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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

Project Number: 6659-22000-025-05
Project Type: Reimbursable

Start Date: Sep 01, 2012
End Date: Aug 31, 2016

Objective:
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.

Approach:
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.

Last Modified: 9/20/2014
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