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Veterinary Genetics Laboratory
Horse Coat Color Tests
Introduction

The basic coat colors of chestnut, bay, brown and black horses are controlled by the interaction between two genes: Extension (gene symbol E) and Agouti (gene symbol A). The Extension gene (red factor) controls the production of red and black pigment. Agouti controls the distribution of black pigment either to a points pattern (mane, tail, lower legs, ear rims) or uniformly over the body. The effects of approximately 10 other genes may modify these pigments to provide an array of colors in the domestic horse ranging from white to black.

The basic colors can be diluted by at least four genes: Cream, Champagne, Dun and Silver. The Cream gene has a dosage effect in that a single copy of Cream produces palominos, buckskins and smoky blacks. Two doses of Cream produce cremellos, perlinos and smoky creams. Champagne, Dun and Silver do not show a dosage effect.

There are several genes responsible for white patterns on horses. White spotting patterns on the base coat color are produced by the Dominant White (one big spot), Appaloosa, Tobiano and Overo genes or as mixed white and colored hair patterns produced by the Grey (progressive whitening with age) and Roan genes. Several genes may be involved in the production of white spotting patterns known as overo. Among those, the gene responsible for the frame-overo pattern is associated with a lethal disease of newborn foals called overo lethal white foal syndrome.

Most color assignments can be correctly made based on physical appearance or phenotype alone. However, genetic testing may be necessary to define phenotypes that are visually ambiguous, such as bays with flaxen manes and tails or chestnuts with dark manes and tails. The same holds true when it is desirable to know which coat colors can be produced by breeding stock. Researchers at the Veterinary Genetics Laboratory and other institutions are working towards the identification of the specific genes and mutations responsible for coat color traits in the horse. In the future, diagnostic tests may be available for all the major coat color genes. Currently, genetic tests are available for: Extension (Red Factor), Agouti, Cream Dilution and Lethal White Overo.

Introduction to Coat Color Genetics
Introduction to Coat Color Genetics

Test Results
Allow 5-10 business days for results.

Detailed coat color information

Red Factor - Extension

The Extension gene (red factor) has two alternative states (alleles). The dominant allele E produces black pigment in the coat. The recessive allele e produces red pigment. Red horses (chestnuts, sorrels, palominos and red duns, to name a few) are homozygous, that is they have two alleles, for the recessive red allele ee. Black pigmented horses (black, bay, brown, buckskin and grullo, to name a few) have at least one E allele. They can be homozygous EE or heterozygous Ee. A horse that is homozygous EE will not produce red offspring, regardless of the color of the mate.

The DNA diagnostic test for red factor can be used to identify those black horses for which neither pedigree nor breeding records is informative for identifying carriers of the recessive red factor. Since red is inherited as a recessive trait, it is relatively easy to start up a breeding program that will produce only red horses. It has been more difficult to initiate a black breeding program as black Ee horses can produce red foals. Prior to the development of this test, only pedigree or breeding records, not phenotype, could provide information about whether black horses are EE or Ee.

Red Factor results are reported as:

  • e: Only the red factor detected. The horse can be assumed to be homozygous for red (ee). The basic color is sorrel or chestnut, but depending on genes at other color loci, the horse could be palomino, red dun, gray, cremello, white or any of these colors with the white hair patterns tobiano, overo, roan or appaloosa.
  • Ee: Both black and red factors detected. The horse can be assumed to be heterozygous for the red factor (Ee). It can transmit either E or e to its offspring. The basic color of the horse will be black, bay or brown, but depending on genes at other color loci, the horse may be buckskin, zebra dun, grullo, perlino, gray, white or any of these colors with the white hair patterns tobiano, overo, roan or appaloosa.
  • E: No red factor detected. The horse can be assumed to be homozygous for black pigment (EE). It cannot have red foals, regardless of the color of the mate. The basic color of the horse will be black, bay or brown, but depending on genes at other color loci, the horse may be buckskin, zebra dun, grullo, perlino, gray, white or any of these colors with the white hair patterns tobiano, overo, roan or appaloosa.

Agouti (Bay/Black)

The Agouti gene controls the distribution of black pigment. The dominant allele A restricts black pigment to the points of the horse (mane, tail, lower legs and ear rims), as seen, for example, in bays and buckskins. The recessive allele a uniformly distributes black pigment over the entire body.

Breeders interested in producing black horses need to have breeding stock carrying the a allele, in addition to the E allele of the Extension gene. Using results from the red factor and agouti tests, click here for a table of breeding schemes to produce black animals.

Agouti results are reported as:

  • A or Aa: Black pigment distributed in point pattern. The basic color of the horse will be bay or brown in the absence of other modifying genes. A has no effect on red pigment (ee).
  • a: Only recessive allele detected. Black pigment distributed uniformly. The basic color of the horse will be black in the absence of other modifying genes.

Cream Dilution Test

The Cream dilution gene is responsible for the palomino, buckskin, smoky black, cremello, perlino and smoky cream coat colors. There are two alleles: CCr and C. CCr is semi-dominant and dilutes red to yellow in single dose (palominos, buckskins, smoky blacks) and to pale cream in double dose (cremellos, perlinos, smoky cream). Cream dilution can have a very subtle effect on black pigment. C is recessive and does not dilute the base color.

Cream Dilution results are reported as:

  • N: Non-dilute. Basic colors are chestnut, bay, black or brown in the absence of other modifying genes.
  • N/Cr: Heterozygous, dilute, one copy of the Cream CCr allele. Chestnut is diluted to palomino; bay is diluted to buckskin and black is diluted to smoky black. These colors can be further modified by the actions of other genes.
  • Cr: Double dilute (two copies of the CCr allele). Chestnut is diluted to cremello; bay is diluted to perlino and black is diluted to smoky cream.

Note: The test offered by VGL is specific for a mutation in exon 2 of the MATP gene that is associated with Cream Dilution. Other dilution genes or mutations that may produce coat colors that phenotypically resemble cream will not be detected by the test.

Pearl Dilution

Horses have four common coat color dilution genes with defined phenotypes: Cream, Dun, Silver and Champagne. Two rare dilution phenotypes have been recognized in Quarter Horses and Spanish horse breeds such as Andalusians and Lusitanos. In Spanish horses, this dilution is known as Pearl. In Quarter Horses and Paints, it has been commonly known as "Barlink Factor". The two dilutions have been assumed to be different. Research at the Veterinary Genetics Laboratory (VGL) on the Quarter Horses/Paints identified a mutation associated with the "Barlink Factor" dilution. Further research has shown that the same mutation is present in Spanish horses with the Pearl phenotype. The presence of this mutation in Quarter Horses and Paints likely reflects the Spanish horse ancestry of these modern breeds. To recognize that this mutation probably originated in Spanish horses, it is appropriate to name it Pearl.

Pearl behaves as a recessive gene with respect to the hair color. One dose of the mutation does not change the coat color of black, bay or chestnut horses. Two doses on a chestnut background produce a pale, uniform apricot color of body hair, mane and tail. Skin coloration is also pale. Pearl is known to interact with Cream dilution to produce pseudo-double Cream dilute phenotypes including pale skin and blue/green eyes.

Pearl Dilution results are reported as:

N/N No evidence of altered sequence detected.
N/Prl One copy of the altered sequence detected. If Cream dilution is also present, a pseudo-double Cream phenotype will result.
Prl/Prl Two copies of the altered sequence detected. On a chestnut base color, a uniform apricot color of body hair, mane and tail will result.

Lethal White Overo

Horse breeding programs specializing in overo have particular challenges compared with programs for other white patterns such as tobiano. Not only is there the possibility of producing a solid dark foal without the overo pattern but there is also the risk of producing an all-white foal that dies of complications from intestinal tract abnormalities (ileocolonic aganglionosis). As far as we are aware, overo horses themselves have no specific health risks. While breeding evidence shows that some overos are heterozygous for a gene that is lethal in the homozygous condition, it has not been easy to identify which horses have the overo gene that is associated with the lethal white foal syndrome. Occasionally even solid-colored horses without obvious body spotting patterns have been reported to produce lethal white foals. Clearly the spotting pattern classified as overo is phenotypically and genetically heterogeneous.

Breeders can test horses for this mutation to avoid producing lethal white foals and to identify new pedigree sources of the overo gene that may be useful in their breeding programs. The gene appears to be associated with horses often characterized as "frame-overos" in Paints and Thoroughbreds, but is also present in some tobiano/overos, some solid-colored (breeding stock Paint) offspring from overo matings, some tobianos and Quarter Horses without obvious evidence of the overo pattern. The gene has also been identified in an overo Miniature Horse.

Using the letter "O" to symbolize the DNA sequence of the lethal white (LW) overo gene and "N" for the sequence of the non-overo, then the lethal white foals can be symbolized as OO, their overo parents as NO and non-overos as NN.

Breeding predictions between LW overos (NO x NO):

N O
N 25% NN solid 25% NO overo
O 25% NO overo 25% OO lethal

Breeding predictions between LW overo and solid (NO x NN): No possibility of lethal white foals.

N O
N 50% NN solid 50% NO overo

We know of no other mutations that are associated with lethal white overo horses. However, owners requesting the diagnostic test should understand that there is the rare possibility that two NN horses could have a lethal white foal due if both the sire and dam carry a mutation at a site other than the one detected by this test.

Sabino 1

Sabino is a generic description for a group of similar white spotting patterns. The sabino pattern is described as irregular spotting usually on the legs, belly and face, often with extensive roaning. A mutation has recently been discovered that produces one type of sabino pattern. It has been named Sabino1 as it is not present in all sabino-patterned horses. More mutations will probably be identified that account for other sabino patterns.

Sabino1 is inherited as an autosomal dominant mutation. One copy of the Sabino1 gene is expected to produce horses with two or more white legs or feet -- often with white running up the anterior part of the leg, an extensive blaze, spotting on the midsection, with jagged or roaned margins to the pattern. Horses with 2 copies of the Sabino1 gene, are at least 90% white and are referred to as Sabino-white.

Sabino1 is most commonly found in Tennessee Walking Horses. Other breeds in which this mutation has been found include: American Miniature Horses, American Paint Horses, Aztecas, Missouri Foxtrotters, Shetland Ponies, Spanish Mustangs and Pony of the Americas. Other breeds of horses that are known to have sabino patterns, such as Clydesdales and Arabians, have so far tested negative for the Sabino1 mutation, although the number of animals tested is low.

Sabino 1 results are reported as:

N/N No evidence of altered sequence detected.
N/SB1 One copy of the Sabino1 gene detected. Horse typically may have 2 or more white legs, blaze, spots or roaning in the midsection and jagged margins around white areas.
SB1/SB1 Two copies of the Sabino1 gene detected. Complete or nearly complete white phenotype expected.

Reference: Brooks S.A. and Bailey E. Exon skipping in the KIT gene causes a Sabino spotting pattern in horses. Mammalian Genome 16:893-902, 2005.

Silver Dilution

The horse Silver dilution gene dilutes black pigment but has no effect on red pigment. The mane and tail are lightened to flaxen or silver gray, and may darken on some horses as they age. A solid black horse with this gene will be chocolate colored with a lightened mane and tail. A bay horse will have the black pigment on the lower legs, mane and tail lightened. Sometimes bay horses with Silver dilution can be mistaken for chestnuts with a flaxen mane and tail. Silver dilution is inherited as a dominant trait. It is known to occur in Rocky Mountain horses and related breeds, Shetland ponies, Icelandic and Morgan horses.

The gene responsible for Silver dilution has been recently identified as PMEL17 by researchers in Sweden. Two single nucleotide substitutions have been found to be associated with the dilution, one in intron 9 -- A (normal) to T (silver) -- and the other in exon 11 -- C (normal) to T (silver). VGL's test for Silver dilution assays both sites.

Silver Dilution results are reported as:

N/N No evidence of altered sequence detected.
N/Z One copy of the altered sequence detected. Black-based horses will be chocolate with flaxen mane and tail. Bay-based horses will have pigment on lower legs lightened and flaxen mane and tail. No effect on chestnut color.
Z/Z Two copies of altered sequence detected. Black-based horses will be chocolate with flaxen mane and tail. Bay-based horses will have pigment on lower legs lightened and flaxen mane and tail. No effect on chestnut color.

Reference: Brunberg E, Andersson L, Cothran G, Sandberg K, Mikko S and Lindgren G. 2006. A missense mutation in PMEL17 is associated with the Silver coat color in the horse. BMC Genetics 7:46

 
Veterinary Genetics Laboratory, One Shields Ave, Davis, CA 95616-8744, Tel 530-752-2211,Email VGL