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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Research » Research » Research Project #439054

Research Project: Dissecting the Cause of Recurrent Blueberry Shock Disease

Location: Horticultural Crops Research

Project Number: 2072-21220-003-033-G
Project Type: Grant

Start Date: Sep 1, 2020
End Date: Oct 31, 2021

Objective:
1. Investigate whether there is a new strain of blueberry shock virus (BlShV) associated with the recurring symptoms and/or identify other agents that may be associated with the phenotype. 2. Develop diagnostic tests to discriminate the recurring from the type strain of BlShV or to detect other agents associated with symptoms. 3. Determine whether the new luteovirus present in plants with recurring shock symptoms is widespread and consistently associated with symptoms when in mixed infections with BlShV.

Approach:
Objective 1 and 2: BlShV sequences generated by next generation sequencing (NGS) from symptomatic samples will be compared to the known sequence of BlShV (non-recurring shock type) to determine whether plants from recurring phenotype harbor a different strain. If the recurring phenotype is associated with a new strain of BlShV, development of an RT-PCR test based on the population structure (diversity) of the virus as identified through NGS will be initiated. Due to the project not being fully funded, only in-silico analysis of the diagnostics will occur, not wet-bench validation. The presence of the type or emerging strains based on amplicon size will be detected; e.g. type strain will amplify a 300 versus 400 base fragment for the emerging counterpart. Alternatively, and depending on sequence variation, Taqman® qRT-PCR assays can be designed with primers common to both strains but using two probes; each specific to one strain of the virus and carries with it a unique fluorophore. Using funds from other grants, RT-PCR tests for the new luteovirus will also be developed. Objective 3: The presence of novel luteovirus and its co-infection with BlShV from additional recurring phenotype samples will be determined using NGS data. To establish a robust association of disease agents, non-symptomatic samples collected from recurring phenotype blueberry orchards for BlShV (ordinary and recurring strain) and novel luteovirus will be further tested.