Abstract
Shot hole disease of stone fruits caused by Thyrostroma carpophilum has become a major threat to stone fruit industry of Jammu and Kashmir, India because of the failure in its management with fungicides. To understand the diversity in shot hole pathogen, a combination of conventional (morphological, cultural and pathological) and molecular (ISSR and ITS markers) approaches were employed to discern variability in 25 isolates of T. carpophilum isolated from peach, plum, apricot, almond and cherry leaves collected from Srinagar, Ganderbal, and Baramulla districts of Jammu and Kashmir, India. The studies revealed a high level of variability among the pathogen. Based on the morpho-cultural and pathological studies, the isolates were grouped into different categories based on colony growth, texture, margin and colour besides change in media colour, incubation period, leaf area infected, etc. Using ISSR markers, a high level of polymorphism in different isolates of T. carpophilum was observed which indicated that these markers are suitable for studying the genetic diversity in this pathogen. Based on dendrogram, the isolates were grouped irrespective of their geographical origin or host species. Phylogenetic analysis of the 25 sequences based on ITS region showed maximum similarity with T. carpophilum (Syn. Wilsonomyces carpophilus) sequences retrieved from NCBI and grouped them in a single clade which proved it as a powerful tool for authentic identification. The pathogen was highly variable based on morpho-cultural, pathological and molecular (ISSR) characterisation.
Similar content being viewed by others
References
Abadio, A. K. R., Lima, S. S., Santana, M. F., Salomao, T. M. F., Sartorato, A., Mizubuti, E. S. G., Araujo, E. F., & Queiroz, M. V. (2012). Genetic diversity analysis of isolates of the fungal bean pathogen Pseudocercospora griseola from central and southern Brazil. Genetics and Molecular Research, 11, 1272–1279.
Adaskaveg, J. E. (1995). Conidial morphology, host colonization and development of shot hole of almond caused by Wilsonomyces carpophilus. Canadian Journal of Botany, 73, 432–444.
Adaskaveg, J. E., Ogawa, J. M., & Butler, E. E. (1990). Morphology and ontogeny of conidia in Wilsonomyces carpophilus, gen. Nov., and comb. nov., causal pathogen of shot hole disease of Prunus species. Mycotaxon, 37, 275–290.
Ahmad, S., Mir, N. A., & Ahmad, S. (1996). Host range of Wilsonomyces carpophilus (Syn. Stigmina carpophila) causing shot hole of almond and other stone fruits. Plant Disease Research, 11, 143–145.
Ahmadpour, A., Ghosta, Y., Javan-Nikkah, M., Fatahi, R., & Ghazanfari, K. (2009a). Isolation and pathogenicity tests of Iranian cultures of the shot hole pathogen of Prunus species, Wilsonomyces carpophilus. Australasian Plant Disease Notes, 4, 133–134.
Ahmadpour, A., Javan-Nikkhah, M., Ghosta, Y., & Fatahi, R. (2009b). Study on some biological and morphological characteristics of Wilsonomyces carpophilus in West Azerbaijan. Rostaniha, 10, 91–109.
Ahmadpour, A., Ghosta, Y., Javan-Nikkhah, M., Fatahi, R., & Ghazanfari, K. (2012a). A study on specificity and host range of Wilsonomyces carpophilus, the causal agent of shot hole disease of stone fruit trees and evaluation of relative resistance of some peach cultivars. Iranian Journal of Plant Protection Sciences, 42, 251–259.
Ahmadpour, A., Ghosta, Y., Javan-Nikkhah, M., Ghazanfari, K., & Fatahi, R. (2012b). Study on morphology, pathogenicity and genetic diversity of Wilsonomyces carpophilus isolates, the causal agent of shot hole of stone fruit trees based on RAPD-PCR in Iran. Archives of Phytopathology and Plant Protection, 45, 2076–2086.
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215, 403–410.
Andotra, P. S., Chib, H. S., & Teng, R. K. (1979). Studies on Stigmina blight-a new threat to stone fruits in Kashmir. Research Development Reporter, 4, 103–106.
Anonymous. (2015a). Areas and production in India for 2014-15. In Washington, DC: Food and agriculture organisation (FAO). United: Nations.
Anonymous. (2015b). Areas and production statement for 2014–15. Government of India, New Delhi: National Horticulture Board.
Anonymous. (2015c). Production and area statement for 2014–15. Jammu and Kashmir: Department of Horticulture, Jammu and Kashmir Government.
Bayraktar, H., & Dolar, F. S. (2009). Genetic diversity of wilt and root rot pathogens of chickpea as assessed by RAPD and ISSR. Turkish Journal of Agriculture and Forestry, 33, 1–10.
Chakraborty, B. N., Chakraborty, U., Dey, P. L., & Rai, K. (2011). rDNA sequence and phylogenetic analysis of Macrophomina phaseolina, root rot pathogen of Citrus reticulata (Blanco). Global Journal of Molecular Sciences, 6, 26–34.
Dar, G. N. & Teng, R. K. (1979). Proceedings of first symposium on “possible improvement in temperate fruit culture” J&K State Srinagar, 13th September, pp. 14-16.
Dar, M. S., Mohammed, I., Sofi, T. A., Ahanger, F. A., Shah, M. D., Ahmad, M., & Padder, B. A. (2015). Distribution of apple scab race Flora and Identification of resistant sources against Venturia inaequalis in Kashmir. Plant Pathology Journal, 14, 196–201.
Ellis, M. B. (1959). Clasterosporium and some allied Dematiaceae-Phragmosporae II. CMI Mycological Paper, 72, 1–75.
Erkal, U. (1973). Studies on shot hole disease (Coryneum beijerinckii Qud) affecting trees in Malatya province. Arastirma Eserlesi Turkiye cum-huryeti Tarim Bakanligi, 33, 139.
Fan, J. Y., Guo, L. Y., Xu, J. P., Luo, Y., & Michailides, T. J. (2010). Genetic diversity of populations of Monilinia fructicola (fungi, Ascomycota, Heliotales) from China. The Journal of Eukaryotic Microbiology, 57, 206–212.
Freeman, S., Minz, D., Jurkevitch, E., Maymon, M., & Shabi, E. (2000). Molecular analyses of Colletotrichum species from almond and other fruits. Phytopathology, 90, 608–614.
Gaumann, E. (1927). The economic significance of our principal plant diseases. Landucrtsch Jahab der Schewiz, 12, 319–324.
Giaretta, D. R., Bogo, A., Coelho, C. M. M., Guidolin, A. F., Adriana, C. M., Dantas, A. C. M., & Gomes, E. A. (2010). ITS-rDNA phylogeny of Colletotrichum spp. causal agent of apple Glomerella leaf spot. Ciencia Rural, 40, 806–812.
Gomez, K. A., & Gomez, A. A. (1984). Statistical procedures for agricultural research. New York: John Wiley & Sons.
Guo, L. D., Xu, L., Zheng, W. H., & Hyde, K. D. (2004). Genetic variation of Alternaria alternata, an endophytic fungus isolated from Pinus tabulaeformis as determined by random amplified microsatellites (RAMS). Fungal Diversity, 16, 53–65.
Haase, F. (1931). Leaf browning and shot hole of sweet cherries in upper Baden. Gemii Sebaii, 77, 113.
Jones, A. L., Shabi, E., & Ehret, G. R. (1987). Genetics of negatively correlated cross-resistance to a N-phenylcarbamate in benomyl-resistant Venturia inaequalis. Canadian Journal of Plant Pathology, 9, 195–199.
Kakvan, N., Zamanizadeh, H., Morid, B., Taheri, H., & Hajmansor, S. (2010). Study on pathogenic and genetic diversity of Alternaria alternate isolated from citrus hybrids of Iran, based on RAPD-PCR technique. European Journal of Experimental Biology, 2, 570–576.
Kanchana-Udomkan, C., Taylor, P. W. J., & Mongkolporn, O. (2004). Development of a bioassay to study anthracnose infection of Capsicumm chinense Jacq. Fruit caused by Colletotrichum capsici. Thai Journal of Agriculture Science, 37, 293–297.
Kerrigan, J., Smith, M. T., Rogers, J. D., Poot, G. A., & Douhan, G. W. (2003). Ascobotryozyma cognata sp. nov., a new ascomycetous yeast associated with nematodes from wood-boring beetle galleries. Mycology Research, 107, 1110–1120.
Lourenco, V., Moya, A., Gonzalez-Candelas, F., Carbone, I., Maffia, L. A., & Mizubuti, E. S. G. (2009). Molecular diversity and evolutionary processes of Alternaria solani in Brazil inferred using genealogical and coalescent approaches. Phytopathology, 99, 765–774.
Mc-Donald, B. A., & Linde, C. (2002). The population genetics of plant pathogens and breeding strategies for durable resistance. Euphytica, 124, 163–180.
Meena, B. S. (2005). Morphological and molecular variability of rice blast pathogen Pyricularia grisea (Cooke) Sacc. Dharwad: MSc. thesis submitted to University of Agricultural Sciences.
Murray, M. G., & Thompson, W. F. (1980). Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research, 8, 4321–4325.
Ogawa, J. M., Zehr, E. I., Bird, G. W., Ritchie, D. F., Uriu, K., & Uyemoto, J. K. (1995). Compendium of stone fruit diseases. St Paul: The American Phytopathological Society Press.
Padder, B. A., Ahmad, M., Shah, M. D., Sofi, T. A., Hamid, A., Sehar, S. & Ahanger, F. A. (2013). Virulence and molecular diversity within Venturia inaequalis isolates from commercial apple cultivars and regions in Kashmir- A North-Western state of India. Journal of Phytopathology, 161, 271–279. https://doi.org/10.1111/jph.12061.
Parisi, L., & Lespinasse, Y. (1996). Pathogenicity of Venturia inaequalis strains of race 6 on apple clones (Malus sp.) Plant Disease, 80, 11179–11183.
Photita, W., Taylor, P. W. J., Ford, R., Hyde, K. D., & Lumyong, S. (2005). Morphological and molecular characterization of Colletotrichum species from herbaceous plants in Thailand. Fungal Diversity, 18, 117–133.
Puttoo, B. L., & Razdan, V. K. (1991). Stigmina blight of cherry: A new record from India. Plant Disease Research, 6, 60.
Ratanacherdchai, K., Wang, H., Lin, F., & Soytong, K. (2010). ISSR for comparison of cross-inoculation potential of Colletotrichum capsici causing chilli anthracnose. African Journal of Microbiology Research, 4, 76–83.
Razdan, V. K., & Puttoo, B. L. (1987). Cultural characteristics of some isolates of Stigmina carpophila causing shot hole of almonds and apricots in Kashmir. International Journal of Tropical Plant Diseases, 5, 103–110.
Rohlf, F. J. (1997). NTSYS-pc (numerical taxonomy and multivariate analysis system), ver 2.02. USA: Applied Biostatistic Inc.
Shukla, H. P., & Bhat, G. N. (1984). Morphology and physiology of Stigmina carpophila causing shot hole disease of almond. Indian Journal of Mycology and Plant Pathology, 14, 178.
Singh, G. (2006). Prevalance and management of leaf spots of peach. Ludhiana: MSc. thesis submitted to Panjab Agricultural University.
Sofi, T. A., Beig, M. A., Dar, G. H., Ahmad, M., Hamid, A., Ahangar, F. A., Padder, B. A., & Shah, M. D. (2013). Cultural, morphological, pathogenic and molecular characterization of Alternaria mali associated with Alternaria leaf blotch of apple. African Journal of Biotechnology, 12, 370–381.
Sukumar, J., & Ramalingam, A. (1981). Detached leaf technique to study leaf spot and other foliar diseases of mulberry. Indian Phytopathology, 34, 110–111.
Sutton, B. C. (1997). On Stigmina, Wilsonomyces and Thyrostroma (Hyphomycetes). Arnoldia, 14, 33–35.
Tamura, S., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30, 2725–2729.
Tejesvi, M. V., Tamhankar, S. A., Kini, K. R., Rao, V. S., & Prakash, H. S. (2009). Phylogenetic analysis of endophytic Pestalotiopsis species from ethnopharmaceutically important medicinal trees. Fungal Diversity, 38, 167–183.
Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994). CLUSTALW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Research, 22, 4673–4680.
Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., & Higgins, D. G. (1997). The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 25, 4876–4882.
Torres-Calzada, C., Tapia-Tussell, R., Higuera-Ciapara, I., & Perez-Brito, D. (2013). Morphological, pathological and genetic diversity of Colletotrichum species responsible for anthracnose in papaya (Carica papaya L). European Journal of Plant Pathology, 135, 67–79.
Tovar-Pedraza, J. M., Ayala-Escobar, V., & Segura-León, O. L. (2013). Thyrostroma carpophilum causing apricot shot-hole in Mexico. Australasian Plant Disease Notes, 8, 31–33.
Tuite, J. (1969). Plant pathologist methods, fungi and bacteria. Miniea Polis, Burgess Publishing. p.239.
Vuillemin, P. (1888). L’ Ascospora beijerinckii et la maladie des cerisiers. Journal of Botany, 2, 255–259.
Walker, S. L., Leath, S., Hagler, J. W. M., & Murphy, J. P. (2001). Variation among isolates of Fusarium graminearum associated with Fusarium head blight in North Carolina. Plant Diseases, 85, 404–410.
Weight, W. R., Smith, M. A., Ramsey, G. B., & Beraha, L. (1960). Observations on pustular spot on peaches. Plant Disease Reporter, 44, 424–425.
White, T. J., Burns, T., Lee, S., & Taylor, J. (1990). Application and direct sequencing of fungal ribosomal RNA genes for phylogenetics. San Diego: A guide to methods and amplifications. Academic Press Inc.
Acknowledgements
The authors are thankful to the Department of Biotechnology, Govt. of India, New Delhi for their financial support.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Ethical statement
This research did not involve any human and/or animal participants.
Conflict of interest
The authors declare that they don’t have any conflict of interests.
Electronic supplementary material
Supplementary Table 1
(DOCX 15 kb)
Rights and permissions
About this article
Cite this article
Nabi, A., Shah, MUD., Padder, B.A. et al. Morpho-cultural, pathological and molecular variability in Thyrostroma carpophilum causing shot hole of stone fruits in India. Eur J Plant Pathol 151, 613–627 (2018). https://doi.org/10.1007/s10658-017-1398-z
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10658-017-1398-z