OMIA:001972-9796 : Coat colour, dun in Equus caballus (horse)

In other species: ass (donkey) , Przewalski's horse

Categories: Pigmentation phene

Possibly relevant human trait(s) and/or gene(s) (MIM number): 601621 (gene)

Links to MONDO diseases: No links.

Mendelian trait/disorder: yes

Mode of inheritance: Autosomal dominant

Considered a defect: no

Key variant known: yes

Year key variant first reported: 2016

Species-specific symbol: D, d1, d2

Species-specific description: "Dun is a wild-type coat color in horses characterized by pigment dilution with a striking pattern of dark areas termed primitive markings." (Imsland et al., 2016). Primitive markings usually appear as a dorsal stripe and bars on the legs. These primitive markings were discussed at some length by Darwin (1859) (chap 5, pp. 163-167).

Inheritance: By studying the results of matings in Icelandic horses, Adalsteinsson (1978) concluded that "a dominant dilution gene, D, converts bay to yellow dun with dark mane and tail, chestnut to yellow dun and dun mane and tail, and black to blue dun (mouse, grullo)". Imsland et al. (2016) described three alleles at the D locus: D for dilution, d1 (non-dun1) for no dilution but primitive markings, and d2 (non-dun2) for no dilution and no primitive markings. D and d1 have dominant modes of inheritance. The d2 allele is recessive and most prevalent among the  common horse breeds. D and d1 are considered ancestral forms of the gene as there were present in horses prior to domestication.

Mapping: Imsland et al. (2016) "mapped the Dun locus to a region on horse chromosome 8 (chr. 8: 18,061,745–18,482,196) using microsatellite markers and then fine-mapped the locus with a 27-SNP panel to a 200-kb region containing only one gene, TBX3"

Molecular basis: Following mapping, the candidate region was DNA sequenced leading to the discovery of a pair of insertions associated with the D and d1 alleles (Imsland et al., 2016). The D allele appears as an 8 bp insertion followed downstream by a 1609 bp insertion. The d1 allele (no dilution but showing primitive markings) appears as an 8 bp insertion followed downstream by a 1610 bp insertion. The d2 allele (described as having no dilution and no primitive markings) is represented in the reference sequence, EquCab 3.0. Imsland et al. (2016) showed that "pigment dilution in Dun horses is due to radially asymmetric deposition of pigment in the growing hair caused by localized expression of the T-box 3 (TBX3) transcription factor in hair follicles, which in turn determines the distribution of hair follicle melanocytes." Furthermore, both d1 and d2 are “regulatory mutations impairing TBX3 expression in the hair follicle, resulting in a more circumferential distribution of melanocytes and pigment granules in individual hairs” resulting in “a more intensely pigmented phenotype”. 

Genetic engineering: Unknown
Have human generated variants been created, e.g. through genetic engineering and gene editing

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
TBX3 T-box 3 Equus caballus 8 NC_009151.3 (20646967..20661149) TBX3 Homologene, Ensembl , NCBI gene


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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 Inferred EVA rsID Year Published PubMed ID(s) Acknowledgements
1028 Non-dun TBX3 nd1 regulatory Naturally occurring variant EquCab2.0 8 Differs from the wild-type allele by a SNP downstream of the wild-type TBX3 sequence (located 1067bp downstream of the start of the larger nd2 deletion described in the nd2 entry), with allele nd1 = T compared with the wild-type D allele = G); an ancient variant 2016 26691985
1029 Non-dun TBX3 nd2 regulatory Naturally occurring variant EquCab2.0 8 A 1609bp deletion (18 227 267–18 227 279; EquCab2) downstream of the wild-type TBX3 sequence plus an 8bp deletion 11 bases upstream of the larger deletion; a recent variant 2016 26691985

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2024). OMIA:001972-9796: 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.

2021 Cieslak, J., Brooks, S.A., Wodas, L., Mantaj, W., Borowska, A., Sliwowska, J.H., Ziarniak, K., Mackowski, M. :
Genetic background of the Polish primitive horse (Konik) coat color variation-new insight into dun dilution phenotypic effect. J Hered 112:436-442, 2021. Pubmed reference: 34432873. DOI: 10.1093/jhered/esab034.
2019 Mackowski, M., Wodas, L., Brooks, S.A., Cieslak, J. :
TBX3 and ASIP genotypes reveal discrepancies in officially recorded coat colors of Hucul horses. Animal 13:1811-1816, 2019. Pubmed reference: 30614426. DOI: 10.1017/S1751731118003506.
2016 Imsland, F., McGowan, K., Rubin, C.J., Henegar, C., Sundström, E., Berglund, J., Schwochow, D., Gustafson, U., Imsland, P., Lindblad-Toh, K., Lindgren, G., Mikko, S., Millon, L., Wade, C., Schubert, M., Orlando, L., Penedo, M.C., Barsh, G.S., Andersson, L. :
Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation that underlies Dun camouflage color in horses. Nat Genet 48:152-8, 2016. Pubmed reference: 26691985. DOI: 10.1038/ng.3475.
1978 Adalsteinsson, S. :
Inheritance of yellow dun and blue dun in the Icelandic toelter horse. Journal of Heredity 69:146-148, 1978. Pubmed reference: 731005.
1859 Darwin, C.R. :
On the Origin of Species by Means of Natural Selection John Murray, London , 1859.

Edit History

  • Created by Frank Nicholas on 22 Dec 2015
  • Changed by Frank Nicholas on 22 Dec 2015
  • Changed by Frank Nicholas on 06 Aug 2016
  • Changed by Frank Nicholas on 12 Feb 2019
  • Changed by Imke Tammen2 on 14 Apr 2024