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

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. The ability of F. avenaceum to cause seed decay may be utilized to deplete the weed seedbank in soil, an important integrated weed management strategy. We developed a SYBR Green I-based real-time polymerase chain reaction (qPCR) assay to efficiently detect and quantify F. avenaceum in soil, wild oat (Avena fatua L.) seed caryopses, and wild oat seed hulls. The primer pair was designed from the translation elongation factor 1-alpha (TEF1) gene. In silico and wet lab testing were done to assess the ability of the primers to bind TEF1 sequences from Fusarium spp. and common soil fungi. The findings indicated that the primers were specific to F. avenaceum, and also recognized GenBank TEF1 accessions annotated as F. arthrosporioides, which has been listed 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. The assay can be used for endpoint PCR as well.