Whole genome sequencing reveals a novel deletion variant in the KIT gene in horses with white spotted coat colour phenotypes.
Abstract: White spotting phenotypes in horses can range in severity from the common white markings up to completely white horses. EDNRB, KIT, MITF, PAX3 and TRPM1 represent known candidate genes for such phenotypes in horses. For the present study, we re-investigated a large horse family segregating a variable white spotting phenotype, for which conventional Sanger sequencing of the candidate genes' individual exons had failed to reveal the causative variant. 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 ~1.9-kb deletion spanning exons 10-13 of the KIT gene (chr3:77,740,239_77,742,136del1898insTATAT). In continuity with previously named equine KIT variants we propose to designate the newly identified deletion variant W22. We had access to 21 horses carrying the W22 allele. Four of them were compound heterozygous W20/W22 and had a completely white phenotype. Our data suggest that W22 represents a true null allele of the KIT gene, whereas the previously identified W20 leads to a partial loss of function. These findings will enable more precise genetic testing for depigmentation phenotypes in horses.
© 2017 Stichting International Foundation for Animal Genetics.
Publication Date: 2017-04-26 PubMed ID: 28444912DOI: 10.1111/age.12556Google Scholar: Lookup
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Summary
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The researchers explored the genomes of horses with various degrees of white spotting to identify the genetic causes. They discovered a novel deletion variant in the KIT gene, designated as W22, that is associated with completely white coat colors, offering a more refined method for genetic testing of color patterns in horses.
Research Background
- The researchers underlined the variability in the extent of white spotting in horse phenotypes, ranging from small patches to completely white coats.
- They identified EDNRB, KIT, MITF, PAX3, and TRPM1 as potential genes impacting these color variations.
- The objective of the study was to review a large horse family exhibiting diverse white spotting, as past efforts to identify the precise variant through Sanger sequencing of individual exons of candidate genes were unsuccessful.
Methodology
- Using whole genome sequencing, the researchers examined data from an affected horse and focused on structural variants in the purported candidate genes.
- The findings highlighted a heterozygous deletion of approximately 1.9 kb size, spanning exons 10-13 of the KIT gene.
- This new deletion variant was named W22, in line with the nomenclature of previously recognized equine KIT variants.
Findings
- The research team studied 21 horses carrying the W22 allele.
- Among these, four horses were compound heterozygous W20/W22 and exhibited a completely white phenotype.
- The data points towards W22 as a null allele of the KIT gene, which indicates an absence of gene function.
- In comparison, the W20 variant seems to cause a partial loss of function.
Conclusion
- The identification of a new deletion variant in the KIT gene for white spotting in horses opens up avenues for more accurate genetic testing for depigmentation phenotypes.
- This can potentially aid breeders and geneticists in understanding and predicting coat color patterns in horses.
Cite This Article
APA
Dürig N, Jude R, Holl H, Brooks SA, Lafayette C, Jagannathan V, Leeb T.
(2017).
Whole genome sequencing reveals a novel deletion variant in the KIT gene in horses with white spotted coat colour phenotypes.
Anim Genet, 48(4), 483-485.
https://doi.org/10.1111/age.12556 Publication
Researcher Affiliations
- Vetsuisse Faculty, Institute of Genetics, University of Bern, 3001, Bern, Switzerland.
- DermFocus, University of Bern, 3001, Bern, Switzerland.
- Vetsuisse Faculty, Institute of Genetics, University of Bern, 3001, Bern, Switzerland.
- DermFocus, University of Bern, 3001, Bern, Switzerland.
- RJC, 53919, Weilerswist, Germany.
- Department of Animal Sciences, University of Florida, Gainesville, FL, 32611-0910, USA.
- Etalon Inc., Menlo Park, CA, 94025, USA.
- Department of Animal Sciences, University of Florida, Gainesville, FL, 32611-0910, USA.
- Etalon Inc., Menlo Park, CA, 94025, USA.
- Vetsuisse Faculty, Institute of Genetics, University of Bern, 3001, Bern, Switzerland.
- DermFocus, University of Bern, 3001, Bern, Switzerland.
- Vetsuisse Faculty, Institute of Genetics, University of Bern, 3001, Bern, Switzerland.
- DermFocus, University of Bern, 3001, Bern, Switzerland.
MeSH Terms
- Alleles
- Animals
- Hair Color / genetics
- Horses / genetics
- Phenotype
- Proto-Oncogene Proteins c-kit / genetics
- Sequence Deletion
Citations
This article has been cited 16 times.- 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).
- Patterson Rosa L, Martin K, Vierra M, Lundquist E, Foster G, Brooks SA, Lafayette C. A KIT Variant Associated with Increased White Spotting Epistatic to MC1R Genotype in Horses (Equus caballus). Animals (Basel) 2022 Aug 2;12(15).
- Bitaraf Sani M, Zare Harofte J, Banabazi MH, Faraz A, Esmaeilkhanian S, Naderi AS, Salim N, Teimoori A, Bitaraf A, Zadehrahmani M, Burger PA, Asadzadeh N, Silawi M, Taghipour Sheshdeh A, Mohammad Nazari B, Faghihi MA, Roudbari Z. Identification of Candidate Genes for Pigmentation in Camels Using Genotyping-by-Sequencing. Animals (Basel) 2022 Apr 23;12(9).
- 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).
- Huang T, Pu Y, Song C, Sheng Z, Hu X. A quantitative trait locus on chromosome 2 was identified that accounts for a substantial proportion of phenotypic variance of the yellow plumage color in chicken. Poult Sci 2020 Jun;99(6):2902-2910.
- Petersen JL, Kalbfleisch TS, Parris M, Tietze SM, Cruickshank J. MC1R and KIT Haplotypes Associate With Pigmentation Phenotypes of North American Yak (Bos grunniens). J Hered 2020 Apr 2;111(2):182-193.
- Nazari-Ghadikolaei A, Mehrabani-Yeganeh H, Miarei-Aashtiani SR, Staiger EA, Rashidi A, Huson HJ. Genome-Wide Association Studies Identify Candidate Genes for Coat Color and Mohair Traits in the Iranian Markhoz Goat. Front Genet 2018;9:105.
- Holl H, Isaza R, Mohamoud Y, Ahmed A, Almathen F, Youcef C, Gaouar S, Antczak DF, Brooks S. A Frameshift Mutation in KIT is Associated with White Spotting in the Arabian Camel. Genes (Basel) 2017 Mar 9;8(3).
- Sorin V, Sanchez MP, Drouilhet L, Tosser-Klopp G, Naji MM, Boichard D, Pausch H, Boussaha M, Leonard AS. Pangenome-based association testing between a structural variant located upstream of the KIT gene and head depigmentation across a diverse panel of cattle breeds. Genet Sel Evol 2026 Feb 26;58(1).
- Sharif MB, Mohaseb AF, Orlando L, Saliari K, Kunst GK, Czeika S, Mashkour M, Cucchi T, Peters J, Trixl S, Mohandesan E. Late Iron Age and Roman equine breeding north of the Alps: Genetic insights and cultural implications. iScience 2025 Sep 19;28(9):113224.
- 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).
- Milia S, Leonard AS, Mapel XM, Bernal Ulloa SM, Drögemüller C, Pausch H. Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle. Genome Res 2025 Apr 14;35(4):1041-1052.
- 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.
- 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.
- 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).
- 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).
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