Abstract:
The swine major histocompatibility complex (MHC) located in SSC7, is a gene dense region with a role in antigen presentation and controlling immune responsiveness. Although highly polymorphic, serological approaches to identify and define alleles have been disappointing. To determine the extent of MHC polymorphisms of class II genes, DNA from divergent world breeds of unrelated pigs was analyzed for SNPs. Primers targeting exon 2 of DQB and DRB were shown to be locus specific and amplified both loci for each animal. Expression of exon 2 PCR amplicons for both genes was verified through sequence analysis revealing 30 haplotypes comprised of over 20 different alleles among the 9 breeds. Located within the two genes were a total of 24 polymorphic sites, 22 of these were located within the antigen recognition site (DRB had two in the alpha helix) where 17 of those were nonsynonymous substitutions (7 synonymous). The breeds analyzed were selected to represent geographic areas in order to determine if haplotype divergence correlated with location of origin. The first group was identified as “Asian” and included Meishan, Erhualian and Lanyu breeds. The second group represented the “British Isles” (Hampshire, Yorkshire and Berkshire breeds) and the third group was identified as “Continental” (Duroc, Large White, and Landrace breeds). Fewer breed specific alleles were observed in breeds selected for lower fat and longer carcasses. SNPs in DRB appear to be under positive Darwinian selection with a dN/dS value of 13 as opposed to DQB with a value of 1 (no selective pressure or purifying selection) To confirm expression of the PCR products and eliminate the possibility of pseudogenes, RT-PCR with primers from intron-exon boundaries were utilized and verified the absence of pseudogene amplification and revealed highest RNA expression in DRB especially in heart, bone marrow, lung, small intestine and lymph node.