Research Article
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Genetic Variability of Small Horse Populations from Greek Islands

Year 2023, Volume: 6 Issue: 2, 117 - 125, 01.03.2023
https://doi.org/10.47115/bsagriculture.1165045

Abstract

In this study, we analyzed microsatellite variation in DNA obtained from hair samples collected from 46 local Greek horse populations originating from the islands of Skyros (Skyros Small Horse; n=9), Rhodes (Rodos Small Horse; n=6), Lesvos (with the traditional miniature Midili Small Horse (n=2) and the larger Lesvos Gaiter (n=22)) and Crete (Messara) (n=7). We used 15 autosomal microsatellite markers (VHL20, HTG4, AHT4, HMS7, HTG6, AHT5, HMS6, ASB2, HTG10, HTG7, HMS3, HMS2, ASB17, ASB23 and LEX33) for the genetic characterization of the above populations and exploration of their genetic structure and diversity levels. A total of 120 alleles were detected across the 15 loci with a minimum of 4 alleles in HTG7 locus and a maximum of 13 alleles in ASB17 locus. Τhe total per population number of alleles was 42 (Skyros Small Horse), 20 (Rodos Small Horse), 71 (Lesvos Gaiter), 52 (Messara breed) and 21 (Midili Small Horse). The effective number of alleles (Ne) per locus ranged from 1.47±0.13 (Rodos Small Horse) to 4.67±0.31 (Lesvos Gaiter). The allelic richness (Ar) was between 1.50±0.12 (Rodos Small Horse) and 2.93±0.08 (Lesvos Gaiter) and the average Polymorphism Information Content (PIC) values varied from 0.200±0.035 (Rodos Small Horse) to 0.733±0.026 (Lesvos Gaiter). No significant deviations from H-W equilibrium were found except for three loci (ASB2, HTG10 and LEX33) in Messara and one locus (ASB23) in Lesvos Gaiter. Τhe inbreeding coefficient (Fis) ranged from -0.130 (Rodos Small Horse) to 0.042 (Lesvos Gaiter). The observed (Ho) and expected (He) multilocus heterozygosity mean estimations were highest in Lesvos Gaiter (0.764±0.027 and 0.783±0.024, respectively) and smallest in Rodos Small Horse (0.300±0.075 and 0.269±0.064, respectively). Across loci, the total genetic diversity HT was 0.741, the diversity among subpopulations HS was 0.621 and the multilocus genetic differentiation GST was 0.161, which was rather high. The population of Rodos Small Horse separated from the remaining horses as shown by factorial correspondence analysis, population assignment and metric multidimensional scaling diagrams. This study highlights the loss of genetic diversity in small isolated horse populations and the urgent need to take protective measures to preserve them.

Supporting Institution

Agricultural University of Athens

References

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  • Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F. 2004. GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5000, Université de Montpellier II, Montpellier, France.
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  • Centre of Animal Genetic Resources of Athens. 2019. URL: http://www.kgbzath.gr (access date: August 10, 2022).
  • Coombs JA, Letcher BH, Nislow KH. 2008. Create: a software to create input files from diploid genotypic data for 52 genetic software programs. Mol Ecol Resour, 8: 578-580. DOI: 10.1111/j.1471-8286.2007.02036.x.
  • Cothran EG, Luis C. 2005. Genetic distance as a tool in the conservation of rare horse breeds. Pub-Eur Assoc Anim Prod, 116: 55.
  • Cothran G, Kostaras N, Juras, R, Conant E. 2010. Genetic diversity in native Greek horses. In: Book of Abstracts of the 61st Annual Meeting of the European Association for Animal Production, August 23-27, Heraklion, Greece, pp: 210.
  • El Mousadik A, Petit RJ. 1996. High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L.) Skeels] endemic to Morocco. Theoret. Appl Genet, 92: 832-839. DOI: 10.1007/BF00221895.
  • Giantsis IA, Diakakis NE, Avdi M. 2020. High frequencies of TNC and COL5A1 genotypes associated with low risk for superficial digital flexor tendinopathy in Greek indigenous horse breeds compared with warmblood horses. J Equine Vet Sci, 92: 103173.
  • Goudet J. 2005. HIERFSTAT, a package for R to compute and test hierarchical F-statistics. Mol Ecol Notes, 5: 184-186.
  • Jombart T. 2008. adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics, 24: 1403-1405.
  • Juras R, Cothran EG, Klimas R. 2003. Genetic analysis of three Lithuanian native horse breeds. Acta Agric Scand (A), 53(4): 180-185.
  • Kakoi H, Tozaki T, Gawahara H. 2007. Molecular analysis using mitochondrial DNA and microsatellites to infer the formation process of Japanese native horse populations. Biochem Genet, 45(3): 375-395.
  • Kostaras N, Papaioannou K, Konstantinidou M. 2021. Greek equine breeds in “Greek Domestic Breeds, A hidden treasure”. AMALTHIA - Network for the protection of Greek indigenous farm animals, Athens, Greece, 1st ed, pp: 152.
  • Laliotis GP, Avdi M. 2017. Genetic diversity assessment of an indigenous horse population of Greece. Biotech Anim Husb, 33(1): 81-90.
  • Nei M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 89(3): 583-590.
  • Nei M. 1987. Phylogenetic trees in molecular evolutionary genetics. Annu Rev Genet, 30: 371-403. DOI: 10.1146/annurev.genet.30.1.371.
  • Nei M, Chesser RK. 1983. Estimation of fixation indices and gene diversities. Annals Human Genet, 47(3): 253-259.
  • Paetkau D, Calvert W, Stirling I, Strobeck C. 1995. Microsatellite analysis of population structure in Canadian polar bears. Mol Ecol, 4(3): 347-354.
  • Paetkau D, Slade R, Burden M, Estoup A. 2004. Genetic assignment methods for the direct, real‐time estimation of migration rate: a simulation‐based exploration of accuracy and power. Mol Ecol, 13(1): 55-65.
  • Papaioannou K, Kostaras N. 2006. Study of the indigenous horse breed of Rhodes, in Greek. AMALTHIA -Network for the P rotection of Greek Indigenous Farm Animals, Athens, Greece, 1st ed, pp: 152.
  • Peakall R, Smouse PE. 2012. GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics, 28: 2537-2539.
  • Promerová M, Andersson LS, Juras R, Penedo MCT, Reissmann M, Tozaki T, Andersson L. 2014. Worldwide frequency distribution of the ‘Gait keeper’mutation in the DMRT 3 gene. Anim Genet, 45(2): 274-282.
  • R Core Team. 2020. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL: https://www.R-project.org/ (access date: September 10, 2021).
  • Rousset F. 2008. Genepop’007: A complete reimplementation of the Genepop. Mol Ecol Resour, 8(1): 103-106.
  • Scherf BD. 2000. World watch list of domestic animal diversity. Food and Agriculture Organization of the United Nations (FAO), Rome, Italy, 3rd ed., pp: 37.
  • Takasu M, Hiramatsu N, Tozaki T, Kakoi H, Nakagawa T, Hasegawa T, Maeda HM, Murase T, Mukoyama H. 2012. Genetic characterization of the endangered Kiso horse using 31 microsatellite DNAs. J Vet Medic Sci, 74(2): 161-166.
  • Thirstrup JP, Pertoldi C, Loeschcke V. 2008. Genetic analysis, breed assignment and conservation priorities of three native Danish horse breeds. Anim Genet, 39(5): 496-505.
  • Van de Goor L, Panneman H, van Haeringen W. 2010. A proposal for standardization in forensic equine DNA typing: allele nomenclature for 17 equine-specific STR loci. Anim Genet, 41(2): 122-127.
Year 2023, Volume: 6 Issue: 2, 117 - 125, 01.03.2023
https://doi.org/10.47115/bsagriculture.1165045

Abstract

References

  • Apostolidis AP, Mamuris Z, Karkavelia E, Alifakiotis T. 2001. Comparison of Greek breeds of horses using RAPD markers. J Anim Breed Genet, 118(1): 47-56.
  • Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F. 2004. GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5000, Université de Montpellier II, Montpellier, France.
  • 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: 68-76.
  • Centre of Animal Genetic Resources of Athens. 2019. URL: http://www.kgbzath.gr (access date: August 10, 2022).
  • Coombs JA, Letcher BH, Nislow KH. 2008. Create: a software to create input files from diploid genotypic data for 52 genetic software programs. Mol Ecol Resour, 8: 578-580. DOI: 10.1111/j.1471-8286.2007.02036.x.
  • Cothran EG, Luis C. 2005. Genetic distance as a tool in the conservation of rare horse breeds. Pub-Eur Assoc Anim Prod, 116: 55.
  • Cothran G, Kostaras N, Juras, R, Conant E. 2010. Genetic diversity in native Greek horses. In: Book of Abstracts of the 61st Annual Meeting of the European Association for Animal Production, August 23-27, Heraklion, Greece, pp: 210.
  • El Mousadik A, Petit RJ. 1996. High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L.) Skeels] endemic to Morocco. Theoret. Appl Genet, 92: 832-839. DOI: 10.1007/BF00221895.
  • Giantsis IA, Diakakis NE, Avdi M. 2020. High frequencies of TNC and COL5A1 genotypes associated with low risk for superficial digital flexor tendinopathy in Greek indigenous horse breeds compared with warmblood horses. J Equine Vet Sci, 92: 103173.
  • Goudet J. 2005. HIERFSTAT, a package for R to compute and test hierarchical F-statistics. Mol Ecol Notes, 5: 184-186.
  • Jombart T. 2008. adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics, 24: 1403-1405.
  • Juras R, Cothran EG, Klimas R. 2003. Genetic analysis of three Lithuanian native horse breeds. Acta Agric Scand (A), 53(4): 180-185.
  • Kakoi H, Tozaki T, Gawahara H. 2007. Molecular analysis using mitochondrial DNA and microsatellites to infer the formation process of Japanese native horse populations. Biochem Genet, 45(3): 375-395.
  • Kostaras N, Papaioannou K, Konstantinidou M. 2021. Greek equine breeds in “Greek Domestic Breeds, A hidden treasure”. AMALTHIA - Network for the protection of Greek indigenous farm animals, Athens, Greece, 1st ed, pp: 152.
  • Laliotis GP, Avdi M. 2017. Genetic diversity assessment of an indigenous horse population of Greece. Biotech Anim Husb, 33(1): 81-90.
  • Nei M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 89(3): 583-590.
  • Nei M. 1987. Phylogenetic trees in molecular evolutionary genetics. Annu Rev Genet, 30: 371-403. DOI: 10.1146/annurev.genet.30.1.371.
  • Nei M, Chesser RK. 1983. Estimation of fixation indices and gene diversities. Annals Human Genet, 47(3): 253-259.
  • Paetkau D, Calvert W, Stirling I, Strobeck C. 1995. Microsatellite analysis of population structure in Canadian polar bears. Mol Ecol, 4(3): 347-354.
  • Paetkau D, Slade R, Burden M, Estoup A. 2004. Genetic assignment methods for the direct, real‐time estimation of migration rate: a simulation‐based exploration of accuracy and power. Mol Ecol, 13(1): 55-65.
  • Papaioannou K, Kostaras N. 2006. Study of the indigenous horse breed of Rhodes, in Greek. AMALTHIA -Network for the P rotection of Greek Indigenous Farm Animals, Athens, Greece, 1st ed, pp: 152.
  • Peakall R, Smouse PE. 2012. GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics, 28: 2537-2539.
  • Promerová M, Andersson LS, Juras R, Penedo MCT, Reissmann M, Tozaki T, Andersson L. 2014. Worldwide frequency distribution of the ‘Gait keeper’mutation in the DMRT 3 gene. Anim Genet, 45(2): 274-282.
  • R Core Team. 2020. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL: https://www.R-project.org/ (access date: September 10, 2021).
  • Rousset F. 2008. Genepop’007: A complete reimplementation of the Genepop. Mol Ecol Resour, 8(1): 103-106.
  • Scherf BD. 2000. World watch list of domestic animal diversity. Food and Agriculture Organization of the United Nations (FAO), Rome, Italy, 3rd ed., pp: 37.
  • Takasu M, Hiramatsu N, Tozaki T, Kakoi H, Nakagawa T, Hasegawa T, Maeda HM, Murase T, Mukoyama H. 2012. Genetic characterization of the endangered Kiso horse using 31 microsatellite DNAs. J Vet Medic Sci, 74(2): 161-166.
  • Thirstrup JP, Pertoldi C, Loeschcke V. 2008. Genetic analysis, breed assignment and conservation priorities of three native Danish horse breeds. Anim Genet, 39(5): 496-505.
  • Van de Goor L, Panneman H, van Haeringen W. 2010. A proposal for standardization in forensic equine DNA typing: allele nomenclature for 17 equine-specific STR loci. Anim Genet, 41(2): 122-127.
There are 29 citations in total.

Details

Primary Language English
Subjects Zootechny (Other)
Journal Section Research Articles
Authors

Myrına Emilio Katsoulakou 0000-0002-2541-8898

Dimitris Papachristou 0000-0002-7605-7455

Nikolaos Kostaras 0000-0003-3863-1302

George Laliotis 0000-0001-6075-7687

Iosif Bizelis 0000-0002-9457-2696

Ernest Gus Cothran 0000-0003-2791-4331

Rytis Juras 0000-0002-7385-0618

Panagiota Koutsouli 0000-0003-4933-635X

Publication Date March 1, 2023
Submission Date September 23, 2022
Acceptance Date January 13, 2023
Published in Issue Year 2023 Volume: 6 Issue: 2

Cite

APA Emilio Katsoulakou, M., Papachristou, D., Kostaras, N., Laliotis, G., et al. (2023). Genetic Variability of Small Horse Populations from Greek Islands. Black Sea Journal of Agriculture, 6(2), 117-125. https://doi.org/10.47115/bsagriculture.1165045

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