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Genetic Evaluation by Microsatellite Loci of Pinus sylvestris L. Plus Trees. P. 48–68

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A.A. Ilinov, B.V. Raevsky

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In this study, a comparative analysis was performed to estimate the genetic diversity levels of Pinus sylvestris L. in 49 seed orchards of I generation and progeny test plantings using 4-nucleus microsatellite loci. The seed orchards are located in the Petrozavodsk and Zaonezhye regions of the Republic of Karelia. The progeny trials were created by half-sibling seed progenies of the clones in the Petrozavodsk seed orchard. Micro-Checker software was used to identify null alleles and exclude genotyping errors. Coefficients of genetic originality were determined by examining the genetic structure of breeding objects in relation to the proportion between the rare and the dominant alleles for each selected tree. A major part of the rarest alleles (27.3–37.0 %) and a small fraction of the most common alleles (3.3–14.8 %) were detected for the distinct range of the pine trees in both seed orchards and test cultures. The largest number (40) of all identified alleles (51) was found in the Petrozavodsk seed orchard. The Hardy-Weinberg test comparing allele rates to expectational values showed a lack of heterozygotes in each category of the empirical substances. The selected material also had high levels of allelic and genetic diversity. The average number of alleles per locus ranged from 7.75 to 10.50. The average effective number was from 5.00 to 6.54. The observed heterozygosity varied from 0.60 to 0.70. The expected heterozygosity was 0.63–0.71. The numerical deviations were statistically insignificant. The AMOVA molecular dispersion result was 5 %, indicating the absence of significant genetic differentiation between the breeding objects. The heterozygote deficiency was caused not only by the presence of null alleles, but also by the selection. Namely, the set of alleles in the experimental material, randomly selected from a limited number of genotypes (clones), may differ from the natural population. The high level of the rarest alleles in the given range of the pine trees can also be explained as a selection effect. The results obtained in this study are important for creating breeding objects with higher genetic value.


Alexey A. Ilinov, Candidate of Agriculture; ResearcherID: L-5854-2013, ORCID:
Boris V. Raevsky*, Doctor of Agriculture Sciences; ResearcherID: K-6424-2018, ORCID:


Forest Research Institute of the Karelian Research Centre of the Russian Academy of Sciences, ul. Pushkinskaya, 11, Petrozavodsk, 185910, Russian Federation;*


Scots pine, microsatellites, coefficient of genetic originality, genetic diversity, forest seed orchards, test cultures

For citation

Ilinov A.A., Raevsky B.V. Genetic Evaluation by Microsatellite Loci of Pinus sylvestris L. Plus Trees. Lesnoy Zhurnal = Russian Forestry Journal, 2023, no. 3, pp. 48–68. (In Russ.).


  1. Ivanovskaya S.I. Evaluation of the Scots Pine (Pinus sylvestris L.) Gene Pool in Plus Stands of Belarus According to Isozyme Analysis. Trudy BSTU, Serie: Lesnoe khozyaistvo, 2014, no. 1, pp. 130–134. (In Russ.).

  2. Ivanovskaya S.I., Barsukova M.M., Revyako I.D., Luferova N.S., Padutov V.E., Revyako I.D. Level of Genetic Variability in Scots Pine Trees of Various Breeding Categories. Problems of Forest Science and Forestry: Proceedings of Forest Institute of the National Academy of Sciences of Belarus. Minsk, 2008, vol. 68, pp. 178–186. (In Russ.).

  3. Ilinov A.A., Raevsky B.V. Comparative Evaluation of the Genetic Diversity of Natural Populations and Clonal Seed Orchards of Pinus sylvestris L. and Picea × fennica (Regel) Kom. in Karelia. Ekologicheskaya genetika = Russian Journal of Genetics, 2015, vol. 13, no. 4, pp. 55–67. (In Russ.).

  4. Ilinov A.A., Raevsky B.V. The Current State of Pinus sylvestris L. Gene Pool in Karelia. Sibirskiy lesnoy zhurnal = Siberian Journal of Forest Science, 2016, no. 5, pp. 45–54. (In Russ.).

  5. Ilinov A.A., Raevsky B.V. Analysis of the Pinus sylvestris L. Plus Tree Gene Pool in Karelia Using Microsatellite Loci. Proceedings of the Karelian RC RAS. 2018, no. 6, pp. 124–134. (In Russ.).

  6. Novikov P.S., Sheikina O.V. ISSR Analysis of Pinus sylvestris Trees of Different Selection Categories. Nauchnyi zhurnal KubGAU = Scientific Journal of KubSAU, 2012, vol. 82, no. 8, pp. 100–112. (In Russ.).

  7. Potokina E.K., Aleksandrova T.G. Methods for Classifying Intraspecific Diversity Based on the Results of Molecular Labeling. Proceedings of All-Russian Conference "Fundamental and Applied Problems of Botany at the Beginning of XXI century", Petrozavodsk, September 22-27, 2008. Petrozavodsk, Karelian RC RAS Publ., 2008, pp. 62–65. (In Russ.).

  8. Raevsky B.V., Schurova M.L. The Method for Breeding and Genetic Assessment of Scotch Pine Clones at Forest Seed Orchards. Sibirskii lesnoi zhurnal = Siberian Journal of Forest Science, 2016, no. 5, pp. 91–98. (In Russ.).

  9. Smirnov E.S. On Coding Traits for Taxonomic Analysis. Zhurnal obshchey biologii = Journal of General Biology, 1971, vol. 32, no. 2, pp. 224–228. (In Russ.).

  10. Stepanova E.M., Goncharenko G.G. Allelic and Genotypic Diversity in Natural and Artificial Forest Stands of Pinus sylvestris. Molodoj uchenyj, 2009, no. 12(12), pp. 122–124. (In Russ.).

  11. Bergmann F., Ruetz W. Isozyme Genetic Variation and Heterozygosity in Random Tree Samples and Selected Orchard Clones from the Same Norway Spruce Populations. Forest Ecology and Management, 1991, vol. 46, no. 1-2, pp. 39–47.

  12. Brown A.H.D., Moran G.F. Isozymes, and the Genetic Resources of Forest Trees. Proceedings of the Symposium on Iso-Zymes of North American Forest Trees and Forest Insects, California, Berkeley, July 27, 1979. California, Berkeley Publ., 1981, pp. 1–10.

  13. Cheliak W.M., Murray G., Pitel J.A. Genetic Effects of Phenotypic Selection in White Spruce. Forest Ecology and Management, 1998, vol. 24, no. 2, pp. 139–149.

  14. Danusevicius D., Lindgren D. Two-Stage Selection Strategies in Tree Breeding Considering Gain, Diversity, Time and Cost. Forest Genetics, 2002, vol. 9, iss. 2, pp. 147–159.

  15. El-Kassaby Y.A., Namkoong G. Genetic Diversity of Forest Tree Plantations: Consequences of Domestication. Consequences of Changes in Biodiversity. Proceedings of IUFRO World Congress. Finland, Tampere, 1995, vol. 2, pp. 218–228.

  16. Elsik C.G., Minihan V.T., Hall S.E., Scarpa A.M., Williams C.G. Low-Copy Microsatellite Markers for Pinus taeda L. Genome, 2000, vol. 43, no. 3, pp. 550–555.

  17. Funda T., Lstiburek M., Lachout P., Klápste J., El-Kassaby Y.A. Optimization of Combined Genetic Gain and Diversity for Collection and Deployment of Seed Orchard Crops. Tree Genetics and Genomes, 2009, vol. 5, no. 4, pp. 583–593.

  18. Haapanen M., Hynynen J., Ruotsalainen S., Siipilehto J., Kilpelyainen M.-L. Realised and Projected Gains in Growth, Quality and Simulated Yield of Genetically Improved Scots Pine in Southern Finland. European Journal of Forest Research, 2016, vol. 135, no. 6, pp. 997–1009.

  19. Ivetić V., Devetaković J., Nonić M., Stanković D., Šijačić-Nikolić M. Genetic Diversity and Forest Reproductive Material – from Seed Source Selection to Planting. IForest: Biogeosciences and Forestry, 2016, vol. 9, no. 5, pp. 801–812.

  20. Knowles P. Comparison of Isozyme Variation Among Natural Stands and Plantations: Jack Pine and Black Spruce. Canadian Journal of Forest Research, 1985, vol. 15, no. 5, pp. 902–908.

  21. Koski V. A Note on Genetic Diversity in Natural Populations and Cultivated Stands of Scots Pine (Pinus sylvestris L.). Investigación Agraria. Sistemas y Recursos Forestales, 2000, vol. 9, no. 1, pp. 89–96.

  22. Ledig F.T. The Conservation of Diversity in Forest Trees: Why and How Should Genes Be Conserved? Bioscience, 1988, vol. 38, no. 7, pp. 471–479.

  23. Ledig F.T. Human Impacts on Genetic Diversity in Forest Ecosystems. Oikos, 1992, vol. 63, no. 1, p. 87.

  24. Lewandowski A., Kowalczyk J., Litkowiec M., Urbaniak L., Rzońca M. Selection of Elite Mother Trees of Scots Pine, and European Larch to Establish 1.5 Generation Seed Orchards. Sylwan, 2017, vol. 161, no. 11, pp. 917–926. (In Polish).

  25. Lindgren D., Prescher F. Optimal Clone Number for Seed Orchards with Tested Clones. Silvae Genetica, 2005, vol. 54, no. 1-6, pp. 80–92.

  26. Lundkvist K. Genetic Structure in Natural and Cultivated Forest Tree Populations. Silva Fennica, 1982, vol. 16, pp. 141–149.

  27. Muller-Starck G. Protection of Genetic Variability in Forest Trees. Forest Genetics, 1995, vol. 2, pp. 121–124.

  28. Namkoong G. Biodiversity – Issues in Genetics, Forestry and Ethics. Forestry Chronicle, 1992, vol. 68, no. 4, pp. 438–443.

  29. Nardin M., Musch B., Rousselle Y., Guerin V., Sanchez L., Rossi J-P., Gerber S., Marin S., Paques L.E., Rozenberg P. Genetic Differentiation of European Larch Along an Altitudinal Gradient in the French Alps. Annals of Forest Science, 2015, vol. 72, no. 5, pp. 517–527.

  30. Peakall R., Smouse P.E. GenAlEx 6.5: Genetic Analysis in Excel. Population Genetic Software for Teaching and Research – an Update. Bioinformatics, 2012, vol. 28, no. 19, pp. 2537–2539.

  31. Soranzo N., Provan J., Powell W. Characterization of Microsatellite Loci in Pinus sylvestris L. Molecular Ecology, 1998, vol. 7, no. 9, pp. 1260–1261.

  32. Stoehr M.U., El-Kassaby Y.A. Levels of Genetic Diversity at Different Stages of the Domestication Cycle of Interior Spruce in British Columbia. Theoretical and Applied Genetics, 1997, vol. 94, no. 1, pp. 83–90.

  33. Van Oosterhout C., Hutchinson W., Wills D., Shipley P. Micro-Checker: Software for Identifying and Correcting Genotyping Errors in Microsatellite Data. Molecular Ecology Notes, 2004, vol. 4, no. 3, pp. 535–538.

  34. Wójkiewicz B., Litkowiec M., Wachowiak W. Contrasting Patterns of Genetic Variation in Core and Peripheral Populations of Highly Outcrossing and Wind Pollinated Forest Tree Species. AoB Plants, 2016, vol. 8, pр. 1–13.


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