Extension, Alezan ou Sorrel

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.