Genetic heterogeneity of white markings in Quarter Horses

White markings are very common in several horse breeds. These patterns are used for breed characterization, for the identification of animals (records) and might be associated with anomalies such as skin problems and deafness. The aim of the study was to perform genome-wide association analysis to identify genomic regions associated with the presence of white markings on the head and legs of Quarter Horses. The horses were from racing lineage and raised in Brazil. Records of 342 individuals and genotypes of 360 animals, genotyped for 63k, were used in a genome-wide association study, using the single-step procedure. Traits under analyses were presence of white markings on the head, forelegs, and hind legs. Few genomic regions influencing the traits were identified. Only one region containing the MC1R gene has been reported previously. The remaining genomic regions were detected for the first time in the present study. Within the genomic windows, some candidate genes were pointed out: ZEB2, KYNU, SLC36A1, STX12, MAP3K6, and GJB2. Markings in horses are characterized by genetic heterogeneity. It means that different genes can give origin to the same phenotype depending on the population. Candidate genes were, herein, described. It will permit future fine mapping studies in Quarter Horses in order to identify their causal mutations and also the development of molecular markers.