Development and Application of a Real-Time Reverse-Transcription PCR and Droplet Digital PCR Assays for the Direct Detection of Potato mop top virus in Soil

Potato mop top virus (PMTV) is a continuing threat to potato production throughout the world. It has the potential to persist in the soil for long periods in the sporosori of its vector Spongospora subterranea f. sp. subterranea, which is as an important source for PMTV infection and dissemination. In this study, we used real-time quantitative reverse-transcription PCR (qRT-PCR) and reverse-transcription droplet digital PCR (RT-ddPCR) assays of the total RNA extracted directly from the soil to develop a simple, fast, and sensitive method to detect PMTV in soil samples using a specific primer with high efficiency despite a minimal amount of viral RNA. The designed primers are resilient in the presence of various PCR inhibitors in the soil when RNA is extracted. Both assays detected PMTV in all soil types used and supported the detection of <10 PMTV copies µl^-1 in the RNA sample. With qRT-PCR, detection was linear, with amplification efficiencies ranging from 93.3 to 105.3% for silt loam, loamy sand, sand, and sandy loam in various experiments with R² > 0.99. Furthermore, the RT-ddPCR assay also demonstrated a high degree of linearity (R² > 0.99 and P < 0.0001) with the RNA extracted from the soil samples representing different textures and physiochemical characteristics that were artificially spiked with infested S. subterranea f. sp. subterranea sporosori. Additionally, both assays successfully detected PMTV in different types of naturally infested soil with PMTV carrying S. subterranea f. sp. subterranea sporosori levels ranging from 6.2 × 10² g^-1 to 1.2 × 10⁶ g^-1 in soils with pH ranging from 4.9 to 7.5 and organic matter ranging from 0.9 to 5.1%, demonstrating the potential to detect PMTV in a wide variety of soils. To our knowledge, this is the first report of the development of real-time PCR and ddPCR methods for the direct detection of a soilborne virus in soil.

Preserved Microarrays for Simultaneous Detection and Identification of Six Fungal Potato Pathogens with the Use of Real-Time PCR in Matrix Format

Fungal diseases of plants are of great economic importance causing 70⁻80% of crop losses associated with microbial plant pathogens. Advanced on-site disease diagnostics is very important to maximize crop productivity. In this study, diagnostic systems have been developed for simultaneous detection and identification of six fungal pathogens using 48-well microarrays (micromatrices) for qPCR. All oligonucleotide sets were tested for their specificity using 59 strains of target and non-target species. Detection limit of the developed test systems varied from 0.6 to 43.5 pg of DNA depending on target species with reproducibility within 0.3-0.7% (standard deviation). Diagnostic efficiency of test systems with stabilized and freeze-dried PCR master-mixes did not significantly differ from that of freshly prepared microarrays, though detection limit increased. Validation of test systems on 30 field samples of potato plants showed perfect correspondence with the results of morphological identification of pathogens. Due to the simplicity of the analysis and the automated data interpretation, the developed microarrays have good potential for on-site use by technician-level personnel, as well as for high-throughput monitoring of fungal potato pathogens.

Matrix approach to the simultaneous detection of multiple potato pathogens by real-time PCR

AIM

Create a method for highly sensitive, selective, rapid and easy-to-use detection and identification of economically significant potato pathogens, including viruses, bacteria and oomycetes, be it single pathogen, or a range of various pathogens occurring simultaneously.

METHODS AND RESULTS

Test-systems for real-time PCR, operating in the unified amplification regime, have been developed for Phytophthora infestans, Pectobacterium atrosepticum, Dickeya dianthicola, Dickeya solani, Ralstonia solanacearum, Pectobacterium carotovorum, Clavibacter michiganensis subsp. sepedonicus, potato viruses Y (ordinary and necrotic forms as well as indiscriminative test system, detecting all forms), A, X, S, M, potato leaf roll virus, potato mop top virus and potato spindle tuber viroid. The test-systems (including polymerase and revertase) were immobilized and lyophilized in miniature microreactors (1·2 μl) on silicon DNA/RNA microarrays (micromatrices) to be used with a mobile AriaDNA^® amplifier.

CONCLUSIONS

Preloaded 30-reaction micromatrices having shelf life of 3 and 6 months (for RNA- and DNA-based pathogens, respectively) at room temperature with no special conditions were successfully tested on both reference and field samples in comparison with traditional ELISA and microbiological methods, showing perfect performance and sensitivity (1 pg).

SIGNIFICANCE AND IMPACT OF THE STUDY

The accurate, rapid and user-friendly diagnostic system in a micromatrix format may significantly contribute to pathogen screening and phytopathological studies.

Sensitivity of Potato Cultivars to Potato mop-top virus-Induced Tuber Necrosis

Potato (Solanum tuberosum) cultivars representing four market classes were assessed for sensitivity to Potato mop-top virus (PMTV)-induced tuber necrosis in three separate trials in a field in North Dakota known to be infested with PMTV. Reverse-transcription polymerase chain reaction confirmed the presence of PMTV in randomly selected samples. Results of tuber necrosis assessments conducted during storage demonstrated that sensitivity to PMTV-induced tuber necrosis among cultivars follows a continuum of tolerant to sensitive. As a group, the russet-skinned cultivars had a lower incidence of tuber necrosis than red-, yellow-, and white-skinned cultivars. The incidence and severity of PMTV-induced tuber necrosis in trial 1 were significantly correlated with those parameters in trial 2 across years. Significant correlations also existed between the incidence of powdery scab on tubers and the incidence of PMTV-induced tuber necrosis in trial 1 across years. A significant correlation was also found between root gall numbers and powdery scab incidence and severity on tubers as well as PMTV-induced tuber necrosis incidence in trial 2. The results of this study provide growers with disease management options by avoiding cultivars highly sensitive to PMTV-induced tuber necrosis development and potentially replacing them with tolerant cultivars in the same market class. It is apparent from these studies that field assessments can be used for the development of PMTV-resistant germplasm for use in future breeding strategies.