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Genetic Disorders - Part II

This is the fourth in a series of five articles aimed at providing knowledge and resources to horse breeders and buyers as well as discussing the thought processes involved in breeding horses. It is also the first of two articles on genetic disorders. The final article in the series will touch on the selection process and breeding theories.

HWAC acknowledges with appreciation the cooperation and funding by the North American Equine Ranching Information Council (NAERIC) to facilitate the series of articles “HORSE BREEDING REALITIES - REPRODUCTIVE MANAGEMENT” composed by Judy Wardrope, JW Equine.

Articles Series

  1. Breeding Realities Introduction

  2. Breeding Realities and Basic Genetics

  3. Genetic Disorders – Part I

  4. Genetic Disorders – Part II

  5. The Selection Process and Breeding Theories


This article will touch on some of the known genetic diseases, disorders and/or syndromes in horses. It will also suggest resources for further investigation. Naturally, other sources of information are available, especially through breed organizations and registries.

HYYP – hyperkalemic periodic paralysis (from “The most-common symptoms of HYPP include muscle tremors, weakness, muscle cramping, yawning, depression, an inability to relax the muscles, sweating, prolapse of the third eyelid, noisy breathing and/or abnormal sounds or whinnies.

“In 1996, AQHA designated HYPP a genetic defect and undesirable trait. Two years later, the Association added that all Impressive-descendent foals born after January 1, 1998, were required to be tested for the disease and parentage verified for registration, with the results placed on the registration certificate. Since 2007, any horses tested as H/H are not accepted for registration with AQHA.”

Impressive, a foal of 1969, became a dominant influence in halter horses in the Quarter Horse, Paint and Appaloosa breeds. It wasn’t until 1992 that this stallion was identified as the propagator of HYPP. Not all descendants of Impressive have HYPP, but all horses with HYPP descended from Impressive. A genetic test became available in 1994.

Further info on HYPP can be found here:

The AQHA has required a five panel test for all breeding stallions since 2015. The panel includes testing for GBED (glycogen branching enzyme deficiency), HERDA (hereditary equine regional dermal asthenia), HYPP (hyperkalemic periodic paralysis), MH (malignant hyperthermia) and PSSM (polysaccharide storage myopathy).

OLWFS - overo lethal white foal syndrome is also known as Lethal white syndrome (LWS), overo lethal white syndrome (OLWS) and lethal white overo (LWO). Affected foals are delivered looking normal and healthy. They are all white or nearly so and have blue eyes, but their colons do not function, meaning they colic within hours and will die within a few days if not euthanized.

SCID – from  “Severe Combined Immunodeficiency (SCID) is a lethal genetic disorder that results in an affected foal being born with a severely weakened immune system. SCID is caused by a mutation in the coding for the enzyme DNA-protein kinase catalytic subunit (DNA-PKcs) located on chromosome 9, which is responsible for the formation of key immune defense molecules. Because the foal’s natural defense system against infection is not functioning properly, by the time they are five months of age, they die of an opportunistic infection (such as pneumonia) or they are euthanized.

A reference list for additional information on SCID can be found at: It states, “SCID is known to be an autosomal recessive trait. ‘Autosomal’ means that there is no sex linkage, so both males and females can be equally affected. ‘Recessive’ means that in order for a foal to be affected, it must have received two copies of the mutated gene, inheriting one copy from each parent. Horses that have one copy of the mutated gene, in combination with one copy of the normal gene, are physically normal but are considered carriers and have a 50% probability, each time they are bred, of passing the mutation along to their offspring. Although the first veterinary publication on SCID appeared in 1973 and the mode of inheritance was determined in 1980, it wasn’t until 1997 that a direct DNA test became commercially available. The use of this test allows breeders to make informed breeding choices and avoid ever breeding an affected foal.”

Other Breed-related Diseases

The Connemara and the Warmblood have two entirely different diseases/syndromes and two entirely different issues concerning them. The Connemara has to contend with a small gene pool, while the warmblood gene pool is vast and horses often ‘migrate’ from registry to registry or are approved by several.

HWSD - Statement re Hoof Wall Separation Disease (HWSD) in Connemaras as shared by the registrar: “In an effort to reduce the number of foals affected by HWSD, the American Connemara Pony Society (ACPS) has adopted the following breeding policy: All breeding stallions must be tested with UC-Davis lab, and the test results reported to the ACPS Registrar. The foals of 2016 by untested stallions will not be registered until the foal is tested for HWSD.

“The ACPS also strongly supports the importance of testing all breeding mares prior to covering. The simple test will be a breeder’s best tool to avoid producing foals affected by the Hoof Wall disease. This policy will reduce the possibility of affected foals if the test results are used responsibly by both the stallion and mare owners.

“The subsequent edit of sentence 2 will be: The foals by untested stallions will not be registered until the foal is tested for HWSD.

“The policy in 2017 became – no foal will be registered until the HWSD [status] is known and recorded. If both parents are N/N, no testing will be done. If either parent is N/HWSD or a carrier, the foal must be tested. The results of the tests will be printed on each registration certificate.”

WFFS - Warmblood Fragile Foal Syndrome: According to Animal Genetics Inc., Warmblood Fragile Foal Syndrome (WFFS) is an autosomal recessive trait, meaning a foal can only be affected if that foal inherits the disease from both parents. Parents that are carriers do not have any symptoms associated with WFFS. However, they will pass on a copy of the defective gene 50% of the time whether bred to a carrier or a non-carrier and regardless of the foal’s gender. If two carriers are bred, the foal has a 25% chance of being affected (a death sentence if carried to term and a likely cause of aborted fetuses), a 50% chance of being a carrier and only a 25% chance of being clear of the defective gene.

In March of 2012, a mare that gave birth to a foal with all the symptoms currently associated with WFFS was at first thought to be a carrier for a different genetic disease, such as Hereditary Equine Regional Dermal Asthenia (HERDA, which was discovered in 2007). When she was found to not be a carrier, exploration of her and some of her relatives led to the identification of the genetic anomaly responsible for WFFS.

A genetic test for Warmblood Fragile Foal Syndrome Type 1 (WFFS), developed by N. Winand, became commercially available in 2013, but there wasn’t that much public talk about the syndrome until 2018.

Now most, if not all, of the warmblood registries have issued statements promoting testing. However, advice regarding choices based on test results is usually not given.

Additional Resources

Dr. Bailey, who is quoted in the previous articles, advises that there is a compendium: Online Mendelian Inheritance in Animals. “It is a database in Sydney, Australia that attempts to keep track of all single genes that have an effect on phenotype in all species. Horses are well represented there.”

Genetic Testing for Horses: What is available and when to use it is available as a pdf document.  Disorders, modes of inheritance as well as the estimated percentages of the population affected are included and the list of breeds is quite extensive, making it well worth the time to read.

This online article - - discusses some of the common genetic diseases from a breed-specific perspective and includes: GBED, HERDA, HYPP and MHS in stock horse breeds; JEB in Belgians and Saddlebreds; LWFS in Paint horses; PSSM1 in stock horse and draft breeds; SCID in Arabians; etc.

Another great article

The article found here includes: CA, JES, LFS and SCID in Arabians; FIS in Fell and Dales ponies; HERDA and HYPP in Quarter Horses; JEB in draft horses; OLWS in Paints; PSSM1 in Quarter Horses and Draft Horses; etc.

This particular article makes several excellent points worth including here: “Because the mass institution of equine chastity belts isn’t feasible, the best way to minimize the perpetuation of genetic disorders is testing. A wide range of tests is currently available and, as we’ve noted, some breed associations...demand proof of certain test results before you can register your horse. Such groups have demonstrated the benefits to this practice.

“’The goal is not to stop breeding carrier horses—and, thus, lose their gene pool—altogether,’ notes the World Arabian Horse Organization. Rather, testing can help breeders avoid crossing carriers with carriers while still retaining those bloodlines’ desirable pedigrees and associated traits.

“In 2013 British researchers highlighted the benefits of genetic testing when they reported that they had identified the genetic mutation responsible for foal immunodeficiency syndrome (FIS) and successfully reduced disease incidence. This disorder, not to be confused with SCID, occurs in Fell and Dales ponies and is caused by a fatal recessive mutation that results in the lack of B lymphocytes. Scientists subsequently developed a test that revealed 38% of tested Fell ponies and 18% of breeding Dales were FIS carriers. After testing and avoiding carrier-to-carrier breeding, the number of affected foals decreased dramatically in just two to three years.” Here’s part of the article’s very important take-home message: It behooves all horse owners to breed responsibly, research a horse’s genetic disease potential prior to purchase, and consider the importance of testing.

Partbreds, Crossbreds and Unregistered

Purebreds are not the only horses to consider when contemplating testing for genetic diseases. Numerous types of crossbreds are commonplace in the horse world: Thoroughbred/Arabian crosses, Quarter Horse/Paint crosses, Thoroughbred/Quarter Horse crosses, Arabian/Saddlebred crosses, Thoroughbred/Connemara crosses, Warmblood/Thoroughbred crosses, etc. And whether a registry offers part-bred papers or not, knowing the ancestry of all horses – even grade horses - is important when it comes to assessing genetic risk factors.


By all means do your own research. You might even want to look at what has happened in the past regarding both dominant and autosomal-recessive syndromes in horses. Pay particular attention to what has happened once a condition was identified, tests were made available, education was provided and the governing bodies either did or did not impose immediate and firm rules. See how many of those that were identified decades ago are still in the afflicted gene pools today. Consider whether the percentages are acceptable and whether best practices were applied.

If the registry or governing body does not have a stated policy regarding test results, it is up to the owners and breeders to decide how to precede once the test results are known. Accountability falls squarely on the shoulders of the people involved whenever a mating happens. Remember what Sir Robert Baker said: “A breeder is one who leaves the breed with more depth of quality than when he started. All others are but multipliers of the species.”

For information and opinion regarding the art of culling, please visit: and read the post entitled The Art of Culling.

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