Haplotype variation, recombination, and gene conversion within the turkey MHC-B locus

Abstract

The major histocompatibility complex (MHC) is a gene dense region with profound effects on the disease phenotype. In many species, characterizations of MHC polymorphisms have focused on identifying allelic haplotypes of the highly polymorphic class I and class II loci through direct immunological approaches such as monoclonal antibodies specific for the major antigens or indirectly through DNA sequence-based approaches. Invariably, these studies fail to assess the broader range of variation at the other loci within the MHC. This study examines variation in the turkey MHC by resequencing 15 interspersed amplicons ( approximately 14 kb) spaced across the MHC-B locus in a representative sampling of 52 commercial birds. Over 200 single nucleotide polymorphisms (SNPs) were identified with high levels of polymorphism (1 SNP/70 bp) and heterozygosity (average minor allele frequency of 0.15). SNP genotypes were used to identify the major haplotypes segregating in the commercial lines. Sequencing of the peptide binding region (PBR, exon 2) of the class IIB loci of select individuals identified 10 PBR alleles/isotypes among the major MHC haplotypes. Examination of pedigreed families provides direct evidence of gene conversion and recombination within the B locus. Results of this study demonstrate the MHC diversity available in commercial flocks and provide genomic resources for studying the effect of this diversity (alleles and/or haplotypes) on disease susceptibility and resistance.

A locus-wide approach to assessing variation in the avian MHC: the B-locus of the wild turkey

“…Analysis was performed using 45 SNVs (42 SNPs and 3 DIPs) with minor allele frequencies (MAFs) of 0.2 or greater that were successfully genotyped on all 40 individuals. An additional haplotype inference analysis included samples from a previous study of commercial turkeys (Chaves et al, 2010) using SNVs of high MAF common among the two groups. Analysis of haplotype relationships was performed using ClustalW (Larkin et al, 2007) and SplitsTree4 (Huson and Bryant, 2006 Figure 1 The turkey MHC-B locus and position of amplicons (arrows) sequenced for haplotype analysis and genetic mapping.…”

“…Samples from the populations studied by Mock et al (2002) were relict, native populations, with presumably higher sequence diversity. Individuals were sequenced at nine interspersed locations across the MHC-B region (Figure 1, Supplementary Table S2) as previously described (Chaves et al, 2010). PCR products were purified using a MinElute PCR Purification Kit (Qiagen, Inc., Valencia, CA, USA) and sequenced with an automated ABI Sequencer (Applied Biosystems, Carlsbad, CA, USA).…”

“…For DGGE, primers (cIIB_DGGE_F-5 0 -AAAA CCCGGAGCCCTTGT-3 0 and cIIB_DGGE_R-5 0 -ACTCA CCGCTCCTCTGCAC-3 0 ) were designed from aligned sequences (Chaves et al, 2010) to simultaneously amplify the highly variable PBR (exon 2) from the three class IIB genes of the B-locus. The designed primers are specific for the MHC-B loci and do not amplify the other known class IIB-like genes that reside outside of the B-locus.…”

“…For example, single loci in the human MHC have 100s of alleles and allelic combinations may generate 10 000s of potential haplotypes (Marsh et al, 2005). In contrast, domestic poultry show more constrained diversity in their MHC (Hosomichi et al, 2008;Chaves et al, 2010) although; a recent study of domestic chickens identified nearly 100 MHC-B haplotypes (Fulton et al, 2006). MHC haplotypes have been found to have strong influences on immune response and disease resistance in chickens.…”

“…Commercial selection has clearly reduced allelic diversity in chicken lines (Muir et al, 2008). A sampling of genetic variation within commercial turkeys shows that some MHC haplotypes occur at high frequency within breeder lines (Chaves et al, 2010).…”