- a mutation of a gene to another form; there may be several
possible alleles for a given locus
- Artificial Selection
- purposeful breeding by man to improve or eliminate a specific characteristic
- chromosome other than the sex chromosomes
- an individual which carries a recessive allele, but is heterozygous, and therefore does not show characteristics
- bodies within a cell nucleus composed of DNA; they carry genetic information
- eliminating animals with undesirable characteristics from the herd
- an allele which will be expressed whether homozygous or heterozygous; it overrides the recessive allele
- deoxyribonucleic acid; genetic material from which chromosomes are made
- a gene at one locus which masks a gene at another locus
- dark pigment which may color the coat, skin, and eyes
- determines a hereditary trait; a segment of a DNA molecule that
instructs a cell to produce a specific protein
- the genes that an individual inherits from both parents; "inward appearance"
- carries two different alleles at a specific locus
- carries two identical alleles at a specific locus
- a gene masked by an epistatic gene
- mating closely related individuals
- Incomplete Dominance
- when a trait is visable when heterozygous, but stronger when homozygous
- Lethal Gene
- a gene whose effect is to kill the carrier; usually recessive (ie Roan)
- the specific site of a gene on a chromosome
- the basic pigment in the coat, skin, and eyes
- Natural Selection
- culling based on "survival of the fittest" without human intervention
- an allele which must be homozygous to be expressed; it will be hidden by the dominant allele
at the locus when heterozygous (both are present)
- Sex linked
- a gene carried on the sex chromosome; usually X
- it might be wise to review Coat Colors before continuing
Notes on Color Genetics
Causes of Color
|Color is due to: ||1) ||the type of pigment deposited on the
|a)eumelanin -dark- (black)
|b)phaeomelanin -light- (chestnut)
|2)||the structure of the pigment
|3)||the distribution of the pigment|
- These factors are controlled by alleles at several loci. We'll start with B
The B locus
- 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.
LIVER CHESTNUT IS NOT GENETICALLY CHESTNUT.
- 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.
|fading black || BB, Bb
|nonfading black ||BB, Bb +certain allele
at separate locus
|fading liver ||bb
|nonfading liver || bb +certain allele at
The A 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
- the A allele CANNOT make a
chestnut horse bay, but
lighten phaeomelanin and
change shade of chestnut.
- A+ epistatic to B
- at allele (at the A locus) - causes a modifying effect.
- - is recessive to A and will
not change bay
- - when homozygous (atat)
or when at 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.
- at 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,
- 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.
- at 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.
|nonfading black ||BB, Bb +certain allele
at separate locus
|fading liver ||bb
|nonfading liver || bb +certain allele at
|Dark seal brown||atatBb
|Light seal brown||atatbb
|Agouti (wild type)||A+_ _ _
The E 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.
The E locus has three possible alleles.
- ED is dominant over the other two alleles.
- The ED allele allows the full extension of the colors
black and liver (B_ and bb) since no phaeomelanin is
- BB or Bb w/ ED is non fading or jet black.
- fading blacks are born mousy, jet blacks are born black
- bb w/ ED is rare nonfading liver.
- ED can completely mask the A locus, THEREFORE ED 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
- 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 ED.
|jet black ||_B_ED_
|nonfading liver|| _bbED_
|fading black||aaB_EE or aaB_Ee
|fading liver ||aabbEE or aabbEe
|chestnut||__ __ ee
|light chestnut||A_ __ ee
|bay||A_B_EE or A_B_Ee
|dark seal brown||at_B_EE or at_B_Ee
|light seal brown ||at_bbEE or at_bbEe|
The Epistatic Modifiers
- The three epistatic modifiers are:
- 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
The G Locus
- 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
- (May be undetectably present
red or black on other coat
- 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
- 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
- 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
- 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
- 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
DILUTED COAT COLORS
- 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
- the C locus affects degree of pigmentation in the hair shaft.
- the ccr allele (mutation of C) dilutes phaeomelanin
- ccr 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: ccr allele is heterozygous w/C (Cccr)
- 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 + Cccr = palomino
- cremello: when ccr is homozygous (ccrccr)
- phaeomelanin is almost entirely absent from the hair shaft so base CHESTNUT is diluted to CREMELLO
- cremello is a double dilution of chestnut
- chestnut + ccrccr = 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
(CC) x (ccrccr)
100% Cccr (palomino)
- variations in palomino coat color:
- different base shades of chestnut.
- other modifying genes
- it has been theorized that the A allele at A locus is necessary for
the expression of ccr at C
- LIVER CHESTNUT WILL NOT BE DILUTED BY THE C LOCUS.
- the ccr allele, on a dark seal brown, will dilute the
phaeomelanin in the red hairs on the muzzle and flanks.
- the ccr 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 ccr 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
- ccr 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 + at and Cccr = Red Dun or Claybank
- this would be "palomino" w/ at causing dorsal stripe, dark points
|Palomino || __ __ Cccree
|Cremello || __ __ ccrccree
|Claybank||at_ __ Cccree
|Buckskin w/dorsal stripe||Aat__CccrE_
|Buckskin w/o dorsal stripe||A_ __CccrE
|Perlino w/dorsal stripe||Aat__ccrccrE_
|Dark seal brown |
|Light seal brown |
The D Locus
- The D locus controls the degree of hair shaft
- 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
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
Why black points is unknown.
|Grulla is traditionally|
considered to be a
dilution of black,
but may actually be a
dilution of seal brown
a grulla has the dorsal stripe
associated w/ at
- 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 at allele may be linked??
Combined Effects of ccr and D
- this would cause dorsal striping
- 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.
yellow mane and tail
|uniform blue grulla |
(dilution of jet black)
|uniform brown grulla||aabb__D_ED_
|blue grulla, black points|
|brown grulla w/dorsal stripe|
|light brown grulla|
w/ dark points and
a dorsal stripe
and dorsal stripe
|Buckskin/dun w/dark points and dorsal stripe||AatB_CccrddE_
|pale palomino||__ __CccrD_ee
|red dun w/dorsal stripe||at_ __CCD_ee|
The F Locus
FLAXEN MANE AND TAIL
- 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.
- ccr 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
The S Locus: SILVER DAPPLE
- 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
- 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