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 onethird of which had minor allele frequencies 40.2 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.

Alpha-Class Glutathione S-Transferases in Wild Turkeys (Meleagris gallopavo): Characterization and Role in Resistance to the Carcinogenic Mycotoxin Aflatoxin B1

“…Recent studies on the major histocompatibility complex (MHC) revealed increased haplotype variability in wild turkey as compared to domestic turkeys [39], [40]. The domestic turkey is recognized as a single breed with eight different varieties defined primarily by plumage color [41], [42].…”

Let's talk turkey: immune competence in domestic and wild fowl

“…However, with the increasing availability of sequence data, it is possible to design primers that amplify target regions and in this issue, Chaves et al (2011) show that singlenucleotide polymorphism haplotyping can be used to capture variation within the MHC-B locus. The authors applied this method to compare MHC diversity of individuals from three different subspecies of wild turkey (Meleagris gallopavo, Figure 1) from the United States with the commercial turkeys.…”