Horse Genome Project


International Equine Genome Mapping Workshop
The 8th Dorothy Russell Havemeyer Foundation International Equine Genome Mapping Workshop took place near Newmarket, UK from July 22 to 25, 2009...[more]

Writers at the Louisville Courier Journal recently won the 2008 Media Eclipse Award for journalism based on an article about Thoroughbred racing and break-downs. They published a 3 part story, including genetics, track surfaces and medications. In connection with the genetics section they interviewed several members of the Horse Genome Project. See the accompanying links for the full stories on the 2008 Media Eclipse Award and the article itself.

Courier-Journal Web site wins award for horse project
Genetics may hold key to Injury-prone horses
[December 2008]

The first draft of the horse genome sequence was recently completed and deposited...
[JAVMA News, April 2007]

Data on Equine Genome Freely Available to Researchers Worldwide
[NIH News, February 2007]

The first genome map of a horse is complete, providing scientists with new tools for investigating equine disease. [ April 2006]



Hair Color has been a topic of fascination for horse owners and breeders since domestication of horses 6,000 years ago.  A horse with a color variation can be more attractive to horse buyers, consequently identifying those genes with economic value. Breeders want to know the likelihood that a horse with a particular color pattern will pass the trait to its offspring.  Sometimes this can be determined by accurately identifying the color and understanding its inheritance.  Sometimes this must be determined by newly developed molecular genetic tests for the genes. 

Chestnut and Black (E):
Early geneticists defined red or black hair color as a product of the “E” locus.  Black is dominant to red.    Horses with black hair may have two copies of the allele for black or they may be carriers of the red allele possessing one copy of each. Horses with chestnut color (red) inherited the gene for red from both parents.  In the 1990s, scientists in Sweden demonstrated that genetic differences in the MC1R gene are responsible for this base coat color in horses.  A molecular DNA test is available to tell if black horses are carriers of the red gene. 

Bay (A):
When black pigment is present a gene called agouti (also the “A” locus) determines whether the pigment is expressed throughout the body or only in the points (legs, tail, mane).  The gene for expression in the points is dominant.  French scientists used the gene map to determine the genetic basis of agouti.  A molecular DNA test is available to tell if bay horses are carriers of the gene for black occurring throughout the body.

Tobiano (TO):
The tobiano gene is responsible for the white patches that occur on the bodies of horses, almost always crossing the midline of the back.  The pattern is popular and found among a large number of horses registered in the Paint Horse Registry.  Tobiano is dominant. One copy of the gene is sufficient to create the pattern.  Usually, there is no difference between patterns on horses with one copy or two copies of the gene.  Since breeders would like to produce offspring with these attractive patterns, they would like to identify horses with two copies of the genes that would be true-breeding for the pattern.  Scientists in California noticed a pattern in which horses with tobiano almost always had the alleles B & S respectively for the Albumin and Gc loci.  They proposed using this test to help identify horses homozygous (two copies) for tobiano.  Recently, scientists in Kentucky identified the probably genetic basis for tobiano patterns and a molecular test has been developed to replace the BS homozygosity test.

Sabino1 (SB1):
Sabino is a white pattern which appears on the lower legs, the belly and produces a blaze on the face. This pattern is common in many breeds of horse and is also prized by breeders.  A University of Kentucky scientist studied DNA from Tennessee Walking horses and identified a genetic cause for sabino. She called this gene sabino1.   Sabino1 was dominant in that a single copy of the gene caused the distinctive white patterns. But two copies of the gene resulted in a horse that was born almost entirely white!  This gene occurs in many horse breeds. But there are similar sabino patterns that are not a result of this gene.  For example, Clydesdale horses are famous for their sabino markings but appear to have a different gene for sabino. (This is not surprising since white Clydesdales are not common.)  Clearly, there are probably several different genes that can cause sabino patterns.  A molecular DNA test is available for sabino1.

Overo (O):
Like tobiano, overo causes extensive white markings on horses and is well represented among horses in the Paint Horse Registry.  Unlike tobiano, overo patterns almost never cross the midline of the back and often look as if they are growing up from the belly.  Overo white patterns are caused by a dominant gene.  However, horses with two copies of the gene are born completely white but with multiple developmental defects resulting in death soon after birth.  (See OLWFS below).  The gene for this pattern was discovered during the same year by scientists from Minnesota, California and Australia. All three scientists recognized similarities between the action of the overo gene in horses and the gene causing Hirschsprung’s disease in humans. The mutation is in a different place in the gene but the effects are similar: white patches and developmental defects.   Horses with one copy of the gene are normal and highly sought by breeders because of their attractive patterns.  A molecular test has been developed to identify the gene. 

Dominant White (W):
The gene for this color is expressed at birth.  Horses are born white with pink skin.  Sometimes the white is not complete and horses will also have colored patches, especially around the ears.  Scientists in Switzerland determined the location of the gene for dominant white and are investigating the molecular genetic basis in Franches Montagnes horses. 

Grey (G):
When the grey gene is present, horses are born with colored hairs, but over time their hair color turns to white.  The process may take up to ten years but eventually the horse appears completely white.  The gene is dominant. Only one copy is needed and there is no known difference between horses with one or two copies of the gene.  Scientists from California, United Kingdom and Switzerland mapped the gene to horse chromosome 25.   Recently, scientists in Sweden identified the genetic basis for grey coat color in horses.  A molecular test may be available soon.

Cream Dilution (CR):
This gene causes a loss of pigment in cells expressing brown or red pigment.  A chestnut horse with the dilution gene becomes a palomino. A bay horse with the dilution gene becomes a buckskin.  The gene is dominant and only one copy is necessary for its effect.  Two copies will cause greater dilution and horses appear almost white.  Scientists in California mapped the gene and a molecular DNA test was subsequently developed by scientists in France.

Silver Dilution (Z):
The silver dilution gene only acts on black pigmented hair.  Horse with the dominant silver gene exhibit a dilution to gray for any black hairs. Scienstists in Sweden discovered the genetic basis for this trait and made a molecular DNA test. 

Appaloosa (LP): 
The Lakota or Nez Pierce Native Americans bred horses with distinctive white color patterns in the American Northwest Territory during the 1800s.  The patterns included white hips with dark spots, white body with dark spots throughout, partial or full roaning (white hairs interspersed with solid color hairs) and more.  In addition appaloosa horses possess characteristics defined as striped hooves, mottled muzzles and white sclera around the eye.  Observations suggested that a single gene determined whether or not the horse had the appaloosa characteristics and a color pattern, while other factors, possibly genes, determined the precise color pattern.  Scientists from Florida and Kentucky determined that the gene for appaloosa is on horse chromosome 1 but work continues to determine which gene is responsible.


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