Equine Genes - Colors & Patterns
As fellow horse enthusiasts, and serious geeks, we started this company to help untangle the meaning of genetics and how it relates to our horses' health. When testing our own horses in the past, we often had questions like: What the heck is Agouti and why do I care? Do I care if my horse is SCID positive? How much should I care? How reliable is the data behind the genetics? One of our missions is to make genetics more understandable, so please, read on. If you have others questions that aren’t answered here, or you would like to let us know how we are doing, please do so! Feel free to contact us at any time, or simply place a test order here.
Below you will find very simple images that represent the basic colors, patterns and modifiers of various horses. Should you like more detailed information, you'll find many links within the descriptors leading you to expanded and detailed information including scientific publications and images.
The ASIP gene, also known as agouti, controls the regional distribution of black pigment. Dominant agouti ("A") pushes the black base color (“E”) to the edges (points) of the horse, resulting in black legs, mane, tail, and ear tips with a reddish body (the bay coat color). A horse needs two recessive "a" alleles to show black throughout the coat. Agouti only affects black pigment, and thus is not visible on a red (chestnut/sorrel) base.
Z Blanco Norsk Stallion pictured - Sired by Friesian Zero Gravity
Black based with a single Dominant White 13 allele
Dominant white (“W”) refers to a class of white spotting patterns in which a horse with one copy generally displays markings on 50-100% of the body. Unlike other extreme white patterns, this trait generally leaves the eyes dark.
(Lethal White Overo)
Gambling Prophecy Stallion pictured - Thank you Prophecy Farms
Black based & one Agouti with a single Lethal White Overo allele
Frame overo (lethal white overo) is a white spotting pattern characterized by patches of white bordered or “framed” by normal pigmentation. It is usually accompanied by blue eyes, and generally white patterning does not cross the topline. While heterozygous horses (LWO/N) only have this white spotting pattern, homozygous foals (LWO/LWO) are born completely white and with megacolon, an abnormal dilation of colon which necessitates immediate euthanasia.
Grey is a modifying allele that causes progressive loss of pigmentation throughout the entire body. Generally, horses are born with a darker coat color than typical, then begin to display some white hairs with the first shedding. The rate of greying is highly variable, though some research suggests horses with two copies (G/G) may grey faster than horses with one copy (G/N).
Research has indicated that between 70-80% of grey horses over the age of 15 have melanomas. Unlike other melanomas, these grey-associated tumors are usually benign and do not generally cause problems for the affected horses.
Cream & Pearl (dilution)
CR/CR=Double Cream Dilution
CR/N=Single Cream Dilution
CR/prl=Cream Pearl Dilution
prl/N=Pearl Carrier (Non-Dilute)
Lusitano Stallion Caetano TH pictured
Red based with two Cream alleles
Cream (sometimes seen as “Crème”) and pearl are two variants of the same gene that dilute coat color. A single CR allele lightens red pigment to gold, but does not affect black pigment. Two CR alleles results in extreme dilution of the hair, skin, and eyes of any color, though black based horses tend to retain more pigment than red based horses.
A single prl allele does not affect the coat color, though may cause some skin lightening/freckling. Horses with two prl alleles are visually similar to horses with the champagne dilution, including skin and eye color. Horses with both a CR and a prl allele are similar to double cream or cream plus champagne dilutions.
SB1/SB1=Max Sabino/Sabino White
Paso Pinto Stallion Curandero TM pictured
Photo credit to Trademark Farms - thank you!
Sabino spotting is characterized by extended white markings on the legs and face, often accompanied by a belly spot and roaning throughout the coat. Unlike other white patterns, sabino horses usually have dark colored eyes. Horses with a single copy of sabino-1 (SB1/N) display this characteristic pattern, whereas horses that have inherited two copies (SB1/SB1) are almost completely white.
Z/Z=Homozygous Silver (MCOA)
Z/N=Heterozygous Silver (Cyst)
Silver is a dominant dilution that only affects black pigmentation. Horses often have a lighter mane and tail. Silver foals are born with striped hooves and white eyelashes. Bay silver horses retain the normal reddish body color combined with diluted legs, which can be misidentified as a chestnut. There has been no documented effect of silver on the coat color of chestnut/sorrel horses.
*Silver also results in equine multiple congenital ocular anomalies (MCOA) syndrome. Heterozygous horses have a mild cyst phenotype, whereas homozygotes display a more severe range of clinical symptoms.
Leopard Complex Spotting
LP/LP=Homozygous LP, CSNB
Leopard complex spotting (or Appaloosa spotting) is a unique group of spotting patterns. One main gene determines whether a horse will express one of the patterns (LP), and other minor factors alter the extent of white spotting. Heterozygous horses usually have oval spots within patterned areas, where homozygotes have few to no such spots.
* Homozygous horses are also affected by congenital stationary night blindness (CSNB), a non-progressive lack of vision in low light conditions.
The MC1R gene, also known as extension, determines whether a horse can produce black pigment. Black ("E") is dominant to red ("e"). Therefore, a horse with the genotype "E/e" (one black and one red allele) has a black base color, but can produce either black or red base offspring. Homozygous black (E/E) horses will always produce black based offspring.
Macchiato (fun fact!)
Photo from Hauswirth et al. 2012
A mutation in the MITF gene, the macchiato coat color was documented in a single Franches-Montagnes stallion. He displayed a dilute coat color, blue eyes, extended face and leg markings, and white on the body. He was also noted as being completely deaf and had low progressive sperm motility.
Tobiano spotting is characterized by large white patches on the limbs and body. Often times, these patches have smooth edges, cross over the topline, and are accompanied by dark eyes. Expression can range from white present only on the legs, to horses nearly completely white. As this trait is dominant, horses with either one (TO/N) or two (TO/TO) copies will have a similar appearance.
Champagne is a dominant dilution that affects all coat colors. Horses with two CH alleles have nearly the same degree of dilution as horses with only one allele. Champagne foals are born with pink skin and blue eyes that slightly darken with age. Adult champagne horses have a distinct pumpkin colored skin with mottling in the hairless regions, as well as amber/green/tan eyes. Horses with multiple dilutions can be difficult to accurately identify color without genetic testing.
The horse pictured above has both champagne and cream dilution. His color is difficult to distinguish from a double cream dilution.
IP/N=IP Female, Lethal Male
Photo from Towers et al. 2013
Incontinencia Pigmenti (IP) is a brindle-like appearance found only in female horses. Affected male embryos die during development in utero. IP foals develop pruritic, exudative lesions soon after birth. The affected regions progress into wart-like lesions and areas of alopecia (hair loss) with occasional wooly hair re-growth. Affected horses display streaks of darker and lighter coat coloration from birth.
* While this is a heritable form of brindling color (as the result of a not-so-desirable skin disease), there are other forms that are either due to non-heritable developmental oddities, or that have yet to be characterized.
* IP is a condition also seen in humans, mice and several other species.
Splashed Whites 1- 7
(SW1, SW2, SW3, SW4, SW5, SW6, SW7)
SW/SW=Homozygous Splashed White
SW/N=Heterozygous Splashed White
Splashed White is a white spotting pattern characterized by large amounts of white on the legs, face, and sometimes tail/belly, giving a horse the appearance of being dipped in paint. Often times, splashed white horses have one or two blue eyes, and may be deaf. SW1 is incompletely dominant, with heterozygotes (SW1/N) displaying "typical" white markings and homozygotes (SW1/SW1) having a classic splashed white appearance. Horses with one copy of any of the other splashed whites (SW2, SW3, SW4, SW5, SW6, SW7) have the typical splashed white appearance.
D/nd1 or D/nd2=Heterozygous Dun
nd1/nd1 or nd1/nd2=Non-Dun
* possible primitive markings (PM)
nd2/nd2=Non-Dun, no PM
Dun is a dominant dilution that affects both pigment types. Although dun is the ancestral color of equids, non-dun is more commonly seen in breeds today. Dun is also associated with an assortment of "primitive markings," such as a characteristic dorsal stripe. Two non-dun variants have been discovered - the nd1 allele is associated with primitive markings in non-dilute horses, whereas the nd2 allele neither shows dilution nor primitive markings.
Pattern-1 is a major effect modifier of leopard complex spotting. While the LP variant itself does not produce much white spotting, the PATN1 variant is associated with white markings over ~50% of the body at birth. Other factors known to influence leopard complex spotting are sex (males with more patterning than females) and coat color (chestnut bases have more white than black bases).
The foal pictured above is heterozygous for both LP and PATN1 (LP/N, PATN1/N).