SNP Identification in Ovine APOM, BAT2 and G6B Genes in the MHC Class III Region and Phylogenetic Analysis in 10 Mammalian Species

The major histocompatibility complex (MHC) genes are associated with genetic resistance and susceptibility to diseases. The MHC class III is very gene dense and contains genes of many types including the complement, heat stress protein and cytokine family genes. We carried out a study to identify single nucleotide polymorphisms (SNPs) in ovine APOM, BAT2 and G6B genes in Nigerian sheep and elucidated their phylogenetic relationships in ten mammalian species. The highest mutation rate of 11 SNPs was observed in G6B gene (3 synonymous and 8 non-synonymous mutations) followed by 10 mutations in BAT2 (1 synonymous and 9 non synonymous mutations) while APOM gene showed the least mutation rate (2 synonymous and 5 non-synonymous mutations). A phylogenetic analysis to compare the sequences in 10 mammalian species (sheep, cattle, pig, monkey, gorilla, giant panda, elephant, rabbit, dog and chimpanzee) was carried out. Our study revealed a lowest average nucleotide substitution per site (Dxy) between sheep and cattle in APOM gene. The higher Dxy values were found between rabbit and dog (4.172), panda and chimpanzee (2.866) and chimpanzee and dog (4.692) indicating small genetic distances. BAT2 gene had the highest Dxy between cattle and chimpanzee (0.094) and rabbit and dog (0.070) which indicated even smaller genetic distances. Sheep and giant panda (12.047) had the highest Dxy in G6B gene. Prediction of protein structures showed that APOM gene consists mainly of beta strands while BAT2 and G6B are mixed structure proteins, consisting of alpha helix, beta strands and random coils. The proteins do not share any similar domain features despite the close proximity of these genes on ovine chromosome 20.