• it might be wise to review Coat Colors before continuing

• These factors are controlled by alleles at several loci. We'll start with B

• controls the formation of the protein framework on which eumelanin is deposited.
• the B allele is the dominant allele at this locus.
• B is the allele for black, a color caused by eumelanin.
• the B allele causes the formation of elongated eumelanin granules. These appear black.
• the b allele is the recessive allele at the B locus.
• b is the allele for liver, also caused by eumelanin.
• the b allele causes the production of small, round or oval eumelanin granules which appear brown and are responsible for the liver coat color.

• BB or Bb = "fading black" shows reddish highlights in the sun
• non fading black results from the effects of another locus on the B locus.

• mutations of the genes at the A(agouti) locus are responsible for changing the primitive equine coat color into the various coat colors of the modern horse.
• agouti is the original wild type coat pattern
• agouti is caused by original A+ allele at the A locus.
• A+ allele dominant over all other alleles at the A locus, but rarely, if ever, occurs in modern day horses. Can be seen in Przewalski's horse on the steppes of Mongolia.
• A+ allele, phenotype:
  • dark points (mane tail legs)
  • coat contains mixture of eumelanin and phaeomelanin in each hairshaft.
  • coat appears gray on neck, back; more yellow on belly

• A allele - bay coat pattern - mutation of A+ allele
• A allele restricts most eumelanin to the points (creating black points) and the rest of the body has some eumelanin, and its abundance in relation to phaeomelanin will determine the exact shade of bay. (ie light bay, dark bay, red bay, liver bay)
• The A allele has an affect on B locus - black and liver horses have eumelanin in their coats; the A allele can restrict this.
• the A allele CANNOT make a chestnut horse bay, but lighten phaeomelanin and change shade of chestnut.
• A+ epistatic to B
• a^t allele (at the A locus) - causes a modifying effect.
  • - is recessive to A and will not change bay
  • - when homozygous (a^ta^t) or when a^t is the dominant allele at the A locus, the genotypically black horse will be dark seal brown and a genotypically liver horse will be light seal brown.
• a^t is associated with a dorsal stripe, but it isn't visible on a dark coat
• dark seal brown - mix of phaeomelanin and eumelanin in coat, w/more eumelanin
• light seal brown - phaeomelanin and liver hairs(eumelanin deposited on round protein granules)
• both seal browns: reddish hair visible on flanks, muzzle, and belly. Legs remain dark.
• a^t allele w/ D dilution gene and genotypically chestnut horse creates RED DUN or CLAYBANK
• D must be present for dun color to be expressed.
• The a allele is recessive to all other alleles at the A locus and does nothing to affect any other locus.
• A horse homozygous for the a allele at the A locus will show coloring with no influence from the A locus.

• The E locus affects the extension of both eumelanin and phaeomelanin throughout the coat.
• The E locus is also called the "extension/restriction locus".
• If one pigment is extended, the other pigment is restricted.

• E^D is dominant over the other two alleles.
  • The E^D allele allows the full extension of the colors black and liver (B_ and bb) since no phaeomelanin is present.
  • BB or Bb w/ E^D is non fading or jet black.
  • fading blacks are born mousy, jet blacks are born black
  • bb w/ E^D is rare nonfading liver.
  • E^D can completely mask the A locus, THEREFORE E^D is epistatic to A, at and a
    • a jet black or nonfading liver horse may carry the allele for bay or brown and not express those colors.
• The e allele is recessive.
• The e allele restricts eumelanin, leaving only phaeomelanin in the coat. Eumelanin is left only in the skin and eyes. The result is chestnut.
• The E allele is the original allele at this locus.
• E allows the expression of genes at other loci. E is dominant to e, but not to E^D.

• The three epistatic modifiers are:
  • Gray
  • Roan
  • Dominant white
• Horse's genotype may be black, liver, bay, brown, etc. and he may be gray, roan or white in phenotype because these colors are epistatic to basic and dilute colors.

• Grey: a progressive silvering that takes place after birth
• horses are born the color they are otherwise genetically coded to be and then fade to gray.
• The G allele prevents pigment form entering the hair shaft, therefore melanin collects in the skin, making grays more susceptible to melanomas. Legs frequently gray later than body. Mane and tail may gray faster or slower than the body.
• The g allele is recessive, and does nothing, allowing the horse to be the color he is otherwise genetically coded to be.
• Homozygous gray (GG) always breeds true.
• fleabitten grey and dapples are caused by unknown modifying alleles
• Bloody Shoulder Markings:
  • permanently restricted areas of dark hair seen ONLY ON GREYS.
  • (May be undetectably present red or black on other coat colors.)
  • commonly on saddle ares may extend to shoulders
  • type of genetic throwback (trait from distant ancestor)
  • occurs only in horses w/Arab blood or ancestry, such as Arabians and Thoroughbreds

• The R locus causes "non progressive silvering", or roaning
• ROANS DO NOT "ROAN OUT" WITH AGE. ROAN COLORING IS PRESENT AT BIRTH.
• Appaloosa Roan follows its own complex rules, and does change with time, often even darkening
• When a roan's skin is injured, hair over scar grows back solid colored.
• hair on a non roan's scar will be roan
• roan on black = blue roan
• roan on chestnut = strawberry roan
• roan on bay = red roan
• ROAN is epistatic to all coat colors (except gray and dominant white.)
• both Rr and G_ = a roan that appears to change
• homozygous R allele at the R locus is lethal (to the embryo)
• When breeding specifically for roan:
  • foal crop is reduced 25%
  • 67% of live foals are roan
• It is impossible to have true breeding roans due to the lethal gene
• mutation at R locus, RnAp allele, produces roaning over hips.
• roan on flanks only caused by unidentified alleles.
• roan and gray undesirable in Paints, Pintos, and Appaloosas because it reduces color contrasts
• roan Rr nonroan rr

• The W locus is epistatic to ALL others.
• Homozygous W (WW) is lethal to the embryo.
• The w allele is recessive and allows expression of color
• True white horses can be distinguished from cremellos and grays because white horses have pink skin, white markings do not show, and dominant white horses are born white.
• Albinoism does not exist in horses, iris is always colored

• believed to be caused by two gene pairs.
• restrict color to one side of the hairshaft, leaving the other side almost transparent.
• pigment almost entirely restricted in cremello, perlino

• the C locus affects degree of pigmentation in the hair shaft.
• the c^cr allele (mutation of C) dilutes phaeomelanin
• c^cr therefore dilutes chestnut, bay, and lighter areas of seal brown, all of which contain phaeomelanin.
• ccr has no noticeable effect on black, liver, or dark areas of seal brown.
• Dilution is present at birth
• palomino: c^cr allele is heterozygous w/C (Cc^cr)
  • phoeomelanin is restricted to one side of the hair shaft so base CHESTNUT coat is diluted to PALOMINO
  • palomino is a single dilution of chestnut
  • chestnut + Cc^cr = palomino
• cremello: when c^cr is homozygous (c^crc^cr)
  • phaeomelanin is almost entirely absent from the hair shaft so base CHESTNUT is diluted to CREMELLO
  • cremello is a double dilution of chestnut
  • chestnut + c^crc^cr = cremello
• it is sometimes difficult to tell cremello from a dominant white, since both have pink skin.
• cremellos have a pale mane and tail, and markings are visable
• a chestnut bred to a cremello will always produce palomino

100% Cc^cr (palomino)

• variations in palomino coat color:
  1. different base shades of chestnut.
  2. other modifying genes
• it has been theorized that the A allele at A locus is necessary for the expression of c^cr at C
• LIVER CHESTNUT WILL NOT BE DILUTED BY THE C LOCUS.
• the c^cr allele, on a dark seal brown, will dilute the phaeomelanin in the red hairs on the muzzle and flanks. ("mealy mouthed")
• the c^cr allele on a bay dilutes the red hairs and = a diluted coat w/black mane and tail. Degree of dilution dependent upon eumelanin : phaeomelanin ratio.
• the c^cr allele, with bay, equals Buckskin
• Buckskin is a single dilution of bay
• the shade of bay affects the shade of buckskin
• while the terms dun and buckskin were once used interchangably, as more genetic research is undergone it becomes more evident that they are seperate, while similar, colors

• c^cr homozygous on a bay coat. phaeomelanin almost entirely restricted from hair shaft.
• Perlino is the double dilution of bay
• claybank MAY be caused by:
  • chestnut + a^t and Cc^cr = Red Dun or Claybank
  • this would be "palomino" w/ a^t causing dorsal stripe, dark points

• The D locus controls the degree of hair shaft pigmentation.
• The D locus affects both phaeomelanin and eumelanin.
• There are two known alleles at the D locus.
• The dominant D allele dilutes both eumelanin and phaeomelanin. It MAY dilute phaeomelanin one shade more than it dilutes eumelanin. Pigment is restricted to one side of the hair shaft.
• The recessive d allele causes no dilution.
• The allele D works the same, homozygous or heterozygous.
• The d allele, when homozygous, causes the D locus to have no control over coat color
• Isabella: uniform yellow dilution of chestnut caused by either DD or Dd at the D locus. With flaxen mane and tail, looks like palomino BUT COULD BREED TRUE when homozygous.
• chestnut + dd = chestnut
• chestnut + flaxen mane and tail + DD = isabella
• Isabella is a single dilution of chestnut
• Grulla: (DD) or (Dd) on black = smokey blue with black points
  
  

  Grulla is traditionally considered to be a dilution of black, but may actually be a dilution of seal brown

  Why black points is unknown.
  but
  a grulla has the dorsal stripe associated w/ a^t
  
• Dilution of liver by the D allele causes a brownish shade of grulla.
• fading liver dilutes lighter
• light seal brown dilutes lighter
• liver bay dilutes lighter w/liver points
• The D allele may dilute eumelanin and phaeomelanin and cause buckskin or dun
• ??the D allele and the a^t allele may be linked??
  • this would cause dorsal striping
  Combined Effects of c^cr and D
  
• combining the two types of dilution genes DOES NOT DOUBLE THE DILUTION
• this may partially account for various shades of buckskin and dun and the confusion around these colors.

• theory one: caused by dilution genes
  • invalid because: some livers and chestnuts have flaxen manes and tails
• theory two: caused by a recessive gene pair
  • invalid because: all palominos would not have flaxen manes and tails if this were true.
• c^cr causes dilution of palomino mane and tail to flaxen
• ff causes flaxen mane and tail in non palomino
• chestnut w/flaxen mane and tail __ __CCddeeff

• found only in Shetlands and Miniatures
• unevenly diluted eumelanin
• almost black to light milk chocolate coat with silver mane and tail and a dark "mask" on the face w/ silver colored dapples.
• originally a dominant mutation in Shetland ponies in England (1886)
• The S allele for silver dappling is dominant to the s allele for no dappling. SS in the homozygous state lightens coat. The S allele in the heterozygous state causes a more striking appearance, especially on a genotypically jet black pony.
• the effects of silver dappling combined with dilution genes causes some of the odd colors seen in the miniature horse
• silver dapple on chestnut results in a dark red chestnut with a flaxen mane and tail, or sometimes a mane and tail with a combination of flaxen and black hairs
• __B_ccddED_SS = chocolate silver dapple w/great contrast