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Population Analysis Identifies 15 Multi-Variant Dominant White Haplotypes in Horses.
Abstract: The influence of a horse's appearance on health, sentimental and monetary value has driven the desire to understand the etiology of coat color. White markings on the coat define inclusion for multiple horse breeds, but they may disqualify a horse from registration in other breeds. In domesticated horses (Equus caballus), 35 KIT alleles are associated with or cause depigmentation and white spotting. It is a common misconception among the general public that a horse can possess only two KIT variants. To correct this misconception, we used BEAGLE 5.4-phased NGS data to identify 15 haplotypes possessing two or more KIT variants previously associated with depigmentation phenotypes. We sourced photos for 161 horses comprising 12 compound genotypes with three or more KIT variants and employed a standardized method to grade depigmentation, yielding average white scores for each unique compound genotype. We found that 7 of the 12 multi-variant haplotypes resulted in significantly more depigmentation relative to the single-variant haplotypes (ANOVA). It is clear horses can possess more than two KIT variants, and future work aims to document phenotypic variations for each compound genotype.
Publication Date: 2024-02-05 PubMed ID: 38338160PubMed Central: PMC10854588DOI: 10.3390/ani14030517Google 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.
- 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 seeks to dispel a general misconception that horses can only possess two variants responsible for coat depigmentation by demonstrating that a horse can possess as many as 15 haplotypes each containing multiple depigmentation related variants.
Objective of the Study
- The researchers aimed to understand the diversity in horse coat color genetics, particularly the variants leading to depigmentation or white spotting on the horse’s coat.
Methodology
- To achieve this, they used advanced sequencing data processed by a software tool called BEAGLE 5.4 to identify haplotypes – or specific sets of genes inherited together from a single parent – which contained two or more depigmentation-related variants.
- They then gathered photographs of 161 horses with 12 different compound genotypes, those with three or more variants, after which they applied a consistent method to estimate the level of depigmentation in each case. This exercise yielded average scores for the extent of white coloration in each unique compound genotype.
Findings
- Through this systematic analysis, the researchers identified a total of 15 such multi-variant haplotypes.
- They found notable differences in depigmentation levels: 7 of the 12 multi-variant haplotypes resulted in significantly more lightening or white coloration compared to single-variant haplotypes. This result was statistically robust, determined via ANOVA (Analysis of Variance), a common statistical test used to compare the means of multiple groups.
Implications and Future Work
- In conclusion, this research clarifies that horses can indeed carry more than two depigmentation variants, thereby offering a more comprehensive understanding of horse coat color genetics.
- Going forward, the researchers intend to document the phenotypic variations (i.e., the observable traits or characteristics) associated with each compound genotype.
Cite This Article
APA
McFadden A, Vierra M, Robilliard H, Martin K, Brooks SA, Everts RE, Lafayette C.
(2024).
Population Analysis Identifies 15 Multi-Variant Dominant White Haplotypes in Horses.
Animals (Basel), 14(3).
https://doi.org/10.3390/ani14030517 Publication
Researcher Affiliations
- Etalon Inc., Menlo Park, CA 94025, USA.
- Etalon Inc., Menlo Park, CA 94025, USA.
- Etalon Inc., Menlo Park, CA 94025, USA.
- Etalon Inc., Menlo Park, CA 94025, USA.
- Department of Animal Sciences, UF Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
- Etalon Inc., Menlo Park, CA 94025, USA.
- Etalon Inc., Menlo Park, CA 94025, USA.
Conflict of Interest Statement
A.M., K.M., M.V., R.E., H.R. and C.L. are affiliated with Etalon Diagnostics which offers commercial diagnostic testing for white-spotting mutations, including Dominant White alleles.
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Citations
This article has been cited 4 times.- Everts RE, Caron R, Foster G, McLoone K, Martin K, Brooks SA, Lafayette C. Identification of Two Genetic Haplotypes Associated with the Roan Coat Color in the American Quarter Horse and Other Equine Breeds. Animals (Basel) 2025 Jun 9;15(12).
- Rodrigues GRD, Cyrillo JNSG, Mota LFM, Schmidt PI, Valente JPS, Oliveira ES, Albuquerque LG, Brito LF, Mercadante MEZ. Effect of genomic regions harboring putative lethal haplotypes on reproductive performance in closed experimental selection lines of Nellore cattle. Sci Rep 2025 Feb 3;15(1):4113.
- 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).
- 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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