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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Production and Genetic Improvement Research Unit » Research » Research Project #438669

Research Project: Virome Associated with Common Grape Virus Diseases in the Pacific Northwest and the Development of New Detection Tools

Location: Horticultural Crops Production and Genetic Improvement Research Unit

Project Number: 2072-21000-057-010-G
Project Type: Grant

Start Date: Aug 1, 2020
End Date: Oct 31, 2024

1. Characterize the virome associated with the grapevine disease complexes in fields. 2. Develop specific tools for detection and differentiation of newly described species and strains of important viruses. 3. Use the developed tools to survey Pacific Northwest states, to get a comprehensive picture of the presence of the novel virus strains. 4. Development of broad-spectrum diagnostic tools like RT-PCR to allow detection in the field.

To characterize the viral population present in the Pacific Northwest (PNW), genomes of viruses will be recovered from previously identified infected plants, exhibiting symptoms corresponding to the main grapevine disease complexes in Idaho and other PNW vineyards. RNA will be extracted from those symptomatic field samples, depleted of ribosomal RNAs, and, after generating a library of cDNAs, submitted to the High-Throughput Sequencing (HTS) technology. Viromes of infected plants will be determined by assembling whole genomes to nearly completion based on HTS reads. Bioinformatic analyses will allow the identification of viral contigs by comparison with a virus database and the characterization of new strains. Re-sequencing of newly described genomes using conventional Sanger method will be applied to specific RT-PCR amplicons, to confirm and check the sequences. Emphasis will be given to viruses responsible for Grapevine Leafroll Disease (GLD), mainly Grapevine leafroll-associated virus-3 (GLRaV-3), and rugose wood complex (RWD), including Grapevine virus A (GVA) and B (GVB), which are the most commonly found in grapevines. The newly discovered sequences will serve as the basis for designing diagnostic primer sets to be used in RT-PCR for (i) specific detection of new strains of relevant pathogenic viruses; and (ii) improvement of current detection assay to detect typical viruses. We then propose to use the newly developed assays in Idaho as well as other PNW states, to assess virus diversity and prevalence in vineyards. Ultimately, these improved detection tools will be available for commercial testing of vegetative material in nurseries, used for propagation and grafting, to prevent an inadvertent dispersal of newly described strains. This will result in improved GLRaV-3 and other common virus detection in plant certification programs.