Here are a list of the known horse colour genes… they are in this format: locus), alleles, series effect of alleles
A) A, a, A+, At: Agouti
The dominant form is A, which, if present in a horse, restricts black to the points. In other words, it keeps black from the body parts, resulting in a bay or other colour with black legs, mane and tail. The recessive or ‘off’ form is a- it does not affect the black in any way; the horse may have black on entire body.
There may be other alleles for Agouti, too: A+ makes the horse a wild (primitive) bay, and At removes light pigment from soft body parts.
Cr) Cr, cr: Cream gene
When two cr genes are present, the horse is not a dilute (palomino, buckskin or the like). When one Cr gene is present, then the body is diluted (bay to buckskin, chestnut to palomino, etc.). When two Cr genes are present, then the horse is what is called a ‘double dilute’: a Cremello or a Perlino (lighter versions of the Palomino and Buckskin, respectively), or Smoky cream (black double dilute)
Ch) Ch, ch: Champagne
The Champagne gene, Ch, dilutes the colour of the horse and also effects eye and skin colour, as well as actual hair build. Horses with the Ch gene will be silvery-chocolate, reddish, or golden in colour with a metallic sheen. Their eyes are amber, and their skin is a pink colour, though not the pink of most horses- it’s a mottled orangey-pink. The hairs of a champagne are actually hollow, so this gene somehow affects more than colour alone. ch is the regular gene, it has no affect.
D) D, d: Dun
The D gene creates a dun horse. It causes pigment to concentrate on one side of the hair, making it a diluted colour. It also gives the horse a dorsal stripe, leg barring, and sometimes other primitive marks. A dun horse is either Dd or DD- by just looking at that animal you cannot tell which. d is the regular allele, no effect.
E) E, e: Extension (black pigment)
The E gene creates black pigmentation; horse may be either EE or Ee. An ee horse will not have any black pigment (chestnut, red roan, palomino, etc.). A horse that is EE or Ee will have black pigment (black, buckskin, grulla, etc).
F) F, f: Flaxen
F creates a flaxen mane and tail, and perhaps lightens the body a bit, in ee horses.
G) G, g: Gray
G is the most dominant gene, and turns any colour to grey. Foals may be born any colour, but lighten with age. In other words, G is epistatic to all other genes. g has no effect.
Lp) Lp, lp: Leopard-complex
Lp creates mottling and spotting characteristics, and allows for different spotting patterns, such as those seen in the Appaloosa. lp has no effect.
N) N, n: White markings
One hypothesis is that the N gene prevents all white markings- even if the horse had sabino or other pinto genes, this would mask them. n allows white markings to occur, and they will if pinto genes are present. It is not known for sure if the N gene exists.
Fr) Fr, fr: Frame
Fr creates the Frame pinto pattern in the horse. Homozygous form (FrFr) is lethal, resulting in an OLWS (overo lethal white syndrome) animal that dies.
P) P, p: Pangare
The Pangare gene, P, lightens the horse’s muzzle, flanks and belly, creating a ‘mealy’ horse.
Rn) Rn, rn: Roan
Creates a mix of light and dark hairs, making roaning.
Sb) Sb, sb: Sabino
The genetic control of sabino is not completely known. It appears to be polygenic, and not a simple dominant like tobiano.
Sc) Sc, sc: Snowcap
Causes pigment loss in the form of snow cap spotting, in the presence of Lp.
Sd) Sd, sd: Dark spots
Causes dark spots in the presence of Lp.
Sn) Sn, sn: Snowflake
Causes white spots (snowflake pattern) in the presence of Lp.
Sv) Sv, sv: Varnish
Causes silvering/varnish effect in the presence of Lp.
Spl) Spl, spl: Splashed White
Causes pigment loss in the form of a Splashed White patterned pinto.
Sty) sty, Sty: Sooty
Causes mixture of black hairs, creating seasonal dapples, or a ‘sooty’ appearance.
To) To, to: Tobiano
Causes pigment loss in the form of a tobiano pinto pattern.
W) W, w: White
Causes pigment loss over entire body in hair and skin, but not eyes; dominant white. There is some doubt as to whether this gene actually exists.
Z) Z, z: Silver
Dilutes black pigment, has no effect on red pigment.
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