Location: National Germplasm Resources Laboratory
Project Number: 8042-22000-302-14-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: May 1, 2016
End Date: Sep 30, 2019
1. Evaluate intercepted potato accessions from the PGQP using all available serological and nucleic acid based assays including protocols currently used in the potato quarantine program. 2. Evaluate intercepted potato accessions from the PGQP using NextGen sequencing technology to 'identify all viruses and virus strains present in these accessions and develop improved and new diagnostic procedures for use in quarantine settings, potato genebank, and the U.S. seed certification programs. 3. Develop and validate detection methods for Tobacco rattle virus and Potato mop top virus in potato quarantine and certification programs.
A collection of 24 potato accessions from PGQP are available to the research team. Seven are potato lines that exhibited virus-like symptoms but tested negative for all the viruses on the diagnostics panel. The additional 17 potato lines are intercepts that tested positive for one or more viruses, some of which are considered exotic. We will initially screen all 24 lines using PGQP and other published protocols followed by Next Generation whole transcriptome shotgun sequencing using an Illumina platform. This approach will validate current techniques (or challenge them if additional viruses are found) and will provide valuable data about the potential for routinely using Next Gen sequencing technology in quarantine settings. We expect to screen for genome variation and identify novel virus strains as well as novel or undetected viruses. Furthermore, we will perform comparative genomic sequence analysis and will develop improved or new diagnostic methods for viruses that are not detected by the current testing protocols. Additionally, we will develop and validate serological and nucleic acid based detection methods for Tobacco rattle virus and Potato mop top virus suitable for use in the USDA quarantine facility. The new tests will be transferred to the Germplasm Quarantine Program and will be included into the standard screening protocols.