sequence characterization of promoter region at the melanocortin-1 receptor (mc1r) gene in karakul sheep breed

the melanocortin-1 receptor mc1r is encoded by the extension locus, playing a fundamental role in the determination of coat color in a number of mammalian species. however, so far there has been no report regarding the single nucleotide polymorphisms (snps) of the mc1r promoter region and the potential association of its snps with coat color in sheep (ovis aries). throughout the present study, the promoter region of the mc1r gene was screened using single strand conformation polymorphism sscp and dna sequencing in the karakul breed of sheep. a total of 4 distinct sscp patterns were observed which revealed 3 novel snps and an insertion/deletion of 26 nucleotides upon sequence analysis in the analyzed population. in silico analysis of the mc1r promoter sequence predicted no consensus tata-box motif at an appropriate position but detected multiple putative transcription factor binding sites for ets, aml-1a , nf-e2, mzf1, usf, oct-1 and gata-1. the analysis of identified polymorphic sites also showed that the polymorphism at nucleotide position -89 relative to the start codon abolishes the usf transcription factor binding site. the snp identified at the -100 position is located within a putative aml-1a transcription factor binding site. the insertion of 26 nucleotides at position -126 made a putative binding site for the mok2 transcription factor. the possible functional activity of the identified genetic variations could be confirmed using gene expression analysis.