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Home / Equine Research Bank / Anim Genet / Screening and detection of chromosomal copy number alteratio...
Animal genetics2021; 52(4); 431-439; doi: 10.1111/age.13077

Screening and detection of chromosomal copy number alterations in the domestic horse using SNP-array genotyping data.

Abstract: Chromosomal abnormalities are a common cause of infertility in horses. However, they are difficult to detect using automated methods. Here, we propose a simple methodology based on single nucleotide polymorphism (SNP)-array data that allows us to detect the main chromosomal abnormalities in horses in a single procedure. As proof of concept, we were able to detect chromosomal abnormalities in 33 out of 268 individuals, including monosomies, chimerisms, and male and female sex-reversions, by analyzing the raw signal intensity produced by an SNP array-based genotyping platform. We also demonstrated that the procedure is not affected by the SNP density of the array employed or by the inbreeding level of the individuals. Finally, the methodology proposed in this study could be performed in an open bioinformatic environment, thus permitting its integration as a flexible screening tool in diagnostic laboratories and genomic breeding programs.
© 2021 Stichting International Foundation for Animal Genetics.
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Publication Date: 2021-05-19 PubMed ID: 34013628DOI: 10.1111/age.13077Google 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.

The research article discusses a new method for identifying chromosomal abnormalities in horses, which are often linked to infertility, using single nucleotide polymorphism (SNP)-array data. This method was successfully used in detecting various types of chromosomal abnormalities in a sample group of horses.

Research Objective

  • The objective of this study was to develop a simple method for identifying chromosomal abnormalities in horses. These abnormalities often result in infertility and are traditionally difficult to detect using automated methods.

Methodology Used

  • The researchers utilized single nucleotide polymorphism (SNP)-array data for the detection of chromosomal abnormalities. This was done by analyzing the raw signal intensity generated by an SNP array-based genotyping platform.
  • The method did not require specific SNP density of the array used or consider the inbreeding level of the horses.

Findings

  • The researchers were successful in identifying chromosomal abnormalities in a total of 33 individuals out of 268, which include monosomies, chimerisms, and male and female sex-reversions. This validated the potency and accuracy of the proposed method.

Implications of the Study

  • The methodology is able to be performed in an open bioinformatic environment, which allows for easy integration as a screening tool in diagnostic laboratories and genomic breeding programs.
  • The identification and understanding of chromosomal abnormalities in horses can contribute to better breeding practices and ultimately to the potential reduction of infertility issues.

Conclusion

  • The study proposes a new, simpler method of identifying chromosomal abnormalities in horses, using SNP-array data. This method can be a crucial tool in reducing infertility problems and enhancing genomic breeding programs in the horse industry.

Cite This Article

APA
Pirosanto Y, Laseca N, Valera M, Molina A, Moreno-Millán M, Bugno-Poniewierska M, Ross P, Azor P, Demyda-Peyrás S. (2021). Screening and detection of chromosomal copy number alterations in the domestic horse using SNP-array genotyping data. Anim Genet, 52(4), 431-439. https://doi.org/10.1111/age.13077

Publication

Animal genetics
ISSN: 1365-2052
NlmUniqueID: 8605704
Country: England
Language: English
Volume: 52
Issue: 4
Pages: 431-439

Researcher Affiliations

Pirosanto, Y
  • Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118 s/n, La Plata, 1900, Argentina.
  • IGEVET (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, UNLP, Calle 60 y 118 s/n, La Plata, 1900, Argentina.
Laseca, N
  • Laboratorio de Diagnóstico Genético Veterinario, Departamento de Genética, Universidad de Córdoba, CN IV KM 396, Edificio Gregor Mendel, Campus Rabanales, Córdoba, 14071, España.
Valera, M
  • Departamento de Agronomía, Escuela Técnica Superior de Ingeniería Agronómica, Universidad de Sevilla, Ctra. de Utrera km 1, Sevilla, 41013, España.
Molina, A
  • Laboratorio de Diagnóstico Genético Veterinario, Departamento de Genética, Universidad de Córdoba, CN IV KM 396, Edificio Gregor Mendel, Campus Rabanales, Córdoba, 14071, España.
Moreno-Millán, M
  • Laboratorio de Diagnóstico Genético Veterinario, Departamento de Genética, Universidad de Córdoba, CN IV KM 396, Edificio Gregor Mendel, Campus Rabanales, Córdoba, 14071, España.
Bugno-Poniewierska, M
  • Katedra Rozrodu, Anatomii i Genomiki Zwierząt Wydział Hodowli i Biologii Zwierząt, Uniwersytet Rolniczy im. Hugona Kołłątaja w Krakowie, al. Mickiewicza 24/28, Krakow, 30-059, Poland.
Ross, P
  • Department of Animal Science, University of California, Davis, One Shields Ave., Davis, CA, 95616, USA.
Azor, P
  • Asociación Nacional de Criadores de Caballos de Pura Raza Española (ANCCE), Edif. Indotorre · Avda. del Reino Unido 11, pl. 3ª 2, Sevilla, 41012, España.
Demyda-Peyrás, S
  • Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118 s/n, La Plata, 1900, Argentina.
  • IGEVET (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, UNLP, Calle 60 y 118 s/n, La Plata, 1900, Argentina.

MeSH Terms

  • Animals
  • Chromosome Aberrations / veterinary
  • DNA Copy Number Variations / genetics
  • Female
  • Genotype
  • Genotyping Techniques / veterinary
  • Horses / genetics
  • Male
  • Polymorphism, Single Nucleotide

Grant Funding

  • PICT2016-0359 / Fondo para la Investigaciu00f3n Cientu00edfica y Tecnolu00f3gica
  • PICT2018-0227 / Fondo para la Investigaciu00f3n Cientu00edfica y Tecnolu00f3gica
  • AGL2017-84217-P / Secretaru00eda de Estado de Investigaciu00f3n, Desarrollo e Innovaciu00f3n

References

This article includes 56 references
  1. Albarella S, De Lorenzi L, Catone G. Diagnosis of XX/XY blood cell chimerism at a low percentage in horses. Journal of Equine Veterinary Science 69, 129-35.
  2. Anaya G, Fernández M.E, Valera M, Molina A, Azcona F, Azor P, Solé M, Moreno-Millán M, Demyda-Peyrás S. Prevalence of twin foaling and blood chimaerism in purebred Spanish horses. The Veterinary Journal 234, 142-4.
  3. Anaya G, Molina A, Valera M, Moreno-Millan M, Azor P, Peral-Garcia P, Demyda-Peyras S. Sex chromosomal abnormalities associated with equine infertility: validation of a simple molecular screening tool in the Purebred Spanish Horse. Animal Genetics 48, 412-9.
  4. Anaya G, Moreno-Millán M, Bugno-Poniewierska M, Pawlina K, Membrillo A, Molina A, Demyda-Peyrás S. Sex reversal syndrome in the horse: four new cases of feminization in individuals carrying a 64, XY SRY negative chromosomal complement. Animal Reproduction Science 151, 22-7.
  5. Bannasch D, Rinaldo C, Millon L, Latson K, Spangler T, Hubberty S, Galuppo L, Lowenstine L. SRY negative 64, XX intersex phenotype in an American saddlebred horse. The Veterinary Journal 173, 437-9.
  6. Beeson S.K, Schaefer R.J, Mason V.C, McCue M.E. Robust remapping of equine SNP array coordinates to Eq쪳. Animal Genetics 50, 114-5.
  7. Berry D.P, Wolfe A, O'Donovan J, Byrne N, Sayers R.G, Dodds K.G, McEwan J.C, O'Connor R.E, McClure M, Purfield D.C. Characterization of an X-chromosomal non-mosaic monosomy (59, X0) dairy heifer detected using routinely available single nucleotide polymorphism genotype data. Journal of Animal Science 95, 1042-9.
  8. Biscarini F, Cozzi P, Gaspa G, Marras G. DetectRUNS: detect runs of homozygosity and runs of heterozygosity in diploid genomes in R. .
  9. Bolormaa S, Gore K, Van Der Werf J.H.J, Hayes B.J, Daetwyler H.D. Design of a low-density SNP chip for the main Australian sheep breeds and its effect on imputation and genomic prediction accuracy. Animal Genetics 46, 544-56.
  10. Bugno M, Słota E, Kościelny M. Karyotype evaluation among young horse populations in Poland. Schweizer Archiv fur Tierheilkunde 149, 227-32.
  11. Bugno M, Słota E, Pieńkowska-Schelling A, Schelling C. Detection of equine X cromosome mosaicism in a mare using an equine X whole chromosome painting probe (WCPP) - a case report. Acta Veterinaria Hungarica 55, 207-12.
  12. Bugno M, Słota E, Zabek T. Two cases of subfertile mares with 64, XX/63, X mosaic karyotype. Annals of Animal Science 1, 7-11.
  13. Demyda-Peyrás S, Anaya G, Bugno-Poniewierska M, Pawlina K, Membrillo A, Valera M, Moreno-Millán M. The use of a novel combination of diagnostic molecular and cytogenetic approaches in horses with sexual karyotype abnormalities: a rare case with an abnormal cellular chimerism. Theriogenology 81, 1116-22.
  14. Demyda-Peyrás S, Membrillo A, Bugno-Poniewierska M, Pawlina K, Anaya G, Moreno-Millán M. The use of molecular and cytogenetic methods as a valuable tool in the detection of chromosomal abnormalities in horses: a case of sex chromosome chimerism in a Spanish Purebred colt. Cytogenetic and Genome Research 141, 277-83.
  15. Dowle M, Srinivasan A. data.table: extension of data.frame. .
  16. Gamo S, Tozaki T, Kakoi H, Hirota K.I, Nakamura K, Nishii N, Almunia J, Takasu M. X monosomy in the endangered Kiso horse breed detected by a parentage test using sex chromosome linked genes and microsatellites. The Journal of Veterinary Medical Science 81, 91-4.
  17. Gel B, Serra E. karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data. Bioinformatics 33, 3088-90.
  18. Goodrich D, Xing T, Tao X, Lonczak A, Zhan Y, Landis J, Zimmerman R, Scott R.T. Jr, Treff N.R. Evaluation of comprehensive chromosome screening platforms for the detection of mosaic segmental aneuploidy. Journal of Assisted Reproduction and Genetics 34, 975-81.
  19. Goszczynski D, Molina A, Terán E, Morales-Durand H, Ross P, Cheng H, Giovambattista G, Demyda-Peyrás S. Runs of homozygosity in a selected cattle population with extremely inbred bulls: descriptive and functional analyses revealed highly variable patterns. PLOS ONE 13, e0200069.
  20. Gunnarsson R, Staaf J, Jansson M. Screening for copy-number alterations and loss of heterozygosity in chronic lymphocytic leukemia - a comparative study of four differently designed, high resolution microarray platforms. Genes Chromosomes and Cancer 47, 697-711.
  21. Hadley W, Romain F, Lionel H, Müller K. dplyr: a grammar of data manipulation. .
  22. Harton G.L, Munné S, Surrey M, Grifo J, Kaplan B, McCulloh D.H, Griffin D.K, Wells D. Diminished effect of maternal age on implantation after preimplantation genetic diagnosis with array comparative genomic hybridization. Fertility and Sterility 100, 1695-703.
  23. Holl H.M, Lear T.L, Nolen-Walston R.D, Slack J, Brooks S.A. Detection of two equine trisomies using SNP-CGH. Mammalian Genome 24, 252-6.
  24. Indahl U.G, Naes T, Liland K.H. A similarity index for comparing coupled matrices. Journal of Chemometrics 32, e3049.
  25. Kalbfleisch T.S, Rice E.S, DePriest M.S. Improved reference genome for the domestic horse increases assembly contiguity and composition. Communications Biology 1, 197.
  26. Kjöllerström H.J, Collares-Pereira M.J, Oom M.M. First evidence of sex chromosome mosaicism in the endangered Sorraia Horse breed. Livestock Science 136, 273-6.
  27. Lear T.L, McGee R.B. Disorders of sexual development in the domestic horse, Equus caballus. Sexual Development 6, 61-71.
  28. Lopes F.B, Wu X.L, Li H, Xu J, Perkins T, Genho J, Ferretti R, Tait R.G. Jr, Bauck S, Rosa G.J.M. Improving accuracy of genomic prediction in Brangus cattle by adding animals with imputed low-density SNP genotypes. Journal of Animal Breeding and Genetics 135, 14-27.
  29. Markello T.C, Carlson-Donohoe H, Sincan M. Sensitive quantification of mosaicism using high density SNP arrays and the cumulative distribution function. Molecular Genetics and Metabolism 105, 665-71.
  30. McCoy A.M, Beeson S.K, Rubin C.-J, Andersson L, Caputo P, Lykkjen S, Moore A, Piercy R.J, Mickelson J.R, McCue M.E. Identification and validation of genetic variants predictive of gait in standardbred horses. PLOS Genetics 15, e1008146.
  31. McGivney B.A, Han H, Corduff L.R, Katz L.M, Tozaki T, MacHugh D.E, Hill E.W. Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population. Scientific Reports 10.
    doi: 10.1038/s41598-019-57389-5google scholar: lookup
  32. Neuhauser S, Handler J, Schelling C, Pieńkowska-Schelling A. Fertility and 63, X mosaicism in a Haflinger Sibship. Journal of Equine Veterinary Science 78, 127-33.
  33. Perdomo-González D.I, Sánchez-Guerrero M.J, Molina A, Valera M. Genetic structure analysis of the Pura Raza Español horse population through partial inbreeding coefficient estimation. Animals 10, 1360.
  34. Petersen J.L, Mickelson J.R, Cothran E.G. Genetic diversity in the modern horse illustrated from genome-wide SNP data. PLOS ONE 8, e54997.
  35. Popova T, Manié E, Stoppa-Lyonnet D, Rigaill G, Barillot E, Stern M.H. Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays. Genome Biology 10, R128.
  36. Power M.M. Chromosomes of the horse. pp. 131-67.
  37. Power M.M, Leadon D.P. Diploid-triploid chimaerism (64, XX/96, XXY) in an intersex foal. Equine Veterinary Journal 22, 211-4.
  38. Pryce J.E, Daetwyler H.D. Designing dairy cattle breeding schemes under genomic selection: a review of international research. Animal Production Science 52, 107-14.
  39. R Core Team. R: A Language and Environment for Statistical Computing v4.0.3 “Bunny-Wunnies Freak Out”. .
  40. Raudsepp T, Chowdhary B.P. The horse pseudoautosomal region (PAR): characterization and comparison with the human, chimp and mouse PARs. Cytogenetic and Genome Research 121, 102-9.
  41. Raudsepp T, Chowdhary B.P. Chromosome aberrations and fertility disorders in domestic animals. Annual Review of Animal Biosciences 4, 15-43.
  42. Raudsepp T, Das P.J, Avila F, Chowdhary B.P. The pseudoautosomal region and sex chromosome aneuploidies in domestic species. Sexual Development 6, 72-83.
  43. Robert P, Escoufier Y. A unifying tool for linear multivariate statistical methods: the RV-coefficient. Journal of the Royal Statistical Society. Series C (Applied Statistics) 25, 257-65.
  44. Saunders I.W, Brohede J, Hannan G.N. Estimating genotyping error rates from Mendelian errors in SNP array genotypes and their impact on inference. Genomics 90, 291-6.
  45. Schaefer R.J, McCue M.E. Equine genotyping arrays. Veterinary Clinics of North America: Equine Practice 36, 183-93.
  46. Schaefer R.J, Schubert M, Bailey E. Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds. BMC Genomics 18, 565.
  47. Shilton C.A, Kahler A, Davis B.W, Crabtree J.R, Crowhurst J, McGladdery A.J, Wathes D.C, Raudsepp T, de Mestre A.M. Whole genome analysis reveals aneuploidies in early pregnancy loss in the horse. Scientific Reports 10.
    doi: 10.1038/s41598-020-69967-zgoogle scholar: lookup
  48. Singh R.R, Mehrotra M, Chen H. Comprehensive screening of gene copy number aberrations in formalin-fixed, paraffin-embedded solid tumors using molecular inversion probe-based single-nucleotide polymorphism array. Journal of Molecular Diagnostics 18, 676-87.
  49. Szczerbal I, Nowacka-Woszuk J, Kopp-Kuhlman C, Mackowski M, Switonski M. Application of droplet digital PCR in diagnosing of X monosomy in mares. Equine Veterinary Journal 52, 627-31.
  50. Tang Y.-C, Amon A. Gene copy-number alterations: a cost-benefit analysis. Cell 152, 394-405.
  51. Thermofisher. Axiom CNV Summary Tool user manual. .
  52. ThermoFisher. Axiom copy number analysis. .
  53. Villagómez D.A.F, Lear T.L, Chenier T, Lee S, McGee R.B, Cahill J, Foster R.A, Reyes E, St John E, King W.A. Equine disorders of sexual development in 17 mares including XX, SRY-negative, XY, SRY-negative and XY, SRY-positive genotypes. Sexual Development 5, 16-25.
  54. Villagómez D.A.F, Pinton A. Chromosomal abnormalities, meiotic behavior and fertility in domestic animals. Cytogenetic and Genome Research 120, 69-80.
  55. Wickham H. ggplot2: Elegant Graphics for Data Analysis. .
  56. Wiggans G.R, Cole J.B, Hubbard S.M, Sonstegard T.S. Genomic selection in dairy cattle: the USDA experience. Annual Review of Animal Biosciences 5, 309-27.

Citations

This article has been cited 7 times.
  1. Demyda-Peyrás S, Laseca N, Anaya G, Kij-Mitka B, Molina A, Karlau A, Valera M. Prevalence of Sex-Related Chromosomal Abnormalities in a Large Cohort of Spanish Purebred Horses. Animals (Basel) 2023 Feb 3;13(3).
    doi: 10.3390/ani13030539pubmed: 36766428google scholar: lookup
  2. Cardinali I, Giontella A, Tommasi A, Silvestrelli M, Lancioni H. Unlocking Horse Y Chromosome Diversity. Genes (Basel) 2022 Dec 2;13(12).
    doi: 10.3390/genes13122272pubmed: 36553539google scholar: lookup
  3. Laseca N, Molina A, Valera M, Antonini A, Demyda-Peyrás S. Copy Number Variation (CNV): A New Genomic Insight in Horses. Animals (Basel) 2022 Jun 2;12(11).
    doi: 10.3390/ani12111435pubmed: 35681904google scholar: lookup
  4. Shaffer LG, Hopp B, Switonski M, Zahand A, Ballif BC. Identification of aneuploidy in dogs screened by a SNP microarray. Hum Genet 2021 Nov;140(11):1619-1624.
    doi: 10.1007/s00439-021-02318-8pubmed: 34287710google scholar: lookup
  5. Zheng W, Ma W, Chen Z, Wang C, Sun T, Dong W, Zhang W, Zhang S, Tang Z, Li K, Zhao Y, Liu Y. DPImpute: A Genotype Imputation Framework for Ultra-Low Coverage Whole-Genome Sequencing and its Application in Genomic Selection. Adv Sci (Weinh) 2025 Apr;12(16):e2412482.
    doi: 10.1002/advs.202412482pubmed: 40013759google scholar: lookup
  6. Valera M, Karlau A, Anaya G, Bugno-Poniewierska M, Molina A, Encina A, Azor PJ, Demyda-Peyrás S. The Use of Genomic Screening for the Detection of Chromosomal Abnormalities in the Domestic Horse: Five New Cases of 65,XXY Syndrome in the Pura Raza Español Breed. Animals (Basel) 2024 Sep 3;14(17).
    doi: 10.3390/ani14172560pubmed: 39272345google scholar: lookup
  7. Laseca N, Anaya G, Peña Z, Pirosanto Y, Molina A, Demyda Peyrás S. Impaired Reproductive Function in Equines: From Genetics to Genomics. Animals (Basel) 2021 Feb 3;11(2).
    doi: 10.3390/ani11020393pubmed: 33546520google scholar: lookup
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