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Home / Equine Research Bank / Genet Mol Biol / Genetic variability in the Skyros pony and its relationship ...
Genetics and molecular biology2011; 34(1); 68-76; doi: 10.1590/S1415-47572010005000113

Genetic variability in the Skyros pony and its relationship with other Greek and foreign horse breeds.

Abstract: In Greece, seven native horse breeds have been identified so far. Among these, the Skyros pony is outstanding through having a distinct phenotype. In the present study, the aim was to assess genetic diversity in this breed, by using different types of genetic loci and available genealogical information. Its relationships with the other Greek, as well as foreign, domestic breeds were also investigated. Through microsatellite and pedigree analysis it appeared that the Skyros presented a similar level of genetic diversity to the other European breeds. Nevertheless, comparisons between DNA-based and pedigree-based results revealed that a loss of genetic diversity had probably already occurred before the beginning of breed registration. Tests indicated the possible existence of a recent bottleneck in two of the three main herds of Skyros pony. Nonetheless, relatively high levels of heterozygosity and Polymorphism Information Content indicated sufficient residual genetic variability, probably useful in planning future strategies for breed conservation. Three other Greek breeds were also analyzed. A comparison of these with domestic breeds elsewhere, revealed the closest relationships to be with the Middle Eastern types, whereas the Skyros itself remained isolated, without any close relationship, whatsoever.
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Publication Date: 2011-03-01 PubMed ID: 21637546PubMed Central: PMC3085377DOI: 10.1590/S1415-47572010005000113Google Scholar: Lookup
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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.

This research studies the genetic diversity of the Skyros pony breed from Greece. The study found that this breed has undergone a loss of genetic diversity, but still maintains a sufficient level of genetic variability, and is genetically distinct from other Greek and global horse breeds.

Research aim and methods

  • This study aimed to examine the genetic diversity in the Skyros pony, which is one of the seven native horse breeds in Greece, and distinctly unique in its physical features.
  • The researchers compared DNA samples from the Skyros pony with other Greek and foreign horse breeds using microsatellite and pedigree analysis.
  • They also analysed genealogical information, looking for common ancestors and patterns of inheritance.

Results and findings

  • The results showed the Skyros pony to have a similar level of genetic diversity as other European horse breeds.
  • However, the comparison of DNA-based and pedigree-based data suggested that the Skyros pony likely suffered a loss of genetic diversity before official breed registration started.
  • Tests found evidence of a recent bottleneck, or reduction in genetic diversity, in two of the three main herds of Skyros ponies.
    This creates a concern for the future sustainability of the breed.
  • Despite these issues, the breed still exhibited high levels of heterozygosity and polymorphism information content, indicating enough residual genetic variability which is important for future breeding strategies and conservation of the breed.

Comparison with other Greek and global breeds

  • Three other Greek horse breeds were also examined as part of the study.
  • Analysis of these breeds showed their closest genetic relationships are with Middle Eastern horse breeds.
  • However, the Skyros pony distinctly lacked any close genetic relationship with other breeds, underscoring its unique genetic make-up.

Implications of the study

  • The results of this study provide valuable information for conservation and breeding strategies, particularly for maintaining the genetic health of the Skyros pony breed.
  • The findings also contribute to the broader body of literature concerning genetic diversity in horse breeds.

Cite This Article

APA
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(1), 68-76. https://doi.org/10.1590/S1415-47572010005000113

Publication

Genetics and molecular biology
ISSN: 1678-4685
NlmUniqueID: 100883590
Country: Brazil
Language: English
Volume: 34
Issue: 1
Pages: 68-76

Researcher Affiliations

Bömcke, Elisabeth
  • Animal Science Unit, Gembloux Agricultural University, Gembloux, Belgium.
Gengler, Nicolas
    Cothran, E Gus

      References

      This article includes 53 references
      1. Aberle KS, Hamann H, Drögemüller C, Distl O. 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 2004 Aug;35(4):270-7.
        pubmed: 15265065doi: 10.1111/j.1365-2052.2004.01166.xgoogle scholar: lookup
      2. Alifakiotis TA. The Indigenous horse of Greece. Ministry of Agriculture; Athens: 2000. p. 38.
      3. Andersson L. The estimation of blood group gene frequencies: a note on the allocation method.. Anim Blood Groups Biochem Genet 1985;16(1):1-7.
        pubmed: 4003853doi: 10.1111/j.1365-2052.1985.tb01445.xgoogle scholar: lookup
      4. Apostolidis AP, Mamuris Z, Karkavelia E, Alifakiotis T. Comparison of Greek breeds of horses using RAPD markers. J Anim Breed Genet 2001;118:47–56.
      5. Aranguren-Mendez J, Jordana J, Gomez M. Genetic conservation of five endangered Spanish donkey breeds. J Anim Breed Genet 2002;119:256–263.
      6. Avdi M, Banos G. Genetic diversity and inbreeding in the Greek Skyros horse. Livest Sci 2008;114:362–365.
      7. Boichard D. PEDIG: A Fortran package for pedigree analysis suited for large populations. Proceedings of the 7th World Congress on Genetics Applied to Livestock Production INRA, Castanet-Tolosan; 2002. p. 38.
      8. Boichard D, Maignel L, Verrier E. The value of using probabilities of gene origin to measure genetic variability in a population. Genet Select Evol 1997;29:5–23.
      9. Bomcke E, Gengler N. Combining microsatellite and pedigree data to estimate relationships among Skyros ponies.. J Appl Genet 2009;50(2):133-43.
        pubmed: 19433910doi: 10.1007/bf03195664google scholar: lookup
      10. Bradley DG, MacHugh DE, Cunningham P, Loftus RT. Mitochondrial diversity and the origins of African and European cattle.. Proc Natl Acad Sci U S A 1996 May 14;93(10):5131-5.
        pmc: PMC39419pubmed: 8643540doi: 10.1073/pnas.93.10.5131google scholar: lookup
      11. Caballero A, Toro MA. Analysis of genetic diversity for the management of conserved subdivided populations. Conserv Genet 2002;3:289–299.
      12. Cañon J, Checa ML, Carleos C, Vega-Pla JL, Vallejo M, Dunner S. The genetic structure of Spanish Celtic horse breeds inferred from microsatellite data.. Anim Genet 2000 Feb;31(1):39-48.
        pubmed: 10690360doi: 10.1046/j.1365-2052.2000.00591.xgoogle scholar: lookup
      13. Cavalli-Sforza LL, Edwards AW. Phylogenetic analysis. Models and estimation procedures.. Am J Hum Genet 1967 May;19(3 Pt 1):233-57.
        pmc: PMC1706274pubmed: 6026583
      14. Chevalet C, de Rochambeau H. Variabilité génétique et contrôle des souches consanguines. Sci Tech Lab 1986;11:251–257.
      15. Cornuet JM, Luikart G. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data.. Genetics 1996 Dec;144(4):2001-14.
        pmc: PMC1207747pubmed: 8978083doi: 10.1093/genetics/144.4.2001google scholar: lookup
      16. Cothran EG, Long YG. A new phenogroup in the horse D system of red cell alloantigens found in the Caspian pony.. Anim Genet 1994 Feb;25(1):49-50.
        pubmed: 8161022
      17. Cothran EG, Luis C. Genetic distance as a tool in conservation of rare horse breeds. In: Bodo I, Alderson L, Langolis B, editors. Conservation Genetics of Endangered Horse Breeds Wageningen. Academic Publishers; Wageningen: 2005. pp. 55–71.
      18. Cothran EG, Santos SA, Mozza MCM, Lear TL, Sereno JRB. Genetics of the Pantaneiro horse of the Pantanal region of Brazil. Genet Mol Biol 1998;21:343–349.
      19. Curik I, Zechner P, Sölkner J, Achmann R, Bodo I, Dovc P, Kavar T, Marti E, Brem G. Inbreeding, microsatellite heterozygosity, and morphological traits in Lipizzan horses.. J Hered 2003 Mar-Apr;94(2):125-32.
        pubmed: 12721224doi: 10.1093/jhered/esg029google scholar: lookup
      20. Dieringer D, Schlötterer C. Microsatellite analyser (MSA): A platform independent analysis tool for large microsatellite data sets. Mol Ecol Notes 2002;3:167–169.
      21. FAO. Secondary Guidelines for Development of National Farm Animal Genetic Resources Management Plans. 1998. p. 215. Management of Small Populations at Risk. Initiative for Domestic Animal Diversity. FAO, Rome.
      22. Felsenstein J. PHYLIP (Phylogeny Inference Package) v 35c. 1993. Department of Genetics, University of Washington.
      23. Flury C, Tapio M, Sonstegard T, Drögemüller C, Leeb T, Simianer H, Hanotte O, Rieder S. Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium.. J Anim Breed Genet 2010 Oct;127(5):339-47.
        pubmed: 20831557doi: 10.1111/j.1439-0388.2010.00862.xgoogle scholar: lookup
      24. Guo SW, Thompson EA. Performing the exact test of Hardy-Weinberg proportion for multiple alleles.. Biometrics 1992 Jun;48(2):361-72.
        pubmed: 1637966
      25. Glowatzki-Mullis ML, Muntwyler J, Pfister W, Marti E, Rieder S, Poncet PA, Gaillard C. Genetic diversity among horse populations with a special focus on the Franches-Montagnes breed.. Anim Genet 2006 Feb;37(1):33-9.
        pubmed: 16441293doi: 10.1111/j.1365-2052.2005.01376.xgoogle scholar: lookup
      26. Gupta AK, Chauhan M, Tandon SN. Genetic diversity and bottleneck studies in the Marwari horse breed.. J Genet 2005 Dec;84(3):295-301.
        pubmed: 16385161doi: 10.1007/bf02715799google scholar: lookup
      27. Juras R, Cothran EG. Microsatellites in Lithuanian native horse breeds: Usefulness for parentage testing. Biologija 2004;4:6–9.
      28. Juras R, Cothran EG, Klimas R. Genetic analysis of three Lithuanian native horse breeds. Acta Agric Scand A 2003;53:180–185.
      29. KIMURA M, CROW JF. THE NUMBER OF ALLELES THAT CAN BE MAINTAINED IN A FINITE POPULATION.. Genetics 1964 Apr;49(4):725-38.
        pmc: PMC1210609pubmed: 14156929doi: 10.1093/genetics/49.4.725google scholar: lookup
      30. Lacy RC. Analysis of founder representation in pedigrees: Founder equivalents and founder genome equivalents. Zoo Biol 1989;8:111–123.
      31. Luikart G, Cornuet JM. Empirical evaluation of a test for identifying recently bottlenecked populations from allele frequency data. Conserv Biol 1998;12:228–237.
      32. Luikart G, Allendorf FW, Cornuet JM, Sherwin WB. Distortion of allele frequency distributions provides a test for recent population bottlenecks.. J Hered 1998 May-Jun;89(3):238-47.
        pubmed: 9656466doi: 10.1093/jhered/89.3.238google scholar: lookup
      33. Luís C, Juras R, Oom MM, Cothran EG. Genetic diversity and relationships of Portuguese and other horse breeds based on protein and microsatellite loci variation.. Anim Genet 2007 Feb;38(1):20-7.
        pubmed: 17257184doi: 10.1111/j.1365-2052.2006.01545.xgoogle scholar: lookup
      34. MacCluer JW, Van de Berg JL, Read B, Ryder OA. Pedigree analysis by computer simulation. Zoo Biol 1986;5:147–160.
      35. Maignel L, Boichard D, Verrier E. Genetic variability of French dairy breeds estimated from pedigree information. Interbull Bull 1996;14:49–54.
      36. Moureaux S, Verrier E, Ricard A, Mériaux JC. Genetic variability within French race and riding horse breeds from genealogical data and blood marker polymorphism. Genet Select Evol 1996;28:83–102.
      37. Nei M. Molecular Evolutionary Genetics. Columbia University Press; New-York: 1987. p. 512.
      38. Ohta T, Kimura M. A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population.. Genet Res 1973 Oct;22(2):201-4.
        pubmed: 4777279doi: 10.1017/s0016672300012994google scholar: lookup
      39. Page RD. TreeView: an application to display phylogenetic trees on personal computers.. Comput Appl Biosci 1996 Aug;12(4):357-8.
        pubmed: 8902363doi: 10.1093/bioinformatics/12.4.357google scholar: lookup
      40. Piry S, Luikart G, Cornuet JM. Bottleneck: A computer program for detecting recent reductions in the effective population size using allele frequency data. J Hered 1999;90:502–503.
      41. Raymond M, Rousset F. GENEPOP v. 1.2: Population genetics software for exact tests and ecumenicism. J Hered 1995;86:248–249.
      42. Rochambeau H de, Fournet-Hanocq F, Vu Tien Khang J. Measuring and managing genetic variability in small populations. Ann Zootech 2000;49:77–93.
      43. Rognon X, Mériaux JC, Verrier E. Caractérisation génétique des races à l'aide des marqueurs moléculaires. 2005. pp. 147–160. In: 31éme Journée de la Recherche Equine, Haras Nationaux.
      44. Royo LJ, Alvarez I, Guttiérez JP, Fernández I, Goyache F. Genetic variability in the endangered Asturcón pony assessed using genealogical and molecular information. Livest Sci 2007;107:162–169.
      45. Sandberg K, Cothran EG. Biochemical genetics and blood groups. In: Bowling AT, Ruvinsky A, editors. The Genetics of The Horse. CABI Publishing; Wallingford: 2000. pp. 85–108.
      46. Solis A, Jugo BM, Mériaux JC, Iriondo M, Mazón LI, Aguirre AI, Vicario A, Estomba A. Genetic diversity within and among four South European native horse breeds based on microsatellite DNA analysis: implications for conservation.. J Hered 2005 Nov-Dec;96(6):670-8.
        pubmed: 16267169doi: 10.1093/jhered/esi123google scholar: lookup
      47. Strom H, Philipsson J. Relative importance of performance tests in horse breeding. Livest Prod Sci 1978;5:303–312.
      48. Takezaki N, Nei M. Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA.. Genetics 1996 Sep;144(1):389-99.
        pmc: PMC1207511pubmed: 8878702doi: 10.1093/genetics/144.1.389google scholar: lookup
      49. Valera M, Molina A, Gutiérrez JP, Gómez J, Goyache F. Pedigree analysis in the Andalusian horse: Population structure, genetic variability and influence of the Carthusian strain. Livest Prod Sci 2005;95:57–66.
      50. VanRaden PM. Efficient methods to compute genomic predictions.. J Dairy Sci 2008 Nov;91(11):4414-23.
        pubmed: 18946147doi: 10.3168/jds.2007-0980google scholar: lookup
      51. Vogelstein B, Gillespie D. Preparative and analytical purification of DNA from agarose.. Proc Natl Acad Sci U S A 1979 Feb;76(2):615-9.
        pmc: PMC382999pubmed: 284385doi: 10.1073/pnas.76.2.615google scholar: lookup
      52. Zafrakas A. The Equine and Its Feeding. 1991. p. 200. Kyriakidis, Thessaloniki. (in Greek).
      53. DAD-IS. Domestic Animal Diversity Information System (DAD-IS), Food and Agriculture Organization of the United Nation. 2007. http://www.fao.org/dad-is/ (September 25, 2008).

      Citations

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      1. Vincelette A. The Characteristics, Distribution, Function, and Origin of Alternative Lateral Horse Gaits.. Animals (Basel) 2023 Aug 8;13(16).
        doi: 10.3390/ani13162557pubmed: 37627349google scholar: lookup
      2. Bozlak E, Radovic L, Remer V, Rigler D, Allen L, Brem G, Stalder G, Castaneda C, Cothran G, Raudsepp T, Okuda Y, Moe KK, Moe HH, Kounnavongsa B, Keonouchanh S, Van NH, Vu VH, Shah MK, Nishibori M, Kazymbet P, Bakhtin M, Zhunushov A, Paul RC, Dashnyam B, Nozawa K, Almarzook S, Brockmann GA, Reissmann M, Antczak DF, Miller DC, Sadeghi R, von Butler-Wemken I, Kostaras N, Han H, Manglai D, Abdurasulov A, Sukhbaatar B, Ropka-Molik K, Stefaniuk-Szmukier M, Lopes MS, da Câmara Machado A, Kalashnikov VV, Kalinkova L, Zaitev AM, Novoa-Bravo M, Lindgren G, Brooks S, Rosa LP, Orlando L, Juras R, Kunieda T, Wallner B. Refining the evolutionary tree of the horse Y chromosome.. Sci Rep 2023 Jun 2;13(1):8954.
        doi: 10.1038/s41598-023-35539-0pubmed: 37268661google scholar: lookup
      3. Kang Z, Shi J, Liu T, Zhang Y, Zhang Q, Liu Z, Wang J, Cheng S. Genome-wide single-nucleotide polymorphism data and mitochondrial hypervariable region 1 nucleotide sequence reveal the origin of the Akhal-Teke horse.. Anim Biosci 2023 Oct;36(10):1499-1507.
        doi: 10.5713/ab.23.0044pubmed: 37170508google scholar: lookup
      4. Klein R, Oláh J, Mihók S, Posta J. Pedigree-Based Description of Three Traditional Hungarian Horse Breeds.. Animals (Basel) 2022 Aug 14;12(16).
        doi: 10.3390/ani12162071pubmed: 36009663google scholar: lookup
      5. Cozzi MC, Valiati P, Longeri M, Ferreira C, Abreu Ferreira S. Genetic Variability Trend of Lusitano Horse Breed Reared in Italy.. Animals (Basel) 2022 Jan 1;12(1).
        doi: 10.3390/ani12010098pubmed: 35011204google scholar: lookup
      6. Funk SM, Guedaoura S, Juras R, Raziq A, Landolsi F, Luís C, Martínez AM, Musa Mayaki A, Mujica F, Oom MDM, Ouragh L, Stranger YM, Vega-Pla JL, Cothran EG. Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites.. Ecol Evol 2020 May;10(10):4261-4279.
        doi: 10.1002/ece3.6195pubmed: 32489595google scholar: lookup
      7. Giontella A, Cardinali I, Lancioni H, Giovannini S, Pieramati C, Silvestrelli M, Sarti FM. Mitochondrial DNA Survey Reveals the Lack of Accuracy in Maremmano Horse Studbook Records.. Animals (Basel) 2020 May 12;10(5).
        doi: 10.3390/ani10050839pubmed: 32408648google scholar: lookup
      8. Cozzi MC, Strillacci MG, Valiati P, Rogliano E, Bagnato A, Longeri M. Genetic variability of Akhal-Teke horses bred in Italy.. PeerJ 2018;6:e4889.
        doi: 10.7717/peerj.4889pubmed: 30202639google scholar: lookup
      9. Lopes MS, Mendonça D, Rojer H, Cabral V, Bettencourt SX, da Câmara Machado A. Morphological and genetic characterization of an emerging Azorean horse breed: the Terceira Pony.. Front Genet 2015;6:62.
        doi: 10.3389/fgene.2015.00062pubmed: 25774165google scholar: lookup
      10. Devi KM, Ghosh SK. Molecular phylogeny of Indian horse breeds with special reference to Manipuri pony based on mitochondrial D-loop.. Mol Biol Rep 2013 Oct;40(10):5861-7.
        doi: 10.1007/s11033-013-2692-2pubmed: 24068432google scholar: lookup
      11. Janova E, Futas J, Klumplerova M, Putnova L, Vrtkova I, Vyskocil M, Frolkova P, Horin P. Genetic diversity and conservation in a small endangered horse population.. J Appl Genet 2013 Aug;54(3):285-92.
        doi: 10.1007/s13353-013-0151-3pubmed: 23649723google scholar: lookup
      12. Petersen JL, Mickelson JR, Cothran EG, Andersson LS, Axelsson J, Bailey E, Bannasch D, Binns MM, Borges AS, Brama P, da Câmara Machado A, Distl O, Felicetti M, Fox-Clipsham L, Graves KT, Guérin G, Haase B, Hasegawa T, Hemmann K, Hill EW, Leeb T, Lindgren G, Lohi H, Lopes MS, McGivney BA, Mikko S, Orr N, Penedo MC, Piercy RJ, Raekallio M, Rieder S, Røed KH, Silvestrelli M, Swinburne J, Tozaki T, Vaudin M, M Wade C, McCue ME. Genetic diversity in the modern horse illustrated from genome-wide SNP data.. PLoS One 2013;8(1):e54997.
        doi: 10.1371/journal.pone.0054997pubmed: 23383025google scholar: lookup
      13. Andersson LS, Swinburne JE, Meadows JR, Broström H, Eriksson S, Fikse WF, Frey R, Sundquist M, Tseng CT, Mikko S, Lindgren G. The same ELA class II risk factors confer equine insect bite hypersensitivity in two distinct populations.. Immunogenetics 2012 Mar;64(3):201-8.
        doi: 10.1007/s00251-011-0573-1pubmed: 21947540google scholar: lookup
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