Journal of Applied Genetics

, Volume 54, Issue 3, pp 285–292 | Cite as

Genetic diversity and conservation in a small endangered horse population

  • Eva Janova
  • Jan Futas
  • Marie Klumplerova
  • Lenka Putnova
  • Irena Vrtkova
  • Mirko Vyskocil
  • Petra Frolkova
  • Petr HorinEmail author
Animal Genetics • Original Paper


The Old Kladruber horses arose in the 17th century as a breed used for ceremonial purposes. Currently, grey and black coat colour varieties exist as two sub-populations with different recent breeding history. As the population underwent historical bottlenecks and intensive inbreeding, loss of genetic variation is considered as the major threat. Therefore, genetic diversity in neutral and non-neutral molecular markers was examined in the current nucleus population. Fifty microsatellites, 13 single nucleotide polymorphisms (SNPs) in immunity-related genes, three mutations in coat colour genes and one major histocompatibility (MHC-DRA) gene were studied for assessing genetic diversity after 15 years of conservation. The results were compared to values obtained in a similar study 13 years ago. The extent of genetic diversity of the current population was comparable to other breeds, despite its small size and isolation. The comparison between 1997 and 2010 did not show differences in the extent of genetic diversity and no loss of allele richness and/or heterozygosity was observed. Genetic differences identified between the black and grey sub-populations observed 13 years ago persisted. Deviations from the Hardy–Weinberg equilibrium found in 19 microsatellite loci and in five SNP loci are probably due to selective breeding. No differences between neutral and immunity-related markers were found. No changes in the frequencies of markers associated with two diseases, melanoma and insect bite hypersensitivity, were observed, due probably to the short interval of time between comparisons. It, thus, seems that, despite its small size, previous bottlenecks and inbreeding, the molecular variation of Old Kladruber horses is comparable to other horse breeds and that the current breeding policy does not compromise genetic variation of this endangered population.


Genetic diversity Old Kladruber horses Endangered horse breed Microsatellites Single nucleotide polymorphisms Immunity-related genes Conservation 



This study was supported by the project of the National Agency for Agricultural Research of the Ministry of Agriculture of the Czech Republic NAZV QH92277.

Conflict of interest

The authors declare no conflict of interest.

Ethical standards

The work performed complied with the current laws and ethical standards of the Czech Republic.

Supplementary material

13353_2013_151_MOESM1_ESM.doc (52 kb)
Table S1 (DOC 51 kb)
13353_2013_151_MOESM2_ESM.doc (125 kb)
Table S2 (DOC 125 kb)
13353_2013_151_MOESM3_ESM.doc (72 kb)
Table S3 (DOC 72 kb)


  1. Aberle KS, Hamann H, Drögemüller C, Distl O (2004) Genetic diversity in German draught horse breeds compared with a group of primitive, riding and wild horses by means of microsatellite DNA markers. Anim Genet 35:270–277PubMedCrossRefGoogle Scholar
  2. Achmann R, Curik I, Dovc P, Kavar T, Bodo I, Habe F, Marti E, Sölkner J, Brem G (2004) Microsatellite diversity, population subdivision and gene flow in the Lipizzan horse. Anim Genet 35:285–292PubMedCrossRefGoogle Scholar
  3. Arcos-Burgos M, Muenke M (2002) Genetics of population isolates. Clin Genet 61:233–247PubMedCrossRefGoogle Scholar
  4. Bömcke E, Gengler N, Cothran EG (2011) Genetic variability in the Skyros pony and its relationship with other Greek and foreign horse breeds. Genet Mol Biol 34:68–76PubMedCrossRefGoogle Scholar
  5. Curik I, Zechner P, Sölkner J, Achmann R, Bodo I, Dovc P, Kavar T, Marti E, Brem G (2003) Inbreeding, microsatellite heterozygosity, and morphological traits in Lipizzan horses. J Hered 94:125–132PubMedCrossRefGoogle Scholar
  6. Díaz S, Giovambattista G, Peral-García P (2005) Polymorphisms of the upstream regulatory region of the major histocompatibility complex DRB genes in domestic horses. Int J Immunogenet 32:91–98PubMedCrossRefGoogle Scholar
  7. Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50Google Scholar
  8. Foulley J-L, Ollivier L (2006) Estimating allelic richness and its diversity. Livest Sci 101:150–158CrossRefGoogle Scholar
  9. Frankham R (1995) Conservation genetics. Annu Rev Genet 29:305–327PubMedCrossRefGoogle Scholar
  10. Futas J, Vychodilova L, Hofmanova B, Vranova M, Putnova L, Muzik J, Vyskocil M, Vrtkova I, Dusek L, Majzlik I, Horin P (2012) Genomic analysis of resistance/susceptibility to melanoma in Old Kladruber greying horses. Tissue Antigens 79:247–248PubMedCrossRefGoogle Scholar
  11. Glowatzki-Mullis ML, Muntwyler J, Pfister W, Marti E, Rieder S, Poncet PA, Gaillard C (2006) Genetic diversity among horse populations with a special focus on the Franches-Montagnes breed. Anim Genet 37:33–39PubMedCrossRefGoogle Scholar
  12. Helyar SJ, Hemmer-Hansen J, Bekkevold D, Taylor MI, Ogden R, Limborg MT, Cariani A, Maes GE, Diopere E, Carvalho GR, Nielsen EE (2011) Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges. Mol Ecol Resour 11(Suppl 1):123–136PubMedCrossRefGoogle Scholar
  13. Horín P, Cothran EG, Trtková K, Marti E, Glasnák V, Henney P, Vyskocil M, Lazary S (1998) Polymorphism of Old Kladruber horses, a surviving but endangered baroque breed. Eur J Immunogenet 25:357–363PubMedCrossRefGoogle Scholar
  14. Jakubec V, Rejfková M, Volenec J, Majzlík I, Vostrý L (2007) Analysis of linear description of type traits in the varieties and studs of the Old Kladrub horse. Czech J Anim Sci 52:299–307Google Scholar
  15. Jakubec V, Vostrý L, Schlote W, Majzlík I, Mach K (2009) Selection in the genetic resource: genetic variation of the linear described type traits in the Old Kladrub horse. Arch Tierzucht 52:343–355Google Scholar
  16. Lazarus R, Vercelli D, Palmer LJ, Klimecki WJ, Silverman EK, Richter B, Riva A, Ramoni M, Martinez FD, Weiss ST, Kwiatkowski DJ (2002) Single nucleotide polymorphisms in innate immunity genes: abundant variation and potential role in complex human disease. Immunol Rev 190:9–25PubMedCrossRefGoogle Scholar
  17. Leroy G, Callède L, Verrier E, Mériaux JC, Ricard A, Danchin-Burge C, Rognon X (2009) Genetic diversity of a large set of horse breeds raised in France assessed by microsatellite polymorphism. Genet Sel Evol 41:5PubMedCrossRefGoogle Scholar
  18. Luís C, Cothran EG, Oom MM, Bailey E (2005) Major histocompatibility complex locus DRA polymorphism in the endangered Sorraia horse and related breeds. J Anim Breed Genet 122:69–72PubMedCrossRefGoogle Scholar
  19. Luís C, Juras R, Oom MM, Cothran EG (2007) Genetic diversity and relationships of Portuguese and other horse breeds based on protein and microsatellite loci variation. Anim Genet 38:20–27PubMedCrossRefGoogle Scholar
  20. Marklund L, Moller MJ, Sandberg K, Andersson L (1996) A missense mutation in the gene for melanocyte-stimulating hormone receptor (MC1R) is associated with the chestnut coat color in horses. Mamm Genome 7:895–899PubMedCrossRefGoogle Scholar
  21. Nei M, Maruyama T, Chakraborty R (1975) The bottleneck effect and genetic variability in populations. Evolution 29:1–10CrossRefGoogle Scholar
  22. O’Brien SJ (1994) Genetic and phylogenetic analyses of endangered species. Annu Rev Genet 28:467–489PubMedCrossRefGoogle Scholar
  23. Petit RJ, El Mousadik A, Pons O (1998) Identifying populations for conservation on the basis of genetic markers. Conserv Biol 12:844–855CrossRefGoogle Scholar
  24. Porter V (2002) Mason’s world dictionary of livestock breeds, types and varieties. Revised by Valeria Porter, 5th edn. CABI Publishing, OxonGoogle Scholar
  25. Rendo F, Iriondo M, Manzano C, Estonba A (2012) Effects of a 10-year conservation programme on the genetic diversity of the Pottoka pony—new clues regarding their origin. J Anim Breed Genet 129:234–243PubMedCrossRefGoogle Scholar
  26. Rieder S, Taourit S, Mariat D, Langlois B, Guérin G (2001) Mutations in the agouti (ASIP), the extension (MC1R), and the brown (TYRP1) loci and their association to coat color phenotypes in horses (Equus caballus). Mamm Genome 12:450–455PubMedCrossRefGoogle Scholar
  27. Rosengren Pielberg G, Golovko A, Sundström E, Curik I, Lennartsson J, Seltenhammer MH, Druml T, Binns M, Fitzsimmons C, Lindgren G, Sandberg K, Baumung R, Vetterlein M, Strömberg S, Grabherr M, Wade C, Lindblad-Toh K, Pontén F, Heldin CH, Sölkner J, Andersson L (2008) A cis-acting regulatory mutation causes premature hair graying and susceptibility to melanoma in the horse. Nat Genet 40:1004–1009PubMedCrossRefGoogle Scholar
  28. Solis A, Jugo BM, Mériaux JC, Iriondo M, Mazón LI, Aguirre AI, Vicario A, Estomba A (2005) Genetic diversity within and among four south European native horse breeds based on microsatellite DNA analysis: implications for conservation. J Hered 96:670–678PubMedCrossRefGoogle Scholar
  29. Thomson RC, Wang IJ, Johnson JR (2010) Genome-enabled development of DNA markers for ecology, evolution and conservation. Mol Ecol 19:2184–2195PubMedCrossRefGoogle Scholar
  30. Volenec J, Jakubec V, Jelínek J, Přibyl J, Záliš N (1995) Analysis of inbreeding of Old Kladrub horses. Sci Agric Bohem 26:279–286Google Scholar
  31. Vostrý L, Kracíková O, Hofmanová B, Czerneková V, Kott T, Přibyl J (2011) Intra-line and inter-line genetic diversity in sire lines of the Old Kladruber horse based on microsatellite analysis of DNA. Czech J Anim Sci 56:163–175Google Scholar
  32. Vychodilova L, Matiasovic J, Bobrova O, Futas J, Klumplerova M, Stejskalova K, Cvanova M, Janova E, Osickova J, Vyskocil M, Sedlinska M, Dusek L, Marti E, Horin P (2013) Immunogenomic analysis of insect bite hypersensitivity in a model horse population. Vet Immunol Immunopathol 152:260–268PubMedCrossRefGoogle Scholar
  33. Vychodilova-Krenkova L, Matiasovic J, Horin P (2005) Single nucleotide polymorphisms in four functionally related immune response genes in the horse: CD14, TLR4, Cepsilon, and Fcepsilon R1 alpha. Int J Immunogenet 32:277–283PubMedCrossRefGoogle Scholar

Copyright information

© Institute of Plant Genetics, Polish Academy of Sciences, Poznan 2013

Authors and Affiliations

  • Eva Janova
    • 1
  • Jan Futas
    • 1
    • 2
  • Marie Klumplerova
    • 1
    • 2
  • Lenka Putnova
    • 3
  • Irena Vrtkova
    • 3
  • Mirko Vyskocil
    • 1
  • Petra Frolkova
    • 1
  • Petr Horin
    • 1
    • 2
    Email author
  1. 1.Department of Animal Genetics, Faculty of Veterinary MedicineUniversity of Veterinary and Pharmaceutical SciencesBrnoCzech Republic
  2. 2.Ceitec VFUUniversity of Veterinary and Pharmaceutical SciencesBrnoCzech Republic
  3. 3.Laboratory of Agrigenomics, Department of Animal Morphology, Physiology and GeneticsMendel UniversityBrnoCzech Republic

Personalised recommendations