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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Emerging Pests and Pathogens Research » Research » Research Project #443053

Research Project: Expanding the Utility of Direct Dormant Tuber Testing

Location: Emerging Pests and Pathogens Research

Project Number: 8062-21000-048-009-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Aug 31, 2022
End Date: Aug 30, 2024

The overall objective of this project is to provide seed certification with protocols for determining disease incidence estimates using dormant tuber testing, minimize parallel, redundant and separate workflows for different pathogens and to help with the implementation of the new procedures. Specific objectives are: 1. Determine if the current dormant tuber testing protocol that is proven effective for Potato Virus Y (PVY) can also be used as a diagnostic for important bacterial pathogens, such as C. sepedonicus (the cause of Bacterial Ring Rot). 2. Validate BRR results obtained from the new protocol with current seed certification protocols 3. Return to previously stored paper cards from 2019 and 2020 samples and based on presence of Tobacco Rattle Virus and Potato Mop Top Virus in samples, evaluate the ability to detect the list of industry communicated highest priority pathogens, vectors and organisms below: a. Spongospora subterranea the vector of PMTV and cause of Powdery Scab b. Stubby-root Nematode species that vector TRV and cause root damage to a wide host range from potato, corn, soybean and even rotational fallow crops such as mustards, and because of host diversity are difficult to control through crop rotation.

Cooperator maintains a bacterial ring rot (BRR) quarantine farm that will be essential in producing field grown tubers in Fall 2022 for sampling to paper cards. This infrastructure is critical since working with the pathogen is not a simple matter from a biological and quarantine perspective. The cooperator's established pipeline for current industry standard BRR testing methods will serve as a comparison and control to the paper tuber collections. To be effective as an early warning screen, we propose to focus upon testing field grown asymptomatic tubers and simulate an infested seed farm and a surveillance screening program that would prevent latent outbreaks from the simulated farm. On farm collection procedures from potatoes, the total nucleic acid extraction and PCR testing are established protocols. This objective will determine if the current dormant tuber sampling method (four biopsy punches per tuber) is sufficient for detection of the BRR pathogen (traditionally detected using incubation of a single core). PMTV/TRV will continue to spread unmonitored and unchecked and could broadly affect commercial potato crop quality. This objective takes advantage of already published qPCR assays. We will apply these well-developed assays to DNA/RNA extracted from samples collected in 2019 and 2020 to test for presence of vectors of these pathogens. If time permits, we will assess samples for the presence of bacterial soft rot pathogens, such as Dickeya sp. and Pectobacterium sp., which are also pathogens of concern for the industry and are poorly understood, and express foliar symptoms differentially based on climate, and potato cultivar. If this approach is successful, it provides the industry with a whole new pipeline for indexing pathogens from soils based on using the tubers as a collection “trap”.