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Home / Equine Research Bank / Animals (Basel) / A KIT Variant Associated with Increased White Spotting Epist...
Animals : an open access journal from MDPI2022; 12(15); 1958; doi: 10.3390/ani12151958

A KIT Variant Associated with Increased White Spotting Epistatic to MC1R Genotype in Horses (Equus caballus).

Abstract: Over 40 identified genetic variants contribute to white spotting in the horse. White markings and spotting are under selection for their impact on the economic value of an equine, yet many phenotypes have an unknown genetic basis. Previous studies also demonstrate an interaction between MC1R and ASIP pigmentation loci and white spotting associated with KIT and MITF. We investigated two stallions presenting with a white spotting phenotype of unknown cause. Exon sequencing of the KIT and MITF candidate genes identified a missense variant in KIT (rs1140732842, NC_009146.3:g.79566881T>C, p.T391A) predicted by SIFT and PROVEAN as not tolerated/deleterious. Three independent observers generated an Average Grade of White (AGW) phenotype score for 147 individuals based on photographs. The KIT variant demonstrates a significant QTL association to AGW (p = 3.3 × 10−12). Association with the MC1R Extension locus demonstrated that, although not in LD, MC1R e/e (chestnut) individuals had higher AGW scores than MC1R E/- individuals (p = 3.09 × 10−17). We also report complete linkage of the previously reported KIT W19 allele to this missense variant. We propose to term this variant W34, following the standardized nomenclature for white spotting variants within the equine KIT gene, and report its epistatic interaction with MC1R.
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Publication Date: 2022-08-02 PubMed ID: 35953947PubMed Central: PMC9367399DOI: 10.3390/ani12151958Google 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.

The research paper delves into the field of genetics, specifically concerning the white spotting on horses. The researchers discovered a new genetic variant contributing to this physical trait, which interacts with the MC1R pigmentation gene.

Introduction

  • The study revolves around investigating the genetics behind the white spotting observed in horses. These markings are not just aesthetically interesting but also have an impact on the economic value of a horse, making it a pertinent area of research in equine science.
  • The focus of this investigation was on two stallions that exhibited an unknown type of white spotting phenomenon. It had been established that over 40 genetic variants contribute to white spotting in horses, and this research sought to determine if there were yet undiscovered variants in the two horses under observation.

Methods and Findings

  • Researchers carried out detailed genetic testing and sequencing on these horses, focusing on possible variants within the KIT and MITF candidate genes.
  • They found a missense variant in KIT, which is a type of genetic change where one DNA base pair is swapped for another, resulting in a different amino acid in the protein that the gene codes for. This specific variant (rs1140732842) was predicted to be deleterious by the genetic analysis tools SIFT and PROVEAN, meaning it was likely to have an adverse effect on the organism.
  • An Average Grade of White (AGW) phenotype score was assessed for 147 individuals by three observers, creating a numerical measure of the white spotting.
  • Statistical analysis showed the newly discovered KIT variant had a significant correlation with this AGW score.

Interactions with the MC1R Extension Locus

  • Association with the MC1R Extension locus was also observed. While not in linkage disequilibrium (LD), which means the allele frequencies of the two genes do not change together, the researchers noticed that horses with the ‘chestnut’ MC1R e/e genotype had higher AGW scores than those with the MC1R E/- genotype.
  • This finding indicates that the KIT genetic variant that they found (termed W34) has an epistatic interaction with the MC1R gene; meaning, the effect of one gene (MC1R) is dependent on the presence of one or more ‘modifier genes’ (in this case, W34).

Linkage to KIT W19 Allele

  • The research also reveals a complete linkage of the newly found KIT W34 variant with a previously reported variant, KIT W19. Having two genetic markers linked together like this may assist with future genetic testing or breeding projects focused on white spotting in horses.

Cite This Article

APA
Patterson Rosa L, Martin K, Vierra M, Lundquist E, Foster G, Brooks SA, Lafayette C. (2022). A KIT Variant Associated with Increased White Spotting Epistatic to MC1R Genotype in Horses (Equus caballus). Animals (Basel), 12(15), 1958. https://doi.org/10.3390/ani12151958

Publication

Animals : an open access journal from MDPI
ISSN: 2076-2615
NlmUniqueID: 101635614
Country: Switzerland
Language: English
Volume: 12
Issue: 15
PII: 1958

Researcher Affiliations

Patterson Rosa, Laura
  • Etalon, Inc., Menlo Park, CA 94025, USA.
Martin, Katie
  • Etalon, Inc., Menlo Park, CA 94025, USA.
Vierra, Micaela
  • Etalon, Inc., Menlo Park, CA 94025, USA.
Lundquist, Erica
  • Etalon, Inc., Menlo Park, CA 94025, USA.
Foster, Gabriel
  • Etalon, Inc., Menlo Park, CA 94025, USA.
Brooks, Samantha A
  • Department of Animal Science, UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA.
Lafayette, Christa
  • Etalon, Inc., Menlo Park, CA 94025, USA.

Conflict of Interest Statement

All authors are affiliated with Etalon Diagnostics, which offers testing for white pattern variants.

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Citations

This article has been cited 6 times.
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