Avian TAP genes : detection of nucleotide polymorphisms and comparative analysis across species

TAP1 and TAP2 genes code for the two subunits of the transporter associated with antigen processing (TAP), and in chicken they are located between the two MHC class I genes. Using primers based on chicken sequences, the genomic regions corresponding to chicken TAP1 exons 6 to 7 and TAP2 exons 4 to 6 (which encode portions of the chicken TAP1 and TAP2 molecules corresponding to the human peptide-binding regions) were amplified and sequenced from chicken (70 birds), turkey (24), pheasant (6), and guinea fowl (7). A total of 80 within-species single nucleotide polymorphisms (SNPs) were identified. None of the chicken SNPs detected here was present in public databases. The SNP frequencies in chicken were 9.57 SNP/kb in TAP1 and 19.16 SNP/kb in TAP2, while turkey showed similar SNP frequencies in the two genes. Putative amino acid sequences were inferred to identify non-synonymous substitutions. The alignment of the consensus polypeptide sequences showed that most of the amino acid variations were conserved or semi-conserved substitutions. In conclusion, a high variability in the level of nucleotide polymorphism was observed within the two genes, with chicken showing the highest polymorphism rate in both genes. Most of the SNPs identified were within introns, and a general conservation of both amino acid numbers and characteristics of residues among and within the species was found. These data underline the functional importance of these molecules, but also suggest their capacity to bind different antigenic peptides.