DNA extraction and electrophoretic visualization for genetic study of gerga and calamansi citrus varieties

Authors

  • Nadia Amida Universitas Bengkulu
  • Florentina Maria Titin Supriyanti Universitas Pendidikan Indonesia

DOI:

https://doi.org/10.30862/accej.v8i2.1085

Keywords:

Citrus calamansi, citrus gerga, CTAB method, DNA isolation, electrophoresis

Abstract

This study aimed to isolate and characterize the genomic DNA of Gerga orange (Citrus gerga) and Calamansi (Citrus microcarpa) using the Cetyl Trimethyl Ammonium Bromide (CTAB) method, followed by agarose gel electrophoresis analysis. The research serves as an initial step toward understanding the genetic relationships among local citrus varieties from Bengkulu, Indonesia. Young leaves were selected as DNA sources due to their metabolically active tissues and relatively low concentrations of secondary metabolites that can inhibit DNA extraction. The isolation procedure included tissue maceration, cell lysis, removal of proteins and polysaccharides, and precipitation of purified DNA. Electrophoresis using a 1 kb DNA ladder revealed distinct genomic DNA bands larger than 10,000 base pairs (bp) in both Gerga (G3) and Calamansi (K3) samples, indicating successful extraction of high-molecular-weight DNA. Subsequent PCR electrophoresis showed approximately 500 bp amplified fragments in the Gerga (G5) and Calamansi (K3) samples, as indicated by the 1 kb DNA ladder. These findings confirm that the CTAB method yields high-quality, intact DNA suitable for further molecular investigations, including genetic identification, phylogenetic reconstruction, and the study of genetic diversity among Bengkulu’s local citrus species.

References

Amida, N., Nahadi, N., Supriyanti, F. M. T., Liliasari, L., Maulana, D., Ekaputri, R. Z., & Utami, I. S. (2024). Phylogenetic analysis of Bengkulu citrus based on DNA sequencing enhanced chemistry students’ system thinking skills: Literature review with bibliometrics and experiments. Indonesian Journal of Science and Technology (IJoST), 9(2). https://doi.org/10.17509/ijost.v9i2.67813

Chen, Y., Liang, Z., Chen, S., Yan, F., He, J., Zhou, Y., & Gao, T. (2024). Unveiling the floral scent dynamics of Calamondin (Citrus × microcarpa) across developmental stages. Separations, 11(12), 359. https://doi.org/10.3390/separations11120359

Chuenwarin, P., Thongleow, S., & Auvuchanon, A. (2022). Genetic relationships analysis of lime and acid citrus by ISSR markers. Thai Agricultural Research Journal, 40(2). https://doi.org/10.14456/thaidoa-agres.2022.16

Dahn, H. A., Mountcastle, J., Balacco, J., Winkler, S., Bista, I., Schmitt, A. D., et al. (2022). Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing. GigaScience, 11, giac068. https://doi.org/10.1093/gigascience/giac068

Kalendar, R., Ivanov, K. I., Samuilova, O., Kairov, U., & Zamyatnin, A. (2023). Isolation of high-molecular-weight DNA for long-read sequencing using a high-salt gel electroelution trap. Analytical Chemistry, 95(48). https://doi.org/10.1021/acs.analchem.3c03894

Kiss, T., et al. (2024). A modified CTAB method for the extraction of high-quality nucleic acids from woody and herbaceous species. Plant Methods, 20(1). https://doi.org/10.1186/s13007-024-01198-z

Nakandala, U. (2025). Citrus genomes: past, present and future. Horticulture Research. https://doi.org/10.1093/hr/uhaf033

Rao, M. J., Zuo, H., & Xu, Q. (2021). Genomic insights into citrus domestication and its important agronomic traits. Plant Communications, 2, 100138. https://doi.org/10.1016/j.xplc.2020.100138

Song, Y., et al. (2024). Unified assembly of chloroplast genomes: a comparative study and application to phylogenomics. Plants/MDPI or related, 10(11), 1218. https://doi.org/10.3390/plants10111218

Wu, Q., Zhu, Y., Zheng, S., Wang, J., Cheng, H., Chen, H., & Zhu, W. (2025). Comparative genomic and phylogenetic analysis of chloroplasts in Citrus paradisi Mac. cv. Cocktail. Genes, 16(5), 544. https://doi.org/10.3390/genes16050544

Xu, L., Liu, Y., & Song, S. (2023). Phylogenetic relationships among Australian native citrus species based upon complete chloroplast genomes and single copy nuclear genes. Tropical Plants, 2023. https://doi.org/10.48130/TP-2023-0021

Zhao, J., Chen, L., & Liu, P. (2023). Evaluation of plant DNA purity and quantification using NanoDrop and Qubit fluorometry. BioTechniques, 75(2), 102–110. https://doi.org/10.2144/btn-2022-0168

Downloads

Published

2025-12-31

How to Cite

Amida, N., & Maria Titin Supriyanti, F. (2025). DNA extraction and electrophoretic visualization for genetic study of gerga and calamansi citrus varieties. Arfak Chem: Chemistry Education Journal, 8(2), 795–801. https://doi.org/10.30862/accej.v8i2.1085

Issue

Vol. 8 No. 2 (2025): Arfak Chem

Section

Articles

License

Copyright (c) 2025 Nadia Amida, Florentina Maria Titin Supriyanti

Creative Commons License

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

License and Copyright Agreement

In submitting the manuscript to the journal, the authors certify that:

  • They are authorized by their co-authors to enter into these arrangements.
  • The work described has not been formally published before, except in the form of an abstract or as part of a published lecture, review, thesis, or overlay journal. Please also carefully read Arfak Chem: Chemistry Education Journal Posting Your Article Policy at http://journalfkipunipa.org/index.php/accej/about
  • That it is not under consideration for publication elsewhere,
  • That its publication has been approved by all the author(s) and by the responsible authorities – tacitly or explicitly – of the institutes where the work has been carried out.
  • They secure the right to reproduce any material that has already been published or copyrighted elsewhere.
  • They agree to the following license and copyright agreement.

Copyright

Authors who publish with Arfak Chem: Chemistry Education Journal agree to the following terms:

  1. Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License (CC BY-ND 4.0) that allows others to share the work with an acknowledgment of the work's authorship and initial publication in this journal.
  2. Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgment of its initial publication in this journal.
  3. Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work.