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United States Department of Agriculture

Agricultural Research Service

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Research Project: A Systems Approach to Managing Microbial Threats to Greenhouse Tomatoes

Location: Vegetable Research

2011 Annual Report


1a.Objectives (from AD-416)
1. To improve plant disease diagnostic technologies for accurate, rapid and cost-effective identification of causal agents in tomato plants at the earliest possible time relative to manifestation of disease symptoms.

2. To elucidate factors affecting the epidemiology of the viroid disease, to evaluate the potential synergistic interaction with Pepino mosaic virus on tomato and to identify vulnerable areas (e.g., seed or alternative host) that could potentially provide innovative and effective disease management opportunities.

3. To develop and evaluate innovative technologies including the use of disinfectants, seed treatment or laser knifes to determine their effectiveness in preventing the highly contagious pathogens (i.e., viroids, PepMV, CMM, and botrytis) from spreading.


1b.Approach (from AD-416)
1. Through gene mining in the GenBank databases, computer-assisted alignment of a group of viroid/virus sequences will be used to identify the conserved genomic regions that can be used for primer and probe design in the development of species-specific or genus-specific Real-time RT-PCR systems. Once the real-time RT-PCR detection system is developed and validated, it will then be used to conduct individual or a panel virus/viroid test to monitor the presence and frequency of certain virus or viroid on tomatoes. This surveillance system will serve to identify the critical control points for these pathogens.

2. To determine the etiology of the emerging tomato stunting chlorosis disorder, pathogenicity tests will be conducted. Presence of a specific viroid or virus will be evaluated through symptom expression on the indicator plants and by confirmation tests using above developed real-time RT-PCR techniques and nucleotide sequencing. To investigate the synergic effect between TCDVd and PepMV, one set of tomato plants will be inoculated with PepMV or TCDVd and another set with a mixed culture of both pathogens. The impact of pathogen infection on plant growth and fruit production will be measured over time. The factors affecting the efficiency of mechanical transmission of TCDVd will be conducted in production greenhouse, in collaboration with cooperating growers, to periodically monitor the occurrence and distribution patterns of TCDVd throughout the tomato growing season.

3. The efficacy of the selected disinfectants will be screened initially through mechanical inoculation of treated TCDVd or PepMV tissue extract on indicator plants and tomato. Any promising disinfectant will be evaluated by simulating crop work practices such as de-leafing, plant training and harvesting using a disinfected cutting knife or pruning shears. Similar efficacy test will be carried out with the newly developed no-contact cutting device(s) (laser and/or water jet knife) that will be developed by one of the project collaborators.

Specialty Crops Research Initiative.


3.Progress Report

This research relates to inhouse objective 1: Elucidate the etiology and epidemiology of Pepino mosaic virus on tomato and Pseudomonas syringae pv. maculicola on vegetable Brassicas to identify vulnerable areas (e.g., seed or alternative host) that provide biologically-based control opportunities.

This project was initiated in early 2011 and a postdoc was only hired for approximately two months (June-July, 2011). Through collaboration with a major greenhouse grower in Mexico, we have identified two emerging diseases infecting greenhouse tomato in Mexico. Through our research, Pepino mosaic virus (PepMV) was first reported in Mexico. Another bacterial disease (Candidatus Liberibacter solanocearum) was identified in a mixed-infection of PepMV and the previously identified Mexican papita viroid. The mixed infection of several pathogens resulted in greater damage to plant health and also complicated decision-making in disease management. To achieve accurate total pathogen identification in field samples, a novel technology with next generation sequencing of small ribonucleic acid (RNA) in plants was used to evaluate viruses in four tomato samples collected in the U.S. and Mexico. This technology was shown to be capable of differentiating pathogen genotypes and for identifying viroids. The virus genome sequences generated by deep sequencing of small interfering RNAs were subsequently confirmed with the conventional nucleotide sequencing technology.


Last Modified: 10/20/2014
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