Location: Vegetable Research
Project Number: 6080-22000-028-13-A
Project Type: Cooperative Agreement
Start Date: Sep 1, 2013
End Date: Jul 31, 2017
1. Develop a global tomato virome and virus distribution map through extensive virus survey and next generation sequencing of small RNAs. 2. Develop tomato translational genomic tools through transcriptome analysis to identify genes that are associated with virus resistance.
The cooperating scientist investigates the natural antiviral responses in plant and invertebrate hosts and the viral counter-defense strategies. Studies from his lab and others have shown that RNA silencing functions as a major natural antiviral defense in plants and invertebrates. In this defense, virus-derived small interfering RNAs (siRNAs) are produced by a host Dicer nuclease and incorporated into an Argonaute protein (AGO)-containing RNA induced silencing complex (RISC) to direct specific degradation of viral RNAs. Antiviral silencing in Arabidopsis thaliana is controlled by multiple cooperative siRNA pathways that involve two Dicer-like proteins (DCL), three AGOs and two cellular RNA-dependent RNA polymerases (RDRs), as well as amplification. As a counter-defense, plant and animal viruses encode essential virulence proteins to suppress the RNA silencing-mediated antiviral defense. Notably, several plant viral suppressors of RNA silencing are recognized by host plants as avirulence protein to trigger R-gene-mediated hyposensitive response. The cooperating scientist's lab was among the first to use viral siRNAs for virus assembly and identification of virus genomes. Specifically, in the current project, he will focus his efforts on viroid identification using a new computational algorithm involving progressive filtering of overlapping small RNAs (PFOR) from total host small RNAs sequences generated in the current global tomato virus survey. In developing tomato translational genomic tools through transcriptome analysis to identify candidate R-genes that are associated with virus resistance, he will also conduct functional gene analysis on the identified R-genes using virus-induced gene silencing (VIGS), artificial miRNA and genetic loss-of-function mutant approaches.