Identification of a Novel Haplotype Associated with the Roan Coat Color in the American Quarter Horse

The roan coat color is described as the dispersion of white hairs within an otherwise solid background color coat. This phenotype is primarily expressed on the body of the horse, with the head and legs exhibiting few to no white hairs. Previous studies mapped the locus for roan to the KIT region and observed linked variants in a small number of breeds. In a recent report we presented evidence for two independent haplotypes, RN1 and RN2, in the KIT region that account for approximately 74% of roan horses. In the current report, using whole genome sequencing for unknown roan samples, we present a third novel allele, RN3, found in American Quarter Horse, that accounts for an additional 75% of horses negative for RN1 and RN2 displaying the roan phenotype. In our sample set of horses, these three haplotypes account for about 80%-90% of roan horses and more than 95% of our Quarter Horse population studied.