Imagine the scenario: A horse owner breeds her bright bay mare to a dark bay stallion, hoping for another flashy bay to shine in the show ring. Instead, out pops a chestnut foal. The owner wonders, ‘How did this happen?’ The answer lies in coat color genetics.

At the 2013 University of Kentucky (UK) Equine Showcase, held Jan. 18 in Lexington, Ky., Kathryn Graves, PhD, the director of the UK Animal Genetic Testing and Research Laboratory, reviewed the basics of equine coat color genetics.

Why should the average horse owner care about the genetics behind their horse’s coat color? Graves explained that some breed registries are either based on horses’ coat colors or have color restrictions. For instance, The American Paint Horse Association, the Appaloosa Horse Club, and the International Buckskin Horse Association, among others, are all color breed organizations, she said. On the other end of the spectrum, some groups like the Friesian Horse Association of North America and the Kentucky Mountain Saddle Horse Association won’t allow horses to be registered if they have certain amounts of white patches, she said. Graves also said that some horsemen believe horses of certain coat colors are easier to market and sell than others. Some owners even opt to have genetic tests run on horses to identify their genotypes (the genetic makeup of a given physical trait), especially if the animals will be used for breeding.

The completion of the equine genome in 2007 opened a door for geneticists to identify mutations for the basic coat colors, as well as modifying genes for other coat colors and spotting patterns, Graves said. In some cases, she said, mutations are considered "silent," meaning there are changes in the DNA but they have no apparent effect on gene function. She cautioned that in some cases genetic mutations related to coat color can have negative effects on horses; she discussed several of these later in the presentation.

Graves also briefly reviewed the key terms "dominant" and "recessive." Dominant means that only one copy of the mutation is needed for it to be expressed outwardly, while recessive means that two copies of the mutation are needed for the trait to be expressed. If a horse carries two copies of the same allele for a gene, he is homozygous (for instance, E/E or e/e, with the lowercase letters indicating recessive genes, and capital letters signifying dominant) for that trait. If he carries one dominant and one recessive allele, then he is heterozygous (E/e) for the trait.

Moving forward, Graves discussed the genetics behind specific equine coat colors.

Base Coat Colors—Horses have three basic coat colors, Graves said: red (or chestnut), bay, and black, all of which are controlled by the interaction of two genes. The Extension (or E) locus gene is instrumental in allowing black pigment to be expressed and the Agouti (or A) locus gene controls the location of black in the horse’s coat. Specifically, the E locus is located on gene MC1R and the A locus is located on gene ASIP. Graves explained that chestnut is a recessive trait, meaning that all chestnut horses have a homozygous (e/e) genotype for that color. The E allele, which is dominant, permits the expression of black pigment; therefore, all black and bay horses have at least one copy of the E allele, Graves explained; they can be either E/E or E/e.

In horses with E/E or E/e genotypes, the A gene determines whether those animals are bay or black. Bay is the dominant phenotype (the physical expression of a genetic trait) between the two, and its genotype is expressed by either E/Aa or E/AA. Black is the recessive coat color, meaning it is always homozygous and expressed as E/aa.

All other equine coat colors and patterns stem from these base coat colors. Graves discussed each color/pattern and its genetics.

Gray—The gray coat color (gene STX17) is represented by a dominant genotype (G/G or G/g), Graves said. These horses are born dark and eventually lose the color pigment in their hair until they are all or nearly all white. To produce a gray horse, at least one parent must contribute a dominant G. Non-gray color horses have two recessive genes (g/g).

Roan—Although gray and roan horses can look similar in some cases, Graves stressed that the genetics behind the two are different. Instead of lightening in color over time, roan horses retain dark heads and legs and have a mixture of white and colored hairs over the rest of the body. The exact mutation behind roan coloring hasn’t been identified yet, but researchers know that it’s linked to the MC1R gene and the KIT gene, which play a role in some pinto horses’ genetics.

Graves then discussed coat spotting patterns that, in most cases, produce horses with a base color spotted with a variety of white patches.

Tobiano—The first spotting pattern Graves discussed was the tobiano pattern, which she said is the most popular genetic test her laboratory carries out. Tobiano horses, she said, generally have dark colored heads with white legs and white patches breaking over the animal’s topline. Graves said chromosomal inversion on the KIT gene helps produce this color pattern: "It’s like the chromosome came out, flipped around, and went back in." Horses with this dominant gene will always produce spotted horses, she said.

Sabino—Sabino is a subclass of the other main painted coat color pattern: overo. Graves said these horses are generally a solid color with white facial markings, white legs, and belly spots. The KIT gene is also involved with creating this color pattern, she said. The most important thing to know about this semidominant trait is that foals with a homozygous genotype can be born all white and healthy (unlike some other white foals that are affected by the deadly overo lethal white syndrome [OLWS]; more on that in a moment). Thus, she stressed, test white foals suspected of having OLWS for the disease before euthanizing them.

Splashed White—Another type of overo coloring is the splashed white pattern, Graves said, which is characterized by similar markings as the sabino pattern. Many splashed white horses have blue eyes, she said. This color pattern is caused by multiple mutations in the genes MITF or PAX3, she said, and these horses are at risk for several different types of health problems, including deafness. One type of MITF mutation (termed SW1) has been identified in several breeds, she said, and homozygotes are viable. A PAX3 mutation (SW2) and another type of MITF mutation (SW3), produce a similar phenotype but are thought to be lethal in the homozygous state.

Frame Overo—This color pattern (characterized by a mostly solid colored horse with white, horizontal patches on the side of the neck and/or belly; white rarely crosses the back between the withers and the tail in frame overos) is produced by a mutation on gene EDNRB, which researchers discovered while searching for the lethal white gene, Graves said. They have identified this pattern in Paints, Quarter Horses, Thoroughbreds, and Tennessee Walking Horses, she noted. As mentioned, two recessive frame overo genes can also produce a foal with OLWS. In these horses, the colon does not develop normally and foals are unable to pass manure; affected foals die or are euthanized within a few days of birth. Because the mutation that causes OLWS is known, breeders can test mares and stallions to reduce the risk of producing an affected foal.

Dominant White—Dominant white horses (those born white with dark eyes–white Thoroughbreds, for example) are produced by 14 to 15 different mutations in the KIT gene, Graves said. She explained that researchers have identified mutations specific to certain families of horses. Thus far, all of these white horses with dark eyes tested have shown a heterozygous genotype.

Appaloosa—The final spotting pattern Graves discussed was the appaloosa or leopard complex spotting (LP) pattern. Researchers still aren’t sure what causes this spotted pattern, but they’ve traced the mutation to the TRPM1 gene, she said. The LP pattern is an incomplete dominant trait, meaning there is a dosage effect (meaning horses with one copy of the mutation are typically a different color than a horse with two copies of the mutation) if the horse has two copies of the mutation, Graves said.

Finally, Graves discussed the dilution patterns, in which a mutated gene dilutes a base color into a variety of different colors.

Cream—The cream dilution (a mutation on gene MATP) produces palomino, buckskin, cremello, perlino, and smokey black coat colors, depending on the number of dilution mutations—one or two–and the horse’s base color, Graves said:

  • A palomino is a chestnut horse that is heterozygous for the cream dilution mutation;
  • A cremello is a chestnut horse homozygous for the cream dilution mutation;
  • A buckskin is a bay horse heterozygous for the cream dilution mutation; and
  • A perlino is a bay horse homozygous for the cream dilution mutation.

Graves noted that a black horse heterozygous for the cream dilution mutation still appears black, but is known as a smokey black; a black horse homozygous for the cream dilution mutation appears perlino and is called a smokey cream.

Champagne—The champagne dilution is caused by a mutation on gene SLC36A1 and is a dominant trait, Graves said. This dilution gene acts solely on the horse’s base color and does not have a dosage effect like the cream dilution gene. It simply lightens the pigment of the horse’s base color. Horses with a black base coat will appear chocolate in color, while chestnut or lighter bay horses will appear gold. Graves said horses with the champagne dilution frequently have blue eyes at birth that become amber-colored in adulthood.

Pearl—Graves said that pearl dilutions (caused by a mutation on gene MATP) are often referred to as the "Barlink factor," as many horses of this color can trace their heritage back to one Paint stallion named Barlink Macho Man. Graves said that one copy of the mutation lightens the horse’s skin and might produce golden undertones to the coat color, while two copies of the mutation produces a diluted base color and might enhance cream and champagne colors.

Dun—The mutation behind the dun coat color is still unknown, Graves said, so there is currently no direct genetic test. Researchers know, however, that it’s a dominant trait affecting the horse’s primary base color. A horse with a black base and the dun mutation would have a grullo coat color; a chestnut base would have a red dun color; and a bay base would have a yellow dun color. All dun horses have dorsal stripes, and many have zebra stripes on their legs, Graves said.

Silver—The final dilution Graves explained is the silver dilution, a phenotype commonly seen in Rocky Mountain Horses, which is caused by a mutation on gene PMEL17. This dominant trait requires either a bay or black base color to be observed; chestnut horses with the mutation will not appear any different than a chestnut without the mutation. This dilution produces a chocolate body color with a flaxen mane and tail.

Graves concluded with a caution to breeders seeking "fancy" coat colors: The mutations that cause those desirable colors can have other undesirable effects. Aside from the aforementioned OLWS, horses with the silver dilution pattern have been known to develop multiple congenital ocular abnormalities, a nonprogressive disease that commonly includes ciliary body cysts (a congenital uveal abnormality) and megaloglobus (eyeball enlargement); homozygotes are more severely affected. Additionally, horses homozygous for the appaloosa mutation are affected by congenital stationary night blindness, which causes a complete lack of night vision.