Haplotype variation, linkage disequilibrium and neutrality test analyses of detected single nucleotide polymorphisms in kisspeptin gene of selected indigenous goat populations in Ethiopia

Abstract

The study was aimed to evaluate the haplotype diversity and patterns of linkage disequilibrium (LD) of Kisspeptin (KISS1) gene in Woyto-Guji and Gondar goat populations in Ethiopia. Target regions of the KISS1 gene which include Exon1 (1210 bp) and Exon2 (325 bp) were amplified. A total of 29 haplotypes in exon1 and three haplotypes in exon2 were detected. The first haplotype of exon2 registered highest haplotype frequency (f=0.947) of all. In exon1, seven haplotypes showed haplotype frequency <1%. Lowest (0.083 for Woyto-Guji and 0.081 for Gondar goats) and modest (0.656 for Woyto-Guji and 0.635 for Gondar goats) average estimates of R2 and |D’| were obtained in LD decay analysis of the haplotypes observed in exon1, respectively. Based on the loci linkage combination analysis, loci 3649, 3808, 3963 and 3989 showed highly significant LD accumulation. The neutrality tests showed significant and negative values of Fs (Fs = -8.098 for Woyto-Guji and Fs = -12.08 for Gondar goat populations) in the goat populations studied; whereas, the Tajima’s D test was positive and non-significant. Overall, remarkable haplotype diversity was observed on the KISS1 gene in the goat populations studied, and measures of LD decays revealed effect of selection implying importance of the target region as a candidate gene for the fecundity trait.