Influence of MC1R Gene Variants on Coat Color of Indicine Cattle Breeds

Indicine cattle display a broad range of coat colors, representing a relevant and breed-defining trait required for registration in breeder association. Among the genes involved in pigmentation, MC1R stands out for modulating the synthesis of melanin-related proteins and remains poorly explored in indicine cattle breeds. Therefore, we aimed to perform fine mapping of the MC1R gene and to evaluate the association between its polymorphisms and coat color as well as skin pigmentation in seven zebu cattle breeds. A total of 295 individuals belonging to Gir, Nelore, Sindi, Indubrasil, Tabapuã, Guzerá, and Brahman cattle breeds were genotyped through PCR-sequencing, followed by estimates of genotypic and allelic frequencies, linkage disequilibrium, and association with phenotypes using the Kruskal-Wallis test. We identified nine polymorphisms: six non-synonymous SNPs, one coding indel, one synonymous SNP, and one 3' downstream SNP. We report, for the first time, the SNP c.274G>A (p.Val92Met), here designated E^Z1, and SNP c.871G>A (p.Ala291Thr) associated with the dark skin phenotype in Gir cattle, here designated E^Z2. Additionally, the indel c.310del was associated with depigmentation in Sindi, Guzerá, and Gir cattle breeds. The variants described herein represent potential molecular markers to support selection strategies targeting desired coat and pigmentation phenotypes.