Location: Fruit and Tree Nut ResearchTitle: Novel primers and sampling for PCR detection of Xylella fastidiosa in peach
Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/20/2018
Publication Date: 2/6/2019
Citation: Chen, C., Bock, C.H., Brannen, P.M. 2019. Novel primers and sampling for PCR detection of Xylella fastidiosa in peach. Phytopathology. 109(2):307-317. https://doi.org/10.1094/PHYTO-11-18-0439-FI.
Interpretive Summary: Phony peach disease (PPD) is caused by the bacterium Xylella fastidiosa (Xf). There is no cure or effective control for PPD. Reliable and reproducible detection of Xf is crucial for early removal of symptomatic trees, a management approach utilized to reduce the spread of PPD. In this study we developed new Xf primers and assessed them in four peach tissue types sampled at three time points using conventional PCR and qPCR. Among the four tissue types, root was the only DNA source for reliable and consistent detection of Xf; none of the other three tissue types tested were reliable, regardless of source trees, primers used, sampling times, or PCR methods (conventional or qPCR).
Technical Abstract: Epidemics of phony peach disease (PPD), caused by Xylella fastidiosa (Xf), are of increasing concern to peach (Prunus persica) producers in the southeastern United States. Primers suitable for both conventional PCR (cPCR) and quantitative PCR (qPCR), along with optimal tissue and sampling time, are needed for comparative and reliable detection of Xf. In this study, we developed and assessed novel primers for Xf and for peach, and compared detection of Xf in four peach tissue types sampled at three time points using both cPCR and qPCR. Primer C06Xf-bamA was extensively tested for reliable detection of Xf due to the more consistent intensity of the cPCR products and the marginally lower average quantification cycle (Cq) values of the qPCR products, compared to the other primers screened. Among the four peach tissue types tested, only root samples demonstrated reliable and consistent detection of Xf; stem, petiole, and leaf samples, regardless of source trees, primers used, sampling times, or PCR methods (cPCR or qPCR), were unreliable for detection, due to insufficient quantity of DNA of Xf in these samples based on the relative quantification assay. The Cq means and ratios were compared and statistically analyzed, to ascertain effects of source tree, tissue type, sampling time, and primer. Differences in detection sensitivity and the Cq means among sampled trees, sampling times, tested primers, and tissues (except root) were not significant or were inconsistent precluding further exploitation. In summary, these novel primers are a useful resource for detecting Xf, and based on our results root is the only tissue type reliable for year-round detection of Xf in peach. Further research on potential utilization of above-ground tissues for PCR detection of Xf are discussed.