Skip to main content
SpringerLink
Log in

Molecular evidence supports hypervariability in Phytophthora colocasiae associated with leaf blight of taro

  • Published:
European Journal of Plant Pathology Aims and scope Submit manuscript

Abstract

The oomycete Phytophthora colocasiae that causes taro leaf blight is the most devastating disease of taro and is widely distributed worldwide. Molecular and phenotypic techniques were employed for assessing and exploiting the genetic variability among four populations of P. colocasiae obtained from a fine spatial scale (multiple leaf blight lesions on single taro leaf). Phenotypic characters such as virulence, morphology and mating type showed no variation. ITS characterization revealed detectable polymorphism among isolates of P. colocasiae. The mean number of haplotypes (H), haplotype diversity (HD), nucleotide diversity (π), and nucleotide substitution rate (θ) among analyzed sequences were 6.75, 1.00, 0.069, and 0.088 respectively. High levels of inter and intra specific variation were detected by random amplified polymorphic DNA (RAPD) assays. Moderate genetic diversity (H = 0.2651) was observed among populations of P. colocasiae. Analysis of molecular variance (AMOVA) confirmed that most of the genetic variability was confined to within a population (63.54 %). The coefficient of genetic differentiation among populations (G ST ) was 0.2007 and estimates of gene flow (Nm) among populations was 1.991 migrants per generation. Cluster analysis using UPGMA revealed that individuals from the same population failed to cluster in one distinct group. The results of the study reveal considerable genetic diversity among and within populations of P. colocasiae obtained from fine spatial scale. The possible mechanisms and implications of this genetic variation are discussed.

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

  • Abu-El Samen, F. M., Secor, G. A., & Gudmestad, N. C. (2003). Genetic variation among asexual progeny of Phytophthora infestans detected with RAPD and AFLP markers. Plant Pathology, 52, 314–325.

    Article  CAS  Google Scholar 

  • Agapow, P. M., & Burt, A. (2001). Indices of multilocus linkage disequilibrium. Molecular Ecology Notes, 1, 101–102.

    Article  CAS  Google Scholar 

  • Caetano-Anollés, G. (1993). Amplifying DNA with arbitrary oligonucleotide primers. Genome Research, 3, 85–94.

    Article  Google Scholar 

  • Cardenas, M., Grajales, A., Sierra, R., Rojas, A., Almario, A. G., Vargas, A., et al. (2011). Genetic diversity of Phytophthora infestans in the Northern Andean region. BMC Genetics, 12, 23.

    Article  PubMed  CAS  Google Scholar 

  • Chang, T. T., Yang, W. W., & Wang, W. Y. (1996). Use of random amplified polymorphic DNA markers for the detection of genetic variation in Phytophthora cinnamomi in Taiwan. Botanical Bulletin of Academia Sinica, 37, 165–171.

    CAS  Google Scholar 

  • Chamnanpunt, J., Shan, W. X., & Tyler, B. M. (2001). High frequency mitotic gene conversion in genetic hybrids of the Oomycete Phytophthora sojae. Proceedings of National Academy of Science USA, 98, 14530–14535.

    Article  CAS  Google Scholar 

  • Cooke, D. E. L., Kennedy, D. M., Guy, D. C., Russel, J., Unkles, S. E., & Duncan, J. M. (1996). Relatedness of groupI species of Phytophthora as assessed by randomly amplified polymorphic DNA (RAPD) and sequences of ribosomal DNA. Mycological Research, 100, 297–303.

    Article  CAS  Google Scholar 

  • Cooke, D. E. L., & Duncan, J. M. (1997). Phylogenetic analysis of Phytophthora species based on ITS1 and ITS2 sequences of the ribosomal RNA gene repeat. Mycological Research, 101, 667–677.

    Article  CAS  Google Scholar 

  • Drenth, A., Janssen, E. M., & Govers, F. (1995). Formation and survival of oospores of Phytophthora infestans under natural conditions. Plant Pathology, 44, 86–94.

    Article  Google Scholar 

  • Drenth, A., Whisson, S. C., Maclean, D. J., Irwin, J. A. G., Obst, N. R., & Ryley, M. J. (1996). The evolution of races of Phytophthora sojae in Australia. Phytopathology, 86, 163–169.

    Article  Google Scholar 

  • Excoffier, L., Smouse, P. E., & Quattro, J. M. (1992). Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131, 479–491.

    PubMed  CAS  Google Scholar 

  • Fry, W. E., & Goodwin, S. B. (1995). Recent migrations of Phytophthora infestans. In L. J. Dowley, E. Bannon, L. R. Cooke, T. Keane, & E. O’Sullivan (Eds.), Phytophthora infestans 150 (pp. 89–95). Dublin: Boole Press.

    Google Scholar 

  • Goodwin, S. B. (1997). The population genetics of Phytophthora. Phytopathology, 97, 462–473.

    Article  Google Scholar 

  • Jackson, G. V. H., Gollifer, D. E., & Newhook, F. J. (1980). Studies on the taro leaf blight fungus Phytophthora colocasiae in the Solomon Islands: control by fungicides and spacing. Annals of Applied Biology, 96, 1–10.

    Article  CAS  Google Scholar 

  • Koh, Y. J., Goodwin, S. B., Dyer, A. T., Cohen, B. A., Ogoshi, A., Sato, N., et al. (1994). Migrations and displacements of Phytophthora infestans in East Asian countries. Phytopathology, 84, 922–927.

    Article  Google Scholar 

  • Lakhanpaul, S., Velayudhan, K. C., & Bhat, K. V. (2003). Analysis of genetic diversity in Indian C. esculenta (Colocasia esculenta (L.)Schott) using random amplified polymorphicDNA (RAPD) markers. Genetic Resources and Crop Evolution, 50, 603–609.

    Article  CAS  Google Scholar 

  • Lebot, V., & Aradhya, K. M. (1991). Isozyme variation in taro (Colocasia esculenta (L.)Schott) from Asia and Oceania. Euphytica, 56, 55–66.

    Google Scholar 

  • Lebot, V., Hartati, S., Hue, N. T., Viet, N. V., Nghia, N. H., & Okpul, T. (2000). Genetic variation in taro (Colocasia esculenta) in SouthEast Asia and Oceania. Twelfth Symposium of the ISTRC. Potential of root crops for food and industrial resources. Sept.10–16, 2000. Tsukuba, Japan, pp. 524–533.

  • Lebot, V., Herail, C., Gunua, T., Pardales, J., Prana, M., Thongjiem, M., et al. (2003). Isozyme and RAPD variation among Phytophthora colocasiae isolates from South East Asia and the Pacific. Plant Pathology, 52, 303–313.

    Article  CAS  Google Scholar 

  • Lewontin, R. C. (1972). The apportionment of human diversity. Evolutionary Biology, 6, 381–398.

    Article  Google Scholar 

  • Librado, P., & Rozas, J. (2009). Dnaspv5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451–1452.

    Article  PubMed  CAS  Google Scholar 

  • Lin, J. M., & Ko, H. W. (2008). Occurrence of isolates of Phytophthora colocasiae in Taiwan with homothallic behavior and its significance. Mycologia, 100(5), 727–734.

    Article  PubMed  CAS  Google Scholar 

  • Lynch, M., & Milligan, B. G. (1994). Analysis of population genetic structure with RAPD markers. Molecular Ecology, 3, 91–99.

    Article  PubMed  CAS  Google Scholar 

  • McDermott, J. M., & McDonald, B. A. (1993). Gene flow in plant pathosystems. Annual Review of Phytopathology, 31, 353–373.

    Article  Google Scholar 

  • Mahuku, G., Peters, R. D., Platt, H. W., & Daay, F. (2000). Random amplified polymorphic DNA analysis of Phytophthora infestans isolates collected in Canada during 1994–96. Plant Pathology, 49, 252–260.

    Article  CAS  Google Scholar 

  • Mantel, N. (1967). The detection of disease clustering and generalized regression approach. Cancer Research, 27, 209–220.

    PubMed  CAS  Google Scholar 

  • Manzanares-Dauleux, M. J., Divaret, I., Baron, F., & Thomas, G. (2001). Assessment of biological and molecular variability between and within field isolates of Plasmodiophora brassicae. Plant Pathology, 50, 165–173.

    Article  CAS  Google Scholar 

  • Meng, X. Q., Soemaker, R. C., & Yang, X. B. (1999). Analysis of pathogenicity and genetic variation among Phytophthora sojae isolates using RAPD. Mycological Research, 103, 173–179.

    Article  Google Scholar 

  • Mishra, A. K., Sharma, K., & Misra, R. S. (2010). Isozyme and PCR-based genotyping of epidemic Phytophthora colocasiae associated with taro leaf blight. Archives of Phytopathology and Plant Protection, 43(14), 1367–1380.

    Article  CAS  Google Scholar 

  • Misra, R. S., Sharma, K., & Mishra, A. K. (2008). Phytophthora leaf blight of Taro (Colocasia esculenta)—a review. The Asian and Australasian Journal of Plant Science and Biotechnology, 2, 55–63.

    Google Scholar 

  • Misra, R. S., Mishra, A. K., Sharma, K., Jeeva, M. L., & Hegde, V. (2011). Characterisation of Phytophthora colocasiae isolates associated with leaf blight of taro in India. Archives of Phytopathology and Plant Protection, 44(6), 581–591.

    Article  Google Scholar 

  • Misra, R. S., & Chowdhury, S. R. (1997). Phytophthora leaf blight disease in taro. Technical Bulletin Series 21, C.T.C.R.I. (ICAR), Trivandrum.

  • Nath, V. S., Sankar, M. S., Hegde, V. M., Jeeva, M. L., Misra, R. S., Veena, S. S., et al. (2012). Analysis of genetic diversity in Phytophthora colocasiae using RAPD markers. The Asian and Australasian Journal of Plant Science and Biotechnology, 6(1), 38–43.

    Google Scholar 

  • Nei, M., & Li, W. H. (1979). Mathematical modelfor studying genetic variation in terms of restriction endonucleases. Proceedings of National Academy of Science, USA, 76, 5269–5273.

    Article  CAS  Google Scholar 

  • Penner, G. A., Bush, A., Wise, R., Kim, W., Domier, L., Kasha, K., et al. (1993). Reproducibility of random amplified polymorphic DNA (RAPD) analysis among laboratories. Genome Research, 12, 341–345.

    Article  Google Scholar 

  • Raciborski, M. (1900). Parasitische Algen und Pilze, Java’s (Java’s Parasitic Algae and Fungi). I. Batavia. (Cited in Waterhouse1970a under P. colocasiae).

  • Rohlf, F. J. (1993). Contributions to morphometrics: Relative warp analysis and an example of its application to mosquito wings. In Marcus et al. (Eds.), Museo Nacional de Ciencias Naturales (pp. 131–159). Madrid

  • Saitou, N., & Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4, 406–425.

    PubMed  CAS  Google Scholar 

  • Schluter, P. M., & Harris, S. A. (2006). Analysis of multilocus fingerprinting data sets containing missing data. Molecular Ecology Notes, 6, 569–572.

    Article  Google Scholar 

  • Sharma, K., Mishra, A. K., & Misra, R. S. (2008). The genetic structure of C. esculenta: a comparison of RAPD and isozyme markers. Plant Biotechnology Reports, 2, 191–198.

    Article  Google Scholar 

  • Sullivan, M. J., Parks, E. J., Cubeta, M. A., Gallup, C. A., Melton, T. A., Moyer, J. W., et al. (2010). An assessment of the genetic diversity in a field population of Phytophthora nicotianae with a changing race structure. Plant Disease, 94(4), 455–460.

    Article  Google Scholar 

  • Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28(10), 2731–2739.

    Article  PubMed  CAS  Google Scholar 

  • Thankappan, M. (1985). Leaf blight of taro-a review. Journal of Root Crops, 11, 223–236.

    Google Scholar 

  • Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994). Clustal-W—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.

    Article  PubMed  CAS  Google Scholar 

  • Van de Peer, Y., & Dewachter, R. (1994). Treecon for Windows-A software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Computer Applications in the Biosciences, 10, 569–570.

    PubMed  Google Scholar 

  • Wang, H. B., Wang, X. M., & Zhu, Z. D. (2003). Analysis of genetic diversity of Phytophthora sojae isolates in China using RAPD. Mycosystema, 22(2), 219–227.

    CAS  Google Scholar 

  • White, T. J., Bruns, T., Lee, S., & Taylor, J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In M. A. Innes, D. H. Gefland, J. Sninsky, & T. J. White (Eds.), PCR protocols: A guide to methods and applications (pp. 315–322). SanDiego: Academic.

    Google Scholar 

  • Yeh, F. C., Boyle, T., Yang, R., Ye, Z., & Xiyan, J. M. (1997). Microsoft window-based freeware for population genetic analysis (POPGENE version 1.31). Edmonton: University of Alberta and Centre for International Forestry Research.

    Google Scholar 

Download references

Acknowledgements

The funding provided for conducting the research work by the Indian Council of Agricultural Research, New Delhi, is gratefully acknowledged. The authors are grateful to Mr. U. Suresh Kumar, DNA examiner, DNA fingerprinting wing, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram for his assistance in DNA sequencing and analysis. The authors express their deep gratitude to the anonymous reviewers for their valuable comments and helpful suggestions throughout the making of this manuscript.

Author information

Authors and Affiliations

  1. Division of Crop Protection, Central Tuber Crops Research Institute, Thiruvananthapuram, 695017, Kerala, India

    Vishnu Sukumari Nath, Muthukrishnan Senthil, Vinayaka Mahabaleswar Hegde, Muthulekshmi Lajapathy Jeeva, Syamala Swayamvaran Veena & Mithun Raj

  2. Regional Centre of CTCRI, Dumduma HBC P.O, Bhubaneswar, 751 019, Orissa, India

    Raj Shekhar Misra

Authors
  1. Vishnu Sukumari Nath
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Muthukrishnan Senthil
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Vinayaka Mahabaleswar Hegde
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Muthulekshmi Lajapathy Jeeva
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Raj Shekhar Misra
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Syamala Swayamvaran Veena
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Mithun Raj
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Vinayaka Mahabaleswar Hegde.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

(DOC 1629 kb)

ESM 2

(DOC 56 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Nath, V.S., Senthil, M., Hegde, V.M. et al. Molecular evidence supports hypervariability in Phytophthora colocasiae associated with leaf blight of taro. Eur J Plant Pathol 136, 483–494 (2013). https://doi.org/10.1007/s10658-013-0181-z

Download citation

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10658-013-0181-z

Keywords

Search

Navigation