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A real-time TaqMan PCR assay to discriminate between pathotype 1 (D1) and non-pathotype 1 (D1) isolates of Synchytrium endobioticum

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Abstract

Synchytrium endobioticum is a severe pathogen of potato causing wart disease. For this obligate fungus many pathotypes exist, which are pathogenic or non-pathogenic to different cultivars of potato. To determine to which pathotype an isolate belongs, two biological assays are used on a set of different potato cultivars: the Spieckermann and the Glynne-Lemmerzahl test. A differential set of cultivars has been recommended by EPPO (European Plant Protection Organization) for these tests. Drawbacks of these tests are that it can take up to several months to score the interaction and results are difficult to score and also often not conclusive. Therefore, possibilities were investigated to look for molecular markers for pathotype specificity. An extremely low level of diversity was observed in a set of eight isolates using CRoPS™ (Complexity Reduction of Polymorphic Sequences) technology. Only 191 sequence polymorphisms were found in 14,660 contigs representing approximately 195 Kb of sequence for eight isolates. Nine sequence polymorphisms could be related to pathotype specificity. Two of these polymorphisms were transferred into a real-time TaqMan PCR assay to discriminate between pathotype specific groups. Validation of the assays was performed using multiple isolates from different countries for which the bioassay had been performed.

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Acknowledgments

This study was supported by the Dutch ministry of Economic Affairs through the Euphresco network. The authors thank colleagues of the dutch Plant Protection Service, Wageningen for valuable discussions and supplying winter spores of Synchytrium endobioticum, compost and infected potato plants. The AFLP patterns and the CRoPS analysis have been performed at Keygene, Wageningen (Hanneke Witsenboer). Collaboration with Ineke van Holst- van den Beld and Margriet Boerma (HLB, Wijster) and with Patricia van Rijswick and Bart van de Vossenberg (NVWA, Wageningen) is highly appreciated. The authors also want to thank the suppliers of wart material (HLB The Netherlands, BBA (now JKI Germany), CSL (now Fera UK) and SASA UK), and/or DNA samples needed for this research as indicated in Tables 1 and 2.

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Authors and Affiliations

  1. Plant Research International BV, P.O. Box 16, 6700 AA, Wageningen, The Netherlands

    Peter J. M. Bonants, Marga P. E. van Gent-Pelzer & Theo A. J. van der Lee

  2. National Plant Protection Organization (NPPO-NL), P.O. Box 9102, 6700 HC, Wageningen, The Netherlands

    Gerard C. M. van Leeuwen

Authors
  1. Peter J. M. Bonants
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  2. Marga P. E. van Gent-Pelzer
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  3. Gerard C. M. van Leeuwen
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  4. Theo A. J. van der Lee
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Correspondence to Peter J. M. Bonants.

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Bonants, P.J.M., van Gent-Pelzer, M.P.E., van Leeuwen, G.C.M. et al. A real-time TaqMan PCR assay to discriminate between pathotype 1 (D1) and non-pathotype 1 (D1) isolates of Synchytrium endobioticum . Eur J Plant Pathol 143, 495–506 (2015). https://doi.org/10.1007/s10658-015-0702-z

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  • DOI: https://doi.org/10.1007/s10658-015-0702-z

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