Genetic Diversity Assessment of Some Salvia Species in the Central Zagros Region Using iPBS Molecular Markers

Hajhadi, Mostafa; Rabiei, Mohammad; Ghorbani Nohooji, Majid; Shiran, Behrouz

doi:10.22034/pgr.2026.2087225.1034

Genetic Diversity Assessment of Some Salvia Species in the Central Zagros Region Using iPBS Molecular Markers

Document Type : Original Article

Authors

Mostafa Hajhadi ¹

Mohammad Rabiei ¹

Majid Ghorbani Nohooji ²

Behrouz Shiran ¹

¹ Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran

² Medicinal Plants Research Institute, ACECR, Karaj, Iran

10.22034/pgr.2026.2087225.1034

Abstract

The genus Salvia is one of the most important genera of medicinal plants in the Lamiaceae family due to its bioactive compounds and pharmaceutical values, requiring the identification and conservation of its genetic resources. Retrotransposon-based molecular markers, particularly inter Primer Binding Site (iPBS) markers, are considered efficient approaches for assessing genetic diversity because of their high ability to detect genetic polymorphism. In this study, the genetic diversity and population structure of 50 ecotypes belonging to seven Salvia species collected from the Central Zagros region of Iran were evaluated using 10 iPBS primers. The results demonstrated the high efficiency of iPBS markers in detecting genetic variation among the studied species. The average percentage of polymorphic bands and polymorphism information content (PIC) were 98.33% and 0.36, respectively. Cluster analysis based on the Dice similarity coefficient and Neighbor-Joining method separated the studied genotypes into distinct genetic groups. The Mantel test showed a significant correlation between the genetic similarity matrix and clustering pattern (r = 0.68, p = 0.002), confirming the reliability of the obtained grouping. Population genetic analysis revealed that S. macrosiphon and S. spinosa populations possessed the highest levels of genetic diversity, indicating their potential as valuable germplasm resources for breeding programs. In contrast, S. reuterana showed the lowest genetic diversity indices and greater genetic distance from other populations, suggesting that it represents a genetically distinct group requiring special attention in conservation and germplasm management. Furthermore, S. multicaulis and S. limbata exhibited considerable genetic differentiation due to their independent positions in the dendrogram and higher genetic distances, highlighting their importance for maintaining genetic diversity within the genus Salvia.

Keywords

Cluster analysis

Genetic variation

Genetic conservation

Retrotransposon

Population structure

Subjects

Molecular Marker

Asghari Mirak, A., Alavikia, S.S. and Mohammadi, S.A. (2022). Investigating genetic diversity and relationships in some henbane (Hyoscyamus spp.) populations based on polymorphisms resulting from retrotransposon insertion. Plant Genetic Researches, 9(1): 117-134 (In Persian). https://doi.org/10.52547/pgr.9.1.9

Biswas, M.K., Baig, M., Cheng, Y.J. and Deng, X.X. (2010). A Retro-transposon based genetic similarity within the genus Citrus and its relatives. Genetic Resources and Crop Evolution, 57:963-972. https://doi.org/10.1007/s10722-010-9533-0

Borna, F., Luo, S., Ahmad, N.M., Nazeri, V., Shokrpour, M. and Trethowan, R. (2017). Genetic diversity in populations of the medicinal plant Leonurus cardiaca L. revealed by inter-primer binding site (iPBS) markers. Genetic Resources and Crop Evolution, 64: 479-492. https://doi.org/10.1007/s10722-016-0373-4

Erbano, M., Schühli, G.S‌. and Santos, É.P. (2015). Genetic variability and population structure of Salvia lachnostachys: implications for breeding and conservation programs. International Journal of Molecular Sciences, 16: 7839-7850. https://doi.org/10.3390/ijms16047839

Haliloğlu, K., Türkoğlu, A., Öztürk, H.I., Özkan, G., Elkoca, E‌. and Poczai, P. (2022). iPBS-retrotransposon markers in the analysis of genetic diversity among common bean (Phaseolus vulgaris L.) germplasm from Türkiye. Genes, 13: 1147- 1150. https://doi.org/10.3390/genes13071147

Kalendar, R., Antonius, K., Smýkal, P. and Schulman, A.H. (2010). iPBS: a universal method for DNA fingerprinting and retrotransposon isolation. Theoretical and Applied Genetics, 121: 1419–1430. https://doi.org/10.1007/s00122-010-1398-2

Kalendar, R‌. and Schulman, A.H. (2014). Transposon-based tagging: IRAP, REMAP, and iPBS. Methods in Molecular Biology, 8: 233-255. https://doi.org/10.1007/978-1-62703-767-9_12

Kalendar, R., Sabot, F., Rodriguez, F., Karlov, G.I., Natali, L‌. and Alix, K. (2021). Editorial: mobile elements and plant genome evolution, comparative analyses and computational tools. Frontiers in Plant Science, 12: 735134. https://doi.org/10.3389/fpls.2021.735134

Kaviani Charati, A., Sabouri, H., Fallahi, H.A. and Jorjani, E. (2016). QTL mapping of spike characteristics in barley using F₃ and F₄ families derived from Badia × Komino cross. Plant Genetic Research, 3(1): 13–28 (In Persian). https://doi.org/10.29252/pgr.3.1.13

Lemos, S.C.M., Silveira, R.L.R., Buuron, S.K., Santos, R.S.M.D‌. and Moro, S.C. (2019). Determining the polymorphism information content of a molecular marker. Gene, 686: 144175. https://doi.org/10.1016/j.gene.2019.144175

Meyer, A., Garcia, A., Souza, A.P‌. and Souza, C.L. (2004). Comparison of similarity coefficients used for cluster analysis with dominant markers in maize (Zea mays L.). Genetics and Molecular Biology, 27: 83-91. https://doi.org/10.1590/S1415-47572004000100014

Mita, P‌. and Boeke, J.D. (2016). How retrotransposons shape genome regulation. Current Opinion in Genetics & Development, 37: 90-100. https://doi.org/10.1016/j.gde.2016.01.001

Mulabagal, V., Lee, C.Y., Lo, S.F., Nalawade, S., Lin, C‌. and Tsay, H.S. (2004). Studies on the production of some important secondary metabolites from medicinal plants by plant tissue cultures. Botanical Bulletin of Academia Sinica, 45: 1-22.

Nadeem, M., Nawaz, M.A., Shahid, M.Q., Doğan, Y., Cömertpay, G., Yildiz, M., Hatipoglu, R., Ahmad, F., Alsaleh, A., Labhane, N., Ozkan, H., Chung, G‌. and Baloch, F. (2017). DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnology & Biotechnological Equipment, 32: 261-285. https://doi.org/10.1080/13102818.2017.1400401

Nei, M‌. and Li, W.H. (1979). Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences of the United States of America, 76: 5269-5273. https://doi.org/10.1073/pnas.76.10.5269

Peakall, R‌. and Smouse, P.E. (2006). GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6: 288-295. https://doi.org/10.1111/j.1471-8286.2005.01155.x

Phong, N.H., Pongnak, W., Soytong, K., Poeaim, S. and Poeaim, A. (2016). Diversity of tea (Camellia sinensis) grown in Vietnam based on morphological characteristics and inter-primer binding sites (iPBS) marker. International Journal of Agriculture and Biology, 18: 385-392. https://doi.org/10.17957/IJAB/15.0100

Sarwat, M., Nabi, G., Das, S‌. and Srivastava, P.S. (2012). Molecular markers in medicinal plant biotechnology: past and present. Critical Reviews in Biotechnology, 32(1): 74-92. https://doi.org/10.3109/07388551.2011.551872

Schulman, A.H., Flavell, A.J., Paux, E‌. and Ellis, T.H. (2012). The application of LTR retrotransposons as molecular markers in plants. Methods in Molecular Biology, 859: 115-153. https://doi.org/10.1007/978-1-61779-603-6_7

Taha, M., Tawfik, A., Mahmoud, A‌. and Mohamed, M. (2024). Assessment of somaclonal variants of Salvia splendens at different subcultures using molecular markers. Assiut Journal of Agricultural Sciences, 55: 78-96. https://doi.org/10.21608/ajas.2024.279071.1349

Vanijajiva, O. and Pornpongrungrueng, P. (2020). Inter-primer binding site (iPBS) markers reveal the population genetic diversity and structure of tropical climbing cissampelopsis (Asteraceae) in thailand. in biodiversitas Journal of Biological Diversity, 21: 1-9. https://doi.org/10.13057/biodiv/d210901

Yuan, Q.J., Zhang, Z.Y., Hu, J., Guo, L.P., Shao, A.J‌. and Huang, L.Q. (2010). Impacts of recent cultivation on genetic diversity pattern of a medicinal plant, Scutellaria baicalensis (Lamiaceae). BMC Genetics, 11: 29. https://doi.org/10.1186/1471-2156-11-29

Zaman, W., Ayaz, A‌. and Park, S. (2025). Climate change and medicinal plant biodiversity: conservation strategies for sustainable use and genetic resource preservation. Genetic Resources and Crop Evolution, 72: 6275-6308. https://doi.org/10.1007/s10722-025-02410-2