Cytochrome c oxidase mRNA as an internal control for detection of Potato virus Y and Potato leafroll virus from single aphids by a co-amplification RT-PCR assay

Evaluation of Various Sources of Viral Infection in Strawberry Fields of Quebec, Canada

The decline of cultivated strawberry (Fragaria × ananassa Duchesne ex Rozier; Rosaceae) observed in the province of Quebec, Canada, between 2012 and 2014 was mostly caused by persistent viruses: strawberry mild yellow edge virus (SMYEV) (Potexvirus; Alphaflexiviridae) and strawberry crinkle virus (SCV) (Cytorhabdovirus; Rhabdoviridae); and semi-persistent viruses: strawberry mottle virus (SmoV) (Secoviridae), strawberry vein banding virus (SVBV) (Caulimovirus; Caulimoviridae), and strawberry pallidosis virus (SPaV) (Crinivirus: Closteroviridae) transmitted by insect vectors. The objective of this study was to determine the sources of viral contamination in commercial strawberry fields in Quebec. Specifically, we wished to 1) determine the prevalence of persistent viruses in winged strawberry aphid Chaetosiphon fragaefolii (Cockerell) (Hemiptera: Aphididae) specimens captured; 2) determine the prevalence of all viruses in wild strawberry Fragaria virginiana Miller plants near commercial plantings; and 3) evaluate the viral contamination of strawberry transplants obtained from nurseries and tested before and after planting in commercial strawberry fields. Results indicated high percentage (38%) of the aphids (n = 205) and high percentage (67%) of F. virginiana patches (n = 12) were infected by strawberry viruses. Ultimately, our results showed a low percentage (5%) of the plants from various nurseries (n = 56) were infected before planting, whereas a third (29%) of the healthy exposed plants in the fields (n = 96) became rapidly infected by insect vectors within a year of having been planted. This study provides significant insights on the relative importance of the various sources of contamination in Quebec strawberry fields: C. fragaefolii versus F. virginiana versus nurseries versus post-nursery infections through exposure to virus-carrying insects.

Uniplex and duplex PCR detection of geminivirus associated with potato apical leaf curl disease in India

Apical leaf curl disease has emerged as a new disease in potato during the last decade in India due to a change in planting date and an increased whitefly population. Its incidence is on the rise threatening the cultivation of potato across the country. Hence, a PCR assay was developed for the detection of Tomato leaf curl New Delhi virus-potato (ToLCNDV-Potato) which is the causal agent of apical leaf curl disease in potato. Primers specific to the coat protein (AV1) and replicase (AC1) gene regions were designed and used for standardization of the PCR. Some of the primers (LCVCPF1/LCVCPR1, LCVREPF2/LCVREPR2, LCrep1F/LCrep2R) could detect the virus in 2.4-0.24pg of total DNA of infected plant. A duplex PCR assay was optimized with the selected coat protein gene specific primers and primers specific to potato urease gene, a housekeeping gene served as an internal check. The suitability of these primers was examined for detection of the virus in 80 potato apical leaf curl disease samples from 11 different potato growing states of India and also from micro-plants grown in tissue culture. The selected coat protein primer pair (LCVCPF1/LCVCPR1) was found to be conserved in all 80 isolates except for a few isolates, which had a single nucleotide substitution in the forward primer sequence. These substitutions did not interfere with amplification of the coat protein gene. The primers could detect the virus using a print-capture PCR assay both in the presence and absence of an internal control. These results indicate the robustness of the PCR assay for virus indexing of mother stocks in the seed production system.

Reference gene selection for gene expression studies using RT-qPCR in virus-infected planthoppers

Background

Planthoppers not only severely affect crops by causing mechanical damage when feeding but are also vectors of several plant virus species. The analysis of gene expression in persistently infected planthoppers might unveil the molecular basis of viral transmission. Quantitative real-time RT-PCR (RT-qPCR) is currently the most accurate and sensitive method used for quantitative gene expression analysis. In order to normalize the resulting quantitative data, reference genes with constant expression during the experimental procedures are needed.

Results

Partial sequences of the commonly used reference genes actin (ACT), α1-tubulin (TUB), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), elongation factor 1 alpha (EF1A), ribosomal protein S18 (RPS18) and polyubiquitin C (UBI) from Delphacodes kuscheli, a planthopper capable of persistently transmitting the plant fijivirus Mal de Río Cuarto virus (MRCV), were isolated for the first time. Specific RT-qPCR primers were designed and the expression stability of these genes was assayed in MRCV-infective and naïve planthoppers using geNorm, Normfinder and BestKeeper tools. The overall analysis showed that UBI, followed by 18S and ACT, are the most suitable genes as internal controls for quantitative gene expression studies in MRCV-infective planthoppers, while TUB and EF1A are the most variable ones. Moreover, EF1A was upregulated by MRCV infection.

Conclusions

A RT-qPCR platform for gene expression analysis in the MRCV-infected planthopper vector Delphacodes kuscheli was developed. Our work is the first report on reference gene selection in virus-infected insects, and might serve as a precedent for future gene expression studies on MRCV and other virus-planthopper pathosystems.

Multiplex PCR for the detection of African cassava mosaic virus and East African cassava mosaic Cameroon virus in cassava

A multiplex PCR was developed for simultaneous detection of African cassava mosaic virus (ACMV) and East African cassava mosaic Cameroon virus (EACMCV) in cassava affected with cassava mosaic disease (CMD). One set of three primers consisting of an upstream primer common for both viruses and two down stream virus-specific primers were designed for simultaneous amplification of 368 base pair (bp) and 650 bp DNA fragments specific to the replicase gene of ACMV and EACMCV, respectively. Similarly, a second set of three primers were designed for simultaneous amplification of 540 bp and 655 bp fragments specific to the coat protein gene of EACMCV and ACMV, respectively. Primers that can amplify a 171 bp fragment of the large subunit of ribulose bisphosphate carboxylase oxygenase L were included as an internal control in these assays to determine the reliability of multiplex PCR. A simplified, cost-effective and rapid sample preparation method was adapted in place of the conventional plant DNA extraction procedure for multiplex PCR detection of ACMV and EACMCV. The method was validated using CMD-infected cassava samples obtained from farmers' fields in Nigeria. The multiplex PCR is useful for reliable assessment of the prevalence of CMBs in epidemiological studies and for crop improvement and phytosanitary programs in African countries.