Part 1: Basic Horse Colour

The first gene we look at is the E or Extention gene. Simply put, it determines RED or BLACK. A horse with two EE or Ee appears black, and ee appears red (chestnut). True black is a fairly uncommon horse coat colour, so where are all the black horses? To answer that, we need the Agouti gene.

	E	E
e	Ee	Ee
e	Ee	Ee

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The Agouti gene A, determines how much black appears on the coat. This gene ONLY acts on black, so chestnut horses are unaffected.
AA: Black is restricted to the points (legs, mane, and tail) Bay
Aa: Black is restricted to the points (legs, mane, and tail) Bay
aa: Black all over (Black)

	A	A
a	Aa	Aa
a	Aa	Aa

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Genotype	Phenotype
EEAA EeAA EEAa EeAa
EEaa Eeaa
eeAA eeAa eeaa

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There is one more gene at the Agouti locus (Locus refers to where on a chromosome the gene is found). It is the A^t or Seal brown, and this third allele has been recognised to explain the colour Seal Brown – a black horse with red/tan muzzle, flank folds, chest, underarms, and inner ears, which is also referred to as ‘Black & Tan’ due to similarities in colour in canines & rabbits (Doberman, Gordon setter, Rottweiler, French bulldog)

AA: Black is restricted to the points (legs, mane, and tail- Bay)- most dominant
Aa: Black is restricted to the points (legs, mane, and tail- Bay)
A^tA^t: Black is somewhat restricted (Seal Brown)
A^ta: Black is somewhat restricted (Seal Brown)
aa: Black all over (Black)- least dominant

Genotype	Phenotype
AA/AAt/aa (Bay)
AtAt (Dark Seal Brown: appears darker than Ata)
Ata (Lighter Seal Brown: appears lighter)
aa (Black)

Some more Seal Brown examples.

Brave from Sand Wash Basin may be a Seal Brown with a more reddish tone or a Bay with an exceptional amount of the Sooty Factor (For a brief review of the sooty factor, go here). The foal shows light areas in the typical locations for Seal Brown (see list below).
Areas with tan/red colour:

• Muzzle- sides, chin, & top. (the very end of the muzzle is usually dark grey)
• Beneath the eyes
• Flank folds (where the hind legs meet the abdomen)
• Underarms
• Chest
• Underbelly
• Front of Stifle (the area just behind the flank fold on the hind leg, ‘knee’)
• Quarters (back of thighs)
• Base of ears
• Ear tips

The first photo is by the talented Kathy Simpson of Rabbitbrush Photography. Used with permission from SWAT: Sand Wash Wild Horse Advocacy Team. The second photo is by Equusferus and Brave clearly demonstrates the lighter “soft areas” (muzzle, beneath the eyes, flank folds, chest, underarms, underbelly, front of the stifle, quarters (backs of the thighs), and inner ears).

Part 1: Review of Inheritance

Presenting a brief review of inheritance. In humans, brown eyes are dominant over blue (except in rare circumstances). We’ll use them as our example. Traits are usually represented by letters. Uppercase is dominant, and lowercase is recessive. Brown eyes =BB, and blue eyes = bb. You have two because you inherit one from each parent. For the biology review, we’ll keep it simple, although eye colour is more complex in reality. Two same letters, BB or bb, indicate the person inherited two of the same gene for eye colour from each parent. This is referred to as homozygous (meaning the same).

	B	B
b	Bb	Bb
b	Bb	Bb

	B	B
b	Bb	Bb
b	Bb	Bb

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Say one parent gives a B and a recessive or lowercase b. The parent has brown eyes but has a hidden recessive b (Bb). This is because B is dominant and overrides the recessive gene b, and the eyes appear brown. If a parent is Bb and they have children with a blue-eyed parent, 50% of the children may have brown eyes, and 50% may have blue. The parents with one dominant and one recessive gene are called heterozygous or “split” for the trait Bb.

	B	b
b	Bb	bb
b	Bb	bb

	B	b
b	Bb	bb
b	Bb	bb

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INCOMPLETE DOMINANCE

“Incomplete Dominance” is where the combination of traits from each parent results in an intermediate colour. In the case of carnations, breeding white and red carnations result in pink flowers; the traits are blended.

	Cr	Cr
Cw	CrCw	CrCw
Cw	CrCw	CrCw

If we take the flowers from above, all pink, and breed them together (second generation), we find the genes align the same way as the parents. C^rC^r= red, C^wC^w= white, and C^wC^r =pink.

	Cr	Cw
Cr	CrCr	CrCw
Cw	CrCw	CwCw

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CODOMINANCE

Some carnations exhibit “Codominance where the trait from each parent is observed without blending, so instead of pink, the flower appears red and white.