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Home / Equine Research Bank / BMC Genomics / A genome-wide investigation of insidious uveitis in Appaloos...
BMC genomics2025; 26(1); 904; doi: 10.1186/s12864-025-12099-3

A genome-wide investigation of insidious uveitis in Appaloosa horses.

Abstract: Equine recurrent uveitis (ERU), an inflammatory eye disease, is the leading cause of blindness among horses. Insidious uveitis, a form of ERU, is especially pervasive within the Appaloosa breed and is highly heritable (h = 0.68-1.0). To date only one risk locus, leopard complex (LP), has been identified, and it explained 0.16-0.33 of the heritability estimate, suggesting that insidious uveitis is a complex genetic disease within the Appaloosa horse breed with multiple unknown predisposing loci. Results: A genome-wide association study (GWAS) using relatedness, LP genotype, sex, and age as covariates was performed on a sample of 96 Appaloosas (36 cases and 60 controls) and identified a 9.7 Kb region of association on ECA X (chrX:14528106-14537812) as significantly associated (P = 2.11 × 10). Sex stratification followed by meta-analysis provided additional support for the association on ECA X (P = 1.35 × 10). A logistic regression model was performed to test for epistasis between LP and the locus on ECA X, and the results did not support an interaction between the two loci. In the second phase of the study, single-nucleotide variants (SNVs) were identified in the region on ECA X by whole genome sequencing (WGS) of 18 horses from the GWAS (9 cases and 9 controls). Five reference markers from the GWAS, two previously associated coat color loci (LP and PATN1), and 102 SNVs were further evaluated in a combined dataset of 157 horses (70 cases and 87 controls, including the original 96 horses from the GWAS). Using logistic regression, none of the SNVs identified from the WGS analysis were significantly associated with phenotype; however, LP and the top three SNP markers from ECA X (ECA X: 14.5 Mb) were significantly associated in the larger dataset (P = 2.34 × 10 and P = 4.06 × 10). Conclusions: In addition to the LP locus, our investigation identified a locus on chromosome X with a significant association to insidious uveitis in Appaloosas. Replication testing in an independent cohort is necessary to determine if this locus is indeed a causal risk locus.
© 2025. The Author(s).
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Publication Date: 2025-10-09 PubMed ID: 41068571PubMed Central: PMC12513139DOI: 10.1186/s12864-025-12099-3Google 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.

Overview

  • This study identifies a genetic region on the X chromosome associated with insidious uveitis, a painful inflammatory eye disease causing blindness in Appaloosa horses, alongside a previously known risk locus.
  • The research suggests that multiple genetic factors contribute to insidious uveitis in this breed, providing a deeper understanding of the disease’s complex genetic basis.

Background

  • Equine recurrent uveitis (ERU) is the primary cause of blindness in horses, characterized by repeated episodes of eye inflammation.
  • Insidious uveitis is a specific form of ERU prevalent in Appaloosa horses, known for its subtle onset but chronic progression.
  • The disease has a very high heritability in this breed, with estimates between 0.68 and 1.0, indicating strong genetic influences.
  • Previously, only one genetic marker, the leopard complex (LP) locus, was linked to the disease but accounted for only a fraction of the genetic risk.

Study Objectives and Design

  • The study aimed to uncover additional genetic loci contributing to insidious uveitis in Appaloosas beyond the known LP locus.
  • A genome-wide association study (GWAS) was conducted using samples from 96 horses (36 affected cases and 60 unaffected controls).
  • Covariates such as genetic relatedness, LP genotype, sex, and age were included in the analysis to control for confounding factors.
  • Follow-up whole genome sequencing (WGS) was performed on a subset of 18 horses (9 cases and 9 controls) to identify single-nucleotide variants (SNVs) in the associated genomic regions.
  • A larger combined dataset of 157 horses was then used to analyze associations of identified variants with disease status.

Key Results

  • The GWAS identified a significant association with a 9.7 Kb region on the X chromosome (ECA X: chrX:14528106-14537812), showing a strong statistical signal.
  • Sex-stratified analysis supported this association, important as the region lies on the sex chromosome where males and females have different genetic architectures.
  • Testing for interaction (epistasis) between the LP locus and the new X chromosome locus indicated no significant interaction, suggesting independent genetic effects.
  • Whole genome sequencing revealed 102 SNVs in the associated X chromosome region, but none of these variants alone were significantly associated in the larger dataset.
  • The LP locus and the top three SNPs from the X chromosome region remained significantly associated with insidious uveitis in the larger sample.

Conclusions and Implications

  • This study expanded understanding of the genetic complexity underlying insidious uveitis in Appaloosa horses by identifying a novel locus on chromosome X linked to disease susceptibility.
  • The findings suggest that multiple independent genetic factors—including LP and the new X chromosome region—contribute to disease risk.
  • The absence of epistasis between these loci implies that they may contribute to disease risk via separate biological pathways.
  • More research, including replication in independent cohorts, is needed to confirm causality and to understand the functional role of the newly identified locus.
  • Ultimately, identifying genetic risk factors aids in potential disease prediction, breeding decisions, and may guide development of treatments or preventative strategies for this blinding disease.

Cite This Article

APA
Kingsley NB, Sandmeyer L, Dwyer A, Langefeld CD, McMullen RJ, McCue M, Lassaline M, Bellone RR. (2025). A genome-wide investigation of insidious uveitis in Appaloosa horses. BMC Genomics, 26(1), 904. https://doi.org/10.1186/s12864-025-12099-3

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 26
Issue: 1
Pages: 904
PII: 904

Researcher Affiliations

Kingsley, N B
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, Davis, CA, 95616, USA.
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, 95616, USA.
Sandmeyer, L
  • Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan , S7N 5B4, Canada.
Dwyer, A
  • Genesee Valley Equine Clinic, LLC, Scottsville, NY, 14546, USA.
Langefeld, C D
  • Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, 27101, USA.
  • Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, 27101, USA.
McMullen, R J
  • Equine Department, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
McCue, M
  • Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA.
Lassaline, M
  • School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
Bellone, R R
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, Davis, CA, 95616, USA. rbellone@ucdavis.edu.
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, 95616, USA. rbellone@ucdavis.edu.

MeSH Terms

  • Animals
  • Horses / genetics
  • Genome-Wide Association Study
  • Horse Diseases / genetics
  • Uveitis / genetics
  • Uveitis / veterinary
  • Male
  • Female
  • Polymorphism, Single Nucleotide
  • Genetic Predisposition to Disease
  • Genotype

Grant Funding

  • D16EQ-028 / Morris Animal Foundation
  • D16EQ-028 / Morris Animal Foundation
  • 22-J / Center for Equine Health
  • 22-J / Center for Equine Health

Conflict of Interest Statement

Declarations. Ethics approval and consent to participate: All protocols were approved by the Institutional Animal Care and Use Committee at the University of California, Davis (18851, 20699, and 22466) or by the Animal Care Committee at the University of Saskatchewan (20110053). All owners provided written informed consent for study participation. Consent for publication: Not applicable. Competing interests: Nicole B. Kingsley and Rebecca R. Bellone are affiliated with the UC Davis Veterinary Genetics Laboratory, a service laboratory offering diagnostic genetic tests for horses and other animal species.

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