base coat

Equine coat color genetics

Equine coat color genetics determine a horse's coat color. All horses begin genetically with a base coat of "red" (chestnut) or "black." This base color is designated as "e" for the recessive red allele and "E" for the dominant black allele. Separate genes or "modifiers" act upon the expression of base colors to create all other equine coat colors.

Coat color alleles affect melanin, the pigment or coloring of the coat. There are two chemically distinct types of melanin: phaeomelanin, which is perceived as red to yellow color, and eumelanin, is perceived as brown to black. All coloration genes in mammals affect either the production or distribution of these two chemicals.

Genes appear in sets of two, with each individual gene "option" being called an allele. Because sex cells (sperm and ova) contain only half the usual number of chromosomes, each parent contributes one allele in each gene set to the ensuing offspring. When an individual's gene set contains two copies of the same allele, it is called homozygous for that gene. When it has two different alleles, it is heterozygous. For a recessive gene to be expressed, it must be homozygous, but a dominant gene will be expressed whether it is heterozygous or homozygous. A horse homozygous for a certain allele will always pass it on to their offspring, while a horse that is heterozygous carries two different alleles and can pass on either one.

Background information

There are currently two major theories of equine coat color genetics: those based on the work of the late Dr. Ann T. Bowling of the University of California, Davis and of Dr. Phillip Sponenberg of Virginia Polytechnic Institute. These theories overlap, and have more similarities than differences.

The terms Alleles and Modifiers are used interchangeably in this article. An allele identified with a capital letter is a dominant gene, one identified with a lower-case letter is a recessive gene.

The genetics of white horse markings are not yet fully understood but are probably influenced by multiple alleles.

''Note: For a quick lesson in genetics and heredity, see the articles on alleles or other footnoted tutorials on inheritance.

Alleles and effects

Alleles Effect of combined pairs of alleles
EE or Ee: Horse forms black pigment in skin and hair.
ee: Horse is chestnut, it has black pigment in skin, but red pigment in hair. White, gray, agouti, roaning, pattern (spotting) and dilution genes will all modify both red and black.
E+ also noted as Ed. E+
Fading and non-fading black: proposed theory, allele yet to be located, does not appear to occur on the same locus as the E and e alleles. E+E+or E+e+: Dominant black, non-fading horse. One theory, unproven and highly unlikely, is that E+ is dominant over agouti.
e+e+: no effect.
Agouti: Acts on "E" to restrict eumelanin, or black pigment, to "points," allowing red coat color to show on body. Has no visible effect on "e" or red, as there is no black pigment to restrict.
AA or Aa horse is a Bay, black hair shows only in points pattern (usually mane, tail, legs, sometimes tips of ears).
aa: No agouti gene. If horse has E allele, then horse will be uniformly black.

WW: Lethal. Embryo reabsorbed or fetus dies en utero.
Ww: Horse has pink skin and white hair, with blue or light-colored eyes. Hair coat is white from birth.
ww: Horse is fully pigmented.
GG or Gg: gray gene. Horse shows progressive silvering with age to white or flea-bitten, but is born a non-gray color. Pigment is always present in skin and eyes at all stages of silvering. Gray horses range from white to dark gray depending on age and the proportion of white hairs in the coat. Horses' coats gray in a manner similar to graying in human hair.
gg: Horse does not gray with aging.
Cr Cr
Cream gene The cream gene is an incomplete dominant.
CC: No dilution factor, horse is fully pigmented. (UC Davis abbreviates as N.)
CCr: Single dilution factor (heterozygous dilute) results in Palomino, Buckskin or Smoky Black. Red pigment is diluted to gold with cream to white mane and tail; black pigment is not visibly altered on black points or black horses, though genetic testing can reveal "smoky black" coloration. (UC Davis abbreviates as N/Cr.)
CrCr Cremello or Perlino: Double dilution factor (homozygous dilute). Red pigment is diluted to a pale cream. Black pigment is diluted to a reddish shade. Skin and eye color are also diluted, skin is pink and blue eyes are common with double diluted creams. (UC Davis abbreviates as Cr.)
DD or Dd: Dun gene Another dilution gene. Horse shows a diluted body color to pinkish-red, yellow-red, yellow or mouse gray and has dark points including dorsal stripe, shoulder stripe and leg barring.
dd: Horse has undiluted coat color.
TOTO or Toto: Tobiano, a form of pinto patterning. Produces regular and distinct ovals or rounded patterns of white and color with a somewhat vertical orientation. White extends across the back, down the legs, but face and tail are usually dark.
toto: No tobiano pattern present.
O Also noted as Fr or FrO O
OO or Oo: Overo or Frame Overo pattern - Pinto horse pattern that forms a solid frame around white spotting. White is usually horizontal in orientation with jagged edges, color crosses the back and legs, face is often white. Overo as an allele is different from overo as a registration since the registration also includes the splash overo and sabino alleles. Homozygous overo is associated with lethal white syndrome, characterized by an incomplete colon and the inability to defecate, which leads to death or humane euthanization within days of birth.
oo: No overo pattern present.
Ch Ch
Champagne: A rare but dominant dilution gene that creates pumpkin-colored freckled skin, amber, greenish, or blue eyes, and gives a bronze cast to hair. The skin surrounding the eye must be pink with freckles in adulthood.
ChCh or Chch: Champagne dilution evident (See Genetic Formulas Chart below.)
chch: No champagne dilution
Prl Prl
Pearl: A new rare recessive dilution gene that looks very much like Champagne. The Pearl gene is sometimes referred to as the "barlink factor." 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.
PrlPrl or Prlprl: No pearl dilution.
prlprl: Pearl dilution evident.
Flaxen: Effects visible on red or chestnut colors only.
FF or Ff: Red points on ee horses.
ff: Flaxen points on ee horses. Proposed theory, allele not located.
Pangare (Mealy): Lightening of hairs in limited regions. The effects of this allele appear in areas of "soft" skin, including the muzzle, behind the elbows, in the flanks, on the buttock, above or around the eyes, and along the belly.
PP or Pp: Mealy or Pangare dilution of pigment.
pp: no mealy looking lightening of pigment. Proposed theory, allele not yet located
Rn Rn
RnRn or Rnrn: roan pattern of white hair mixed in with base color. There probably is no lethal roan question.
rnrn: No roan pattern.
Rb Rb
Rabicano: Partial roaning with ‘coon’ tail markings. Thought to be a dominant gene by Sponenberg.
RbRb or Rbrb: Rabicano markings.
rbrb: No rabicano traits.
Sb Sb
Sabino - Assorted pinto or roan-like markings.
Sabino may be polygenic (a gene-complex rather than a single gene pair), caused by several different genes. Recognized by abundant white on the legs, belly spots or body spots that are can be flecked and roaned, chin spots, or white on the face extending past the eyes. Sabino is registered as overo by some registries, but is not the overo or frame overo allele. No risk of lethal white, though some "Fully expressed" sabinos may be completely white in coat color.
SbSb or Sbsb: Sabino markings.
sbsb: No sabino markings.
SB1:The only Sabino gene currently detected by DNA testing, however does not appear to be the gene that creates sabino coloring in Arabians or Clydesdales.
Spl Spl
Splash, Splashed White - A type of pinto horse coloring recorded in the overo family, but possibly related to other genes. Resembles reverse tobiano with white moving from the bottom of the horse towards the top. The horse's head will look as if dunked in bucket of white paint. Commonly has blue eyes.
SplSpl or Splspl: Splashed markings. Splash is not associated with frame overo lethal white syndrome.
splspl: No splashed markings. Alternate theory: Incomplete dominant. SplSpl:classic Splash markings.Splspl:socks, face markings, may be small in the "normal" marking range or into the pinto range with or without blue eyes. splspl causes no white at all.
Sty Sty
StySty or Stysty: The Sooty effect is of black hairs mixed into a body coat or any other color, may create dark bays or "brown" horses and liver chestnut. Is most visible on Buckskin or Palomino.
stysty: No black mixed into coat. Proposed theory, allele not yet located.
ZZ or Zz: Silver dapple - Dilutes eumelanin or black pigment. Converts black to brown with white mane and tail or results in silver coloring.
zz: No silver dapple.
Lp Lp
Appaloosa or Leopard spotting gene. Produces coat spotting patterns, mottling over otherwise dark skin, striped hooves and white sclera around the eye.

Genetic formulas and color definitions

Partial list of Genetic Formulas and Color Definitions
Chart based on Dr. Bowling's Genetic Formulas
W White
G Gray
E, A, CC, dd, gg, ww, toto Bay or Brown
E, aa, CC, dd, gg, ww, toto Black
ee, aa, CC, dd, gg, ww, toto Red: Sorrel or Chestnut
E, A, CCr, dd, gg, ww, toto Buckskin
ee, CCr, dd, gg, ww, toto Palomino
ee, CrCr Cremello
E, CrCr Perlino
E, A, CC, D, gg, ww, toto Yellow or "buckskin" Dun
E, aa, CC, D, gg, ww, toto Mouse Dun, Blue Dun or Grulla
E,A,CC,D Dun, "Zebra" Dun, "Bay" Dun, Classic Dun
ee, CC, D, gg, ww, toto Red Dun
gg, E, aa, CC, dd, RN Blue Roan
gg, E, A, CC, dd, RN Bay Roan
gg, ee, CC, dd, RN Red Roan
gg, E, A, CCr, dd, RN Buckskin Roan (Red Roan) 
gg, ee, CCr, dd, RN Palomino Roan (Red Roan)
gg, E, A, CC, D, RN Buckskin Roan (Red Roan)
gg, E, aa, CC, D, RN Mouse Dun Roan, Grulla Roan, or Blue Roan&
gg,ee, CC, D, RN  Red Dun Roan (Red Roan)
gg, E, A, CC, dd, gg, ww, TO Bay Tobiano
gg, ee, CC, D, gg, ww, TO Red Dun Tobiano
gg, Ch, ee, aa, CC, dd, gg, ww, toto Gold Champagne - looks like Palomino
gg, Ch, E, A, CC, dd, gg, ww, toto Amber Champagne
gg, Ch, E, aa, CC, dd, gg, ww, toto Classic Champagne
gg, Ch, ee, CcrCcr Ivory Champagne
gg, E, aa, CC, dd, TO, Sb Black Sabino-Tobiano (Tovero without lethal white.)
gg, E, aa, CC, dd, TO, O Black Tobiano-Overo (Tovero carrying lethal white.) 
ee, CCr, dd, gg, ww, TO Palomino Tobiano Paint
gg, ee, aa, CC, dd, TO, Spl Red Tobiano-Splash (Tovero without lethal white.)

Lethal roan question

Hintz, H. F. and VanVleck, L. D., published 1979. "Lethal Dominant Roan in Horses". Journal of Heredity, 70:145-146. This study, based on percentages of roan foals thrown by roan parents, popularized the idea of Lethal Roan Syndrome. The study did not include direct genetic analysis and assumed fetus absorption preventing birth. Similar studies suggested that roan-to-roan breedings were lethal because the resulting embryos were absorbed. This was thought to be true because homozygous roans, horses that carried two alleles for the roan characteristic, were rare.

A recent genetic study of roans by Dr. Bowling refuted Hintz and VanVleck’s inferences. Using genetic analysis, Dr. Bowling found several homozygous roans and no evidence of a Lethal Roan Syndrome.

See also


Sources and external links

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