ND5-ND6 of mitochondrial dna as a molecular marker for differentiations of two repair and uterine nelma herds "Kubenskaya" and "Obskaya"

The purpose of the work is to evaluate the possibility of using the ND5/ND6 mtDNA site as a polymorphic marker for nelma differentiation using the example of two repair and brood herds of nelma "Kubenskaya" and "Obskaya" of the Forvat fish farm in the Leningrad region. 
Materials and Methods. Nelma haplotyping by PCR-RDF based on polymorphism of restriction sites of endonuclease enzymes and determination of the nucleotide sequence by Sanger sequencing of the ND5/ND6 mtDNA region. 
Results. The features of the ND5/ND6 nucleotide sequence presented in the work in representatives of the genus Stenodus had not previously been considered as an informative molecular genetic marker. It was found that the nelma from the repair and broodstock formed from the producers of Lake Kubensky demonstrates genetic differences from the repair and broodstock of the nelma from the Ob River. The analyzed mtDNA region can be used as a molecular genetic marker when carrying out nelma haplotyping at fish hatcheries in samples of a significant volume to control measures to restore geographically remote natural populations of nelma.

1. Dryagin P. A. Questions of the phylogeny of whitefishes (Coregonidae) / P. A. Dryagin, P. L. Pirozhnikov, V. V. Pokrovsky // Eighth session of the Scientific Council of SevNIORH. Petrozavodsk. – 1969. – P. 90—92.

2. Reshetnikov Yu. S. Ecology and systematics of whitefish // M.: Nauka. – 1980. – 263 p.

3. Bernatchez L. Integrating molecular genetics and ecology in studies of adaptive radiation: whitefish, Coregonus sp., as a case study / L. Bernatchez, A. Chouinard, G. Lu // Biol. J. Linn. Soc. – 1999. – V. 68. — P. 173—194.

4. Sendek D. S. Electrophoretic studies of Coregonid fishes from across Russia / D. S. Sendek // Advances in Limnology. – 2002. – Vol. 57. – P. 35—55.

5. Popov I. Yu. The Quintessence of Evolution / Popov I. Yu., Sendek D. S. // Evolutionary Biology: History and Theory. St. Petersburg: SPbFIET. – 2003. – P. 172–189.

6. Politov D. V. Molecular phylogeography of Palearctic and Nearctic ciscoes. / D. V. Politov, J. W. Bickham, J. C. Patton // Annales Zoologici Fennici. – 2004 – Vol. 41. —P. 13–23.

7. Borovikova E. A. Systematic position and origin of whitefishes (Coregonus, Coregonidae, Osteichthyes) of Europe. Genetic approach / E. A. Borovikova, A. A. Makhrov // Advances in modern biology. - 2009. — Vol. 129. – № 1. — P. 58—66.

8. Borovikova E. A. Molecular genetic studies in solving problems of phylogeny and phylogeography of whitefishes (Coregonidae) / E. A. Borovikova // Transactions of the I. D. Papanin Institute of Biology of Inland Waters, Russian Academy of Sciences. — 2016. — № 73 (76). — P. 46—63.

9. Bochkarev N. A. Taxonomic status and origin of some ecological forms of whitefish of the species Coregonus lavaretus (L.) from Siberian water bodies / N. A. Bochkarev, E. I. Zuikova, D. V. Politov // Genetics. — 2017. — Vol. 53. — № 8. — P. 922—932. doi: 10.7868/S0016675817080033.

10. Berg L. S. Freshwater fishes of the USSR and adjacent countries. Part 1. Publishing House of the USSR Academy of Sciences, Moscow-Leningrad, 1948. — p. 466.

11. Bernatchez L. Phylogenetic relationships among the subfamily Coregoninae as revealed by mitochondrial DNA restriction analysis. / L. Bernatchez, F. Colombani, J. J. Dodson // Journal of Fish Biology. – 1991. – Vol. 39. – P. 283–290.

12. Bodaly R. A. Genetic comparisons of New and Old World coregonid fishes./ R. A. Bodaly, J. Vuorinen et al. // Journal of Fish Biology. – 1991. – Vol. 38. – P. 37–51.

13. Lockwood S. F. Phylogenetic relationships among members of the Coregoninae inferred from direct sequencing of PCR-amplified mitochondrial DNA. / S. F. Lockwood, R. E. Dillinger et al. // Canadian Journal of Fisheries and Aquatic Sciences. – 1993. – Vol. 50 – P. 2112–2118.

14. Sajdak S. L. Phylogenetic relationships among Coregonus species inferred from the DNA sequence of the first internal transcribed spacer (ITS1) of ribosomal DNA / S. L. Sajdak, R. B. Phillips // Canadian Journal of Fisheries and Aquatic Sciences. – 1997. – Vol. 54. – P. 1494–1503.

15. Reist J. D. The phylogeny of New- and Old World coregonine fishes as revealed by sequence variation in a portion of the d-loop of mitochondrial DNA / J. D. Reist, L. D. Maiers et al. // Biology and Management of Coregonid Fishes. – Advances in Limnology. – 1998 – Vol. 50. – P. 323–339.

16. Baldina S. N. Genetic relationships of the Ussuri cisco, Coregonus ussuriensis Berg 1906, in view of mtDNA data / S. N. Baldina, N. Y. Gordon, D. V. Politov // Biology and Management of Coregonid Fishes. Advances in Limnology. – 2007. – Vol. 60 – P. 83–89.

17. Crete-Lafreniere A. Framing the Salmonidae Family hylogenetic Portrait: A More Complete Picture from Increased taxon Sampling / A. Crete-Lafreniere, L. K. Weir, L. Bernatchez // PLoS ONE. – 2012. – 7(10).

18. Politov D. V. Coregonids of Russia: Evolutionary genetic approach in assessment of the current state of biodiversity / D. V. Politov // Fundamental and Applied Limnology / Archiv for Hydrobiologie. – 2017. – Vol. 189(3). – P. 181—192.

19. Golovanova T. S. Allozyme variability of whitefish and nelma Stenodus leucichthys / T. S. Golovanova, D. G. Maldov, et al. // Voprosy rybovodstva. – 2000. – Vol. 1. – № 2. – P. 95–96.

20. Golovanova T. S. Application of RAPD-PCR analysis to study intraspecific variability of whitefish and nelma (Stenodus leucichthys) / T. S. Golovanova, S. I., et al. // II Biology, bioengineering of breeding and industrial cultivation of whitefish: Proceedings of the scientific and production meeting. Tyumen. – 2001. – P. 37–41.

21. Golovanova T. S. Analysis of genetic variability of whitefish and nelma Stenodus leucichthys (Guldenstadt, 1772) in connection with the tasks of artificial reproduction // Abstract of Cand. Sci. (Biol.). Moscow: VNIIPRKh, 2004 – 24 p.

22. Kottelat M., Freyhof J. Handbook of European freshwater fishes, 2007 – p. 640.

23. Shestakov A. V. Materials on the biology of nelma (Stenodus leucichthys nelma) of the middle reaches of the Anadyr River / A. V. Shestakov, S. I. Grunin // Readings in memory of Vladimir Yakovlevich Levanidov. — 2005. – Issue 3. — P. 552—556.

24. Popov P. A. Fishes of Siberia: distribution, ecology, catch: monograph. Novosibirsk: Publishing house of Novosibirsk. state University, 2007. – 526 p.

25. Zadelenov V. A. Nelma Stenodus leucichthys nelma (Pallas, 1773) (Salmoniformes, Coregonidae) of the Yenisei River: population structure, fishery, reproduction / V. A. Zadelenov, E. V. Derbineva // Vopr. Fisheries. — 2020. – Vol. 21. — № 2. — P. 156—168.

26. Bukhardinova M. V. Distribution and migration cycle of nelma Stenodus leucichthys nelma (Pallas, 1773) / M. V. Bukhardinova // Bulletin of Astrakhan State Technical University. — 2022. — № 1. — Vol. 73. — P. 16—24.

27. Tikhonov A. V. Animals of Russia. Red Book / Moscow: Rosman, 2012 – 241 p.

28. Titenkov I. S. Kubenskaya nelma / Moscow: Fisheries, 1961. – 52 p.

29. Red Data Book of the Russian Federation. Animals / Moscow: AST Astrel, 2001 – 862 p.

30. Konovalov A. F. Experiment with artificial reproduction of nelma Stenodus leucichthys nelma in the Lake Kubenskoye basin / A. F. Konovalov, M. Ya. Borisov, N. V. Dumnich // Bulletin of fishery sciences. – 2016. – Vol. 3. – № 4 (12). – P. 12–19.

31. Aljanabi S. M., Martinez I. Universal and rapid salt-extraction of high-quality genomic DNA for PCR-based techniques / S. M. Aljanabi, I. Martinez // Nucleic Acids Res. — 1997 – V. 25.

32. Gharrett A. J. Phylogeographic analysis of mitochondrial DNA variation in Alaskan coho salmon, Oncorhynchus kisutch. / A. J. Gharrett, A. K. Gray, V. Brykov // Fishery Bulletin. — 2001 – Vol. 99(4). – P. 528–544.

33. Brown W. M. Rapid evolution of animal mitochondrial DNA / W. M. Brown, M. George, A. C. Wilson // Ibid. 1979 – V. 76. – P. 1967—1971.

34. NEBcutter V2.0 2025. URL: https://nc2.neb.com/NEBcutter2/?noredir (дата обращения: 18.07.2025).