Sampling source
The samples consisted of fruit from a 6-year-old commercial plum (Prunus domestica L.) cv. Red Lyon orchard located in the Libertador Bernardo O'Higgins region of Chile. To identify trees infected with plum pox virus, leaves were collected from four cardinal points of each tree, individually labeled and kept at a temperature between 8°C and 10°C until further processing. PPV identification in the samples was performed by RT-PCR using universal primers described in the literature (Sánchez-Navarro et al., 2005) (Table 1). Positive trees were marked in the field.
Table 1
Primers for molecular analyses
Organism | Primer name | Sequence 5´- 3´ | Fragment Size | Annealing Temperature | Reference |
Plum pox virus | PPV-9196 PPV-9506 | CAATAAAGCCATTGTTGGATC CTCTGTGTCCTCTTCTTGTG | 313pb | 50°C | Sánchez-Navarro et al., 2005 |
Gen nad5 | Nad5-F Nad5-R | GATGCTTCTTGGGGCTTCTTGTT CTCCAGTCACCAACATTGGCATAA | 181pb | 62°C | Menzel et al., 2002 |
Experimental design
The experiment was carried out during two consecutive seasons (2020–2021 and 2021–2022). During the first season (2020–2021) a total of 36 fruit with evident PPV symptoms were randomly collected at the time of the commercial harvest, from ten trees marked as infected with plum pox virus.
During the second season (2021–2022) the number of samples was increased. A total of fruit with evident PPV symptoms were collected randomly at the time of commercial harvest from twenty-eight trees marked as infected with plum pox virus. The results of from each experiment were analyzed separately, using a completely randomized design.
Treatments
The fruit samples were divided into the following treatments: Treatment 1 (T1): Freshly harvested fruit; Treatment 2 (T2): Fruit harvested and stored at 0°C for 7 days; Treatment 3 (T3): Fruit harvested and stored at 0°C for 15 days. The fruit in the T1 treatment were kept at room temperature for 18 hours before being analyzed. The fruit in the T2 and T3 treatments were packed in plastic boxes with a perforated bag with 0.3% ventilated area and arranged in a honeycomb tray. These were precooled to 4°C for 18 hours and then placed in a regular air cold chamber (atmospheric conditions) at 0°C, with an average of 75% relative humidity.
The relative accumulation of PPV-D RNA in fruit of each treatment was determined using semi-quantitative reverse transcription polymerase chain reaction (RT-PCR).
RNA extraction
Total nucleic acids (TNAs) were extracted from leaf samples using the silica capture method (Foissac et al., 2000) with minor modifications. 100 mg of tissue from each leaf sample was homogenized with 1 mL extraction buffer (4 M guanidinium thiocyanate, 0.2 M sodium acetate, 25 mM EDTA, 1 M potassium acetate, 2.5% (w/v) PVP-40, 1% 𝛃-mercaptoethanol). After centrifugation at 900 g for 4 minutes, 500 µL of the supernatant was mixed with 100 µL of 10% (w/v) N-lauroylsarcosine and incubated at 70°C for 10 minutes with occasional stirring. After another centrifugation at 12,500 g for 6 minutes, 300 µL of the supernatant was mixed with 300 µL of 6 M sodium iodide, 150 µL of 95% ethanol, and 25 µL of 1 g mL-1 silica. This mixture was incubated for 10 min at room temperature and then centrifuged at 5000g for 1 minute to precipitate the silica. The precipitate was washed twice with 500 µL of wash buffer (20 mM Tris-HCl pH 7.5, 100 mM NaCl, 1 mM EDTA, and 50% ethanol) and centrifuged at 5000g for 1 minute. Finally, 50 µL of nuclease-free water (Molecular Biology Grade Water, Corning™) was added to elute the TNAs and stored at -80°C.
TNAs were extracted from fruit peel using the same procedure as described above, except that 300 mg of peel from the symptomatic zone was taken from each fruit. In Season 1 (2020–2021) 36 fruit were evaluated, with 12 fruit per treatment. In Season 2 (2021–2022) 180 fruit were evaluated, with 60 fruit per treatment.
For each sample (leaves and fruit), the TNAs were treated with DNase (RQ1 RNase-Free DNase, Promega Corporation) to eliminate all DNA. A reaction mixture was prepared with 4 µL of TNAs, 0.5 µL of DNase, 0.5 µL of buffer DNase I 10X (Promega Corporation), and incubated at 37°C for 30 minutes. Then 0.5 µL of stop solution (Promega Corporation) was added to inactivate the DNase, and the reaction mixture was incubated at 65°C for 10 minutes.
RT-PCR and semi-quantitative PCR
cDNA was synthesized by mixing the RNA with 0.4 µL Random Primers (200ng µL-1, Invitrogen™) and 0.9 µL nuclease-free water (Molecular Biology Grade Water, Corning™), incubating at 70°C for 5 minutes, then cooling on ice for 5 minutes to prevent secondary structure formation. Then we added 4 µL M-MLV 5X reaction buffer (Promega Corp.), 1 µl dNTPs (10mM, Thermo Scientific™), 1 µL M-MLV Reverse Transcriptase (200U µL-1, Promega Corp.), and 0.5 µL RiboLock RNase Inhibitor (40U µL-1, Thermo Scientific™), following this thermal protocol: 25°C for 5 minutes, 37°C for 60 minutes, and 70°C for 15 minutes. PPV fragments were amplified using PPV-9196/PPV-9506 primers (Table 1) that amplify fragments of 313 bp. The PCR reaction mixture was prepared as follows: 4 µL 5x GoTaq® Flexi buffer (Promega Corp.), 1.6 µL MgCl2 solution (25mM, Promega Corp.), 0.4 µL dNTPs (10mM, Thermo Scientific™), 0.4 µL forward primer, 0.4 µL reverse primer (both described in Table 1), 0.13 µL GoTaq® DNA polymerase (5UµL-1, Promega Corp.), and 2 µL of template. A volume of 20 µL was completed with nuclease-free water (Molecular Biology Grade Water, Corning™). Negative controls were prepared by replacing the template volume with nuclease-free water, and positive controls were prepared using known PPV-infected samples as the template. The PCR cycling conditions were 94°C (3 min) followed by 40 cycles of denaturation at 94°C (30 s), annealing at 50°C (30 s) and extension at 72°C (30 s), with a final extension at 72°C for 7 min.
Semi-quantitative PCR were performed to analyze the fruit samples. A PCR was performed for the constitutive gene nad5 using Nad5-F/Nad5-R primers (Table 1) as an internal control, to determine the levels of PPV RNA relative to this gene. The PCR for PPV was performed using PPV-9196/PPV-9506 primers (Table 1). The same reaction mixture was used for both the PPV and nad5 PCRs. To ensure that differences in the amplified concentration were due to different levels of viral RNA among the samples, an optimization of the number of PCR cycles for each reaction was made; the optimal number of cycles was defined as the number that produced a well-defined band without saturated DNA. The PCR cycling conditions were 94°C (3 minutes) followed by 30 (for nad5) or 24 (for PPV PCR) cycles of denaturation at 94°C (30 seconds), annealing at 50°C or 62°C (30 seconds) (for PPV-9196/PPV-9506 or Nad5-F/Nad5-R respectively) and extension at 72°C (30 seconds), with a final extension at 72°C for 7 minutes. Amplified fragments were observed on 1.5% agarose gels in 0.5X TBE Buffer with 0.05 µL mL-1 SafeView, using the 100pb GeneRuler™ standard (Fermentas). A volume of 7 µL of the amplified product was loaded, and the gels were run at 90 V for 25 minutes. The gels were analyzed using a transilluminator (WiseDoc WGD-30S, Daihan Scientific Co Ltd, Korea) and the Wise CaptureII program (Daihan Scientific Co).
The results of the semi-quantitative PCR assay were analyzed using ImageJ v1.53f51 software (National Institutes of Health, USA), which can be used to quantify the density of the bands observed in each electrophoresis gel. The values obtained were normalized in relation to the density measured in the samples of the nad5 gene and then graphed in relation to the RNA accumulation in Treatment T1, which served as a control for this purpose.
Statistical analysis and graphic representation
Data from each experiment were analyzed separately using one-way analysis of variance (ANOVA). The PPV/NAD5 ratio was compared between treatments with Tukey’s Honestly Significant Difference test at P ≤ 0.05. All statistical analyses were performed using InfoStat software version 2020 (InfoStat Transfer Center, FCA, National University of Cordoba, Argentina). To graph the relative accumulation of PPV viral RNA between treatments, the average of ratio PPV/Nad5 in the control treatment (T1) was considered as 100%. Therefore, the results of T2 and T3 are represented as percentages relative to the control treatment.