The broad goal of this research was to examine the nature of the Melanocortin receptor 1 (MC1R) locus on the coat color phenotype of seven goat breeds with different color coat. Blood samples were collected from five Iranian indigenous (Khalkhal, Markhor, Naeini, Najdi and Tali) and two exotic (Cashmere and Saanen) goat breeds. Polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) technique and DNA sequencing were used to detect polymorphism of the MC1R gene. Digestion of polymerase chain reaction products with EarIrevealed two alleles of A and B and three genotypes of AA, AB and BB. The observed allele size was similar to previous reports. The genotype and gene frequencies for each breed were determined and shown to be variable among the breeds. In the goat breeds with black / brown coat color, AA genotype showed a higher frequency than white color goat breeds. In this aspect, Tali had only AA and B genotypes and Cashmere had AB and BB genotypes. Comparison of genotype frequencies using χ2 test showed significant (P<0.01) differences between colored and white coat phenotypes. The Lys226Arg (A676G) mutation of the MC1R was verified by sequencing distinguished the B allele from the A allele. The phylogenetic tree also separated these breeds into two clusters, including exotic breeds with white / yellow coat color and indigenous breeds with black/brown phenotype. A replacement mutation was verified in Lys to Arg at position 676 bp. In conclusion, the results of this study confirmed the previous findings on MC1R gene as a useable tool for breed identification and white mohair marketing and production.
