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Determination of DNA Methylation Modes of Coriander Plant (Coriandrum sativum) Under Salt Stress Using RAPD Markers

Year 2024, Volume: 7 Issue: 1, 1 - 9, 30.06.2024
https://doi.org/10.46876/ja.1410871

Abstract

Epigenetics pertains to heritable alterations in gene expression and function that occur without modifications to the DNA base sequence. Among the extensively researched epigenetic mechanisms in plants are DNA methylation and chemical modifications in histone proteins. In the realm of epigenetic exploration, a variety of techniques are employed for both low- and high-throughput DNA methylation detection. One low-throughput approach involves the utilization of an enzyme-based method for detecting DNA cytosine methylation. This technique was applied to investigate DNA cytosine methylation in randomly selected genes within salt-treated coriander (Coriandrum sativum) seedlings, renowned for their biological activities and therapeutic potential. The study facilitates comprehension of epigenetic modifications in plant genotypes and an assessment of the biological implications of these alterations. The research employed the touch-down polymerase chain reaction methylation-sensitive-randomly amplified polymorphic DNA (TD-MS RAPD) technique to unveil cytosine methylation polymorphism between tissue samples collected at 12 and 24 hours from coriander seedlings subjected to salt stress. Genomic DNA samples extracted from coriander seedlings (Cemre) underwent treatment with the methylation-insensitive MspI restriction enzyme and the methylation-sensitive HpaII restriction enzyme prior to touch-down polymerase chain reactions. Methylation polymorphisms were identified using three primers (OPA 05, OPD 01, OPH 10) out of the 9 oligonucleotide primers employed, with samples taken at hourly intervals. The TD-MS-RAPD-PCR method presents an economical approach requiring basic equipment. Implementation involves a standard DNA thermal cycler and DNA gel electrophoresis system. Notably, cytosine methylation polymorphism determined by this method exhibited minimal variance across applications. The findings indicate a low level of polymorphism between two distinct salt treatments (100mM-200mM). Moreover, when scrutinizing methylation in tissue samples obtained from coriander seedlings at hourly intervals, no discernible methylation differences were observed between the samples collected at the 12th and 24th hours.

References

  • Ali, Y., Aslam, Z., Ashraf, M., & Tahir, G. R. (2004). Effect of salinity on chlorophyll concentration, leaf area, yield and yield components of rice genotypes grown under saline environment. International Journal of Environmental Science and Technology, 1(3), 221-225.
  • Al-Lawati, A., Al-Bahry, S., Victor, R., Al-Lawati, A. H., & Yaish, M. W. (2016). Salt stress alters DNA methylation levels in alfalfa (Medicago spp). Genetics and Molecular Research, 15(1), 15018299.
  • Arzani, A., & Ashraf, M. (2016). Smart engineering of genetic resources for enhanced salinity tolerance in crop plants. Critical Review Plant Science, 35, 146-189.
  • Ashraf, M., & Ali, Q. (2008). Relative membrane permeability and activities of some antioxidant enzymes as the key determinants of salt tolerance in canola (Brassica napus L.). Environmental and Experimental Botany, 63, 266-273.
  • Aydın, A., & Özden, E. (2021). Bazı Tef Genotiplerinde RAPD Markırları Kullanılarak Genetik Varyasyonun Belirlenmesi. Journal of the Institute of Science and Technology, 11(özel sayı), 3496-3506.
  • Aydın, A., İnce, A. G., Uygur Gocer, E., & Karaca, M. (2018). Single cotton seed DNA extraction without the use of enzymes and liquid nitrogen. Fresenius Environmental Bulletin and Advances in Food Sciences, 27, 6722-6726.
  • Berwal, M. K., & Ram, C. (2018). Superoxide dismutase: a stable biochemical marker for abiotic stress tolerance in higher plants. In A. De Oliveira (Ed.), Abiotic and Biotic Stress in Plants. IntechOpen. https://doi.org/10.5772/intechopen.82079
  • Demirel, F., Türkoğlu, A., Haliloğlu, K., Eren, B., Özkan, G., Uysal, P., ... & Bocianowski, J. (2023). Mammalian sex hormones as steroid-structured compounds in wheat seedling: Template of the cytosine methylation alteration and retrotransposon polymorphisms with iPBS and CRED-iBPS techniques. Applied Sciences, 13(17), 9538.
  • Eren, B., Türkoğlu, A., Haliloğlu, K., Demirel, F., Nowosad, K., Özkan, G., ... & Bocianowski, J. (2023). Investigation of the influence of polyamines on mature embryo culture and DNA methylation of wheat (Triticum aestivum L.) using the machine learning algorithm method. Plants, 12(18), 3261.
  • Karaca, M., Aydın, A., & İnce, A. G. (2019). Cytosine methylation polymorphisms in cotton using TD-MS-RAPD-PCR. Modern Phytomorphology, 13, 13-19.
  • Karaca, M., İnce, A. G., Uygur-Gocer, E., & Aydın, A. (2016). Bisulfite primer pairs for analysis of cotton (Gossypium spp.) DNA methylation. Journal of Scientific and Engineering Research, 3, 656-662.
  • Karaca, M., İnce, A. G., Elmasulu, S. Y., Onus, A. N., & Turgut, K. (2005). Coisolation of genomic and organelle DNAs from 15 genera and 31 species of plants. Analytical Biochemistry, 34, 353-355.
  • Kulak, M., & Aydın, A. (2023). Role of beneficial elements in epigenetic regulation of plants in response to abiotic stress factors. In Beneficial Chemical Elements of Plants: Recent Developments and Future Prospects (pp. 22-37).
  • Leena, M. A., & Kakoli, R. (2012). Centralized database security in cloud. International Journal of Advanced Research in Computer and Communication Engineering, 1(8), 50-68.
  • Mishra, D., Gunasekaran, A., Papadopoulos, T., & Hazen, B. (2017). Green supply chain performance measures: a review and bibliometric analysis. Sustainable Production and Consumption, 10, 85-99.
  • Moradi, P., & Zavareh, M. (2013). Effects of salinity on germination and early seedling growth of chickpea (Cicer arietinum L.) cultivars. International Journal of Farming and Allied Sciences, 2(3), 70-74.
  • Önder, A. (2018). Coriander and its phytoconstituents for the beneficial effects. In H. A. El-Shemy (Ed.), Potential of Essential Oils. IntechOpen. https://doi.org/10.5772/intechopen.78656
  • Salmon, A., Clotault, J., Jenczewski, E., Chable, V., & Manzanares-Dauleux, M. J. (2008). Brassica oleracea displays a high level of DNA methylation polymorphism. Plant Science, 174(1), 61-70.
  • Scandalios, J. G. (1993). Oxygen stress and superoxide dismutases. Plant Physiology, 101(1), 7.
  • Sheldon, A. R., Dalal, R. C., Kirchhof, G., Kopittke, P. M., & Menzies, N. W. (2017). The effect of salinity on plant-available water. Plant Soil, 418, 477-491.
  • Adams, P., Thomas, J. C., Vernon, D. M., Bohnert, H. J., & Jensen, R. G. (1992). Distinct cellular and organismic responses to salt stress. Plant and Cell Physiology, 33(8), 1215-1223.
  • Türkoğlu, A., Haliloğlu, K., Demirel, F., Aydın, M., Çiçek, S., Yiğider, E., ... & Niedbała, G. (2023c). Machine learning analysis of the impact of silver nitrate and silver nanoparticles on wheat (Triticum aestivum L.): Callus induction, plant regeneration, and DNA methylation. Plants, 12(24), 4151.
  • Türkoğlu, A., Haliloğlu, K., Tosun, M., Bujak, H., Eren, B., Demirel, F., ... & Niedbała, G. (2023b). Ethyl methanesulfonate (EMS) mutagen toxicity-induced DNA damage, cytosine methylation alteration, and iPBS-retrotransposon polymorphisms in wheat (Triticum aestivum L.). Agronomy, 13(7), 1767.
  • Türkoğlu, A., Haliloğlu, K., Tosun, M., Szulc, P., Demirel, F., Eren, B., ... & Niedbała, G. (2023a). Sodium azide as a chemical mutagen in wheat (Triticum aestivum L.): Patterns of the genetic and epigenetic effects with iPBS and CRED-iPBS techniques. Agriculture, 13(6), 1242.
  • Yilmaz, A., Yilmaz, H., Turan, S., Celik, A., Nadeem, M. A., Demirel, F., ... & Arslan, M. (2022). Biotechnological advancements in coriander (Coriandrum sativum L.). Avrupa Bilim ve Teknoloji Dergisi(35), 203-220.

Tuz Stresi Altındaki Kişniş Bitkisinin (Coriandrum sativum) DNA Metilasyon Modlarının RAPD Markırları ile Belirlenmesi

Year 2024, Volume: 7 Issue: 1, 1 - 9, 30.06.2024
https://doi.org/10.46876/ja.1410871

Abstract

Epigenetik, gen ifadesi ve fonksiyonundaki kalıtsal değişiklikleri tanımlayan bir alanı ifade eder, ancak DNA baz değişimi olmaksızın gerçekleşir. Bitkilerde en çok incelenen epigenetik mekanizmalar, DNA metilasyonu ve histon proteinlerindeki kimyasal modifikasyonlardır. Epigenetik araştırmalarda, düşük ve yüksek işlem hacimli DNA metilasyon tespiti için çeşitli teknikler kullanılmaktadır. Düşük işlem hacimli tekniklerden biri, enzim tabanlı DNA sitozin metilasyonunu belirleme yaklaşımıdır. Bu yöntem, biyolojik aktiviteleri ve terapötik potansiyeli olan tuz uygulaması yapılan kişniş (Coriandrum sativum) fidelerinde rastgele genlerdeki DNA sitozin metilasyonunu incelemek amacıyla kullanılmaktadır. Bu çalışma, bitki genotiplerindeki epigenetik değişiklikleri anlamamıza ve bu değişikliklerin biyolojik etkilerini değerlendirmemize olanak tanır. Bu çalışmada tuz stresine maruz kalan kişniş fidelerinden 12. ve24. Saatlerde alınan doku örnekleri arasındaki sitozin metilasyon polimorfizmini ortaya koymak için touch-down polimeraz zincir reaksiyonları metilasyon duyarlı-rastgele arttırılmış polimorfik DNA (TD-MS RAPD) tekniği uygulanmıştır. Kişniş fidelerinden (Cemre) genomik DNA örnekleri izole edilmiş ve DNA izolatı touch- metilasyona duyarsız olan MspI restriksiyon enzimi ve metilasyona duyarlı HpaII restriksiyon enzimi ile kesilmiştir. Kullanılan 9 oligonükleotid primerinden üç primer (OPA 05-OPD 01-OPH 10) uygulamalar ve saatlik alınan örnekler arasında metilasyon polimorfizmleri belirlenmiştir. TD-MS-RAPD-PZR metodu, basit ve temel cihazlar gerektiren ekonomik bir yaklaşımdır. Bu yöntem, standart bir DNA termal döngü cihazı ve DNA jel elektroforezi sistemi kullanılarak kolayca uygulanabilir. Bu metotla belirlenen sitozin metilasyon polimorfizmi uygulamalar arsında oldukça düşüktür. İki farklı tuz uygulaması arasında (100mM-200mM) düşük düzeyde polimorfizm olduğu sonucuna varılmıştır. Saatlik alınan kişniş fidelerinden elde edilen doku örneklerindeki metilasyona bakıldığında ise 12’nci ve 24’üncü saatlerde alınan örnekler arasında bir metilasyon farkı tespit edilmemiştir.

References

  • Ali, Y., Aslam, Z., Ashraf, M., & Tahir, G. R. (2004). Effect of salinity on chlorophyll concentration, leaf area, yield and yield components of rice genotypes grown under saline environment. International Journal of Environmental Science and Technology, 1(3), 221-225.
  • Al-Lawati, A., Al-Bahry, S., Victor, R., Al-Lawati, A. H., & Yaish, M. W. (2016). Salt stress alters DNA methylation levels in alfalfa (Medicago spp). Genetics and Molecular Research, 15(1), 15018299.
  • Arzani, A., & Ashraf, M. (2016). Smart engineering of genetic resources for enhanced salinity tolerance in crop plants. Critical Review Plant Science, 35, 146-189.
  • Ashraf, M., & Ali, Q. (2008). Relative membrane permeability and activities of some antioxidant enzymes as the key determinants of salt tolerance in canola (Brassica napus L.). Environmental and Experimental Botany, 63, 266-273.
  • Aydın, A., & Özden, E. (2021). Bazı Tef Genotiplerinde RAPD Markırları Kullanılarak Genetik Varyasyonun Belirlenmesi. Journal of the Institute of Science and Technology, 11(özel sayı), 3496-3506.
  • Aydın, A., İnce, A. G., Uygur Gocer, E., & Karaca, M. (2018). Single cotton seed DNA extraction without the use of enzymes and liquid nitrogen. Fresenius Environmental Bulletin and Advances in Food Sciences, 27, 6722-6726.
  • Berwal, M. K., & Ram, C. (2018). Superoxide dismutase: a stable biochemical marker for abiotic stress tolerance in higher plants. In A. De Oliveira (Ed.), Abiotic and Biotic Stress in Plants. IntechOpen. https://doi.org/10.5772/intechopen.82079
  • Demirel, F., Türkoğlu, A., Haliloğlu, K., Eren, B., Özkan, G., Uysal, P., ... & Bocianowski, J. (2023). Mammalian sex hormones as steroid-structured compounds in wheat seedling: Template of the cytosine methylation alteration and retrotransposon polymorphisms with iPBS and CRED-iBPS techniques. Applied Sciences, 13(17), 9538.
  • Eren, B., Türkoğlu, A., Haliloğlu, K., Demirel, F., Nowosad, K., Özkan, G., ... & Bocianowski, J. (2023). Investigation of the influence of polyamines on mature embryo culture and DNA methylation of wheat (Triticum aestivum L.) using the machine learning algorithm method. Plants, 12(18), 3261.
  • Karaca, M., Aydın, A., & İnce, A. G. (2019). Cytosine methylation polymorphisms in cotton using TD-MS-RAPD-PCR. Modern Phytomorphology, 13, 13-19.
  • Karaca, M., İnce, A. G., Uygur-Gocer, E., & Aydın, A. (2016). Bisulfite primer pairs for analysis of cotton (Gossypium spp.) DNA methylation. Journal of Scientific and Engineering Research, 3, 656-662.
  • Karaca, M., İnce, A. G., Elmasulu, S. Y., Onus, A. N., & Turgut, K. (2005). Coisolation of genomic and organelle DNAs from 15 genera and 31 species of plants. Analytical Biochemistry, 34, 353-355.
  • Kulak, M., & Aydın, A. (2023). Role of beneficial elements in epigenetic regulation of plants in response to abiotic stress factors. In Beneficial Chemical Elements of Plants: Recent Developments and Future Prospects (pp. 22-37).
  • Leena, M. A., & Kakoli, R. (2012). Centralized database security in cloud. International Journal of Advanced Research in Computer and Communication Engineering, 1(8), 50-68.
  • Mishra, D., Gunasekaran, A., Papadopoulos, T., & Hazen, B. (2017). Green supply chain performance measures: a review and bibliometric analysis. Sustainable Production and Consumption, 10, 85-99.
  • Moradi, P., & Zavareh, M. (2013). Effects of salinity on germination and early seedling growth of chickpea (Cicer arietinum L.) cultivars. International Journal of Farming and Allied Sciences, 2(3), 70-74.
  • Önder, A. (2018). Coriander and its phytoconstituents for the beneficial effects. In H. A. El-Shemy (Ed.), Potential of Essential Oils. IntechOpen. https://doi.org/10.5772/intechopen.78656
  • Salmon, A., Clotault, J., Jenczewski, E., Chable, V., & Manzanares-Dauleux, M. J. (2008). Brassica oleracea displays a high level of DNA methylation polymorphism. Plant Science, 174(1), 61-70.
  • Scandalios, J. G. (1993). Oxygen stress and superoxide dismutases. Plant Physiology, 101(1), 7.
  • Sheldon, A. R., Dalal, R. C., Kirchhof, G., Kopittke, P. M., & Menzies, N. W. (2017). The effect of salinity on plant-available water. Plant Soil, 418, 477-491.
  • Adams, P., Thomas, J. C., Vernon, D. M., Bohnert, H. J., & Jensen, R. G. (1992). Distinct cellular and organismic responses to salt stress. Plant and Cell Physiology, 33(8), 1215-1223.
  • Türkoğlu, A., Haliloğlu, K., Demirel, F., Aydın, M., Çiçek, S., Yiğider, E., ... & Niedbała, G. (2023c). Machine learning analysis of the impact of silver nitrate and silver nanoparticles on wheat (Triticum aestivum L.): Callus induction, plant regeneration, and DNA methylation. Plants, 12(24), 4151.
  • Türkoğlu, A., Haliloğlu, K., Tosun, M., Bujak, H., Eren, B., Demirel, F., ... & Niedbała, G. (2023b). Ethyl methanesulfonate (EMS) mutagen toxicity-induced DNA damage, cytosine methylation alteration, and iPBS-retrotransposon polymorphisms in wheat (Triticum aestivum L.). Agronomy, 13(7), 1767.
  • Türkoğlu, A., Haliloğlu, K., Tosun, M., Szulc, P., Demirel, F., Eren, B., ... & Niedbała, G. (2023a). Sodium azide as a chemical mutagen in wheat (Triticum aestivum L.): Patterns of the genetic and epigenetic effects with iPBS and CRED-iPBS techniques. Agriculture, 13(6), 1242.
  • Yilmaz, A., Yilmaz, H., Turan, S., Celik, A., Nadeem, M. A., Demirel, F., ... & Arslan, M. (2022). Biotechnological advancements in coriander (Coriandrum sativum L.). Avrupa Bilim ve Teknoloji Dergisi(35), 203-220.
There are 25 citations in total.

Details

Primary Language Turkish
Subjects Plant Biotechnology in Agriculture
Journal Section Research Articles
Authors

Emine Uygur Göçer 0000-0002-6967-7357

Early Pub Date June 30, 2024
Publication Date June 30, 2024
Submission Date December 27, 2023
Acceptance Date January 10, 2024
Published in Issue Year 2024 Volume: 7 Issue: 1

Cite

APA Uygur Göçer, E. (2024). Tuz Stresi Altındaki Kişniş Bitkisinin (Coriandrum sativum) DNA Metilasyon Modlarının RAPD Markırları ile Belirlenmesi. Journal of Agriculture, 7(1), 1-9. https://doi.org/10.46876/ja.1410871