Knowledge gaps, research needs, and opportunities in plant disease diagnostic assay development and validation

Authors: GEISER, DAVID - Pennsylvania State University; Martin, Frank; ESPINDOLA, ANDRES - Oklahoma State University; BROWN, JUDITH - University Of Arizona; BELL, TERRENCE - Pennsylvania State University; YANG, YINONG - Pennsylvania State University; KANG, SEOGCHAN - Pennsylvania State University

Submitted to: PhytoFrontiers
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/1/2023
Publication Date: 2/26/2023
Citation: Geiser, D., Martin, F.N., Espindola, A.S., Brown, J.K., Bell, T., Yang, Y., Kang, S. 2023. Knowledge gaps, research needs, and opportunities in plant disease diagnostic assay development and validation. PhytoFrontiers. 3(1):51-63. https://doi.org/10.1094/PHYTOFR-05-22-0057-FI.
DOI: https://doi.org/10.1094/PHYTOFR-05-22-0057-FI

Interpretive Summary: This manuscript describes needed research and technological approaches that are important for developing molecular diagnostic assays for detection of economically important plant pathogens to ensure the assays perform properly under a range of conditions.

Technical Abstract: Disease diagnostics is a core endeavor in the field of plant pathology because it supports disease prediction and management, monitoring and quarantine, research in etiology and epidemiology, screening and breeding disease-resistant germplasm, and the production and movement of pathogen-free plants. Needs for faster diagnostic methods with enhanced specificity and sensitivity are heightened by the external forces of climate change, population growth, and increased global trade. Technological advances and research over the last quarter century present opportunities to develop more sensitive, specific, and informative diagnostic assays for these purposes, and to implement them more rapidly in response to emerging diseases. We are positioned to create 1) genomics-enabled analyses of plant pathogenic taxa to develop improved markers for diagnosis; 2) more sensitive and specific application of nucleic acid markers to determine the presence of a known or potential plant pathogen in the midst of other non-pathogenic organisms in a given sample (infected plant, germplasm/seed, soil, irrigation water), and if present, whether it is metabolically active; 3) implementation of novel, robust technologies that provide diagnostic information quickly and reliably from challenging samples; and 4) purposefully organized data and materials in advance of emergencies aimed at quick-starting diagnostics development and validation of pathogen targets. These advances will require collaboration and coordination of efforts between 1) scientists describing and curating the diversity of microbial taxa, and their natural histories in agricultural and other ecosystems; 2) data scientists capable of creating and maintaining cyberinfrastructure for adapting data to diagnostic purposes; 3) scientists engineering and validating diagnostic methods; 4) field scientists and growers/stakeholders who will utilize diagnostic tools; and 5) regulators who oversee diagnostics in a legal and policy context. Such community efforts will facilitate disease control and management, monitoring and quarantine, and assist agricultural industries in providing improved disease-free and or -resistant cultivars, seeds and nursery products.