Skip to main content
SpringerLink
Log in

Population genetic structure of Rhizoctonia solani AG1IA from rice field in North India

  • Published:
Phytoparasitica Aims and scope Submit manuscript

Abstract

Rhizoctonia solani AG1IA is an important fungal pathogen causing significant yield and quality losses in rice production. However, little is known about the levels of genetic diversity and structure of this pathogen in North India. Out of 240 samples collected from different rice-growing regions of North India, 112 isolates were identified as R. solani AG1IA subgroups using species-specific primers. All 112 isolates were organized into four groups on the basis of percent disease index (PDI). The majority of the isolates were weakly virulent. Population genetic analysis was performed within and between populations using inter simple sequence repeat (ISSR) markers. A total of 8249 alleles were identified from the 112 isolates of R. solani AG1IA through analysis of the ten inter simple sequence repeat markers. All the ten ISSR markers were polymorphic. The average number of bands per primer was 7.3 which ranged in size from 250 to 1500 bp. Genetic structure of the isolates using inter simple sequence repeat primers showed high degree of polymorphism (PIC ≥0.81). The analysis of molecular variance (AMOVA) indicated that most of the genetic diversity occurred within populations (60%), while the variability among populations and among regions contributed 25 and 15%, respectively. Overall, the present study reveals that a large variation exists among rice-infecting isolates of R. solani AG1IA in North India. Fingerprinting of the isolates using ISSRs along with phenotypic characterization and virulence analysis will help epidemiological studies that can provide new insights into pathogen biology and disease spread.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Bhaktavatsalam, G., Satyanarayana, K., Reddy, A. P. K., & John, V. T. (1978). Evaluation for sheath blight resistance in rice. International Rice Research Newsletter, 3, 9–10.

    Google Scholar 

  • Ciampi, M. B., Kuramae, E. E., Fenille, R. C., Meyer, M. C., Souza, N. L., & Ceresini, P. C. (2005). Intraspecific evolution of Rhizoctonia solani AG1IA associated with soybean and rice in Brazil based on polymorphisms at the ITS-5.8S rDNA operon. European Journal of Plant Pathology, 113, 183–196.

    Article  CAS  Google Scholar 

  • David Paulraj, R.S. (2003). Molecular strategies for management of sheath blight (ShB) and bacterial blight (BB) diseases of rice through pathogen population analysis and breeding disease resistance (Ph.D. thesis, Chennai, India), University of Madras.

  • Dubey, S. C., Tripathi, A., & Upadhyay, B. K. (2012). Molecular diversity analysis of Rhizoctonia solani isolates infecting various pulse crops in different agro-ecological regions of India. Folia Microbiologia, 57, 513–524.

    Article  CAS  Google Scholar 

  • Garcia, V. G., Onco, M. A. P., & Susan, V. R. (2006). Review, biology and systematic of the form genus Rhizoctonia. Spanish Journal of Agricultural Research, 4, 55–59.

    Article  Google Scholar 

  • González, N., Godoy-Lutz, G., Steadman, J. R., Higgins, R., & Eskridge, K. M. (2012). Assessing genetic diversity in the web blight pathogen Thanatephorus cucumeris (anamorph = Rhizoctonia solani) subgroups AG 1-IE and AG 1-IF with molecular markers. Journal of General Plant Pathology, 78, 85–98.

    Article  Google Scholar 

  • Guillemaut, C., Edel-Hermann, V., Camporota, P., Alabouvette, C., Richard-Molard, M., & Steinberg, C. (2003). Typing of anastomosis groups of Rhizoctonia solani by restriction analysis of ribosomal DNA. Canadian Journal of Microbiology, 49, 556–568.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Jayaprakashvel, M., & Mathivanan, N. (2012). Morphological and pathological variation of rice sheath blight inciting south Indian Rhizoctonia solani isolates. Archives of Phytopathology and Plant Protection, 45, 455–467.

    Article  Google Scholar 

  • Kashyap, P. L., Rai, S., Kumar, S., Srivastava, A. K., Anandaraj, M., & Sharma, A. K. (2015). Mating type genes and genetic markers to decipher intraspecific variability among Fusarium udum isolates from pigeonpea. Journal of Basic Microbiology, 55, 846–856.

    Article  CAS  PubMed  Google Scholar 

  • Khush, G. S. (2005). What it will take to feed 5.0 billion rice consumers in 2030. Plant Molecular Biology, 59, 1–6.

    Article  CAS  PubMed  Google Scholar 

  • Kumar, M., Singh, V., Singh, N., & Vikram, P. (2008). Morphological and virulence characterization of Rhizoctonia solani causing sheath blight of rice. Environmental Ecology, 26, 1158–1166.

    Google Scholar 

  • Linde, C. C., Zala, M., Paulraj, R. S. D., McDonald, B. A., & Gnanamanickam, S. S. (2005). Population structure of the rice sheath blight pathogen Rhizoctonia solani AG1-IA from India. European Journal of Plant Pathology, 112, 113–121.

    Article  CAS  Google Scholar 

  • Lore, J. S., Jain, J., Hunjan, M. S., Gargas, G., Mangat, G. S., & Sandhu, J. S. (2015). Virulence spectrum and genetic structure of Rhizoctonia isolates associated with rice sheath blight in the northern region of India. European Journal of Plant Pathology, 143, 847–860.

    Article  CAS  Google Scholar 

  • Lore, J. S., Vikal, Y., Hunjan, M. S., Goel, R. K., Bharaj, T. S., & Raina, G. L. (2011). Genotypic and pathotypic diversity of Xanthomonas oryzae pv. oryzae, the cause of bacterial blight of rice in Punjab State of India. Journal of Phytopathology, 159, 479–487.

    Article  CAS  Google Scholar 

  • Manian, S. (1982). Studies on the sheath blight disease of rice. Ph.D. Thesis, University of Madras, Madras, p. 121.

  • Matsumoto, M. (2002). Trials of direct detection and identification of Rhizoctonia solani AG1 and AG2 subgroups using specifically primed PCR analysis. Mycoscience, 43, 185–189.

    Article  CAS  Google Scholar 

  • Mishra, P. K., Gogoi, R., Singh, P. K., Borah, J., & Rai, S. N. (2015). Genotypic variability in isolates of Rhizoctonia solani from rice, maize and green gram. Indian Phytopathology, 68, 56–62.

    Google Scholar 

  • Mohammadi, M., Banihashemi, M., Hedjaroude, G. A., & Rahimani, H. (2003). Genetic diversity among Iranian isolates of Rhizoctonia solani anastomosis group 1 subgroups based on isozyme analysis and total soluble protein pattern. Journal of Phytopathology, 151, 162–170.

    Article  CAS  Google Scholar 

  • Nadarajah, K., Omar, N. S., Rosli, M. M., & Tze, O. S. (2014). Molecular characterization and screening for sheath blight resistance using malaysian isolates of Rhizoctonia solani. BioMed Research International, 2014, 434257.

    Article  PubMed  PubMed Central  Google Scholar 

  • Neeraja, C. N., Shenoy, V. V., Reddy, C. S., & Sarma, N. P. (2002). Isozyme polymorphism and virulence of Indian isolates of the rice sheath blight fungus. Mycopathologia, 159, 101–108.

    Article  Google Scholar 

  • Padasht-Dehkaei, F., Ceresini, P. C., Zala, M., Okhovvat, S. M., Nikkhah, M. J., & McDonald, B. A. (2013). Population genetic evidence that basidiospores play an important role in the disease cycle of rice-infecting populations of Rhizoctonia solani AG-1 IA in Iran. Plant Pathology, 62, 49–58.

    Article  Google Scholar 

  • Parmeter Jr., J. R., & Whitney, H. S. (1970). In J. R. Parmerter Jr. (Ed.), Taxonomy and nomenclature of the imperfect state. In: Rhizoctonia solani biology and pathology (pp. 7–19). Berkeley: University of California Press.

    Google Scholar 

  • Peakall, R., & Smouse, P. E. (2012). GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics, 28, 2537–2539.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pudovkin, A. I., Zaykin, D. V., & Hedgecock, D. (1996). On the potential for estimating the effective number of breeders from heterozygote-excess in progeny. Genetics, 144, 383–387.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rohlf, F. J. (2004). NTSYS-pc numerical taxonomy and multivariate analysis system. Version 2.11V. Setauket, NY: Exeter Software.

    Google Scholar 

  • Rosewich, U. L., Pettway, R. E., McDonald, B. A., & Kistler, H. C. (1999). High levels of gene flow and heterozygote excess characterize Rhizoctonia solani AG-1IA (Thanatephorus cucumeris) from Texas. Fungal Genetics and Biology, 28, 148–159.

    Article  CAS  PubMed  Google Scholar 

  • Schneider, J. H. M., Schilder, M. T., Dijst, G. (1997). Characterisation of Rhizoctonia solani AG2 isolates causing bare patch in held grown tulips in the Netherlands. European Journal of Plant Pathology, 103, 265–79.

  • Sharma, N. R., Teng, P. S., & Olivares, P. M. (1990). Comparison of assessment methods for rice sheath blight disease. Philippines Phytopathology, 26, 20–24.

    Google Scholar 

  • Shu, C.-W., Zou, C.-J., Chen, J.-L., Tang, F., Yi, R.-H., & Zhou, E.-X. (2014). Genetic diversity and population structure of Rhizoctonia solani AG-1 IA, the causal agent of rice sheath blight, in South China. Canadian Journal of Plant Pathology, 36, 179–186.

    Article  CAS  Google Scholar 

  • Singh, J., & Singh, R. S. (1994). Variability in cultural characteristics of Rhizoctonia solani isolates from black scurf of potato. Plant Disease Research, 9, 61–65.

    Google Scholar 

  • Singh, V., Singh, U. S., Singh, K. P., Singh, M., & Kumar, A. (2002). Genetic diversity of Rhizoctonia solani by morphological characteristics, pathogenicity, anastomosis behaviour and RAPD fingerprinting. Journal of Mycology and Plant Pathology, 32, 332–344.

    CAS  Google Scholar 

  • Stevens Johnk, J., & Jones, R. K. (1994). Comparison of whole-cell fatty acid compositions in intra-specific groups of Rhizoctonia solani AG-1. Phytopathology, 84, 271–275.

    Article  Google Scholar 

  • Susheela, K., & Reddy, C. S. (2013). Variability in Rhizoctonia solani (AG1IA) isolates causing sheath blight of rice in India. Indian Phytopathology, 66, 341–350.

    Google Scholar 

  • Taheri, P., Gnanamanickam, S., & Hofte, M. (2007). Characterization, genetic structure, and pathogenicity of Rhizoctonia spp. associated with rice sheath blight diseases in India. Phytopathology, 97, 373–383.

    Article  CAS  PubMed  Google Scholar 

  • Tsai, W.H. (1973). Variation in cultural characteristics and pathogenecity of single basidiospores of Thanatephorus cucumeris (Frank) Donk, causing sheath blight of rice. M.S. Thesis, University of Philippines, Philippines p.85.

  • Vijayan, M., & Nair, C. M. (1985). Anastomosis group of isolates of Rhizoctonia solani (Thanatephorus cucumeris) causing sheath blight of rice. Current Science, 54, 289–291.

    Google Scholar 

  • Wang, L., Liu, L. M., Hou, Y. X., Li, L., & Huang, S. W. (2015). Pathotypic and genetic diversity in the population of Rhizoctonia solani AG1IA causing rice sheath blight in China. Plant Pathology, 64, 718–728.

    Article  CAS  Google Scholar 

  • Wang, L., Liu, L. M., Wang, G. Z., & Huang, S. W. (2013). Genetic structure and aggressiveness of Rhizoctonia solani AG1IA, the cause of sheath blight of rice in southern China. Journal of Phytopathology, 161, 753–762.

    Article  CAS  Google Scholar 

  • Wang, Y., Pinson, S. R. M., Fjellstrom, R. G., & Tabien, R. E. (2011). Phenotypic gain from introgression of two QTL, qSB9-2 and qSB12-1, for rice sheath blight resistance. Molecular Breeding, 30, 293–303.

    Article  CAS  Google Scholar 

  • Wheeler, B. E. J. (1969). An introduction to plant diseases (p. 301). London: Wiley.

    Google Scholar 

  • Willocquet, L., Jagjeet, S. L., 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.

    Article  Google Scholar 

  • Yugander, A., Ladhalakshmi, D., Prakasham, V., Mangrauthia, S. K., Prasad, M. S., Krishnaveni, D., Madhav, M. S., Sundaram, R. M., & Laha, G. S. (2015). Pathogenic and genetic variation among the isolates of Rhizoctonia solani (AG 1-IA), the rice sheath blight pathogen. Journal of Phytopathology, 163, 465–474.

    Article  CAS  Google Scholar 

  • Zheng, A., Lin, R., Zhang, D., Qin, P., et al. (2013). The evolution and pathogenic mechanisms of the rice sheath blight pathogen. Nature Communications, 4, 1424.

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhong, T. W., Wei, Z., Qi, O. Z., Wen, L. C., Zun, Z. G., Kun, W. Z., & Li, Y. (2007). Analyses of temporal development and yield losses due to sheath blight of rice (Rhizoctonia solani AG1IA). Agricultural Sciences of China, 6, 1074–1081.

    Article  Google Scholar 

  • Zou, C. J., Tang, F., Yang, M., He, X. X., Li, X. J., & Zhou, E. X. (2011). Studies on biological characteristics and pathogenicity differentiation of rice sheath blight pathogen from three provinces in south China. Chinease Journal of Rice Science, 2, 206–212.

    Google Scholar 

Download references

Acknowledgements

Authors acknowledge Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, for providing all the required facilities to conduct this research smoothly.

Author information

Authors and Affiliations

  1. ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh, 275103, India

    Sanjay Kumar Goswami & Prem Lal Kashyap

  2. Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, UP, 221005, India

    Vineeta Singh

  3. ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, Haryana, 132001, India

    Prem Lal Kashyap

Authors
  1. Sanjay Kumar Goswami
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Vineeta Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Prem Lal Kashyap
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Prem Lal Kashyap.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest regarding this research work.

Electronic supplementary material

Fig. S1

(DOCX 2051 kb)

Fig. S2

(DOCX 783 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Goswami, S.K., Singh, V. & Kashyap, P.L. Population genetic structure of Rhizoctonia solani AG1IA from rice field in North India. Phytoparasitica 45, 299–316 (2017). https://doi.org/10.1007/s12600-017-0600-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12600-017-0600-3

Keywords

Search

Navigation