Analysis of polymorphisms in the major expressed class I locus (B-FIV) of the chicken

We analyzed the polymorphic nature of eleven alleles expressed by the major class I locus (B-FIV) in chickens. Similar to mammalian class I loci, the nucleotide substitutions with high variability occur in exons 2 and 3 encoding the alpha1 and alpha2 domains. However, the nonsynonymous to synonymous ratio of nucleotide substitutions in exon 3 encoding the alpha helix and beta sheets is reversed compared with HLA. The region of exon 3 encoding the alpha2 helix demonstrates a much lower nonsynonymous to synonymous ratio, suggesting evolutionary selection of a more conserved alpha2 helix in B-FIV compared with HLA. Amino acid residues with high Wu-Kabat variability are typically located in positions predicted to impact antigen presentation. B-FIV amino acid residues predicted to interact with the CDR1alpha region of the T-cell receptor (Tcr) demonstrate less variability than in mouse and human class I alleles. The combination of a reduced nonsynonymous to synonymous ratio in exon 3 encoding the alpha2 helix and the limited variability in CDR1alpha contact residues is discussed with regard to concerted evolution between a minimal major histocompatibility complex and compaction of Tcr variable gene segments in the chicken.