Nucleotide sequence variability analysis of Major Histocompatibility Complex Class II DQA1 gene in Nigerian goats

Abstract

Major Histocompatibility Complex (MHC) molecules loaded with peptides derived from invading pathogens are recognised by the immune system to produce a highly effective and specific response against foreign pathogens. A 310-bp fragment of exon 2 of the MHC Class II DQA1 gene was amplified in 27 animals made up of three major Nigerian goat breeds [West African Dwarf (WAD), Red Sokoto (RS) and Sahel (SH)]. Twenty amino acid polymorphic sites were found in Nigerian goats. Comparison of predicted amino acid residues of DQA1 exon 2 alleles of Nigerian goats with similar alleles from other caprine species revealed considerable congruence in amino acid substitution pattern. A significant positive selection signature was detected at the DQA1 locus of Nigerian goats in that non-synonymous substitutions occurred at a faster rate compared to synonymous substitutions (dN:dS ratio = 1.28 ; Z-Statistics= 1.634; P<0.05). The evolutionary tree constructed using UPGMA, revealed that the southern WAD goat appeared to be more related to the northern RS than SH goat at the DQA1 locus. It will be interesting therefore, for future studies to investigate the association of the genetic variants in DQA1 gene of Nigerian goats with resistance/susceptiblity to diseases in order to conserve these precious animal genetic resources.