Quantitative PCR for detection and quantification of Phytophthora cactorum in the cultivation of strawberry

E. Verdecchia, A. Ceustermans, D. Baets, J. Ferreira, P. Bonants, P. Melis, W. Van Hemelrijck, D. Bylemans, H. Rediers*, B. Lievens*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

4 Citations (Scopus)

Abstract

In this study, we report on the development of two quantitative PCR assays for the detection and quantification of the soilborne plant pathogen Phytophthora cactorum causing root and crown rot of strawberry. The assays rely on the use of SYBR Green I chemistry and use the internal transcribed spacer region 2 (ITS2) and the Ras-related protein gene Ypt1 as detection markers. An extensive list of Phytophthora isolates was included in the study to evaluate assay specificity. High specificity was obtained when Ypt1 was used as detection marker, with cross-reactions only occurring with the closest relatives of P. cactorum, including P. hedraiandra, P. idaei and P. pseudotsugae. In contrast, the ITS-based assay was less specific, resulting in a larger number of cross-reactions (eight species when tested at 10 pg DNA). In sensitivity tests, P. cactorum DNA was detected down to 10 fg using the ITS-based assay, while the limit of detection (LOD) for the Ypt1-based assay was 1 pg DNA, irrespective of the presence of background DNA from strawberry or soil. When strawberry, growth substrate and soil samples were spiked with a 10-fold dilution series of P. cactorum zoospores, the LOD for the ITS-based assay was 10 zoospores g−1 plant material, growth substrate or soil. The limit of quantification (LOQ) of the assay was 109 zoospores g−1 plant material, 15.8 zoospores g−1 growth substrate, and 106 zoospores g−1 soil. For the Ypt1-based assay, the LOD and LOQ values were 1000 and 5910 zoospores g−1 plant material, 1000 and 1818 zoospores g−1 growth substrate, and 1000 and 3823 zoospores g−1 soil, respectively. In terms of detection, analysis of field samples suggested that the Ypt1-based assay almost performed equally well compared to the ITS-based assay, especially for plant and growth substrate samples. Further, our results showed that both qPCR assays outperformed classical plating, illustrating their power to be used for diagnostic purposes. Interestingly, P. cactorum was also detected in soil and growth substrate samples from areas with no symptoms, suggesting that the assays can also aid in early pathogen detection before the disease manifests.

Original languageEnglish
Pages (from-to)867-882
JournalEuropean Journal of Plant Pathology
Volume160
Issue number4
Early online date27 Apr 2021
DOIs
Publication statusPublished - 2021

Keywords

  • Detection
  • Diagnostics
  • Phytophthora
  • qPCR
  • Quantification
  • Strawberry

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