Improved RNA extraction and one-tube RT-PCR assay for simultaneous detection of control plant RNA plus several viruses in plant extracts

A multiplex polymerase chain reaction method for reliable, sensitive and simultaneous detection of multiple viruses in citrus trees

A multiplex polymerase chain reaction (mPCR) assay was developed to detect six RNA and one DNA citrus virus: Citrus leaf rugose virus (CLRV), Citrus psorosis virus (CPsV), Citrus tatter leaf virus (CTLV), Citrus tristeza virus (CTV), Citrus variegation virus (CVV), Citrus yellow mosaic virus (CYMV), and Indian citrus ringspot virus (ICRSV) from citrus plants. These seven viruses are classified in six different virus genera. Degenerate primers were designed based on the respective virus isolate sequence data available from the GenBank and were used for reliable detection of the different viruses by simplex- and mPCR. The sensitive and simultaneous detection of RNA and DNA viruses using the mPCR decreases the risk of contamination, saves time and reduces the cost as compared to other conventional methods for citrus virus detection. Seven different fragments (245-942 bp) specific to the viruses were simultaneously amplified using mPCR and were identified on the basis of their molecular sizes. The consistent results of the mPCR were compared with simplex PCR for detection of each virus pathogen. The mPCR results were confirmed with sequencing analysis. The mPCR provides a useful rapid method for detecting multiple viruses in citrus plants that will aid in the production of virus-free citrus plants for certification programs.

Field Evaluation of Tomato Hybrids Engineered with Tomato spotted wilt virus Sequences for Virus Resistance, Agronomic Performance, and Pollen-Mediated Transgene Flow

ABSTRACT Tomato hybrids obtained from homozygous progeny of line 30-4, engineered for Tomato spotted wilt virus (TSWV) resistance, were tested under field conditions in two locations with their corresponding nontransgenic hybrids. No transgenic hybrid became infected, but 33 to 50% of plants of each nontransgenic hybrid became infected with a severe reduction of marketable fruit production. The transgenic hybrids conformed to the standard agronomic characteristics of the corresponding nontransgenic ones. Fruit were collected from the nontransgenic plots included in the experimental field and from border rows, and seed were used to estimate the flow of the transgene via pollen. No transgene flow was detected in the protected crops; however, in the open field experiment, 0.32% of tomato seedlings were found to contain the genetic modification. Immunity to TSWV infection in 30-4 hybrids was confirmed in laboratory conditions using mechanical inoculation and grafting. Thrips inoculation in leaf discs of line 30-4 demonstrated that TSWV replication was inhibited at the primary infection site but not in leaf discs of a commercial hybrid containing the naturally occurring resistance gene Sw-5. Due to the high economic value of tomato crops worldwide and the importance of TSWV, the engineered resistance described here is of practical value for breeding into cultivars of commercial interest, because it could be combined with naturally occurring resistance, thus greatly reducing the ability of the virus to develop resistance-breaking strains.

A method for isolating functional RNA from callus of Dendrobium candidum contented rich polysaccharides

Isolation of high-quality RNA from Dendrobium candidum is particularly difficult. D. candidum contains considerable amounts of polysaccharides that coprecipitate with RNA, which render RNA unsuitable for either cDNA synthesis and/or PCR amplification. In this paper, a rapid and efficient method was described for functional RNA isolation from the callus of D. candidum. The procedure included: (i) an extraction with phenol and isopropyl alcohol, to remove proteins and polyphenols; (ii) purifications by lithium chloride, pre-cooled (-20 degrees C) ethanol successively to remove polysaccharides. The method resulted in high-quality RNA suitable for DDRT-PCR and cDNA library analysis finally.

Phenotypic and genotypic expression of self-incompatibility haplotypes in Arabidopsis lyrata suggests unique origin of alleles in different dominance classes

The highly divergent alleles of the SRK gene in outcrossing Arabidopsis lyrata have provided important insights into the evolutionary history of self-incompatibility (SI) alleles and serve as an ideal model for studies of the evolutionary and molecular interactions between alleles in cell-cell recognition systems in general. One tantalizing question is how new specificities arise in systems that require coordination between male and female components. Allelic recruitment via gene conversion has been proposed as one possibility, based on the division of DNA sequences at the SRK locus into two distinctive groups: (1) sequences whose relationships are not well resolved and display the long branch lengths expected for a gene under balancing selection (Class A); and (2) sequences falling into a well-supported group with shorter branch lengths (Class B) that are closely related to an unlinked paralogous locus. The purpose of this study was to determine if differences in phenotype (site of expression assayed using allele-specific reverse transcription-polymerase chain reaction) or function (dominance relationships assayed through controlled pollinations) accompany the sequence-based classification. Expression of Class A alleles was restricted to floral tissues, as predicted for genes involved in the SI response. In contrast, Class B alleles, despite being tightly linked to the SI phenotype, were unexpectedly expressed in both leaves and floral tissues; the same pattern found for a related unlinked paralogous sequence. Whereas Class A included haplotypes in three different dominance classes, all Class B haplotypes were found to be recessive to all except one Class A haplotype. In addition, mapping of expression and dominance patterns onto an S-domain-based genealogy suggested that allelic dominance may be determined more by evolutionary history than by frequency-dependent selection for lowered dominance as some theories suggest. The possibility that interlocus gene conversion might have contributed to allelic diversity is discussed.

Multiplexed RT-PCR for streamlined detection and separation of barley and cereal yellow dwarf viruses

Two novel multiplexed RT-PCR assays that can efficiently detect and distinguish among different barley and cereal yellow dwarf viruses (B/CYDVs) are described. The basic multiplex can produce two fragments simultaneously, a approximately 830-bp fragment indicating the presence of the BYDV-PAV, BYDV-MAV, or BYDV-SGV viruses and a approximately 372-bp fragment indicating the presence of the CYDV-RPV, BYDV-RMV, or BYDV-GPV viruses. The enhanced multiplex produces two additional fragments, which further differentiate between BYDV-PAV, BYDV-MAV, and BYDV-SGV. These assays fulfill the critical need for a streamlined diagnostic procedure for B/CYDVs that can be cost-effectively applied to large numbers of small samples. The assays are useful not only in the basic diagnosis of B/CYDVs, but also for studies examining the ecological roles of B/CYDVs in natural systems and for longer-term epidemiological studies of grasses and cereals.

A one-step reverse transcription-polymerase chain reaction system for the simultaneous detection and identification of multiple tospovirus infections

ABSTRACT A one-step reverse transcription-polymerase chain reaction (RT-PCR) method has been developed for the simultaneous detection and identification of multiple tospoviruses that infect plants. The RT-PCR system is composed of six primers in a single tube: a universal degenerate primer and five virus species-specific primers. Amplifications resulted in an 848-bp PCR product for Watermelon silver mottle virus, 709-bp for Tomato spotted wilt virus, 589-bp for Impatiens necrotic spot virus, 511-bp for Melon yellow spot virus, and a 459-bp amplicon for Iris yellow spot virus. This system enables the simultaneous detection of at least three types of tospovirus infections, in addition to their species identities, from five possible tospoviruses studied, on the basis of their S RNA combinations. This multiplex RT-PCR system was applied to the detection of tospovirus in ornamental crops cultivated in fields and shows potential for epidemiological studies.

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.

Detection of Geminiviruses in Sweetpotato by Polymerase Chain Reaction

Geminivirus infection of sweetpotato (Ipomoea spp.) germplasm acquired from foreign regions is common. Graft inoculation of the indicator host, Ipomoea setosa, is the accepted detection method for these viruses, but the assay is laborious and requires up to 8 weeks. When infected sweetpotato is subjected to meristem tip culture to eliminate these viruses, the eradication rate is low. In this study, a polymerase chain reaction (PCR) detection assay was developed for the detection of geminiviruses in a variety of sweetpotato cultivars. Different methods were evaluated to extract nucleic acids suitable for PCR from Ipomoea spp., and a reliable and simple extraction method was developed for large-scale sample preparation. PCR products of the expected sizes were amplified from infected plants using degenerate and virus-specific primers, but not from noninoculated indicator plants. PCR assays using three primer pairs detected nine uncharacterized isolates of the geminiviruses in sweetpotato from Asia and America. However, the best PCR result was obtained with degenerate primers SPG1/SPG2, which detected a Taiwan isolate of Sweet potato leaf curl virus (SPLCV-Taiwan) in a sample diluted to 10^-9. Viral identities of three amplicons from SPLCV-Taiwan were confirmed by sequencing. The degenerate primers had a broader detection range than virus-specific primers; therefore, they were used to detect geminiviruses in in vitro plantlets and greenhouse-grown sweetpotato plants, and in several Ipomoea hosts. PCR was shown to be as reliable for virus detection as grafting.

Comparative Infection Progress Analysis of Lettuce big-vein virus and Mirafiori lettuce virus in Lettuce Crops by Developed Molecular Diagnosis Techniques

ABSTRACT Nonisotopic molecular dot blot hybridization technique and multiplex reverse transcription-polymerase chain reaction assay for the specific detection of Lettuce big-vein virus (LBVV) and Mirafiori lettuce virus (MiLV) in lettuce tissue were developed. Both procedures were suitable for the specific detection of both viruses in a range of naturally infected lettuce plants from various Spanish production areas and seven different cultivars. The study of the distribution of both viruses in the plant revealed that the highest concentration of LBVV and MiLV occurred in roots and old leaves, respectively. LBVV infection progress in a lettuce production area was faster than that observed for MiLV. In spite of different rates of virus infection progress, most lettuce plants became infected with both viruses about 100 days posttransplant. The appearance of both viruses in lettuce crops was preceded by a peak in the concentration of resting spores and zoosporangia of the fungus vector Olpidium brassicae in lettuce roots.

Barley yellow dwarf virus and Cereal yellow dwarf virus Quantification by Real-Time Polymerase Chain Reaction in Resistant and Susceptible Plants

ABSTRACT Reliable detection and quantification of barley and cereal yellow dwarf viruses (YDVs) is a critical component in managing yellow dwarf diseases in small grain cereal crops. The method currently used is enzyme-linked immunosorbent assay (ELISA), using antisera against the coat proteins that are specific for each of the various YDVs. Recently, quantitative real-time reverse-transcription polymerase chain reaction (Q-RT-PCR) has been used to detect bacterial and viral pathogens and to study gene expression. We applied this technique to detect and quantify YDVs using primers specific for Barley yellow dwarf virus-PAV (BYDV-PAV) and Cereal yellow dwarf virus-RPV (CYDV-RPV) coat protein genes because of the higher sensitivity of RT-PCR and the advantage of using a real-time PCR instrument. This Q-RT-PCR was used to detect BYDV and CYDV, and to examine disease development in a resistant wheatgrass, a resistant wheat line, a susceptible wheat line, and a susceptible oat line. BYDV-PAV and CYDV-RPV were detected as early as 2 and 6 h, respectively, in susceptible oat compared with detection by ELISA at 4 and 10 days postinoculation. BYDV-PAV RNA accumulated more rapidly and to a higher level than CYDV-RPV RNA in both oat and wheat, which may account for PAV being more prevalent and causing more severe viral disease than CYDV. Q-RT-PCR is reproducible, sensitive, and has the potential to be used for examining yellow dwarf disease and as a rapid diagnostic tool for YDVs.

Innovative tools for detection of plant pathogenic viruses and bacteria

Detection of harmful viruses and bacteria in plant material, vectors or natural reservoirs is essential to ensure safe and sustainable agriculture. The techniques available have evolved significantly in the last few years to achieve rapid and reliable detection of pathogens, extraction of the target from the sample being important for optimising detection. For viruses, sample preparation has been simplified by imprinting or squashing plant material or insect vectors onto membranes. To improve the sensitivity of techniques for bacterial detection, a prior enrichment step in liquid or solid medium is advised. Serological and molecular techniques are currently the most appropriate when high numbers of samples need to be analysed. Specific monoclonal and/or recombinant antibodies are available for many plant pathogens and have contributed to the specificity of serological detection. Molecular detection can be optimised through the automatic purification of nucleic acids from pathogens by columns or robotics. New variants of PCR, such as simple or multiplex nested PCR in a single closed tube, co-operative-PCR and real-time monitoring of amplicons or quantitative PCR, allow high sensitivity in the detection of one or several pathogens in a single assay. The latest development in the analysis of nucleic acids is micro-array technology, but it requires generic DNA/RNA extraction and pre-amplification methods to increase detection sensitivity. The advances in research that will result from the sequencing of many plant pathogen genomes, especially now in the era of proteomics, represent a new source of information for the future development of sensitive and specific detection techniques for these microorganisms.

Multiplex RT-PCR detection of four aphid-borne strawberry viruses in Fragaria spp. in combination with a plant mRNA specific internal control

The principal aphid-borne viruses infecting Strawberry (Fragaria spp.) Strawberry crinkle virus (SCV), Strawberry mild yellow edge virus (SMYEV), Strawberry mottle virus (SMoV) and Strawberry vein banding virus (SVBV) can cause serious crop losses. In this paper, a multiplex reverse transcriptase polymerase chain reaction (RT-PCR) method is described for the simultaneous detection of all four viruses in combination with a plant mRNA specific internal control which can be used as an indicator of the effectiveness of the extraction and RT-PCR. In total, 18 strawberry isolates infected naturally were analysed by this method. Every combination of RNA virus was able to be detected and a full complement of all four viruses were found together in three isolates, all taken from wild strawberry (Fragaria chiloensis (L.) Duch.) in Chile. The upper detection limit for the four viruses was at an extract dilution of 1/200. The broad applicability of the RNA specific internal control primers-which produced a PCR fragment of the expected size in 25 of 27 plant species tested-combined with improvements, made in extraction methods described provides potentially a standard method for comparable RT-PCR analyses in a wide variety of plant species.

Multiplex RT-PCR-ELISA compared with bioassay for the detection of four apple viruses

A sensitive and reliable multiplex RT-PCR-ELISA technique for the detection of Apple chlorotic leaf spot virus, Apple stem pitting virus, Apple mosaic virus and Apple stem grooving virus was developed. This technique is compared with the method used commonly for indexing by woody indicators, which is time consuming and expensive. For the RT-PCR-ELISA technique, the amplified products were labeled with digoxigenin during the RT-PCR by incorporation of a digoxigenin labeled primer. After hybridization of the PCR products to specific capture oligonucleotides, which were bound covalently to the surface of NucleoLink strips, anti-digoxigenin antibodies were used for detection. More than 100 samples were tested in parallel by indexing and multiplex-RT-PCR-ELISA. All infections detected by woody indicators were also detected by multiplex RT-PCR-ELISA. Furthermore, additional infections were only found by multiplex RT-PCR-ELISA. The colourimetric detection of multiplex-RT-PCR products was at least as sensitive and sometimes slightly more sensitive than detection by gel electrophoresis. The results show that this molecular technique is more reliable for the detection of the above mentioned apple viruses than indexing by woody indicators, thereby helping to reduce cost and time during the certification of plant material.

A spot nested RT-PCR method for the simultaneous detection of members of the Vitivirus and Foveavirus genera in grapevine

A reverse transcription (RT) polymerase chain reaction (PCR) assay was developed to allow rapid, and simultaneous detection of Vitivirus and Foveavirus sequences in two steps. The method involved a one-step RT-PCR, in which the combination of degenerate deoxyinosine-substituted primers amplified part of the polymerase region of both genera, followed by a nested PCR amplification that increased specificity and sensitivity of detection. The increase in sensitivity also permitted the use of a simple and rapid template preparation protocol, involving the spotting of plant sap extract on a nylon membrane. Consistent amplification with infected grapevine plants was possible after inclusion of additives for inhibiting polyphenolic compounds during template preparation. This spot nested RT-PCR method can reliably detect virus species of both genera in grapevine allowing simple, fast, and cost-effective analysis of a large number of samples in certification schemes.

Multiplex Detection of Criniviruses Associated with Epidemics of a Yellowing Disease of Tomato in Greece

Since 1997, a yellowing disease has been observed in greenhouse tomato (Lycopersicon escu-lentum). By 2001, the disease was widespread, including open field tomato crops, and in most cases its incidence was 80 to 90% or even 100%. Epidemics in glasshouses were mainly associated with high populations of the whitefly Trialeurodes vaporariorum and Bemisia tabaci, the major whitefly pests in vegetable crops in Greece. The main leaf symptoms were severe yellowing, rolling, and brittleness. Samples from symptomatic plants were analyzed by polymerase chain reaction (PCR) and shown to be infected with Tomato infectious chlorosis virus (TICV) and Tomato chlorosis virus (ToCV) (family Closteroviridae, genus Crinivirus). TICV was found in 164 of 183 symptomatic samples, while ToCV was less representative (25/183). Sequence comparisons of the amplified 229-bp and 466-bp products revealed 99 and 100% identity with the reported sequences of TICV and ToCV, respectively. A reverse transcription (RT) multiplex PCR assay using a simple sample preparation procedure was developed to allow rapid, specific, and simultaneous detection of both ToCV and TICV sequences in two steps. The method involves a one-tube RT-PCR step in which the combination of primers amplifies part of the heat shock protein to homologue gene of both ToCV and TICV, followed by a multiplex nested PCR amplification. This is the first report of TICV and ToCV in Greece and, as far as we know, the first report of TICV in Europe.

Simultaneous RT/PCR detection and differentiation of arabis mosaic and grapevine fanleaf nepoviruses in grapevines with a single pair of primers

The movement protein genes from several isolates of ArMV and GFLV of different geographical origins were amplified by RT/PCR using degenerate primers, cloned and sequenced. A single pair of degenerate primers was designed from these sequences to allow the simultaneous amplification of parts of the movement protein genes of ArMV and GFLV. Their use in an immunocapture-RT/PCR for the detection of ArMV or GFLV in infected grapevines proved to be ten times more sensitive than the corresponding ArMV or GFLV ELISA tests. A Sph1 restriction site found in the sequences corresponding to the amplified products from the GFLV isolates, but not in the amplified products from the ArMV isolates, allowed the differentiation between ArMV and GFLV in the infected grapevines by a Sph1 restriction digestion of the amplified products.

Detection of four apple viruses by multiplex RT-PCR assays with coamplification of plant mRNA as internal control

Two multiplex RT-PCR assays with specific coamplification of plant mRNA as an internal control from total nucleic acids are described for the parallel detection of Apple chlorotic leaf spot virus, Apple stem pitting virus, Apple mosaic virus and Apple stem grooving virus. All are important economically and common pathogens in commercial apple and pear cultivars, except for Apple mosaic virus. Four virus specific primer pairs and one primer pair which allows the specific amplification of mRNA of the mitochondrial nad5 gene are described. Specificity of all primer pairs was confirmed by sequencing the RT-PCR products. A range of different virus isolates from various geographic origins could be detected by these multiplex RT-PCR assays all year round. Viruses were detected reliably in composite extracts at a ratio of one part total nucleic acid extract from an infected sample mixed with 39 parts of extract from healthy samples. The use of the internal control minimizes the risk of obtaining false negative RT-PCR results, which is desirable for routine testing, and avoids the need to eliminate contaminating DNA in extracts. To our knowledge, this is the first report on the use of a specific internal RNA control from total nucleic acids. The multiplex RT-PCR assays described are reliable, rapid and sensitive methods for the detection of these viruses, and may replace techniques need commonly like indexing by woody indicators or ELISA.

Single-step multiplex RT-PCR for simultaneous and colourimetric detection of six RNA viruses in olive trees

A single-step multiplex RT-PCR was developed for the simultaneous and colourimetric detection of six RNA viruses (Cucumber mosaic virus, Cherry leaf roll virus, strawberry latent ringspot virus, Arabis mosaic virus, Olive latent-1 virus and Olive latent-2 virus) which infect olive trees. Six compatible primer set for one-step RT-PCR amplification in a single closed-tube and 3' digoxigenin labelled probes were designed in optimal, specific and conserved regions. The method has been assessed with 195 Spanish field olive trees, suggesting that approximately 1.5% of the tested material was infected by Cucumber mosaic virus and 0.5% by Cherry leaf roll virus. This method saves time and reagent costs compared with monospecific RT-PCR which needs several reactions for the same number of tests. Using colourimetric detection, it is possible to analyse many samples, it increases sensitivity 10-fold, and whilst facilitating the interpretation of results, it avoids the use of gels and the toxic ethidium bromide. The method could be used routinely for sanitary and certification programmes.

RT-PCR Based Detection of Rupestris stem pitting associated virus Within Field-Grown Grapevines Throughout the Year

The presence of Rupestris stem pitting associated virus (RSPaV) can go unnoticed since symptoms appear only if additional viruses are present. Detection by reverse transcription-polymerase chain reaction (RT-PCR) is possible; however, this assay could be unreliable if the tissue that is being tested has detection-interfering compounds, or if the virus has a low titer. This paper reports on (i) use of a recently developed extraction method and internal control to determine which tissues from field-grown grapevines yield extracts that are reliable for virus detection by RT-PCR, and (ii) a survey for RSPaV of different tissues from the Vitis vinifera varieties Riesling, Chardonnay, Cabernet Franc, Merlot, Sauvignon Blanc, Pinot Noir, and Gamay, as well as from the rootstocks 3309 and Riparia, which were harvested in Ontario, Canada, at different times of the year. Amplifiable extracts were obtained from virtually all bud, shoot tip, seed, and cane samples tested. Detectable amounts of RSPaV were generally found in all tissues of infected plants except young buds collected in the summer. A combination of three single buds from dormant canes, less time-consuming than the preparation of cane shavings, was a reliable source for RSPaV detection.