Candidate SNPs for chicken immune response genes

Chicken MHC is located on microchromosome 16 (GGA16). On the same chromosome, class I-like and IIβ-like genes are clustered within the Rfp-Y region. From previous studies, both loci seem to be associated to some viral disease positive outcomes. In the present study the MHC genes Tapasin, TAP1 and TAP2 and the Rfp-Y genes YFV and YFVI were analised in several commercial lines and indigenous breeds to identify new SNPs within the two regions. DNA sequences were edited and processed using Phred. Database searches (EMBL, GenBank) and initial sequence comparisons were carried out with BLASTn. The polymorphism identification analyses were carried out by the CAP3 and ClustalW multiple alignment programs. The sequence data here produced were further analysed with the PolyBayes SNP discovery pipeline established at PTP, Italy. Tapasin, TAP1 and TAP2 genes showed a low level of within/between breed polymorphism. On the other hand, YFV and YFVI genes showed an higher level of polymorphism with within/between breed nucleotide substitution rates ranging between 6% in the exons and 20% in the intronic regions. Several of these base substitutions are non-synonymous and when located within exonic regions can be of great consequence as they could affect the final phenotype. Therefore, most of the here presented SNPs will likely be invaluable tools in future association studies.