Assessment of genetic diversity in Colletotrichum sp. causing cucumber anthracnose using random amplified polymorphic DNA and inter-simple sequence repeat markers
,
,
,
and
*
Article Sidebar
Full Text: 
PDF
Main Article Content
Abstract
Anthracnose caused by Colletotrichum sp. is an important disease causing severe damage to the quality and yield of cucumbers in the Mekong Delta of Viet Nam. This study was conducted to assess the genetic diversity of Colletotrichum isolates collected from the Mekong Delta using 13 random amplified polymorphic DNA (RAPD) and 10 inter-simple sequence repeat (ISSR) primers. In addition, associations between these molecular markers and pathogenicity were explored using stepwise multiple regression analysis (MRA). The molecular markers showed high percentages of polymorphic bands (71-100%). Similarity coefficients among the isolates (74-82%) derived from the combined RAPD-ISSR data indicated a moderate to high level of genetic similarity. Two isolates, DT and CT, had the highest similarity coefficients. A total of 13 significant alleles were found to be associated with disease severity and AUDPC indices. S1189-458 and ISSR848-675 were the most significant alleles associated with both disease severity and AUDPC indices. Overall, RAPD and ISSR markers are useful for assessing genetic diversity, while their association with pathogenicity requires further validation.
Article Details
Conflict of Interest
© 2026 The authors. This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License.
References
Esfahani, M. N. (2018). Analysis of virulence and genetic variability of Alternaria alternata associated with leaf spot disease in potato plants in Iran. Acta Mycologica, 53(1), 1105. https://doi.org/10.5586/am.1105
FAO. (2025). Crops and livestock products. https://www.fao.org/faostat/en/#data/QCL
He, J., Li, D. W., Zhu, Y. N., Si, Y. Z., Huang, J. H., Zhu, L. H., Ye, J. R., & Huang, L. (2022). Diversity and pathogenicity of Colletotrichum species causing anthracnose on Cunninghamia lanceolata. Plant Pathology, 71(8), 1757–1773. https://doi.org/10.1111/ppa.13611
Istvan, L. J., & Istvan, L. S. (2019). GelAnalyzer (Version 19.1). http://www.gelanalyzer.com/index.html
Jebaraj, M. D., Aiyanathan, K. E. A., & Nakkeeran, S. (2017). Virulence and genetic diversity of Sclerotium rolfsii Sacc. infecting groundnut using nuclear (RAPD & ISSR) markers. Journal of Environmental Biology, 38(1), 147–159. https://doi.org/10.22438/jeb/38/1/ms-274
Kodama, S., Bissaro, B., Berrin, J. G., & Kubo, Y. (2023). Plant surface signal sensing and infection-related morphogenesis of Colletotrichum orbiculare. Physiological and Molecular Plant Pathology, 124, 101979. https://doi.org/10.1016/j.pmpp.2023.101979
Kumar, N., Jhang, T., S., S., & Sharma, T. R. (2011). Molecular and pathological characterization of Colletotrichum falcatum infecting subtropical Indian sugarcane. Journal of Phytopathology, 159(4), 260–267. https://doi.org/10.1111/j.1439-0434.2010.01759.x
Mahmodi, F., Kadir, J. B., Puteh, A., Pourdad, S. S., Nasehi, A., & Soleimani, N. (2014a). Genetic diversity and differentiation of Colletotrichum spp. isolates associated with leguminosae using multigene loci, RAPD and ISSR. Plant Pathology Journal, 30(1), 10–24. https://doi.org/10.5423/PPJ.OA.05.2013.0054
Mahmodi, F., Kadir, J., & Puteh, A. (2014b). Genetic diversity and pathogenic variability of Colletotrichum truncatum causing anthracnose of pepper in Malaysia. Journal of Phytopathology, 162(7–8), 456–465. https://doi.org/10.1111/jph.12213
Matsuo, H., Ishiga, Y., Kubo, Y., & Yoshioka, Y. (2022). Colletotrichum orbiculare strains distributed in Japan: race identification and evaluation of virulence to cucurbits. Breeding Science, 72(4), 306–315. https://doi.org/10.1270/jsbbs.22011
Mo, J., Zhao, G., Li, Q., Solangi, G. S., Tang, L., Guo, T., Huang, S., & Hsiang, T. (2018). Identification and Characterization of Colletotrichum Species Associated with Mango Anthracnose in Guangxi, China. Plant Disease, 102(7), 1283–1289. https://doi.org/10.1094/PDIS-09-17-1516-RE
Neto, J. A. da S., Ambrósio, M. M. de Q., Araújo, M. B. M., da Silva, R. M., Pinto, P. S. L., & Holanda, I. S. A. (2022). Morphological, molecular and pathogenic characterization of Colletotrichum gloeosporioides isolated from mango. Revista Caatinga, 35(3), 514–527. https://doi.org/10.1590/1983-21252022v35n302rc
Nga, N. T. T., Lan, T. B., & Giao, B. T. (2011). Evaluation pathogenicity of Colletotrichum lagenarium causing anthracnose disease on watermelon and study biological control the disease by rhizobacteria in greenhouse condition. The 10th National Conference of the Phytopathological Society of Viet Nam (pp. 135–145).
Omri, A., Abdelhamid, S., Benincasa, C., Araouki, A., Ayadi, M., Gharsallaoui, M., & Gouiaa, M. (2021). Genetic diversity and association of molecular markers with biochemical traits in Tunisian olive cultivars. Genetic Resources and Crop Evolution, 68, 1181–1197. https://doi.org/10.1007/s10722-020-01058-4
Palacioglu, G., Bayraktar, H., Özer, G. (2020). Genetic variability of Colletotrichum lindemuthianum isolates from Turkey and resistance of Turkish bean cultivars. Spanish Journal of Agricultural Research, 18(3), e1005. https://doi.org/10.5424/sjar/2020183-16398
Palenchar, J., Treadwell, D. D., Datnoff, L. E., & Gevens, A. J. (2009). Cucumber anthracnose in Florida. Florida: University of Florida.
Patel, P., Rajkumar, B. K., Parmar, P., Shah, R., & Krishnamurthy, R. (2018). Assessment of genetic diversity in Colletotrichum falcatum Went accessions based on RAPD and ISSR markers. Journal, Genetic Engineering and Biotechnology, 16(1), 153–159. https://doi.org/10.1016/j.jgeb.2017.11.006
Pavlícek, A., Hrdá, S., & Flegr, J. (1999). Free-Tree--freeware program for construction of phylogenetic trees on the basis of distance data and bootstrap/jackknife analysis of the tree robustness. Application in the RAPD analysis of genus Frenkelia. Folia Biologica, 45(3), 97–99.
Pineda-Vaca, D., Flores-Méndez, G., Fernández-Pavía, S. P., Santillán-Mendoza, R., Montero-Castro, J. C., Garay-Serrano, E., Ortega-Arreola, R., & Rodríguez-Alvarado, G. (2025). Genetic diversity of Colletotrichum siamense causing mango anthracnose in the state of Jalisco, Mexico, based on ISSR markers. Canadian Journal of Plant Pathology, 47(4), 339-355. https://doi.org/10.1080/07060661.2025.2462658
Powell, W., Morgante, M., Andre, C., Hanafey, M., Vogel, J., Tingey, S., & Rafalski, A. (1996). The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Molecular Breeding, 2, 225–238. https://doi.org/10.1007/BF00564200
Ratanacherdchai, K., Wang, H. K., Lin, F. C., & Soytong, K. (2007). RAPD analysis of Colletotrichum species causing chilli anthracnose disease in Thailand. Journal of Agricultural Technology, 3(2), 211-219.
Roberts, P. D., Vallad, G., Zhang, S., Dufault, N., & Paret, M. (2023). Anthracnose on Cucurbits in Florida. EDIS, 2023(3). https://doi.org/10.32473/edis-pp370-2023
Rohlf, F. J. (2000). NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System Version 2.1. New York: Exeter Publishing Setauket.
Rojas-Martínez, R. I., Zavaleta-Mejía, E., Nieto-Ángel, D., & Acosta-Ramos, M. (2008). Virulence and Genetic Variation of Isolates of Colletotrichum gloeosporioides (Penz.) Penz. and Sacc. on Mango (Mangifera indica L.) cv. Haden. Revista Mexicana de Fitopatología, 26, 21–26.
Samba, N., Nunomura, O., Nakano, A., & Tsukagoshi, S. (2023). Effective training methods for cucumber production in newly developed nutrient film technique hydroponic system. Horticulturae, 9(4), 478. https://doi.org/10.3390/horticulturae9040478
Sambrook, J., Fritsch, E. F., & Maniatis, T. (1989). Molecular Cloning: A Laboratory Manual. Vol. 68, Society. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
Sangdee, A., Sachan, S., & Khankhum, S. (2011). Morphological, pathological and molecular variability of Colletotrichum capsici causing anthracnose of chilli in the North-east of Thailand. African Journal of Microbiology Research, 5(25), 4368–4372. https://doi.org/10.5897/AJMR11.476
Simko, I., & Piepho, H. P. (2012). The area under the disease progress stairs: Calculation, advantage, and application. Phytopathology, 102(4), 381–389. https://doi.org/10.1094/PHYTO-07-11-0216
Tovar-Pedraza, J. M., Mora-Aguilera, J. A., Nava-Díaz, C., Lima, N. B., Michereff, S. J., Sandoval-Islas, J. S., Câmara, M. P. S., Téliz-Ortiz, D., & Leyva-Mir, S. G. (2020). Distribution and Pathogenicity of Colletotrichum Species Associated With Mango Anthracnose in Mexico. Plant Disease, 104(1), 137–146. https://doi.org/10.1094/PDIS-01-19-0178-RE
Villa-Rivera, M. G., Conejo-Saucedo, U., Lara-Marquez, A., Cano-Camacho, H., Lopez-Romero, E., & Zavala-Paramo, M. G. (2017). The role of virulence factors in the fathogenicity of Colletotrichum sp. Current Protein and Peptide Science, 18(10), 1005–1018. https://doi.org/10.2174/1389203717666160813160727
Wang, Y., Chen, J. Y., Xu, X., Cheng, J., Zheng, L., Huang, J., & Li, D. W. (2020). Identification and characterization of Colletotrichum species associated with anthracnose disease of Camellia oleifera in China. Plant Disease, 104(2), 474–482. https://doi.org/10.1094/PDIS-11-18-1955-RE
Williams, J. G., Kubelik, A. R., Livak, K. J., Rafalski, J. A., & Tingey, S. V. (1990). DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research, 18(22), 6531–6535. https://doi.org/10.1093/nar/18.22.6531