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ARS Home » Crop Production and Protection » Research » Research Project #438176

Research Project: Quantification Assays for Predictive Modeling Tool Initiative Samples

Location: Crop Production and Protection

Project Number: 0500-00102-001-001-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Jun 5, 2020
End Date: Jun 4, 2024

1) Development of validated, quantifiable assays for specific diseases of concern to each RAC; and 2) In-lab high-throughput testing of field samples of crop residues and/or soil to quantify pathogen loads. Then during the growing season, we can test seed and plant tissue, as well as field-supplied air samples to detect and quantify spores of various diseases, assuming the genetic markers exist for the spores in question.

1) Assay Development: The Research Area Committee (RAC) for corn has identified its three priorities as Grey Leaf Spot, Bacterial Leaf Streak, and Northern Corn Leaf Blight. NAGC has already developed and validated quantifiable assays for these three diseases. The cotton RAC has identified its top two priorities as Target Spot or Corynespora leaf spot and Grey or Areolate Mildew. Unfortunately, genetic markers for these two are not currently available to NAGC so we will work with the University of Tennessee on Target Spot and the University of Georgia on Areolate Mildew, to identify genetic markers, and then develop and validate assays for the quantification of the diseases. The wheat RAC has identified Stem or Black Rust, Wheat Stripe or Yellow Rust, Leaf or Brown Rust and Wheat Powdery Mildew. NAGC will first research each disease to determine if genetic markers have been identified, and if so, to then develop and validate quantifiable assays for the three highest priority diseases as determined by the wheat RAC. All of these pathogens will need assays that have to be validated for air-borne spore sampling. 2) In-Lab Testing: In order to help researchers focus resources on field-based study, data collection and analysis, NAGC will test 6,750 samples at no cost to the researchers. This equates to approximately 2,250 samples for each RAC. These testing services will be provided to each researcher on a confidential basis. Follow-up reports will go to the researcher and any other parties the researcher may designate. It will be up to the researcher to submit data to Los Alamos National Laboratory (LANL). LANL will aggregate this information to help further the development of the predictive modeling tool. The validated, quantifiable assays that are ready to use are the highest in-lab testing priority. This includes the assays for Northern Corn Leaf Blight, Gray Leaf Spot and Bacterial Leaf Streak in corn. NAGC can accept samples at any time. Next are those assays that will be in development during the 2020 season. This includes tests for Leaf, Stem and Stripe Rust in wheat, and working on Target Spot and Areolate Mildew in cotton. It is expected that the majority of samples received will be for soil and/or crop residue testing. NAGC can also provide quantifiable testing for plant tissue and seed if the researcher so desires. Regardless of the substrate, molecular assays rely on quality sampling procedures in order to produce quality results. To this end, NAGC has developed separate sampling procedures that the researcher can follow for soil, crop residue, plant tissue and seed. Quantification of air-borne pathogens via spore sampling will be more difficult since the capture efficiency and gain factors vary for different spore monitor designs, hence numerical values in a given field could vary based on what kind of spore monitor is used. Because of these differences, standardized numerical values may not be possible for the next couple of years, but it may be possible to establish numerical values for each monitor design. NAGC can assist the RACs in this area.