2011 Annual Report 1a.Objectives (from AD-416) The objectives of this cooperative research are to:. 1)genotypically and phenotypically characterize plant pathogens that cause diseases of crops grown in cereal-based cropping systems,. 2)to genotypically and phenotypically characterize microbial biocontrol agents that suppress plant pathogens in these cropping systems, and. 3)to determine the molecular genetic and biochemical basis of plant-microbe interactions and plant defense. 1b.Approach (from AD-416) Plant pathogens and their biocontrol agents will be characterized through a combination of molecular fingerprinting techniques and methods of classical plant pathology and microbiology. The population structures of pathogens and biocontrol agents will be determined by statistical analysis of DNA banding patterns generated by techniques such as rep-PCR and RAPDs, RFLPs, and AFLPs, and by sequence analysis of 16S rDNA and key genes. Results of genotypic and phenotypic analyses will be compared. Plant-microbe interactions will be characterized using a combination of laboratory, greenhouse and field studies, and molecular biology and bioanalytical tools. Biologically active metabolites produced by pathogens and antagonists will be characterized using techniques such as high performance liquid chromatography (HPLC) and mass spectrometry. 3.Progress Report Progress aligns with objectives 1,2,3, and 4 from parent project. Root diseases, including take-all, Pythium, Rhizoctonia and common root rots, and Fusarium crown rot, cause billions in losses annually to U.S. wheat and barley growers. For most of these diseases, there are no resistant varieties and chemical treatments are not available or perform inconsistently. Modern farming practices of direct seeding and intensive cereal production increase severity of root diseases. Researchers at Washington State University, in collaboration with ARS scientists at Pullman, WA, used a combination of molecular fingerprinting techniques, conventional and real-time polymerase chain reaction (PCR) and methods of classical plant pathology and mycology to characterize the genetic diversity present in populations of soilborne pathogens including Pythium, Gaeumannomyces, Pratylenchus, Hederodera, Fusarium and Rhizoctonia that attack crops grown in cereal-based production systems. Methods to rapidly isolate fungal and nematode DNA from soil were developed and commercialized, allowing detection and quantification of pathogens in soil by using real-time PCR. Knowledge of pathogen population structure and virulence insures that research to develop resistant wheat, barley, and canola germplasm utilizes pathogen isolates typical of field populations. This work provides to growers a direct test for determining the risk from pathogens present in their fields. Phenazine-1-carboxylic acid was isolated from roots of wheat and barley grown in fields throughout the low precipitation zone of the Columbia Plateau. Current studies indicate a role for phenazine-1-carboxylate (PCA) in suppression of Rhizoctonia or mobilization of minerals. PCA was shown to be produced in the rhizosphere of wheat throughout the entire growing season. Collectively, these findings will hasten the development of biocontrol technology, a sustainable approach to control root diseases in cereal-based production systems. Progress on this project is monitored by weekly conversations with the collaborator.