FREE SHIPPING over $40
OVER 9000 FIVE-STAR REVIEWS
5% OFF ALL SUBSCRIPTIONS
100% HAPPINESS GUARANTEE
Analyze Diet
0
Home / Equine Research Bank / Genes (Basel) / Breed Distribution and Allele Frequencies of Base Coat Color...
Genes2022; 13(9); doi: 10.3390/genes13091641

Breed Distribution and Allele Frequencies of Base Coat Color, Dilution, and White Patterning Variants across 28 Horse Breeds.

Abstract: Since domestication, horses have been selectively bred for various coat colors and white spotting patterns. To investigate breed distribution, allele frequencies, and potential lethal variants for recommendations on genetic testing, 29 variants within 14 genes were investigated in 11,281 horses from 28 breeds. The recessive chestnut ea allele in melanocortin 1 receptor (MC1R) (p.D84N) was identified in four breeds: Knabstrupper, Paint Horse, Percheron, and Quarter Horse. After filtering for relatedness, ea allele frequency in Knabstruppers was estimated at 0.035, thus illustrating the importance of testing for mate selection for base coat color. The Rocky Mountain Horse breed had the highest allele frequency for two of the dilution variants under investigation (Za.f. = 0.32 and Cha.f. = 0.026); marker-assisted selection in this breed could aid in the production of horses with desirable dilute coats with less severe ocular anomalies caused by the silver (Z) allele. With regard to white patterning, nine horses homozygous for the paired box 3 (PAX3) splashed white 2 (SW2) allele (p.C70Y) and six horses homozygous for the KIT proto-oncogene, receptor tyrosine kinase (KIT) sabino 1 (SB1) allele (ECA3g.79544206A>T) were identified, thus determining they are rare and confirming that homozygosity for SW2 is not embryonic lethal. The KIT dominant white 20 (W20) allele (p.R682H) was identified in all but three breeds: Arabian (n = 151), Icelandic Horse (n = 66), and Norwegian Fjord Horse (n = 90). The role of W20 in pigmentation across breeds is not well understood; given the different selection regimes of the breeds investigated, these data provide justification for further evaluating the functional role of this allele in pigmentation. Here, we present the largest dataset reported for coat color variants in horses to date, and these data highlight the importance of breed-specific studies to inform on the proper use of marker-assisted selection and to develop hypotheses related to pigmentation for further testing in horses.
Get Full Text
Publication Date: 2022-09-13 PubMed ID: 36140807PubMed Central: PMC9498372DOI: 10.3390/genes13091641Google Scholar: Lookup
The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
LinkedInCopy
  • Journal Article
  • Research Support
  • Non-U.S. Gov't

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research study investigates the distribution and frequency of genetic variants involved in determining a horse’s coat color and white spotting patterns across 28 different horse breeds, in an attempt to provide recommendations for genetic testing and mate selection in these breeds.

Background of Research

  • The main focus of the research was on evaluating the distribution and frequencies of 29 genetic variants across 14 different genes in a sample of 11,281 horses belonging to 28 breeds. These genetic variants were known to influence the base coat color, dilution, and white patterning in horses.
  • Genetic testing can aid in identifying these variants, assisting breeders to select breeding mates and produce offspring with desirable coat colours and patterns.
  • The study advanced our understanding of horse genetics and coat patterns, while also providing practical information for breeders.

Main Findings

  • The research found that the recessive chestnut ‘ea’ allele in melanocortin 1 receptor (MC1R), an essential gene for determining coat color, was present in four breeds: Knabstrupper, Paint Horse, Percheron, and Quarter Horse. The allele frequency was notably significant in Knabstrupper horses, emphasizing the need for genetic testing for better mate selection in this breed.
  • The study found that the Rocky Mountain Horse breed had the highest frequency of two known ‘dilution’ variants of coat color. Practising marker-assisted selection in this breed could help breed horses with desirable dilute coats and less severe eye anomalies caused by the Silver ‘Z’ allele.
  • The research identified a number of horses homozygous (carrying two copies of the variant) for two specific variants associated with white patterning, confirming that being homozygous for these variants is not lethal to horse embryos. This information is crucial for successful breeding programs.
  • The dominant white 20 allele (W20), known to influence the horse’s pigmentation, was found in all but three horse breeds. However, its actual role in pigmentation across different breeds and its potential value in breeding programs remains unclear and is recommended for further research.

Significance and Conclusions

  • The research provides the largest dataset to date regarding genetic variants associated with coat color in horses, thereby providing crucial insights for breeders and geneticists alike.
  • The data collected demonstrates the importance of breed-specific studies for determining the effects of different genetic variants on coat color and patterns. It also opens avenues for further research into horse pigmentation genetics.
  • Aside from contributing to the knowledge of horse genetics, these findings have practical implications in the field of horse breeding, particularly in selecting breeding mates to produce offspring with preferred coat colors and spotting patterns. They can also inform the application of marker-assisted selection and the development of theories related to pigmentation for further testing.

Cite This Article

APA
Avila F, Hughes SS, Magdesian KG, Penedo MCT, Bellone RR. (2022). Breed Distribution and Allele Frequencies of Base Coat Color, Dilution, and White Patterning Variants across 28 Horse Breeds. Genes (Basel), 13(9). https://doi.org/10.3390/genes13091641

Publication

Genes
ISSN: 2073-4425
NlmUniqueID: 101551097
Country: Switzerland
Language: English
Volume: 13
Issue: 9

Researcher Affiliations

Avila, Felipe
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA.
Hughes, Shayne S
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA.
Magdesian, K Gary
  • Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA.
Penedo, Maria Cecilia Torres
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA.
Bellone, Rebecca R
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA.
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA.

MeSH Terms

  • Animals
  • Gene Frequency / genetics
  • Horses / genetics
  • Phenotype
  • Protein-Tyrosine Kinases
  • Receptor, Melanocortin, Type 1 / genetics
  • Silver

Conflict of Interest Statement

F.A., S.S.H., M.C.P., and R.R.B are affiliated with the Veterinary Genetics Laboratory, a laboratory offering parentage and diagnostic DNA tests in horses and other species.

References

This article includes 42 references
  1. Ludwig A, Pruvost M, Reissmann M, Benecke N, Brockmann GA, Castaños P, Cieslak M, Lippold S, Llorente L, Malaspinas AS. Coat color variation at the beginning of horse domestication.. Science 2009;324:485.
    doi: 10.1126/science.1172750pmc: PMC5102060pubmed: 19390039google scholar: lookup
  2. Marklund L, Moller MJ, 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.. Mamm. Genome 1996;7:895–899.
    doi: 10.1007/s003359900264pubmed: 8995760google scholar: lookup
  3. Bellone RR, Avila F. Genetic testing in the horse.. Vet. Clin. N. Am. Equine Pract. 2020;36:211–234.
    doi: 10.1016/j.cveq.2020.03.003pubmed: 32534857google scholar: lookup
  4. Rieder S, Taourit S, Mariat D, Langlois B, Guérin 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). Mamm. Genome 2001;12:450–455.
    doi: 10.1007/s003350020017pubmed: 11353392google scholar: lookup
  5. Sponenberg DPB, Bellone RR. Equine Color Genetics.. 4th ed. John Wiley & Sons, Inc.; Hoboken, NJ, USA: 2017.
  6. Wagner HJ, Reissmann M. New polymorphism detected in the horse MC1R gene.. Anim. Genet. 2000;31:289–290.
    doi: 10.1046/j.1365-2052.2000.00655.xpubmed: 11086549google scholar: lookup
  7. 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. 2016;57:519–525.
    doi: 10.1007/s13353-016-0352-7pubmed: 27194311google scholar: lookup
  8. Andersson LS, Wilbe M, Viluma A, Cothran G, Ekesten B, Ewart S, Lindgren G. Equine multiple congenital ocular anomalies and silver coat colour result from the pleiotropic effects of mutant PMEL.. PLoS ONE 2013;8:e75639.
    doi: 10.1371/journal.pone.0075639pmc: PMC3781063pubmed: 24086599google scholar: lookup
  9. Andersson LS, Axelsson J, Dubielzig RR, Lindgren G, Ekesten B. Multiple congenital ocular anomalies in Icelandic horses.. BMC Vet. Res. 2011;7:21.
    doi: 10.1186/1746-6148-7-21pmc: PMC3125316pubmed: 21615885google scholar: lookup
  10. Imsland F, McGowan K, Rubin CJ, Henegar C, Sundström E, Berglund J, Schwochow D, Gustafson U, Imsland P, Lindblad-Toh K. Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation that under-lies Dun camouflage color in horses.. Nat. Genet. 2016;48:152–158.
    doi: 10.1038/ng.3475pmc: PMC4731265pubmed: 26691985google scholar: lookup
  11. Mariat D, Taourit S, Guérin G. A mutation in the MATP gene causes the cream coat colour in the horse.. Genet. Sel. Evol. 2003;35:119.
    doi: 10.1186/1297-9686-35-1-119pmc: PMC2732686pubmed: 12605854google scholar: lookup
  12. Holl HM, Pflug KM, Yates KM, Hoefs-Martin K, Shepard C, Cook DG, Lafayette C, Brooks SA. A candidate gene approach identifies variants in SLC45A2 that explain dilute phenotypes, pearl and sunshine, in compound heterozygote horses.. Anim. Genet. 2019;50:271–274.
    doi: 10.1111/age.12790pubmed: 31006892google scholar: lookup
  13. Cook D, Brooks S, Bellone R, Bailey E. Missense mutation in exon 2 of SLC36A1 responsible for champagne dilution in horses.. PLoS Genet. 2008;4:e1000195.
    doi: 10.1371/journal.pgen.1000195pmc: PMC2535566pubmed: 18802473google scholar: lookup
  14. Tanaka J, Leeb T, Rushton J, Famula TR, Mack M, Jagannathan V, Flury C, Bachmann I, Eberth J, McDonnell SM. Frameshift Variant in MFSD12 Explains the Mushroom Coat Color Dilution in Shetland Ponies.. Genes 2019;10:826.
    doi: 10.3390/genes10100826pmc: PMC6827053pubmed: 31635058google scholar: lookup
  15. Brooks SA, Gabreski N, Miller D, Brisbin A, Brown HE, Streeter C, Mezey J, Cook D, Antczak DF. Whole-genome SNP association in the horse: Identification of a deletion in myosin Va responsible for Lavender Foal Syndrome.. PLoS Genet. 2010;6:e1000909.
    doi: 10.1371/journal.pgen.1000909pmc: PMC2855325pubmed: 20419149google scholar: lookup
  16. Martin K, Rosa LP, Vierra M, Foster G, Brooks SA, Lafayette C. De novo mutation of KIT causes extensive coat white patterning in a family of Berber horses.. Anim. Genet. 2020;52:135–137.
    doi: 10.1111/age.13017pubmed: 33111383google scholar: lookup
  17. Rosa LP, Martin K, Vierra M, Foster G, Brooks SA, Lafayette C. Two variants of KIT causing white patterning in stock-type horses.. J. Hered. 2021;112:447–451.
    doi: 10.1093/jhered/esab033pubmed: 34223905google scholar: lookup
  18. Esdaile E, Till B, Kallenberg A, Fremeux M, Bickel L, Bellone RR. A de novo missense mutation in KIT is responsible for dominant white spotting phenotype in a Standardbred horse.. Anim. Genet. 2022;53:534–537.
    doi: 10.1111/age.13222pubmed: 35641888google scholar: lookup
  19. Rosa LP, Martin K, Vierra M, Foster G, Brooks SA, Lafayette C. Non-frameshift deletion on MITF is associated with a novel splashed white spotting pattern in horses (Equus caballus). Anim. Genet. 2022;53:538–540.
    doi: 10.1111/age.13225pubmed: 35672910google scholar: lookup
  20. Magdesian KG, Tanaka J, Bellone RR. A De Novo MITF Deletion Explains a Novel Splashed White Phenotype in an American Paint Horse.. J. Hered. 2020;111:287–293.
    doi: 10.1093/jhered/esaa009pmc: PMC7238438pubmed: 32242630google scholar: lookup
  21. Haase B, Brooks SA, Tozaki T, Burger D, Poncet PA, Rieder S, Hasegawa T, Penedo C, Leeb T. Seven novel KIT mutations in horses with white coat colour phenotypes.. Anim. Genet. 2009;40:623–629.
    doi: 10.1111/j.1365-2052.2009.01893.xpubmed: 19456317google scholar: lookup
  22. Dürig N, Jude R, Holl H, Brooks SA, Lafayette C, Jagannathan V, Leeb T. Whole genome sequencing reveals a novel deletion variant in the KIT gene in horses with white spotted coat colour phenotypes.. Anim. Genet. 2017;48:483–485.
    doi: 10.1111/age.12556pubmed: 28444912google scholar: lookup
  23. Magdesian KG, Williams DC, Aleman M, Lecouteur RA, Madigan JE. Evaluation of deafness in American Paint Horses by phenotype, brainstem auditory-evoked responses, and endothelin receptor B genotype.. J. Am. Vet. Med. Assoc. 2009;235:1204–1211.
    doi: 10.2460/javma.235.10.1204pubmed: 19912043google scholar: lookup
  24. Bellone RR. Genetics of equine ocular disease.. Vet. Clin. N. Am. Equine Pract. 2020;36:303–322.
    doi: 10.1016/j.cveq.2020.03.009pubmed: 32654784google scholar: lookup
  25. Rine J, Metallinos DI, Bowling AT. A missense mutation in the endothelin-B receptor gene is associated with Lethal White Foal Syndrome: An equine version of Hirschsprung Disease.. Mamm. Genome 1998;9:426–431.
    doi: 10.1007/s003359900790pubmed: 9585428google scholar: lookup
  26. Bellone RR, Holl H, Setaluri V, Devi S, Maddodi N, Archer S, Sandmeyer L, Ludwig A, Foerster D, Pruvost M. Evidence for a Retroviral Insertion in TRPM1 as the Cause of Congenital Stationary Night Blindness and Leopard Complex Spotting in the Horse.. PLoS ONE 2013;8:e78280.
    doi: 10.1371/journal.pone.0078280pmc: PMC3805535pubmed: 24167615google scholar: lookup
  27. Fung T, Keenan K. Confidence Intervals for Population Allele Frequencies: The General Case of Sampling from a Finite Diploid Population of Any Size.. PLoS ONE 2014;9:e85925.
    doi: 10.1371/journal.pone.0085925pmc: PMC3897575pubmed: 24465792google scholar: lookup
  28. UC Davis Veterinary Genetics Laboratory–Full Color/Pattern Panel. [(accessed on 20 November 2021)]. Available online: https://vgl.ucdavis.edu/panel/full-coat-color-pattern-panel.
  29. UC Davis Veterinary Genetics Laboratory–Mushroom. [(accessed on 20 November 2021)]. Available online: https://vgl.ucdavis.edu/test/mushroom.
  30. Peakall R, Smouse PE. GENALEX 6: Genetic analysis in Excel. Population genetic software for teaching and research.. Mol. Ecol. Notes 2006;6:288–295.
    doi: 10.1111/j.1471-8286.2005.01155.xpmc: PMC3463245pubmed: 22820204google scholar: lookup
  31. Peakall R, Smouse PE. GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research-an update.. Bioinformatics 2012;28:2537–2539.
    doi: 10.1093/bioinformatics/bts460pmc: PMC3463245pubmed: 22820204google scholar: lookup
  32. Brooks SA, Bailey E. Exon skipping in the KIT gene causes a Sabino spotting pattern in horses.. Mamm. Genome 2005;16:893–902.
    doi: 10.1007/s00335-005-2472-ypubmed: 16284805google scholar: lookup
  33. Brooks SA, Lear TL, Adelson DL, Bailey E. A chromosome inversion near the KIT gene and the Tobiano spotting pattern in horses.. Cytogenet. Genome Res. 2007;119:225–230.
    doi: 10.1159/000112065pubmed: 18253033google scholar: lookup
  34. Holl HM, Brooks SA, Archer S, Brown K, Malvick J, Penedo MCT, Bellone RR. Variant in the RFWD3 gene associated with PATN1, a modifier of leopard complex spotting.. Anim. Genet. 2016;47:91–101.
    doi: 10.1111/age.12375pubmed: 26568529google scholar: lookup
  35. Hauswirth R, Haase B, Blatter M, Brooks S, Burger D, Drögemüller C, Gerber V, Henke D, Janda J, Jude R. Mutations in MITF and PAX3 cause “splashed white” and other white spotting phenotypes in horses.. PLoS Genet. 2012;8:e1002653.
    doi: 10.1371/journal.pgen.1002653pmc: PMC3325211pubmed: 22511888google scholar: lookup
  36. Hauswirth R, Jude R, Haase B, Bellone RR, Archer S, Holl H, Brooks SA, Tozaki T, Penedo MCT, Rieder S. Novel variants in the KIT and PAX3 genes in horses with white-spotted coat colour phenotypes.. Anim. Genet. 2013;44:763–765.
    doi: 10.1111/age.12057pubmed: 23659293google scholar: lookup
  37. Brooks SA, Palermo KM, Kahn A, Hein J. Impact of white-spotting alleles, including W20, on phenotype in the American Paint Horse.. Anim. Genet. 2020;51:707–715.
    doi: 10.1111/age.12960pubmed: 32686191google scholar: lookup
  38. Druml T, Grilz-Seger G, Neuditschko M, Horna M, Ricard A, Pausch H, Brem G. Novel insights into Sabino1 and splashed white coat color patterns in horses.. Anim. Genet. 2018;49:249–253.
    doi: 10.1111/age.12657pmc: PMC6001536pubmed: 29635692google scholar: lookup
  39. Rockwell H, Mack M, Famula T, Sandmeyer L, Bauer B, Dwyer A, Lassaline M, Beeson S, Archer S, McCue M. Genetic investigation of equine recurrent uveitis in Appaloosa horses.. Anim. Genet. 2020;51:111–116.
    doi: 10.1111/age.12883pubmed: 31793009google scholar: lookup
  40. Sandmeyer LS, Kingsley NB, Walder C, Archer S, Leis ML, Bellone RR, Bauer BS. Risk factors for equine recurrent uveitis in a population of Appaloosa horses in western Canada.. Vet. Ophthalmol. 2020;23:515–525.
    doi: 10.1111/vop.12749pubmed: 32086865google scholar: lookup
  41. Pielberg GR, Golovko A, Sundström E, Curik I, Lennartsson J, Seltenhammer MH, Druml T, Binns M, Fitzsimmons C, Lindgren G. A cis-acting regulatory mutation causes premature hair graying and susceptibility to melanoma in the horse.. Nat. Genet. 2008;40:1004–1009.
    doi: 10.1038/ng.185pubmed: 18641652google scholar: lookup
  42. Henkel J, Lafayette C, Brooks SA, Martin K, Patterson-Rosa L, Cook D, Jagannathan V, Leeb T. Whole-genome sequencing reveals a large deletion in the MITF gene in horses with white spotted coat colour and increased risk of deafness.. Anim. Genet. 2019;50:172–174.
    doi: 10.1111/age.12762pubmed: 30644113google scholar: lookup

Citations

This article has been cited 6 times.
  1. Lin S, Yang M, Zhu W, Yang C, Chen Y, Cong P, Liu X, He Z. Heterozygous deletion of exon 17 of the Kit gene impairs mouse spermatogenesis by attenuating MAPK-ERK signaling. Biol Res 2025 May 13;58(1):28.
    doi: 10.1186/s40659-025-00609-2pubmed: 40355978google scholar: lookup
  2. Bacon EK, Donnelly CG, Bellone RR, Haase B, Finno CJ, Velie BD. Preliminary investigation of potential links between pigmentation variants and opioid analgesic effectiveness in horses during cerebrospinal fluid centesis. BMC Vet Res 2024 Jul 12;20(1):311.
    doi: 10.1186/s12917-024-04139-zpubmed: 38997753google scholar: lookup
  3. Durward-Akhurst SA, Marlowe JL, Schaefer RJ, Springer K, Grantham B, Carey WK, Bellone RR, Mickelson JR, McCue ME. Predicted genetic burden and frequency of phenotype-associated variants in the horse. Sci Rep 2024 Apr 10;14(1):8396.
    doi: 10.1038/s41598-024-57872-8pubmed: 38600096google scholar: lookup
  4. Mura MC, Carcangiu V, Cosso G, Columbano N, Sanna Passino E, Luridiana S. Discrepancies between Genetic and Visual Coat Color Assignment in Sarcidano Horse. Animals (Basel) 2024 Feb 6;14(4).
    doi: 10.3390/ani14040543pubmed: 38396512google scholar: lookup
  5. McFadden A, Vierra M, Robilliard H, Martin K, Brooks SA, Everts RE, Lafayette C. Population Analysis Identifies 15 Multi-Variant Dominant White Haplotypes in Horses. Animals (Basel) 2024 Feb 5;14(3).
    doi: 10.3390/ani14030517pubmed: 38338160google scholar: lookup
  6. McFadden A, Vierra M, Martin K, Brooks SA, Everts RE, Lafayette C. Spotting the Pattern: A Review on White Coat Color in the Domestic Horse. Animals (Basel) 2024 Jan 30;14(3).
    doi: 10.3390/ani14030451pubmed: 38338094google scholar: lookup
Subscribe to our newsletter
Join 99,344 horse owners like you who receive our email updates on horse health and nutrition.