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Open AccessArticle

Comprehensive Real-Time RT-PCR Assays for the Detection of Fifteen Viruses Infecting Prunus spp.

1
Department of Plant Pathology, University of California-Davis, Davis, CA 95616, USA
2
Department of Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA
3
Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA
*
Author to whom correspondence should be addressed.
These authors equally contributed to this work.
Plants 2020, 9(2), 273; https://doi.org/10.3390/plants9020273
Received: 28 January 2020 / Revised: 14 February 2020 / Accepted: 17 February 2020 / Published: 19 February 2020
(This article belongs to the Special Issue Diagnosis and Control of Plant Viral Diseases)
Viruses can cause economic losses in fruit trees, including Prunus spp., by reducing yield and marketable fruit. Given the genetic diversity of viruses, reliable diagnostic methods relying on PCR are critical in determining viral infection in fruit trees. This study evaluated the broad-range detection capacity of currently available real-time RT-PCR assays for Prunus-infecting viruses and developed new assays when current tests were inadequate or absent. Available assays for 15 different viruses were exhaustively evaluated in silico to determine their capacity to detect virus isolates deposited in GenBank. During this evaluation, several isolates deposited since the assay was designed exhibited nucleotide mismatches in relation to the existing assay’s primer sequences. In cases where updating an existing assay was impractical, we performed a redesign with the dual goals of assay compactness and comprehensive inclusion of genetic diversity. The efficiency of each developed assay was determined by a standard curve. To validate the assay designs, we tested them against a comprehensive set of 87 positive and negative Prunus samples independently analyzed by high throughput sequencing. As a result, all the real-time RT-PCR assays described herein successfully detected the different viruses and their corresponding isolates. To further validate the new and updated assays a Prunus germplasm collection was surveyed. The sensitive and reliable detection methods described here will be used for the large-scale pathogen testing required to maintain the highest quality nursery stock. View Full-Text
Keywords: Prunus spp.; viruses; genetic diversity; detection; real-time RT-PCR; high throughput sequencing Prunus spp.; viruses; genetic diversity; detection; real-time RT-PCR; high throughput sequencing
MDPI and ACS Style

Diaz-Lara, A.; Stevens, K.; Klaassen, V.; Golino, D.; Al Rwahnih, M. Comprehensive Real-Time RT-PCR Assays for the Detection of Fifteen Viruses Infecting Prunus spp.. Plants 2020, 9, 273.

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