Color Testing

Color Testing

Color Testing

We offer more than a dozen color tests, each described here. Pricing and and details can be found in the submission form below.

Color Testing Submission Form


Kathryn Graves

Associate Professor
Director of Genetic Testing

(859) 218-1193 341 Gluck Equine Research Center 1400 Nicholasville Rd. Lexington, KY 40546

Types of Color Tests

Dun is a color pattern characterized by dilution of the base coat color as well as primitive markings such as a dorsal stripe, facial masking and barring on the legs. Dun is dominant and only one copy of the normal Dun locus at the TBX3 gene is required for the phenotype to be expressed. There is no dosage effect, so that horses exhibit the same phenotype whether they are heterozygous or homozygous for Dun. Dun is actually the ancestral coat color in horses, and horses that are not dun are the ones that have mutations, known as Non-Dun1 and Non-Dun2. Non-Dun1 horses have variations within the TBX3 gene that allow them to exhibit primitive markings without the coat color dilution. Non-Dun2 horses have a large deletion within the TBX3 gene, and thus do not have primitive markings or the coat color dilution. A black horse with Dun is called grullo or grulla, chestnut horses with Dun are called red or claybank duns, and bay horses with Dun are called yellow duns or simply dun.

WHY TEST: If an owner wishes to know if their horse is homozygous or heterozygous for Dun the Dun test alone is appropriate. This test does not distinguish between Non-Dun1 and Non-Dun2 if the horse is heterozygous for Dun or homozygous for Non-Dun. Dilute coat colors, such as palomino and perlino, may make it difficult to see primitive markings. If both the sire and dam of a horse are NOT dun, then the offspring cannot be dun. The Non-Dun1 test would be used in cases where a horse exhibits primitive markings but tests negative for dun or in cases where the owner wants to determine if their horse is a true dun or a Non-Dun1 horse on a different dilute coat color. The Non-Dun1 mutation can cause confusion, especially in a buckskin horse, because the horse may have a dorsal stripe and other primitive markings which would mimic Dun.

The A locus can be thought of as the gene that determines if a horse is bay or black, although other genes come into play. A horse that has at least one dominant "A" allele will be bay if it also possesses at least one "E" allele. A horse that is homozygous recessive for "a", that is "aa", will be black if it also possesses a "E" allele. All black horses are "EE or Ee and aa".

WHY TEST: If a horse is homozygous for "e", it will have a sorrel or chestnut base coat regardless of what genes it carries at the A locus. Thus a chestnut horse may be able to produce blacks if it carries an "a" allele and is bred to another horse carrying the "a" allele and a "E". If a person has a black horse and wants to know if a breeding to a chestnut horse will produce a black, the black horse needs to tested for the E locus and the chestnut horse needs to be tested for the A locus. A black horse that tests homozygous for "a" must also be homozygous for "E" to produce 100% blacks/bays/buckskins.

The dominant PATN1 mutation acts in concert with the LP mutation to increase the amount of white in horses that carry both mutations. Horse that do not have the LP mutation, but have PATN1, show no effect. However, horses that are heterozygous or homozygous for LP and also have PATN1 exhibit the Leopard Spotting pattern. Horses that are homozygous for both mutations exhibit a few spot or no spot pattern.

WHY TEST: Breeders wishing to plan matings that produce horses with appaloosa coloration, especially the leopard pattern.

We now offer the test for the mutation responsible for the Champagne factor in horses. The mutation was discovered here at the University of Kentucky. The Champagne gene is a dilution gene often confused with the Cream dilution gene. Unlike horses carrying a single Cream gene, Champagne horses have pink skin which becomes mottled in exposed areas such as the muzzle. Also Champagne foals are born with blue eyes that later darken to hazel or brown. A true black horse can mask the presence of the Cream gene, but a black horse carrying the Champagne gene is generally a chocolate color. There is no added effect if a horse carries two copies of the Champagne gene, whereas the homozygotes for the Cream gene create a more dilute horse with pink skin (cremellos and perlinos). Therefore the ability to test for the Champagne gene can distinguish homozygotes from heterozygotes, as well as more clearly determine the genotype of dilute pigmented horses.

The cream gene, designated Cr, is a dominant dilution gene that causes a reduction in red pigment in the body hair and mane and tail hair. It acts on any base color- therefore a sorrel horse that inherits one copy of the Cr allele is palomino (ee, Cr/cr), a sorrel that inherits a Cr from each parent is Cr/Cr and is a cremello (ee, Cr/Cr). A bay horse that inherits a Cr allele from one parent is a buckskin (E/-, Cr/cr), while one that is homozygous for Cr is a perlino (ee, Cr/Cr). True black horses can mask the presence of the Cr gene, so it is possible for a black horse to produce palominos or buckskins. Cream is a different gene than Dun, which is also a dilution gene. In general, dun horses have a dorsal stripe.

WHY TEST: Owners of a black horse with a palomino or buckskin parent may want to determine if the horse carries an unexpressed Cr allele. Horses carrying the champagne gene may be confused with horses carrying the Cr gene-this test will verify if the horses indeed possess the Cr allele. It will also determine if a dun or gray horse may also possess a Cr allele.

The Extension locus is another gene related to color, and determines whether a horse has black “points” as in the bay coat color pattern (the mane, tail, legs and tips of the ears are black). The allele responsible for this pattern is designated as E, the capital letter indicating it is dominant. The alternative allele, e, is recessive, and when a horse has two copies of this allele, as in ee, the horse lacks black pigment in the extremities, as in chestnut horses. For owners of a bay or black horse that want to know if that horse is homozygous for the Extension locus, and thus will always have offspring with black points, a DNA-based test is available.

Gray is caused by a dominant mutation, therefore a gray horse has at least one copy of the gray gene and must have at least one gray parent.  Gray causes a horse to progressively lighten as it ages, regardless of other color genes the horse possesses. The ultimate effect is that the horse will become totally white or flea-bitten gray. The skin remains black unless the horse has other genes that result in pink skin. The test we offer ONLY determines if the horse carries the Gray mutation, it cannot distinguish with confidence whether the horse carries one or two copies of the mutation.  The test is useful to determine if a horse will turn gray as it ages, or if the horse has such a dilute phenotype that it is difficult to determine if it also has the gray mutation.

Pearl is a mutation in the SLC45A2 gene, the same gene where the Cream dilution mutation occurs. It is a recessive mutation, so horses with only one copy of the mutation show no effect. Horses homozygous for Pearl (prl/prl) exhibit a dilute phenotype similar to Champagne. Pearl dilution is found primarily in Iberian breeds such as the Andalusian and Lusitano, as well as certain families of Paint and Quarter Horses.

WHY TEST: Dilute phenotypes such as cremello, perlino, ivory champagne, etc. may be hard to distinguish without testing for the actual mutations present. For example, a horse carrying one copy of Cream and one copy of Pearl may look like a Cream homozygote, but such a horse is capable of producing a non-dilute foal if the foal inherits only the prl mutation, which has no effect if only one copy is present.

The Silver Dapple mutation results in a chocolate colored horse that has a lighter mane and tail.  It is most commonly found in pony breeds and gaited horse breeds such as the Rocky Mountain Horse. The mutation requires the presence of at least one E allele to be expressed. Therefore genetically black or bay horses alone express it if they carry one or two Z alleles. A chestnut horse (ee) may carry a Z allele, but there is no effect on color. It is thought that horses homozygous for the Z allele have a whiter mane and tail than the heterozygotes.

The lab offers testing to determine homozygosity for the Tobiano (spotted) gene. Since the tobiano color pattern is valued and is dominant, horses that possess two copies of the gene (homozygous) are of special value to breeders, as ALL their offspring will inherit the tobiano color pattern. We no longer perform the serum protein test based on blood types due to its low reliability. Instead, Genetic Testing at Gluck is proud to offer the most reliable test for the Tobiano spotting pattern yet developed. Dr. Samantha Brooks, a former graduate student at UK's Department of Veterinary Science, discovered an inversion on chromosome 3 that appears to be 100% concordant with the presence of the tobiano pattern. This test replaces the former double marker test previously offered. Please be advised that Tobiano testing reports will reflect this change.

Sabino is a Paint color pattern that is variably expressed and can range from white stockings and a blaze to white leg and face markings and extensive white spreading up from the belly into the body area. The mutation we detect is indicative of the Sabino1 gene. Homozygous sabinos may have more extensive white than heterozygous horses. There is more than one sabino gene so that a horse that appears to have the sabino pattern may test negative for the Sabino1 gene. So far all horses that test positive for Sabino1 have the sabino pattern.

We offer testing for the three most common Splashed White mutations, SW1, SW2 and SW3. SW2 is due to a mutation in the PAX3 gene and SW1 and SW3 are mutations that occur in the MITF gene. All of the mutations are dominant and cause variable white spotting patterns, which can include a wide blaze, belly spots, extensive white leg markings and blue eyes. Deafness can also occur and is most often associated with SW2. Extreme expression of Splashed White is often described as the horse looking like it was dipped in white paint, with the legs and abdomen being white while the upper half of the horse is dark. However, horses with a splashed white mutation can also have minimal markings. Horses can have combinations of the SW mutations and SW1 and SW2 homozygotes can occur. No SW3 homozygotes have been found and it is assumed that this is a lethal genotype.

WHY TEST: Breeders interested in producing white-patterned horses that want to increase their chances of producing horses with white-spotting. Horses carrying one or more of the SW mutations may produce additional white when crossed with horses carrying other white-spotting mutations such as tobiano and frame overo (OLWS carriers). Breeders may also want to avoid matings where both the sire and dam have SW3, which can result in early pregnancy loss.

Also known as appaloosa spotting, the leopard complex mutation in the TRPM1 gene is responsible for a white coat pattern with or without pigmented spots. The appaloosa pattern is variable, ranging from only minimal appaloosa features such as a white sclera, striped hooves and mottled skin, to overall white patterning with pigmented spots (leopard) or roaning. The LP locus interacts with the PATN1 locus, which increases the amount of white. A health concern is present in horses homozygous for the LP mutation. Horses that are LP/LP have Congenital Stationary Night Blindness (CSNB), which limits the horse’s ability to see in low light conditions. The LP mutation is an incomplete dominant, meaning the horse will exhibit an intermediate phenotype with characteristics associated with both the normal and LP genotype.

WHY TEST: To determine if a minimally marked animal carries the LP mutation or not. It is also important to test when making breeding decisions if the breeder wishes to avoid having foals affected with CSNB.

A large number of “W” mutations have been identified in the horse KIT gene that are associated with all-white or increased white phenotype. Some of these mutations are only found in specific families of horses. The W20 mutation is found in a number of breeds. Horses homozygous for W20 generally exhibit white facial and leg markings. When W20 occurs with the presence of other KIT mutations, such as Tobiano and Sabino or other W mutations, it can greatly increase the amount of white. Horses can be homozygous for W20.

WHY TEST: For breeders interested in producing white-patterned horses, the presence of W20 can increase the chances of producing horses with white markings when combined with other white-pattern mutations.

Roan is a coat color pattern characterized by white hairs mixed with base color hairs throughout the body, with the head and legs exhibiting only the base-coat color.  It is a dominant color pattern, meaning that if a horse has only one copy of the Roan mutation, it will exhibit the Roan phenotype.  This also means that in order for a horse to be roan, at least one parent must also be roan.

The test for Roan does not detect the actual mutation that causes the roan coat color pattern. The single nucleotide variant (SNV) does not affect the protein-coding sequence of the KIT gene.  This SNV is therefore designated as a MARKER for Roan. This marker was found NOT to be linked to the roan coat color in several pony breeds and the original study only confirmed the linkage in Swedish Trotters and Belgian draft horses.

The significance of a marker test compared to a direct test for the causative mutation is that there may not be 100% concordance of the SNV with the color pattern. Therefore horse owners should exercise caution when advertising that their horse is homozygous (or heterozygous) for roan.

Contact Information

Dr. Dan Howe
Interim Director, Gluck Equine Research Center

437 Gluck Equine Research Center 1400 Nicholasville Rd. Lexington, KY 40546-0099

(859) 218-1113