About

Dr. Rebecca R. Bellone is a professor involved in veterinary genetics research at UC Davis, with a focus on equine genetic projects. Her research interests include investigating traits in horses that are economically and medically important, serving as models for other species including humans. She specializes in the genetics of ocular disorders, pigmentation, and their connections, with a long-standing passion for studying the genetics of Appaloosa spotting patterns. Her team discovered the mutation responsible for leopard complex spotting (LP mutation), which is associated with white spotting patterns and congenital stationary night blindness (CSNB) in horses. They also identified a second gene, PATN1, that modifies the size of white patterns. Her work includes developing genetic tests for these traits, which are offered at the UC Davis Veterinary Genetics Laboratory. Dr. Bellone’s team is actively investigating other genes influencing pigmentation and ocular conditions, such as Equine Recurrent Uveitis (ERU) and ocular squamous cell carcinoma, identifying genetic risk factors and contributing to improved clinical management. Her research extends to understanding genetic diversity and health traits in breeds like the Standardbred, aiming to develop tools for informed breeding and management decisions. She is dedicated to training graduate and undergraduate students, leading a team that collaborates with scientists globally to advance knowledge in equine genetics.

Research topics

• Biology
• Genetics
• Cell biology
• Pathology
• Computational biology
• Surgery
• Medicine
• Physiology

Selected publications

• An intronic variant in Ferredoxin Reductase (FDXR) creates a cryptic exon in Quarter Horses with Equine Juvenile Spinocerebellar Ataxia

  PLoS Genetics · 2026-05-20

  articleOpen access

  Equine Juvenile Spinocerebellar Ataxia (EJSCA) is a novel autosomal recessive neurologic disease in Quarter Horses. Affected foals display a progressive proprioceptive ataxia by 1-5 weeks of age, leading to recumbency and necessitating euthanasia. Whole genome sequencing was performed on 7 EJSCA cases and unaffected horses that included 4 obligate carriers, 4 unaffected half or full-siblings, and 28 unrelated, unaffected control Quarter Horses. An 82 kb region of association was identified (EquCab3.0, chr11: 6963986-7045999), containing 9 candidate SNPs across four genes (FADS6, FDXR, GRIN2C and TMEM104). Decreased FDXR mRNA expression and a cryptic exon was identified in spinal cord tissue from EJSCA cases via RNA-sequencing. One of the 9 associated SNPs (FDXR-203 c.177 + 1778G > C) was the eighth base pair of this cryptic exon. Affected foals were all homozygous for the variant. Protein concentrations of FDXR were lower in EJSCA cases in spinal cord and liver compared to unaffected controls. The FDXR-203 c.177 + 1778G > C mutation represents the first non-coding neurological genetic variant in horses. Additionally, this is the first genetic cause of a degenerative axonopathy in the horse and a spontaneous disease model to study FDXR pathology in humans.

  PublisherDOI

• Spatial transcriptomics defines the cell-specific RNA landscape of equine dorsal root ganglia

  Veterinary Pathology · 2025-02-06 · 1 citations

  articleOpen access

  Equine spinal neurodegenerative conditions are frequently encountered in sport and racing horses and may be career-ending diagnoses. To further define the spatial transcriptomic landscape of equine dorsal root ganglia (DRG) in healthy adult horses, we investigated gene expression differences in distinct DRG regions using the GeoMx Digital Spatial Profiling from NanoString. Four human cell markers demonstrated high fidelity for equine cells; microtubule-associated protein 2 (MAP2), myelin basic protein (MBP), allograft inflammatory 104 factor 1/ionized calcium-binding adaptor molecule 1 (IBA1/AIF1), and Syto83 nuclear marker. Geometric regions of interest were then selected as MBP-rich, IBA1-high, and IBA1-low, and gene expression was compared. Experimental validation was achieved, with genes involved in myelination enriched in MBP-rich regions, and the identification of glia-specific genes enriched in IBA1-high regions. Thus, spatial transcriptomics with human cell markers was successful in equine DRG and can now be applied to determine cell-specific transcriptional changes during disease states.

  PublisherDOI

• Annotation of cis-regulatory-associated histone modifications in the genomes of two Thoroughbred stallions

  Frontiers in Genetics · 2025-02-27 · 1 citations

  articleOpen access

  The Functional Annotation of Animal Genomes (FAANG) consortium aims to annotate animal genomes across species, and work in the horse has substantially contributed to that goal. As part of this initiative, chromatin immunoprecipitation with sequencing (ChIP-seq) was performed to identify histone modifications corresponding to enhancers (H3K4me1), promoters (H3K4me3), activators (H3K27ac), and repressors (H3K27me3) in eight tissues from two Thoroughbred stallions: adipose, parietal cortex, heart, lamina, liver, lung, skeletal muscle, and testis. The average genome coverage of peaks identified by MACS2 for H3K4me1, H3K4me3, and H3K27ac was 6.2%, 2.2%, and 4.1%, respectively. Peaks were called for H3K27me3, a broad mark, using both MACS2 and SICERpy, with MACS2 identifying a greater average number of peaks (158K; 10.4% genome coverage) than SICERpy (32K; 24.3% genome coverage). Tissue-unique peaks were identified with BEDTools, and 1%-47% of peaks were unique to a tissue for a given histone modification. However, correlations among usable reads, total peak number, and unique peak number ranged from 0.01 to 0.92, indicating additional data collection is necessary to parse technical from true biological differences. These publicly available data expand a growing resource available for identifying regulatory regions within the equine genome, and they serve as a reference for genome regulation across healthy tissues of the adult Thoroughbred stallion.

  PublisherOA PDFDOI

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

  BMC Genomics · 2025-10-09

  articleOpen accessSenior author

  Abstract Background 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 2 = 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 −8 ). Sex stratification followed by meta-analysis provided additional support for the association on ECA X ( P = 1.35 × 10 −8 ). 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 LP = 2.34 × 10 −6 and P X = 4.06 × 10 −5 ). Conclusion 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.

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• Identification of a cryptic exon in FDXR associated with equine juvenile spinocerebellar ataxia in Quarter Horses

  Journal of Equine Veterinary Science · 2025-05-01

  article
  PublisherDOI

• Evidence of de novo variant in FBN1as the potential cause of congenital bilateral ectopia lentis in a crossbred horse

  Research Square · 2025-08-29

  preprintOpen accessSenior author
  PublisherOA PDFDOI

• Using STR Data to Investigate the Impact of the Studbook Cap on Genetic Diversity in the American Standardbred Horse from 1998 to 2021

  Genes · 2025-06-27

  articleOpen accessSenior authorCorresponding

  Background/Objectives: Standardbreds, a breed of horses used in harness racing at either the trot or the pace, established a closed studbook in 1973. Concerns about genetic diversity within the breed led the United States Trotting Association (USTA) to establish a limit of mares bred per stallion (i.e., a studbook cap) in 2009. Here, we aimed to evaluate the impact of the breeding restrictions on genetic diversity between and among subpopulations. Methods: Sixteen short tandem repeats (STRs) were analyzed across a dataset of 176,424 Standardbreds foaled in the United States between 1998 and 2021. We examined allelic richness (Na), number of effective alleles (Ne), expected heterozygosity (HE), observed heterozygosity (HO), inbreeding coefficient (FIS), and fixation index (FST) across 24 years, differentiating by gate type, and comparing pre-(1998–2009) and post-(2010–2021) studbook cap periods using regression analysis. Results: Our results support decreased genetic diversity for both trotters and pacers over time. However, pacing Standardbreds exhibited significantly slower rates of decrease in genetic diversity after the 2009 studbook cap, as evidenced by Ne, HE, and FIS (PBonferroni < 0.01). Additionally, moderate levels of genetic differentiation were found between trotters and pacers (0.05 < FST < 0.09), which increased over time. Conclusions: Given that the rate of loss of diversity does not appear to differ pre and post studbook cap in trotters and that there is an increase in genetic differentiation between the groups over time, developing additional breeding tools and strategies is necessary to help the subpopulation mitigate further decline.

  PublisherOA PDFDOI

• A de novo FBN1 variant likely causes congenital bilateral ectopia lentis in a crossbred horse

  Scientific Reports · 2025-10-24

  articleOpen accessSenior authorCorresponding

  Although several inherited ocular disorders have been extensively studied in horses, few reports of equine ectopia lentis exist and no genetic investigations have been reported. Ectopia lentis in humans and other species is reported to be caused by trauma, genetic variants, and systemic diseases. The most commonly reported genetic causes are dominant alleles in FBN1. Here we examined a 3-day old Oldenburg x Thoroughbred colt due to concerns over bilateral ocular anomalies and hypothesized that either a recessively inherited allele or a dominant de novo allele was the genetic cause. Examination revealed bilateral microphakia and spherophakia with medioventral lens subluxation. Histopathology of the globes was consistent with ectopia lentis. Whole genome sequencing of the affected foal was conducted, and forty-six candidate genes were evaluated for SNVs and small INDELS. Testing both hypotheses, 82 variants were identified, of which 69 were present in publicly available data from 504 horses and not investigated further. Of the 13 remaining variants, two variants were found in 3' UTRs (ADAMTS17 and OAF), ten were intronic, and one was a coding variant located in the FBN1 gene encoding fibrillin-1 (FBN1:p.(Ala882Val)). This variant was also computationally predicted to be deleterious to protein function, including in silico modelling of FBN1 which suggests that 882Val impacts disulfide bond formation by Van der Waals clashing in a hybrid domain of the protein. The affected foal was confirmed by Sanger sequencing to be heterozygous for this variant and his clinically unaffected dam, reportedly unaffected sire, and five paternal half-siblings were homozygous for the reference allele. Additionally, the homologous human substitution is reported to be pathogenic, causing Marfan syndrome with a dominant mode of inheritance, of which ectopia lentis is a common feature. These findings support the de novo hypothesis with FBN1:p.(Ala882Val) as the likely cause of ectopia lentis in this foal, the first genetic explanation for this condition in the horse. Given the role of FBN1 in ectopia lentis in humans and other species, FBN1 should be evaluated as a potential candidate when other horses with this condition are identified.

  PublisherOA PDFDOI

• Allele Frequencies and Genotypes for the <i>Ryanodine Receptor 1</i> Variant Causing Malignant Hyperthermia and Fatal Rhabdomyolysis With Hyperthermia in Horses

  Journal of Veterinary Internal Medicine · 2025-04-29 · 1 citations

  articleOpen accessSenior authorCorresponding

  BACKGROUND: Fatal anesthesia-induced malignant hyperthermia (MH) and rhabdomyolysis with hyperthermia documented in Quarter Horses (QH) breeds are caused by a missense variant in the ryanodine receptor 1 gene (RYR1: XP_023505430.1.:p.(R2454G), designated as MH). The reported cases to date have all been heterozygous, and the allele frequency is suspected to be low. OBJECTIVE: To determine an accurate estimate of MH allele frequency in multiple horse breeds and investigate whether homozygous animals exist in the population. ANIMALS: In total, 159 227 horses from 16 breeds who were either submitted for clinical evaluation (n = 1500) or genetic testing (n = 157 727) were included. METHODS: Prospective study using banked DNA samples from two diagnostic laboratories determined the presence, zygosity, and estimated population MH allele frequencies. RESULTS: The MH allele was exclusively detected in 391 QH, 18 Paints (PT), one Appaloosa (AP), and one QH-Clydesdale cross with similar allele frequencies (QH = 0.0013 and PT and AP = 0.0012). In cases submitted for clinical evaluation, death occurred as anesthesia-induced MH or severe acute rhabdomyolysis with hyperthermia (≥ 42°C, 107.6°F) in 51% of N/MH horses. Nineteen of the 20 fatal cases were young males (median: 9 years old, range: 9 months-14 years). No MH homozygotes were detected in either cohort evaluated. CONCLUSIONS AND CLINICAL IMPORTANCE: Homozygotes for the MH allele were not identified, and thus might be incompatible with life, but additional testing is needed to confirm. Although the allele frequency was low, being heterozygous poses a risk of death if anesthesia, stress, concurrent illness, breeding, or other stresses occur.

  PublisherOA PDFDOI

• Genetic testing as a tool for diagnosis of congenital stationary night blindness (CSNB) in white spotted breeds in Poland

  Journal of Equine Veterinary Science · 2025-02-26 · 1 citations

  articleSenior author
  PublisherDOI

Frequent coauthors

• Carrie J. Finno

  University of California, Davis

  53 shared

• Jessica L. Petersen

  University of Nebraska–Lincoln

  43 shared

• Theodore S. Kalbfleisch

  University of Kentucky

  34 shared

• Sichong Peng

  University of California, Davis

  27 shared

• Kelly E. Knickelbein

  Cornell University

  22 shared

• M. C. T. Penedo

  University of California, Davis

  22 shared

• Tomasz Szmatoła

  University of Agriculture in Krakow

  18 shared

• Mary E. Lassaline

  University of Pennsylvania

  17 shared

Labs

• Equine Genetic Projects of Dr. Rebecca BellonePI