Genetic Profiling of Regional Oregano Accessions (Thymus vulgaris L.) from Sivas/Divriği Using SCoT Molecular Markers

Abstract

This study investigates the genetic diversity among different Thymus vulgaris L. genotypes using the SCOT (Start Codon Targeted) marker system. A total of 136 bands were obtained from 15 markers, of which 106 were polymorphic, with an average of 9.07 bands per primer. The SCOT markers yielded a polymorphism rate of 77.9%. In order to interpret the genetic distance among Juglans regia L. genotypes, a UPGMA dendrogram was constructed using MVSP 3.22 software. According to the resulting dendrogram, the lowest similarity (0.593) was observed between samples W6 and W26, while the highest similarity (0.970) was observed between W1 and W4, followed by 0.962 between W4 and W5. Principal Component Analysis (PCA) was also conducted using MVSP 3.22. The PCA results revealed a homogeneous distribution and wide variation. The UPGMA dendrogram and PCA analysis were consistent with each other. The SCOT analyses conducted on walnut genotypes provide highly valuable information for assessing the level of genetic diversity, understanding population structure, and selecting superior individuals. Such studies contribute to the conservation of genetic resources and support the development of new cultivars with high yield, disease resistance, and strong adaptation to climate change in future breeding programs. Based on this study, SCOT analyses demonstrate that the Sivas province constitutes an important genetic diversity reservoir and that oregano genotypes possess rich genetic variation.

Keywords

• Thymus vulgaris L.
• genetic diversity
• SCOT

Investigation of Genetic Polymorphism in Selected Thyme (Thymus vulgaris L.) Accessions Using SCoT Molecular Markers

Abstract

Identifying plant species and evaluating their variation should not be based solely on morphological characteristics. Such studies should be expanded through biochemical and DNA analyses. In this context, the aim of our study is to reveal the genetic diversity of some thyme (Thymus) samples naturally growing in the flora of Divriği district of Sivas province, and to contribute to the sustainable conservation of natural resources as well as to determine their agricultural utilization potential. Additionally, this study aims to explore the use of SCoT (Start Codon Targeted) markers in evaluating the diversity among different thyme genotypes. The plants were collected from their natural habitats, and DNA was extracted from fresh leaves using the CTAB method. A total of 36 SCoT markers were screened in the samples and the 14 most polymorphic markers were selected for analysis. In this study, a total of 169 bands were obtained from the 14 SCoT primers used to determine the genetic relationships among the thyme samples. Among these, 141 bands were polymorphic, resulting in a polymorphism rate of 83.43%. The data obtained allowed for the construction of a dendrogram grouping the analyzed ecotypes according to their similarity indices. According to the UPGMA dendrogram and the correlation matrix generated from the SCoT molecular data, the lowest similarity (0.326) was observed between samples G12 and G17, while the highest similarity (0.854) was found between G8 and G10. As a result, it was demonstrated that evaluating variation in Thymus species and establishing similarity indices using SCoT markers is possible, providing a solid basis for advanced molecular genetic analyses.

Keywords

• Thymus vulgaris L.
• SCOT
• genetic diversity

References

1. Ahmed AR, Soliman KA, Al-Senosy NK, Omar SA (2022). Genetic polymorphisms of four Egyptian plant species using some molecular markers techniques RAPD, ISSR, and SCoT. Journal of Agricultural Chemistry and Biotechnology 13(1), 21-24.
2. Alqahtani MM, Abdein MA, Abou El-Leel OF (2020). Morphological and molecular genetic assessment of some Thymus species. Biosciences Biotechnology Research Asia 17(1), 103-113.
3. Amiot J, Salmon Y, Collin C, Thompson JD (2005). Differential resistance to freezing and spatial distribution in a chemically polymorphic plant Thymus vulgaris. Ecology Letters 8(4), 370-377.
4. Basch E, Ulbricht C, Hammerness P, Bevins A, Sollars D (2004). Thyme (Thymus vulgaris L.), thymol. Journal of Herbal Pharmacotherapy 4(1), 49-67.
5. Beicu R, Popescu S, Neacsu A, Imbrea IM (2020). Applicability of ScoT (Start Codon Targeted) markers in evaluation of Thymus genetically variability. Research Journal of Agricultural Science 52(1), 24-30.
6. Celep F, Dirmenci T (2017). Systematic and biogeographic overview of Lamiaceae in Türkiye. Natural Volatiles and Essential Oils 4(4), 14-27.
7. Doyle JJ, Doyle JL (1990). Isolation of plant DNA from fresh tissue. Focus 12, 13-15.
8. El-Demerdash ESS, Elsherbeny EA, Salama YAM, Ahmed MZ (2019). Genetic diversity analysis of some Egyptian Origanum and Thymus species using AFLP markers. Journal of Genetic Engineering and Biotechnology 17, 1-11.

9. Elsherbeny E, Eldemerdash ES (2019). Genetic diversity among Thymus spp. using RAPD and ISSR markers. Egyptian Journal of Desert Research 69(2), 91-106.
10. Fafal T, Kayalar H, Birim D, Armağan G, Tüzün BS, Taştan P, Kıvcak B (2024). Assessment of antioxidant and neuroprotective activity of plants from the Lamiaceae family. İstanbul Journal of Pharmacy 54(3), 403-408.
11. Gavarić N, Kladar N, Mišan A, Nikolić A, Samojlik I, Mimica-Dukić N, Božin B (2015). Postdistillation waste material of thyme (Thymus vulgaris L., Lamiaceae) as a potential source of biologically active compounds. Industrial Crops and Products 74, 457-464.
12. Gouyon PH, Vernet P, Guillerm JL, Valdeyron G (1986). Polymorphisms and environment: the adaptive value of the oil polymorphisms in Thymus vulgaris L. Heredity 57(1), 59-66.
13. György Z, Incze N, Pluhár Z (2020). Differentiating Thymus vulgaris chemotypes with ISSR molecular markers. Biochemical Systematics and Ecology 92, 104118.
14. Karagöz H, Hosseinpour A, Karagöz FP, Cakmakci R, Haliloglu K (2022). Dissection of genetic diversity and population structure in oregano (Origanum acutidens L.) genotypes based on agro-morphological properties and start codon targeted (SCoT) markers. Biologia 77(5), 1231-1247.
15. Khalil R, Khalil R, Li Z (2012). Determination of genetic variation and relationship in Thymus vulgaris populations in Syria by random RAPD markers. Plant Biosystems-An International Journal Dealing with all Aspects of Plant Biology 146 (sup1), 217-225.
16. Kovach WL (2007). MVSP-A MultiVariate Statistical Package for Windows, ver. 3.1. Kovach Computing Services, Pentraeth Wales, UK.
17. Koyuncu O, Yaylaci O, Öztürk D, Potoglu Erkara I, Savaroglu F, Akcoskun O, Ardic M (2010). Risk categories and ethnobotanical features of the Lamiaceae taxa growing naturally in Osmaneli (Bilecik/Türkiye) and environs. Biological Diversity and Conservation 3(3), 31-45.
18. Miraj S, Kiani S (2016). Study of pharmacological effect of Thymus vulgaris: A review. Der Pharmacia Lettre 8(9), 315-320.
19. Mishra SP, Sarkar U, Taraphder S, Datta S, Swain D, Saikhom R, Laishram M (2017). Multivariate statistical data analysis-principal component analysis (PCA). International Journal of Livestock Research (7), 60–78.
20. Prasanth Reddy V, Ravi Vital K, Varsha PV, Satyam S (2014). Review on Thymus vulgaris traditional uses and pharmacological properties. Medicinal and Aromatic Plants 3(164), 2167-0412.
21. Rustaiee AR, Yavari A, Nazeri V, Shokrpour M, Sefidkon F, Rasouli M (2013). Genetic diversity and chemical polymorphism of some Thymus species. Chemistry & Biodiversity 10(6), 1088-1098.
22. Sayed Ibrahim A, Çelik C, Karakurt Y, Sevindik E (2024). Physiological, biochemical, and molecular characterization of some cucumber (Cucumis sativus L.) genotypes. International Journal of Vegetable Science 30(6), 673-694.
23. Shabnum S, Wagay MG (2011). Essential oil composition of Thymus vulgaris L. and their uses. Journal of Research and Development 11, 83-94.
24. Shayan A, Shokrpour M, Nazeri V, Babalar M, Mehrabi A (2025). Assessment of diversity and genetic differentiation in polycross-derived populations of Thymus daenensis using ISSR and SCoT markers. Genetic Resources and Crop Evolution 72, 4931–4945. https://doi.org/10.1007/s10722-024-02214-w
25. Thompson JD, Tarayre M, Gauthier P, Litrico I, Linhart YB (2004). Multiple genetic contributions to plant performance in Thymus vulgaris. Journal of Ecology 99(1), 45-56.
26. Vernet P, Gouyon RH, Valdeyron G (1986). Genetic control of the oil content in Thymus vulgaris L: a case of polymorphism in a biosynthetic chain. Genetica 69(3), 227-231.