Morpho-Molecular Identification of Plant Pathogen Infecting Bulb Onion (Allium cepa L.) Production Under Protected Cultivation
DOI:
https://doi.org/10.11594/Keywords:
Alternaria porri, ITS rDNA, Mixed fungal infection, Nigrospora sphaerica, Purple blotchAbstract
This study was conducted to identify the fungal pathogen associated with bulb onion production under protected cultivation through combined morphological and molecular identification. Onion leaves showing yellowing, wilting, and purple-to-black lesions were collected from infected plants and subjected to fungal isolation, morphological examination, pathogenicity testing, and molecular analysis. Based on colony and spore characteristics, together with the results of pathogenicity test, the pathogen was identified as Alternaria porri, which is the causal agent of purple blotch disease, fulfilling Koch’s postulates. However, molecular identification based on Internal Transcribed Spacer (ITS) ribosomal DNA sequencing revealed high similarity (98.58– 98.79%) to Nigrospora sphaerica. This difference may be attributed to the faster growth rate and dominance of N. sphaerica in vitro, which likely overshadowed the slower-growing A. porri during DNA amplification and sequencing. Phylogenetic analysis additionally supported the clustering of isolates within the N. sphaerica clade, distinct from A. porri. The contrasting morphological and molecular findings show the occurrence of mixed fungal infections, where A. porri acts as the primary pathogen, and N. sphaerica functions as a secondary colonizer or opportunistic fungus. These results show the limitations of single-method identification and point out the need to integrate morphological, pathogenicity, and molecular approaches for accurate pathogen diagnosis in complex disease systems.
Downloads
References
Abdel-Hafez, S. I. I., Abo-Elyousr, K. A. M., & Abdel-Rahim, I. R. (2015). Leaf surface and endophytic fungi associated with on-ion leaves and their antagonistic activity against Alternaria porri. Czech Mycology, 67(1), 1–22.
Agrios, G. N. (2005). Plant pathology (5th ed.). Elsevier Academic Press.
Barnett, H. L., & Hunter, B. B. (1999). Illustrat-ed genera of imperfect fungi (4th ed.). APS Press.
Black, L. L., Koike, S. T., O’Brien, R. G., & Han-son, P. (2012). Compendium of onion and garlic diseases and pests (2nd ed.). APS Press.
Dar, G. H., Beig, M. A., Bhat, J. A., & Bhat, N. A. (2020). Morphological and molecular characterization of Alternaria porri caus-ing purple blotch disease in onion. Jour-nal of Plant Pathology, 102(2), 559-567.
Dhingra, O. D., & Sinclair, J. B. (1995). Basic plant pathology methods (2nd ed.). CRC Press.
Dutt, V., Sharma, S., & Singh, R. (2022). Mixed fungal infections and their role in plant disease development. Plant Pathology Journal, 38(2), 89–101.
Leslie, J. F., & Summerell, B. A. (2006). The Fusarium laboratory manual. Blackwell Publishing.
Manjunatha, N., Sharma, J., Pokhare, S. S., Sharma, K. K., Agarrwal, R., Hinge, V. R., Adiver, S. S., Gawande, S. P., Somkuwar, R. G., Jadhav, V. T., Ghadge, S. B., Bidwe, M. G., Bicchal, A., Ukale, A. S., & Marathe, R. A. (2022). Characterization of Alter-naria and Colletotrichum species associ-ated with pomegranate (Punica gran-atum L.) in Maharashtra State of India. Journal of Fungi, 8(10), 1040. https://doi.org/10.3390/jof8101040
Meena, M., Gupta, S. K., Swapnil, P., Zehra, A., Dubey, M. K., & Upadhyay, R. S. (2017).
Alternaria toxins: Potential virulence fac-tors and genes related to pathogenesis. Frontiers in Microbiology, 8, 1451. https://doi.org/10.3389/fmicb.2017.01451
Miller, M. E., & Lacy, M. L. (1995). Purple blotch of onion. Plant Disease, 79(3), 242–248.
Schoch, C. L., Seifert, K. A., Huhndorf, S., Rob-ert, V., Spouge, J. L., Levesque, C. A., & Chen, W. (2012). Nuclear ribosomal in-ternal transcribed spacer (ITS) region as a universal DNA barcode marker for fun-gi. Proceedings of the National Academy of Sciences, 109(16), 6241–6246. https://doi.org/10.1073/pnas.1117018109
Schwartz, H. F., & Mohan, S. K. (2008). Com-pendium of onion and garlic diseases and pests (2nd ed.). American Phytopatholog-ical Society.
Simmons, E. G. (2007). Alternaria: An identifi-cation manual. CBS Fungal Biodiversity Centre.
Suheri, H., & Price, T. V. (2001). The epidemi-ology of purple leaf blotch on leeks in Victoria, Australia. European Journal of Plant Pathology, 107(5), 503–510.
Tamura, K., & Nei, M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Bi-ology and Evolution, 10(3), 512–526. https://doi.org/10.1093/oxfordjournals.molbev.a040023
Wang, M., Liu, F., Crous, P. W., & Cai, L. (2017). Phylogenetic reassessment of Nigrospo-ra: Ubiquitous endophytes, plant and human pathogens. Persoonia, 39, 118–142. https://doi.org/10.3767/persoonia.2017.39.06
Woudenberg, J. H. C., Seidl, M. F., Groenewald, J. Z., & Crous, P. W. (2014). Alternaria section Alternaria: Species, formae spe-ciales or pathotypes? Studies in Mycology, 75, 1–21. https://doi.org/10.3114/sim0015
Downloads
Published
Data Availability Statement
All data generated or analyzed during this study are included in this article. Additional data are available from the corresponding author upon reasonable request.
Issue
Section
Categories
License
Copyright (c) 2026 Jennifer P. Celades, Marilyn M. Belarmino, Catherine C. Arradaza, Robelyn T. Piamonte, Zenaida C. Gonzaga
This work is licensed under a Creative Commons Attribution 4.0 International License.
Authors who publish with this journal agree to the following terms:
Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
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 acknowledgement of its initial publication in this journal.
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 (See the Effect of Open Access).
