Comparison of Primer Types to Produce Fungal DNA Fragment from Garlic Plant Root Samples

Fibrianti Shinta Dewi, Abdul Latief Abadi, Muhammad Akhid Syib'li

Abstract


Fusarium wilt disease caused by Fusarium oxysporum f.sp cepae is a widespread and dangerous diseases in garlic commodities. The combination of AMF and Bacillus amyloliquefaciens can be an effective solution to reduce losses due to attacks by these pathogens. The PCR technique is initial method that has proven to be significant in detecting fungal target DNA so that the effectiveness of biological agents can be determined. The aim of this study is to compare the types of primers that are effective for use in detecting fungal groups in PCR. This research was conducted in October 2023 - November 2024. The types of primers compared were ITS1-F/ITS4-R and LSU200A-F/LSU476-R with spectophotometry and fluometry quantification. The results show that ITS1-F/ITS4-R forms DNA band with a size of 700 bp, while LSU200A-F/LSU476-R had a size of 290-300 bp. The electropherogram also showed differences in DNA distribution which confirmed the results on agarose more specifically in the range 19-12,999 bp. In general, these results prove that the two types of primers have different abilities in fragmenting target DNA. This knowledge can help in detecting DNA at an early stage which can be used in various analyzes that can help in integrated plant disease management.


Keywords


Fusarium wilt, Garlic, ITS1-F/ITS4-R, LSU200A-F/LSU476-R, DNA

Full Text:

PDF

References


Asemaninejad, A., Weerasuriya, N., Gloor, G. B., Lindo, Z., & Thorn, G. (2016). New primers for discovering fungal diversity using nuclear large ribosomal DNA. PLoS ONE, 11(7). https://doi.org/10.1371/journal.pone.0159043

Bunu, S. J., Otele, D., Alade, T., & Dodoru, R. (2020). Determination of serum DNA purity among patients undergoing antiretroviral therapy using NanoDrop-1000 spectrophotometer and polymerase chain reaction. Biomedical and Biotechnology Research Journal, 4(3), 214–219. https://doi.org/10.4103/bbrj.bbrj_68_20

Dewanata, P. A., & Mushlih, M. (2021). Differences in DNA Purity Test Using UV-Vis Spectrophotometer and Nanodrop Spectrophotometer in Type 2 Diabetes Mellitus Patients. Indonesian Journal of Innovation Studies, 15. https://doi.org/10.21070/ijins.v15i.553

Hikmatyar, M. F., Royani, J. I., & Dasumiati. (2015). Isolasi dan Amplifikasi DNA Keladi Tikus (Thyponium flagelliform) untuk Identifikasi Keragaman Genetik. Jurnal Bioteknologi & Biosains Indonesia, 2(2), 42–48.

Hussing, C., Kampmann, M. L., Mogensen, H. S., Børsting, C., & Morling, N. (2018). Quantification of massively parallel sequencing libraries - A comparative study of eight methods. Scientific Reports, 8(1). https://doi.org/10.1038/s41598-018-19574-w

Jian, F., Yan-hong, B., Yun-long, W., & Jian-zhou, J. (2010). Detection and Identification of Enterohemorrhagic Escherichia coli O157:H7 using Agilent 2100 Bioanalyzer. [IEEE].

Kalman, B., Abraham, D., Graph, S., Perl-Treves, R., Harel, Y. M., & Degani, O. (2020). Isolation and identification of Fusarium spp., the causal agents of onion (Allium cepa) basal rot in Northeastern Israel. Biology, 9(4). https://doi.org/10.3390/biology9040069

Lee, E. Y., Lee, E. J., Yoon, H., Lee, D. H., & Kim, K. H. (2020). Comparison of four commercial kits for isolation of urinary cell-free DNA and sample storage conditions. Diagnostics, 10(4). https://doi.org/10.3390/diagnostics10040234

Nachamkin, I., Panaro, N. J., Li, M., Ung, H., Po Ki Yuen, Kricka, L. J., & Wilding, P. (2001). Agilent 2100 bioanalyzer for restriction fragment length polymorphism analysis of the Campylobacter jejuni flagellin gene. Journal of Clinical Microbiology, 39(2), 754–757. https://doi.org/10.1128/JCM.39.2.754-757.2001

Ponti, G., Maccaferri, M., Manfredini, M., Kaleci, S., Mandrioli, M., Pellacani, G., Ozben, T., Depenni, R., Bianchi, G., Pirola, G. M., & Tomasi, A. (2018). The value of fluorimetry (Qubit) and spectrophotometry (NanoDrop) in the quantification of cell-free DNA (cfDNA) in Malignant melanoma and prostate cancer patients. Clinica Chimica Acta, 479, 14–19. https://doi.org/10.1016/j.cca.2018.01.007

Rashad, Y. M., Abbas, M. A., Soliman, H. M., Abdel-Fattah, G.-D. G., & Abdel-Fattah, G. M. (2020). Phytopathologia Mediterranea Synergy between endophytic Bacillus amyloliquefaciens GGA and arbuscular mycorrhizal fungi induces plant defense responses against white rot of garlic and improves host plant growth. Phytopathologia Mediterranea, 59(1), 169–186. https://doi.org/10.14601/Phyto-11019

Setiati, N., Partaya, & Hidayah, N. (2020). The use of two pairs primer for CO1 gene amplification on traded stingray at fish auction Tasik Agung Rembang. Journal of Physics: Conference Series, 1567(3). https://doi.org/10.1088/1742-6596/1567/3/032056

Singha, I. M., Kakoty, Y., Unni, B. G., Das, J., & Kalita, M. C. (2016). Identification and characterization of Fusarium sp. using ITS and RAPD causing fusarium wilt of tomato isolated from Assam, North East India. Journal of Genetic Engineering and Biotechnology, 14(1), 99–105. https://doi.org/10.1016/j.jgeb.2016.07.001




DOI: https://doi.org/10.21776/ub.rjls.2023.010.03.3

Refbacks

  • There are currently no refbacks.


Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.