Evaluation of ISSR Primer Applicability for Interspecific Differentiation of Marchantia from West Java
DOI:
https://doi.org/10.15575/biodjati.v11i1.54766Keywords:
genetic markers, Inter Simple Sequence Repeat, Marchantia, molecular fingerprintingAbstract
Liverworts of the genus Marchantia play important ecological roles in humid tropical ecosystems; however, molecular marker evaluation for tropical taxa remains limited. This study aimed to assess the amplification performance and cross-species applicability of selected Inter Simple Sequence Repeat (ISSR) primers for interspecific molecular differentiation of Marchantia species from West Java, Indonesia. Four species (M. emarginata, M. geminata, M. paleacea, and M. polymorpha) were analyzed using five ISSR primers. Genomic DNA was extracted using a modified CTAB protocol and amplified through single-primer ISSR-PCR assays. Amplification profiles were scored as the presence or absence of dominant bands. Three primers (F218, F231, and F209) generated clear and reproducible multi-locus banding patterns, producing a total of 21 scorable fragments, whereas BS537 and BS3 failed to amplify detectable products. Polymorphism Information Content (PIC), interpreted as an index of band discrimination capacity across species, ranged from 0.70 to 0.91, with F209 and F218 showing the highest informativeness. The results demonstrate that the selected ISSR primers enable reliable interspecific discrimination among the taxa examined and provide a practical framework for preliminary molecular screening of tropical bryophytes. These findings support the use of validated ISSR primers in future taxonomic and comparative genetic studies of non-model liverwort species.
References
Aboul-Maaty, N. A.-F., & Oraby, H. A.-S. (2019). Extraction of high-quality genomic DNA from different plant orders applying a modified CTAB-based method. Bulletin of the National Research Centre, 43(1), 25. DOI: https://doi.org/10.1186/s42269-019-0066-1
Aguado-Ramsay, P., Lara, F., Cuerdo, M., & Draper, I. (2025). Optimizing DNA extraction protocols for bryophytes: Insights from Orthotrichaceae. Applications in Plant Sciences, 13(6), e70028. DOI: https://doi.org/10.1002/aps3.70028
Amiteye, S. (2021). Basic concepts and methodologies of DNA marker systems in plant molecular breeding. Heliyon, 7(10). DOI: https://doi.org/10.1016/j.heliyon.2021.e08093
Araújo, F. dos S., Bruno, R. de L. A., Arriel, N. H. C., de Medeiros, E. P., de Lima, L. M., de Souza, M. A., de Andrade, A. P., Silva, R. A. R., Felix, F. C., & da Silva Belarmino, K. (2023). Genetic polymorphism detection in brazilian perennial cottons (Gossypium spp.) using an ISSR marker system and its application for molecular interspecific differentiation. Molecular Biology Reports, 50(4), 3001–3009. DOI: https://doi.org/10.1007/s11033-022-08165-8
Bellini, E., Bandoni, E., Giardini, S., Sorce, C., Spanò, C., Bottega, S., Fontanini, D., Kola, A., Valensin, D., Bertolini, A., Saba, A., Paoli, L., Andreucci, A., Li, M., Varotto, C., & Sanità di Toppi, L. (2023). Glutathione and phytochelatins jointly allow intracellular and extracellular detoxification of cadmium in the liverwort Marchantia polymorpha. Environmental and Experimental Botany, 209, 105303. DOI: https://doi.org/10.1016/j.envexpbot.2023.105303
Bowman, J. L., Arteaga-Vazquez, M., Berger, F., Briginshaw, L. N., Carella, P., Aguilar-Cruz, A., Davies, K. M., Dierschke, T., Dolan, L., Dorantes-Acosta, A. E., Fisher, T. J., Flores-Sandoval, E., Futagami, K., Ishizaki, K., Jibran, R., Kanazawa, T., Kato, H., Kohchi, T., Levins, J., … Zachgo, S. (2022). The renaissance and enlightenment of Marchantia as a model system. The Plant Cell, 34(10), 3512–3542. DOI: https://doi.org/10.1093/plcell/koac219
Brilhante, B. D., Santos, T. D., Santos, P. H., Kamphorst, S. H., Neto, J. D., Rangel, L. H., Valadares, F. V, de Almeida, R. N., Rodrigues, R., Júnior, A. C., & Moulin, M. M. (2021). Phenotypic and Molecular Characterization of Brazilian Capsicum Germplasm. Agronomy, 11(5). DOI: https://doi.org/10.3390/agronomy11050854
Brzyski, J. R., Adams, K. J., Walter, C. M., Gale, K. H., & Nicholas Mcletchie, D. (2012). Characterization of 12 polymorphic microsatellite markers in the liverwort Marchantia inflexa (Marchantiaceae). American Journal of Botany, 99(11), e440–e442. DOI: https://doi.org/10.3732/ajb.1200187
Buczkowska, K., Rabska, M., Gonera, P., Pawlaczyk, E. M., Wawrzyniak, P., Czołpińska, M., & Bączkiewicz, A. (2016). Effectiveness of ISSR markers for determination of the Aneura pinguis cryptic species and Aneura maxima. Biochemical Systematics and Ecology, 68, 27–35. DOI: https://doi.org/10.1016/j.bse.2016.06.013
Doğan, B., Çelik, M., Ünal, M., Sefali, A., Martin, E., & Kaya, A. (2016). Study of phylogenetic relationship of Turkish species of Matthiola (Brassicaceae) based on ISSR amplification. Turkish Journal of Botany, 40(2), 130–136. DOI: https://doi.org/10.3906/bot-1412-34
Dong, Z., Qi, J., Zhang, Y., Li, G., & Minaeifar, A. A. (2020). Species relationship and population structure analysis in Allochrusa (Caryophylloideae, Caryophyllaceae) using ISSR molecular markers. Phytotaxa, 460(3 SE-Article), 201–213. DOI: https://doi.org/10.11646/phytotaxa.460.3.3
Dos Santos, L. F., De Oliveira, E. J., Dos Santos Silva, A., De Carvalho, F. M., Costa, J. L., & Pádua, J. G. (2011). ISSR markers as a tool for the assessment of genetic diversity in Passiflora. Biochemical Genetics, 49(7–8), 540–554. DOI: https://doi.org/10.1007/s10528-011-9429-5
Gradstein, S. R., Churchill, S. P., & Salazar-Allen, N. (2001). Guide to the Bryophytes of Tropical America. Memoirs of the New York Botanical Garden, 86, 1–577.
Hancı, F., & Paşazade, E. (2025). A Comparison of Efficiency Parameters of SRAP and ISSR Markers in Revealing Variation in Allium Germplasm. Horticulturae, 11(3). DOI: https://doi.org/10.3390/horticulturae11030294
Ho, V. T., Ngo, T. K. A., Phan, T. H. T., Ta, T. T. T., & Tran, T. K. P. (2021). Genetic diversity among passion fruit (Passiflora edulis) accessions of Southern Vietnam using RAPD and ISSR markers. Sabrao Journal of Breeding and Genetics, 53(1), 1–14.
Jamil, A., Razzaq, K., Rajwana, I. A., Naz, A., Akhtar, G., Ullah, S., Faried, H. N., Hussain, S. B., Li, Y., Amin, M., Sher, M. A., Altaf, M. T., Hassan, H., Ahmed, M. A. A., Alfarraj, S., & Ansari, M. J. (2022). Characterization of indigenous phalsa (Grewia subinequalis) genotypes using morphological traits and ISSR markers. Journal of King Saud University - Science, 34(7), 102237. DOI: https://doi.org/10.1016/j.jksus.2022.102237
Lücking, R., Moncada, B., & Dal Forno, M. (2023). PhyloKey: a novel method to rapidly and reliably identify species in complex, species-rich genera, and an opportunity for “non-molecular museomics.” Lichenologist, 55(5), 181–192. DOI: https://doi.org/10.1017/S0024282923000415
Mint Abdelaziz, S., Medraoui, L., Alami, M., Pakhrou, O., Makkaoui, M., Ould Mohamed Salem Boukhary, A., & Filali-Maltouf, A. (2020). Inter simple sequence repeat markers to assess genetic diversity of the desert date (Balanites aegyptiaca Del.) for Sahelian ecosystem restoration. Scientific Reports, 10(1), 1–8. DOI: https://doi.org/10.1038/s41598-020-71835-9
Mo, X., Gao, J., Gao, L., Mo, X., Gao, J., & Gao, L. (2013). Characterization of Microsatellite Markers and Their Application to Genetic Diversity Analysis of Brachypodium sylvaticum var. breviglume from Yunnan, China. American Journal of Plant Sciences, 4(7), 1427–1434. DOI: https://doi.org/10.4236/ajps.2013.47174
Nowaczyński, F., Nicoletti, R., Zimowska, B., & Ludwiczuk, A. (2025). Marchantia polymorpha as a Source of Biologically Active Compounds. Molecules, 30(3), 1–19. DOI: https://doi.org/10.3390/molecules30030558
Ongom, P. O., Fatokun, C., Togola, A., Salvo, S., Oyebode, O. G., Ahmad, M. S., Jockson, I. D., Bala, G., & Boukar, O. (2021). Molecular Fingerprinting and Hybridity Authentication in Cowpea Using Single Nucleotide Polymorphism Based Kompetitive Allele-Specific PCR Assay. Frontiers in Plant Science, 12(734117). https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2021.734117
Peng, Y., Nafee-Ul, A., Liu, M., He, Q., & Liang, Z. (2023). Assessment of Genetic Diversity in Bupleurum spp. Basing Agronomic Traits, Medicinal Components and ISSR Markers. In Genes (Vol. 14, Issue 4, p. 951). DOI: https://doi.org/10.3390/genes14040951
Petolescu, C., Sarac, I., Popescu, S., Tenche-Constantinescu, A.-M., Petrescu, I., Camen, D., Turc, A., Fora, G. C., Turcus, V., Horablaga, N. M., Gorinoiu, G., Mariana, G., & Onisan, E. (2024). Assessment of Genetic Diversity in Alfalfa Using DNA Polymorphism Analysis and Statistical Tools. Plants, 13(20). h DOI: ttps://doi.org/10.3390/plants13202853
Polaiah, A. C., Damor, P. R., Reddy, R. N., Manivel, P., Shivakumara, K. T., Suthar, M. K., Thondaiman, V., Manjesh, G. N., Bindu, K. H., & Kumar, J. (2023). Development of genomic SSR markers in Gymnema sylvestre (Retz.) R.Br. ex Sm. using next generation DNA sequencing and their application in genetic diversity analysis. Journal of Applied Research on Medicinal and Aromatic Plants, 34, 100455. DOI: https://doi.org/10.1016/j.jarmap.2022.100455
Poveda, J. (2020). Marchantia polymorpha as a model plant in the evolutionary study of plant-microorganism interactions. Current Plant Biology, 23, 100152. DOI: https://doi.org/10.1016/j.cpb.2020.100152
Sakhravi, A., Dehdari, M., & Fahliani, R. A. (2023). Genetic relationships among common bean (Phaseolus vulgaris L) genotypes using ISSR markers. Gene Reports, 32, 101797. DOI: https://doi.org/10.1016/j.genrep.2023.101797
Serrote, C. M. L., Reiniger, L. R. S., Silva, K. B., Rabaiolli, S. M. dos S., & Stefanel, C. M. (2020). Determining the Polymorphism Information Content of a molecular marker. Gene, 726, 144175. DOI: https://doi.org/10.1016/j.gene.2019.144175
Söderström, L., Hagborg, A., Von Konrat, M., Bartholomew-Began, S., Bell, D., Briscoe, L., Brown, E., Cargill, D. C., Costa, D. P., Crandall-Stotler, B. J., Cooper, E. D., Dauphin, G., Engel, J. J., Feldberg, K., Glenny, D., Robbert Gradstein, S., He, X., Heinrichs, J., Hentschel, J., … Zhu, R. L. (2016). World checklist of hornworts and liverworts. PhytoKeys, 59(1), 1–828. DOI: https://doi.org/10.3897/phytokeys.59.6261
Susilo, Handayani, H., Darmayani, S., Shofi, M., & Puji Raharjeng, A. R. (2018). RAPD Analysis of the Genetic Diversity among Accessions of Micropropagation Bananas from Indonesia. Journal of Physics: Conference Series, 1114(1). DOI: https://doi.org/10.1088/1742-6596/1114/1/012137
Susilo, & Meitiyani. (2018). Genetic variation of three bruguiera species from Karimunjawa Islands detected by using RAPD molecular markers. Asian Journal of Plant Sciences, 17(4), 198–203. DOI: https://doi.org/10.3923/ajps.2018.198.203
Tahir, N., Lateef, D., Rasul, K., Rahim, D., Mustafa, K., Sleman, S., Mirza, A., & Aziz, R. (2023). Assessment of genetic variation and population structure in Iraqi barley accessions using ISSR, CDDP, and SCoT markers. Czech Journal of Genetics and Plant Breeding, 59(3), 148–159. DOI: https://cjgpb.agriculturejournals.cz/artkey/cjg-202303-0004.php
Tran, D. H., Dao, T. H., Ngo, X. B., Nguyen, V. H., Dao, T. V, & Nguyen, T. D. (2025). Genetic Diversity of Peach (Prunus persica) Accessions Collected in Northern Vietnam Using ISSR Markers. Diversity, 17(3). DOI: https://doi.org/10.3390/d17030151
Wang, L., Wan, M.-C., Liao, R.-Y., Xu, J., Xu, Z.-G., Xue, H.-C., Mai, Y.-X., & Wang, J.-W. (2023). The maturation and aging trajectory of Marchantia polymorpha at single-cell resolution. Developmental Cell, 58(15), 1429-1444.e6. DOI: https://doi.org/10.1016/j.devcel.2023.05.014
Wu, F., Cai, G., Xi, P., Guo, Y., Xu, M., & Li, A. (2024). Genetic Diversity Analysis and Fingerprint Construction for 87 Passionfruit (Passiflora spp.) Germplasm Accessions on the Basis of SSR Fluorescence Markers. In International Journal of Molecular Sciences (Vol. 25, Issue 19, p. 10815). DOI: https://doi.org/10.3390/ijms251910815
Downloads
Published
How to Cite
Issue
Section
Citation Check
License
Copyright (c) 2026 Jurnal Biodjati
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
Copyright and Attribution:
Copyright of published in Jurnal Biodjati is held by the journal under Creative Commons Attribution (CC-BY-NC-ND) copyright. The journal lets others distribute and copy the article, create extracts, abstracts, and other revised versions, adaptations or derivative works of or from an article (such as an tranlation), include in collective works (such as an anrhology), text or data mine the article, as long as they credit the author(s), do not represent the author as endorsing their adaptation of the article and do not modify the article in such a way as to damage the author's honor or reputation.
Permissions:
Authors wishing to include figures, tables, or text passages that have already been published elsewhere and by other authors are required to obtain permission from the copyright owner(s) for both the print and online format and to include evidence that such permission has been granted when submitting their papers. Any material received without such evidence will be assumed to originate of one of the authors.
Ethical matters:
Experiments with animals or involving human patients must have had prior approval from the appropriate ethics committee. A statement to this effect should be provided within the text at the appropriate place. Experiments involving plants or microorganisms taken from countries other than the authors own must have had the correct authorization for this exportation.
