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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Sustainable Agricultural Systems Laboratory » Research » Research Project #443270

Research Project: Development of Genomic Tools for Control and Characterization of Rhizoctonia solani and Other Soil-borne Plant Pathogens

Location: Sustainable Agricultural Systems Laboratory

Project Number: 8042-21220-259-000-D
Project Type: In-House Appropriated

Start Date: Jun 7, 2022
End Date: Jun 7, 2027

Objective 1. Enhance and utilize Rhizoctonia solani pangenomic database to improve pathogen identification accuracy and characterize pathogenic mechanisms. Objective 2. Determine the impact of cropping system and soil edaphic factors on populations of pathogenic and non-pathogenic soil-borne fungi. Objective 3: Develop biological control agents for soil-borne pathogens, including Rhizoctonia solani, of field and nursery crops.

Planned research is directed at managing important diseases caused by soil-borne plant pathogens that negatively impact farmers' livelihoods in the Mid-Atlantic region of the United States and elsewhere. A major emphasis of this research is developing sustainable disease management tools for pathogens from the Rhizoctonia solani species complex. For Objective 1 the Rhizoctonia solani pangenomic database (RsolaniDB), developed during the prior project, will be enhanced using newly generated near-chromosome-level genome assemblies. This enhanced RsolaniDB will be used to develop molecular probes for the detection and differentiation of R. solani isolates in farm fields. Specific identification technologies are required to ensure the use of appropriate controls, as isolates from this species complex can be morphologically similar but vary widely in sensitivity to chemical or biocontrol measures. The enhanced RsolaniDB will also be used to develop knowledge concerning mechanisms of pathogenicity of poorly studied isolates from the R. solani species complex. For this patho-genomic analysis of select genomes in RsolaniDB will be conducted. Also, RNAseq will be used to carry out temporal, differential gene expression analysis of interactions between a R. solani isolate and known host and non-host crops. Differential expression of R. solani genes during interactions with the host and non-host crops will provide insights into genes involved in pathogenicity and host range of this pathogen. For Objective 2 we will analyze the impact of corn, wheat, and soybean cropping systems used in the mid-Atlantic region on the ecology of R. solani. Modern microbiome molecular approaches will be used on DNA extracted from soil samples from fields used for these cropping systems. Amplicon sequencing of ribosomal markers (ITS for fungi and 16S V4 for bacteria) will provide a description of fungi, including species from the R. solani species complex, and bacteria in the different cropping system fields. Discoveries will result in best management cropping practices to minimize the inoculum of R. solani and disease in farm fields. For Objective 3, environmentally friendly biocontrol options for R. solani isolates and the critical soil-borne plant pathogens Pythium ultimum and Sclerotinia sclerotiorum will be developed. Omics approaches will be used to determine mechanisms of biocontrol. Using this multipronged approach of specific identification, development of environmentally sound biocontrol options, and best management practices to minimize inoculum and disease, this project will improve control of important soil-borne diseases and improve sustainability of farming systems in the Mid-Atlantic region and elsewhere.