Arabian Horses

…and inherited genetic disease

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Horse’s Name:  Habibi
VG ID:  000100
Date: 20 October 2021

The Arabian Inheritance

The Arabian is the oldest recorded horse breed, stretching back 2,000 years.

It’s dish-shaped nose, large eyes, arched neck, and high tail carriage shows off the breed’s beauty, making it one of the most recognizable breeds of horse in the world, valued as a cultural symbol, a source of wealth, or military companion.

Renowned for its tolerance to heat and graceful athleticism, their bones dense and strong, the Arabian is an endurance athlete without peer.

For several centuries, Arabians have been exported from their ancestral homelands resulting in horses that excel in showing and racing. Over this period, Arabians have been bred to infuse Arabian traits into other horses.

However, selection during breeding for these stunning traits has meant some inherited genetic diseases now proliferate among Arabians and horses with Arabian bloodlines.

The genes that cause these inherited genetic diseases are carried by up to 13% of Arabians. Not knowing which horses carry these genes dramatically increases the risk of breeding horses who then produce an incurable, diseased foal.

Conversely, knowing that your horse is free of these specific disease genes means it can be bred to any horse, safe in the knowledge that none of the four Arabian diseases will manifest in the foal.

Hello and Welcome

Here’s a quick summary of your horse’s results.

Cerebellar Abiotrophy

The TOE1 Gene

Result: G/A

Your horse has ONE cerebellar abiotrophy gene variant present.

This means that your horse does not have the disease but is a carrier of the variant.

Your horse has a 50% chance to pass this gene variant to their foal. Any resulting foal could be negative, a carrier, or have the disease, based on the genetics of the breeding partner.

Lavender Foal Syndrome

The MYO5A Gene

Result: Not deleted / Deleted

Your horse has ONE lavender foal syndrome gene variant present.

This means that your horse does not have the disease but is a carrier of the variant.

Your horse has a 50% chance to pass this gene variant to their foal. Any resulting foal could be negative, a carrier, or have the disease, based on the genetics of the breeding partner.

Occipitoatlantoaxial Malformation

The HODX3 Gene

Result: Deleted / Deleted

Your horse has TWO occipitoatlantoaxial malformation gene variants present.

This means that your horse has occipitoatlantoaxial malformation.

This horse will pass on the genetic variant for occipitoatlantoaxial malformation. Any resulting foal will be a carrier, or have the disease, based on the genetics of the breeding partner.

Severe Combined Immunodeficiency Disease

The PRKDC Gene

Result: Not deleted / Deleted

Good news!

Your horse is clear of severe combined immunodeficiency disease and does not carry the variant.

Your horse cannot pass on the SCID gene variant.

Understanding Your Test Results

We don’t want your horse’s results to be a pile of meaningless letters or dashes that are hard to interpret.

We use two terms that might be unfamiliar: variant and carrier

A variant is a change in the DNA sequence of a gene. This change influences how the gene works. This variant change could be benign and have no effect on gene function. Or, it could be harmful and cause disease.

Every horse has two copies of each gene: one gene from each parent.

A carrier is a horse with only one copy of a genetic variant from one parent. A carrier has a single copy in cells of their body but it’s just there, not causing any problems.

A carrier could potentially pass this variant on to its offspring, but a second copy of the variant from the other parent is needed in the offspring to cause the disease. Thus, matings between a carrier and a diseased horse, or between two carriers, could produce an affected foal.

On the other hand, matings between two non-carrier horses cannot produce an affected foal.

Since many genetic conditions reveal themselves only when two copies of the diseased gene are inherited by a foal, a well-known stallion who is a carrier of an inherited disease can quickly spread the diseased variant across the world.

Similarly, if a population of horses derives from a small herd of breeding stock, and one or more of them is a carrier of a genetic disease, then that diseased gene copy is likely to spread throughout the growing population quickly.

Testing for diseased variants can help breeders identify carriers among breeding stock and reduces the risk of producing affected foals through careful matings.

With a good understanding of the genetic risks involved, Arabian breeders can gradually reduce the number of carriers over several generations, while still maintaining genetic diversity, and breeding for desirable traits.

Let’s look at your horse’s genome

Cerebellar Abiotrophy

A progressive disease of the brain

Result: G/A

Your horse has ONE cerebellar abiotrophy gene variant present.

This means that your horse does not have the disease but is a carrier of the variant.

Your horse has a 50% chance to pass this gene variant to their foal. Any resulting foal could be negative, a carrier, or have the disease, based on the genetics of the breeding partner.

What is cerebellar abiotrophy?

Cerebellar abiotrophy is the most reported brain disease in horses. This condition is caused by the loss of brain cells (called Purkinje cells) in the cerebellum (the part of the brain that controls a horse’s sensory perception and the ability to coordinate physical movements).

What are the symptoms?

The most common symptoms seen in cerebellar abiotrophy are: 

  • Head tremors; manifested by high-frequency jerking of the head.
  • Stiff or exaggerated paddling gait from the shoulder.
  • Difficulty getting up, backing up, in tight turns.
  • Uncontrolled movements.

Symptoms may be confused with other causes of severe locomotion problems, e.g., a head injury or wobblers syndrome, because the disease affects the neurons that control balance. There is no cure for cerebellar abiotrophy, but it’s not contagious, and there are ways to prevent it through responsible breeding practices.

How is it inherited?

Cerebellar abiotrophy is a recessive condition, which means your horse must have two copies of the diseased gene to be affected. However, as your horse has only one copy of the diseased gene, it is a carrier of the gene, which can be passed to its foal.

How common is it?

It’s estimated that up to 9 percent of Arabian Horses carry this gene.

Breeding Implications for your horse

Horses with just one diseased gene variant are clinically unaffected and can live normal lives without any limitations on performance.

If you choose to breed your horse with another horse that also carries this diseased gene variant, then there is:

  • A 25% chance the foal will have cerebellar abiotrophy.
  • A 50% chance the foal will be a carrier of the diseased gene variant like your horse.
  • A 25% chance that the foal will not be a carrier of the diseased gene variant.

It’s important to be aware of this when choosing a mate.

If you breed your horse with a mate that is not a carrier of the cerebellar abiotrophy genetic variant, then there is:

  • A 50% chance the foal will carry the diseased gene variant, like your horse.

A 50% chance the foal will not be a carrier of the diseased gene variant.

Genomic Details

Cerebellar abiotrophy is caused by a disease gene variant of the TOE1 gene that is on chromosome 18. This gene is thought to be involved in the development of Purkinje neurons, which help to coordinate movement in the part of the brain called the cerebellum. When these Purkinje neurons do not form, the horse has coordination and movement problems.

The mutation that causes cerebellar abiotrophy is a switch in one of the four base pairs that make up a DNA molecule. Guanine (G) is replaced by Adenine (A) changing the protein of the TOE1 gene. Therefore, a horse’s genetic result for cerebellar abiotrophy can be one of three possibilities:

  1. G/G: Normal. Does not have the disease, nor carries a diseased gene variant.
  2. G/A: Carrier. Does not have the disease, but carries one diseased gene variant from one parent, which might be passed to the foal.
  3. A/A: Diseased. Has the genetic disease. The horse has inherited the diseased variant from both parents. One diseased gene variant will be passed to their foal.

Lavender Foal Syndrome

A lethal disorder of the brain that produces a distinctive coat color

Result: not deleted / deleted

Your horse has ONE lavender foal syndrome gene variant present.

This means that your horse does not have the disease but is a carrier of the variant.

Your horse has a 50% chance to pass this gene variant to their foal. Any resulting foal could be negative, a carrier, or have the disease, based on the genetics of the breeding partner.

What is lavender foal syndrome?

Lavender foal syndrome (LFS) is a universally fatal genetic disease affecting newborn foals. Affected foals are often a pale color with a pink or lavender tinge. They are born alive but cannot stand or nurse and have neurologic symptoms such as seizures, leg paddling, and arched necks. Since there is no effective treatment available, foals normally pass away within a few days or are humanely euthanized.

What are the symptoms?

The most common symptoms seen in lavender foal syndrome are:

  • Lavender, silver, or pink coat color.
  • Inability to stand.
  • Hyperextension of limbs.
  • Paddling motion with legs.
How is it inherited?

Lavender foal syndrome is a recessive condition, which means your horse must have two copies of the diseased gene to be affected. However, as your horse has only one copy of the diseased gene, it is a carrier of the gene, which can be passed to its foal.

How common is it?

It’s estimated that 10 percent of Egyptian Arabian Horses carry this gene. It’s less common in non-Egyptian Arabian horse bloodlines, where its prevalence is only 1.8 percent.

Breeding Implications for your horse

Carriers of lavender foal syndrome are clinically unaffected and can live normal lives without any limitations on performance.

If you choose to breed your horse with another horse that also carries this diseased gene variant, then there is:

  • A 25% chance the foal will have lavender foal syndrome.
  • A 50% chance the foal will be a carrier of the diseased gene variant like your horse.
  • A 25% chance that the foal will not be a carrier of the diseased gene variant.

 It’s important to be aware of this when choosing a mate.

If you breed your horse with a mate that is not a carrier of the lavender foal syndrome genetic variant, then there is:

  • A 50% chance the foal will carry the diseased gene variant, like your horse.
  • A 50% chance the foal will not be a carrier of the diseased gene variant.

Genomic Details

The mutation that causes lavender foal syndrome is a deletion in the MYO5A gene. Part of the gene is deleted or lost from the genome. Therefore, the instructions from the MYO5A gene are abnormal. This small deletion interferes with the function of melanocytes (cells in the skin’s outer layer that produce pigment) and in brain neurons. This results in the distinctive coat color of lavender foal syndrome and the tragic neurological symptoms.

A horse’s genetic result for lavender foal syndrome can be one of three possibilities:

  1. Not deleted / Not Deleted: Normal. Does not have the disease, nor carries a diseased gene variant.
  2. Not deleted / Deleted: Carrier. Does not have the disease, but carries one diseased gene variant from one parent, which might be passed to the foal.
  3. Deleted / Deleted: Diseased. Has the genetic disease. The horse has inherited a diseased variant from both parents.

Occipitoatlantoaxial malformation

A bone abnormality at the base of the skull that can lead to weakness or paralysis

Result: deleted / deleted

Your horse has TWO occipitoatlantoaxial malformation gene variants present.

This means that your horse has occipitoatlantoaxial malformation.

This horse will pass on the genetic variant for occipitoatlantoaxial malformation. Any resulting foal will be a carrier, or have the disease, based on the genetics of the breeding partner.

What is occipitoatlantoaxial malformation?

Occipitoatlantoaxial malformation (OAAM1) is an inherited genetic disease caused by the HOXD3 gene that causes the bones of the neck at the base of the skull to fuse together, resulting in a loss of coordination and sometimes paralysis.

What are the symptoms?

Symptoms range from mild incoordination and weakness of the limbs to paralysis of both front and hind legs. Mild cases may not show manifestations of the disease until the horse is several years old.  

The most common symptoms seen in OAAM1 are:

  • Abnormal head and neck carriage.
  • Clicking sound when moving the neck.
  • Poor balance.
  • Visible deformities along the spine.
  • Restricted head and neck movement.
How is it inherited?

The OAAM1 form of occipitoatlantoaxial malformation is a recessive condition, which means your horse must have two copies of the diseased gene to be affected. As your horse has two copies of the disease gene it has inherited a diseased copy from both parents.

 

Some horses classified as affected by genetic testing of OAAM1 show no symptoms for months or even years, however due to a lack of effective treatment or cure, horses are usually humanely euthanized. Consult with your veterinarian for more help and advice.

Breeding Implications for your horse

Since this horse has two copies of the diseased gene variant for occipitoatlantoaxial malformation it should not be allowed to breed.

If you breed your affected horse with another horse that carries the diseased gene variant for this disease, then there is:

  • A 50% chance the foal will have occipitoatlantoaxial malformation just like your horse.
  • A 50% chance they will be a carrier of the diseased gene variant.

Genomic Details

The mutation that is thought to cause OAAM1 is a deletion in HOXD3 gene. This is when part of the gene, or several base pairs, are deleted. However, this deletion is an association with OAAM1. How the gene mutation causes OAAM1 is not currently known. Indeed, some Arabian horses with this mutation can have a less severe form of OAAM1. Moreover, there are other types of occipitoatlantoaxial malformation that are not caused by this specific deletion.

A horse’s genetic result for OAAM1 can be one of three possibilities:

  1. Not deleted / Not Deleted: Normal. Does not have the disease, nor carries a diseased gene variant.
  2. Not deleted / Deleted: Carrier. Does not have the disease, but carries one diseased gene variant from one parent, which might be passed to the foal.
  3. Deleted / Deleted: Diseased. Has the genetic disease. The horse has inherited the diseased variant from both parents. One diseased gene variant will be passed to their foal.

Severe combined immunodeficiency disease (SCID)

Poor immunity leading to early death

Result: Not Deleted / Not Deleted

Good news!

Your horse is clear of severe combined immunodeficiency disease and does not carry the variant.

Your horse cannot pass on the SCID gene variant.

What is severe combined immunodeficiency disease?

Severe combined immunodeficiency disease is an inherited genetic disease caused by the PRKDC gene. This mutation impairs the mechanism necessary to make functional immune cells and they never develop a functional immune system. Foals usually appear healthy at birth but die of infection within the first 6 months. This is a lethal condition. Sadly, there is no cure or treatment.

What are the symptoms?

The most common symptoms seen in SCID are:

  • Weight loss.
  • Coughing.
  • Lameness.
  • Fever.
How is it inherited?

Severe combined immunodeficiency disease is a recessive condition, which means your horse must have two copies of the diseased gene to be affected. Your horse has not inherited any copies of this diseased gene variant from either parent.

How common is it?

It’s estimated that up to 8.5% percent of Arabian Horses carry this gene. It may also occur in breeds carrying Arab bloodlines.

Breeding Implications for your horse

Your horse can be safely mated to non-carrier horses without any risk of the foal suffering from the disease or carrying the diseased gene variant.

 If you breed your horse to an SCID carrier there is a 50% chance the foal could be a carrier of the diseased gene variant. However, that foal will be healthy and unaffected by the disease.

Thanks to genetic testing over the past decade, the percentage of SCID carriers and affected foals has been noticeably reduced, which clearly testifies to the influence of testing Arabian breeding stock.

Genomic Details

The mutation that causes severe combined immunodeficiency disease (SCID) is a deletion in the PRKDC gene. This is when part of the gene, or several base pairs, are deleted. A small deletion of 5 base pairs on this gene reduces the activity of a protein called DNA-PK. When this happens, there is a profound reduction in B and T cells that help the immune system to fight infections and viruses. This means the foal completely lacks an immune system, dying before the age of three months.

A horse’s genetic result for severe combined immunodeficiency disease (SCID) can be one of three possibilities:

  1. Not deleted / Not Deleted: Normal. Does not have the disease, nor carries a diseased gene variant.
  2. Not deleted / Deleted: Carrier. Does not have the disease, but carries one diseased gene variant from one parent, which might be passed to the foal.
  3. Deleted / Deleted: Diseased. Has the genetic disease. The horse has inherited the diseased variant from both parents. One diseased gene variant will be passed to their foal.

Questions?

It’s normal to feel concerned about your horse.

Reach out to us for a personal consultation, and we’ll walk you through your results or advise on the best breeding decisions.

You can also contact us if you have an inherited disease running through a pedigree. We’ll do our best to figure it out, then advise you on best breeding practice.

Should you think your horse already has one of these serious diseases then we encourage you to speak to your veterinarian for the best clinical advice.

Victory Genomics

 www.victorygenomics.com  

info@victorygenomics.com

  

Should we discover something new, then we’ll let you know, with no need for any additional tests or samples to be mailed in. We already have everything we need to look out for the DNA of your horse for their entire lifetime. No more tests or samples are needed.

This report is based on the latest genomic sequencing technology and scientific research that is regularly reviewed by the Victory Genomics Expert Team.

In the future, newly discovered genetic mutations could also cause similar diseases in this report. We’re working hard to find out.