Name: E Extension Red Factor
Brand: Equigerminal
Price: 43.05 EUR

About

The Extension locus controls pigment production, red and/or black. The E allele is the dominant allele and determines the production of black pigment. The e allele is the recessive allele and determines the production of red pigment.

Why test?

Horses have only three base coat colours: bay (A/- E/-), chestnut (-/- e/e) or black (a/a E/-). The base colour alone does not dictate the horse's coat, because there are many other genes that modify the base colour: they can dilute it, depigment it or add white spotting or other patterns to it.

In the absence of variants in the other modifier genes, the horse shows the base coat phenotype.

The base coat colour is determined by the sum of two loci, Agouti and Extension.

A/- E/-: bay base colour. The dominant A allele restricts the black pigment produced by the E allele to the points.
a/a E/-: black base colour. The homozygous recessive a/a only gives a black base colour because Extension dictates that black pigment is produced.
-/- e/e: chestnut base colour. An e/e horse only produces red pigment and, as it has no black pigment, it is not affected by Agouti.

Clinical signs

Bay (A/- E/-). The dominant A allele restricts black pigment to the points: mane, tail, lower legs and ear rims. The body ranges from light bay to very dark bay.

Black (a/a E/-). Uniform black over the whole horse, including mane, tail and legs.

Chestnut (-/- e/e). Red pigment only, from light chestnut to very dark chestnut, with a mane and tail that are darker, the same shade or flaxen. Agouti has no visible effect on a -/- e/e horse.

The base coat alone does not dictate the horse's coat, because there are many other genes that modify the base coat: they can dilute it, depigment it or add white spotting or other patterns to it. Phenotypes that can be confused:

Very dark bay (A/- E/-) and black (a/a E/-)
Black (a/a E/-) faded by the sun
Very dark chestnut (-/- e/e) and black (a/a E/-)
Chestnut (-/- e/e) with flaxen mane and tail, and palomino
Sooty, which darkens the back
Dilutions, which change the base coat
Grey, which progressively depigments the base coat

Transmission

What breeders need to know about base coat colour:

Two black base colour a/a E/e horses mated together can produce foals with a black (a/a E/-) or chestnut (a/a e/e) base colour.
Two chestnut base colour (-/- e/e) horses mated together can only produce foals with a chestnut base colour (-/- e/e).
Two bay base colour A/a E/e horses mated together can produce foals with a bay (A/- E/-), black (a/a E/-) or chestnut (-/- e/e) base colour.
A bay base colour A/A E/E horse can never produce foals with a black (a/a E/-) or chestnut (-/- e/e) base colour, whatever the mating partner.

Mendelian probability for each foal from mating two bay base colour A/a E/e horses:

56.25% bay base colour: A/- E/-
18.75% black base colour: a/a E/-
25% chestnut base colour: -/- e/e

Why is it so important to test bay and black base colour horses?

Because horses with the same base colour can have different genotypes, and that changes the foals they can produce.

Bay base colour horses:

A/A E/E: only produces foals with a bay base colour (A/- E/-), whatever the mating partner.
A/a E/E: carries the recessive a allele. Never produces foals with a chestnut base colour (-/- e/e). Mated with another carrier of the a allele, or with an a/a horse, it can produce foals with a black base colour (a/a E/-).
A/A E/e: carries the recessive e allele. Never produces foals with a black base colour (a/a E/-). Mated with another carrier of the e allele, or with a -/- e/e horse, it can produce foals with a chestnut base colour (-/- e/e).
A/a E/e: carries the recessive a allele and the recessive e allele. Can produce foals with a bay (A/- E/-), black (a/a E/-) or chestnut (-/- e/e) base colour.

Black base colour horses:

a/a E/E: never produces foals with a chestnut base colour (-/- e/e), whatever the mating partner.
a/a E/e: carries the recessive e allele. Mated with another carrier of the e allele, or with a -/- e/e horse, it can produce foals with a chestnut base colour (-/- e/e).

By appearance, these horses are identical. Only the DNA test shows which is which.

And that is why it is important to choose the mating partner carefully.

Prevention

100% probability of foals with a chestnut base coat -/- e/e. Both parents must have a chestnut base coat -/- e/e. The parents' Agouti genotype does not change the foal's base coat, but it is passed on.

Foals with a black base coat a/a E/-. Each parent must have at least one recessive a allele (A/a or a/a) and at least one of the parents must have the E allele. For a 100% probability of foals with a black base coat, both parents must be a/a and at least one must be E/E. Two a/a E/e horses mated together: 75% black base coat a/a E/- and 25% chestnut base coat a/a e/e.

100% probability of foals with a bay base coat A/- E/-. At least one parent must be A/A and at least one parent must be E/E. An A/A E/E horse produces 100% foals with a bay base coat, whatever the mating partner.

Base coat selection. To select against a chestnut base coat, use at least one E/E parent. To select against a black base coat, use at least one A/A parent.

The Agouti genotype of a chestnut base coat horse matters. An a/a e/e horse passes the a allele to 100% of its foals. Mated with a black base coat a/a E/E horse, it produces 100% foals with a black base coat a/a E/e.

Base coat should not be the only criterion for choosing a mating partner.

Results

Bay: A/- E/-
• Extension: E/E or E/e

Black: a/a E/-
• Extension: E/E or E/e

Chestnut: -/- e/e
• Extension: e/e

Sample

Hair roots: 20 to 40 hairs pulled (not cut) from the mane or tail, with the roots. Tape them inside the marked area of the printable submission form. Hairs without roots cannot be analysed.

Blood: 5 mL of whole blood in a K3-EDTA tube, collected by a veterinarian. Label the tube with the horse's name and send it with the submission form.

Keep samples dry and at room temperature, and do not freeze them. Do not send hair that is wet, mouldy or soiled with bedding or faeces.

Turnaround

Standard processing: results within 5 to 10 working days of the sample arriving at the laboratory. Shipping is arranged and paid for by the client, and transit time is not included in the 5 to 10 working days.

Samples that fail DNA extraction or amplification are repeated at no extra cost, which may add a few working days. We will contact you if a new sample is needed.

How it works

🛒 Buy the test: select and buy the test online.

📧 Receive the instructions: after payment is confirmed, you receive the sample collection instructions by e-mail.

📄 Complete the form: print and complete the submission form with the animal’s identification.

✨ Collect the sample: pull 20 to 40 hair roots with the bulb and stick them in the marked area of the form, or ask your veterinarian to collect blood in a K3-EDTA tube.

📮 Send it to the laboratory: Equigerminal, S.A., HIESE, Rua da Quinta do Sobreiro, 25, Quinta Vale do Espinhal, 3230-343 Penela, PORTUGAL.

📊 Receive the report: the certified report is issued as soon as the analysis is validated.

FAQs

What is the difference between genotype and phenotype?
The genotype is what is written in the horse's DNA. It cannot be seen. The phenotype is what can be seen: in this case, the coat.
For each gene, the horse has two alleles: one inherited from the dam and one from the sire. We write, for example, A/a E/e.
Two horses can look the same and be different in their DNA. An A/A E/E horse and an A/a E/e horse both have a bay base coat. The A/a E/e horse can have foals with a black or chestnut base coat; the A/A E/E horse only has foals with a bay base coat.

What is the difference between base coat and the animal's coat?
The base coat is the starting point. There are only three: bay, black and chestnut. It is decided by two genes, Agouti and Extension.
Then other modifier genes can change the base coat: dilute it (make it lighter), depigment it (remove colour) or add white spotting and other patterns. The end result is the animal's coat, the one we see.
Examples:
• Palomino: chestnut base coat with one Cream allele.
• Buckskin: bay base coat with one Cream allele.
• Grey: any of the three base coats, progressively depigmented by Grey with age.
If the other modifier genes have no variants, the animal's coat is the same as the base coat.

What does each locus do?
The horse can produce two pigments: black pigment and red pigment.
Extension decides which one is produced. With at least one E allele, the horse produces black pigment. With e/e, the horse only produces red pigment.
Agouti decides where the black pigment goes. With at least one A allele, black pigment stays only on the points (mane, tail, lower legs and ear rims): bay base coat. With a/a, black pigment covers the whole body: black base coat.

Why is an e/e horse always chestnut base coat?
An e/e horse only produces red pigment. Agouti only acts on black pigment. Without black pigment, Agouti has nothing to act on, and the horse has a chestnut base coat -/- e/e, whatever its Agouti. But the Agouti alleles remain in the DNA and are passed on to the foals.

Why is an a/a horse black base coat only if it has the E allele?
a/a puts black pigment over the whole body. But there is only black pigment if the horse has at least one E allele. So: a/a E/- is black base coat; a/a e/e is chestnut base coat.

What does the dash in A/- or -/- mean?
The dash means "any allele". It is used when that allele does not change the base coat.
• A/- E/- can be A/A E/E, A/a E/E, A/A E/e or A/a E/e: all have a bay base coat.
• -/- e/e can be A/A e/e, A/a e/e or a/a e/e: all have a chestnut base coat.

If I can already see my horse's coat, what is the test for?
Because looking at the horse does not show what it can pass on to its foals. An A/A E/E horse and an A/a E/e horse look the same, but have different foals. Only the DNA test shows which is which.

Can two bay base coat horses mated together have a foal with a black or chestnut base coat?
Yes, if both are A/a E/e. Mendelian probability for each foal:
• 56.25% bay base coat A/- E/-
• 18.75% black base coat a/a E/-
• 25% chestnut base coat -/- e/e

Can two black base coat horses mated together have a foal with a chestnut base coat?
Yes, if both are a/a E/e. Mendelian probability for each foal:
• 75% black base coat a/a E/-
• 25% chestnut base coat a/a e/e

What foals do two chestnut base coat horses mated together have?
100% foals with a chestnut base coat -/- e/e, because both can only pass on the e allele.

Which horse has 100% foals with a bay base coat?
An A/A E/E horse. It always passes the A allele and the E allele to every foal. So all foals have a bay base coat A/- E/-, whatever the other parent.

How to get foals with a black base coat?
For it to be possible: each parent must have at least one a allele, and at least one of the parents must have the E allele.
For a 100% probability: both parents must be a/a and at least one must be E/E.

Why does this test matter to breeders of black horses?
The Friesian horse is always black. In Portugal, the Coudelaria Ortigão Costa breeds only black Pure Blood Lusitano horses. To keep a black base coat in every foal, the breeder must know which breeding horses are a/a E/E and which carry the e allele (a/a E/e). Two a/a E/e horses mated together have a 25% probability of a foal with a chestnut base coat a/a e/e. An a/a E/E stallion has 100% foals with a black base coat with any a/a mare. Only the DNA test identifies the carriers.

Can a chestnut base coat horse have foals with a black base coat?
Yes, if it has the a allele (A/a e/e or a/a e/e). Example: an a/a e/e horse mated with an a/a E/E horse has 100% foals with a black base coat a/a E/e. That is why the Agouti of a chestnut base coat horse counts when choosing the mating partner.

How to tell a very dark bay base coat from a black base coat?
By eye it can be difficult. With the DNA test it is certain: bay base coat A/- E/-; black base coat a/a E/-.

My grey horse does not show its base coat. Can it be tested?
Yes. Grey progressively depigments the coat with age, but the DNA does not change. The test determines the base coat the horse was born with.

At what age can a horse be tested?
At any age. The DNA is the same from birth.

When will I receive the results?
Within 5 to 10 working days of the sample arriving at the laboratory. The certified report is sent as soon as the analysis is validated.

For Professionals

Genetic information for veterinarians, geneticists and laboratories.

Extension (E) locus – MC1R gene (melanocortin 1 receptor), ECA3

Function: controls pigment production, red and/or black.
E allele: functional dominant allele. Determines the production of black pigment.
e allele: recessive allele. Determines the production of red pigment.
eᵃ allele: second recessive allele associated with a chestnut base coat.

Variants at the Extension locus

e (Marklund et al., 1996): SNP (single nucleotide polymorphism) with an amino acid change. NC_009146.3:g.36979560C>T; NM_001114534.1:c.248C>T; NP_001108006.1:p.(Ser83Phe). Identifiers: rs68458866; OMIA variant 154.
eᵃ (Wagner and Reissmann, 2000): SNP with an amino acid change. NM_001114534.1:c.250G>A; p.(Asp84Asn). Described in Belgian Draft (Wagner and Reissmann, 2000), also reported in Black Forest, and found in Knabstrupper, Paint Horse, Percheron and Quarter Horse (Avila et al., 2022).

Inheritance

The e and a alleles are autosomal recessive (OMIA: code A, autosomal).

Breed distribution

Avila et al. (2022) tested 11,281 horses from 28 breeds and found the e and a alleles in all of them: Andalusian, Appaloosa, Arabian, Connemara Pony, Dutch Warmblood, Gypsy Cob, Gypsy Vanner, Hanoverian, Icelandic Horse, Knabstrupper, Lusitano, Miniature Horse, Missouri Fox Trotter, Morgan Horse, Mustang, Norwegian Fjord Horse, Oldenburg, Paint Horse, Percheron, Pony of the Americas, Pura Raza Española, Quarter Horse, Rocky Mountain Horse, Shetland Pony, Standardbred, Tennessee Walking Horse, Thoroughbred and Welsh Pony.

Key references

Marklund L, Moller MJ, Sandberg K, Andersson L (1996). A missense mutation in the gene for melanocyte-stimulating hormone receptor (MC1R) is associated with the chestnut coat color in horses. Mamm Genome 7:895-899. PMID 8995760.
Rieder S, Taourit S, Mariat D, Langlois B, Guerin G (2001). Mutations in the agouti (ASIP), the extension (MC1R), and the brown (TYRP1) loci and their association to coat color phenotypes in horses. Mamm Genome 12:450-455. doi:10.1007/s003350020017. PMID 11353392.
Wagner HJ, Reissmann M (2000). New polymorphism detected in the horse MC1R gene. Anim Genet 31:289-290. doi:10.1046/j.1365-2052.2000.00655.x. PMID 11086549.
Avila F, Hughes SS, Magdesian KG, Penedo MCT, Bellone RR (2022). Breed distribution and allele frequencies of base coat color, dilution, and white patterning variants across 28 horse breeds. Genes 13:1641.
Henner J, Poncet PA, Aebi L, Hagger C, Stranzinger G, Rieder S (2002). Horse breeding: genetic tests for the coat colors chestnut, bay and black. Schweiz Arch Tierheilkd 144:405-412.