Identification of a Novel Haplotype Associated with Roan Coat Color in American Quarter Horses.
Abstract: Roan coat color is described as the dispersion of white hairs within an otherwise solid background-color coat. This phenotype is primarily expressed on the body of the horse, with the head and legs exhibiting few or no white hairs. Previous studies mapped the locus for roan to the region and observed linked variants in a small number of breeds. Recently, we reported evidence for two independent haplotypes, and , in the region, which account for approximately 38% and 36% of roan horses, respectively. In the current report, using whole genome sequencing for unknown roan samples. We present a third novel haplotype, , found in American Quarter Horses, that accounts for an additional 30% of American Quarter Horses negative for and that display the roan phenotype. Within this haplotype, we observe a variant chr3:79656505 (G > A), which we believe is a founder allele for the RN3 haplotype. In our sample set of horses, these three haplotypes account for more than 95% of the American Quarter Horse population studied and about 50-60% of roan horses in other breeds. Using whole genome sequencing of distantly related animals with a particular phenotype, together with a larger number of control horses, improves the odds of finding linked and/or causative variants.
Publication Date: 2025-08-14 PubMed ID: 40867714PubMed Central: PMC12383168DOI: 10.3390/ani15162386Google Scholar: Lookup
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- Journal Article
Summary
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Overview
- The study identifies a new genetic haplotype associated with the roan coat color in American Quarter Horses, expanding understanding of the genetic basis for this phenotype.
- This third haplotype explains a significant portion of roan horses previously unaccounted for by two known haplotypes.
Background
- Roan coat color in horses is characterized by a mixture of white hairs on a solid background coat, mostly visible on the body but sparing the head and legs.
- Previous research mapped roan-related genetic variants to a specific region on chromosome 3.
- Two independent haplotypes, RN1 and RN2, were earlier reported to explain about 38% and 36% of roan cases respectively.
Research Objective
- The study aimed to identify genetic factors accounting for roan phenotypes in American Quarter Horses that were negative for the known RN1 and RN2 haplotypes.
- Researchers used whole genome sequencing (WGS) on these unknown roan samples to find new causative variants.
Methods
- Whole genome sequencing was conducted on American Quarter Horses showing the roan phenotype but lacking the RN1 and RN2 haplotypes.
- Additional sequencing of control horses without roan phenotype was used to compare and validate findings.
Main Findings
- Discovery of a novel third haplotype, designated RN3, associated with the roan coat color in American Quarter Horses.
- The RN3 haplotype explains approximately 30% of roan horses that were negative for the earlier RN1 and RN2 haplotypes.
- A specific genetic variant at position chr3:79656505 (G > A) within this RN3 haplotype is proposed as a founder allele responsible for this phenotype.
- Together, RN1, RN2, and RN3 haplotypes account for more than 95% of roan American Quarter Horses in the sample set.
Broader Implications
- These three haplotypes explain about 50–60% of roan horses in other breeds, suggesting shared genetic mechanisms across breeds.
- The identification of multiple independent haplotypes highlights genetic complexity and diversity in the expression of coat color traits.
- Whole genome sequencing of phenotypically affected but genetically unexplained animals improves the likelihood of discovering new causative variants.
Conclusion
- The study advances the genetic understanding of roan coat color in horses by identifying a novel haplotype in American Quarter Horses.
- This work enhances genetic testing approaches to predict or identify roan phenotype carriers in breeding programs.
- It emphasizes the value of comprehensive genome sequencing and large sample comparisons for complex trait dissection.
Cite This Article
APA
Everts RE, Caron R, Foster G, McLoone K, Simiele L, Martin K, Brooks SA, Lafayette C.
(2025).
Identification of a Novel Haplotype Associated with Roan Coat Color in American Quarter Horses.
Animals (Basel), 15(16), 2386.
https://doi.org/10.3390/ani15162386 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.
- 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.
Conflict of Interest Statement
All authors are affiliated with Etalon, Inc., which offers diagnostic testing for coat color and disease testing.
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