Characterization and Evaluation of Melanocortin 4 Receptor (MC4R) Gene Effect on Pork Quality Traits in Pigs

This study aimed to investigate the single nucleotide polymorphisms (SNPs) of the porcine MC4R gene and validate the effect of the MC4R genotype for marker assisted selection (MAS). Six amplicons were produced to analyze the entire base sequences of the porcine MC4R gene and six SNPs were detected (c.-780C greater than G, c.-135C greater than T, c.175C greater than T-Leu59Leu, c.707A greater than G-Arg236His, c.892A greater than G-Asp298Asn, and c.*430A greater than T). Linkage disequilibrium (LD) of the six SNPs was analyzed by performing haploid analysis. There was a perfect linkage disequilibrium in c.-780C greater than G, c.-135C greater than T, c.175C greater than T-Leu59Leu, c.707A greater than G-Arg236His, and c.*430A greater than T. Only the c.892A greater than G (Asp298Asn) SNP showed a very low LD with an r² value of 0.028 and the D' value of 0.348. As a result, the two SNPs-c.707A greater than G (Arg236His) and c.892A greater than G (Asp298Asn)-were selected to extract the genotype frequencies from the 5 pig breeds by using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) genotype analysis method. The SNP frequency of c.707A greater than G (Arg236His) indicated the presence of the A (His) allele only in Yorkshire, while the G allele was fixed in the KNP, Landrace, Berkshire, and Duroc. Association analysis was carried out in 484 pigs with the c.707A greater than G (Arg236His) SNP and the meat quality traits of four different pig cross populations: a significant association was noted in crude fat, sirloin moisture, meat color, and the degree of red and yellow coloration. The frequency of the c.892A greater than G(Asp298Asn) SNP genotype varied among the breeds; while Duroc showed the highest frequency of the A (Asn) allele, KNP showed the highest frequency of the G (Asp) allele. Association analysis was carried out in 1126 pigs with the c.892A greater than G (Asp298Asn) SNP and the meat quality traits of four pig populations: a highly significant linkage was noted in the back-fat thickness (P less than 0.002). It was found that the back-fat thickness was higher in individuals with the AA genotype than in those with the AG or GG genotype. Thus, in this study, we verified that the c.892A greater than G (Asp298Asn) SNP in the pig MC4R gene has a sufficient effect as a gene marker for MAS in Korean pork industry.