Equine Coat Color Genetics
Lesson Nine
The Appaloosa
Like the terms
“Paint” and “Pinto”, “Appaloosa” refers to both a breed and a color. Like those terms, when capitalized it means a
horse of that breed, and when not, it means the color. Just as the terms “paint” and (more commonly)
“pinto” are used to refer to horses of any breed with white body spotting, so
has the term “appaloosa” been used to refer to that pattern, regardless of
breed. In Europe it is usually called
“spotted”. Although the Appaloosa breed
gave its name to the color, it is far from the only breed in which the pattern
occurs. Spotted horses have been found
in Chinese art dating back as far as 500 BC. By the 1300s they were
common in Spain and by the early 1800s their presence was well established on
the North American continent as the horse of the Nez Perce Indians. Tribal legend of the Nez Perce indicate that
the first '"spotted horses" arrived aboard a Russian ship in the
early 1700s. The horses were traded to Indians in the northwest who in turn traded them to the Nez Perce. Other stories credit Cortez and the early
Spanish explorers with the infusion of the Appaloosa into the Americas in the
early 15th century.
The breed
registry for the Appaloosa horse is the Appaloosa Horse Club (ApHC)
http://www.appaloosa.com/
This registry
has standardized names for the various types of appaloosa patterning and
characteristics, as the Paint and Pinto registries did with pattern names like tobiano, overo, and so on.
As with the pinto spotting patterns, the size of the white areas is
independent of the actual pattern gene, so can vary from large to small.
A group of
researchers and Appaloosa breeders formed a project to identify and map the
Appaloosa genetics. You can read more on
The Appaloosa Project at: https://www.appaloosaproject.co/
Appaloosa Characteristics
Just as the Dun
gene causes a set of specific “dun-factor” markings, and the Champagne gene
causes a unique skin color, the appaloosa color comes with some special characteristics
of its own, in addition to any colorful pattern the horse may carry (or
not). These characteristics are varnish
roan, mottled skin, white sclera, and striped hooves. Another characteristic which is quite common
but not universal is a short, sparse mane and tail (in the Appaloosa breed this
is often called a “rat tail” and is considered a sign of “old blood” or
“foundation” type); this trait is one that most breeders have been trying to eliminate,
with some success, so it apparently is not caused by the actual appaloosa color
genes.
Mottled Skin
This
characteristic is unique to the appaloosa color, and is visible wherever there
is bare skin - on
the face, udder or sheath, and under the tail.
It can vary from horse to horse, and can also increase over time, but
there should be at least some mottling present.
Not to be confused with the speckled champagne skin, which is pinkish
with tiny dark spots that look like they were dabbed on with a brown or black
felt-tip marker, the appaloosa mottling looks like pink spots on a dark
base.
White Sclera
The sclera is
the white part of the eye which encircles the iris (the colored portion). The
white sclera of the human eye is visible all the time, but horses typically do
not have much white sclera visible unless they are looking forward or back. The appaloosa's is more readily visible at all
times. While the visible white sclera is
considered an appaloosa trait, by itself it is not sufficient to prove a horse
is appaloosa, because it can occur randomly on other colors and breeds,
especially if there is a large amount of white on the face.
Striped Hooves
Bold
and clearly defined vertical stripes on the hooves of the dark legs, either
dark with tan stripes, or tan with dark stripes, is an appaloosa trait. If the horse happens to
have white markings on its legs (unrelated to its appaloosa color), those
hooves won’t be striped. Striped
hooves alone are not proof of appaloosa color, because other things can cause
them. Some Cream dilutes have vertical
stripes on their hooves, but this is much more subtle. Silver dapples can have very bold, distinct
stripes, especially when young. When
horses with white leg markings have ermine spots in them,
that can create a stripe below each spot. For comparison, here are some examples of
non-appaloosa hoof striping.
palomino striped
hoof silver dapple striped hoof ermine spots with stripes
Varnish roan or
“appy roan”
Appaloosas
have a specific type of roaning which is different
from the true roan and other types of roan that we discussed earlier. This roaning is
typically called Varnish Roan. Appaloosa
roaning is somewhat like grey in that it is
progressive over time (although the horse won’t go completely white as a grey
would). They start out dark, like a
grey, and the roaning increases from year to
year. Like grey, it may be obvious at
the first shedding, or they may stay dark for several years, but eventually it
will occur. Although the appearance can
be mistaken for other types of roan, or even grey, there are differences. The lightest area tends to be over the hips
(which may or may not be spotted), and the roaning is
not as uniform as other types of roan.
There are darker areas where the bones are closer to the skin, such as the
point of hip and elbow, stifle, lower legs, the frontal bones of the face and
above the eye. The ears are also usually
dark. These areas may stay dark all the
horse’s life.
Varnish
roan
Appaloosa Patterns
In
addition to the above general appaloosa characteristics, appaloosas usually
have some sort of pattern. Some don’t,
and are “only” varnish roan, but the patterning is highly desirable and
breeders strive to produce them.
Just
as the Paint and Pinto registries standardized pattern terms such as Tobiano and Overo, Appaloosas have their own pattern terms
as well. (In other breeds where these
patterns occur, they may or may not use the same terminology, but for the most
part they have been pretty universally adopted.) White patterning that covers all or almost
all of the body is called Leopard, while white patterning that covers the
hindquarters is called Blanket. The
white areas can contain spots, or not (more on that later). A leopard without spots is called a
“few-spot” and a blanket without spots is called a “snowcap”.
Leopard
is used when the horse is 60% or more white.
It’s not uncommon for them to retain a good deal of dark color on the
head and legs. If the white patterning
extends up onto the neck and shoulder, but doesn’t cover them entirely, this is
commonly called a “near-leopard” or “suppressed leopard”.
Leopard Near-leopard
“Few-spot”
leopard Few-spot
Blanket is used for a white marking
that does not go farther forward than the withers. They can be just a small area on the top of
the hips, or extend all the way down under the belly. The Appaloosa registry has five
classifications of blankets depending on how much of the body they cover.
Small blanket Larger blanket
Snowcap
Snowcap
Another pattern is called
Snowflake. This is not actually white
patterning, and it’s not known what exactly causes it; most likely it’s a stage
that some varnish roans go through, but that is not known for certain yet. This is when there are many white spots on a
dark background.
Snowflake Snowflake
How it works
The Appaloosa coloring is a bit
more complex than any others so far. The
reason for this is because it’s not just one gene. Think back to when we looked at the base
colors, and remember how it takes a combination of two separate genes to get a
bay – at least one “E” so that it can make black pigment, and then at least one
“A” so the black is restricted to the points, instead of covering the whole
body. Recall how a red horse might have
any of the different genes at the Agouti locus, but because there’s no black
pigment for it to act on, there’s no visible effect. The appaloosa colors are similar to
that.
The first gene is called “LP” for
Leopard Complex. It was named long ago,
before much was known about genetics, and is actually a slight misnomer now –
this is the gene that gives the appaloosa characteristics listed above – the
mottled skin, visible sclera, striped hooves, and varnish roan. It does not actually cause
the pattern labeled Leopard. LP is the
basic appaloosa gene, without which a horse would not be any of the appaloosa
colors, but additional genes are needed to get the white patterning. Without those pattern genes, the horse will
be “just” a varnish roan with appaloosa characteristics. The LP gene is another incomplete
dominant. This should be a familiar term
by now. When heterozygous, any white patterning
on the horse will contain dark (base color) spots that do not roan out over
time as the varnish roan progresses (these would be the leopards and
blankets). When homozygous, the white
areas will have no spots or only a few little ones (these would be the fewspots and snowcaps).
Some experts also state that the heterozygous ones have dark hooves with
light stripes, while the homozygous ones have light hooves with dark stripes
(on legs without any white markings, of course).
When homozygous, the LP gene also
causes night blindness (full name: Congenital Stationary Night Blindness). Most horses see much better
in the dark than humans, but horses with night blindness see very little in the
dark. Surprisingly, they seem to cope
with this very well, as with the Splash pintos that are deaf. It took a long time for us humans to realize
that these horses were deaf, or night-blind, as the case may be. This condition is in place from birth and
does not change throughout their lives.
It is commonly believed that
appaloosas in general tend to be more prone to uveitis, another eye condition,
but there is no solid evidence linking it to the appaloosa genes. Most experts think it’s caused by some sort
of virus, but it’s not known why appaloosas would be more susceptible.
The LP gene is located on
chromosome 1, and was isolated in 2013.
There is now a test for it.
But in addition to LP, an entirely
different, separate gene is needed to get the white patterning. So far only one has been isolated, in 2015. It’s located on chromosome 3, and was named
PATN1. It is a simple dominant. PATN1 causes the leopard/fewspot
pattern, defined as 60-100% white. Like
the various pinto-spotting genes, there are undoubtedly other factors that
influence the amount of white. Usually
leopards are white all over the body, with some dark on the head and legs. But some have mixed or even dark areas
extending back from the head, even including the whole neck and chest
sometimes. These are commonly called
“semi-leopard” or “suppressed leopard”.
In the past it could be hard to tell for sure whether a horse was a
semi-leopard or an extended-blanket pattern, but now that there is a test for
the PATN1 gene, this can be determined.
A horse that has one or two PATN1 genes, and one LP gene, will be a
leopard appaloosa: white covering all or
most of the body, with dark (base color) spots scattered throughout. The spots are often larger and more numerous
over the hindquarters. A horse that has
one or two PATN1 genes, and two LP genes, will be a few-spot appaloosa: white covering all or most of the body, with
no (or a very few small) spots. A horse
that is homozygous for both, LP/LP + PATN1/PATN1 will, when bred to solid
mates, produce 100% leopard patterned offspring.
When the research into the pattern
genes was underway, it was hoped that there would be a second gene (which would
be named PATN2) that causes the blanket pattern. Unfortunately, no such gene has been found. The researchers now believe that the blanket
patterns are probably caused by many pattern genes, each of which has a small
effect, so that a horse with a very small blanket might have just one of these
genes, while a horse with an extensive blanket would have several of these
genes. And such a horse could pass on
none, or some, or all of them, so that its offspring would range from no
blanket, through various sizes of blankets, to ones that looked the parent,
with smaller numbers at each extreme.
This does appear to be the way they produce. But these pattern genes have not been
identified yet. It may be that some of
the white-spotting (“W”) genes in the KIT complex can affect appaloosa patterns
as well.
There
is a nice article on the Appaloosa Project website which has illustrated
Punnett Square examples demonstrating the odds of various results when breeding
Appaloosas, here:
The interesting thing about this “two-genes-needed”
inheritance of the appaloosa color, is that horses can
carry the various pattern genes without showing any outward sign of it, if they
don’t have at least one LP gene. We have
seen similar situations before; for instance a red-based horse can carry a
Silver gene without showing it, even though it’s dominant, because Silver only
affects black pigment and the red horse has none. And as previously mentioned,
a red-based horse does not show which genes it carries at the Agouti locus,
since they too only affect black pigment.
It is completely unknown what percentage of solid-colored horses in
breeds that once came in appaloosa colors but no longer do,
or which go back to “unknowns” fairly recently, could possibly be
carrying PATN1 and whatever other patterning genes that cause the blanket
pattern. It explains how the rare
“crop-out” appaloosa can appear in breeds that were thought not to have those
colors, such as the Quarter Horse and Tennessee Walking Horse. One parent carried the pattern gene, unseen
for generations, and the other parent had the LP gene although misidentified as
a regular roan, or thought to be grey, or even covered up by an actual grey or
roan color. The foal gets both, and -
surprise – an appaloosa baby.
As mentioned at the beginning, the
appaloosa coloring is very old. It
appears to have been popular at various times in history, and then fallen out
of favor at other times. While it would
be easy enough for a breed to eliminate LP because it’s visible (especially if
that breed didn’t have any roans or greys for it to be mistaken for), the PATN
genes would not be as easy to remove from the gene pool, since they are invisble without LP.
It would be a fascinating project to test a large number of solid
colored horses from breeds which once had the coloring, or ties to breeds that
did, and see if any are carrying PATN1.