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Pre-domestication (Wild Horses, 35,000–10,000 years ago)

The Early Domestication period at Botai

The Early Domestication period at Botai spanned from 3500 BCE to 3000 BCE. The three primary coat colours of bay, black, and chestnut spread widely while dun remained present but became less common (Outram et al., 2009).

The Bronze Age spanned from 3000 BCE until 1000 BCE.

The domestic horse population started to develop new genetic traits, which included the cream dilution (CR) responsible for palomino and buckskin colours and the silver dilution (Z) that lightens black pigmentation and creates flaxen manes and tails (Reissmann & Ludwig, 2013). The presence of pinto spotting (tobiano/overo) in horses from Hungary and Siberia became evident through ancient DNA analysis during the time period between 2500 BCE and 2000 BCE (Ludwig et al., 2009). The research of Wutke et al. (2016) discovered tobiano spotting in horses from Botai, Kazakhstan, and Germany, which dates back to 3600–3300 BCE and 3300 BCE, respectively, showing that tobiano existed during the first domestication period. The first appearance of polygenic white markings, which include stars, blazes, socks, and stockings, occurred in Bronze Age genomes as evidence of early selection for decorative traits (Pruvost et al., 2011).

The Iron Age and Antiquity (1000 BCE to 500 CE)

The STX17 duplication, known as the grey mutation, emerged between 200 BCE and 200 CE, and then spread quickly because people valued its visual appeal and symbolic meaning (Royo et al., 2008). The grey horse colouration emerges at birth but develops depigmentation as the animal ages, which distinguishes it from previous stable genetic mutations. The frequency of sabino and tobiano spotting patterns rose significantly during the Late Bronze and Iron Ages until tobiano reached its peak at 19% in Iron Age horses (Wutke et al., 2016). The depiction of pinto and leopard-spotted horses in Scythian, Celtic, and Roman art from ancient times demonstrates that patterned horse coats became widespread throughout Eurasia (Ludwig et al., 2009).

The Early Modern Period (500 CE to 1500 CE).

The research by Wutke et al. (2016) demonstrates that the occurrence of spotted and diluted coat patterns decreased dramatically throughout the Middle Ages, while solid coat colours, particularly chestnut, became more prevalent. The Roman Empire’s collapse and subsequent decline in breeding practices reduced the need for horse identification. Additionally, possible religious and cultural meanings associated with apocalyptic riders and church art may have contributed to this colour shift. The pearl dilution allele first appeared in medieval Iberian, German, and Slovakian horses, according to Wutke et al. (2016), but its presence remained limited to Iberian regions. The Iberian and baroque breeds maintained their preference for grey horses while Spanish-introduced leopard-spotted horses evolved into the contemporary Appaloosa breed (Wutke et al., 2016). The period between 1500 CE and the present day marks the beginning of the Post-Medieval to Modern era.

The roan pattern emerged as a result of the KIT allele, but scientists discovered it through European draft breeds before it spread to American stock horses (Holl et al. 2019). The KIT gene mutation SB1 leads to irregular white markings on legs and face with roaned edges, which scientists discovered in Clydesdales and Tennessee Walkers during the domestication period (Haase et al. 2007). The genetic basis of Rabicano remains unknown; however, scientists agree it developed during the domestication period because it affects Arabians and Thoroughbreds (Imsland et al. 2015). The genetic basis of flaxen remains unknown because it lightens chestnut manes and tails through multiple genetic factors. At the same time, sooty creates dark hair patterns on the topline, which scientists first documented during modern times (Holl et al. 2019). The mushroom dilution mutation in Shetland ponies results from a recessive MFSD12 mutation, which produces a sepia-colored chestnut coat with lightened mane and tail, and scientists believe it emerged recently (Ishida et al. 2015). The champagne dilution mutation in SLC36A1 occurred within the past few hundred years and now affects many American stock and gaited breeds (Cook et al. 2008). The pearl gene functions as a recessive dilution factor, which comes from Iberian origins and produces pale coat colours when horses have two copies of the gene or when they carry the cream gene (Wutke et al. 2016). The Dominant White alleles represent the newest group of mutations, which include more than 30 independent KIT mutations that result in white or nearly white foals at birth, and these mutations emerged during the last few centuries from specific founder horses in Thoroughbreds, Arabians, and Quarter Horses (Haase et al. 2009).

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Chronological Order of Horse Coat Colors

Pre-domestication (Pleistocene / Ice Age Horses, >30,000 years ago)
Bay (wild-type) — ancestral color.
Dun (primitive dilution with dorsal stripe, leg barring).
Black (MC1R mutation).
Chestnut (MC1R e/e mutation).
Leopard complex (Appaloosa spotting, LP) — confirmed ~25,000 years ago (Pech-Merle cave horses).
Pangaré (mealy shading, light muzzle/belly, primitive modifier).
Sooty (countershading/black hairs through coat).

Early Domestication (Botai ~3500–3000 BCE)
Polygenic white markings (stars, blazes, socks, stockings).
Tobiano spotting — detected in Eneolithic/Copper Age horses (~3600–3300 BCE; Botai and Germany)

Bronze Age (3000–1000 BCE)
Cream dilution (CR) — palomino, buckskin.
Silver dilution (Z) — dilutes black, light mane/tail.
Sabino-1 (SB1, KIT) — introduced after domestication; confirmed in Bronze Age samples.

Iron Age / Antiquity (1000 BCE–500 CE)
Grey (STX17 duplication) — appears ~200 BCE–200 CE.

Medieval (500–1500 CE)
Pearl dilution (prl, MATP gene) — first detected in medieval Iberian and European horses

Post-Medieval to Modern (1500 CE–present)
Roan (KIT allele) — absent in ancient DNA, appears in European draft breeds, later in stock breeds.
Rabicano — flank/tailhead roaning, genetic basis unknown, only in domestic horses.
Flaxen — light mane/tail on chestnut; polygenic modifier.
Mushroom (MFSD12 mutation) — sepia chestnut, Shetland ponies.
Champagne (SLC36A1 mutation) — American stock and gaited breeds.
Dominant White (multiple KIT mutations, W1–W30+ ) — independent, breed-specific, recent mutations.

Summary
Oldest: Bay, dun, black, chestnut, leopard complex (Ice Age horses).
Early domestication (~3500 BCE): white markings, tobiano.
Bronze Age: cream, silver, sabino.
Iron Age (~200 BCE): grey.
Medieval (~500–1500 CE): pearl.
Modern (1500 CE–present): roan, rabicano, flaxen, mushroom, champagne, dominant white.(Palomino, Buckskin, Smokey Black),

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Dr. Meredith Hudes-Lowder
September 13, 2025

References

• Cook, D., Brooks, S., Bellone, R., & Bailey, E. (2008). Missense mutation in exon 2 of SLC36A1 responsible for champagne dilution in horses. Genomics, 92(2), 93–98.
• Haase, B., Brooks, S. A., Schlumbaum, A., Azor, P. J., Bailey, E., Alaeddine, F., … Poncet, P. A. (2007). Allelic heterogeneity at the equine KIT locus in dominant white (W) horses. PLoS Genetics, 3(11), e195.
• Haase, B., Rieder, S., Tozaki, T., & Brooks, S. A. (2009). Five novel KIT mutations in horses with white coat colour phenotypes. Animal Genetics, 40(5), 623–629. https://
• Holl, H. M., Brooks, S. A., Bailey, E., & Mack, M. (2019). Equine coat color genetics. In T. R. Famula, E. Cothran, & M. Bowling (Eds.), Equine Genetics (2nd ed., pp. 83–104). Wiley.
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• Ishida, N., Hasegawa, T., Takeda, K., Sakagami, M., Onuki, A., Inoue-Murayama, M., … Mukoyama, H. (2015). A frameshift mutation in the MFSD12 gene is associated with the mushroom coat color dilution in Shetland ponies. BMC Genetics, 16, 101.
• Ludwig, A., Pruvost, M., Reissmann, M., Benecke, N., Brockmann, G. A., Castaños, P., … Hofreiter, M. (2009). Coat color variation at the beginning of horse domestication. Science, 324(5926), 485.
• Outram, A. K., Stear, N. A., Bendrey, R., Olsen, S., Kasparov, A., Zaibert, V., Thorpe, N., & Evershed, R. P. (2009). The earliest horse harnessing and milking. Science, 323(5919), 1332–1335.
• Pruvost, M., Bellone, R., Benecke, N., Sandoval-Castellanos, E., Cieslak, M., Kuznetsova, T., … Ludwig, A. (2011). Genotypes of predomestic horses match phenotypes painted in Paleolithic cave art. Proceedings of the National Academy of Sciences, 108(46), 18626–18630.
• Royo, L. J., Álvarez, I., Beja-Pereira, A., Molina, A., Fernández, I., Jordana, J., Gómez, E., Goyache, F., & Cañón, J. (2008). The origins of the grey phenotype in horses. Nature Genetics, 40(8), 1004–1007.
• Reissmann, M., & Ludwig, A. (2013). Pleiotropic effects of coat colour-associated mutations in humans, mice and other mammals. Seminars in Cell & Developmental Biology, 24(6–7), 576–586.
• Wutke, S., Benecke, N., Sandoval-Castellanos, E. et al. Spotted phenotypes in horses lost attractiveness in the Middle Ages. Sci Rep 6, 38548 (2016). https://doi.org/10.1038/srep38548