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EquiGenes

Understanding horse coat colors

Understanding coat colors

Two bay horses can have a chestnut foal. A dark foal can grow into an almost white gray while keeping the genetic information for its birth color. To understand why, start with the visible coat, then explore the inheritance behind it. The gene articles explain pigment production, coat lightening and progressive graying. The pattern articles focus on patches, spots and mixtures of white and colored hair. Both sections explain genetics, using different visible features as a starting point.

Explanations and diagrams reviewed on 3 November 2026

The ideas you need before reading a DNA result

Four questions for understanding a coat

  1. Base color

    Can the hair make black pigment, and where is it distributed? This gives chestnut, bay or black.

  2. Dilution

    Does an inherited variant lighten the pigment? Its effect also depends on the starting base.

  3. Pattern

    Are there white patches, colored spots or white hairs mixed among the colored ones?

  4. Graying

    Does more white hair appear with age while the original base remains genetically present?

Read these as four questions about the same horse, not four compulsory stages in its development. Start with the base, then ask whether a dilution, a pattern or graying helps explain what you see. A horse may combine several of them or have none of these additional effects.

One gene, a version from each parent

DNA carries biological instructions. A gene is a stretch of those instructions involved in a function, such as pigmentation. Different versions at the same genetic location are called alleles. For the autosomal locations discussed here, meaning those on non-sex chromosomes, a horse normally receives one allele from each parent. The two may be identical or different; they are two versions of one gene, not separate genes for each color.

Two pigments explain the three base colors

Horse hair has two main pigments: black-brown eumelanin and red-yellow pheomelanin. Extension, the MC1R gene, determines whether the hair can make black pigment. Its E version allows this. Without E, the pairs e/e, e/eᵃ and eᵃ/eᵃ give a chestnut base. The rarer eᵃ is another recessive version. Agouti, the ASIP gene, has versions written A and a that affect where black pigment appears. When the hair can produce black pigment, A/A and A/a restrict most of it to the mane, tail and lower legs, giving bay. With a/a, the base is black. Dilutions, white patterns and graying can then change the appearance of these bases.

What dominant and recessive mean

A dominant effect can appear with one relevant allele. A recessive effect generally needs two relevant copies, so a horse with one copy can carry and pass on the variant without showing that effect. With incomplete dominance, one and two copies produce different effects, as they do for Cream. Dominance describes the effect of a particular genetic combination. It does not tell you whether an allele is common or healthier, or guarantee the same appearance in every horse.

One effect can hide another

Dilutions change how pigment looks, white patterns change where colored and white hair appear, and Gray gradually adds more white hairs. A horse can have several of these effects together. In a chestnut e/e, for example, Agouti cannot visibly restrict black pigment because the hair produces none. The Agouti alleles are still present and can be passed on. An interaction in which one genetic location changes or hides the effect of another is called epistasis.

The genetic result and the visible coat are different things

A genotype describes the allele combination at the genetic locations being considered. A phenotype is a feature you can observe. Two horses with the same tested variants may still differ in shade, amount of white or changes with age. Other genetic factors, season, clipping and lighting also affect what you see. A test result can explain a color category without predicting the outline of every white patch.

Some variants travel together

DNA is organized into chromosomes. Genetic locations, or loci, on the same chromosome may be inherited together: this is linkage. Extension, MC1R, and KIT, a gene involved in several white patterns, are both on horse chromosome 3. The combination on one chromosome is called a haplotype. Exchange between chromosome copies, called recombination, can separate linked variants. Their position alone therefore does not give one universal inheritance percentage. Before multiplying probabilities from different genes, check whether treating them as independent is justified.

Sources for this explanation [1] · [3] · [4] · [5] · [9] · [10]

Extension and Agouti: the combinations behind each base

Read each line from left to right: the pair at Extension (MC1R), then the pair at Agouti (ASIP). These lists show the combinations that can give each base, not their probabilities in a cross.

Chestnut

No black hair pigment: chestnut base

9 combinations

MC1RASIP
  • e/eA/A
  • e/eA/a
  • e/ea/a
  • e/eᵃA/A
  • e/eᵃA/a
  • e/eᵃa/a
  • eᵃ/eᵃA/A
  • eᵃ/eᵃA/a
  • eᵃ/eᵃa/a

Bay

Black hair pigment can be produced

6 combinations

MC1RASIP
  • E/EA/A
  • E/EA/a
  • E/eA/A
  • E/eA/a
  • E/eᵃA/A
  • E/eᵃA/a

Black

Black hair pigment can be produced

3 combinations

MC1RASIP
  • E/Ea/a
  • E/ea/a
  • E/eᵃa/a
The lists show the 18 possibilities in this Extension and Agouti model, including the rare Extension version eᵃ: nine chestnut combinations, six bay and three black. They are not 18 equally likely outcomes of a mating. The parents’ own combinations determine what they can pass on and each foal’s probabilities. Dilutions, white patterns, graying and other modifiers are excluded here; the lists describe the base rather than the complete coat.

Two E/e parents: how one foal inherits its pair

MC1R

Both demonstration horses have the exact pair shown. These examples explain inheritance; they do not use the mare and stallion entered in the calculator.

MareE/e

StallionE/e

Mare: E/e × Stallion: E/e
Mare ↓ / Stallion →E50%e50%
E50%E/E25%E/e25%
e50%E/e25%e/e25%

All possible pairs at each conception

  1. E/E25%

    Two copies of E

  2. E/e50%

    One E and one e

  3. e/e25%

    Two copies of e

This example assumes both parents have been tested as E/e. Each passes E or e with a 50% chance. The four equally likely routes give 25% E/E, two routes to E/e at 25% each (50% together), and 25% e/e. Only e/e is chestnut-based in this cross. Each conception is independent: earlier foals do not change these chances, and four births need not follow the proportions. Other genes can still change the visible coat.

Genes: what produces and changes the color

Start with chestnut, bay and black, then explore the changes that can lighten those bases or make the hair turn gray. Each article explains the visible effect, the letters used in test results, how parents pass the variants on and what the evidence can tell us about testing or health.

Cream: one copy and two copies have different effects

These three horses all have a chestnut base. In this example, with no Pearl allele or other coat modifiers, zero, one and two copies of Cr produce chestnut, palomino and cremello respectively. Here N means the allele without Cream; laboratory notation must always be read with its test key. These drawings compare the effect, not an exact shade or a diagnosis from a photograph.

Gray changes the hair, not the inherited birth base

  1. At birth: bay base

  2. As it grays: more white hairs

  3. Later: the coat may be very pale

Follow one example horse with a bay base. White hairs increase as it grays, but the inherited information for its bay base stays the same. The drawings show a possible progression rather than fixed ages or a forecast for every horse. A very pale adult coat does not replace its original genetic base.

Patterns: where the color and white appear

Large white patches, small colored spots and white hairs mixed through the body can have different causes. The articles help you recognize the main arrangements and understand their inheritance. A familiar pattern name does not always identify one particular variant, and several patterns can occur together.

Compare four ways color and white can be arranged

Tobiano

This example has large white patches crossing the back and extending toward the legs.

Frame overo

White patches appear on the sides, with colored areas framing them along the back.

Leopard complex

The drawing shows colored spots on a mainly white coat. The leopard complex includes other appearances too.

Classic roan

White hairs mix with colored body hairs. Here, the head and lower legs retain more color.

These examples help compare characteristic arrangements, not identify a horse from one outline. Each pattern varies, and several can overlap or partly hide one another. The drawings do not predict a foal’s exact markings; the articles explain the inheritance and relevant tests.
KIT region · TO

Tobiano

White patches that often cross the back

Tobiano produces white patches, often crossing the back. A horse can carry one or two copies of the associated DNA variant, and the amount of white does not reliably distinguish them.

Read the article : Tobiano
Molecular cause unresolved

Rabicano

White hairs concentrated near the flanks and tailhead

Rabicano describes white hairs concentrated especially around the flanks and tailhead. Researchers have studied a candidate DNA region, but the cause and a universal model of inheritance remain unconfirmed.

Read the article : Rabicano
Unresolved · EDN3-region research

Pangaré or mealy

Lighter areas around the muzzle and underside

Pangaré lightens the muzzle, belly and other local areas without producing the unpigmented white patches seen in spotting patterns. Researchers have proposed candidate DNA regions, but no single molecular explanation or diagnostic test applies to all horses.

Read the article : Pangaré or mealy
Unresolved · ASIP/RALY-region research

Sooty or shaded

Understanding dark shading within a coat

Sooty describes dark hairs or shading over a coat, often most visible along the upper body. Studies of bay shade offer leads, but they do not yet explain every horse given this description.

Read the article : Sooty or shaded

How to observe a horse before choosing a genetic explanation

1.Compare the whole coat

Look at the mane, tail, lower legs, white areas, skin and eyes. Photographs of both sides in natural light are useful. A light mane or a dark dorsal stripe is a starting clue, but neither establishes a genotype alone. Compare the combination of features with the relevant article.

2.Keep photographs from different ages

Save foal photographs and record dates, season and clipping. A gray keeps the inherited base it had at birth even as more white hairs appear. Following the same horse over time helps distinguish progressive graying from a pattern that already mixed white and colored hair.

3.Record what is known and how it is known

Keep coat observations, registration records and laboratory results separate. Family coat colors and confirmed parentage can guide what to investigate, but cannot reveal every allele. If a result is missing, record it as unknown. A horse that has not been tested should not be treated as having a negative result.

4.Use the actual report for health questions

Some coat color variants also affect other functions. The specific variant, the inherited combination and the strength of the evidence matter more than the coat name alone. For a breeding or health decision, take the laboratory reports and the horse’s clinical history to a veterinarian. A coat description cannot diagnose an individual animal.

Reading a DNA test: five things to check

Begin with the laboratory’s letter definitions. N usually means the reference result for the variant being examined; it does not mean that the gene is absent. On a Cream report, N/N means no detected copies of the tested Cream variant. The Cream variant is written Cr; N/Cr has one copy and can pass it on. Neither result describes every variant of the Cream gene, scientifically SLC45A2, or every cause of a pale coat.

Check the horse’s identity, the report date and the precise list of variants covered. A panel tests several variants together, but its name does not guarantee its contents. A negative result means the covered variants were not detected. It cannot exclude variants outside the panel, recently discovered causes or mechanisms that have not yet been identified.

Check what the test measures. Detecting the presence of a variant is different from identifying both inherited versions or counting repeated DNA segments. For example, UC Davis’s gray presence/absence test does not establish whether a horse has one or two gray alleles or which version it carries. Its separate copy-number test provides more detail, with limits explained in the Gray article.

Check whether the test examines the causal variant—the DNA change responsible for the effect—or a nearby linked marker. A marker is a DNA signpost, and its usefulness must be demonstrated for the population concerned. If appearance and result seem inconsistent, ask the laboratory to review which variants the test covers and the sample details. Interpret the result alongside coat observations and, for health questions, a veterinary assessment.

This guide covers more traits than the calculator currently models. Read the articles to understand a trait, and use the calculator for the combinations it supports. A trait appearing in the guide does not mean it is included in a calculation.

Sources for this explanation [2] · [8] · [6] · [7]

Open the coat calculator

Words you will meet in the articles

Gene
A stretch of DNA involved in a biological function. Many genes contribute to a horse’s pigmentation.
Allele
A version at a particular genetic location. At the locations on non-sex chromosomes described here, a horse normally inherits one allele from each parent.
Locus
A genetic location: an address in the DNA. The plural is loci.
Genotype
The inherited allele combination being described. E/e, for example, records two different versions of Extension, the gene MC1R.
Phenotype
What can be observed, such as coat color, white markings or a change with age. It does not reveal every inherited variant.
Homozygous
Having two identical alleles at the location considered, such as E/E or e/e at Extension.
Heterozygous
Having two different alleles at the location considered, such as E/e at Extension.
Epistasis
An interaction in which one genetic location changes or hides another’s effect. For example, a chestnut inherits Agouti alleles, but they cannot change the visible distribution of black pigment because its hair produces none.
Penetrance
Among individuals with a particular genotype, the proportion that actually shows the associated trait.
Expressivity
The way a trait varies among individuals that show it, such as differences in how much white appears on the coat.
Haplotype
A set of variants carried together on one copy of a chromosome, which can matter when predicting linked inheritance.

Sources for this explanation [2]

Where the explanations come from

Laboratory resources explain which variants are tested and how to read their results. Research papers describe the evidence, discoveries and remaining uncertainties. Each article links its explanations to the relevant sources. Published titles stay in their original language so you can find the exact work.

  1. 1 · Laboratory explanation

    UC Davis VGL — Equine Coat Color Genetics
  2. 2 · Laboratory explanation

    UC Davis VGL — Genetics Glossary
  3. 3 · Laboratory explanation

    UC Davis VGL — Red Factor
  4. 4 · Laboratory explanation

    UC Davis VGL — Agouti (Bay/Black)
  5. 5 · Laboratory explanation

    UC Davis VGL — Cream
  6. 6 · Laboratory explanation

    UC Davis VGL — Gray Presence/Absence
  7. 7 · Laboratory explanation

    UC Davis VGL — Gray Copy Number
  8. 8 · Laboratory explanation

    UC Davis VGL — Full Color/Pattern Panel
  9. 9 · Research paper

    Rieder et al. (2001) — Mutations in ASIP, MC1R and TYRP1 and their association to horse coat colour
  10. 10 · Research paper

    A KIT Variant Associated with Increased White Spotting Epistatic to MC1R Genotype in Horses (2022)
  11. 11 · Research paper

    Hammons et al. (2021) — Variation of pigmentation intensity within the chestnut coat colour
  12. 12 · Research paper

    Bisbee et al. (2020) — Identification of a novel missense variant in SLC45A2 associated with dilute snowdrop phenotype in Gypsy horses
  13. 13 · Laboratory explanation

    LABOGEN — Snowdrop: genetic testing and interpretation
  14. 14 · Research paper

    Marklund et al. (1996) — MC1R and chestnut coat colour
  15. 15 · Research paper

    Mariat et al. (2003) — A mutation in the MATP gene causes the cream coat colour in the horse
  16. 16 · Laboratory explanation

    UC Davis VGL — Pearl
  17. 17 · Research paper

    Holl et al. (2019) — SLC45A2 variants, pearl and sunshine
  18. 18 · Research paper

    Sevane et al. (2019) — Molecular evidence for pearl dilution
  19. 19 · Laboratory explanation

    UC Davis VGL — Dun Dilution
  20. 20 · Research paper

    Imsland et al. (2016) — TBX3 and Dun camouflage colour
  21. 21 · Laboratory explanation

    UC Davis VGL — Champagne
  22. 22 · Research paper

    Cook et al. (2008) — SLC36A1 and champagne dilution
  23. 23 · Laboratory explanation

    UC Davis VGL — Silver and Multiple Congenital Ocular Anomalies
  24. 24 · Research paper

    Brunberg et al. (2006) — PMEL17 and Silver coat colour
  25. 25 · Research paper

    Andersson et al. (2013) — Ocular anomalies and Silver result from mutant PMEL
  26. 26 · Laboratory explanation

    UC Davis VGL — Mushroom
  27. 27 · Research paper

    Tanaka et al. (2019) — MFSD12 explains Mushroom dilution in Shetland ponies
  28. 28 · Research paper

    Rosengren Pielberg et al. (2008) — STX17, graying and melanoma susceptibility
  29. 29 · Research paper

    Rubin et al. (2024) — STX17 copy number, speed of greying and melanoma incidence
  30. 30 · Research paper

    Magdesian et al. (2009) — Evaluation of deafness in American Paint Horses by phenotype, brainstem auditory-evoked responses, and endothelin receptor B genotype
  31. 31 · Research paper

    Aleman et al. (2014) — Brainstem auditory evoked responses in an equine patient population: Part I — Adult horses
  32. 32 · Research paper

    McFadden et al. (2023) — Two Novel Variants in MITF and PAX3 Associated With Splashed White Phenotypes in Horses
  33. 33 · Laboratory explanation

    UC Davis VGL — Tobiano
  34. 34 · Research paper

    Brooks et al. (2007) — A chromosome inversion near the KIT gene and the Tobiano spotting pattern in horses
  35. 35 · Laboratory explanation

    UC Davis VGL — Lethal White Overo
  36. 36 · Research paper

    Santschi et al. (1998) — Endothelin receptor B polymorphism associated with lethal white foal syndrome in horses
  37. 37 · Research paper

    Santschi et al. (2001) — Incidence of the endothelin receptor B mutation that causes lethal white foal syndrome in white-patterned horses
  38. 38 · Laboratory explanation

    UC Davis VGL — Sabino 1
  39. 39 · Research paper

    Brooks & Bailey (2005) — Exon skipping in the KIT gene causes a Sabino spotting pattern in horses
  40. 40 · Research paper

    Druml et al. (2018) — Novel insights into Sabino1 and splashed white coat color patterns in horses
  41. 41 · Laboratory explanation

    UC Davis VGL — Splashed White Mutations SW1–SW8
  42. 42 · Research paper

    Hauswirth et al. (2012) — Mutations in MITF and PAX3 cause splashed white and other white spotting phenotypes in horses
  43. 43 · Research paper

    Magdesian et al. (2020) — De novo MITF deletion explains a novel splashed white phenotype in an American Paint Horse
  44. 44 · Laboratory explanation

    UC Davis VGL — Dominant White Mutations W5, W10, W13, W20 and W22
  45. 45 · Research paper

    Haase et al. (2007) — Allelic heterogeneity at the equine KIT locus in dominant white horses
  46. 46 · Research paper

    Haase et al. (2009) — Seven novel KIT mutations in horses with white coat colour phenotypes
  47. 47 · Laboratory explanation

    UC Davis VGL — Leopard complex, congenital stationary night blindness and uveitis
  48. 48 · Research paper

    Bellone et al. (2013) — Evidence for a retroviral insertion in TRPM1 as the cause of congenital stationary night blindness and leopard complex spotting in the horse
  49. 49 · Laboratory explanation

    UC Davis VGL — Appaloosa Pattern-1
  50. 50 · Research paper

    Holl et al. (2016) — Variant in the RFWD3 gene associated with PATN1, a modifier of leopard complex spotting
  51. 51 · Laboratory explanation

    UC Davis VGL — Roan zygosity test
  52. 52 · Research paper

    Voß et al. (2020) — Coat color roan shows association with KIT variants and no evidence of lethality in Icelandic horses
  53. 53 · Research paper

    Everts et al. (2025) — Identification of two genetic haplotypes associated with the roan coat color in the American Quarter Horse and other equine breeds
  54. 54 · Research paper

    Everts et al. (2025) — Identification of a novel haplotype associated with roan coat color in American Quarter Horses
  55. 55 · Research paper

    Esdaile (2021) — Short Tandem Repeat Analysis of Genetic Diversity Metrics in American Standardbreds and an Investigation on the Cause of the Rabicano Coat Color Phenotype Utilizing Short and Long Read Sequencing Methods (UC Davis MSc thesis, chapter 3)
  56. 56 · Research paper

    Fegraeus et al. (2018) — A potential regulatory region near EDN3 may control both harness racing performance and coat color variation in horses
  57. 57 · Research paper

    Abitbol et al. (2015) — An ASIP missense mutation associated with the no light points phenotype in donkeys
  58. 58 · Research paper

    Corbin et al. (2020) — An independent locus upstream of ASIP controls variation in the shade of the bay coat colour in horses
  59. 59 · Conference abstract

    Kotiščak et al. (2024) — Effect of Raly gene on coat colour in equids (conference abstract, p. 60)
  60. 60 · Research paper

    Horecká et al. (2017) — Standardization of methodology for polymorphism detection in ASIP, MC1R and MATP genes in relation to colour in horses
  61. 61 · Laboratory explanation

    UC Davis VGL — Brindle coat texture
  62. 62 · Research paper

    Murgiano et al. (2016) — An intronic MBTPS2 variant results in a splicing defect in horses with brindle coat texture