Understanding Coat Color and SynchroGait Testing Results
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.
Agouti results are reported as:
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A/A
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2 copies of agouti present. If present, black pigment is restricted to the points.
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A/a
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1 copy of agouti. If present, black pigment is restricted to the points.
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a/a
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If present, black pigment is distributed uniformly over the body.
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Red Factor
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:
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e/e
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Only red factor detected. Basic color is red in the absence of modifying genes.
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E/e
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Both black and red factors detected.
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E/E
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No red factor detected. Offspring cannot be chestnut/sorrel.
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Cream
The Cream dilution gene is responsible for the palomino, buckskin, smoky black, cremello, perlino and smoky cream coat colors. There are two alleles: Cr and N. Cr 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. N is recessive and does not dilute the base color.
Cream Dilution results are reported as:
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N/N
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No copies of Cream dilution detected.
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N/Cr
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1 copy of Cream dilution detected.
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Cr/Cr
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2 copies of Cream dilution detected
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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.
Dominant White Mutations – W5, W10 and W20
The KIT gene has crucial function for the development of blood, gonadal and pigmentary tissues. Mutations that affect normal functioning of KIT gene products often result in lack of pigment cells (melanocytes) in the skin and hair follicles which leads to white patterning in horses known as Dominant White or White. Dominant White patterns are variable ranging from minimal Sabino-like spotting to all-white phenotypes. Eye color of Dominant White horses is typically brown. Studies of inherited white phenotypes in different breeds have shown that these arise as independent mutations. More than 20 different KIT mutations associated with white patterns have been identified to date. Except for W20, most of the known Dominant White mutations arose recently and are restricted to specific lines within breeds.
The Veterinary Genetics Laboratory offers a test for the W5, W10 and W20 mutations to owners who want to breed horses for Dominant White or to determine the genetic status of horses with unknown white patterns.
W5 is found in descendants of the Thoroughbred stallion Puchilingui. W10 is found in descendants of the Quarter Horse stallion GQ Santana. Because of the nature of the molecular change, it is thought that only horses that carry one copy of W5 or W10 are viable but this remains to be confirmed. W20 is a much older mutation that is found in many breeds and that has a subtle effect on the amount of white expressed. It appears to increase the expression of white in combination with other white pattern genes. Unlike W5 and W10, the homozygous condition (W20/W20) is not lethal.
Dominant White results are reported as:
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Genotype
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Interpretation
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N/N
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No evidence of altered sequences for W5, W10 or W20 mutations detected.
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N/W5
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One copy of W5 mutation detected. Horse will display some degree of white spotting but the specific pattern cannot be predicted.
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W5/W10
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One copy each of W5 and W10 detected. Horse will display white spotting and may be completely white.
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W5/W20
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One copy each of W5 and W20 detected. Horse will display white spotting and may be completely white.
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W5/W5
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Two copies of W5 mutation detected. Horse will display white spotting and may be completely white.*
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N/W10
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One copy of W10 mutation detected. Horse will display some degree of white spotting but the specific pattern cannot be predicted.
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W10/W20
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One copy each of W10 and W20 detected. Horse will display white spotting and may be completely white.
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W10/W10
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Two copies of W10 mutation detected. Horse will display white spotting and may be completely white.*
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N/W20
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One copy of W20 mutation detected. W20 has subtle or no effect on white spotting. Horse may display extended white markings.
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W20/W20
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Two copies of W20 mutation detected. W20 has subtle or no effect on white spotting. Horse may display extended white markings.
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* Homozygous W5/W5 and W10/W10 horses may not be viable. This result may only be found in aborted fetuses produced in matings between two W5 or W10 carriers.
References:
Haase B, Brooks SA, Schlumbaum A, Azor PJ, Bailey E, Alaeddine F, Mevissen M, Burger D, Poncet PA, Rieder S, Leeb T. Allelic heterogeneity at the equine KIT locus in dominant white (W) horses. PLoS Genet. Nov;3(11): e195, 2007.
Haase B, Brooks SA, Tozaki T, Burger D, Poncet P -A, Rieder S, Hasegawa T, Penedo C, Leeb T. Seven novel KIT mutations in horses with white coat colour phenotypes. Animal Genetics 40:623-629, 2009.
Haase B, Rieder S, Tozaki T, Hasegawa T, Penedo MCT, Jude R, Leeb T. Five novel KIT mutations in horses with white coat colour phenotypes. Animal Genetics 42:337-338, 2011.
Dun Dilution - Direct Test
Dun is a dominant dilution gene of equines characterized by lightening of the body color, leaving the head, lower legs, mane and tail undiluted. Dun is also typically characterized by “primitive markings” consisting of a dark dorsal stripe and sometimes leg barring, shoulder stripes and concentric marks on the forehead (spiderwebbing, cobwebbing). Dun with primitive markings is considered the “wild-type state” and is found in wild equids such as Przewalski horses, zebras and wild asses. The expression of the primitive markings (with or without dun) in the domestic horse is variable, with the dark dorsal stripe being the most consistent and visible feature. Dun dilutes both red and black pigment, and the resulting colors range from apricot, golden, dark gray, olive and many more subtle variations. Dun is present in many breeds of horses including (but not limited to) Appaloosa, Bashkir Curly, Iberian horse breeds (rare, except in Sorraias), Icelandic Horse, Mustang, Norwegian Fjord, Paint, Paso Fino, Peruvian Paso, Quarter Horse and several of the pony breeds. The names assigned to the various dun shades vary by breed.
A team of researchers has recently shown that Dun dilution results from radially asymmetric deposition of pigment in the growing hair controlled by localized expression of the TBX3 gene in hair follicles. The absence of Dun dilution (more circumferential distribution of pigment in the hair) results from a 1,617 bp deletion of DNA that impairs TBX3 expression in hair follicle. An additional SNP change was shown to govern the presence or absence of primitive markings. Three variants in DNA sequence explain phenotypes related to Dun dilution – D (presence of dun dilution and primitive markings), nd1 (not Dun-diluted; primitive markings are present but expression is variable), nd2 (1,617 bp deletion, not Dun-diluted, primitive markings absent). With respect to variant interactions, D is dominant over nd1 and nd2; nd1 is dominant over nd2.
The VGL offers a DNA test that will provide information for both dun dilution and the primitive markings. Below is a table with nomenclature for the variants and interpretation of results.
Dun dilution results are reported as:
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D/D
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2 copies of Dun dilution detected.
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D/nd1
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1 copy of Dun dilution and 1 copy of nd1.
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D/nd2
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1 copy of Dun dilution and 1 copy of nd2.
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nd1/nd1
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Horse is not Dun dilute but may have primitive markings.
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nd1/nd2
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Horse is not Dun dilute but may have primitive markings.
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nd2/nd2
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Horse is not Dun dilute. Primitive markings are absent.
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Reference:
Imsland F, McGowan K, Rubin CJ, Henegar C, Sundström E, Berglund J, Schwochow D, Gustafson U, Imsland P, Lindblad-Toh K, Lindgren G, Mikko S, Millon L, Wade C, Schubert M, Orlando L, Penedo MC, Barsh GS, Andersson L. Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation that underlies Dun camouflage color in horses. Nature Genetics 2015 Dec 21. doi: 10.1038/ng.3475
Gray
The Gray gene causes progressive depigmentation of the hair, often resulting in a coat color that is almost completely white by the age of 6-8 years. Horses that inherit progressive Gray can be born any color, then begin gradually to show white hairs mixed with the colored throughout the body. Usually the first signs of gray hair can be found on the head, particularly around the eyes. Gray is dominant, therefore a single copy of this gene will cause a horse to turn gray. If a horse has two copies of Gray, all offspring of this horse will be gray. Research indicates that horses with one copy of Gray often retain some of the original pigment while homozygotes tend to progress to almost completely white. Gray is found in many breeds and is the predominant color of the Lippizaner breed.
Gray horses have a high incidence of dermal melanomas that are commonly seen around the tail and head. Over 70% of Gray horses older than 15 years will develop melanoma. Gray homozygotes are more likely to develop melanoma than heterozygotes. Gray horses that are homozygous for non-agouti (“aa” genotype at the Agouti locus) also have a higher risk for melanoma. Many Gray horses show depigmentation of the skin around the eyes, mouth and anus but there are no health risks associated with this condition.
Researchers at Uppsala University in Sweden discovered that a 4.6 kilobases duplication in intron 6 of gene syntaxin 17 (STX17) produces progressive graying in horses.
Gray results* are reported as:
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N/N
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No copies of the gray gene. Horse will not turn gray.
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N/G
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One copy of the gray gene. Horse will turn gray and approximately 50% of offspring will be gray.
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G/G
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Two copies of the gray gene. Horse will turn gray and all offspring will be gray.
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Reference:
Pielberg G.R., Golovko A., Sundstrom E. et al. A cis-acting regulatory mutation causes premature hair graying and susceptibility to melanoma in the horse.Nature Genetics, 40 (8):1004-1009 (2008).
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):
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N
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O
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N
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25% NN solid
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25% NO overo
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O
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25% NO overo
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25% OO lethal
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Breeding predictions between LW overo and solid (NO x NN): No possibility of lethal white foals.
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N
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O
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N
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50% NN solid
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50% NO overo
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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.
Sabino 1 is inherited as an autosomal dominant mutation. One copy of the Sabino 1 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.
Sabino 1 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.
Sabino 1 results are reported as:
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N/N
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No copies of Sabino 1 detected.
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N/SB1
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1 copy of Sabino 1 detected.
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SB1/SB1
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2 copies of Sabino 1 detected.
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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
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 identified as PMEL17 with a mutation in exon 11 being responsible for the dilute phenotype described above. Research has also confirmed the Silver dilution mutation to be associated with Multiple Congenital Ocular Abnormalities syndrome (MCOA), a wide range of ocular defects occurring in the anterior and posterior segment of the eye. The severity of the syndrome is dosage related, thus horses with 1 copy of Silver have less severe signs than those with 2 copies of the mutation. To avoid producing offspring with severe MCOA, breeders should not breed 2 Silver dilute horses together.
Silver Dilution results are reported as:
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N/N
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No copies of Silver dilution detected.
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N/Z
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One copy of Silver dilution detected.
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Z/Z
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Two copies of Silver dilution detected. Horse is expected to have MCOA abnormalities.
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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
Andersson LS, Wilbe M, Viluma A, Cothran G, Ekesten B, Ewart S, and Lindgren G. 2013. EquineMultiple Congenital Ocular Anomalies and Silver Coat Colour Result from the Pleiotropic Effects of Mutant PMEL PLoS One. 2013 Sep 23;8(9):e75639.
Splashed-White
Splashed white is a variable white spotting pattern characterized primarily by large, broad blaze, extended white markings in legs, variable white spotting on belly, and often blue eyes. Some, but not all, splashed white horses are also deaf. Four mutations have been identified – SW-1, SW-2, SW-3 and SW4 – that cause splashed white phenotypes in horses. SW1 and SW3 are mutations in the MITF gene. SW2 and SW4 are mutations in the PAX3 gene. SW-1 is found in several breeds - Quarter Horse, Paint, Morgan Horse, 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. SW2 is currently considered not homozygous lethal based on a single SW2/SW2 horse. Horses that have SW2 may be deaf. Based on predictions from other species, SW-3 may be homozygous lethal but there is no confirmatory evidence. The current recommendation is that mating of two horses that carry SW-3 should be avoided. The rare SW-4 mutation has been identified in the Appaloosa breed and may cause a splashed white or a broad blaze.
Splashed white mutations are inherited as dominant traits with variable expression, which means that one copy of a SW mutation will produce a white spotting phenotype with variable amount of white. Horses that carry combinations of the splashed white mutations, tobiano or lethal white overo can display extensive white patterning or be white.
The VGL offers genetic tests for the 4 splashed white mutations SW-1, SW-2, SW-3 and SW-4.
Results are reported as:
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Splashed White (SW1, SW3)
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N/N
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No copies of SW1 or SW3 detected.
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N/SW1
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1 copy of SW1 detected.
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SW1/SW1
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2 copies of SW1 detected.
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N/SW3
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1 copy of SW3 detected.
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SW3/SW3
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2 copies of SW3 detected.
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SW1/SW3
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1 copy of SW1 and 1 copy of SW3 detected.
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Splashed White (SW2, SW4)
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N/N
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No copies of SW2 or SW4 detected.
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N/SW2
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1 copy of SW2 detected.
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SW2/SW2
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2 copies of SW2 detected.
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N/SW4
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1 copy of SW4 detected.
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SW4/SW4
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2 copies of SW4 detected.
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SW2/SW4
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1 copy of SW2 and 1 copy of SW4 detected.
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References:
R Hauswirth, B Haase, M Blatter, SA Brooks, D Burger, C Drögemüller, V Gerber, D Henke, J Janda, R Jude, KG Magdesian, JM Matthews, P-A Poncet, V Svansson, T Tozaki, L Wilkinson-White, MCT Penedo, S Rieder and T Leeb. Mutations in MITF and PAX3 cause ‘‘Splashed White’’ and other white spotting phenotypes in horses. Plos Genetics 2012, 8(4) e1002653.
Hauswirth R1, Jude R, Haase B, Bellone RR, Archer S, Holl H, Brooks SA, Tozaki T, Penedo MC, Rieder S, Leeb T. Novel variants in the KIT and PAX3 genes in horses with white-spotted coat colour phenotypes. Anim Genet. 2013, 44 (6):763-765. doi: 10.1111/age.12057. Epub 2013 May 9.
SynchroGaitTM
Summary about the three different genetic classes
AA Horses
Are most often easy gaited horses. In a study of Morgan horses, we had only three AA horses but they were all classified as five-gaited (walk, trot, gallop, amble, and pace).
AA Icelandic horses have the potential to perform flying pace - given other factors such as correct training, conformation and character. They can also amble and most of them do so easily and naturally. There is a high frequency of AA horses in gaited breeds worldwide.
CA Horses
Can often but not always amble. In Morgan horses, almost half (41%) of the CA horses were classified as three-gaited and 55% as four-gaited (ambling + basic gaits).
In Icelandic horses, the vast majority can amble, but they cannot perform flying pace. On average they obtain higher scores for the basic gaits than AA Icelandic horses (CC horses unavailable for comparison). Some of the CA horses may not show ambling easily at the beginning of their training. The genotype may therefore be “hidden” in a three-gaited horse because the horse has not been trained to amble.
Locomotion is a complex trait
Gaits in horses are influenced by several factors, both genetic and environmental. The summary above is what we see most often, but there are exceptions. Horses can to some extent be trained to re-shape their natural pattern of locomotion. Conformation also has an impact on the gaits and we have had reports of CC horses that are gaited and AA horses that seem unable to perform pace. However, these instances are quite rare and the gait-gene has a proven dramatic impact on horses’ gaits.
Used with permission from the UCDavis Veterinary Genetics Lab