Scientists Identify Fungal Disease Culprits with Molecular Genetics

A new method that rapidly detects the "genetic fingerprints" of fungi responsible for millions of dollars in losses in western wheat has been developed by Agricultural Research Service (ARS) scientists in Pullman, Wash.

Though not ready for commercial use, the real-time quantitative polymerase chain reaction (PCR) assays set the stage for building a comprehensive risk-management database that will help farmers decide the best way to counter the fungi, based on how many of them are present in the soil, as well as other factors such as prevailing conditions, the type of crop grown, and other variables.

Patricia Okubara, Timothy Paulitz and Kurtis Schroeder at the ARS Root Disease and Biological Control Research Unit in Pullman developed the assays, which now detect 10 Pythium and seven Rhizoctonia species. In May, the team began collaborating with Harry Kreeft and Jim Torell, with Western Laboratories of Parma, Idaho, to explore the assays' commercial potential and eventual use in gathering fungal data for the risk-management system.

In the Pacific Northwest, fungal diseases of seedlings and roots in spring and winter wheat cost growers from $50 million to $70 million annually in yield losses. In Washington State, Rhizoctonia root rot is so severe that some wheat growers have abandoned the practice of direct-seeding, a planting technique that conserves water and topsoil, notes Okubara.

The assay her team developed uses laboratory-built molecules called primers to detect specific sequences of fungal DNA in soil or plant samples. The primers bind with the sequences and prepare them for PCR amplification, which generates millions of copies. A fluorescent signal that's measured and displayed on a computer screen at each amplification cycle's end indicates how much of the pathogen is present in the original sample.

The assays' chief advantages over conventional methods are speed, specificity and sensitivity. Before, it was necessary to culture the fungi, examine their features under a microscope and conduct greenhouse trials to observe disease symptoms--a weeks-long process. The assays yield results in one day.

ARS is a scientific research agency of the U.S. Department of Agriculture.