Specific Detection of Cherry Mottle Leaf Virus Using Digoxigenin-Labeled cDNA Probes and RT-PCR

Pathogen testing and certification of Vitis and Prunus species

Strategies to screen horticultural crops for graft-transmissible agents, particularly viruses and phytoplasmas, have advanced substantially over the past decade. Tests used for Vitis and Prunus are reviewed in detail, including both biological indexing procedures and laboratory-based assays. Despite advances in laboratory molecular-based detection techniques, a strong case is presented for the continued use of slower biological tests in programs requiring high levels of confidence in detection of pathogens that must be excluded from valuable germplasm.

RT-PCR and Dot Blot hybridization methods for a universal detection of tospoviruses

Transcriptase reverse - polymerase chain reaction (RT-PCR) and dot blot hybridization with digoxigenin-labeled probes were applied for the universal detection of Tospovirus species. The virus species tested were Tomato spotted wilt virus, Tomato chlorotic spot virus, Groundnut ringspot virus, Chrysanthemum stem necrosis virus, Impatiens necrotic spot virus, Zucchini lethal chlorosis virus, Iris yellow spot virus. Primers for PCR amplification were designed to match conserved regions of the tospovirus genome. RT-PCR using distinct primer combinations was unable to simultaneously amplify all tospovirus species and consistently failed to detect ZLCV and IYSV in total RNA extracts. However, all tospovirus species were detected by RT-PCR when viral RNA was used as template. RNA-specific PCR products were used as probes for dot hybridization. This assay with a M probe (directed to the G1/G2 gene) detected at low stringency conditions all Tospovirus species, except IYSV. At low stringency conditions, the L non-radioactive probe detected the seven Tospovirus species in a single assay. This method for broad spectrum detection can be potentially employed in quarantine services for indexing in vitro germplasm.

Molecular Evidence of the Relationship Between a Virus Associated with Flat Apple Disease and Cherry rasp leaf virus as Determined by RT-PCR

Flat apple disease-associated virus (FAV) was mechanically transmitted to the propagation host Chenopodium quinoa and double-stranded (ds)RNA recovered using CFII chromatography. Purified dsRNA was used to generate cDNA clones which were sequenced and the information used to design oligonucleotide primers for reverse transcription-polymerase chain reaction (RT-PCR) and tube capture (TC)/RT-PCR analyses. Oligonucleotide primers for RT-PCR analysis and dot blot hybridization using digoxigenin-labeled cDNA clones were used for the detection of FAV and Cherry rasp leaf virus (CRLV) in C. quinoa, in leaf and bud wood tissue of apple, or both. Primers JQ3D33FF/FR amplified a virus-specific 429-bp fragment and reliably detected all isolates of FAV and CRLV tested by RT-PCR and TC/RT-PCR. Primers JQ2C1FF/FR amplified a 370-bp fragment and detected FAV and some isolates of CRLV. Comparison of amino acid residues derived from the 429-bp fragments of FAV and CRLV gave 95% identity. The RT-PCR assays provided strong evidence of a relationship between FAV and CRLV. These assays were also used to confirm virus elimination in apple plants after heat therapy. Western blot analysis of FAV revealed capsid protein subunits of approximately 22 and 24 kDa. Our data support biological and serological evidence that FAV and CRLV are isolates of the same virus. Searches of the database produced sequence matches only with RNA2 of Apple latent spherical virus (ALSV), a new member of the family Comoviridae. This suggests that both primer pairs presumably target regions on RNA2 of FAV/CRLV and that these viruses may be more closely related to ALSV than to other members of this family.

Impacts of Molecular Diagnostic Technologies on Plant Disease Management

Detection and diagnosis of plant viruses has included serological laboratory tests since the 1960s. Relatively little work was done on serological detection of plant pathogenic bacteria and fungi prior to the development of ELISA and monoclonal antibody technologies. Most applications for laboratory-based tests were directed at virus detection with relatively little emphasis on fungal and bacterial pathogens, though there was some good work done with other groups of plant pathogens. With the advent of molecular biology and the ability to compare regions of genomic DNA representing conserved sequences, the development of laboratory tests increased at an amazing rate for all groups of plant pathogens. Comparison of ITS regions of bacteria, fungi, and nematodes has proven useful for taxonomic purposes. Sequencing of conserved genes has been used to develop PCR-based detection with varying levels of specificity for viruses, fungi, and bacteria. Combinations of ELISA and PCR technologies are used to improve sensitivity of detection and to avoid problems with inhibitors or PCR often found in plants. The application of these technologies in plant pathology has greatly improved our ability to detect plant pathogens and is increasing our understanding of, their ecology and epidemiology.

A simple and reliable protocol for the detection of apple stem grooving virus by RT-PCR and in a multiplex PCR assay

Primers were identified which amplify specifically a 499 bp fragment in the coat protein coding region of apple stem grooving virus (ASGV) genome. These primers were used in various RT-polymerase chain reaction (PCR) analyses for the detection of ASGV in Chenopodium quinoa, Nicotiana occidentalis, and in species of Malus and Pyrus. Isolates of ASGV in Malus and Pyrus from locations in Canada, China, Israel, Japan, Nepal, Pakistan, South Africa, and the U.S.A. were reliably detected in leaf and bark (budwood) tissue. Storage of the tissues at -80 degrees C for more than 4 months did not affect the reliability of detection by immunocapture (IC) RT-PCR. Triton-X was not necessary for the detection of ASGV by IC/RT-PCR, and it was also possible to combine the antibody incubation and virus sap incubation into a single step without any obvious loss in sensitivity. A Tube Capture (TC) RT-PCR procedure was developed that eliminated the need for antibody binding of the virus. Phosphate buffered saline with 2% PVP was identified as the most effective sample-grinding buffer for the detection of ASGV by IC/RT-PCR and TC/RT-PCR. TC/RT-PCR facilitated the simultaneous detection (multiplex PCR) of ASGV and cherry mottle leaf virus.

Single primer pair designs that facilitate simultaneous detection and differentiation of peach mosaic virus and cherry mottle leaf virus

Peach mosaic virus (PMV) and cherry mottle leaf virus (CMLV) are viruses which are related serologically and share common Prunus hosts, but cause distinct diseases. An RT-PCR procedure using a single oligonucleotide primer pair that allows simultaneous detection and differentiation of the two viruses was developed. A sense primer with 100% complementarity to PMV and 83% complementarity to the corresponding site of the CMLV genome was combined with either of two antisense primers (one of PMV origin and the other of CMLV origin) with 3' end complementarity at variable sites. This allowed the differential amplification of PMV and CMLV specific fragments, 419 and 705 bp, respectively. When oligo (dT) was used to generate the cDNA template, differential amplification was not observed, only amplification of the homologous virus associated with the antisense primer. This indicates polyadenylation of both viruses. Incorporation of the antisense primer into cDNA at the reverse transcription step was shown to be essential for this approach. The PMV primer pair reliably detected all isolates of PMV tested by RT-PCR analysis, both in peach leaf and budwood tissue.