PRE Coat Color Genetics: The Definitive Scientific Guide

In the international market for the Pura Raza Española, excellence is not measured by height or trot extension alone. Chromotrichology — the science that studies coat colour — has become an indispensable asset-auditing tool. For the breeder seeking differentiation and the investor demanding certainty, understanding the genetic code behind a horse's appearance is the only way to eliminate risk and guarantee long-term profitability.

01 The Genetic Foundation: The Three Base Colours

Every colour in the PRE arises from the interaction of two genes: Extension (MC1R) and Agouti (ASIP). Without these two pillars, no later dilution or modification would exist.

• Bay

  E_ A_ gg
  The most representative base coat in the PRE (~23% of the 2024 ANCCE census). The Agouti gene restricts black pigment to the points — mane, tail and lower legs — producing the characteristic contrast between a mahogany body and black points. It is the necessary base for Buckskin and the chestnut-based Pearl colours.
• Black

  E_ aa gg
  Prized for its elegance and lower frequency (~2%). The absence of the Agouti gene lets black pigment spread evenly across the whole body. An essential base for Smoky Black and black-based Pearl colours.
• Chestnut

  ee
  The base of the red colour range (~13%). Produced by the total absence of black pigment as a homozygous recessive at Extension. Agouti is irrelevant in this genotype. An indispensable condition for Palomino, Cremello and chestnut-based Pearl (Isabela).

02 The Grey Gene (STX17): The PRE's Dominant Trait

Grey is not a colour in itself but a postnatal modifier that triggers progressive depigmentation over the horse's lifetime. It is the dominant gene par excellence in the PRE, present in around 57% of the census — an unusually high frequency compared with any other breed in the world.

Its molecular mechanism involves duplication of the STX17 gene on chromosome 25, which affects skin melanocytes. The result is a horse born with colour that progressively lightens until it reaches flea-bitten grey or pure white at maturity.

Homozygous (GG)

The horse will always be grey and 100% of its offspring will be grey, regardless of the breeding partner. This trait makes it a first-rate genetic-planning tool for breeders working with special colour lines: it guarantees visibility and coverage in the grey market.

Heterozygous (Gg)

The horse is grey but passes on a non-grey allele (g) in 50% of cases. Crossed with a non-grey horse, it statistically produces 50% grey foals and 50% coloured foals, keeping the production of special colours alive.

03 The Cream Gene (SLC45A2): Dilutions and the 2020 ANCCE Nomenclature

The Cream gene (mutation c.457G>A in SLC45A2) is an incomplete dominant: one copy produces visible dilution, but it's the second copy that radically transforms the phenotype. On 11 March 2020, ANCCE updated its official nomenclature to align with international laboratories.

Single Dilutions — one Cream copy (Cr/cr)

These coats keep dark skin and brown eyes. They are the most common in the PRE's special-colour market.

Double Dilutions — two Cream copies (Cr/Cr)

These produce horses with pink skin and pale eyes (blue or greenish), traits that make them easy to identify visually and place them in the market's highest-value segments.

04 The Pearl Gene (Prl / SLC45A2): The PRE's Recessive Jewel

Unlike Cream, the Pearl gene (mutation c.985G>A, also in the SLC45A2 gene but at a different position) follows a recessive inheritance pattern. A single Pearl allele produces no visible dilution: the carrier horse (N/Prl) looks normal. Its effects, however, emerge in two specific situations of high breeding value.

Isabela — double Pearl (Prl/Prl)

When a horse inherits two Pearl alleles, one of the most exclusive and highly sought phenotypes in the Iberian market results. Isabela horses show a unique metallic sheen, pink skin, pale eyes and a coat with highlights ranging from champagne to pale gold. They are classified by underlying genetic base:

• Bay Isabela

  E_ A_ Prl/Prl
  Warm golden tones with metallic highlights. Slightly darker points. Pink skin, pale eyes.
• Chestnut Isabela

  ee Prl/Prl
  The brightest variant. Cream-champagne coat with intense sheen, no dark points.
• Black Isabela

  E_ aa Prl/Prl
  Cool cream or silvery tones. The black base lends a particular nuance that sets it apart from the other variants.

Cream-Pearl Combinations (Cr/Prl)

The compound heterozygote Cream-Pearl produces coats visually very similar to double Cream dilutions — pink skin, pale eyes — but with a different genetic makeup that allows both genes to be passed on to offspring simultaneously. This trait gives it superior breeding value.

05 Full Table: Cream × Pearl Interactions

The table below sets out every possible combination between the Cream-gene status and the Pearl-gene status, across each of the three genetic bases.

06 The Dun Gene (TBX3): Dilution and Primitive Markings

The Dun gene, mediated by the TBX3 transcription factor, is an active diluter — it doesn't just add decorative markings, it reduces pigment intensity across the body — combined with the appearance of characteristic primitive markings: a dorsal stripe, leg barring and a possible shoulder stripe.

There are three allelic variants with distinct phenotypic effects — a critical nuance for correctly interpreting DNA analysis:

• D (Classic Dun)

  D/nd2 or D/nd1
  Produces true dilution of the base colour (Dun Buckskin, Grullo, Red Dun) combined with obvious primitive markings. Extremely rare in purebred PRE.
• nd1 (Pseudo-Dun)

  nd1/nd2 or nd1/nd1
  Produces primitive markings without dilution of the base colour. Estimated frequency f = 0.79 in the PRE (Avila et al., 2022): explains why many grey or bay PRE horses show a dorsal stripe without being genetically true Dun.
• nd2 (Wild-type)

  nd2/nd2
  Standard allele with no effect. Produces neither dilution nor primitive markings.

07 White Patterns in the PRE

Roan (KIT)

Roan is a uniform dilution pattern that mixes white and pigmented hairs across the body while keeping the head and legs coloured. It is dominant and stable throughout life, without the progressive lightening seen in Grey. Uncommon in purebred PRE (<2% of the census).

Splashed White — Discovered in the PRE (2023)

A white pattern marked by symmetrical facial patches (forehead and jaw), blue eyes and a white belly. In 2023, McFadden et al. published in the Journal of Equine Veterinary Science the discovery of two new PRE-specific alleles: SW9 and SW10, identified for the first time exclusively in this breed — confirming the PRE's genetic uniqueness on a global scale.

Tobiano

The best-known irregular white-spotting pattern in pinto horses. Practically non-existent in registered purebred PRE (ANCCE); its presence in a horse declared as purebred PRE would require pedigree verification.

08 Genes Not Present in the Purebred PRE

Scientific rigour also requires pointing out what is not documented in the breed, to avoid unsupported claims that could compromise a breeder's or investor's credibility.

• Champagne (SLC36A1)

  Ch
  Produces characteristic freckled skin, amber eyes and a metallic-sheen dilution over the base colour. Not documented in genomic studies of the purebred PRE (Cook et al., 2008; Avila et al., 2022). Its presence in a horse registered as purebred PRE would require pedigree review for possible historical crossbreeding.
• Silver (PMEL17)

  Z
  Selectively dilutes black pigment, affecting points and mane but not a chestnut body. First detected in the PSL (Avila 2022). No published data on its presence in the purebred PRE. Relevant in the PSL because of historical crossbreeding with Nordic and mountain breeds.