Adaptive selection at agouti gene inferred breed specific selection signature within the indigenous goat populations

Objective The aim of this study was to calculate selection signatures at possible loci leading to population differentiation, as well as pattern of selection of agouti gene within the local goat breeds and its correlation among other animal species to reveal molecular evolution. Methods The high Fst outlier method corresponding to Fst distribution was used to identify the loci subject to positive selection. According to the empirical distribution of Fst estimates, we selected the SNPs having high Fst outlier corresponded to the upper 1% of the distribution as the loci under selection. In five goat populations 14 SNPs were determined from 14 genes to be subjected to natural or artificial selection. The selective pressures were measured with the non-synonymous to synonymous substitution rate ratio ω (dN/dS), where ω=1, ω<1 and ω>1 correspond to neutral, purifying and positive selection, respectively. Results The loci were analyzed for positive selection and the most locus undergone positive selection was Agouti-2. Positive selection of agouti gene was analyzed with FDIST analysis using outlier approach, agouti gene showed a significant positive selection in the outlier area as there was a strong evidence of positive selection for this locus because of its low heterozygosity. Analysis showed that previously agouti gene was initially under purified selection, but now is under adaptive positive selection. The data was explored by two sets of nested models (M1-M2; M7-M8) and LRT was concluded by using likelihood estimates. The nucleotide sequence of goat agouti gene showed closer coding sequence similarity to agouti gene of sheep (99.3%), buffalo (98.3%) cattle (98%), and wild yak (95.3%) and human (85.5%). Conclusion This study provides strong evidence of breed specific selection of the agouti gene within the indigenous goat breeds. We also demonstrate comprehensive approaches formulating systemic searches for genes; that have undergone positive selection in lineages.