Location: Small Grains and Potato Germplasm Research
Project Number: 2050-21000-036-004-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: May 1, 2020
End Date: Oct 31, 2023
Objective:
1. Validate for diagnostic methods for S. subterranea and Potato Mop Top Virus and determine inoculum thresholds for disease.
2. Develop optimum sampling strategy for S. subterranea and PMTV for field soil
3. Determine the relative importance of seed and soil-borne inoculum
4. Evaluate integrated management strategies for the pathogen.
5. Creating a decision support system integrating diagnostic results, chemical applications, varietal resistance and cultural methods.
Approach:
We will use real-time PCR (TaqMan) as this the most sensitive method which can tolerate humic acid PCR inhibitors typically present in soil. Since several published assays exist for these pathogens, in addition to several in-house unpublished assays, the University of Idaho (UI)-Parma lab will compare each assay in terms of key diagnostic attributes (specificity, sensitivity, repeatability etc.) and select the two most effective assays for each pathogen. The end user of the assays, which will be front-line diagnostic labs, typically require an additional quality check or confirmation assay. Therefore, two assays for each pathogen target will be selected for full validation. The performance of the most effective assays will be confirmed by Washington State University (WSU)-Pullman. Using an iterative approach, a method based on paramagnetic beads for extracting both DNA and RNA will be developed for bulk soil samples. This will be evaluated for both Potato Mop Top Virus (PMTV) and Tobacco rattle virus (TRV) also and tomato/tobacco plant bait testing used as standard tests for comparison. This soil nucleic acid extraction development work will be conducted at WSU-Pullman and verified at UI-Parma.
In the first year of the project ARS-Aberdeen will grid sample an infested field and UI–Parma will process the samples. We will use a kriging approach to produce soil distribution field maps from this field plus two others previously sampled in 2019 by ARS-Aberdeen and UI-Parma in east and west Idaho respectively. From the resulting pathogen distribution maps, UI-Parma can determine an optimum sampling strategy to test for the pathogens (the number of subsamples required over a given area for a representative sample).
The UI-Parma lab will use a rapid nucleic acid extraction method for DNA and RNA to test the best assays from objective 1. In addition, we will collect soil samples from 100 fields in the first two years of the project using optimum sampling strategy determined in objective 1. ARS-Aberdeen will coordinate soil sampling working with industry consultants to ensure cost effective sampling.
In the first year of the project we will collaborate with a Northwest Potato Research Consortium project evaluating eight different potato varieties for resistance to powdery scab. We will take pre-plant soil samples and test tuber samples originating from this trial. This, combined with greenhouse studies at UI-Parma, will enable us to determine risk thresholds for each variety. With key varieties, WSU-Pullman will use RNAseq to study gene expression to investigate the mechanisms of resistance or tolerance in greenhouse studies, it is likely multiple resistance mechanisms are present in different varieties. Data from the RNAseq work will enable us to determine timing and development of infection and will inform the design of field trials in Idaho planned for years 2 and 3. In the field trials, we will evaluate a range of existing chemical treatments (such as Omega and Moncut) with plant health promoters, variety and other cultural practices as informed in year 1 of the project.
