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Home / Equine Research Bank / Anim Genet / Whole-genome sequencing reveals a large deletion in the MITF...
Animal genetics2019; 50(2); 172-174; doi: 10.1111/age.12762

Whole-genome sequencing reveals a large deletion in the MITF gene in horses with white spotted coat colour and increased risk of deafness.

Abstract: White spotting phenotypes in horses are highly valued in some breeds. They are quite variable and may range from the common white markings up to completely white horses. EDNRB, KIT, MITF, PAX3 and TRPM1 represent known candidate genes for white spotting phenotypes in horses. For the present study, we investigated an American Paint Horse family segregating a phenotype involving white spotting and blue eyes. Six of eight horses with the white-spotting phenotype were deaf. We obtained whole-genome sequence data from an affected horse and specifically searched for structural variants in the known candidate genes. This analysis revealed a heterozygous ~63-kb deletion spanning exons 6-9 of the MITF gene (chr16:21 503 211-21 566 617). We confirmed the breakpoints of the deletion by PCR and Sanger sequencing. PCR-based genotyping revealed that all eight available affected horses from the family carried the deletion. The finding of an MITF variant fits well with the syndromic phenotype involving both depigmentation and an increased risk for deafness and corresponds to human Waardenburg syndrome type 2A. Our findings will enable more precise genetic testing for depigmentation phenotypes in horses.
© 2019 Stichting International Foundation for Animal Genetics.
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Publication Date: 2019-01-15 PubMed ID: 30644113DOI: 10.1111/age.12762Google Scholar: Lookup
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  • Journal Article

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 investigates the genetic cause of the white spotting phenotype and related deafness in certain breeds of horses. A genome analysis of affected horses from an American Paint Horse family revealed a large deletion in the MITF gene, which may be responsible for these conditions.

Objective of the Study

  • The study aimed to identify the genetic cause behind a unique phenotype in horses where the animals exhibit white spotting and blue eyes. This set of characteristics were observed in an American Paint Horse family where six out of eight horses showing these traits were reportedly deaf. By performing a whole-genome sequence analysis on the affected horses, the researchers hoped to isolate the responsible gene variant.

Methodology

  • Whole-genome sequencing was performed on a horse with the mentioned phenotype. The researchers carried out a detailed search for structural variants in the known candidate genes (EDNRB, KIT, MITF, PAX3, TRPM1) that might be responsible for this genetic characteristic.
  • The specific structural variant they found was a large, heterozygous deletion spanning exons 6-9 of the MITF gene.
  • The researchers then carried out PCR (Polymerase Chain Reaction) and Sanger sequencing to confirm the breakpoints of the deletion.
  • PCR-based genotyping was then done on all eight available affected horses from the family to check if they carried the same deletion.

Findings

  • The researchers found that all eight horses from the family who exhibited the phenotype carried the same deletion in the MITF gene.
  • The presence of this MITF variant correlates with the observed syndromic phenotype involving both depigmentation (white spotting) and increased risk for deafness. This similarity suggests a syndromic disorder akin to human Waardenburg syndrome type 2A, which also involves depigmentation and increased risk of deafness.
  • Based on the observed variant, the researchers believe genetic testing can be fine-tuned to accurately predict depigmentation phenotypes in horses.

Cite This Article

APA
Henkel J, Lafayette C, Brooks SA, Martin K, Patterson-Rosa L, Cook D, Jagannathan V, Leeb T. (2019). 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, 50(2), 172-174. https://doi.org/10.1111/age.12762

Publication

Animal genetics
ISSN: 1365-2052
NlmUniqueID: 8605704
Country: England
Language: English
Volume: 50
Issue: 2
Pages: 172-174

Researcher Affiliations

Henkel, J
  • Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.
  • DermFocus, University of Bern, 3001, Bern, Switzerland.
Lafayette, C
  • Etalon Inc., Menlo Park, CA, 94025, USA.
Brooks, S A
  • Department of Animal Sciences, University of Florida, Gainesville, FL, 32611-0910, USA.
Martin, K
  • Etalon Inc., Menlo Park, CA, 94025, USA.
Patterson-Rosa, L
  • Department of Animal Sciences, University of Florida, Gainesville, FL, 32611-0910, USA.
Cook, D
  • Etalon Inc., Menlo Park, CA, 94025, USA.
Jagannathan, V
  • Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.
  • DermFocus, University of Bern, 3001, Bern, Switzerland.
Leeb, T
  • Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.
  • DermFocus, University of Bern, 3001, Bern, Switzerland.

MeSH Terms

  • Animals
  • Color
  • Deafness / genetics
  • Deafness / veterinary
  • Female
  • Gene Deletion
  • Horse Diseases / genetics
  • Horses / genetics
  • Male
  • Microphthalmia-Associated Transcription Factor / genetics
  • Microphthalmia-Associated Transcription Factor / metabolism
  • Pigmentation / genetics
  • Risk Factors
  • Whole Genome Sequencing / veterinary

Grant Funding

  • 31003A_172964 / Swiss National Science Foundation

Citations

This article has been cited 7 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. Jia X, Ding P, Chen S, Zhao S, Wang J, Lai S. Analysis of MC1R, MITF, TYR, TYRP1, and MLPH Genes Polymorphism in Four Rabbit Breeds with Different Coat Colors.. Animals (Basel) 2021 Jan 5;11(1).
    doi: 10.3390/ani11010081pubmed: 33466315google scholar: lookup
  5. Silva ILS, Junqueira GSB, Oliveira CAA, Costa RB, DE Camargo GMF. Inconsistencies in horse coat color registration: A case study.. J Equine Sci 2020 Oct;31(3):57-60.
    doi: 10.1294/jes.31.57pubmed: 33061785google scholar: lookup
  6. 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 May 20;111(3):287-293.
    doi: 10.1093/jhered/esaa009pubmed: 32242630google scholar: lookup
  7. Raudsepp T, Finno CJ, Bellone RR, Petersen JL. Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post-genome era.. Anim Genet 2019 Dec;50(6):569-597.
    doi: 10.1111/age.12857pubmed: 31568563google scholar: lookup
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