Quantitative Real-Time PCR Assay for the Detection of Pectobacterium parmentieri, a Causal Agent of Potato Soft Rot
Abstract
:1. Introduction
2. Results
2.1. Phylogenetic Analysis
2.2. Search for Species-Specific Primers
2.3. Primary Analysis by Conventional PCR
2.4. qPCR Analysis on an Extended Set of Strains
2.5. Sensitivity
2.6. Assays of Plant Samples
3. Discussion
4. Materials and Methods
4.1. Phylogenetic Analysis
4.2. Search for Species-Specific Sequences and Primer Design
4.3. Bacterial Strains, Media and Culture Conditions
4.4. Genomic DNA Isolation
4.5. PCR Conditions
4.6. Plasmid Construction for Sensitivity Assay
4.7. qPCR
4.8. Testing the Detection System on Artificially Infected Tubers
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Conflicts of Interest
References
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Type | Sequence |
---|---|
F primer | TAT CGC TGG CTC AGG CAA TT |
R primer | TAC GCT GCG CAT ACT TGG AA |
Probe | (6-FAM)-CGCCCGGG-(dT-BHQ-1)-GCCCAAGATATGACTT-(Pi) |
Amplicon | TATCGCTGGCTCAGGCAATTGAAAAAAACGATGAATCAGAAGTCAAAAAACTTTCAGCTCATACGGACCTAAATCGCCCGGGTGCCCAAGATATGACTTTACTATTCTTCGCGATGCAAAATAGTTATGACAAACAAGCCAAACATTTGTCGATAGTCTCATATTTGGTTAGTGCCGGAGCAAGTCCATTACAGAAAGTTCCAAGTATGCGCAGCGTA |
№ | Plasmid | DNA | ||||
---|---|---|---|---|---|---|
Copies Per Reaction | Cq | SD | Copies Per Reaction | Cq | SD | |
1 | 1.4 × 1010 | 8.01 | 0.12 | 1.68 × 107 | 16.29 | 0.37 |
2 | 1.48 × 109 | 11.83 | 0.21 | 1.68 × 106 | 20.48 | 0.36 |
3 | 1.48 × 108 | 15.27 | 0.15 | 1.68 × 105 | 24.62 | 0.01 |
4 | 1.48 × 107 | 19.04 | 0.71 | 1.68 × 104 | 27.20 | 2.90 |
5 | 1.48 × 106 | 22.90 | 0.57 | 1.68 × 103 | 29.92 | 1.25 |
6 | 1.48 × 105 | 25.67 | 1.72 | 168 | 34.60 | 1.80 |
7 | 1.48 × 104 | 29.37 | 3.07 | 16.8 | 36.20 | 0.37 |
8 | 1.48 × 103 | 32.59 | 0.70 | 1.68 | - | - |
9 | 148 | 33.95 | 1.72 | 0.16 | - | - |
Incubation, h | Cq | SD | Copies/mL |
---|---|---|---|
Control (120 h) | 38.32 | 0.00 | 6.92 |
72 | 31.03 | 0.67 | 1.06 × 103 |
96 | 27.38 | 0.67 | 1.3 × 104 |
120 | 20.76 | 1.05 | 1.3 × 106 |
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Lukianova, A.A.; Evseev, P.V.; Stakheev, A.A.; Kotova, I.B.; Zavriev, S.K.; Ignatov, A.N.; Miroshnikov, K.A. Quantitative Real-Time PCR Assay for the Detection of Pectobacterium parmentieri, a Causal Agent of Potato Soft Rot. Plants 2021, 10, 1880. https://doi.org/10.3390/plants10091880
Lukianova AA, Evseev PV, Stakheev AA, Kotova IB, Zavriev SK, Ignatov AN, Miroshnikov KA. Quantitative Real-Time PCR Assay for the Detection of Pectobacterium parmentieri, a Causal Agent of Potato Soft Rot. Plants. 2021; 10(9):1880. https://doi.org/10.3390/plants10091880
Chicago/Turabian StyleLukianova, Anna A., Peter V. Evseev, Alexander A. Stakheev, Irina B. Kotova, Sergey K. Zavriev, Alexander N. Ignatov, and Konstantin A. Miroshnikov. 2021. "Quantitative Real-Time PCR Assay for the Detection of Pectobacterium parmentieri, a Causal Agent of Potato Soft Rot" Plants 10, no. 9: 1880. https://doi.org/10.3390/plants10091880