Horse Coat Colours Presentation 2008

Horse Coat Colours and 

Markings 

Cindy Harper 

Onderstepoort Laboratory for Applied 

Veterinary Genetics

Basic Colours 

Black 

Bay 

Chestnut

Genetic Control of the Basic Colours 

• Melanocytes produce melanin pigment 

• 2 Pigments responsible for coat and skin 

colour – eumelanin (black and brown) and 

phaeomelanin (red and yellow) 

• Colour genes control either the pigment 

producing cell or pigment production 

• 2 genes control the main colour switches 

in horses 

Extension (E) and Agouti (A)

Genetics 

Sire 

Dam 

Locus (address of a gene and each has a 

name) occurs on a pair of chromosomes – 1 

from sire and 1 from dam 

Form of gene (allele) on 1 chromosome of pair 

can be same as on other – homozygosity 

Or different – heterozygosity 

Different – dominant and recessive where 1 

allele is expressed and other is not 

Function: Gene that codes for protein 

Protein: Effect e.g. stimulates melanocyte to 

produce eumelanin 

Chromosome pair 

Result: Black horse

The Extension Gene/Locus (E) 

• Difference between black and red lies in the action of 1 

gene – MC1R 

• Allele symbols are E and e 

E extends black (eumelanin( 

eumelanin) ) in coat 

e extends red (phaeomelanin( 

phaeomelanin) ) in coat 

Combination of alleles at the extension locus: 

EE 

Ee 

ee 

Allows black in the coat: Black, brown, bay, 

buckskin, grullo 

Black in the skin but not in the coat: Chestnut, 

palomino

Black Pattern 

The Agouti Gene / Locus (A) 

AA 

Aa 

Black pattern limited to the legs , mane and tail 

aa 

Black distributed uniformly through the coat 

The combination of alleles at the extension and agouti 

genes / loci control the basic colour of the horse

Interaction between Extension and 

Agouti 

EEAA 

EEAa 

EeAA 

EeAa 

Black in coat 

Black at the points 

Bay, Brown 

EEaa 

Eeaa 

eeAa 

eeAA 

eeaa 

Black in coat 

Black throughout coat 

Only red in the coat coat 

Black, 

Chestnut,

Red Factor (e) 

• Extension locus – 2 alleles E and e 

ee breeding principles 

Chestnut + chestnut = all 

chestnut 

e 

e 

e 

ee 

ee 

e 

ee 

ee

Red Factor (Ee( 

Ee) 

and Black Pattern factor (Aa( 

Aa) 

Sire: eeAa 

chestnut 

eA ea 

chestnut + chestnut = All 

chestnut 

Extension (red) locus 

dominant over the Agouti 

(black) locus 

Dam: eeaa 

chestnut 

ea 

ea 

eeAa 

eeAa 

eeaa 

eeaa


Ee) 


Aa) 

Sire: EEaa 

black 

Ea 

Ea 

Dam: eeAA 

chestnut 

eA 

eA 

EeAa 

Bay 

EeAa 

Bay 

EeAa 

Bay 

EeAa 

Bay


Ee) 


Aa) 

Sire: Eeaa 

black 

Ea 

ea 

Dam: Eeaa 

black 

Ea 

ea 

EEaa 

Black 

Eeaa 

Black 

Eeaa 

Black 

eeaa 

Chestnut

Breeding Black 

• Avoid recessive e! 

Genetic test for E/e 

Is this a true black (aa( 

aa) ) or dark bay / brown 

(Aa)? 

Genetic test for A/a

Principle 

Each horse has all the genes that can possibly code for any colour, BUT an 

individual allele combination that in total gives it a specific appearance! 

Extension Locus 

E e 

Agouti Locus 

A A 

Cream Locus 

CR N 

Grey Locus 

g g 

Tobiano Locus 

TO N 

1 

2 

3 

4 

5 

Genotype: E/e A/A N/CR g/g N/TO 

Phenotype: Diluted Bay (Buckskin) Nongrey 

with a Tobiano Paint pattern

What colour?

Basic Colour Modification 

Sooty / Shaded 

Black hairs between coat hairs 

Bay – topline to extensive covering most of 

the body



Bay – extensive shading 

“Brown” 

How to distinguish from true black? 

Genetic test aa – black / Aa or AA - brown

The Brown Gene 

• There is a brown gene – (TYRP1) dilutes 

black to chocolate 

• Most obvious in dogs, but not common 

colour in horses and chocolate and dun 

horses are caused by other genes

When is a horse Brown?! 

• Brown in horses is a term used to 

describe a shade of bay in horses. 

• Some breeders describe all bays with 

shading / sootiness as Brown 

• Some breeders describe all bays 

regardless of shading as bays 

• Most commonly breeders describe the 

dark, extensively shaded bay as 

brown and all other bays as bay 

• Heritability?

Brown Heritability 

• Some believe that brown can be bred and is in fact a 

sub-division of the agouti locus or extension locus (A t or 

E B ) 

• Black is allowed in the coat and is more extensive than 

the points in a bay 

• This would support the proposal that brown (“extensive( 

bay”) ) is heritable and “breedable”

Colour terms 

• Terms that describe a phenotype – what 

you see 

• Depend on breed / society / country / 

individual 

• Only right or wrong is to find and test the 

actual genetic control! 

• FEI rulebook states that the definition of 

colour differs according to country.



Chestnut – usually distributed throughout 

the coat 

Liver Chestnut


Mealy 

• Mealy causes lighter areas on 

the belly, muzzle, inner legs, 

and over the eyes. It is 

usually ignored in color 

description. 

• Black - Seal brown (test aa is 

modified black / Aa or AA is 

bay with lots of shading) 

• Chestnut to sorrel for 

breeders of draft horses

Mealy 

Dun 

Bay

Bay 

• Black Points 

• Legs 

• Ear tips 

• Mane 

• Tail

Variations of Bay

Black 

• No Brown in coat 

• White markings are 

allowed 

•Genetic test aa vs Aa 

or AA and EE or Ee

Feature of Bay vs Black 

• A black horse, even with a sun-bleached 

hair coat will have solid black hairs around 

the eye. 

Bay 

Black

Chestnut 

e 

e 

e 

ee 

ee 

e 

ee 

ee 

Recessive traits are expressed 

phenotypically when in homozygous form! 

Red coat throughout – no black points.

Chestnut Modifications 

Liver 

Flaxen 

Flaxen and 

mealy

White on basic coat 

• Any white or white pattern is 

SUPERIMPOSED on a basic colour 

• Cover the whole or part of the horse 

• Pattern – name 

Grey 

Roan 

Roaning 

Spotting 

Paints 

White markings

Grey 

• Born any colour – becomes grey 

• Usually starts on head and is progressive 

• Speed of greying individual 

• Gradual process – 

completely white with pigmented 

skin

Grey Breeding 

• Dominant trait GG and Gg 

– always grey i.e. a horse 

does not carry a hidden 

grey gene 

• A grey foal must have at 

least 1 grey parent! 

• Homozygous grey + non 

grey 100% Grey 

g 

G 

Gg 

G 

Gg 

g 

Gg 

Gg

Grey Breeding 

• A horse can have any combination of base coat 

genes, but G overrides all 

e/e a/a N/RN to/to C/C G/g = GREY 

• Grey is going to obliterate any other colour pattern 

• 2 greys can 

• produce 

a non-grey 

• DNA Test 

available 

G 

G 

GG 

g 

Gg 

g 

Gg 

gg

Grey Variations 

• Variations of grey can given different 

names: 

Rose grey 

Steel grey 

Fleabitten grey 

Dapple grey

Roan 

• Permanent colour, , white does not progress 

with age! 

• Dark head and limbs 

• Characteristic inverted “V” above knees

Roan Genetics 

• RN is caused by a dominant gene. 

RNrn or rnrn (not roan) – no test yet 

• THUS: A roan must have 1 roan parent! 

• Homozygous dominant roan RNRN = lethal 

resorption?

Roan Variations 

Chestnut Roan 

Blue Roan

Rabicano / Roaning 

• Rabicano, , also called white ticking or 

roaning, , is characterized by limited roaning 

in a specific pattern, usually in the flank, sides 

and the tailhead 

• Also in breeds which do not possess any true 

roan Thoroughbreds and Arabians

Spots 

• THE LEOPARD COMPLEX 

• Produced by a the leopard gene complex (Lp( 

Lp) 

• It is a dominant trait – patterns produced by 

modifier genes 

• Not all horses with the dominant leopard allele 

(Lp)) will be spotted but indicators of this gene 

include: 

• White sclera 

• Mottled skin 

• Striped hooves

Leopard Breeding 

• Occurs in many breeds but in some it is a 

fixed characteristic 

Appaloosa, Knapstrup, Noriker 

• Dominant Lp allele expresses a pattern 

• Pattern depends on modifiers 

• Horse with a specific pattern can produce 

the whole range of patterns depending on 

the modifiers in its gene complex 

• No specific test

Leopard Patterns 

• Leopard

Blanket

Varnish Roan 

• Not Rn or G 

• Lp spotting complex gene with 

characteristics and may have leopard spots 

• Mottled skin, color mainly on bony points 

(on the face, usually in a distinct V on the 

bridge of the nose; on the cheeks, point of 

shoulder, elbows, knees, point of hips, hock) 

and it can be seasonal as well 

• Roans (RN) are roan from birth, varnish 

roans are born quite solid with some spots 

and "roan out" as they age

Varnish Roan Variations

Leopard Variations 

Small Blanket 

Extensive Solid Blankets 

Extensive Spotted Blanket or Near Leopard 

Leopards with various sized spots

Paints 

• Basic colour with a white pattern 

superimposed 

• Patterns are controlled by separate genes and 

are heritable 

• Extent of pattern can vary

Tobiano 

• Most legs white 

• White crosses the topline 

• General head markings (may 

have no head markings) 

• Mixed tail 

• Regular Edges 

• Dominant gene TO/TO or 

N/TO 

• Direct Genetic Test available

Tobiano Variations

Frame Overo 

• Dark legs 

• White patches on the 

sides 

• Irregular Edges 

• Extensive head 

markings 

• Tail one colour

Frame Overo

OLWS 

• Frame Overo is associated with 

Lethal White Foal Syndrome 

(LWF) 

• Mutation in gene supposedly 

produces frame overo – O/O 

• Test for this mutation 

• Some solids carry the O mutation 

(N/O) 

• N/O x N/N – always to avoid 

lethal 

• O/O solid white foal with 

incomplete intestinal 

development

Sabino 

• Legs extensively white – edges 

mottled 

• White mottled body spots with 

ticking and roaning 

• Extensively marked faces with 

white chin 

• Polygenic trait 

• 1 sabino pattern test available – 

N/SB1 or SB1/SB1 – extensive 

white sabino but no lethal

Sabino Variations 

• Paint pattern but occurs in many breeds

Splashed White 

• Legs, body and face 

are white 

• Edges of markings 

are crisp 

• Dipped into white 

paint

Dilution Factors 

• Cream 

• Dun 

• Silver 

• Champagne

Cream Dilution 

• Caused by Dilution factor Cr at the cream locus 

• Incomplete dominant gene, which means that it 

is expressed to some degree when there is only 

one copy of the gene and to a greater degree 

when there are 2 copies 

• DNA test available 

• 1 copy of dilution factor N/Cr 

Dilutes only red to yellow 

Does not dilute black

Palomino 

ee N/Cr 

Chestnut

Buckskin 

EEAa or EeAa and N/Cr 

Bay

Sooty Buckskin 

EEAa or EeAa and N/Cr 

Shaded Bay

Smoky Black 

Ee or EE and aaN/Cr 

Both tested to carry the cream dilution factor 

Can produce palomino, buckskin and double 

dilutes even though it looks black


• 2 copies of dilution factor Cr/Cr 

Dilutes red and black 

Pink skin and blue eyes (not albinos) 

Diluted Chestnut 

= Cremello 

Diluted Bay 

= Perlino


• DNA-tested: 

TOto EE aa Cr/Cr 

Diluted Black 

= Smoky Cream

Grey vs. Cremello

Dun 

• Dilution Factor + Primitive Marking Factor: Linked 

• Primitive marks are the colour of the undiluted base 

colour 

• Simple dominant gene 

DNDN – dun 

DNdn – dun 

dndn – not dun 

• Dilutes all colours to a certain extent 

• Yellow colour more tan than cream dilution 

• Manes, tails and primitive markings colour of non- 

diluted base colour 

• No direct DNA test (zygosity( 

test based on pedigree 

and other markers)

Primitive Markings 

• List (dorsal stripe) 

• Zebra stripes 

• Withers stripe 

• Cobwebbing on face

Bay with dun gene – zebra 

dun 

Classic Fjord colour 

Dun Variations

Dun Variations 

Chestnut : orange 

+ red points 

Red Dun 

Black : mouse / smoky 

coloured horse with black 

points 

Grullo

Silver / Taffy (aus( 

aus) 

• Silver gene (Z) is a simple 

dominant 

• Dilutes black but not red 

• Results in colors that are frequently confused with 

chestnut, but that lack the redness of chestnut 

• Lightens manes, tails, and lower legs to flaxen or silver 

grey, or can leave them relatively unchanged 

• Gene has been identified and test is available 

N/N – no silver mutation present 

Z/N or Z/Z – silver mutation present

Silver Variantions 

N/Z or ZZ 

• Bay-based horses will have chocolate lower limbs with 

flaxen mane and tail and red body 

• Red Silver

Silver Variantions 

N/Z or ZZ 

• Black-based / Brown horses will be chocolate with flaxen 

mane and tail 

• Chocolate Silver or Silver Dapple

Silver Characteristics 

Progressive colour that changes with age 

Foals often have silver eyelashes

Silver Variations 

• Chestnut will not be affected but may be confused with 

bay silver 

Chestnut confirmed silver carrier

Champagne 

• Simple dominant gene that dilutes hair pigment from 

black to brown and red to gold 

• N/Ch and Ch/Ch 

• The skin of Champagne-diluted horses is 

pinkish/lavender toned and becomes speckled with age; 

the speckling is particularly noticeable around the eye, 

muzzle, under the tail 

• The eye color is blue-green at birth and darkens to 

amber as the horse ages. 

• DNA test is available

Champagne 

Variations 

•Chestnut (red) diluted to 

gold body colour with 

flaxen mane and tail 

•Bay diluted to a tan 

body color with brown 

points 

•Black to a darker tan 

body with brown points

Champagne Variations 

Pinkish skin 

Blue to amber eyes 

Speckles

Horse Colour can be confusing without 

genetic testing 

Palomino N/Cr 

Chocolate Silver 

Z/Z or N/Z 

Flaxen Chestnut

Horse Colour can be confusing without 

genetic testing 

Smoky Cream 

E a/a Cr/Cr 

Perlino 

E A Cr/Cr 

Champagne Grullo 

a/a DN Ch

White 

• No albinos 

• No W/W lethal 

• N/W true white 

• Spot and paint patterns – extensive 

• Grey – pigmented skin and eyes 

• Cremello and Perlino

Horse Coat Colours Presentation 2008

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