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ARS Home » Pacific West Area » Salinas, California » Crop Improvement and Protection Research » Research » Publications at this Location » Publication #351042

Research Project: Management of Pathogens for Strawberry and Vegetable Production Systems

Location: Crop Improvement and Protection Research

Title: Development of molecular methods to detect Macrophomina phaseolina from strawberry plants and soil

item Burkhardt, Alyssa
item RAMON, MARINA - Former ARS Employee
item SMITH, BRETT - Former ARS Employee
item KOIKE, STEVE - Trical Inc
item Martin, Frank

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/4/2018
Publication Date: 6/7/2018
Citation: Burkhardt, A.K., Ramon, M.L., Smith, B., Koike, S.T., Martin, F.N. 2018. Development of molecular methods to detect Macrophomina phaseolina from strawberry plants and soil. Phytopathology.

Interpretive Summary: This manuscript describes the development of a diagnostic assays using DNA based tools for rapid detection and quantification of a pathogen capable of causing significant losses of commercial strawberry plants. Its availability will simplify and speed up the diagnostics of this pathogen.

Technical Abstract: Macrophomina phaseolina is a broad-host range fungus that shows some degree of host preference on strawberry, and causes symptoms including charcoal rot and root rot. Recently, this pathogen has impacted strawberry production as fumigation practices have changed, leaving many growers in California and around the world in need of accurate, rapid diagnostic tools for M. phaseolina in soil and infected plants. This study uses next-generation sequencing and comparative genomics to identify a locus that is unique to isolates within a main genotype shared by a majority of isolates that infect strawberry. This locus was used to develop a quantitative single tube nested TaqMan qPCR assay which is able to detect as little as 2-3 microsclerotia/gram of soil with 100% genotype specificity. An isothermal assay using recombinase polymerase amplification (RPA) was developed from the same locus and has been validated on over 200 infected strawberry plants with a diagnostic sensitivity of 93% and a diagnostic specificity of 99%. Together, this work demonstrates the value of using new approaches to identify loci for detection and provides valuable diagnostic tools that can be used to monitor soil and plant samples for M. phaseolina.