MHC class I BFIV gene polymorphisms in four Chinese native chicken breeds

•Characteristics of MHC I BFIV molecules in 4 Chinese native breeds were obtained.•There was no correlation between geography and genotype among MHC I BFIV molecules.•Most polymorphism was found in a1 and a2 regions which include the residues of the PBR.•The chicken and human MHC I molecules had the similar structural features.

The major histocompatibility complex (MHC) includes the most polymorphic genes in vertebrates, and balancing selection has been proposed as a main evolutionary force. Here we present one of the first data sets examining the genetic characteristics of chicken MHC I BFIV molecules in four Chinese native breeds, sourced from different regions in China. In all, 89 BFIV alleles were isolated from 102 individuals sampled, and 13 repeated alleles were observed. No significant correlation was found between genetic differentiation and geographical distance in the phylogenetic tree. BFIV genes exhibited a high level of nucleotide polymorphisms, and most of the polymorphic sites were located in the peptide-binding region (PBR) encoded in exons 2 and 3. A comparison of the three-dimensional structures of PBRs in chicken BFIV and human HLA-A molecules revealed evident structural and functional similarities. The results suggested that MHC I molecules had similar structural features in different species.