Evolutionary history of DLA class II haplotypes in canine diabetes mellitus through single nucleotide polymorphism genotyping

Abstract

Strong linkage disequilibrium (LD) is a characteristic of the major histocompatibility complex (MHC) region, as well as the genome in general in dogs as a consequence of demographic changes with domestication. Disease association studies of MHC haplotypes may be affected by high LD and the resultant shared genetic backgrounds of haplotypes giving associations with linked but non-causative mutations, and also by convergent haplotypes, in which combinations of alleles have arisen independently. This study provides preliminary tools for dog leukocyte antigen (DLA) class II haplotype analysis with 102 single nucleotide polymorphisms (SNPs) identified in 14.6 kb and genotyping of 20 of these SNPs to tag haplotypes in 60 dogs with diabetes mellitus and in 49 non-diabetic dogs. The pattern of LD and analysis of SNP patterns indicated combinations of exon 2 alleles have arisen through both recombination and convergence. For exon 2 haplotypes associated with susceptibility or protection from diabetes mellitus, a region of fixed differences in SNPs across the DQ region was observed, suggesting a region outside exon 2 may be implicated in disease association. Four new DQB1 promoter alleles restricted to diabetic dogs were identified, as well as a substitution difference in the X1 box of the DQB1 promoter that will potentially modify the effect of the protective haplotypes within diabetic dogs.

Expanded dog leukocyte antigen (DLA) single nucleotide polymorphism (SNP) genotyping reveals spurious class II associations

“…Since both linkage disequilibrium (LD) and allelic content vary for different HLA haplotypes (Horton et al, 2008), this may be true for the DLA. The exon 2 ‘alleles’ may represent different haplotypes that appear to be identical due to convergence (Seddon et al, 2010). When Seddon et al (2010) sampled SNPs from the MHC class II region to evaluate canine cases and controls for type I diabetes, it was concluded that the published class II association with type I diabetes (Kennedy et al, 2006a), could be outside the DRB1/DQA1/DQB1 exon 2 region or within a region larger than just exon 2.…”

“…The exon 2 ‘alleles’ may represent different haplotypes that appear to be identical due to convergence (Seddon et al, 2010). When Seddon et al (2010) sampled SNPs from the MHC class II region to evaluate canine cases and controls for type I diabetes, it was concluded that the published class II association with type I diabetes (Kennedy et al, 2006a), could be outside the DRB1/DQA1/DQB1 exon 2 region or within a region larger than just exon 2. It is also possible that associations are more complex than those involving a single haplotype (Seddon et al, 2010).…”

“…When Seddon et al (2010) sampled SNPs from the MHC class II region to evaluate canine cases and controls for type I diabetes, it was concluded that the published class II association with type I diabetes (Kennedy et al, 2006a), could be outside the DRB1/DQA1/DQB1 exon 2 region or within a region larger than just exon 2. It is also possible that associations are more complex than those involving a single haplotype (Seddon et al, 2010). Differentiation of each of these possibilities should be possible when genotyping SNPs across the extended DLA region for disease association studies.…”

“…The long regions in LD are homozygous for breed-specific phenotypes, and show a mosaic pattern of short ancestral haplotype blocks that are shared between different breeds (Karlsson et al, 2007). It is expected that disease association studies of DLA haplotypes will be affected by breed-specific long LD blocks as well as the restricted number of breed-specific DLA haplotypes, giving associations with linked but non-causative mutations (Seddon et al, 2010). …”

Evaluation of DLA promoters in Doberman hepatitis

“…In dogs, only one study has been conducted on the MHC class II promoters and their role in the regulation of the MHC class II genes (23). In canine diabetes mellitus, both protective and susceptibility MHC class II haplotypes have been found, suggesting a complex interaction between the MHC class II and canine diabetes mellitus (23). In this study, a variable site was identified within the promoter DQBp X1‐box, where protective alleles in diabetic dogs, but not in other dogs, had an A nucleotide in their promoter sequence.…”