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United States Department of Agriculture

Agricultural Research Service

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Research Project: Understand Global Virus Distribution in Tomato and Developing Translational Genomic Tools to Accelerate Breeding for Virus Resistance

Location: Vegetable Research

2013 Annual Report

1a.Objectives (from AD-416):
1. Develop a comprehensive global tomato virus distribution map through extensive virus survey in association with major U.S. and international seed companies using next generation sequencing technologies, computational sequence analysis, to characterize and detect new viruses and viroids.

2. Develop tomato translational genomic tools for virus resistance through RNA-Seq whole transcriptome analysis upon virus infection, functional analysis of the identified candidate genes for virus resistance, single nucleotide polymorphism (SNP) identification and association analysis, and molecular marker development to accelerate tomato breeding for resistance by pyramiding multiple virus resistance for tomato spotted wilt virus (TSWV) and tomato yellow leaf curl virus (TYLCV).

3. Assess the economical impact of viral diseases and benefits of using virus resistant cultivars to tomato growers including seed and chemical costs, market structure, formal and informal relationships between seed producers, tomato growers, packers and processors.

4. Develop an outreach program to communicate the outcomes of this project to stakeholders and the general public.

1b.Approach (from AD-416):
Survey, sample collection in 2-3 countries in different continents through collaboration with seed pathologists with at least 3 samples per location. (3 x 6 x 3 x 3 = 162 samples);sRNA library preparation for a total of 162 preparations; Illumina sequencing (Cornell genomic center): libraries can be multiplexed for saving costs; Computer-based sequence analysis of small RNAs for virus identification; Confirmation of viral sequence by Sanger-sequencing; Characterization and molecular detection of new viruses and viroids; Characterization of novel viruses or viroids; Determine the seed transmissibility of new viruses; Joint development of detection technologies(antibody or primers for polymerase chain reaction).

Using microRNA or a virus-induced gene silencing system to conduct functional gene analysis on the identified putative disease resistance candidate genes; Evaluate SNP mutations between resistant and susceptible parent lines and their association with disease resistance in the segregating populations (F1, F2, BC1); Molecular marker (CAPS) development; Selection and generation of breeding materials to achieve a multiple virus resistance through gene pyramiding using marker assisted selection; Evaluate potential economical losses due to virus disease infection; Conduct feasibility study on the need in developing a new technology and new cultivar; Determine economical benefits in adaptation of the new technology.

Create a project website for the understanding of a global distribution of viruses and viroids in tomato; Educate the public on the new technology for disease diagnosis, virus detection and disease resistance; Develop a workshop to teach tomato breeders in using marker assisted selection; Develop an extension booklet such as focus on tomato.

3.Progress Report:

The research in this subordinate project relates to inhouse project Objective 1: Develop sensitive diagnostic tools for the emerging viral diseases of greenhouse tomatoes and bacterial diseases on vegetable Brassicas. Tomato (Solanum lycopersicum L.), which originated in South America, is one of the most widely grown vegetables in the world. The modern transportation system, the increasing global seed trade, and the off-shore hybrid seed production have created greater opportunities for broader geographic distribution of viruses and other pathogens in tomato and other crops. Although general virus detection methods (including serological and molecular) for a number of tomato viruses are very useful, for new or emerging viruses and viroids such detection methods may not be available. Since there are more than 100 viruses infecting tomato plants, choosing which viruses to be tested is a challenging task. For new or emerging viruses without a priori knowledge, effective management relies on timely identification and characterization of the causal agent(s) of a disease. In recent years, next-generation sequencing technologies have been applied to plant virus identification. One of the promising technologies is the deep sequencing and assembly of virus-derived small RNAs (sRNAs). In collaboration with seed companies, a new research project was initiated in 2012 to conduct a global survey of tomato viruses and viroids using deep sequencing of sRNAs. Several hundreds of samples have been collected in over 10 major tomato seed producing countries around the world, and nearly 100 sRNA libraries were generated and sequenced with the Illumina HiSeq system. A bioinformatics pipeline for efficient identification of known and novel viruses and viroids was developed based on assembly of sRNA sequences and alignment to known viruses in the GenBank, as well as, prediction through conserved domain analysis.

In benefit-cost analysis for prevention or reduction of viral diseases affecting tomato crops, two modeling components will contribute to this analysis. We will develop a bioeconomic model of tomato diseases. We will also develop a global trade model because the tomato market in the United States is heavily impacted by global market activities. Our model will be used to evaluate policy options to control tomato diseases. Developing this model requires substantial data. We are pursuing several sources by working closely with project scientists, seed companies and trade organizations to understand the plant pathology and specific concerns the industry has, which will be a key to accurate economic modeling. The project scientists visited several U.S. seed companies, which provided links to local industry groups, as well as, references to the American Seed Trade Association and the International Seed Federation. Working with these institutions will help us incorporate seed health, quality, and phytosanitary requirements into our model. Tomatoes are the second most important vegetable crop in the world after potatoes, and tomato seeds are traded globally, therefore our model must account for imports and exports around the world. Global Trade Information Services, Inc. (GTI) publishes monthly official government trade statistics for more than 80 countries. We are working to gain access to this database to incorporate this highly detailed trade information into our model to estimate key supply and demand parameters.

This is the first year progress report in the 4-year project. It is anticipated that once the project is completed, a comprehensive tomato virus and viroid inventory and a general global virus distribution map will be generated. The success of this project will lead us to determine reasonable phytosanitary requirements, to conduct proper risk assessment, and to recommend suitable disease management strategies to prevent or minimize viral infections affecting tomato productions.

Last Modified: 8/1/2014
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