European Journal of Plant Pathology

, Volume 143, Issue 4, pp 847–860 | Cite as

Virulence spectrum and genetic structure of Rhizoctonia isolates associated with rice sheath blight in the northern region of India

  • J. S. Lore
  • J. Jain
  • M. S. Hunjan
  • G. Gargas
  • G. S. Mangat
  • J. S. SandhuEmail author


Rhizoctonia solani Kuhn, a highly variable pathogen, causes sheath blight of rice globally leading to serious yield losses under favourable environmental conditions. Sixty-four Rhizoctonia isolates collected from diverse rice growing agro-ecological zones of the north Indian state of Punjab were analyzed for species identification, genetic diversity, morphological features and virulence pattern. Accurate identification of the fungal species using internal transcribed spacer species-specific primers confirmed presence of R. solani (84.4 %), R. oryzae-sativae (10.9 %), R. oryzae (1.5 %) and mixed infection of these Rhizoctonia sp. Genetic structure of the isolates resolved using inter simple sequence repeat primers revealed high degree of polymorphism (PIC value ranging from 0.80 to 0.90), clustering the pathogen population into four major groups. The virulence pattern of 18 isolates representing genetically diverse groups generated by ISSR profile was quantified on seven rice genotypes/cultivars i.e., Tetep, Jasmine 85, Te-Qing, D-256, D-6766, PR108 and PAU201 with different levels of resistance to rice sheath blight. The hierarchical cluster analysis based on different disease variables classified isolates into six main groups. Reaction of individual isolate to each genotype revealed different levels of virulence pointing towards high evolutionary potential, thus enabling it to adapt to diverse geographical regions.


Genetic diversity ISSR markers ITS markers Rhizoctonia spp. Rice sheath blight Virulence 



Dr C. M. Vera Cruz, International Rice Research Institute, the Philippines is thankfully acknowledged for generously providing the seed material.

Supplementary material

10658_2015_736_MOESM1_ESM.docx (20 kb)
Supplementary Table 1 Morphological characters of Rhizoctonia isolates (DOCX 20 kb)
10658_2015_736_MOESM2_ESM.pptx (148 kb)
Supplementary Fig. 1 PCR amplification of Rhizoctonia isolates using R. solani specific ITS primers (M; Gene ruler molecular weight marker, catalogue # SM0311), isolates are abbreviated in Table 1 (PPTX 147 kb)
10658_2015_736_MOESM3_ESM.pptx (304 kb)
Supplementary Fig. 2 PCR amplification of Rhizoctonia isolates using R. oryzae-sativae specific primers (M;Promega molecular weight marker, catalogue # G7511), isolates are abbreviated in Table 1 (PPTX 303 kb)
10658_2015_736_MOESM4_ESM.pptx (264 kb)
Supplementary Fig. 3 PCR amplification of Rhizoctonia isolates using R. oryzae specific primers (M;Promega molecular weight marker, catalogue # G7511), isolates are abbreviated in Table 1 (PPTX 264 kb)
10658_2015_736_MOESM5_ESM.pptx (518 kb)
Supplementary Fig. 4 a DNA profile of Rhizoctonia isolates obtained with ISSR primer R28 (M; Gene ruler molecular weight marker, catalogue # SM0311). The serial number 1 to 55 are shown in Table 1 b DNA profile of Rhizoctonia isolates obtained with ISSR primer R30 (M; Gene ruler molecular weight marker, catalogue # SM0311). The serial number 1 to 55 are shown in Table 1 (PPTX 517 kb)
10658_2015_736_MOESM6_ESM.pptx (1.3 mb)
Supplementary Fig. 5 a-c Different types of sclerotia arrangement in Rhizoctonia isolates. a) scattered arrangement b) ring in centre c) ring in centre and at periphery (PPTX 1336 kb)
10658_2015_736_MOESM7_ESM.pptx (69 kb)
Supplementary Fig. 6 Dendogram showing different groups of Rhizoctonia isolates according to their morphological characters (PPTX 68 kb)
10658_2015_736_MOESM8_ESM.pptx (69 kb)
Supplementary Fig. 7 Dendogram showing different groups of Rhizoctonia isolates according to their virulence spectrum (PPTX 69 kb)
10658_2015_736_MOESM9_ESM.pptx (666 kb)
Supplementary Fig. 8 a-b Reaction of Rhizoctonia isolates on rice cultivar Jasmine 85. a) Shb-1105 showing lower lesion length compared to b) Shb-905 (PPTX 665 kb)


  1. Anderson, N. A. (1982). The genetics and pathology of Rhizoctonia solani. Annual Review of Phytopathology, 20, 329–347.CrossRefGoogle Scholar
  2. Anonymous. (2012). Production oriented survey. Hyderabad: Directorate Rice Research.Google Scholar
  3. Banniza, S., & Rutherford, M. A. (2001). Diversity of isolates of Rhizoctonia solani AG-1 IA and their relationship to other anastomosis groups based on pectic zymograms and molecular analysis. Mycological Research, 105, 33–40.CrossRefGoogle Scholar
  4. Banniza, S., Sy, A. A., Bridge, P. D., Simons, S. A., & Holderness, M. (1999). Characterization of populations of Rhizoctonia solani in paddy rice fields in Cote d’ Ivoire. Phytopathology, 89, 414–420.CrossRefPubMedGoogle Scholar
  5. Burpee, L. L., & Martin, B. (1992). Biology of Rhizoctonia species associated with turfgrass. Plant Disease, 76, 112–117.CrossRefGoogle Scholar
  6. Carling, D. E., Pope, E. J., Brainard, K. A., & Carter, D. A. (1999). Characterization of mycorrhizal isolates of Rhizoctonia solani from an orchid, including AG-12, a new anastomosis group. Phytopathology, 89, 942–946.CrossRefPubMedGoogle Scholar
  7. Carling, D. E., Baird, R. E., Gitaitis, R. D., Brainard, K. A., & Kuninaga, S. (2002). Characterization of AG-13, a newly reported anastomosis group of Rhizoctonia solani. Phytopathology, 92, 893–899.CrossRefPubMedGoogle Scholar
  8. Chahal, K. S., Sokhi, S. S., & Rattan, G. S. (2003). Investigations on sheath blight of rice in Punjab. Indian Phytopathology, 56, 22–26.Google Scholar
  9. Channamallikarjuna, V., Sonah, H., Prasad, M., Rao, G. J. N., Chand, S., Upreti, H. C., Singh, N. K., & Sharma, T. R. (2010). Identification of major quantitative trait loci qSBR11-1 for sheath blight resistance in rice. Molecular Breeding, 25, 155–166.CrossRefGoogle Scholar
  10. Duncan, S., Barton, J. E., & O’Brien, P. A. (1993). Analysis of variation in isolates of Rhizoctonia solani by random amplified polymorphic DNA assay. Mycological Research, 97, 1075–1082.CrossRefGoogle Scholar
  11. Gangopadhyay, S., & Chakrabarti, N. K. (1982). Sheath blight of rice. Annual Review of Plant Pathology, 61, 451–460.Google Scholar
  12. Gou, Q., Kamio, A., Sharma, B. S., Sagara, Y., Arakawa, M., & Inagaki, K. (2006). Survival and subsequent dispersal of rice sclerotial disease fungi, Rhizoctonia oryzae and Rhizoctonia oryzae-sativae in paddy fields. Plant Disease, 90, 615–622.CrossRefGoogle Scholar
  13. Guleria, S., Aggarwal, R., Thind, T. S., & Sharma, T. R. (2007). Morphological and pathological variability in rice isolates of Rhizoctonia solani and molecular analysis of their genetic variability. Journal of Phytopathology, 155, 654–661.CrossRefGoogle Scholar
  14. Johanson, A., Turner, H. C., McKay, G. J., & Brown, A. E. (1998). A PCR-based method to distinguish fungi of the rice sheath-blight complex, Rhizoctonia solani, R. oryzae, and R. oryzae-sativae. FEMS Microbiology Letters, 162, 289–294.CrossRefPubMedGoogle Scholar
  15. Khodayari, M., Safaie, H., & Shambakhsh, M. (2009). Genetic diversity of Iranian AG1-IA isolates of Rhizoctonia solani, the cause of rice sheath blight, using morphological and molecular markers. Journal of Phytopathology, 157, 708–714.CrossRefGoogle Scholar
  16. Linde, C. C., Zala, M., Pauraj, R. S. D., McDonald, B. A., & Gnanamanickam, S. S. (2005). Population structure of the rice sheath blight pathogen Rhizoctonia solani AG-1 1A from India. European Journal of Plant Pathology, 112, 113–121.CrossRefGoogle Scholar
  17. Liu, G., Jia, Y., Correa-Victoria, F. J., Prado, G. A., Yeaton, K. M., Mcclung, A., & Correll, J. C. (2009). Mapping quantitatively trait loci responsible for resistance to sheath blight in rice. Phytopathology, 99, 1078–1084.CrossRefPubMedGoogle Scholar
  18. Lore, J. S., Hunjan, M. S., Singh, P., Willocquet, L., Sri, S., & Savary, S. (2013). Phenotyping of partial physiological resistance to rice sheath blight. Journal of Phytopathology, 161, 224–229.CrossRefGoogle Scholar
  19. Murry, M. G., & Thompson, W. F. (1980). Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research, 8, 4321–4325.CrossRefGoogle Scholar
  20. Ou, S. H. (1985). Rice diseases (2nd ed.). Kew Surrey: Commonwealth Mycological Institute.Google Scholar
  21. Pan, X. B., Rush, M. C., Sha, X. Y., Xie, Q. J., Linscombe, S. D., Stetina, S. R., & Oard, J. H. (1999). Major gene, non-allelic sheath blight resistance from the rice cultivars Jasmine 85 and Te-Qing. Crop Science, 39, 338–346.Google Scholar
  22. Perrier, X., Flori, A., & Bannot, F. (2003). Data analysis methods. In P. Hamon, M. Seguin, X. Perrier, & J. C. Glaszmann (Eds.), Genetic diversity of cultivated tropical plants (pp. 43–76). Montpellier: Enfield, Science Publishers.Google Scholar
  23. Pillai, P. K., & Singh, V. P. (1994). Differential reaction of rice cultivars to isolates of Rhizoctonia solani. Indian Phytopathology, 47, 96–98.Google Scholar
  24. Pinson, S. R. M., Capdevielle, F. M., & Oard, J. H. (2005). Confirming QTLs and finding additional loci conditioning sheath blight resistance in rice using recombinant inbred lines. Crop Science, 45, 503–510.CrossRefGoogle Scholar
  25. Savary, S., Willocquet, L., Elazegui, F. A., Castilla, N., & Teng, P. S. (2000). Rice pest constraints in tropical Asia: quantification of yield losses due to rice pests in a range of production situations. Plant Disease, 84, 357–369.CrossRefGoogle Scholar
  26. Sharma, M., Gupta, S. K., & Sharma, T. R. (2005). Characterization of variability in Rhizoctonia solani by using morphological and molecular markers. Journal of Phytopathology, 153, 449–456.CrossRefGoogle Scholar
  27. Singh, V., Singh, U. S., Singh, K. P., Singh, M., & Kumar, A. (2002). Genetic diversity of Rhizoctonia solani isolates from rice differentiation by morphological characteristics, pathogenicity, anastomosis behaviour and RAPD fingerprinting. Journal of Mycology and Plant Pathology, 32, 332–334.Google Scholar
  28. Taheri, P., Gnanamanickam, S., & Hoffe, M. (2007). Characterization, genetic structure and pathogenicity of Rhizoctonia spp. associated with rice sheath diseases in India. Phytopathology, 97, 373–383.CrossRefPubMedGoogle Scholar
  29. Toda, T., Mushika, T., & Hyakumachi, M. (2004). Development of specific PCR primers for the detection of Rhizoctonia solani AG 2–2 LP from the leaf sheaths exhibiting large-patch symptom on zoysia grass. FEMS Microbiology Letters, 232, 67–74.CrossRefPubMedGoogle Scholar
  30. Willocquet, L., Lore, J. S., Srinivasachary, S., & Savary, S. (2011). Quantification of the components of resistance to rice sheath blight using a detached tiller test under controlled conditions. Plant Disease, 95, 1507–1515.CrossRefGoogle Scholar

Copyright information

© Koninklijke Nederlandse Planteziektenkundige Vereniging 2015

Authors and Affiliations

  1. 1.School of Agricultural BiotechnologyPunjab Agricultural UniversityLudhianaIndia
  2. 2.Department of Plant Breeding and GeneticsPunjab Agricultural UniversityLudhianaIndia
  3. 3.Department of Plant PathologyPunjab Agricultural UniversityLudhianaIndia

Personalised recommendations