PCR Optimization Prior to Genetic Diversity Assessment of Sesame (Sesamum indicum L.) Genotypes Using Inter-Primer Binding Site (IPBS) Markers
Genetic Diversity Assessment of Sesame
DOI:
https://doi.org/10.33687/ricosbiol.03.012.94Keywords:
local sesame lines, IPBS, optimal annealing temperatures, molecular markerAbstract
This study aimed to accurately and reliably determine the genetic diversity among sesame (Sesamum indicum L.) genotypes, which is an important oil crop. To achieve this, Polymerase Chain Reaction (PCR) conditions based on Inter-Primer Binding Site (IPBS) molecular markers were optimized to reveal genetic variation, which forms the basis of plant breeding programs. For the methodology, DNA was isolated from fresh sesame leaves grown under controlled conditions using the CTAB method and analyzed from 50 local sesame lines. Since PCR success is directly dependent on the specificity of the primers and reaction parameters like temperature, the gradient temperature PCR method was applied using 22 different iPBS primers to determine the optimal annealing temperatures. According to the findings, 20 out of the 22 primers successfully generated polymorphic bands, revealing genetic diversity. Determining the optimal PCR conditions was critical for identifying the binding temperature at which iPBS primers exhibited the highest polymorphism. For example, Primer 2277 showed high amplification and activity at 47.6 and 50.9°C, while Primer 2218 was highly active at 50.9°C. This optimization establishes a precise molecular foundation that will contribute to future sesame breeding programs.
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References
Al-Obaidi, Z. (2015). Optimisation of standard PCR programme. Kerbala Journal of Pharmaceutical Sciences, 10(1), 42–57. https://iasj.rdd.edu.iq/journals/journal/issue/14024
Doyle, J. J., & Doyle, J. L. (1990). A rapid total DNA preparation procedure for fresh plant tissue. Focus, 12, 13–15. https://api.semanticscholar.org/CorpusID:90972282
Erkoç, K., Işık, M. İ., Erkol, Ş., Aras, T., & Şakiroğlu, M. (2024, December 03-04). Onobrychis cinsinin genetik varyasyonunun tanımlanması için primer arası bağlanma yerine (iPBS işaretleyicileri) dayalı PCR analizinin optimizasyonu [Optimisation of PCR analysis based on interprimer binding sites (iPBS markers) for the characterisation of genetic variation in the genus Onobrychis]. 3rd International Conference on Recent Academic Studies, Konya, Türkiye. https://as-proceeding.com/index.php/icras/3rdicras2024
Erkol, Ş., Işık, M. İ., Armağan, M., & Aras, T. (2024, May 16-17). SCoT DNA markörleri ile Gundelia L.'nin genetik çeşitliliğinin belirlenmesi için PCR analizinin optimizasyonu [Optimisation of PCR analysis for determining the genetic diversity of Gundelia L. using SCoT DNA markers]. 3rd International Conference on Engineering, Natural and Social Sciences, Konya, Türkiye. https://www.icensos.com/
Hadeithi, Z. S. M., & Jasim, S. A. (2021). Study of plant genetic variation through molecular markers: An overview. Journal of Pharmaceutical Research International, 33(45B), 464–473. https://doi.org/10.9734/jpri/2021/v33i45B32828
Lakhanpaul, S., Singh, V., Kumar, S., Bhardwaj, D., & Bhat, K. V. (2012). Sesame: Overcoming the abiotic stresses in the queen of oilseed crops. In N. Tuteja, S. S. Gill, A. F. Tiburcio, & R. Tuteja (Eds.), Improving crop resistance to abiotic stress (pp. 1251–1283). Wiley-VCH Verlag GmbH & Co. KGaA. https://doi.org/10.1002/9783527632930.ch48
Mahyar, Z., & Fatemeh, N. (2021, February 16-19). SCoT-PCR optimization in Halocnemum strobilaceum L. [Poster presentation]. 21st National & 9th International Conference of Biology, Semnan University, Semnan, Iran.
Özer, G., Sameeullah, M., Bayraktar, H., & Göre, M. (2017). Genetic diversity among phytopathogenic Sclerotiniaceae, based on retrotransposon molecular markers. Phytopathologia Mediterranea, 56(2), 251–258. https://doi.org/10.14601/Phytopathol_Mediterr-20379
Saxena, K., & Bisen, R. (2017). Use of RAPD marker for the assessment of genetic diversity of sesame (Sesamum indicum L.) varieties. International Journal of Current Microbiology and Applied Sciences, 6(5), 2523–2530. https://doi.org/10.20546/ijcmas.2017.605.283
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Copyright (c) 2025 Eliş Seval, POLAT BÜŞRA, KIZILGEÇİ FERHAT, TÜRKOĞLU ARAS, Mehmet YILDIRIM
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