Analysis of genetic relationships of genotypes of the genus Rosa L. from the collection of Nikita Botanical Gardens using ISSR and IRAP DNA markers

In connection with the development of breeding and the creation of new plant varieties, the problem of their genotyping and identification is becoming increasingly important, therefore the use of molecular methods to identify genetic originality and assess plant genetic diversity appears to be relevant. As part of the work performed, informative ISSR and IRAP DNA markers promising for the study of genetic diversity of the Rosa L. genus were sought and applied to analysis of genetic relationships among 26 accessions of the genus Rosa L. from the gene pool collection of Nikita Botanical Gardens. They included 18 cultivated varieties and 8 accessions of wild species. The species sample included representatives of two subgenera, Rosa and Platyrhodon. The subgenus Platyrhodon was represented by one accession of the species R. roxburghii Tratt. Cultivated roses were represented by varieties of garden groups hybrid tea, floribunda, and grandiflora. The tested markers included 32 ISSRs and 13 IRAPs. Five ISSR markers (UBC 824, ASSR29, 3A21, UBC 864, and UBC 843) and three IRAPs (TDK 2R, Сass1, and Сass2) were chosen as the most promising. They were used for genotyping the studied sample of genotypes. In general, they appeared to be suitable for further use in studying the genetic diversity of the genus Rosa L. The numbers of polymorphic fragments ranged from 12 to 31, averaging 19.25 fragments per marker. For markers UBC 864 and UBC 843, unique fingerprints were identified in each accession studied. The genetic relationships of the studied species and varieties of roses analyzed by the UPGMA, PCoA, and Bayesian methods performed on the basis of IRAP and ISSR genotyping are consistent with their taxonomic positions. The genotype of the species R. roxburghii of the subgenus Platyrhodon was determined genetically as the most distant. According to clustering methods, the representative of the species R. bengalensis did not stand out from the group of cultivated varieties. When assessing the level of genetic similarity among the cultivated varieties of garden roses, the most genetically isolated varieties were ‘Flamingo’, ‘Queen Elizabeth’, and ‘Kordes Sondermeldung’; for most of the other varieties, groups of the greatest genetic similarity were identified. This assessment reflects general trends in phylogenetic relationships, both among the studied species of the genus and among cultivated varieties.

1. Arzate-Fernandez A.M., Miwa M., Shimada T., Yonekura T., Ogawa K. Genetic diversity of Miyamasukashi-yuri (Lilium maculatum Thunb. var. bukosanense), an endemic and endangered species at Mount Buko, Saitama, Japan. Plant Species Biol. 2005;20:57-65.

2. Atienza S.G., Torres A.M., Millan Т., Cubero J.I. Genetic diversity in Rosa as revealed by RAPDs. Agric. Conspec. Sci. 2005;70(3): 75-85.

3. Bruneau A., Starr J.R., Joly S. Phylogenetic relationships in the genus Rosa: new evidence from chloroplast DNA sequences and an appraisal of current knowledge. Syst. Bot. 2007;32(2):366-378.

4. El-Assal S.E.-D., El-Awady M.A., El-Tarras A., Shehab G. Assessing the genetic relationship of taif rose with some rose genotypes (Rosa sp.) based on random amplified polymorphic DNA, inter simple sequence repeat and simple sequence repeat markers. Am. J. Biochem. Biotechnol. 2014;10(1):88-98. DOI 10.3844/ajbbsp.2014.88.98.

5. Ena A.V. Natural Flora of the Crimean Peninsula. Simferopol’, 2012. (in Russian)

6. Fougère-Danezan M., Joly S., Bruneau A., Gao X.-F., Zhang L.-B. Phylogeny and biogeography of wild roses with specific attention to polyploids. Ann. Bot. 2015;115(2):275-291.

7. Jan C.H., Byrne D., Manhart J., Wilson H. Rose germplasm analysis with RAPD markers. HortSci. 1999;34(2):341-345.

8. Jawdat D., Al-Faoury H., Ayyoubi Z., Al-Safadi B. Molecular and ecological study of Eryngium species in Syria. Biologia. 2010;65(5): 796-804. DOI 10.2478/s11756-010-0086-7.

9. Koopman W.J.M., Wissemann V., De Cock K., Van Huylenbroeck J., De Riek J., Sabatino G.J.H., Visser D., Vosman B., Ritz C.M., Maes B., Werlemark G., Nybom H., Debener T., Linde M., Smulders M.J.M. AFLP markers as a tool to reconstruct complex relationships: a case study in Rosa (Rosaceae). Am. J. Bot. 2008;95(3): 353-366.

10. Korkmaz M., Dogan N.Y. Analysis of genetic relationships between wild roses (Rosa L. spp.) growing in Turkey. Erwerbs-Obstbau. 2018;60(4):305-310. DOI 10.1007/s10341-018-0375-9.

11. Krishna Parvathaneni R., Natesan S., Arunachalam Devaraj A., Muthuraja R., Venkatachalam R., Prathap Subramani A., Laxmanan P. Fingerprinting in cucumber and melon (Cucumis spp.) genotypes using morphological and ISSR markers. J. Crop Sci. Biotech. 2011; 1:39-43. DOI 10.1007/s12892-010-0080-1.

12. McFarland H. Modern Roses 12. Shreveport: The American Rose Society, 2007.

13. Millan T., Osuna F., Cobos S., Torres A.M., Cubero J.I. Using RAPDs to study phylogenetic relationships in Rosa. Theor. Appl. Genet. 1996;92:273-277.

14. Murray M.G., Thompson W.F. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 1980;10:4321-4325.

15. Plugatar S.A., Klymenko Z.K., Plugatar Yu.V., Mitrofanova I.V. Garden roses: results of introduction and selection in Nikita botanical garden. Acta Hortic. 2017;1167:177-180. DOI 10.17660/ActaHortic.2017.1167.27.

16. Plugatar’ Yu.V. Nikitsky Botanical Gardens as a scientific institution. Vestnik RAN = Herald of the Russian Academy of Sciences. 2016; 86(2):120-126. DOI 10.7868/S0869587316010096. (in Russian)

17. Shanzer I.A. The taxonomy and phylogeny of wild rose species (Rosa) in the light of molecular data. In: Modern Botany in Russia: Proceedings of the 13th Congress of the Russian Botanical Society and the Conference “Scientific Bases for Protection of the Volga Region”. Tolyatti, 2013;1:272-273. (in Russian)

18. Shanzer I.A. Reticular evolution in the genus Rosa L.: paleobotanical findings, morphological systematics, and molecular data. Paleobotanicheskiy Vremennik. Prilozhenie k Zhurnalu “Lethaea Rossica” = Paleobotanical Chronicle: Supplement to the journal “Lethaea Rossica”. 2015;2:161-164. (in Russian)

19. Schanzer I.A., Vagina A.V. ISSR (Inter Simple Sequence Repeat) markers reveal natural intersectional hybridization in wild roses [Rosa L., sect. Caninae (DC.) Ser. and sect. Cinnamomeae (DC.) Ser.]. Wulfenia. 2007;14:1-14.

20. Senkova S., Ziarovska J., Bezo M., Stefúnova V., Razna K. Utilization of IRAP technique for plums genotypes differentiation. Biosci. Res. 2013;10(1):1-7.

21. Suprun I.I., Kolomiec T.M., Malyarovskaya V.I., Sokolov R.N., Samarina L.S., Slepchenko N.A. Testing ISSR DNA markers for genotyping rare plant species of the Western Caucasus: Lilium caucasicum Miscz. ex Grossh., Galánthus woronowii Kolak., Pancratium maritimum. Nauchnyy Zhurnal KubGAU = Proceedings of the Kuban State Agrarian University. 2014;103(09). http://ej.kubagro.ru/2014/09/pdf/37.pdf (in Russian)

22. Wissemann V., Ritz C.M. The genus Rosa (Rosoideae, Rosaceae) revisited: molecular analysis of nrITS-1 and atpB-rbcL intergenic spacer (IGS) versus conventional taxonomy. Bot. J. Linn. Soc. 2005; 147(3):275-290.

23. Yuying S., Xiajun D., Fei W., Binhuaa C., Zhihonga G., Zhena Z. Analysis of genetic diversity in Japanese apricot (Prunus mume Sieb. et Zucc.) based on REMAP and IRAP molecular markers. Sci. Hortic. 2011;132:50-58. DOI 10.1016/j.scienta.2011.10.005.