Location: National Germplasm Resources Laboratory
Project Number: 8042-22000-324-002-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Jul 15, 2024
End Date: Dec 31, 2025
Objective:
Collect field samples from grower fields and preliminarily screen symptomatic and atypical PTNRD samples using currently deployed diagnostic tool. Sequence samples using high throughput sequencing (HTS) for a comprehensive overview of the phytosanitary status of potato samples.
Approach:
1. Potato tuber samples will be collected from the San Luis Valley Research Center (SLVRC), Colorado, and visually assessed for external and internal necrosis and further selected for additional characterization. Tubers with virus-like necrotic symptoms will be tested for PVY, PMTV, and TRV using ELISA, IC-RT-PCR, and RT-qPCR. A total of at least 60 samples with tuber necrosis symptoms and positive to one or more of the necrotic-inducing viruses or negative to all tested viruses will be selected for library preparation and high throughput sequencing (HTS). Samples with novel viruses will also be completely sequenced, including terminal sequence ends.
2. Virus sequence data will be collated and used for a comparative genomic analysis for each of PVY, PMTV, and TRV. Recombinant analysis will be performed to identify potential recombinants or exotic strains. Sequences from the public database will also be included for comparison purposes. The sequence data will be leveraged for evaluating in silico currently used primers and probes for PCR detection assays of PVY, PMTV and TRV.
3. A field trial will be carried out at SLVRC in a field with PMTV infection history. The potato cultivar Shepody will be used due to its susceptibility to Spongospora subterranea f. sp. subterranea (Sss) and PMTV. A randomized complete block design will be used with three blocks and six in-furrow treatments, including Root Shield Plus (Trichoderma harzianum Rifai strain T-22), Tenet WP (Trichoderma gamsii and Trichoderma asperellum), SoilGard 12G (Gliocladium virens strain GL-21), Double Nickel (Bacillus amyloliquefaciens strain D747), Non-treated control, and Synthetic fungicide (Quadris Opti). Each plot will consist of four rows with 30 plants per row. The treatments will be evaluated for disease severity, pathogen loads, and yield. Soil will be sampled from each plot (two central rows) twice, before planting and after vine-kill. Soil samples will be quantified for Sss using a qPCR assay. Root galls will be assessed before vine-kill on 6 plants per plot. Also, tubers will be scored and tested (50 tubers per plot, a total 900 tubers) for powdery scab after harvest, PMTV using ELISA and tuber necrosis score simultaneously. The yield from field plots will be determined from harvesting two central rows per plot.
