Major histocompatibility complex (MHC) class II genes are cell surface molecules with roles in intercellular recognition, discrimination between self and non-self and humoral and cell-mediated immune responses. We amplified a 228-bp fragment of exon 2 of MHC DQB1 gene in 60 animals made up of the three major Nigerian goat breeds [West African Dwarf (WAD), Red Sokoto (RS) and Sahel (SH)]. Comparison of predicted amino acid residues of Nigerian goats with similar alleles from other ruminants revealed considerable similarity in amino acid substitution pattern. Twenty polymorphic positions were identified, four of which are located in the peptide binding region of goat DQB1 locus. However, seven of the amino acid substitutions were peculiar to Nigerian goats compared to published caprine sequences. A significantly (P<0.01) higher rate of non-synonymous substitutions per non-synonymous site (dN) than synonymous substitutions per synonymous site (dS) at the DQB1 locus suggests that allelic sequence evolution at this locus may be driven by balancing selection. In-silico functional analysis of non-synonymous mutations obtained using PANTHER revealed that three of the amino acid substitutions at the peptide binding region (Y27S, T29N and D57T) did not impair protein function. Based on neighbor-joining phylogenetic tree (UPGMA) derived from consensus sequences, the northern SH and RS goats are closer at this locus compared to the southern WAD goats. Our results provide the first description of Nigerian goat DQB1 sequence polymorphism; information that might be used in the search of association with disease resistance.
Key words: MHC Class II genes, DQB1, Exon 2, Polymorphisms, Nigerian, Goats