Genetics Index

Horses come in a variety of colors and color mixes. How does this happen? What can this mean? Are certain colors prone to certain problems? Does it ever make a difference in breeding? Are certain colors more desirable than others? Do breeders breed for certain colors?


Mapping the Equine Genome

The Horse Genome Project made it much easier to breed for specific colors. There are horse coat colors and patterns can be traced back to red, black and bay. "Two genes control how these colors are expressed. The Extension (or E) locus gene determines whether black pigment will be expressed somewhere in the coat, and the Agouti (or A) locus gene defines where the black will be expressed. All bay and black horses have at least one copy of the E allele. And because the A gene determines the black's location, it's the determining factor of whether a horse is black all over or just has black points (legs, tail, mane). The chestnut color, on the other hand, is a recessive trait, so horses must have two alleles for it to show up (e/e). All other coat colors are variations on these three colors...." There are coat colr tests that can be done that cost $25.00 and up They must be done by a licensed lab.

The Mapping of the Equine Genome also has helped to avoid many of the serious health implications through the understanding of genetic information that flag hereditary diseases.


What is a mutation?

"A mutation is a permanent change in a gene's DNA sequence that occurs during cell division. Both a sire and dam can pass hereditary mutations to their offspring. In domestic animals such as horses, breeders have, over time, selected for coat color-related mutations because they produced unusual or desirable patterns. This has caused many mutations to eventually became fixed in the population...Prehistoric horses were primarily dark colors prior to domestication, as evidenced by genetic tests German researchers performed on ancient horse remains (Ludwig 2009). ..."

Now Penedo's specialty is the cream and pearl dilution-a mutation that dilutes a base coat color (which can be either black, bay, or chestnut) into a variety of different colors, such as cremello, buckskin, or perlino. And, like most equine geneticists, she also keeps a close eye on the mutations that cause white coat patterning or white spotting.

In many disciplines it's highly favorable (or, in the case of color breeds, required) to produce a horse with flashy white markings or spots. But, Penedo cautions, it's also risky. That's because the mutation that produces the white patches found in the main frame overo patterns (white patches centered in the body and neck and framed by colored areas) is the same mutation that produces the deadly overo lethal white syndrome (OLWS).

Heterozygosity (one copy of the mutated form of the gene and one normal copy) for the OLWS mutation produces an attractive white spotting pattern in breeds such as Paints, Quarter Horses, Thoroughbreds, and Tennessee Walking Horses-basically, a foal with striking markings born without incident. A horse that inherits two copies of the mutant gene, however, is born completely white and possesses the major developmental defects that define OLWS.

"These are major genes that are affected," says Penedo. "They're involved with cell development and the proliferation and migration of cells through embryonic development-they don't simply determine coat color."

More specifically, foals born with OLWS lack the ability to pass food through the gut and excrete waste, causing them to become impacted and die within a few days. Most are euthanized at birth. Because of the fatal consequences now definitively associated with breeding two overo-pattern horses, most owners of horses that clearly carry the overo gene test their stock before breeding.

Genetic testing remains important, however, for breeders of all colors with Paint or stock horse ancestry, because the American Paint Horse Association notes there are records of two apparently nonspotted parents producing frame overos. Testing has revealed that these horses are actually frame overos whose body color is so dark it overpowers any spots.

"Horses can appear a solid color with minimal white markings and can still carry the overo gene," Graves says. "And a lot of Paint horses have mixed patterns that may mask the more obvious markings of an overo."

On the flip side, Graves says, it is important to know the parents' genotypes before you assume a white foal is has OLWS. Not all pure-white foals are overo; healthy white foals might actually be sabino-patterned. While sabino is a subclass of overo, it doesn't carry the mutation responsible for OLWS.

Other Problem-Causing Colors

Overo lethal white syndrome is the only known fatal disease associated with a coat color gene mutation, but that doesn't mean other coat types don't also cause problems.

The same genes that cause Appaloosas' distinctive spotted coat pattern, the LP (leopard complex) mutation, can cause adverse effects in these horses. Appaloosas that have two copies of the dominant form of LP are commonly afflicted with congenital (present at birth) stationary night blindness (CSNB). This inherited disorder makes it difficult or even impossible for the horse to see in the dark. Many Appaloosa owners might not even realize their horse is affected but, if they do, they can make simple equine management changes to accommodate the problem.

The bigger issue, notes Penedo, is that breeders continue to produce primarily white Appaloosas, which are associated with the LP mutation. "Sure, you can change the way horses are handled and trained to accommodate for night blindness, but there are some consequences associated with it," she says.

A similar problem is associated with the silver gene: It produces a very attractive color dilution on black-based horses (such as the Rocky Mountain Horse's chocolatey coat and flaxen mane and tail), but two copies of the silver mutation gene result in multiple congenital ocular defects that impair vision.

"Take into account the function and marketability of your horse as a whole - because (when you breed) you may not get the color you want!"

Dr. Kathryn Graves

While these health effects are widely known (and tested for), many geneticists conjecture there are other white-spotted mutations that cause mares to resorb or abort fetuses. But because there's currently a limited field of genetic tests, it's nearly impossible to draw definitive conclusions. Coats of Many Colors (And a Few Surprises, Too)

The ability to define mutations and the genes associated with specific coat colors through relatively inexpensive genetic testing has greatly reduced the number of surprises born. In Graves' laboratory at the University of Kentucky, the most popular test is for tobiano spotting. Horses that are homozygous for tobiano will always produce spotted foals, regardless of their mate; this is desirable if you are breeding for spots. Other owners want to know what color they need to breed their horse to in order to achieve, say, a blue roan or a cream dilution color.

"There are a couple of tricky inheritance things that take people by surprise sometimes," Graves says. "For example, if you breed a palomino to a black horse, hoping to get palomino or buckskin, you need to know that black can mask the cream. Alternatively, you might have a black horse that throws palominos-and that can be quite a surprise!"

Similarly, breeding a bay to a chestnut can result in a jet-black horse, thanks to the way the two genes interact. Another variable color is gray, as horses are typically born dark, then get progressively lighter. Graves recalls a gray Quarter Horse stallion in Kentucky that sired quite a few palominos and buckskins, because his gray color masked the fact that he was actually a palomino. "People weren't too happy when he was throwing cream, as that wasn't nearly so desirable in the hunter-under-saddle classes they were breeding for," Graves says. "You need to get an idea of the colors that are in a horse's pedigree, because they may very well pop up."

Color preference certainly varies among the disciplines, but Penedo and Graves both emphasize the importance of breeding for healthy animals first, with priorities such as color falling second. They also caution that, while genetic testing has greatly improved the accuracy of color prediction, there is still an element of genetic variability (remember Thunderhead, sorrel Flicka's throwback white colt?).

"Even if you produce a horse that isn't a fancy color, consider what his value will be if he has good conformation, as compared to a flashy horse that has conformation problems," Graves says. "Take into account the function and marketability of your horse as a whole-because you may not get get the color you want!"

Seek the advice of a qualified veterinarian before proceeding with any diagnosis, treatment, or therapy.

For More Information:

How Your Horse Got His Color (And Why You Should Care)
Horse Color Information (Genetics)
Equine coat color genetics
Introduction to Coat Color Genetics
Horse Colors and Markings
Genome Sequence, Comparative Analysis, and Population Genetics of the Domestic Horse
Horse Color Breeding Charts
Genetic Problems in Horses
Molecular Tests for Coat Colours in Horses
Pinto or Paint?
Tobiano, Overo, Sabino, Tovero
First posted: June 12, 2018
Last update: Jan 21, 2020