Genetic Testing

The HHSA offers a very convenient way for members to do genetic tests on their HHSA registered horses through the lab. Horse owners do not need to collect any further samples to have these tests done unless on rare occasion the lab has an insufficient sample to complete the tests. The tests can be done with the DNA already on file from registration.

The following tests are most common, but others can also be done on request.

Please see the form below for pricing information and to organise the tests. Further detail on the tests available are below.

FFS1 (Fragile Foal Syndrome Type 1)

Fragile Foal Syndrome type 1 (FFS1) is a genetic connective tissue disorder caused by a mutation in the PLOD1 gene. It is inherited in an autosomal recessive pattern, meaning a foal must inherit two copies of the mutated gene (one from each parent) to be affected. This is why it is very important to test your mare if you are looking at using a stallion that is a known carrier, or vice versa.

⚠️ What Happens to Affected Foals?
Foals with two copies of the FFS1 gene (FFS1/FFS1) are born with:

• Extremely fragile, hyperextensible skin
• Joint laxity
• Severe lesions or tearing of skin from normal handling
• In many cases, are stillborn or euthanised shortly after birth

FFS1 is 100% fatal in affected foals.

Possible test results:

📌 Key Point for Breeders:
Carrier horses (N/FFS1) are completely normal and healthy, but should never be bred to another carrier, because there’s a 25% chance of producing a fatally affected foal.

FFS1 testing is a simple, one-time genetic test that can prevent heartbreak and financial loss in breeding. Many affected foals are also lost in-utero and this could explain why some stallions and mare combinations did not work (before we had the test available). Many responsible breeders today treat it like they do WFFS (Warmblood Fragile Foal Syndrome)—as standard pre-breeding protocol.

If your mare has these bloodlines up close it would be worth testing as these stallions are carriers: Corrado I, Caretino, Carthago, Balou du Rouet, Don Schufro, Fursten-Look, Top Gear, Furst Toto. Most licensed stallions should have their status readily available but if you have any questions please contact the HHSA or stallion owners.

PSSM1 Testing

Polysaccharide Storage Myopathy Type 1 (PSSM1) is a genetic muscle disorder that affects thousands of horses across various breeds, especially those bred for performance. While the condition can be managed with proper care, it starts with one critical step: genetic testing.

PSSM1 is a heritable metabolic muscle disease caused by a mutation in the GYS1 gene, which controls how muscle cells store and use glycogen (sugar). Horses with this mutation store excess glycogen, which disrupts normal muscle function.

What Does the Test Look For?

PSSM1 testing is a DNA test that checks whether a horse carries a mutation in the GYS1 gene. This gene mutation is autosomal dominant, meaning even one copy can cause symptoms.

Not every horse that carries the gene will show signs, but clinical symptoms may include:

• Muscle stiffness or cramping
• “Tying up” (exertional rhabdomyolysis)
• Reluctance to move or exercise intolerance
• Sweating and shifting weight post-exercise
• Muscle atrophy over time

These signs often appear after rest, light work, or diet changes. Why Test?

In competition: Understand if performance issues are related to genetics or training.
Early detection allows you to manage the horse’s diet and exercise program to reduce symptoms.
In breeding: Avoid crossing two carriers, and reduce risk of passing the gene to foals.

Coat Colour Tests

Understanding Coat Colour Genetics: Red/Black Factor & Agouti Explained

Coat colour is more than just aesthetics—it’s written in a horse’s DNA. Two of the most common tests used to determine a horse’s base colour are the Red/Black Factor (Extension gene) and the Agouti gene.

Red/Black Factor (Extension Gene – “E”)

This test determines details of a horse’s black or red based coat colour.

• EE (Homozygous Black):
  The horse has two copies of the black allele and will always produce black pigment. This means it will be black-based and can never produce a chestnut foal, even when bred to a chestnut.
• Ee (Heterozygous Black):
  The horse carries one black and one red gene. It will appear black-based (e.g., bay, black, brown) but can pass on a red gene and potentially produce a chestnut foal depending on the mate’s genetics.
• ee (Homozygous Red):
  The horse has two copies of the red gene and cannot produce black pigment. It will be red-base in colour (for our purposes most likely chestnut), regardless of any other modifiers.

Example Result: EE
This horse is black-based and cannot produce a red (chestnut) foal.

🟤 Agouti Gene (“A”)

The Agouti gene controls the distribution of black pigment—specifically, whether black pigment is restricted to certain areas of the body (like the points: legs, mane, tail), or the entire body.

• AA (Homozygous Agouti):
  The horse will have black pigment restricted to the points, making it bay. If the horse is EE or Ee (can produce black), Agouti will always turn it bay.
• Aa (Heterozygous Agouti):
  Also results in a bay coat, but the horse carries one non-agouti gene and could pass on the ability to produce black offspring if bred to another black-producing horse.
• aa (No Agouti):
  No restriction of black pigment. If the horse has black genes (EE or Ee), it will appear black.

Agouti has no visible effect on chestnut (ee) horses.

🧪 Example Result: Aa
The horse is black-based and carries one Agouti gene. This means it will appear bay, but can produce black foals if passed the non-agouti gene.

🐴 Putting It All Together: Example – EE Aa

This horse:

• Is black-based (EE), so it cannot produce chestnut foals.
• Carries one Agouti gene (Aa), so black pigment is restricted, and the horse will appear bay.
• Can pass on either the A (Agouti) or a (non-Agouti) allele to its offspring.

Breeding Implications:
This horse will always pass on black pigment and may produce bay or black offspring depending on the mate’s genetics.

Brown Coat Colour – A Shade of Bay

• Genetically, most “brown” horses test as Ee or EE (black-based) with At (a variant of the Agouti gene).
• The Agouti gene controls where the black pigment appears. While Aa or AA restricts black pigment to the points (producing a bay), the At allele is thought to produce a darker, more uniformly shaded bay—what many people visually identify as “brown.”
• Brown horses often have lighter or “mealy” areas around the eyes, muzzle, and flanks, which distinguishes them from true black horses.

Black Horses

• Genetically EE or Ee and aa (no Agouti gene to restrict pigment).
• The entire coat is black with no lighter areas or red tones.

Dominant White (W) Gene Series – W20, W5, W10, W22

The Dominant White (W) variants are mutations of the KIT gene, which controls pigmentation in the coat.

• Horses with one or two copies of certain W variants often have extensive white markings or even fully white coats.
• The term “Dominant” means that one copy of the gene can influence the coat colour.
• These mutations vary in strength, and some are more subtle (like W20), while others are more likely to produce dramatic white expression (like W5 or W10).

🔎 W20

• One of the most common KIT variants in many breeds, including warmbloods and Thoroughbreds.
• W20 alone often produces modest white markings, such as socks, blazes, or high white.
• However, when combined with other W variants (or other white spotting genes like Sabino or Tobiano), W20 can enhance white expression significantly.

Possible Results:

• N/W20: One copy – may cause subtle white markings.
• W20/W20: Two copies – usually more noticeable white, but still variable.

✅ Safe to breed. Not associated with health problems.

🔎 W5

• A stronger white mutation, often associated with extensive white markings or nearly all-white coats.
• Less common and found in specific breeds.
• Expression is highly variable, but it tends to produce more dramatic white than W20.

Possible Results:

• N/W5: Likely to show significant white, possibly with a white face and high white legs.
• W5/W5: Thought to be lethal in utero (foals likely don’t survive)- Do not breed two W5 carriers together (not likely with Warmbloods, but important to keep in mind)

🔎 W10

• Another rare but highly expressive white mutation.
• Like W5, W10 is associated with extensive or full-body white.
• Occurs in certain lines (e.g., some Quarter Horses and Paints).

Possible Results:

• N/W10: Likely shows bold white markings or nearly white coat.
• W10/W10: Also believed to be lethal in homozygous form. Again, avoid pairing W10 carriers in breeding.

🔎 W22

• A newer, less studied variant in the W series.
• Typically produces minimal to moderate white, depending on other genetic influences.
• May enhance white in combination with W20 or other spotting genes.

Possible Results:

• N/W22: May show moderate white markings.
• W22/W22: Not well documented yet; likely viable, but more data is needed.

🧬 Sabino 1 (SB1) – White Spotting Gene

What is Sabino?

Sabino is a white spotting pattern controlled (in some cases) by a specific gene known as Sabino 1 (SB1). It’s a mutation of the KIT gene, the same gene family involved in many white patterns like Tobiano, Roan, and Dominant White.

Not all sabino-like patterns are caused by SB1—SB1 is just one tested version. Other sabino-type patterns may be caused by other KIT variants (or even untested genes), especially in breeds where SB1 is rare or absent.

The SB1 gene causes:

• High white leg markings
• Bold, often jagged white face markings (like blazes or snips)
• White extending up the belly or flanks
• Roaning or speckling at the edges of white areas
• Irregular spotting, especially on the lower body

Some SB1 horses can appear nearly solid with minimal white, while others are very flashy.

Summary:

• SB1 is a testable sabino gene causing flashy white markings.
• One copy gives typical sabino markings.
• Two copies can produce nearly white horses with pigmented skin.
• SB1 is safe to breed, even in homozygous form.