A comparison of standard and high-fidelity PCR in the detection of Sclerotium rolfsii and a Dickeya sp. from Phalaenopsis orchids

The polymerase chain reaction (PCR) has become widely used in phylogenetic and genomic analyses, plant-disease diagnoses, and to examine pathogen diversity. However, standard PCR usually does not amplify sequences of more than 5 kb and can be inhibited by plant cellular contents including host genomic DNA when used for the detection of plant pathogens directly from plant tissue. The high-fidelity PCR has been used to detect a number of microbes while in the presence of host genomic DNA and is more efficient than the standard PCR. In this study, high-fidelity and standard PCRs were used to detect S. rolfsii and a Dickeya sp. directly from inoculated orchids. The high-fidelity PCR could detect the presence of the pathogen in all inoculated plants, while the standard PCR could detect only the positive controls. These results indicate that the high-fidelity PCR may enable a dramatic improvement in the detection of a wide range of plant pathogens, especially when low template concentration, contaminating or competitor DNA, or amplification inhibitors exist in a given sample.