OMIA:001216-9796 : Coat colour, roan in Equus caballus (horse)

In other species: dog , pig , taurine cattle , goat , sheep , alpaca

Categories: Pigmentation phene

Links to possible relevant human trait(s) and/or gene(s) in OMIM: 184745 (gene) , 611664 (trait)

Mendelian trait/disorder: yes

Mode of inheritance: Autosomal

Considered a defect: no

Key variant known: no

Key variant is published: no

Species-specific symbol: Rn

Inheritance: Hintz and van Vleck (1979) provided convincing evidence that roan coat colour in Belgian horses is due to heterozygosity for an autosomal gene that is lethal when homozygous. However, as reported by Grilz-Seger et al. (2020), "The hypothesis of the lethality in homozygous roan horses currently has been disputed by Sponenberg and Bellone (2017) . . . , who postulate the existence of homozygous roan horses." The results of Grilz-Seger et al. (2020), described below, confirm the existence of "living homozygous Rn/Rn horses". Voß et al. (2020) also provided evidence of viable homozygotes in the Icelandic breed: "The breeding data analysis showed a 0.87:1 roan to non-roan ratio for roan × non-roan matings (n = 3795) while roan × roan matings (n = 67) resulted in a 4.6:1 ratio of roan to non-roan foals. For roan × non-roan matings, we would expect a ratio of 1:1 roan to non-roan offspring. The expected ratio for roan × roan matings under the assumption of Rn being lethal in the homozygous state is 2:1 roan to non-roan offspring. Both observed ratios differ significantly from the expected ratio".

Mapping: Roan is one of three coat-colour loci that belong to equine linkage group 2 (later shown to be on chromosome ECA3): the other two loci are tobiano and chestnut (Extension)(Andersson and Sandberg, 1982; Marklund et al., 1994)

Markers: Twenty-three years later, Grilz-Seger et al. (2020) conducted a GWAS in the Noriker breed that confirmed KIT as the major candidate gene, and identified a SNP "(ECA3:g.79,543.439 A > G) in the intron 17 of the KIT gene" as a strong marker for roan in the Noriker breed. These authors also reported "two deletions in the downstream region (ECA3:79,533,217_79,533,224delTCGTCTTC; ECA3:79,533,282_79,533,285delTTCT) and a 3 bp deletion combined with 17 bp insertion in intron 20 of KIT (ECA3:79,588,128_79,588,130delinsTTATCTCTATAGTAGTT) . . . [that] Within the Noriker sample, . . . were in complete linkage disequilibrium (LD) with the identified top SNP". Voß et al. (2020) "detected eight variants within the KIT gene that had significant association with roan in Icelandic horses. Variants in KIT that were reported to be associated with roan in other breeds were not found."

Molecular basis: Building on the results of work showing that dominant white coat colour in pigs is due to a mutation at the KIT gene (see OMIA 000209), Marklund (1997) reported very strong evidence that the KIT gene in horses is the gene for roan coat colour: a linkage study revealed zero recombinantion between Roan and KIT, and a 79 bp insertion between exons 1 and 2 of the KIT gene, creating a frameshift mutation, was associated with the Roan phenotype. However, definitive evidence of a causative mutation is still lacking.

Prevalence: Grizl-Seger et al. (2020): "The G -allele of the top associated SNP was present in other roan horses, namely Quarter Horse, Murgese, Slovenian, and Belgian draught horse, while it was absent in a panel of 15 breeds, including 657 non-roan horses. In further 379 gray Lipizzan horses, eight animals exhibited a heterozygous genotype (A/G)".

Breed: Noric (Horse) (VBO_0001030).
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
KIT v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog Equus caballus 3 NC_009146.3 (79618685..79536564) KIT Homologene, Ensembl , NCBI gene

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2020). OMIA:001216-9796: 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.
McFadden, A., Vierra, M., Martin, K., Brooks, S.A., Everts, R.E., Lafayette, C. :
Spotting the pattern: A review on white coat color in the domestic horse. Animals (Basel) 14:451, 2024. Pubmed reference: 38338094. DOI: 10.3390/ani14030451.
2022 Voß, K., Blaj, I., Tetens, J.L., Thaller, G., Becker, D. :
Roan coat color in livestock. Anim Genet 53:549-556, 2022. Pubmed reference: 35811453. DOI: 10.1111/age.13240.
2020 Grilz-Seger, G., Reiter, S., Neuditschko, M., Wallner, B., Rieder, S., Leeb, T., Jagannathan, V., Mesarič, M., Cotman, M., Pausch, H., Lindgren, G., Velie, B., Horna, M., Brem, G., Druml, T. :
A genome-wide association analysis in Noriker horses identifies a SNP associated with roan coat color. J Equine Vet Sci 88:102950, 2020. Pubmed reference: 32303326. DOI: 10.1016/j.jevs.2020.102950.
Voß, K., Tetens, J., Thaller, G., Becker, D. :
Coat Color Roan Shows Association with <i>KIT</i> Variants and No Evidence of Lethality in Icelandic Horses. Genes (Basel) 11, 2020. Pubmed reference: 32580410. DOI: 10.3390/genes11060680.
2017 Sponenberg, P.L., Bellone, R.R. :
Equine Color Genetics, 4th Edition Wiley-Blackwell, Hoboken, NJ , 2017.
2009 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.
1999 Marklund, S., Moller, M., Sandberg, K., Andersson, L. :
Close association between sequence polymorphism in the KIT gene and the roan coat color in horses Mammalian Genome 10:283-288, 1999. Pubmed reference: 10051325.
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.
1979 Hintz, H.F., Van Vleck, L.D. :
Lethal dominant roan in horses Journal of Heredity 70:145-146, 1979.

Edit History

  • Created by Frank Nicholas on 06 Sep 2005
  • Changed by Frank Nicholas on 14 Oct 2011
  • Changed by Frank Nicholas on 20 Apr 2020
  • Changed by Frank Nicholas on 30 Jun 2020