University of Oulu

Feau, N. , Ojeda, D. I., Beauseigle, S. , Bilodeau, G. J., Brar, A. , Cervantes‐Arango, S. , Dale, A. L., Dhillon, B. , Hammett, C. , Herath, P. , Shamoun, S. F., Tsui, C. K., Tanguay, P. and Hamelin, R. C. (2019), Improved detection and identification of the sudden oak death pathogen Phytophthora ramorum and the Port Orford cedar root pathogen Phytophthora lateralis. Plant Pathol, 68: 878-888. doi:10.1111/ppa.13015

Improved detection and identification of the sudden oak death pathogen Phytophthora ramorum and the Port Orford cedar root pathogen Phytophthora lateralis

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Author: Feau, N.1; Ojeda, D. I.1,2; Beauseigle, S.1,3;
Organizations: 1Faculty of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
2Department of Forest Genetics and Biodiversity, Norwegian Institute of Bioeconomy Research (NIBIO), Høgskoleveien 8, 1433, Ås, Norway
3Biopterre, 1642 rue de la Ferme, Sainte‐Anne‐de‐la‐Pocatière, QC, G0R 1Z0, Canada
4Ottawa Plant Laboratory, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON, K2H 8P9, Canada
5Department of Ecology and Genetics, University of Oulu, Oulu, Finland
6GC‐New Construction Materials, FPInnovations, Vancouver, BC, Canada
7Department of Plant Pathology, University of Arkansas at Fayetteville, Fayetteville, AR, USA
8Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada
9Division of Pathology Sciences, Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar
10Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 rue du PEPS, Quebec, QC, G1V 4C7, Canada
11Foresterie et géomatique, Institut de Biologie Intégrative des Systèmes, Laval University, Quebec city, Quebec, Canada
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 1.3 MB)
Persistent link: http://urn.fi/urn:nbn:fi-fe2019092730120
Language: English
Published: , 2019
Publish Date: 2019-09-27
Description:

Abstract

Early detection provides the best way to prevent introduction and establishment of alien plant pathogens. Amplification of DNA by PCR has revolutionized the detection and monitoring of plant pathogens. Most of those assays rely on the amplification of a fraction of the genome of the targeted species. With the availability of whole genomes for a growing number of fungi and oomycetes it is becoming possible to compare genomes and discover regions that are unique to a target organism. This study has applied this pipeline to develop a set of hierarchical TaqMan real‐time PCR detection assays targeting DNA of all four Phytophthora ramorum lineages, and a closely related species, P. lateralis. Nine assays were generated: three targeting DNA of all P. ramorum lineages, one for each lineage of P. ramorum, one for P. lateralis and one targeting DNA of P. ramorum and P. lateralis. These assays were very accurate and sensitive, ranging from 98.7% to 100% detection accuracy of 2–10 gene copies of the targeted taxa from pure cultures or inoculated tissues. This level of sensitivity is within the lowest theoretical limit of detection of DNA. It is expected that these assays will be useful because of their high level of specificity and the ease with which they can be multiplexed because of the inherent flexibility in primer and probe design afforded by their lack of conservation in non‐target species.

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Volume: 68
Issue: 5
Pages: 878 - 888
DOI: 10.1111/ppa.13015
OADOI: https://oadoi.org/10.1111/ppa.13015
Type of Publication: A1 Journal article – refereed
Field of Science: 1183 Plant biology, microbiology, virology
Subjects:
NA1
NA2
Funding: This work was supported by Genome Canada's Large‐Scale Applied Research Program (LSARP projects #2112 and 10106) and Genome Canada's Genomic Application Partnership Program (GAPP 6102) with additional funding from Genome B.C., Genome Quebec, Canadian Food Inspection Agency, Natural Resources Canada and FPInnovations. The authors declare no conflict of interest.
Copyright information: © 2019 The Authors. Plant Pathology published by John Wiley & Sons Ltd on behalf of British Society for Plant Pathology. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
  https://creativecommons.org/licenses/by/4.0/