Avian TAP1 and TAP2 genes: polymorphisms and haplotypes

TAP1 and TAP2 are the two subunits of the transporter associated with antigen processing (TAP). TAP role is the transport of peptides, that will be specifically loaded onto the Major Histocompatibility Complex (MHC) class I molecules for the antigen presentation, from the cytoplasm into the endoplasmic reticulum. Chicken TAP1 and TAP2 genes are located inside the MHC, between the two class I genes. TAP1 includes 11 exons and TAP2 includes 9 exons. Aim of the present work is the discovery and validation of Single Nucleotide Polymorphisms (SNPs) within these two genes and the study of the haplotypes. Chicken and turkey sequences of the regions spanning from TAP1 exon 5 to exon 6 and from TAP2 exon 4 to exon 6 were obtained by direct sequencing of specifically amplified fragments. The sequences were so aligned to investigate the intra- and inter-species polymorphisms and the SNP discovery was carried out using the PolyBayes program. Eighteen TAP1 putative SNPs were identified in chicken and seven in turkey. Twenty-four TAP2 putative SNPs were detected in chicken and eleven in turkey. The analysis of chicken polymorphisms showed that most of the SNPs did not show a breed specific pattern. Only one breed presented a specific SNP, that was not identified in the other breeds. A second specific SNP was identified in a small number of broilers. On the other hand, turkey sequences showed higher nucleotide substitution between the commercial line and the local breeds in both TAP1 and TAP2 genes. Polypeptide sequences were inferred from nucleotide sequences and aligned to identify synonymous and non-synonymous substitutions. The polymorphic sites identified in this work were further used in the identification of haplotypes for these two genes. Haplotypes were reconstructed using the FASTPHASE software. Differences among haplotype frequencies in different species and breeds were tested for significance. No significant differences were found for TAP1. Significant differences (P