FREE SHIPPING over $40
OVER 10000 FIVE-STAR REVIEWS
5% OFF ALL SUBSCRIPTIONS
100% HAPPINESS GUARANTEE
Analyze Diet
0
The Journal of heredity2020; 111(3); 287-293; doi: 10.1093/jhered/esaa009

A De Novo MITF Deletion Explains a Novel Splashed White Phenotype in an American Paint Horse.

Abstract: Splashed white is a coat color pattern in horses characterized by extensive white patterning on the legs, belly, and face often accompanied by blue eyes and deafness. Three mutations in microphthalmia-associated transcription factor (MITF) and two mutations in Paired Box 3 (PAX3) have been identified that explain splashed white patterns (SW1-SW5). An American Paint Horse stallion with a splashed white phenotype and blue eyes, whose parents were not white patterned, was negative for the 5 known splashed white variants and other known white spotting alleles. This novel splashed white phenotype (SW6) was hypothesized to be caused by a de novo mutation in MITF or PAX3. Analysis of whole-genome sequencing using the EquCab3.0 reference genome for comparison identified an 8.7 kb deletion in MITF on ECA16 (NC_009159.3:g.21551060-21559770del). The deletion encompassed part of intron 7 through the 3' UTR of exon 9 of MITF, including the helix-loop-helix DNA-binding domain (ENSECAT00000006375.3). This variant is predicted to truncate protein and impair binding to DNA. Sanger sequencing confirmed the stallion was heterozygous for the MITF deletion. No single nucleotide polymorphisms (SNPs) or structural variants were identified in PAX3 or any of the other candidate genes that were unique to the stallion or predicted to affect protein function. Genotyping five of the stallion's splashed white offspring, including one all white foal, found that they were also heterozygous for the deletion. Given the role of MITF in producing white pattern phenotypes, and the predicted deleterious effect of this mutation, this 8.7 kb deletion is the likely causal variant for SW6.
© The American Genetic Association 2020.
Get Full Text
Publication Date: 2020-04-04 PubMed ID: 32242630PubMed Central: PMC7238438DOI: 10.1093/jhered/esaa009Google 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.

This research explores a unique color pattern, known as splashed white, found in an American Paint Horse that couldn’t be explained by standard genetic variants. The study identifies a new genetic mutation in the Microphthalmia-associated Transcription Factor (MITF), potentially responsible for this different color pattern.

Introduction

  • The study focuses on a specific horse color pattern known as splashed white. This pattern is typically associated with white markings on the legs, belly, and face of the horse, often accompanied by blue eyes and potential deafness.
  • Genetically, the splashed white phenotype is known to be caused by mutations in the MITF and PAX3 genes.
  • However, an American Paint Horse displaying this pattern showed no existing variants in these genes, piquing the researchers’ interest and prompting this study.

Basis of the Study

  • An American Paint Horse stallion exhibited splashed white pigmentation and blue eyes, although its parents didn’t have this white pattern. When tested, the stallion didn’t carry any of the five known splashed white variants or other known white spotting alleles, indicating a potential new variant, SW6.
  • The researchers hypothesized that this novel pattern could be due to a de novo mutation in either the MITF or PAX3 genes – de novo meaning it hadn’t occurred in the parents but had newly emerged in the stallion.

Findings

  • Using the EquCab3.0 reference genome for comparison, the researchers analyzed whole-genome sequencing data and discovered a unique 8.7 kb deletion in the MITF gene on the stallion’s ECA16 chromosome.
  • The deletion spanned part of intron 7 through the 3′ UTR of exon 9 of MITF, including the helix-loop-helix DNA-binding domain. This alteration could truncate protein and impair DNA binding, thus causing the unique color pattern.
  • Upon further analysis, the researchers found that the stallion was heterozygous for the MITF deletion, meaning it carried both a normal and a mutated copy of the gene.
  • No unique single nucleotide polymorphisms (SNPs) or structural variants in PAX3 or any other candidate genes that could have influenced the phenotype were found in the stallion.

Confirmation of Findings

  • The research team also confirmed their findings through genetic testing of five of the stallion’s splashed white offspring, including one all-white foal. All offspring also were heterozygous for the deletion. This reinforces the belief that this novel MITF deletion could be the cause of the SW6 variant.

Conclusion

  • The study concludes that the identified 8.7 kb deletion in the MITF gene might be the causal mutation for the novel splashed white phenotype, named SW6, as this gene is known for producing white pattern phenotypes, and the mutation is predicted to have a detrimental effect.

Cite This Article

APA
Magdesian KG, Tanaka J, Bellone RR. (2020). A De Novo MITF Deletion Explains a Novel Splashed White Phenotype in an American Paint Horse. J Hered, 111(3), 287-293. https://doi.org/10.1093/jhered/esaa009

Publication

The Journal of heredity
ISSN: 1465-7333
NlmUniqueID: 0375373
Country: United States
Language: English
Volume: 111
Issue: 3
Pages: 287-293

Researcher Affiliations

Magdesian, K Gary
  • Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California-Davis, Davis, CA.
Tanaka, Jocelyn
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA.
Bellone, Rebecca R
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA.
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA.

MeSH Terms

  • Animals
  • Gene Deletion
  • Hair Color / genetics
  • Horses / genetics
  • Male
  • Microphthalmia-Associated Transcription Factor / genetics
  • Mutation
  • PAX3 Transcription Factor / genetics
  • Phenotype
  • Sequence Analysis, DNA

References

This article includes 26 references
  1. Amyere M, Vogt T, Hoo J, Brandrup F, Bygum A, Boon L, Vikkula M. KITLG mutations cause familial progressive hyper- and hypopigmentation.. J Invest Dermatol 2011 Jun;131(6):1234-9.
    pubmed: 21368769doi: 10.1038/jid.2011.29google scholar: lookup
  2. Bellone RR, Holl H, Setaluri V, Devi S, Maddodi N, Archer S, Sandmeyer L, Ludwig A, Foerster D, Pruvost M, Reissmann M, Bortfeldt R, Adelson DL, Lim SL, Nelson J, Haase B, Engensteiner M, Leeb T, Forsyth G, Mienaltowski MJ, Mahadevan P, Hofreiter M, Paijmans JL, Gonzalez-Fortes G, Grahn B, Brooks SA. 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(10):e78280.
    pmc: PMC3805535pubmed: 24167615doi: 10.1371/journal.pone.0078280google scholar: lookup
  3. Bendl J, Musil M, Štourač J, Zendulka J, Damborský J, Brezovský J. PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions.. PLoS Comput Biol 2016 May;12(5):e1004962.
    pmc: PMC4880439pubmed: 27224906doi: 10.1371/journal.pcbi.1004962google scholar: lookup
  4. Blatter M, Haase B, Gerber V, Poncet PA, Leeb T, Rieder S, Henke D, Janett F, Burger D. [Clinical evaluation of the new coat colour macchiato in a male Franches-Montagnes horse].. Schweiz Arch Tierheilkd 2013 Apr;155(4):229-32.
    pubmed: 23531944doi: 10.1024/0036-7281/a000451google scholar: lookup
  5. Brooks SA, Bailey E. Exon skipping in the KIT gene causes a Sabino spotting pattern in horses.. Mamm Genome 2005 Nov;16(11):893-902.
    pubmed: 16284805doi: 10.1007/s00335-005-2472-ygoogle scholar: lookup
  6. 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(3-4):225-30.
    pubmed: 18253033doi: 10.1159/000112065google scholar: lookup
  7. Chandra Mohan SLN. Case of Waardenburg Shah syndrome in a family with review of literature.. J Otol 2018 Sep;13(3):105-110.
    pmc: PMC6291636pubmed: 30559775doi: 10.1016/j.joto.2018.05.005google scholar: lookup
  8. Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.. Fly (Austin) 2012 Apr-Jun;6(2):80-92.
    pmc: PMC3679285pubmed: 22728672doi: 10.4161/fly.19695google scholar: lookup
  9. 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 Jun;49(3):249-253.
    pmc: PMC6001536pubmed: 29635692doi: 10.1111/age.12657google scholar: lookup
  10. Grill C, Bergsteinsdóttir K, Ogmundsdóttir MH, Pogenberg V, Schepsky A, Wilmanns M, Pingault V, Steingrímsson E. MITF mutations associated with pigment deficiency syndromes and melanoma have different effects on protein function.. Hum Mol Genet 2013 Nov 1;22(21):4357-67.
    pmc: PMC3888191pubmed: 23787126doi: 10.1093/hmg/ddt285google scholar: lookup
  11. Hauswirth R, Haase B, Blatter M, Brooks SA, Burger D, Drögemüller C, Gerber V, Henke D, Janda J, Jude R, Magdesian KG, Matthews JM, Poncet PA, Svansson V, Tozaki T, Wilkinson-White L, Penedo MC, Rieder S, Leeb T. Mutations in MITF and PAX3 cause "splashed white" and other white spotting phenotypes in horses.. PLoS Genet 2012;8(4):e1002653.
    pmc: PMC3325211pubmed: 22511888doi: 10.1371/journal.pgen.1002653google scholar: lookup
  12. Hauswirth R, Jude R, Haase B, Bellone RR, Archer S, Holl H, Brooks SA, Tozaki T, Penedo MC, Rieder S, Leeb T. Novel variants in the KIT and PAX3 genes in horses with white-spotted coat colour phenotypes.. Anim Genet 2013 Dec;44(6):763-5.
    pubmed: 23659293doi: 10.1111/age.12057google scholar: lookup
  13. 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 Apr;50(2):172-174.
    pubmed: 30644113doi: 10.1111/age.12762google scholar: lookup
  14. Baranowska Körberg I, Sundström E, Meadows JR, Rosengren Pielberg G, Gustafson U, Hedhammar Å, Karlsson EK, Seddon J, Söderberg A, Vilà C, Zhang X, Åkesson M, Lindblad-Toh K, Andersson G, Andersson L. A simple repeat polymorphism in the MITF-M promoter is a key regulator of white spotting in dogs.. PLoS One 2014;9(8):e104363.
    pmc: PMC4130573pubmed: 25116146doi: 10.1371/journal.pone.0104363google scholar: lookup
  15. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform.. Bioinformatics 2009 Jul 15;25(14):1754-60.
    pmc: PMC2705234pubmed: 19451168doi: 10.1093/bioinformatics/btp324google scholar: lookup
  16. Mack M, Kowalski E, Grahn R, Bras D, Penedo MCT, Bellone R. Two Variants in SLC24A5 Are Associated with "Tiger-Eye" Iris Pigmentation in Puerto Rican Paso Fino Horses.. G3 (Bethesda) 2017 Aug 7;7(8):2799-2806.
    pmc: PMC5555483pubmed: 28655738doi: 10.1534/g3.117.043786google scholar: lookup
  17. 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 Nov 15;235(10):1204-11.
    pubmed: 19912043doi: 10.2460/javma.235.10.1204google scholar: lookup
  18. Metallinos DL, Bowling AT, Rine J. 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 Jun;9(6):426-31.
    pubmed: 9585428doi: 10.1007/s003359900790google scholar: lookup
  19. Philipp U, Lupp B, Mömke S, Stein V, Tipold A, Eule JC, Rehage J, Distl O. A MITF mutation associated with a dominant white phenotype and bilateral deafness in German Fleckvieh cattle.. PLoS One 2011;6(12):e28857.
    pmc: PMC3236222pubmed: 22174915doi: 10.1371/journal.pone.0028857google scholar: lookup
  20. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. Integrative genomics viewer.. Nat Biotechnol 2011 Jan;29(1):24-6.
    pmc: PMC3346182pubmed: 21221095doi: 10.1038/nbt.1754google scholar: lookup
  21. Seitz JJ, Schmutz SM, Thue TD, Buchanan FC. A missense mutation in the bovine MGF gene is associated with the roan phenotype in Belgian Blue and Shorthorn cattle.. Mamm Genome 1999 Jul;10(7):710-2.
    pubmed: 10384045doi: 10.1007/s003359901076google scholar: lookup
  22. Vachtenheim J, Borovanský J. "Transcription physiology" of pigment formation in melanocytes: central role of MITF.. Exp Dermatol 2010 Jul 1;19(7):617-27.
    pubmed: 20201954doi: 10.1111/j.1600-0625.2009.01053.xgoogle scholar: lookup
  23. Wang HH, Chen HS, Li HB, Zhang H, Mei LY, He CF, Wang XW, Men MC, Jiang L, Liao XB, Wu H, Feng Y. Identification and functional analysis of a novel mutation in the SOX10 gene associated with Waardenburg syndrome type IV.. Gene 2014 Mar 15;538(1):36-41.
    pubmed: 24440785doi: 10.1016/j.gene.2014.01.026google scholar: lookup
  24. Weich K, Affolter V, York D, Rebhun R, Grahn R, Kallenberg A, Bannasch D. Pigment Intensity in Dogs is Associated with a Copy Number Variant Upstream of KITLG.. Genes (Basel) 2020 Jan 9;11(1).
    pmc: PMC7017362pubmed: 31936656doi: 10.3390/genes11010075google scholar: lookup
  25. Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden TL. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction.. BMC Bioinformatics 2012 Jun 18;13:134.
    pmc: PMC3412702pubmed: 22708584doi: 10.1186/1471-2105-13-134google scholar: lookup
  26. Zhang H, Luo H, Chen H, Mei L, He C, Jiang L, Li JD, Feng Y. Functional analysis of MITF gene mutations associated with Waardenburg syndrome type 2.. FEBS Lett 2012 Nov 30;586(23):4126-31.
    pubmed: 23098757doi: 10.1016/j.febslet.2012.10.006google scholar: lookup

Citations

This article has been cited 10 times.
  1. Avila F, Hughes SS, Magdesian KG, Penedo MCT, Bellone RR. Breed Distribution and Allele Frequencies of Base Coat Color, Dilution, and White Patterning Variants across 28 Horse Breeds. Genes (Basel) 2022 Sep 13;13(9).
    doi: 10.3390/genes13091641pubmed: 36140807google scholar: lookup
  2. Guo Q, Jiang Y, Wang Z, Bi Y, Chen G, Bai H, Chang G. Genome-Wide Analysis Identifies Candidate Genes Encoding Beak Color of Duck. Genes (Basel) 2022 Jul 18;13(7).
    doi: 10.3390/genes13071271pubmed: 35886054google scholar: lookup
  3. Esdaile E, Kallenberg A, Avila F, Bellone RR. Identification of W13 in the American Miniature Horse and Shetland Pony Populations. Genes (Basel) 2021 Dec 14;12(12).
    doi: 10.3390/genes12121985pubmed: 34946933google scholar: lookup
  4. Jafari H, Abebe BK, Cong L, Ahmed Z, Zhaofei W, Sun M, Muhatai G, Chuzhao L, Dang R. Review: Genomic insights into the adaptive traits and stress resistance in modern horses. Stress Biol 2026 Jan 12;6(1):5.
    doi: 10.1007/s44154-025-00274-1pubmed: 41521281google scholar: lookup
  5. Kassymbekova SN, Bimenova ZZ, Iskhan KZ, Sobiech P, Jastrzebski JP, Brym P, Babis W, Kalykova AS, Otebayev ZM, Kabylbekova DI, Baneh H, Romanov MN. Uncovering Genetic Diversity and Adaptive Candidate Genes in the Mugalzhar Horse Breed Using Whole-Genome Sequencing Data. Animals (Basel) 2025 Sep 11;15(18).
    doi: 10.3390/ani15182667pubmed: 41007912google scholar: lookup
  6. Obradovic NA, McFadden A, Martin K, Vierra M, McLoone K, Martin E, Thomas A, Everts RE, Brooks SA, Lafayette C. Three Novel KIT Polymorphisms Found in Horses with White Coat Color Phenotypes. Animals (Basel) 2025 Mar 22;15(7).
    doi: 10.3390/ani15070915pubmed: 40218308google scholar: lookup
  7. Dai D, Sari EM, Si J, Ashari H, Dagong MIA, Pauciullo A, Lenstra JA, Han J, Zhang Y. Genomic analysis reveals the association of KIT and MITF variants with the white spotting in swamp buffaloes. BMC Genomics 2024 Jul 24;25(1):713.
    doi: 10.1186/s12864-024-10634-2pubmed: 39048931google scholar: lookup
  8. Liu X, Peng Y, Zhang X, Wang X, Chen W, Kou X, Liang H, Ren W, Khan MZ, Wang C. Coloration in Equine: Overview of Candidate Genes Associated with Coat Color Phenotypes. Animals (Basel) 2024 Jun 17;14(12).
    doi: 10.3390/ani14121802pubmed: 38929421google scholar: lookup
  9. Rudd Garces G, Farke D, Schmidt MJ, Letko A, Schirl K, Abitbol M, Leeb T, Lyons LA, Lühken G. PAX3 haploinsufficiency in Maine Coon cats with dominant blue eyes and hearing loss resembling the human Waardenburg syndrome. G3 (Bethesda) 2024 Sep 4;14(9).
    doi: 10.1093/g3journal/jkae131pubmed: 38869246google scholar: lookup
  10. 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 99,727 horse owners like you who receive our email updates on horse health and nutrition.