Equine Coat
Color Genetics
Lesson One
Introduction
to Horse Color Genetics
It is fairly common to hear comments in the horse industry like "Why should you care about colors?" and "A good horse is never a bad color," and so on. While it's true that color is a superficial characteristic of lesser importance than conformation, temperament, and ability, there are certainly many good horses to choose from and, all other things being equal, there is no reason not to choose, or breed for, a color that you prefer. Everyone has different color preferences in everything from the clothes we wear to the car we drive, and horses are no different. It's a nearly universal question from anyone who has a mare in foal - "What color baby will I get?"
There's
another reason that learning about colors is useful. Genetics can be a mysterious, confusing
branch of science. For the most part,
the inner workings of the
Basic Genetics
Before we start discussing specific coat colors, a refresher on basic genetics might be useful.
Inside
the nucleus of every cell are the chromosomes.
Chromosomes are made up of
When
cells divide for growth, a duplicate copy of every chromosome is made, and then the cell splits
into two, with exactly the same genetic material in each one. This is called mitosis. But when reproductive cells are being made
(eggs and sperm), the chromosomes are duplicated but then only one of each pair
goes into the new cell. This is called
meiosis. As a result, each egg and sperm
cell contains only one copy of each chromosome and therefore one copy of each
gene. Upon fertilization,
the single chromosomes find their corresponding mate and pair back up. The
resulting individual again has two genes at each location – one from each
parent.
An analogy
that helps to visualize this process is this:
Imagine you have a set of beaded bracelets. There are 23 on each arm (humans have 23
pairs of chromosomes). The ones on the
right came from your mom, and the ones on the left came from your dad. Bracelet #1 on the right and #1 on the left
have exactly the same number and size and shape of beads, but the colors might
be different. The same is true for
bracelet #2 on the right and #2 on the left; the beads match up as far as how
many, what sequence they are in, sizes and shapes, but the colors may or may
not be the same. And so on down the
line. A particular type of bead may come
in many different colors, but you can only have any two colors, since you have
only two bracelets. The bracelets
represent the chromosomes, the beads represent the genes, and the colors of the
beads represent the alleles. Now,
imagine taking them all off, shuffling them around for a bit, then lining them
all up again – the two #1s together, the two #2s together, and so on – and then
putting one of each pair on the arm of each of two children. Now picture your spouse doing the same thing,
mixing up the bracelets, and then putting one of each pair on each child. Now your children have 23 bracelets on each
arm, one set from each parent, but a completely new and unique mixture.
Gene Relationships
Genes and alleles interact in a few different ways. The most common is what is known as “simple dominant”. This is when there are two different alleles possible for the gene, and one is dominant, meaning that if it is present it will show, and the other one is recessive, meaning that it does not show if there is a dominant allele present; the recessive allele is only visible when there is no other kind present. In other words, it must be homozygous for the recessive allele in order for it to show. The dominant allele is represented by an upper-case letter, and the recessive allele by a lower-case letter. A classic example is the color grey. There are two possible alleles of the Grey gene. The dominant G causes the horse to turn grey, and the recessive g has no effect, causing the horse to be not-grey. With simple dominants, it does not matter whether the horse has one copy of the dominant allele (is heterozygous, or G/g in this case) or whether it has two copies of the dominant allele (is homozygous, or G/G in this case) – it will look the same either way. So, if you look at a horse and it is not grey, you know that it must be g/g since recessive alleles must be homozygous to be visible. But you cannot tell by looking at it whether a grey horse is G/G or G/g. When you have a horse that is homozygous for a simple dominant gene, you can guarantee that it will pass on that color every time.
Another way some alleles interact is called “incomplete dominant”. It is still a dominant gene, meaning only one copy is needed to be expressed, but in this case it means that there is a different expression when homozygous vs. heterozygous. A classic example is the Cream gene. The recessive allele cr has no effect, leaving the color unchanged. One copy of the dominant Cr causes red hair to be diluted to golden, causing palominos and buckskins. And two copies of the Cr dilutes the hair to a cream color, and makes the skin pink and the eyes blue. Before this was understood, people were frustrated that their palominos did not breed true. Now that it is understood, breeders know that all they need to do is breed chestnuts to cremellos and they will get a palomino every time. Some of the white spotting genes are also incomplete dominants, but the expression of these is complicated by the fact that there are other factors (mostly unknown at this time) that affect how much white a horse ends up with.
Another relationship is called “codominant”. This means that when heterozygous, both alleles are expressed equally. The typical example of this is blood types in people. There is a type A and a type B, and if someone gets one of each, they express both, and are type AB. There is no horse color gene with this kind of relationship known at this time, but it’s possible some may end up being that way.
Another kind of relationship is called “intermediate”. For example, in cattle, if you breed a red to a white you get a roan. There is nothing like this in horse colors, but it’s interesting nonetheless.
When there are more than two different kinds of alleles possible for a given locus, it gets confusing. In the past it was thought that there would be a clear “order” of dominance. For example, the Agouti gene has three known alleles (and likely more yet to be found). A causes bay, and is dominant over the others. a causes black, and is recessive to all the others. The third is called At and causes seal brown. For many years it had been assumed that A was clearly dominant over At which was clearly dominant over a. But now that a large number of horses have been tested, we find that horses that are At/At are on average lighter colored than horses that are At/a, although not enough that you could tell them apart visually. The numbers are not large enough yet, but it’s possible that horses that are A/A are on average lighter than horses that are A/a. However, it is difficult to pinpoint it, because bay and brown phenotypes overlap a good deal anyway, influenced by other genes such as shade, sooty, etc. At any rate, it’s not a clear simple dominant/recessive relationship, nor a clear incomplete dominant one.
All of the above relationships are referring to the interaction between different alleles of the same gene. The terms “dominant” and “recessive” are not used for interactions between different genes. When one gene hides the expression of another gene, the term used for that is “epistatic”. For example, grey horses will eventually turn white. They are still whatever color they would have been if they didn’t have a Grey gene, whatever color they were born as, but over time the grey color progresses until it hides whatever was underneath. So Grey is said to be epistatic to all other colors. Genes that cause white spotting are the same. Whatever parts are white, completely hide whatever color was there underneath.
When genes are linked:
Most of the genes affecting horse colors are scattered about on different chromosomes. This means that they are independently assorted. Let’s say you have a horse that is palomino, and also has a Dun gene (this combo is commonly called dunalino). He has a 50-50 chance of passing on each of those color genes. So, from nondilute mares he would be expected to have 25% nondilute foals, 25% Dun only, 25% Cream only, and 25% both Cream and Dun. However, there are a few genes that are located on the same chromosome, in close proximity to each other, so they tend to be passed on together the vast majority of the time. These genes are said to be “linked”. We will discuss these in more detail for those colors, but a common example is tobiano. The Tobiano gene is located right next to the Extension gene, so a horse that has T and E on one chromosome, and t and e on the other, will sire 50% black-based tobianos, and 50% red solids (from mares who don’t have either to contribute) rather than the 25/25/25/25 odds in the previous example. Comparing it to the bracelet analogy, it’s like Cr and D are on separate bracelets, so each child has an equal chance of getting either, or both, or none. But the E and the T are on the same bracelet, so there are only two options – both or none.
About those
gene abbreviations
You may see various different ways of writing gene symbols. If you have taken a general genetics class, you know that typically the abbreviation for the gene name is used, followed by the abbreviation for the allele in superscript. This method is common in human genetics because there are many more genes known, and each gene may have several alleles which might be labeled a, b, c, d, etc. But with horse color genes, that method has been dropped since the majority of them have only two possible alleles so they are simply one letter, with the dominant one capital and the recessive one lowercase. So it’s redundant and confusing to write both the gene name and the allele name every time. You may see it that way in some older books, but typically now just the abbreviation for the allele is used. Normally this is a single letter, but some have a two-letter abbreviation due to there being more than one color/gene starting with the same letter, or there being more than two possible alleles for a gene.
The various testing labs also have different ways of writing the results. Remember they are showing you the results of a specific test, not the genetic makeup of the horse. So for example if you test for grey, and the horse is heterozygous, you would write that in genetic terms as G/g; however the testing lab might write it as “G/N” meaning one G was found (the N for none found). Or if no grey gene was found, genetically that would be called g/g, but the lab might report it as “N/N”, meaning none found, or negative for that trait.
Predicting Gene Combinations - The
The
last concept to be mastered before we begin our discussion of the genetics of
specific coat colors is how to predict the possible gene combinations that
could occur from the mating of two horses. The
To
use the
(See following graphic.)
STEP 2
Across
the top, place each one of the genes contributed by the stallion into a
separate column.
For
this example, let’s assume the stallion is homozygous recessive for black
pigment, or “ee”
STEP 3
Down
the left side, place each one of the possible genes contributed by the mare
into a separate row.
Let’s
assume this mare is Heterozygous for black pigment, or “Ee”
STEP 4
To
create a mating, enter the gene notation from the top of the column into the
blank boxes in the table.
STEP 5
Now
add the gene notation at the left side of each row into each mating box.
The
resulting table, above, indicates the E/e gene combinations possible from the
mating of this stallion to this mare. In this example, foals from this cross have a
50% chance of getting the “Ee” combination (2 x 25%)
and a 50% chance of getting the “ee” combination (2 x
25%).
The
concept of a "cross", as in a particular stallion crossed with a
particular mare, is abbreviated "x".
Thus, the mating above would be abbreviated ee x Ee = 50% Ee, 50% ee
A
foal is considered to be by a stallion, and out of a mare. Thus, the foal resulting from the mating
above is by an ee stallion, and out of an Ee mare. One easy
way to remember how these terms are used is to keep in mind that the foal
literally comes out of the mare when it is born. (You may see people stating they have a foal
“out of” a particular stallion, but anyone who makes that mistake will quickly
be branded as the rankest sort of amateur.)
Summary: basic terms and definitions
Chromosome - shaped like
miniature strings, the chromosomes are in the nucleus of every cell, and
contain the
Gene - the section of
Locus - the location on the
chromosome for a specific gene. Every gene occupies a certain place on a
certain chromosome. You could think of
it as the gene's "address".
Allele - the different types
of expression of each gene. For instance, the Grey gene is at the G locus, and
there are two possible alleles there, called "G" (which causes grey)
and "g" (which has no effect, thus causing non-grey). All horses have two alleles for every gene,
one from each parent. Some genes have only two different possible alleles, but
some have more possible alleles, although each individual horse has only two of
them. The term "gene" is often used interchangeably with
"allele" in general use (i.e. "my horse has a grey gene").
Homozygous - means that both of the
alleles at a specific gene locus are the same, i.e. "G/G" or
"g/g".
Heterozygous - means that the
alleles at a specific gene locus are different, i.e. "G/g".
Expression - the effect that a
specific gene has on the horse's appearance.
("what does it do?" or "what will I see if my horse has
this gene?")
Dominant - means that if this
allele is present, it will be expressed, even if there is only one. There is usually no visual difference between
a horse with one copy of a particular dominant gene (heterozygous) and one with
two copies of the gene (homozygous).
Only one is needed; another one has no further effect. The dominant allele is abbreviated as an
upper-case letter.
Recessive - the opposite of
dominant, it means that this allele will only be expressed if there is no
dominant allele to "cover it up". For example, grey ("G")
is dominant over non-grey ("g").
If both alleles are present, the "G" will express itself and
the "g" will not. It takes two "g" alleles to express the
recessive, non-grey, color. The
recessive allele is abbreviated as a lower-case letter. It's important to remember that dominant and
recessive only refer to interactions between different alleles of the SAME gene
-- i.e., grey is dominant over non-grey, NOT grey is dominant over bay.
Incomplete Dominant - this term
doesn't mean the gene is "partly dominant" -- it is still a dominant
gene. It means that there is a different
appearance depending on whether the horse has one allele, or two. There are several horse color genes known to
be incomplete dominants at this time.
The Cream gene is a typical example -- a chestnut horse with one Cream
gene is a palomino, while a chestnut horse with two Cream genes is a cremello.
Mutation - when new cells are
being made, the chromosomes are duplicated so that there is an exact copy of
each one in the new cell. Sometimes
there is a mistake in the copying process, a "glitch" of some sort,
and a little bit of
Genotype - a word meaning the entire
genetic makeup of the horse; what genes are actually present, whether visible
or not.
Phenotype - a word meaning the
visible effects of the genetic makeup of the horse; only what you actually can
see.
Just what do we know about equine
colors?
Equine coat colors have often been a great cause of confusion. There are tremendous ranges of shades within a color, and various colors without recognized names, and regional terms for colors vary widely. Some of their methods of inheritance (especially of "shade") are not understood. Then there are colors which appear to the eye to be identical, but are caused by completely different genes/alleles.
Breed associations have contributed to the confusion. Registries use phenotype, or what the horse "looks like", when labeling colors, not caring about the genotype, or what the horse actually is, genetically. They recognize only a limited number of colors each, which vary from registry to registry, and sometimes change from year to year, and often have different definitions from one registry to another. It is generally not a good idea to take the horse's "registered-as" color as the final word on what color it truly is.
Color
genetics is one of those areas where new discoveries are happening all the
time.
There are many color genes that can be tested for now, with more being found all the time. Here are some labs that test for various color genes.
Color
Testing Resources:
UC Davis: http://www.vgl.ucdavis.edu/services/coatcolorhorse.php
Pet
Animal
Genetics: http://www.animalgenetics.us/Equine/Equine_Index.asp
VetGen: http://www.vetgen.com/equine.html
Equine Genome Mapping Project
The
Horse Genome Project is a collaborative effort by many research partners in
Scientists in recent years have been able to map the entire equine genome. More information on the Equine Genome Mapping project may be found at the University of Kentucky. The site is located here: http://www.uky.edu/Ag/Horsemap/welcome.html . If you are interested in exploring equine genetics in general, there is plenty of interesting information there.
(This class will not focus on the mapping project; however, references to findings will be noted.)
***A Word About Spelling
We understand that an emphasis on
correct spelling, grammar and punctuation is not as strong as it used to
be. Nevertheless, if you are going to be
discussing serious topics, such as science and genetics, you should expect that
if you misspell common words, people will naturally draw conclusions about your
level of education or intelligence. Go
ahead and write “CU L8R” when texting your friends, but take the time to use
proper English when writing about horse colors.
All the teachers, scientists and anyone over 40 in your audience will
thank you.
Don’t count on a spell-checker to
fix things. Conformation and
confirmation are both real words, but with very different meanings. Dominant and dominate are both real words,
but with very different meanings.
Lightning and lightening, sight and site, right and rite, and so on,
same thing. Spell-checkers won’t catch
these kind of mistakes. On the other
hand, one might expect a spell-checker to catch common misspellings that are
not real words, but judging by the frequency these are seen, apparently they do
not. Nite, lite and brite are not real
words. Shiney,
smokey, and scarey are not
real words. Creme
is not a word (in English). If you come
across a website about horse colors (or anything else) and the person is
consistently misspelling common words like smoky and cream, it’s very
reasonable to wonder what else is inaccurate there.