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De Coster T, Zhao Y, Tšuiko O, Demyda-Peyrás S, Van Soom A, Vermeesch JR, Smits K. Genome-wide equine preimplantation genetic testing enabled by simultaneous haplotyping and copy number detection. Sci Rep 2024; 14:2003. [PMID: 38263320 PMCID: PMC10805710 DOI: 10.1038/s41598-023-48103-7] [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: 06/28/2023] [Accepted: 11/22/2023] [Indexed: 01/25/2024] Open
Abstract
In different species, embryonic aneuploidies and genome-wide errors are a major cause of developmental failure. The increasing number of equine embryos being produced worldwide provides the opportunity to characterize and rank or select embryos based on their genetic profile prior to transfer. Here, we explored the possibility of generic, genome-wide preimplantation genetic testing concurrently for aneuploidies (PGT-A) and monogenic (PGT-M) traits and diseases in the horse, meanwhile assessing the incidence and spectrum of chromosomal and genome-wide errors in in vitro-produced equine embryos. To this end, over 70,000 single nucleotide polymorphism (SNP) positions were genotyped in 14 trophectoderm biopsies and corresponding biopsied blastocysts, and in 26 individual blastomeres from six arrested cleavage-stage embryos. Subsequently, concurrent genome-wide copy number detection and haplotyping by haplarithmisis was performed and the presence of aneuploidies and genome-wide errors and the inherited parental haplotypes for four common disease-associated genes with high carrier frequency in different horse breeds (GBE1, PLOD1, B3GALNT2, MUTYH), and for one color coat-associated gene (STX17) were compared in biopsy-blastocyst combinations. The euploid (n = 12) or fully aneuploid (n = 2) state and the inherited parental haplotypes for 42/45 loci of interest of the biopsied blastocysts were predicted by the biopsy samples in all successfully analyzed biopsy-blastocyst combinations (n = 9). Two biopsies showed a loss of maternal chromosome 28 and 31, respectively, which were confirmed in the corresponding blastocysts. In one of those biopsies, additional complex aneuploidies not present in the blastocyst were found. Five out of six arrested embryos contained chromosomal and/or genome-wide errors in most of their blastomeres, demonstrating their contribution to equine embryonic arrest in vitro. The application of the described PGT strategy would allow to select equine embryos devoid of genetic errors and pathogenetic variants, and with the variants of interest, which will improve foaling rate and horse quality. We believe this approach will be a gamechanger in horse breeding.
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Affiliation(s)
- T De Coster
- Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, Merelbeke, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
| | - Y Zhao
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - O Tšuiko
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - S Demyda-Peyrás
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Department of Animal Production, Veterinary School, National University of La Plata, La Plata, Argentina
| | - A Van Soom
- Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, Merelbeke, Belgium
| | - J R Vermeesch
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - K Smits
- Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, Merelbeke, Belgium.
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AbouEl Ela NH, El Araby IE, Saleh AA, Abd El-Fattah AH, Hagag NM, Brooks SA, Radwan MA, Kalbfleisch T. Evidence for origin of Lavender Foal Syndrome among Egyptian Arabian horses in Egypt. Equine Vet J 2022; 55:487-493. [PMID: 35665534 DOI: 10.1111/evj.13604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/14/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Lavender Foal Syndrome (LFS) is a fatal hereditary condition that is inherited in an autosomal recessive pattern. This detrimental mutation is more common in Arabian foals of Egyptian origin than foals from other bloodlines. Heterozygous horses are carriers of the LFS trait and appear normal, while recessive homozygous foals died shortly after birth due to serious complications. In Egypt, in 2014, an Egyptian foal died after manifestations of neurological signs and abnormal coat colour as LFS signs. Therefore, it is important to identify LFS carriers in the population of Arabian horses in Egypt and to encourage improvement of the Arabian horse industry in Egypt by constructing a breeding system based on genetic background in order to avoid mating between carriers and reduce financial losses from deaths of affected foals. OBJECTIVES To establish a PCR-based test for detecting the MYO5A gene mutation causing LFS in the registered Arabian horse population in Egypt prior to breeding. STUDY DESIGN Cross sectional survey (n = 170) plus targeted sampling (n = 30). METHODS A total of 200 samples were collected from an Arabian farm in Egypt and some of them were traced for LFS based on the farm records. The LFS genotypes were identified using the PCR-RFLP technique, fragment analysis followed by sequence analysis. RESULTS The overall mutated allele and genotype frequencies (N/L) were 0.08 and 16%, respectively. CONCLUSION The observed frequency of heterozygotes suggests foals affected with LFS will be produced among Arabian horses in Egypt. Therefore, screening of the entire population for this mutation should be undertaken in the breeding program. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | - Iman E El Araby
- Animal Wealth Development Department, Faculty of Veterinary Medicine, Zagazig University, Egypt
| | - Ayman A Saleh
- Animal Wealth Development Department, Faculty of Veterinary Medicine, Zagazig University, Egypt
| | - Amir H Abd El-Fattah
- Animal Wealth Development Department, Faculty of Veterinary Medicine, Zagazig University, Egypt
| | - Naglaa M Hagag
- Genome Research Unit, Animal Health Research Institute, Agricultural Research Center, Egypt
| | - Samantha A Brooks
- Department of Animal Sciences, UF Genetics Institute, University of Florida, USA
| | - Mohamed A Radwan
- Genome Research Unit, Animal Health Research Institute, Agricultural Research Center, Egypt
| | - Ted Kalbfleisch
- Department of Veterinary Science, College of Agriculture, Food, and Environment, University of Kentucky, USA
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Investigation of Cerebellar Abiotrophy (CA), Lavender Foal Syndrome (LFS), and Severe Combined Immunodeficiency (SCID) Variants in a Cohort of Three MENA Region Horse Breeds. Genes (Basel) 2021; 12:genes12121893. [PMID: 34946842 PMCID: PMC8701198 DOI: 10.3390/genes12121893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 11/24/2022] Open
Abstract
Genetic disorders in horses are mostly fatal or usually cause significant economic losses for breeders and owners. Here we studied a total of 177 Arabian, Barb and Arab-Barb horses from the Middle East and North Africa (MENA) using Sanger Sequencing and PCR-ACRS (polymerase chain reaction—artificially created restriction site) approaches to examine the genetic disorders in the studied horse breeds. We identified the genetic variations related to Cerebellar Abiotrophy (CA), Severe Combined Immunodeficiency (SCID) occurrence, and the studied population was free of the mutant allele determined Lavender Foal Syndrome (LFS). Overall, presented data showed that 15 of the studied horses are carriers of two genetic disorders; the investigated horse population showed that five Arabian horses were heterozygous for the CA-associated SNP (rs397160943). The SCID-deletion TCTCA within PRKDC was detected in ten horses (nine Arabian horses and one Arab-Barb horse). This investigation shows the importance of testing these breeds for genetic disorders to avoid further spread of deleterious variants
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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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Bugno-Poniewierska M, Stefaniuk-Szmukier M, -Kajtoch AP, Fornal A, Piórkowska K, Ropka-Molik K. Genetic screening for cerebellar abiotrophy, severe combined immunodeficiency and lavender foal syndrome in Arabian horses in Poland. Vet J 2019; 248:71-73. [PMID: 31113566 DOI: 10.1016/j.tvjl.2019.04.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 04/24/2019] [Accepted: 04/24/2019] [Indexed: 02/05/2023]
Abstract
The highly selective breeding of Arabian horses results in inbreeding depression and genetic disorders, thereby causing significant economic loss. The Polish population of Arabians has a great impact on many breeding programmes. The aim of the current study was to monitor genetic variants involved in the most common genetic disorders of this breed. A total of 808 elite Arabian horses were screened for cerebellar abiotrophy (CA), severe combined immunodeficiency (SCID) and lavender foal syndrome (LFS) genetic disorders by Sanger sequencing and allelic discrimination methods. The investigated population was clear of LFS. The unfavourable SCID allele was detected in three heterozygous horses (q = 0.00185). Regarding CA, the minor allele frequency was q = 0.04029. This is the first report of SCID carriers in Poland. This investigation demonstrates the value of genetic testing to support breeding decisions and to facilitate genetic disease monitoring.
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Affiliation(s)
- Monika Bugno-Poniewierska
- Department of Animal Reproduction, University of Agriculture, al. Mickiewicza 24/28, 30-059 Kraków, Poland
| | - Monika Stefaniuk-Szmukier
- Department of Horse Breeding, University of Agriculture, al. Mickiewicza 24/28, 30-059 Kraków, Poland.
| | - Agata Piestrzyńska -Kajtoch
- Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland
| | - Agnieszka Fornal
- Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland
| | - Katarzyna Piórkowska
- Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland
| | - Katarzyna Ropka-Molik
- Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland
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AbouEl Ela NA, El-Nesr KA, Ahmed HA, Brooks SA. Molecular Detection of Severe Combined Immunodeficiency Disorder in Arabian Horses in Egypt. J Equine Vet Sci 2018; 68:55-58. [PMID: 31256889 DOI: 10.1016/j.jevs.2018.05.210] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/12/2018] [Accepted: 05/21/2018] [Indexed: 11/18/2022]
Abstract
Severe combined immunodeficiency (SCID) is a fatal genetic disorder and one of the common genetic diseases of the Arabian horse. The genetic mutation responsible for this disease is a five base pair deletion (TCTCA) in the DNA-protein kinase catalytic subunit gene. Severe combined immunodeficiency is a recessive autosomal genetic disorder with 25% chance inheritance of the disease among the progeny of carrier parents. It causes complete absence of certain immune cells, like B and T lymphocytes, leaving foals with immunodeficiency and exposing them to early death within 4 to 6 months. This study aimed to establish a reliable DNA test for detection of asymptomatic SCID carriers in the Egyptian Arabian horse population and to re-examine cases of unexplained foal death to exclude presence of SCID disease. Samples collected from live horses were chosen at random from the registered population, as well as postmortem samples from reported cases died at different ages in Arabian farms. Among these samples, we did not identify SCID carriers. Improved SCID diagnostic assays will help in selection within breeding programs to avoid carrier-to-carrier mating and the birth of clinically affected foals. This will have a positive effect on the financial value of Arabian horse production by decreasing economic losses due to affected foal deaths, extended veterinary care, and intensive but futile treatments. Application of the DNA test overall Egyptian population is recommended.
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Affiliation(s)
- Nahla A AbouEl Ela
- Genome Research Unit, Animal Health Research Institute, Dokki, Giza, Egypt; Biotechnology and Life Science Department, Faculty of Postgraduate Studies for Advanced Sciences, Beni-Suef University, Beni-Suef, Egypt.
| | - Khalid A El-Nesr
- Biotechnology and Life Science Department, Faculty of Postgraduate Studies for Advanced Sciences, Beni-Suef University, Beni-Suef, Egypt; Pathology Department, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef, Egypt
| | - Hanaa A Ahmed
- Genome Research Unit, Animal Health Research Institute, Dokki, Giza, Egypt
| | - Samantha A Brooks
- Department of Animal Sciences, University of Florida, Gainesville, FL
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Efendić M, Maćešić N, Samardžija M, Vojta A, Korabi N, Capak H, Sušnić MA, Žaja IŽ, Pećin M, Babić NP. Determination of Sublethal Mutation Causing Lavender Foal Syndrome in Arabian Horses From Croatia. J Equine Vet Sci 2018. [DOI: 10.1016/j.jevs.2017.11.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Aleman M, Finno CJ, Weich K, Penedo MCT. Investigation of Known Genetic Mutations of Arabian Horses in Egyptian Arabian Foals with Juvenile Idiopathic Epilepsy. J Vet Intern Med 2017; 32:465-468. [PMID: 29171123 PMCID: PMC5787150 DOI: 10.1111/jvim.14873] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 09/22/2017] [Accepted: 10/12/2017] [Indexed: 12/18/2022] Open
Abstract
Background The carrier status of lavender foal syndrome (LFS), cerebellar abiotrophy (CA), severe combined immunodeficiency (SCID), and occipitoatlantoaxial malformation (OAAM1) in foals with juvenile idiopathic epilepsy (JIE) is unknown. Hypothesis/Objectives To determine the carrier status of LFS, CA, SCID, and OAAM1 in foals with JIE. Animals Ten foals with JIE. Materials and Methods Archived DNA samples were tested for known genetic mutations causing LFS, CA, SCID, and OAAM1. The inclusion criteria consisted of having been diagnosed with JIE by ruling out other causes of seizures in foals and supported by electroencephalographic examination. Results Ten Egyptian Arabian horses (5 females and 5 males) were phenotyped as foals with JIE by electroencephalography (EEG). All foals were negative for the genetic mutations that cause LFS, CA, SCID, and OAAM1 except for 1 foal that was a carrier of CA. Conclusions and Clinical Importance Juvenile idiopathic epilepsy of Egyptian Arabian foals and LFS appear to be phenotypically and genetically distinct disorders. There was no apparent association between JIE and LFS, CA, SCID, and OAAM1.
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Affiliation(s)
- M Aleman
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA
| | - C J Finno
- School of Veterinary Medicine, Population Health and Reproduction, University of California Davis, Davis, CA
| | - K Weich
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA
| | - M C T Penedo
- School of Veterinary Medicine, Veterinary Genetics Laboratory, University of California Davis, Davis, CA
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Diseases of the Nervous System. Vet Med (Auckl) 2017. [PMCID: PMC7322266 DOI: 10.1016/b978-0-7020-5246-0.00014-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Affiliation(s)
- E Bailey
- MH Gluck Equine Research Center, University of Kentucky - Veterinary Science, Lexington, USA
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The Arabian horse SCIDs to a halt. Lab Anim (NY) 2014; 43:49. [PMID: 24451352 DOI: 10.1038/laban.467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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