Genetic characterisation of buffalo MHC (Bubu)-DQB cDNA molecule

Abstract

A 771 nucleotide long cDNA molecule corresponding to major histocompatibility complex (MHC)-DQB gene was amplified, cloned and sequenced from water buffalo (Bubalus bubalis). Open reading frame of the Bubu-DQB sequence was short by three nucleotides from the DQB genes of the other ruminants. Nucleotide similarity of Bubu-DQB was highest with cattle DQB alleles (84–97%), followed by goat (88.8%) and sheep (87.5%). The sequence comparison revealed that the DQB gene was highly variable in buffalo particularly, in exon 2 (β1 domain). A total of 45 amino acid substitutions were identified in Bubu-DQB compared to cattle DQB*0101 sequence, with a maximum (27) in β1 domain. The residues involved in antigen binding and heterodimer formation were found to be different in buffalo DQB sequence compared to other species. Phylogenetic study showed that the Bubu-DQB has evolved prior to the diversification of common DQB alleles in ruminants. Our study revealed the high genetic variation in the DQB gene in buffalo, which might have generated to recognise species specific antigens.