General Description of Roan

The roan coat color is described as the dispersion of white hairs within an otherwise solid color coat. This phenotype is primarily expressed on the body of the horse, including the barrel, hips, chest, shoulders, neck and upper legs with the head and lower legs exhibiting few to no white hairs. Previous research mapped a locus for roan to the KIT region and observed linked markers in a small number of breeds. However, utilizing those linked markers to determine the Roan genotype in other breeds has seen limited success.

The roan mutation is dominant, meaning that the coat color of a horse with at least one roan allele is generally observed as a roan and called as such, regardless of the underlying coat color. If the coat color is known, it is identified with “red roan”, “blue roan”, “dun roan” etc.

Etalon has discovered three haplotypes (RN1, RN2, RN3) that segregate with a roan haplotype each.

Etalon conducted a comprehensive study with a total of 3,000+ equine samples. Fro the 3,000 samples received, 250+ samples were reported as Roan. The following data is from our 250+ Roan samples.

Roan 1 (RN1) is present in about 38% of the roan horses studied, and found present in multiple breeds such as American Quarter Horse, American Paint Horse, Noriker Horse, Mustang, Gypsy Horse, Welsh Pony and Cob, Mangalarga Marchador, Percheron, Belgian Draft, European Brabant, Missouri Fox Trotter, and Curly Horse. Within the Quarter Horse breed, we looked at the extended pedigrees of several individuals (allbreedpedigree.com), and assuming a dominant trait, we found this to be the Roan haplotype traced to the Burnett roan mare(U0069050). One major Quarter Horse sire likely contributing this Roan haplotype to the modern breed is [Red Man](Red Man) (née 1935).

Roan 2 (RN2) is present in about 36% of the roan horses studied. This associated haplotype is present in fewer breeds, all based on North American ancestry including the American Quarter Horse, Mustang, Curly Horse, and American Paint Horse (Table 2). Within the American Quarter Horse breed, using the same pedigree analysis as described for Roan 1, we found this to be the Roan haplotype that can be traced to the Burns mare (U0069059) and her offspring Oral’s Kitten. This seems a newer haplotype as it is present only in breeds that originated in the US. It is currently propagated by the influential sires Metallic Cat and Peptoboonsmal.

Read the RN1 & RN2 Paper Here

Roan 3 (RN3) is present in about 15% of horse samples tested. This allele is mostly present in the American Quarter Horse. Using the same pedigree analysis as described for Roan 1, we found this to be the Roan haplotype that can be traced to the Kitch Roan mare (U0073276) and her offspring Margie Star. This seems a newer haplotype as it is present only in breeds that originated in the US. Within the American Quarter Horse it is currently likely propagated by the influential sires Zippos Mr Good Bar, VS Code Blue, and VS Code Red.

Read the RN3 Paper Here

The three identified Roan alleles account for ~85-90% of the 250+ Roan samples tested in Etalon's comprehensive Roan study. Thus there are about 10-15% of Roan samples that currently cannot be identified. Etalon's team has seen evidence that additional alleles may be present and discovery work is in progress.

Overall, The RN1 allele was present in 3%, the RN2 allele in 3%, the RN3 allele in 1%, and the unknown allele(s) in 1% of all the 3,000+ horses we have analyzed. In conclusion, Roan is present in about 7% of all 3,000+ horses tested in total.

It is also important to note that Roan is not lethal. Horses can safely inherit multiple Roan alleles from one or both parents. Roan Horses can also safely inherit two different Roan haplotypes (e.g., RN1/RN2, RN2/RN3, RN1/RN3). Etalon currently has at least 3 recorded cases of compound heterozygous horses in the Roan study so far.

We would like to emphasize that these haplotypes are based on association only, they are so-called tag-SNPs, and do not likely include the causal mutation. Tag-SNPs are SNPs that have been found to segregate with the specific trait of interest, in this case roan coat color, but themselves do not cause roan. RN1 to RN3 are indications to discern the origin of the associated haplotypes, and future research will decide whether these are truly different alleles or mere variations of different chromosomal blocks inherited from the roan parent that includes the actual roan causing variant. THey all may lead to the same causal variant. Further research into the genetic basis of the collection of roan phenotypes needs to be performed and is ongoing.

Gene Information

KIT is a tyrosine kinase receptor that is vital for normal development. Mutations in other species have led to white spotting, anemia, sterility, and certain types of tumors. However, no negative health effects associated with roan have been documented to date in the horse. The various KIT alleles and variants encompass a variety of mutations, all resulting in changes to the encoded protein.

References

Everts, R. E., Caron, R., Foster, G., McLoone, K., Simiele, L., Martin, K., Brooks, S. A., & Lafayette, C. (2025). Identification of a Novel Haplotype Associated with the Roan Coat Color in the American Quarter Horse. Preprints. https://doi.org/10.20944/preprints202506.2208.v1

Everts, R. E., Caron, R., Foster, G., McLoone, K., Martin, K., Brooks, S. A., & Lafayette, C. (2025). Identification of Two Genetic Haplotypes Associated with the Roan Coat Color in the American Quarter Horse and Other Equine Breeds. Animals, 15(12), 1705. https://doi.org/10.3390/ani15121705

Marklund, S., Moller, M., Sandberg, K., & Andersson, L. (1999). Close association between sequence polymorphism in the KIT gene and the roan coat color in horses. Mammalian genome : official journal of the International Mammalian Genome Society, 10(3), 283–288. https://doi.org/10.1007/s003359900987

D. Phillip Sponenberg, Henry T. Harper, Anne L. Harpar, Direct evidence for linkage of roan and extension loci in Belgian horses, Journal of Heredity, Volume 75, Issue 5, September 1984, Pages 413–414, https://doi.org/10.1093/oxfordjournals.jhered.a109968

Grilz-Seger, G., Reiter, S., Neuditschko, M., Wallner, B., Rieder, S., Leeb, T., Jagannathan, V., Mesarič, M., Cotman, M., Pausch, H., Lindgren, G., Velie, B., Horna, M., Brem, G., & Druml, T. (2020). A Genome-Wide Association Analysis in Noriker Horses Identifies a SNP Associated With Roan Coat Color. Journal of equine veterinary science, 88, 102950. https://doi.org/10.1016/j.jevs.2020.102950

Voß, K., Tetens, J., Thaller, G., & Becker, D. (2020). Coat Color Roan Shows Association with KIT Variants and No Evidence of Lethality in Icelandic Horses. Genes, 11(6), 680. https://doi.org/10.3390/genes11060680