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ARS Home » Pacific West Area » Pullman, Washington » WHGQ » Research » Publications at this Location » Publication #353263

Research Project: Biology, Ecology, and Genomics of Pathogenic and Beneficial Microorganisms of Wheat, Barley, and Biofuel Brassicas

Location: Wheat Health, Genetics, and Quality Research

Title: Real-time PCR quantification of Fusarium avenaceum in soil and seeds

item POLLARD, ANNE - Washington State University
item Okubara, Patricia

Submitted to: Journal of Microbial Methods
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/12/2018
Publication Date: 12/17/2018
Citation: Pollard, A.T., Okubara, P.A. 2018. Real-time PCR quantification of Fusarium avenaceum in soil and seeds. Journal of Microbial Methods. 157:21-30.

Interpretive Summary: We developed a molecular diagnostic assay for a common soilborne pathogen of crop plants found in the Pacific Northwest, USA and throughout the world. This pathogen is being studied for its differential ability to cause decay of wild oat seed, while leaving wheat seed relatively free of decay. The assay is useful for quantifying the pathogen in soil, seeds and hulls.

Technical Abstract: The pathogenic fungus Fusarium avenaceum infects a broad range of plant hosts across the globe. While primarily soilborne, F. avenaceum can colonize all plant tissues, including buds, seeds, fruits, stems, crowns, and roots, resulting in significant crop yield reductions and economic losses for growers. In addition to its impact on crop productivity, F. avenaceum produces toxic metabolites that can be transferred to humans and livestock through consumption of infected foods. We developed a SYBR Green I-based real-time polymerase chain reaction assay to efficiently detect and quantify F. avenaceum in soil, seed caryopses, and seed hulls. The primer pair was designed from the translation elongation factor 1-alpha (TEF1) gene. In silico testing was done to predict the ability of the primers to bind TEF1 sequences from Fusarium spp. and common soil fungi. The findings indicated the primers were specific to F. avenaceum, and also recognized GenBank TEF1 accessions annotated as F. arthrosporioides, which has been described as a foliar pathogen of wheat in Oregon, and conspecific with F. avenaceum. Standard curves of F. avenaceum DNA diluted with soil, caryopsis, or hull extracts indicated primer amplification efficiency was not significantly affected by PCR inhibitors. This real-time PCR assay effectively assesses the presence and abundance of F. avenaceum and its close relative F. arthrosporioides, if present, in soil and seed tissues.