Variation of goat interferon regulatory factor 3 gene and its implication in goat evolution

Members of the interferon regulatory factor (IRF) gene family are major regulators of host defense in vertebrates, controlling many different aspects of the innate and adaptive immune responses. Among these, IRF3 plays important roles in many biological processes. Considering that immune systems are crucially fundamental for the survival and evolution of all species, patterns of selection and polymorphisms in innate immune loci are of significant interest in molecular evolution research. We assembled and evaluated 1353 bases on the encoding regions of the IRF3 gene in domesticated goats from Nigeria (West Africa), Ethiopia (East Africa), Iran (West Asia) and China (East Asia) and in wild goat (Capra aegagrus). The sequence diversity in domesticated goats was quite low but significantly different from that of wild goats. The Fu and Li's tests were significant and positive, while the Tajima's D test was significant but negative, suggesting a deviation from neutrality. Two of the six observed haplotypes across all the sequences were common in Asian goats. Two haplotypes were shared with wild goat, by West African Dwarf (WAD) and African Borena goats. In assessing the mode of evolutionary activity affecting the evolution of the gene, we found that the codon models dN/dS ratio for all goats was greater than a unit (1.667; P = 0.025). Likelihood ratio test (LRT) to compare the models used was significant (24.56; P < 0.001). Positive diversifying selection inferred with recent evolutionary changes in domesticated goat IRF3 led us to conclude that the gene evolution has been influenced by domestication process in goats.