Allelic and Genotypic Distribution in Single Nucleotide Polymorphism (SNP) G.676A > G of Melanocortin-1 Receptor (MC1R) Gene in Indonesian Goat Breeds

The melanocortin-1 receptor (MC1R) gene has been investigated by many studies regarding the pigmentation variation in various species. In order to determine its allelic and genotypic distribution, we sequenced the goat MC1R gene from 78 individuals in ten populations (Gembrong, Senduro, Ettawa Grade, Boerawa, Boerka, Kosta, Samosir, Muara, Boer and Kacang). Direct sequencing method was performed to detect the single nucleotide polymorphisms (SNPs). Three SNPs (g.676A>G, g.748G>T and g.801C>G) were identified in the gene target. The SNP g.676 A > G was used to genotype the investigated animals by using polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) method with EarI restriction enzyme. In all studied populations, the A allele had the highest frequency (83%) and the G allele had the lowest frequency (17%). The frequency of homozygous AA genotype was the highest (90%) in Kacang goats, while that of heterozygous AG genotype was fixed in Senduro and Boer goats. Analysis of observed heterozygosity, expected heterozygosity, Nei’s (1973) expected heterozygosity, and Shannon index were found to be 0.3425, 0.2858, 0.2838 and 0.4578, respectively.The distribution of MC1R gene in overall breeds confirmed with Hardy-Weinberg equilibrium (P>0.05).