNPs for genotyping. SNP haplotyping provides a means to identify both divergent haplotypes and homozygous individuals for assessment of immunological variation in wild and domestic populations.
authors.affiliation: Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St Paul, USA.
authors.forename: L D
authors.initials: LD
authors.lastname: Chaves
authors.forename: G M
authors.initials: GM
authors.lastname: Faile
authors.forename: J A
authors.initials: JA
authors.lastname: Hendrickson
authors.forename: K E
authors.initials: KE
authors.lastname: Mock
authors.forename: K M
authors.initials: KM
authors.lastname: Reed
mesh_terms: D000483:Alleles; D000818:Animals; D058645:Denaturing Gradient Gel Electrophoresis; D056426:Genetic Loci; D014644:Genetic Variation; D005838:Genotype; D006239:Haplotypes; D008285:Major Histocompatibility Complex / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D014422:Turkeys / Q000235:genetics*