2006 Annual Report 4d.Progress report. This project is assigned to National Program Plant Diseases, NP 303 This report serves to document research conducted under a Specific Cooperative Agreement between ARS and Washington State University. Additional details of the research can be found in the report for the parent project 5248-22000-008-00D, NP 303, Plant Diseases. Root diseases including take-all, Pythium root rot, Rhizoctonia root rot, common root rot, and Fusarium foot rot cause nearly $3 billion in losses annually to wheat and barley growers in the U.S. Unfortunately, for most of these diseases resistant varieties are not available and chemical treatments are not available or perform inconsistently. The modern cereal production practice of direct seeding, which is used to control soil erosion, exacerbates the incidence and severity of root diseases. Researchers at Washington State University, in collaboration with ARS scientists at Pullman, WA, have used a combination of molecular fingerprinting techniques, real-time PCR and methods of classical plant pathology and microbiology to characterize the genetic diversity present in populations of important soilborne pathogens including Pythium spp. and Rhizoctonia spp. that attack crops grown in cereal-based cropping systems. Methods to rapidly and efficiently isolate Pythium and Rhizoctonia DNA from soil were developed, which allow detection and quantification of these pathogens in field soil by using real-time PCR and species specific primers. Knowledge of pathogen population structure and virulence is critical in order to insure that research to develop resistant wheat, barley, canola and legume germplasm will utilize pathogen isolates typical of field populations in the Pacific Northwest. This work also provides to growers a direct test for determining the risk from soilborne pathogen present in their fields. The build-up of naturally-occurring populations of 2,4-diacetylphloroglucinol (DAPG)-producing Pseudomonas fluorescens during wheat monoculture is responsible for the suppression of take-all disease of wheat in some suppressive soils. A quantitative real-time PCR SYBR Green assay was developed to quantify populations of four of the 22 genotypes of DAPG-producing P. fluorescens known to occur in soils worldwide. The results of this study demonstrate that it is possible to quantify DAPG producers directly from soil DNA and thus provide growers with an assessment of the suppressiveness of their soil to take-all. Novel antifungal, biocontrol metabolites such as phloroglucinols and phenazines responsible for suppression of root pathogens were characterized by mass spectrometry. These studies will hasten the development of biological control technology, which is an environmentally friendly and sustainable approach to control root diseases in modern cereal-based production systems. Accomplishment align with Components 1,2 and 4 of NP 303.