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United States Department of Agriculture

Agricultural Research Service

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

Location: Wheat Health, Genetics, and Quality Research

Project Number: 2090-22000-017-00-D
Project Type: In-House Appropriated

Start Date: Mar 5, 2017
End Date: Mar 4, 2022

Objective:
The long-term objective of this project is to develop biologically based technologies for controlling soilborne pathogens of wheat, barley and brassica crops grown as part of cereal-based production systems. Three specific objectives will be addressed over the next five years. Objective 1: Define the pathogen diversity, host range, and geographical distribution of fungal and nematode root pathogens, especially those causing emerging diseases in cereal-based cropping systems in the Pacific Northwest. Subobjective 1A: Using conventional and molecular techniques, determine the biogeographical distribution and risk of emerging and chronic pathogens and diseases. Subobjective 1B: Examine the genetic and pathogenic diversity of emerging and chronic pathogens. Subobjective 1C: Develop and evaluate agronomic, genetic and cultural methods of root disease management. Objective 2: Determine the soil microorganisms, microbial communities, and molecular mechanisms that promote or reduce plant health in wheat, barley and canola in the Pacific Northwest. Subobjective 2A: Determine how cultural practices and chemical inputs affect the plant and soil microbiomes in wheat cropping systems. Subobjective 2B: Characterize the rhizosphere microbiome of wheat in take-all decline soils. Subobjective 2C: Evaluate the effect of the wheat cultivar on the robustness of biological control by Pseudomonas spp. and in take-all decline soils. Objective 3: Identify and characterize molecular mechanisms of host-microbe interactions, including the action of host genes governing disease resistance and biological control against soilborne pathogens of wheat, barley and canola. Subobjective 3A: Identify host responses to soilborne pathogens, biocontrol bacteria and bacterial metabolites. Subobjective 3B: Identify and characterize germplasm with resistance to soilborne pathogens.

Approach:
Biological control of soilborne fungal pathogens such as Gaeumannomyces, Rhizoctonia, Pythium, Fusarium and plant-parasitic nematodes by naturally-occurring and recombinant microorganisms will be developed and quantified in agricultural soils. Molecular approaches will be used to detect and quantify soilborne pathogens and their microbial antagonists, and next-generation sequencing will be used to characterize the microbiomes of conducive and suppressive soils and the rhizosphere of small grain crops. Genetic determinants and molecular mechanisms responsible for root colonization and pathogen suppression will be characterized with emphasis on the genetics and regulation of phenazine and phloroglucinol biosynthesis in vitro and in situ. The genetic and physiological diversity of populations of root pathogens and their microbial antagonists, and influence of cropping systems on pathogens and antagonists will be determined. Genomes of pathogens and antagonists will be sequenced and analyzed. New sources and mechanisms of host resistance will be identified. Practical disease control will be accomplished by maximizing the activity of natural biocontrol agents.

Last Modified: 10/18/2017
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