OMIA:001199-9796 : Coat colour, extension in Equus caballus (horse)

In other species: lorises , coyote , dog , red fox , American black bear , domestic cat , jaguar , ass (donkey) , Przewalski's horse , pig , Arabian camel , reindeer , taurine cattle , indicine cattle (zebu) , goat , sheep , rabbit , Mongolian gerbil , domestic guinea pig , domestic yak , fallow deer , alpaca , gray squirrel , raccoon dog , antarctic fur seal , woolly mammoth , rock pocket mouse , oldfield mouse , lesser earless lizard , Geoffroy's cat , jaguarundi , Colocolo , little striped whiptail , water buffalo , Arctic fox

Categories: Pigmentation phene

Links to possible relevant human trait(s) and/or gene(s) in OMIM: 266300 (trait) , 155555 (gene)

Mendelian trait/disorder: yes

Mode of inheritance: Autosomal

Considered a defect: no

Key variant known: yes

Year key variant first reported: 1996

Cross-species summary: The extension locus encodes the melanocyte-stimulating hormone receptor (MSHR; now known as MC1R). This receptor controls the level of tyrosinase within melanocytes. Tyrosinase is the limiting enzyme involved in synthesis of melanins: high levels of tyrosinase result in the production of eumelanin (dark colour, e.g. brown or black), while low levels result in the production of phaeomelanin (light colour, e.g. red or yellow). When melanocyte-stimulating hormone (MSH) binds to its receptor, the level of tyrosinase is increased, leading to production of eumelanin. The wild-type allele at the extension locus corresponds to a functional MSHR, and hence to dark pigmentation in the presence of MSH. As explained by Schneider et al. (PLoS Genet 10(2): e1004892; 2015), "The most common causes of melanism (black coat) mutations are gain-of-function alterations in MC1R, or loss-of function alterations in ASIP, which encodes Agouti signaling protein, a paracrine signaling molecule that inhibits MC1R signaling". Mutations in MC1R have been associated with white colouring in several species.

Species-specific name: Chestnut

Species-specific description: Various theories on the inheritance of horse coat colours have existed for many decades. Since the 1990s, the full force of molecular biology has been brought to bear on this topic. The first results of such work in horses were reported by Marklund et al. (1996) (see below).

Inheritance: The autosomal recessive inheritance of chestnut was first reported by Hurst (1906), soon after the rediscovery of Mendelism. This conclusion was rigorously (and erroneously) opposed by Weldon (1906).

Molecular basis: By cloning and sequencing a very likely comparative candidate gene (based on the very reasonable assumption that chestnut coat colour in horses is due to an allele at the extension locus), Marklund et al. (1996) showed that chestnut coat colour in 12 different breeds is due to a missense mutation in the gene for melanocyte-stimulating hormone receptor (MSHR or MC1R).

Breeds: American Trotter (Horse) (VBO_0000899), Arab (Horse) (VBO_0000905), Belgian Draft (Horse) (VBO_0000915), Black Forest (Horse) (VBO_0017099), Clydesdale (Horse) (VBO_0000934), Freiberger (Horse) (VBO_0000965), Icelandic Horse (Horse) (VBO_0000991), Morgan (Horse) (VBO_0001022), Quarter Horse (Horse) (VBO_0001057), Shetland Pony (Horse) (VBO_0001066), Thoroughbred (Horse) (VBO_0001083), Warmblood (Horse) (VBO_0017483), Welsh Pony (Horse) (VBO_0001091).
Breeds in which the phene has been documented. (If a likely causal variant has been documented for the phene, see the variant table breeds in which the variant has been reported).

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
MC1R melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) Equus caballus - no genomic information (-..-) MC1R Homologene, Ensembl , NCBI gene


By default, variants are sorted chronologically by year of publication, to provide a historical perspective. Readers can re-sort on any column by clicking on the column header. Click it again to sort in a descending order. To create a multiple-field sort, hold down Shift while clicking on the second, third etc relevant column headers.

WARNING! Inclusion of a variant in this table does not automatically mean that it should be used for DNA testing. Anyone contemplating the use of any of these variants for DNA testing should examine critically the relevant evidence (especially in breeds other than the breed in which the variant was first described). If it is decided to proceed, the location and orientation of the variant sequence should be checked very carefully.

Since October 2021, OMIA includes a semiautomated lift-over pipeline to facilitate updates of genomic positions to a recent reference genome position. These changes to genomic positions are not always reflected in the ‘acknowledgements’ or ‘verbal description’ fields in this table.

OMIA Variant ID Breed(s) Variant Phenotype Gene Allele Type of Variant Source of Genetic Variant Reference Sequence Chr. g. or m. c. or n. p. Verbal Description EVA ID Year Published PubMed ID(s) Acknowledgements
154 American Trotter (Horse) Arab (Horse) Belgian Draft (Horse) Clydesdale (Horse) Freiberger (Horse) Icelandic Horse (Horse) Morgan (Horse) Quarter Horse (Horse) Shetland Pony (Horse) Thoroughbred (Horse) Warmblood (Horse) Welsh Pony (Horse) Coat colour, chesnut MC1R e missense Naturally occurring variant EquCab3.0 3 NC_009146.3:g.36979560C>T NM_001114534.1:c.248C>T NP_001108006.1:p.(S83F) rs68458866 1996 8995760 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. Breed information updated based on PMID: 38600096
155 Belgian Draft (Horse) Coat colour, chesnut MC1R e^a missense Naturally occurring variant EquCab3.0 3 NC_009146.3:g.36979562G>A NM_001114534.1:c.250G>A NP_001108006.1:p.(D84N) rs3443929753 2000 11086549 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. Breed information updated based on PMID: 38600096

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2024). OMIA:001199-9796: Online Mendelian Inheritance in Animals (OMIA) [dataset].


Note: the references are listed in reverse chronological order (from the most recent year to the earliest year), and alphabetically by first author within a year.

2024 Durward-Akhurst, S.A., Marlowe, J.L., Schaefer, R.J., Springer, K., Grantham, B., Carey, W.K., Bellone, R.R., Mickelson, J.R., McCue, M.E. :
Predicted genetic burden and frequency of phenotype-associated variants in the horse. Sci Rep 14:8396, 2024. Pubmed reference: 38600096. DOI: 10.1038/s41598-024-57872-8.
Mura, M.C., Carcangiu, V., Cosso, G., Columbano, N., Sanna Passino, E., Luridiana, S. :
Discrepancies between genetic and visual coat color assignment in Sarcidano horse. Animals (Basel) 14:543, 2024. Pubmed reference: 38396512. DOI: 10.3390/ani14040543.
2022 Ji, R.L., Tao, Y.X. :
Melanocortin-1 receptor mutations and pigmentation: Insights from large animals. Prog Mol Biol Transl Sci 189:179-213, 2022. Pubmed reference: 35595349. DOI: 10.1016/bs.pmbts.2022.03.001.
2021 Hammons, V., Ribiero, L., Munyard, K., Sadeghi, R., Miller, D., Antczak, D., Brooks, S.A. :
GWAS identifies a region containing the SALL1 gene in variation of pigmentation intensity within the chestnut coat color of horses. J Hered 112:443-6, 2021. Pubmed reference: 34343312. DOI: 10.1093/jhered/esab037.
2020 Nguyen, T.B., Paul, R.C., Okuda, Y., LE, T.N.A., Pham, P.T.K., Kaissar, K.J., Kazhmurat, A., Bibigul, S., Bakhtin, M., Kazymbet, P., Maratbek, S.Z., Meldebekov, A., Nishibori, M., Ibi, T., Tsuji, T., Kunieda, T. :
Genetic characterization of Kushum horses in Kazakhstan based on haplotypes of mtDNA and Y chromosome, and genes associated with important traits of the horses. J Equine Sci 31:35-43, 2020. Pubmed reference: 33061782. DOI: 10.1294/jes.31.35.
2019 Fawcett, J.A., Sato, F., Sakamoto, T., Iwasaki, W.M., Tozaki, T., Innan, H. :
Genome-wide SNP analysis of Japanese Thoroughbred racehorses. PLoS One 14:e0218407, 2019. Pubmed reference: 31339891. DOI: 10.1371/journal.pone.0218407.
Grilz-Seger, G., Druml, T., Neuditschko, M., Mesarič, M., Cotman, M., Brem, G. :
Analysis of ROH patterns in the Noriker horse breed reveals signatures of selection for coat color and body size. Anim Genet 50:334-346, 2019. Pubmed reference: 31199540. DOI: 10.1111/age.12797.
Shang, S., Yu, Y., Zhao, Y., Dang, W., Zhang, J., Qin, X., Irwin, D.M., Wang, Q., Liu, F., Wang, Z., Zhang, S., Wang, Z. :
Synergy between MC1R and ASIP for coat color in horses (Equus caballus)1. J Anim Sci 97:1578-1585, 2019. Pubmed reference: 30785190. DOI: 10.1093/jas/skz071.
2016 Finn, J.L., Haase, B., Willet, C.E., van Rooy, D., Chew, T., Wade, C.M., Hamilton, N.A., Velie, B.D. :
The relationship between coat colour phenotype and equine behaviour: A pilot study. Applied Animal Behaviour Science 174:66-69, 2016. DOI: 10.1016/j.applanim.2015.11.004.
Jacobs, L.N., Staiger, E.A., Albright, J.D., Brooks, S.A. :
The MC1R and ASIP coat color loci may impact behavior in the horse. J Hered 107:214-9, 2016. Pubmed reference: 26884605. DOI: 10.1093/jhered/esw007.
Martin, L., Damaso, N., Mills, D., Martin, L., Damaso, N., Mills, D. :
Detection of single nucleotide polymorphisms (SNP) in equine coat color genes using SNaPshotTM multiplex kit or pluronic F-108 tri-block copolymer and capillary electrophoresis. Electrophoresis 37:2862-2866, 2016. Pubmed reference: 27542347. DOI: 10.1002/elps.201600245.
Reissmann, M., Musa, L., Zakizadeh, S., Ludwig, A. :
Distribution of coat-color-associated alleles in the domestic horse population and Przewalski's horse. J Appl Genet 57:519-525, 2016. Pubmed reference: 27194311. DOI: 10.1007/s13353-016-0352-7.
2013 Petersen, J.L., Mickelson, J.R., Rendahl, A.K., Valberg, S.J., Andersson, L.S., Axelsson, J., Bailey, E., Bannasch, D., Binns, M.M., Borges, A.S., Brama, P., da Câmara Machado, A., Capomaccio, S., Cappelli, K., Cothran, E.G., Distl, O., Fox-Clipsham, L., Graves, K.T., Guérin, G., Haase, B., Hasegawa, T., Hemmann, K., Hill, E.W., Leeb, T., Lindgren, G., Lohi, H., Lopes, M.S., McGivney, B.A., Mikko, S., Orr, N., Penedo, M.C., Piercy, R.J., Raekallio, M., Rieder, S., Røed, K.H., Swinburne, J., Tozaki, T., Vaudin, M., Wade, C.M., McCue, M.E. :
Genome-wide analysis reveals selection for important traits in domestic horse breeds. PLoS Genet 9:e1003211, 2013. Pubmed reference: 23349635. DOI: 10.1371/journal.pgen.1003211.
Switonski, M., Mankowska, M., Salamon, S. :
Family of melanocortin receptor (MCR) genes in mammals-mutations, polymorphisms and phenotypic effects. J Appl Genet 54:461-72, 2013. Pubmed reference: 23996627. DOI: 10.1007/s13353-013-0163-z.
Teixeira, R.B., Rendahl, A.K., Anderson, S.M., Mickelson, J.R., Sigler, D., Buchanan, B.R., Coleman, R.J., McCue, M.E. :
Coat color genotypes and risk and severity of melanoma in gray Quarter horses. J Vet Intern Med 27:1201-8, 2013. Pubmed reference: 23875712. DOI: 10.1111/jvim.12133.
2010 Bellone, RR. :
Pleiotropic effects of pigmentation genes in horses. Anim Genet 41 Suppl 2:100-10, 2010. Pubmed reference: 21070283. DOI: 10.1111/j.1365-2052.2010.02116.x.
Li, B., He, XL., Zhao, YP., Wang, XJ., Manglai, D., Zhang, YR. :
[Molecular basis and applicability in equine color genetics]. Yi Chuan 32:1133-40, 2010. Pubmed reference: 21513164.
2009 Kakoi, H., Tozaki, T., Nagata, S., Gawahara, H., Kijima-Suda, I. :
Development of a method for simultaneously genotyping multiple horse coat colour loci and genetic investigation of basic colour variation in Thoroughbred and Misaki horses in Japan. J Anim Breed Genet 126:425-31, 2009. Pubmed reference: 19912416. DOI: 10.1111/j.1439-0388.2009.00841.x.
Lewin, H.A. :
Genetics. It's a bull's market. Science 324:478-9, 2009. Pubmed reference: 19390037. DOI: 10.1126/science.1173880.
Ludwig, A., Pruvost, M., Reissmann, M., Benecke, N., Brockmann, G.A., Castaños, P., Cieslak, M., Lippold, S., Llorente, L., Malaspinas, A.S., Slatkin, M., Hofreiter, M. :
Coat color variation at the beginning of horse domestication. Science 324:485, 2009. Pubmed reference: 19390039. DOI: 10.1126/science.1172750.
Rendo, F., Iriondo, M., Manzano, C., Estonba, A. :
Identification of horse chestnut coat color genotype using SNaPshot. BMC Res Notes 2:255, 2009. Pubmed reference: 20015355. DOI: 10.1186/1756-0500-2-255.
Rieder, S. :
Molecular tests for coat colours in horses. J Anim Breed Genet 126:415-24, 2009. Pubmed reference: 19912415. DOI: 10.1111/j.1439-0388.2009.00832.x.
2008 Royo, L.J., Fernández, I., Azor, P.J., Alvarez, I., Pérez-Pardal, L., Goyache, F. :
Technical note: a novel method for routine genotyping of horse coat color gene polymorphisms. J Anim Sci 86:1291-5, 2008. Pubmed reference: 18310485. DOI: 10.2527/jas.2007-0498.
2003 Andersson, L. :
Melanocortin receptor variants with phenotypic effects in horse, pig, and chicken Annals of the New York Academy of Sciences 994:313-8, 2003. Pubmed reference: 12851331.
2002 Henner, J., Poncet, P.A., Aebi, L., Hagger, C., Stranzinger, G., Rieder, S. :
Horse breeding: genetic tests for the coat colors chestnut, bay and black. Results from a first study in the Swiss Franches-Montagnes horse breed. 144:405-412, 2002. Pubmed reference: 12224446.
2001 Knyazev, S.P., Reissmann, M., Wagner, H.J., Kurai, M.V., Samovolov, N.V. :
Analysis of the genetic structure of the breeding nucleus of the Russian population of thoroughbred horses by the extension locus molecular DNA typing Russian Journal of Genetics 37:1161-1164, 2001.
Rieder, S., Taourit, S., Mariat, D., Langlois, B., Guerin, G. :
Mutations in the agouti (ASIP), the extension (MC1R), and the brown (TYRP1) loci and their association to coat color phenotypes in horses (Equus caballus) Mammalian Genome 12:450-455, 2001. Pubmed reference: 11353392. DOI: 10.1007/s003350020017.
2000 Wagner, H.J., Reissmann, M. :
New polymorphism detected in the horse MC1R gene. Anim Genet 31:289-90, 2000. Pubmed reference: 11086549.
1997 Sponenberg, D.P., Weise, M.C. :
Dominant black in horses Genetics Selection Evolution 29:403-408, 1997.
1996 Kriegesmann, B., Jansen, S., Bishop, M., Brenig, B. :
The equine MSH-R TaqI RFLP is not informative for hair colour in Arabian horses Animal Genetics 27:64, 1996. Pubmed reference: 8624048.
Marklund, L., Moller, M.J., Sandberg, K., Andersson, L. :
A missense mutation in the gene for melanocyte-stimulating hormone receptor (MC1R) is associated with the chestnut coat color in horses Mammalian Genome 7:895-899, 1996. Pubmed reference: 8995760.
1994 Marklund, S., Ellegren, H., Eriksson, S., Sandberg, K., Andersson, L. :
Parentage Testing and Linkage Analysis in the Horse Using a Set of Highly Polymorphic Microsatellites Animal Genetics 25:19-23, 1994. Pubmed reference: 8161016.
1984 Sponenberg, D.P., Harper, H.T., Harper, A.L. :
Direct evidence for linkage of roan and extension loci in Belgian horses. J Hered 75:413-4, 1984. Pubmed reference: 6481131.
1982 Anderson, L., Sandberg, K. :
A linkage group composed of 3 coat colour genes and 3 serum protein loci in horses Journal of Heredity 73:91-94, 1982. Pubmed reference: 7096983.
1909 Bateson, W. :
Mendel’s Principles of Heredity. Cambridge University Press, London , 1909. URL:
1906 Hurst, C.C. :
On the inheritance of coat colour in horses. Proceedings of the Royal Society of London, Series B 77:388-394, 1906. DOI: 10.1098/rspb.1906.0026.
Weldon, W.F.R. :
Note on the offspring of thoroughbred chestnut mares Proceedings of the Royal Society of London, Series B 17:394-398, 1906. DOI: 10.1098/rspb.1906.0027.

Edit History

  • Created by Frank Nicholas on 12 Sep 2010
  • Changed by Frank Nicholas on 11 Sep 2011
  • Changed by Frank Nicholas on 09 Dec 2011
  • Changed by Frank Nicholas on 03 Sep 2012
  • Changed by Frank Nicholas on 27 Feb 2013
  • Changed by Frank Nicholas on 28 Sep 2015
  • Changed by Imke Tammen2 on 08 Aug 2021
  • Changed by Imke Tammen2 on 28 Aug 2021
  • Changed by Imke Tammen2 on 04 Jun 2024