Horses have two main skin pigment types that are responsible for the coat colour. One pigment type is dark (black or brown/bay) and the other one is red. The many colours and shades in between are the result of genes that regulate penetration, strength and distribution of the two main pigment types.
A black or brown/bay coat colour can only arise if a horse is either a non-carrier (E/E) or a carrier (E/e) for the red coat colour. The Agouti gene determines whether the horse develops a black or a brown coat. A horse homozygous for the recessive allele of the Agouti gene (a/a) is black. In a carrier or non-carrier horse (A/a or A/A), the black pigment appears only in certain areas like mane or tail and the horse is brown/bay. The colour inheritance for specific pairings follows the same rules as described for the red factor. For breeding purposes, the Agouti gene is mainly important as a “hidden” feature in red coloured horses.
Similar to the gene for the colour cream, the gene for champagne causes a lightening of the basic colour. The champagne gene is dominant and homozygous and heterozygous genotypes are almost indistinguishable phenotypically. The basic colours are modified as follows: Chestnut is diluted to Gold-Champagne, bay is diluted to Amber-Champagne and black is diluted to Classic-Champagne. Champagne coloured horses are born with unpigmented skin that develops black spots during the first days of life. In most cases the eyes are blue but darken as the horse gets older.
Another gene, MATP, determines the different variations of the colour cream. Depending on the expression of the basic colours chestnut, brown or black several variations of the colour cream are possible. Horses that do not carry the gene for the colour cream (c/c) show one of the basic colours chestnut, brown or black. Horses that carry one copy of the cream gene (C/c) show diluted colours: Chestnut is diluted to palomino; bay is diluted to buckskin and black is diluted to smoky black Horses that carry two copies of the cream gene (C/C) show double diluted colours: Chestnut is diluted to cremello; bay is diluted to perlino and black is diluted to smoky cream. Our test specifically detects a mutation in the MATP gene, which has been shown to be responsible for the described cream colours. Other genes or mutations causing similar coat colours are not identified by this test.
In 2000, a Quarter Horse named GQ Santana was born with a KIT gene white mutation (called W10) and became a prominent stallion in both AQHA and APHA. Horses with the W10 mutation have pink skin where the hair is white and the eyes have normal pigmentation and are rarely blue. VGL offers a test for the W10 mutation to owners who want to breed horses for this white pattern or to determine the genetic status of horses that descend from GQ Santana, but have minimal white spotting. W10 is inherited as a dominant trait; horses that carry W10 will display some degree of white patterning. Homozygous W10/W10 horses may not be viable. This result may only be found in aborted fetuses produced in matings between two W10 carriers.
Dun is a dominant gene that dilutes the color of body hair, leaving the points and head unaffected. Dun horses also show "primitive markings" consisting of a dark dorsal stripe, leg barring, shoulder stripes and concentric marks on the forehead (spiderwebbing, cobwebbing). The dorsal stripe appears to be a consistent feature of dun horses while the other "primitive marks" vary and may not all be present, or visible. The effect of the Dun gene on the base colors of chestnut, bay and black produces horses with shades that range from apricot, golden, dark gray, olive, and many, more subtle, variations. Dun is inherited independently of other coat color genes and can occur in combination with any other genes that modify the base colors. The specific mutation that causes Dun has not yet been identified, and there is no direct test for the gene. VGL has identified DNA markers associated with Dun that can be used to determine if a horse has the Dun gene and how many copies.
A mutation in the gene STX17 causes the greying phenotype in horses. Horses with this mutation are born coloured but gradually lose their hair pigmentation (not skin pigmentation) until they are grey or white at an age of about 6–8 years. The mode of inheritance is autosomal dominant. Heterozygous horses will be grey-white and, in most cases, never be completely white. Some horses show some speckling or a “flea bitten” pattern. Horses that are homozygous for the mutation will be completely white at an early age. Horses with the grey mutation show a high incidence of dermal melanomas (70–80% of Grey horses older than 15 years have melanomas) and reduced longevity. Homozygous carriers of the grey gene as well as horses born with a black coat seam to have a higher risk to develop melanomas compared to horses born with a brown coat.
A single autosomal dominant gene, leopard complex (LP), is responsible for different spotting patterns while modifier genes are thought to play a role in determining the amount of white patterning that is inherited. These patterns are called from lightest to darkest: „few spot leopard“, „leopard“, „snowcap blanket“, „blanket with spots“, „varnish roan (marble)“, „snowflake“, „frosted“, „speckled“ and „mottled“. Homozygosity for LP (LP/LP) is directly associated with congenital stationary night blindness (CSNB) in Appaloosa horses. Heterozygous carriers (LP/lp) are not affected. CSNB is characterized by impaired vision in dark conditions, and is present at birth.
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. In Spanish horses, this dilution is known as Pearl. In Quarter Horses and Paints, it has been commonly known as "Barlink Factor". Pearl is known to interact with Cream dilution to produce pseudo-double Cream dilute phenotypes including pale skin and blue/green eyes.
The extension (E) locus determines the red factor (colour: chestnut, sorrel, ...). The dominant allele at this locus (E) leads to the expression of the pigment Eumelanin and the colour brown or black develops. If a horse is homozygous for the recessive form of this allele (e/e), Pheomelanin is synthesized and this horse will be red. A horse that is heterozygous at the E-locus (E/e) will be either black or brown depending on the Agouti-locus. If a horse is homozygous (e/e) for the mutation, it will be red and all of its offspring will receive the mutated form of the gene (e). If such a horse is bred to a horse that does not carry the mutation (E/E), no red colour will result. Offspring with genotype E/e carries the mutation for red colour but is not red himself. If two carrier horses (E/e) are bred, red coloured offspring can result. If a non-carrier horse (E/E) is bred, its offspring will never be red coloured, even if the pairing is with a genetic carrier (E/e). However, such a pairing will result in 50% carriers (E/e) for the mutation.
Roan is a white patterning coat color trait of intermixed white and colored hairs in the body while the head, lower legs, mane and tail remain colored. Roan horses are born with the pattern, though it may not be obvious until the foal coat is shed. The white and colored hairs are evenly mixed in horses that inherit the classic Roan gene, which can differentiate this from several mimic patterns called roaning. Roaning patterns tend to be uneven in the distribution of white hairs and the inheritance of roaning has not been defined. Although it has been suggested that Roan is a homozygous lethal, evidence from the Quarter Horse breed indicates otherwise. Production records have documented the existence of Roan Quarter Horses that produce 100% Roan foals. DNA tests have confirmed homozygosity in the genomic region that contains the Roan gene. Roan is inherited as a dominant gene but the specific mutation has not yet been identified, so there is no direct test for the gene. VGL has identified DNA markers in Quarter Horses and Paints associated with Roan that can be used to determine if a horse has the roan gene and how many copies.
Horses with Sabino-1 show a spotting pattern characterized by white patches of varying sizes and irregular forms and borders. The spots mainly occur on the face, lower legs, and belly. Sometimes interspersed white hairs on the midsection or all over the body can be seen. The spotting pattern can be seen in horses that are heterozygous for the Sabino trait. The coat of homozygous horses is almost completely white. So far, one gene responsible for the Sabino trait, could be identified and characterized (Sabino-1) but it is likely that additional genes are involved in the development of this colour pattern.
The gene for silver is another gene causing a lightening of the basic colour. The silver-gene has no impact on pheomelanin like the genes for cream and champagne and only leads to brightening of black coloured areas. Especially black coloured hair of mane and tail appears brighter because of the occurrence of white and grey hairs. The gene for silver is inherited autosomal-dominant and one copy of the gene is sufficient for the phenotype.
Splashed white is a variable white spotting pattern characterized primarily by extremely large blaze, extended white markings in legs, variable white spotting in belly, and often blue eyes. Some, but not all, splashed white horses are also deaf. Recent research has identified 3 mutations – SW-1, SW-2 and SW-3 - that cause splashed white phenotypes in horses. SW-1 has been found in several breeds - Quarter Horse, Paint, Trakehner, Miniature Horse, Shetland Pony and Icelandic Horse – and may be present in other breeds as well. Horses homozygous for SW-1 (SW1/SW1) have been identified, which suggests that this mutation is not homozygous lethal. SW-2 and the rare SW-3 occur exclusively in certain lines of Quarter Horses and Paints. Based on predictions from other species, SW-2 and SW-3 may be homozygous lethals and thus matings of two horses that carry SW-2 or SW-3 should be avoided. Horses that carry combinations of the splashed white mutations, tobiano or lethal white overo can display extensive white patterning or be white.
Tobiano is the most frequent paint pattern in horses. Horses exhibiting the tobiano spotting are characterized by white, unpigmented areas with distinct borders that cross the dorsal midline and include at least one if not all of the four legs. The amount of white spotting can vary from very small (penny-size) areas on the lower legs to large white areas covering the entire body. The Tobiano pattern is inherited as a dominant trait and horses with the genotype N/Tob and Tob/Tob develop the characteristic colour pattern.
Each characteristic is evaluated separately and the genotype for each trait is analysed as follows. Two copies for each characteristic exist in the genome of an animal. Therefore, the outcome are three possible genotypes for either recessive or dominant trait:
Recessive trait: Genotype N/N: This animal does not inherit the mutation coding for the characteristic. The animal will never pass a mutated allele to it's offspring.
Genotype N/mut: This animal posses one copy of the mutated allele, which makes it a carrier for the trait. It won't exhibit the phenotype. The offspring of the carrier inherit the mutated allele with 50% probability.
Genotype mut/mut: Carrying two mutated copies of the allele, this animal will exhibit the trait phenotypically. Additionally, 100% of it's offspring inherit the mutated allele.
Dominant trait: Genotype n/n: This animal does not inherit the mutation and does not exhibit the characteristic. The animal will never pass a mutated allele to it's offspring.
Genotype n/Mut: This animal posses one copy of the mutated allele and exhibits the phenotype of the trait. The offspring of the carrier inherit the mutated allele with 50% probability.
Genotype Mut/Mut: Carrying two mutated copies of the allele, this animal will exhibit the phenotype of the trait. Additionally, 100% of it's offspring inherit the mutated allele. Some dominant traits lead to diseases if the animal posses two mutataed alleles.