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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; 14:8396. [PMID: 38600096 PMCID: PMC11006912 DOI: 10.1038/s41598-024-57872-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
Disease-causing variants have been identified for less than 20% of suspected equine genetic diseases. Whole genome sequencing (WGS) allows rapid identification of rare disease causal variants. However, interpreting the clinical variant consequence is confounded by the number of predicted deleterious variants that healthy individuals carry (predicted genetic burden). Estimation of the predicted genetic burden and baseline frequencies of known deleterious or phenotype associated variants within and across the major horse breeds have not been performed. We used WGS of 605 horses across 48 breeds to identify 32,818,945 variants, demonstrate a high predicted genetic burden (median 730 variants/horse, interquartile range: 613-829), show breed differences in predicted genetic burden across 12 target breeds, and estimate the high frequencies of some previously reported disease variants. This large-scale variant catalog for a major and highly athletic domestic animal species will enhance its ability to serve as a model for human phenotypes and improves our ability to discover the bases for important equine phenotypes.
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Affiliation(s)
- S A Durward-Akhurst
- Department of Veterinary Clinical Sciences, University of Minnesota, C339 VMC, 1353 Boyd Avenue, St. Paul, MN, 55108, USA.
| | - J L Marlowe
- Department of Veterinary Clinical Sciences, University of Minnesota, C339 VMC, 1353 Boyd Avenue, St. Paul, MN, 55108, USA
| | - R J Schaefer
- Department of Veterinary Population Medicine, University of Minnesota, 225 VMC, 1365 Gortner Avenue, St. Paul, MN, 55108, USA
| | - K Springer
- Department of Veterinary Population Medicine, University of Minnesota, 225 VMC, 1365 Gortner Avenue, St. Paul, MN, 55108, USA
| | - B Grantham
- Interval Bio LLC, 408 Stierline Road, Mountain View, CA, 94043, USA
| | - W K Carey
- Interval Bio LLC, 408 Stierline Road, Mountain View, CA, 94043, USA
| | - R R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
- Population Health and Reproduction and Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - J R Mickelson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 295F Animal Science Veterinary Medicine Building, 1988 Fitch Avenue, St. Paul, MN, 55108, USA
| | - M E McCue
- Department of Veterinary Population Medicine, University of Minnesota, 225 VMC, 1365 Gortner Avenue, St. Paul, MN, 55108, USA
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Aleman M, Benini R, Elestwani S, Vinardell T. Juvenile idiopathic epilepsy in Egyptian Arabian foals, a potential animal model of self-limited epilepsy in children. J Vet Intern Med 2024; 38:449-459. [PMID: 38041837 PMCID: PMC10800229 DOI: 10.1111/jvim.16965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/17/2023] [Indexed: 12/04/2023] Open
Abstract
BACKGROUND Juvenile idiopathic epilepsy (JIE) is categorized as a generalized epilepsy. Epilepsy classification entails electrocortical characterization and localization of epileptic discharges (ED) using electroencephalography (EEG). HYPOTHESIS/OBJECTIVES Characterize epilepsy in Egyptian Arabian foals with JIE using EEG. ANIMALS Sixty-nine foals (JIE, 48; controls, 21). METHODS Retrospective study. Inclusion criteria consisted of Egyptian Arabian foals: (1) JIE group diagnosed based on witnessed or recorded seizures, and neurological and EEG findings, and (2) control group of healthy nonepileptic age-matched foals. Clinical data were obtained in 48 foals. Electroencephalography with photic stimulation was performed under standing sedation in 37 JIE foals and 21 controls. RESULTS Abnormalities on EEG were found in 95% of epileptic foals (35 of 37) and in 3 of 21 control asymptomatic foals with affected siblings. Focal ED were detected predominantly in the central vertex with diffusion into the centroparietal or frontocentral regions (n = 35). Generalization of ED occurred in 14 JIE foals. Epileptic discharges commonly were seen during wakefulness (n = 27/37 JIE foals) and sedated sleep (n = 35/37 JIE foals; 3/21 controls). Photic stimulation triggered focal central ED in 15 of 21 JIE foals. CONCLUSIONS AND CLINICAL IMPORTANCE Juvenile idiopathic epilepsy has a focal onset of ED at the central vertex with spread resulting in clinical generalized tonic-clonic seizures with facial motor activity and loss of consciousness. Electroencephalography with photic stimulation contributes to accurate phenotyping of epilepsy. Foals with this benign self-limiting disorder might serve as a naturally occurring animal model for self-limited epilepsy in children.
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Affiliation(s)
- Monica Aleman
- Department of Medicine and Epidemiology, School of Veterinary MedicineUniversity of CaliforniaDavisCaliforniaUSA
| | - Ruba Benini
- Division of Pediatric Neurology, Sidra MedicineDohaQatar
| | - Sami Elestwani
- Division of Pediatric Neurology, Sidra MedicineDohaQatar
| | - Tatiana Vinardell
- Equine Veterinary Medical CenterDohaQatar
- Present address:
Equine Precision TherapyMazyBelgium
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Alhaddad H, Powell BB, Pinto LD, Sutter N, Brooks SA, Alhajeri BH. Geometric morphometrics of face profile across horse breeds and within Arabian horses. J Equine Vet Sci 2024; 132:104980. [PMID: 38070586 DOI: 10.1016/j.jevs.2023.104980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/08/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023]
Abstract
Horse traits under selection are largely quantitative and affected by multiple genes. Horse face shape is an example of a continuous trait, which due to the reliance on observational assessments, is classified into; "dished", "straight", and "roman-nosed". This categorization is often inadequate to convey the full spectrum of the face shape variation especially for genetic studies. The first objective of the current study was to use geometric morphometric methods to quantitatively phenotype face shapes and examine its variation across horse breeds. The second objective was to analyze the face shape variation within Arabian horses since face shape is (1) favored, valued, and genetically selected in certain lineages (e.g. Egyptian), (2) is evaluated by registries and scored in shows, and (3) in its extreme forms pose health concerns. We digitized landmarks on lateral profile photos, particularly on the dorsal curvature of the rostrum, and subjected these landmarks to Generalized Procrustes Analysis to generate independent shape and size variables which were statistically compared across breeds and within Arabians. Horse breeds varied in nasal curvature, ranging from extremely concave to extremely convex, with over 70 % of horse breeds exhibiting intermediate concavity (i.e., straight profile). Interestingly, Arabian horses possessed the highest diversity in face profile and individuals clustered into three distinct shape sub-groups (one dished and two straight profile clusters). Our quantitative phenotyping method can be the basis of future genetic studies of facial profile within Arabian lineages as a favored traits and potentially manage its extreme forms as a likely genetic disease.
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Affiliation(s)
- H Alhaddad
- Department of Biological Sciences, Kuwait University, Shadadiya, Kuwait.
| | - B B Powell
- Department of Animal Science, UF Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - L Del Pinto
- Biology Department, La Sierra University, Riverside, California, USA
| | - N Sutter
- Biology Department, La Sierra University, Riverside, California, USA
| | - S A Brooks
- Department of Animal Science, UF Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - B H Alhajeri
- Department of Biological Sciences, Kuwait University, Shadadiya, Kuwait
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Ciosek J, Kimes A, Vinardell T, Miller DC, Antczak DF, Brooks S. Juvenile idiopathic epilepsy in Arabian horses is not a single-gene disorder. J Hered 2023; 114:488-491. [PMID: 37145017 DOI: 10.1093/jhered/esad029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 05/04/2023] [Indexed: 05/06/2023] Open
Abstract
Valued for their temperament, beauty, athletic ability, and exhibition in the show ring, Arabian horses are an important component of the horse industry. Juvenile idiopathic epilepsy (JIE), a seizure disorder, is most often reported in Arabian foals from birth to 6 months of age. Affected foals exhibit tonic-clonic seizures lasting as long as 5 min and risking secondary complications like temporary blindness and disorientation. Some foals outgrow this condition, while others die or suffer lifelong complications if not treated. Previous work suggested a strong genetic component to JIE and proposed JIE to be a single-gene trait. In this work, we conducted a genome wide association study (GWAS) in 60 cases of JIE and 120 genetically matched controls, identifying loci suggesting JIE is not caused by a single locus. Coat color (chestnut, gray) phenotypes were used as positive control traits to assess the efficacy of GWAS in this population. Future work will attempt to future define candidate regions and explore a polygenic mode of inheritance.
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Affiliation(s)
- Julia Ciosek
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
| | - Abigail Kimes
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
| | - Tatiana Vinardell
- Equine Veterinary Medical Center, Hamad Bin Khalifa University, Doha, Qatar
| | - Donald C Miller
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Douglas F Antczak
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Samantha Brooks
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
- UF Genetics Institute, University of Florida, Gainesville, FL, USA
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Polani S, Dean M, Lichter-Peled A, Hendrickson S, Tsang S, Fang X, Feng Y, Qiao W, Avni G, Kahila Bar-Gal G. Sequence Variant in the TRIM39-RPP21 Gene Readthrough is Shared Across a Cohort of Arabian Foals Diagnosed with Juvenile Idiopathic Epilepsy. JOURNAL OF GENETIC MUTATION DISORDERS 2022; 1:103. [PMID: 35465405 PMCID: PMC9031527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Juvenile idiopathic epilepsy (JIE) is a self-limiting neurological disorder with a suspected genetic predisposition affecting young Arabian foals of the Egyptian lineage. The condition is characterized by tonic-clonic seizures with intermittent post-ictal blindness, in which most incidents are sporadic and unrecognized. This study aimed to identify genetic components shared across a local cohort of Arabian foals diagnosed with JIE via a combined whole genome and targeted resequencing approach: Initial whole genome comparisons between a small cohort of nine diagnosed foals (cases) and 27 controls from other horse breeds identified variants uniquely shared amongst the case cohort. Further validation via targeted resequencing of these variants, that pertain to non-intergenic regions, on additional eleven case individuals revealed a single 19bp deletion coupled with a triple-C insertion (Δ19InsCCC) within the TRIM39-RPP21 gene readthrough that was uniquely shared across all case individuals, and absent from three additional Arabian controls. Furthermore, we have confirmed recent findings refuting potential linkage between JIE and other inherited diseases in the Arabian lineage, and refuted the potential linkage between JIE and genes predisposing a similar disorder in human newborns. This is the first study to report a genetic variant to be shared in a sub-population cohort of Arabian foals diagnosed with JIE. Further evaluation of the sensitivity and specificity of the Δ19InsCCC allele within additional cohorts of the Arabian horse is warranted in order to validate its credibility as a marker for JIE, and to ascertain whether it has been introduced into other horse breeds by Arabian ancestry.
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Affiliation(s)
- S Polani
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - M Dean
- National Cancer Institute, Division of Cancer Epidemiology & Genetics, Laboratory of Translational Genomics, USA
| | - A Lichter-Peled
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - S Hendrickson
- Department of Biology, Shepherd University, Shepherdstown, USA
| | | | - X Fang
- BGI-Shenzhen, Shenzhen, China
| | - Y Feng
- BGI-Shenzhen, Shenzhen, China
| | - W Qiao
- BGI-Shenzhen, Shenzhen, China
| | - G Avni
- Medisoos Equine Clinic, Kibutz Magal, Israel
| | - G Kahila Bar-Gal
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
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Abstract
Neurologic disease in horses can be particularly challenging to diagnose and treat. These diseases can result in economic losses, emotional distress to owners, and injury to the horse or handlers. To date, there are 5 neurologic diseases caused by known genetic mutations and several more are suspected to be heritable: lethal white foal syndrome, lavender foal syndrome, cerebellar abiotrophy, occipitoatlantoaxial malformation, and Friesian hydrocephalus. Genetic testing allows owners, breeders, and veterinarians to make informed decisions when selecting dams and sires for breeding or deciding the treatment or prognosis of a neurologic animal.
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Affiliation(s)
- Lisa Edwards
- Department of Veterinary Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Room 4206 Vet Med 3A One Shields Avenue, Davis, CA 95616, USA
| | - Carrie J Finno
- Department of Veterinary Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Room 4206 Vet Med 3A One Shields Avenue, Davis, CA 95616, USA.
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Abstract
The Arabian horse, one of the world’s oldest breeds of any domesticated animal, is characterized by natural beauty, graceful movement, athletic endurance, and, as a result of its development in the arid Middle East, the ability to thrive in a hot, dry environment. Here we studied 378 Arabian horses from 12 countries using equine single nucleotide polymorphism (SNP) arrays and whole-genome re-sequencing to examine hypotheses about genomic diversity, population structure, and the relationship of the Arabian to other horse breeds. We identified a high degree of genetic variation and complex ancestry in Arabian horses from the Middle East region. Also, contrary to popular belief, we could detect no significant genomic contribution of the Arabian breed to the Thoroughbred racehorse, including Y chromosome ancestry. However, we found strong evidence for recent interbreeding of Thoroughbreds with Arabians used for flat-racing competitions. Genetic signatures suggestive of selective sweeps across the Arabian breed contain candidate genes for combating oxidative damage during exercise, and within the “Straight Egyptian” subgroup, for facial morphology. Overall, our data support an origin of the Arabian horse in the Middle East, no evidence for reduced global genetic diversity across the breed, and unique genetic adaptations for both physiology and conformation.
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Campbell MLH, McNamee MJ. Ethics, Genetic Technologies and Equine Sports: The Prospect of Regulation of a Modified Therapeutic Use Exemption Policy. SPORT ETHICS AND PHILOSOPHY 2020. [DOI: 10.1080/17511321.2020.1737204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- M. L. H Campbell
- Department of Production and Population Sciences, The Royal Veterinary College, South Mymms, UK
| | - M. J. McNamee
- School of Sport and Exercise Sciences, Swansea University, Swansea, UK
- Faculty of Kinesiology and Rehabilitation Sciences, KU Leuven, Leuven, Belgium
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Wright S. Highlights of recent clinically relevant papers. EQUINE VET EDUC 2018. [DOI: 10.1111/eve.12932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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