Development of three duplex real-time RT-PCR assays for the sensitive and rapid detection of a phytoplasma and five viral pathogens affecting stone fruit trees

Selection and Validation of Reference Genes for Gene Expression Studies Using Quantitative Real-Time PCR in Prunus Necrotic Ringspot Virus-Infected Cucumis sativus

Several members of the genus Ilarvirus infect fruit trees and are distributed worldwide. Prunus necrotic ringspot virus (PNRSV) is one of the most prevalent viruses, causing significant losses. Cucumissativus can be infected by several ilarviruses, leading to obvious symptoms, including PNRSV, which suggests that cucumbers could be good hosts for the study of the pathogenesis of ilarviruses. Real-time quantitative PCR is an optimal choice for studying gene expression because of its simplicity and its fast and high sensitivity, while its accuracy is highly dependent on the stability of the reference genes. In this study, we assessed the stability of eleven reference genes with geNorm, NormFinder, ΔCt method, BestKeeper, and the ranking software, RefFinder. The results indicated that the combined use of EF1α and F-BOX was the most accurate normalization method. In addition, the host genes AGO1, AGO4, and RDR6 were selected to test the reliability of the reference genes. This study provides useful information for gene expression analysis during PNRSV infection and will facilitate gene expression studies associated with ilarvirus infection.

Duplex PCR assay for detection of chickpea chlorotic dwarf virus and peanut witches' broom phytoplasma in chickpea

A duplex PCR assay was standardized by optimizing PCR reaction constituents and cycles for the simultaneous detection of chickpea chlorotic dwarf virus (CpCDV) and a peanut witches' broom (PnWB) phytoplasma associated with the chickpea stunt disease. Coat protein gene and tuf gene specific primers for CpCDV and phytoplasmas were used. Different concentrations of the PCR components such as Taq polymerase, primers and PCR annealing temperature were standardized for the identification of the two agents by a duplex PCR assay. Expected amplicons of 590 bp for CpCDV and 1090 bp for phytoplasmas were consistently amplified from the symptomatic chickpea tissues. That resulted in equally efficient and sensitive in detecting single or mixed infection of CpCDV and PnWB phytoplasma in 148 symptomatic chickpea stunt samples collected in two states of India. The results indicate the robustness in the detection of pathogens present in chickpea showing stunt disease and for theoretical use in epidemiological studies that would help the appropriate disease management strategies.