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

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 or no white hairs. Previous studies mapped the locus for roan to the KIT region and observed linked variants in a small number of breeds. Recently, we reported evidence for two independent haplotypes, RN1 and RN2, in the KIT region, which account for approximately 38% and 36% of roan horses, respectively. In the current report, using whole genome sequencing for unknown roan samples. We present a third novel haplotype, RN3, found in American Quarter Horses, that accounts for an additional 30% of American Quarter Horses negative for RN1 and RN2 that display the roan phenotype. Within this haplotype, we observe a variant chr3:79656505 (G > A), which we believe is a founder allele for the RN3 haplotype. In our sample set of horses, these three haplotypes account for more than 95% of the American Quarter Horse population studied and about 50–60% of roan horses in other breeds. Using whole genome sequencing of distantly related animals with a particular phenotype, together with a larger number of control horses, improves the odds of finding linked and/or causative variants.