The identification of representatives of the genus Ovis by microsatellite markers

The identification of wildlife species belonging to the same genus is important for population genetics, for detection of hybrids in contact zones, as well as for forensics and for monitoring to create the conservation programs for genetic recourses. The most informative method in wildlife species is the cross-species amplification of DNA marker panels designed for domestic relatives. In this regard, the purpose of our work was to perform the identification of species of the genus Ovis based on microsatellite markers of the domestic sheep. The materials for our research included three groups of argali (n = 7, n = 6, n = 16), mouflon (n = 22); snow sheep, including the Yakut subspecies from several ranges (n = 17, n = 11, n = 21, n = 10), and the Chukchi subspecies (n = 3); domestic sheep (n = 35). Analysis of the NeighborNet revealed that snow sheep formed own remote cluster (D_N = 1.544 to 2.225, 1.685 to 2.424, 1.674 to 2.454 between snow sheep and mouflon domestic sheep and argali, respectively). The remaining species under the study formed two clusters: the first included groups of argali, and the second comprised of mouflons and domestic sheep. PCoA showed that the first principal coordinate clearly divided snow sheep from the remaining groups (Fst = 0.304, 0.333, 0.378 between snow sheep and domestic sheep, argali, mouflon, respectively). The second principal coordinate separated the Chukchi from the Yakut bighorns and groups of argali from domestic sheep and mouflon, respectively. To determine the individual belonging to the group, a cluster analysis was carried out in the STRUCTURE program. At K = 2, mouflons formed a shared cluster with domestic sheep, while snow sheep and argali included in the other cluster. At K = 3, snow sheep and argali formed own clusters. At K = 5, each specie had own cluster. The average membership criterions were Q_{3 / 5} = 0.976 ± 0.004 for domestic sheep, Q_{2/ 5} = 0.980 ± 0.004 for mouflons and and Q_{5 / 5} = 0.962 ± 0.011 for snow sheep. Regarding the argali group, its membership criterion was lower (Q_{1 / 5} = 0.747 ± 0.072). At K = 6, the Chukchi bighorns (Q_{4 / 6} = 0.991 ± 0.001) clearly separate from their Yakut relatives (Q_{6 / 6} = 0.947 ± 0.014). Thus, we demonstrated that the resolving power of ten microsatellite markers of domestic sheep is sufficient to identify wild representatives of the genus Ovis.

Ovis genus, domestic sheep, wild relatives, argali, snow sheep, mouflons, microsatellite loci, identification

1. Arif I. A. DNA marker technology for wildlife conservation / I. A. Arif, H. A. Khan, A. H. Bahkali, A. A. Al Homaidan, A. H. Al Farhan, M. Al Sadoon, M. Shobrak // Saudi Journal of Biological Sciences. - 2011. - № 18. - P. 219-225.

2. Ogden R. Wildlife DNA forensics-bridging the gap between conservation genetics and law enforcement / R. Ogden, N. Dawnay, R. McEwing // E. Species Res. - 2009. - № 9. -P. 179-195.

3. Rezaei H. R. Evolution and taxonomy of the wild species of the genus Ovis (Mammalia, Artiodactyla, Bovidae) / H. R. Rezaei, S. Naderia, I. C. Chintauan-Marquiera, S. Jordan, P. Taberlet, A. T. Virk, H. R. Naghash, D. Rioux, M. Kaboli, G. Luikart, F. Pompanon // Molecular Phylogenetics and Evolution. - 2010. - № 54. - P. 315-326.

4. Feng J. Genetic differentiation of argali sheep Ovis ammon in Mongolia revealed by mitochondrial control region and nuclear microsatellites analyses / J. Feng, M. R. Frisina, M. S. Webster, G. Ulziimaa // Journal of the Bombay Natural History Society. - 2009. - № 106(1). - P. 38-44.

5. Fahmi A. I. Genetic Variation in Captive Herd of Arabian Oryx Using RAPD and ISSR Markers / Fahmi A. I., Al-Otaibi S. A. // African Journal of Biotechnology. - 2011. - № 10(27). - P. 5251-5262.

6. Budowle B. Forensics and mitochondrial DNA: applications, debates, and foundations / B. Budowle, M. W. Allard, M. R. Wilson, R. Chakraborty // Annu Rev Genomics Hum Genet. - 2003. - № 4. -P. 119-141.

7. Kol N. V. Polymorphism of ISSR-PCR markers in Tuvinian population of Reindeer Rangifer tarandus / N. V. Kol, O. E. Lazebny // Russ. J. Genet. - 2006. - № 42. - P. 1466 -1469.

8. Столповский Ю. А. Сравнительный анализ полиморфизма ISSR-маркеров в популяциях яка (Bos mutus) и гибридов F1 между яком и крупным рогатым скотом в Саяно-Алтайском регионе / Ю. А. Столповский, Н. В. Кол, А. Н. Евсюков, Л. В. Нестерук, Ч. М. Доржу, Ц. Цендсурэн, Г. Е. Сулимова // Генетика. - 2014. - № 50 (10). - С. 1163

9. Gaponova I. I. Comparative analysis of polylocus spectra of ISSR-PCR markers in dogs, jackals and wolves / I. I. Gaponova, V. I. Glazko, T. V. Blokhina, E. A. Knyaseva, T. T. Glazko // Central European Journal of Zoology. - 2017. - Т. 1. № 3. - С. 4 -18.

10. Serra I. A. Comparison of ISSR and SSR markers for analysis of genetic diversity in the seagrass Posidonia oceanica / I. A. Serra, G. Procaccini, M. C. Intrieri, M. Migliaccio, S. Mazzuca, A. M. Innocenti1 // Marine Ecology Progress Series. - 2007. - №8. - P. 71 -79.

11. Miller J. M. A genome-wide set of SNPs detects population substructure and long-range linkage disequilibrium in wild sheep / J. M. Miller, J. Poissant, J. W. Kijas, D. W. Coltman, the International Sheep Genomics Consortium //Molecular Ecology Resources. -2011. - № 11(2). - P. 314 - 322.

12. Garvin M. R. Application of single nucleotide polymorphisms to non-model species: a technical review / M. R. Garvin, K. Saitoh, A. J. Gharrett //Molecular Ecology Resources. - 2010.- №10.- P. 915 -934.

13. Ogden R. The use of cross-species genome-wide arrays to discover SNP markers for conservation genetics: a case study from Arabian and scimitar-horned oryx / R. Ogden, J. Baird, H. Senn, R. McEwing // Conservation Genetics Resources. - 2012.- №4. - P. 471 - 473.

14. Kharzinova V. R.A study of applicability of SNP chips developed for bovine and ovine species to whole-genome analysis of reindeer Rangifer Tarandus / V. R. Kharzinova, A. A. Sermyagin, E. A. Gladyr, G. Brem, N. A. Zinovieva, I. M. Okhlopkov //Journal of Heredity. - 2015. - № 106(6). - P. 758 -761.

15. Kim K.-S. Cross-Species Amplification of Bovidae Microsatellites and Low Diversity of the Endangered Korean Goral / K. S. Kim, M.-S. Min, J.-H. An, H. Lee // Journal of Heredity. - 2004. - № 95 (6). - P. 521-525.

16. Marín J. C. Cross-amplification of nonspecific microsatellites markers: a useful tool to study endangered/vulnerable species of southern Andes deer / J. C. Marín, P. Orozco-ter Wengel, K. Romero, J. P. Vásquez, V. Varas, J. A. Vianna // Genet Mol. Res. - 2014. - №13 (2). - P. 3193-3200.

17. Nguyen T. T. Genomic conservation of cattle microsatellite loci in wild gaur (Bos gaurus) and current genetic status of this species in Vietnam / T. T. Nguyen, S. Genini, L. C. Bui, P. Voegeli, G. Stranzinger, J. P. Renard, J. C. Maillard, B. X. Nguyen // BMC Genet. - 2007. - №6. - P.77.

18. Gutierrez E. Genetic variation and population structure in desert bighorn sheep: implications for conservation / E. Gutierrez, S. Kalinowski, W. Boyce, P. Hedrick // Conservation Genetics. - 2000. -№1(1). - P. 3-15.

19. Poissant J. Genome-wide cross-amplification of domestic sheep microsatellites in bighorn sheep and mountain goats / J. Poissant, A. B. Shafer, C. S. Davis, J. Mainguy, J. T. Hogg, S. D. Côté, D. W. Coltman // Mol Ecol Resour. - 2009 - № 9(4). - P. 1121-6.

20. Abad-Zavaleta J. Genetic diversity analysis of two desert bighorn sheep (Ovis canadensis mexicana) population in Mexico / J. Abad-Zavaleta, A. M. Sifuente-Rincon, A. Lafon-Terrazas, J. Gutierrez-Alderete, E. Gonzalez-Rodriguez, J. A. Ortega-Gutierrez, S. Del Moral, C. A. Meza-Herrera // Tropical and Subtropical Agroecosystems. - 2011. - № 14. - P.171 - 178.

21. Worley K. Population genetic structure of North American thin horn sheep (Ovis dalli) / K. Worley, C. Strobeck, S. Arthur, J. Carey, H. Schwantje, A. Veitch, D. W. Coltman // Molecular Ecology. - 2004. - №13(9). - P. 2545 -2556.

22. Petit E. Genetic structure of populations of the Mediterranean mouflon (Ovis gmelinl) / E. Petit, S. Aulagnier, R. Bon, M. Dubois, B. Crouau-Roy //Journal of Mammalogy. - 1997. - № 78 (2). - P. 459-467.

23. Sadeghi B. Genetic Diversity of Tandureh Mouflon Population / B. Sadeghi // Acta Vet Eurasia. - 2018. - № 44. - P. 20-25.

24. Nei. M. Molecular Evolutionary Genetics, Columbia University Press, NewYork, 1987

25. Peakall R. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research -an update / R. Peakall, P. E. Smouse // Bioinformatics. - 2012. - № 28. - P. 2537-2539

26. Huson D. H. Application of Phylogenetic Networks in Evolutionary Studies / D. H. Huson, D. Bryant //Molecular Biology and Evolution. - 2006. - № 23 (2). - P. 254-267.

27. Prichard J. K. Inference of population structure using multilocus genotype data / J. K. Prichard, M. Stephens, P. Donnelly // Genetics. - 2000. - №55. - P. 945-959.

28. Hartl D. L., Clark A. G. Principles of population genetics, United Kingdom: Sunderland, 1997.

29. Денискова Т. Е. Сравнительное исследование информативности STR и SNP маркеров для внутривидовой и межвидовой дифференциации рода Ovis / T. Е. Денискова, Сермягин А.А., В. А. Багиров, И. М. Охлопков, Е. А. Гладырь, Р. В. Иванов, Г. Брем, Н. А. Зиновьева // Генетика. - 2016. - № 52(1). - С. 90-96.

30. Vigne J. D. The origins of animal domestication and husbandry: a major change in the history of humanity and the biosphere / J. D. Vigne // C R Biol. - 2011. - №334(3). - P. 171-181.