Equine Coat Color Genetics
Lesson Two
Base Colors
The "base colors" of
chestnut, black, bay, and brown are the starting point for understanding color
inheritance. Why do we call them
"base colors"? Partly tradition
-- that's just the way it has been for a long time. And partly because they are the
"base", or what is underneath, every other color. It's important to understand that, for
instance, grey is not a color of its own, but rather a grey horse started out
as one of these colors and then had the grey gene added on top of that
"base color". Likewise,
buckskin is not a color of its own, but rather, is a bay horse with a Cream
gene added, making it diluted (lighter).
And so on.
Color in mammals is caused by a pigment
called melanin. In horses, melanin
appears in two forms, eumelanin (black) and phaeomelanin (red).
These two pigments are the source of every horse color. All of the many
shades and colors that can occur are caused by these two pigments, and the various
modifying genes that cause them to be lighter or darker or to have white added
in various ways. All horses can make red pigment (although it may be
modified or hidden), but only some horses can make black pigment. If a
horse has black pigment, that doesn't necessarily mean it will be black colored
-- various other genes can modify or restrict the black pigment.
To understand the base colors, it's
important to remember that they are caused by the interaction of two separate,
independent genes. For
whatever reason this concept is difficult for beginners sometimes. Once you get it, though, you'll be able to
answer questions like: "If chestnut is recessive to black,
and black is recessive to bay, then how did I get a bay foal from black x
chestnut parents?"
Two
Genes
The first gene is called the
"Extension" gene. (You don't
have to remember the name. In
horse-color lingo we just call it "E".) It was named that because the dominant
allele, E, "extends" the eumelanin
(black pigment). The recessive allele, e,
blocks the eumelanin (when homozygous – remember, a
recessive gene must be homozygous to show), leaving only phaeomelanin
(red pigment). If a horse has at least
one E, then it can make black pigment, and if both black and red are
present, then logically, we would only see the black, unless something is
restricting it in some way. So the horse
will look black. (The red tones will
often become visible when the horse gets sunbleached,
though.) Horses with at least one E allele are called “black-based”
colors, because they have black pigment.
Therefore, e/e would give a red (chestnut/sorrel) horse, E/E
would give a black-based horse which cannot produce a chestnut foal, and E/e
would give a black-based horse that can produce a chestnut foal.
The second gene is called the
"Agouti" gene. (Again, no need to remember the name if you don't want to. Just remember "A".) It was named that because it was thought to
be similar to the color of a South American rodent of the same name. The term was used in mouse color genetics to
refer to a gene that controls the distribution of eumelanin,
and apparently the name carried over to the horse gene as well; although we now
know they are not really the same, it does have the same purpose -- it controls
the distribution of the black pigment.
One very important thing to remember is that since this gene only
affects black pigment, it will do absolutely nothing to a red (e/e)
horse, since they have no black to be affected.
Yet the red horse still has two Agouti genes just like every other
horse; although you can't see which genes they have, they will be passed on
just like any other gene.
The Agouti locus is somewhat unusual
in that, unlike most horse color genes, which only have two possible alleles,
for example E and e, or G and g, this one has at least three and quite likely
four or more different possible alleles.
Each horse can still only have two, of course, one from each parent. But there are more possible
combinations. Over the years there has
been plenty of speculation about the workings of the Agouti genes. But nowadays the actual gene locus has been
identified, and there are tests for two of the alleles. In addition we have many decades of
observation and breeding records, so that the actions of at least three of the
alleles are reasonably well understood.
They are:
A, which is dominant,
causes the black pigment to be restricted to the horse's points (mane, tail,
legs, eartips), leaving the rest of the body red,
therefore making the horse bay. This is
the most common horse color in many breeds.
a,
which is recessive, does not restrict the eumelanin
in any way, but allows it to be fully expressed all over the horse's body,
therefore making the horse black. It is
more common in some breeds and less common in others.
At,
which is dominant to a but recessive to A,
restricts the black pigment only slightly, leaving the horse mostly black but
with tan or red areas at the muzzle, flanks, and underbelly, therefore making the
horse seal brown.
There
is also a variation of bay called "wild bay" which is lighter, with
very little black on the legs. It has
been theorized to be caused by an Agouti allele called A+, thought to be dominant over all the other alleles at the A locus. However it has not been found yet at this
time, and if the A+ allele is
dominant over all the others as is theorized, then one should never occur from
two regular bay parents, and this result has been reported. More research is needed to determine whether
“
So, the combined action of
these two genes, the "E" and "A" locuses,
give us the four base colors as follows:
Chestnut (called
Sorrel in some breeds)
e/e,
with any two Agouti genes (which are not visible)
The whole horse will be some shade
of red, which can range from very light to very dark. The mane and tail are often the same color
as the body, but may be darker or lighter.
If they are much lighter, a blonde shade, it’s called flaxen.
How to Breed for the Color Chestnut (or Sorrel)
If chestnut
is your favorite color, you're in luck:
it is the easiest to produce. Red
parents only produce red foals.
Because all red horses are homozygous for the recessive allele (e/e),
one truism in breeding horses is red x red = red.
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e |
e |
|
e |
ee |
ee |
|
e |
ee |
ee |
Chestnuts can also be produced
from two heterozygous black-based horses (E/e)
about 25% of the time.
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E |
e |
|
E |
EE |
Ee |
|
e |
Ee |
ee |
Chestnut/sorrel
(red) is a valuable color when trying to breed other colors based on the red
color.
Palominos, cremellos, gold champagnes, red roans and red duns are all
built upon the basic red color.
It is
possible to test for the presence of the recessive e gene. While this has little
value for breeders of red horses, it does help breeders of black-based horses
to determine whether their horses are homozygous or heterozygous for the
dominant E
gene. This is referred to as a “red-factor” test.
Chestnut foal color
Foals are generally much lighter
at birth than their adult color.
Chestnut foals are usually a light red at first, but they can change
drastically when the foal-coat sheds out.
Red and red-based (palomino, red dun, red roan, etc.) foals usually have
pinkish skin at birth, which darkens up quickly. Foals of all colors are usually born with
very light legs. This makes it difficult to tell whether there are white
markings on the legs. Although you may
not be able to tell until they shed off, the hoof color does provide a
clue. The hoof of newborn red horses is
grayish in color where the leg is going to shed off red. Where the leg is going to shed off white the
hoof will be cream or white. This does
create a change in the color of hoof, but may be difficult to see.
This foal was light at 6 weeks
old: 
And shed out much darker by 4
months old: 
These are more typical after-shedding foal shades: 
Black
E/E or E/e, and a/a
The horse is black all over,
including the muzzle, flanks and underbelly.
However, blacks are notorious for fading when exposed to the sun, so
depending on the time of year, they may appear quite reddish or even yellowish,
and may only look really black for a few weeks after shedding out. The mane and tail may get quite reddish from
sun exposure, especially at the tips.
It's not known at this time why most blacks fade but some do not, and
it's not known whether there is a genetic basis for that, but in any case, if
there is, it has nothing to do with the E and A genes.
The “a” allele contains a deletion in
the gene that renders the Agouti non-functional. Therefore, instead of being restricted to the
points, the black pigment is free to cover the entire body. The mutation causing the “a” allele has been isolated and
there is a test for it. This is of
little use for an obviously black horse, but is helpful in many other cases
such as where sunbleaching has raised doubts about
whether the horse is truly black, or in cases where a breeder would want to
know whether a bay horse is carrying a copy of “a”, or for a chestnut whose Agouti status is not visible, or a grey
or dilute whose base color is uncertain.
How
to Breed for the Color
The best
way to produce black horses is to breed two homozygous black horses. Two
homozygous blacks (E/E, a/a) will produce homozygous black
foals 100% of the time.
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E, a |
E, a |
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E, a |
EEaa |
EEaa |
|
E, a |
EEaa |
EEaa |
A
homozygous black (E/E, a/a) bred to a heterozygous black (E/e, a/a)
will also produce 100% black foals because the homozygous black will pass a
black (E) gene 100% of the time.
50% of the offspring will be heterozygous, and 50% will be homozygous.
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E, a |
E, a |
|
E, a |
EEaa |
EEaa |
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e, a |
Eeaa |
Eeaa |
However, the best two heterozygous black (E/e, a/a)
horses can do is to produce 75% black foals.
The remaining 25% will be chestnut.
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E, a |
e, a |
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E, a |
EEaa |
Eeaa |
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e, a |
Eeaa |
eeaa |
Black foal color
Black foals are usually not born
black, but rather a pewter-grey color, turning black when the foal coat sheds
out around 3-6 months old. The foal coat
can get surprisingly light before it sheds out.
Many breeders have been fooled into thinking they had a grulla foal by a black baby coat. Some black foals are jet black right from
birth, though. No one knows why. The black-at-birth ones are not the same ones
that do not sunbleach later in life.
This one was born black: 
This one is a more typical black
foal color: 
This one is at maximum fading
right before shedding out: 
(Hard as it may be to believe
that is a black, here is the same horse as a 2 year old) : 
Bay
E/E
or E/e, and at least one A
The bay's body color will be some shade
of red or reddish-brown, ranging from light golden-red “sandy bay” to very dark
“mahogany bay”; the points (mane, tail, legs, eartips)
are black. A very dark sooty bay can
look like a seal brown; only genetic testing can tell them apart.
This mare is a sooty bay who varies tremendously from season to season, looking brown
sometimes and bay other times. She is
not seal brown (per testing and foal colors). These pictures are all the same
horse.
The next picture is of a bay horse that
has a large amount of flaxen in his tail.
This occurs on occasion. It
usually disappears with age, but may persist throughout the horse’s life. His legs are almost as red as a “
How to Breed for the Color
If one parent is homozygous for
black (E/E) and for the bay Agouti (A/A), then all foals will be bay. The only thing such a horse can pass on is E and A, and it only takes one of each to cause the bay color. Even if bred to a chestnut with only black
agouti (e/e, a/a) the results still
give all bays, although they will all be heterozygous.
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E, A |
E, A |
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e, a |
EeAa |
EeAa |
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e, a |
EeAa |
EeAa |
Normally with a dominant gene, you
need at least one parent with the color to get a foal with that color. However, because of the two-gene interaction
that causes the bay color, a chestnut x black cross can produce bay under the
right circumstances.
In this example, a chestnut mare (e/e) carrying one A
gene (A/a) has been bred to a
homozygous black (E/E, a/a). This
cross produces a 50% chance of a bay and a 50% chance of a black.
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E, a |
E, a |
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e, A |
EeAa |
EeAa |
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e, a |
Eeaa |
Eeaa |
Bay foal color
Like most
colors, bays are typically much lighter at birth than their adult color. Sometimes they can be mistaken for a
chestnut. The legs especially tend to be
light, but there is usually at least some black in the mane and tail. They also have dark skin right from birth,
unlike chestnut foals which usually have pinkish skin at birth (this may,
however, be a very subtle difference).
These are
fairly typical bay foals. The legs are
not black yet, but the body color is about the same as the dam. Mane and tail are black.
This is an extra-light bay
foal. The second picture is of the same
foal, on the right, with a chestnut foal on the left, showing the difference in
color tone.
Seal Brown
E/E
or E/e; and At/At or At/a
Also called just "brown",
or "black-bay" in some breeds; it is also called "black and
tan" in some countries. The horse will be mostly black, with reddish or
tan highlights in specific areas, often called the “soft spots”: typically the muzzle, flanks, underbelly, and
girth areas. The darkest shades of seal brown are nearly all black except for a
little tan at the muzzle and flank, while the lighter ones have more extensive
lighter areas. These are often strongly
dappled in the summer coat. A very sooty
bay can look just like a seal brown.
The “At” allele contains a mutation that makes the Agouti gene less
effective. It isn’t totally
non-functional, as the “a”
allele is, but the black pigment is not nearly as restricted as it would be
with the “A” allele. The black pigment is restricted only a
little, so the red is visible in just a few spots. The “At”
mutation has been found, and there is a test for it. It’s at a different place on the Agouti gene
than the “a” mutation, so they are
two separate tests.
One interesting finding that has
come out of several years of testing is that the “classic Seal Brown phenotype”
– black with tan muzzle and flanks – almost always tests E/E, At/a. Some studies have
shown a general tendency for bay horses to be darker in shade when they are E/E, as opposed to E/e. The seal browns that
are lighter, that could (visually) just as easily be sooty bay, almost always
test At/At. This raises some interesting questions. Perhaps it’s not as cut-and-dried as was
thought previously, i.e. that there is a strict heirarchy
of dominance from A to At to a.
Considering the function of the Agouti gene (to restrict black pigment
to the points), it makes sense that a partially impaired allele would work a
little better when there are two copies of it, and a little worse when there is
just one copy combined with a totally nonfunctional allele. Combined with the often-darker-shade of E/E, and we get a much more gradual
range of shades than simply “bay or brown”.
Over time, more and better testing will tease out the details of whether
there really is a genetic difference in shades, or if it is pure coincidence.
How to Breed for the Color
Breeders
for many decades have observed that Brown x Brown will produce brown and black,
but not bay. Plenty of classic seal brown
(phenotype) horses have had chestnut foals, proving they are E/e, but statistics do seem to indicate
that the color is more likely to be associated with E/E. If you really want to
be guaranteed a seal brown foal, find parents that are both E/E, and one is tested to be At/At, and the other a/a.
This should guarantee you the desired outcome.
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E, At |
E, At |
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E, a |
EEAta |
EEAta |
|
E, a |
EEAta |
EEAta |
Seal Brown foal color
Seal Brown foals are, like other colors,
typically lighter at first. Generally
they look like a bay foal, but often somewhat darker. Often the legs will already be black, or more
so than a bay foal. A dark “cape” of
black hairs over the shoulders is common.
Many times it is not possible to tell bay and brown foals apart, though.
This
one is fairly typical: 
The
above foal is darker than most at this age.
This
foal, newborn color: 
shed out at 3 months old to this: 
Modifiers
At this point
you are probably thinking, OK, so there are only four genetically separate base
colors….. that
doesn’t explain the huge variety of colors that we see.
There are
additional factors which are called “Modifiers” as a general category. These modifiers alter the visual appearance
of the colors. Some of the variation in
color is environmental -- some colors are commonly lighter in winter coat and
darker in summer coat, and the sun does unpleasant things to most black
hair. Some is nutritional – there are
cases of malnourished horses turning a much different shade when properly
fed. And some is likely genetic, but the
genetic mechanism of all of the following modifiers is unknown at this time. That’s why we call them “modifiers” instead
of “genes”.
These
categories do overlap to some degree.
For example, most horses that are a very dark shade usually have some
degree of sooty as well, and most horses that are an extremely light shade
probably have some pangare as well. Sooty often causes dapples.
Shade: This describes variations within
a basic color group resulting in light to dark color variations.
On a
chestnut, this can result in colors from light peachy red (looking like a red dun
or almost palomino) to dark liver, almost purple, or nearly black.
Keep in mind that both of the
above horses are genetically red (e/e). If you were to test these horses they would
test identically for the red gene (e/e).
On a bay, this can result in
colors from light golden-red or tan (looking almost buckskin), to deep dark red
bodied (often called “mahogany bay”).
On a seal
brown, this can result in colors from jet black with a little tan on the side of
the muzzle, to dark bay looking.
On a black,
we typically don’t expect to see variations in shade, but some horses are just
“light black” even though testing negative for all known dilutions. Some blacks sunbleach
out much faster than others. These differences
may be caused by shade.
Sooty: This refers to the presence of black hairs which appear
“overlaid” on the regular body color. Most often this is noticeable across the
back, shoulder and croup, with the lower body appearing lighter. Some extremely sooty horses appear nearly
black.
This mare was thought to be seal
brown, until testing was available, but is actually a very dark, very sooty,
bay. (In addition to testing negative
for “At”, she later also proved she
was bay by producing bay and buckskin foals by sires who
had no “A” allele to contribute.)
Sooty would
naturally not be expected to be visible on black or seal brown horses, since
they already have black hairs in those areas.
When sooty is quite extensive, it can make bay look like
brown, chestnut look like black, and palomino look like silver dapple.
There is some debate about whether sooty actually adds black
hairs to chestnuts and palominos, which are e/e and “should not” be able to produce black pigment. There are basically two theories; one is that
whatever the sooty gene is, it actually does “override” the e, and allows black pigment to be
produced; the other is that sooty hairs on e/e
horses, no matter how black they look to our eyes, are really very dark
red. One piece of evidence that strongly
suggests the first theory is correct, is the way sooty acts on
single-cream-dilute (palomino and buckskin) horses. Since the Cream gene when heterozygous does
not affect black pigment, only red, and since sooty buckskins and palominos
have what looks to be black hairs on their bodies (a strong contrast against
the diluted-to-yellow red hairs), it suggests those hairs are indeed
black. By comparison, other types of dilutes
such as Dun and Champagne do not look sooty, and this is likely because if they
do have the sooty gene, the black hairs would be diluted right along with the
red ones, so there would be little contrast.
The term
“smutty” was also used in the past, to mean sooty. However with the meaning of that word
changing over time, from “dirty” as in dirt, to “dirty” as in obscene, the term
has been dropped from color descriptions for the most part. You may see it used in older literature.
Countershading: This term is used by some to mean the same thing as Sooty,
but some consider it something different.
Sometimes it is used to mean the typical shading of foal coats, where
they are darker over the top and lighter on the underparts. Non-Dun dorsal stripes are commonly called countershading.
Mealy or Pangare:
This causes
pale areas on the lower belly, in the flank area, behind the elbows, inside the
legs, on the lower legs, on the muzzle and over the eyes. This modification can
occur on any base color and the effect varies from minimal, very subtle and
easily missed, to extensive, causing dramatic paleness to the body. In the
American Southwest, it is often referred to as “muley",
after a mule's coloration. It is more
common in draft and pony breeds. It’s
also very common for foals of all breeds to have lots of pangare
and then outgrow it as they mature.
chestnut Belgian showing mealy/pangare
Dapples: Dapples are round spots of a different shade (usually
lighter). They may be actual different
colored hairs, or a slight difference in shade or reflectivity that is only
visible from certain angles. Dapples are
common during shedding, and may occur during one season but not another (either
summer or winter coat). Some colors are
known for being dappled quite often, i.e. grey, but dapples can occur on any
color. The type that come and go are
likely caused by environmental factors, but the kind that persist year round
seem to have a genetic basis, as they often run in families (it may be that
they are an expression of sooty, however).
This is a black horse that is sunbleached, revealing faint dapples.
Typical dapples on a palomino.
These are called “reverse
dapples”, darker spots instead of lighter ones, on a
champagne.