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ARS Home » Southeast Area » Charleston, South Carolina » Vegetable Research » Research » Research Project #423023

Research Project: Characterization, Etiology, and Disease Management for Vegetable Crops

Location: Vegetable Research

Project Number: 6080-22000-025-000-D
Project Type: In-House Appropriated

Start Date: May 1, 2012
End Date: Apr 30, 2017

1. Develop sensitive diagnostic tools for the emerging viral diseases of greenhouse tomatoes and bacterial diseases on vegetable brassicas. 1.A. Develop loop-mediated isothermal amplification (LAMP) and siRNA deep sequencing techniques for viral disease diagnosis on tomatoes. 1.B. Develop real-time polymerase chain reaction (PCR) techniques for species-specific detection of phytopathogenic bacteria on vegetable Brassica. 2. Characterize the etiology of emerging diseases of vegetables and identify critical factors affecting the epidemiology of those diseases. 2.A. Determine the seed-transmission potential of tomato viroids and characterize the synergistic interactions between tomato viroids and Pepino mosaic virus on tomato. 2.B. Determine environmental factors influencing bacterial leaf blight on vegetable Brassica. 3. Characterize and develop host resistance to effectively manage viral and Fusarium wilt diseases on watermelon. 3.A. Determine inheritance of, and develop molecular markers linked to virus resistance in watermelon and bottle gourd. 3.B. Identify new sources of resistance to Fusarium wilt race 2 in watermelon and determine inheritance of identified resistance.

Relative to Objective 1, several molecular detection techniques, including real-time RT-PCR, loop-mediated isothermal amplification (LAMP) and small RNA deep sequencing, will be used to study viral diseases of tomato, and develop strain-specific detection assays for Pepino mosaic virus (PepMV), pospiviroids, and the bacterium Liberibacter solanacearum. A combination of targeted and whole genome sequencing of select Pseudomonas syringae and P. cannabina strains will be conducted and analyzed using appropriate bioinformatics tools. Species-specific primer sets will be developed to detect P. cannabina pv. Alisalensis. Primer sensitivity will also be tested on related and nonrelated bacterial isolates from various sources. For Objective 2, the potential of transmitting tomato viroids on tomato seed and any synergistic interactions between the viroids and PepMV on tomato will be analyzed using newly developed, sensitive detection methods. If seed transmissibility of viroids on tomato is confirmed, a reliable seed health assay will be developed to select clean plants for the generation of viroid-free seed. The influence of environmental factors (e.g., humidity and temperature) on bacterial leaf blight of leafy green Brassicas will be studied under controlled conditions. Seed transmissibility, alternate hosts, and survivability of the bacterial pathogens will also be examined. Under Objective 3, molecular markers linked to resistance to viruses, including Papaya ringspot virus (PRSV) and Watermelon mosaic virus (WMV) in watermelon and its rootstock (bottle gourd), will be identified by analyzing candidate disease resistance genes (elongation factor sequences) associated with virus resistance in segregating populations (F2, F3, and BC1). PCR-based genetic analysis will also be applied to identify DNA markers linked to single or multiple virus (PRSV, WMV and ZYMV) resistance. Aided by marker-assisted selection (MAS), resistant lines of watermelon and bottle gourd will be developed. Inheritance of new sources of resistance to Fusarium wilt (FW) race 2 in watermelon will be elucidated using F2, F3, and recombinant inbred populations. Marker discovery will be conducted using Illumina Next-Generation sequencing, and markers for FW resistance will be mapped and tested for use in MAS.