National Agricultural Genotyping Center (NAGC)

Goal #1

Shorten turnaround time between development and validation for specific pathogen tests within and among commodity groups.

There is an ongoing need to make a variety of pathogen tests available to the NPMTI and the agricultural community. Diagnostic laboratories with specialized equipment and experienced personnel can quickly assess and optimize quantitative-based tests for use across commodity groups.

Milestones/Performance Expectations:

  • Evaluate and, if necessary, modify published quantitative tests for pathogens related to NPMTI goals.
  • Rapidly create novel quantitative tests if no published tests have been developed.

Performance Measures:

  • Validation of published and novel tests for use in the NPMTI.
    • Development of Standard Operating Procedures (SOPs) that are accessible to NPMTI teams
  • Improve methodological standards for molecular-based data collection.
    • Provide a resource hub for all commodity groups on standard practices in quantification of pathogens.
    • Provide proficiency tests and support to collaborating laboratories that collect pathogen quantification data.

Research Needs:

  • Collection and subsequent access to isolates and pure cultures or pathogens across the participating US regions. Successful detection of isolates that represent a wide geographic distribution will provide evidence of a robust diagnostic assay.
  • Validate detecting and quantifying the target pathogens from a variety of substrates, including those that may impact quantitative diagnostic tests (e.g., soil types).
  • Develop standard operations procedures (SOPs) that can provide a level of standardization for molecular diagnostics for model inputs.

Outputs: Year 1

  • Corn Group – Provide laboratory support for DNA extraction and molecular assay deployment and validation for Northern Corn Leaf Blight (NCLB) and Gray Leaf Spot (GLS) in soil and residue.
  • Cotton Group – Begin assay development and validation for Target Spot, Areolate Mildew, and viral targets.
  • Wheat Group – Begin validating spore testing using NAGC’s Wheat Rust Panel and optimize assay for Parastagonospora leaf blotch.

Year 5

  • Continue to increase NAGC’s test menu to encompass 2-3 pathogen targets per year for each commodity group participating in NPMTI. With the inclusion of more commodity groups, we expect to have a diverse diagnostic menu.

 Anticipated Impact:

Expanded menu of pathogen tests that have been standardized to minimize noise in the predictive model that may occur due to differences in pathogen quantification protocols (e.g., reagents, diagnostic chemistry).

Goal #2

Provide high-throughput testing support to participating research institutions

NPMTI network needs to maintain test capacity and shorten turnaround time to make progress on predicting disease risk in near real-time. Additionally, some groups that excel with in-field research, may not have the molecular diagnostic capabilities to include pathogen data in their research program.

Milestones/Performance Expectations:

  • Maintain an up-to-date menu of pathogen tests.

Performance Measures:

  • Maximized capacity for pathogen testing and analysis.

Research Needs:

  • Update equipment and optimize techniques for high-throughput testing and large sample volumes.

Outputs: Year 1

  • Corn group – Test residue and soil samples for NCLB and GLS from field study sites.
  • Cotton group – Begin preliminary testing for Target Spot, Areolate Mildew, and viral targets.
  • Wheat group – Test spore traps samples and other substrates for wheat rusts.

Year 5

  • Increase output of sample testing for all three groups and any additional commodity groups that are involved in the NPMTI.

Anticipated Impact:

Increased use of high-throughput testing facility allows researchers that do not have molecular laboratory equipment and experience to allocate their limited resources away from repetitive testing of bulk samples. This goal will also allow increased accessibility of molecular diagnostics to research groups with field data that do not have molecular laboratory equipment or experience.

Goal #3

Research & Development in the next generation of quantitative technology for pathogens.

The variability of pathogen pressure across the US will likely require in-field technology to provide near real-time inputs for the predictive model at finer scales. The latest point-of-use or other human diagnostic technology are often transferable to the agricultural sector, yet are not thoroughly tested.

Milestones/Performance Expectations:

  • Test point-of-use diagnostics for their applicability for in-field pathogen data
  • Develop in-field test protocols
  • Continual examination of novel chemistries and technologies for rapid nucleic acid extraction of complex substrates and pathogen quantification.

Performance Measures:

  • Transfer of laboratory-based pathogen tests to a point-of-use test that is quantitative or semi-quantitative
  • Integration of advancements in diagnostics that improve the throughput and accuracy of pathogen data collection.

Research Needs:

  • Compare the practicality of several in-field technologies that have shown promise in literature for point of use pathogen tests.
  • Better understand the limitations of in-field tests for predictive modeling of agricultural pathogens.
  • Assess in-field technologies that may be easily and quickly modified or adapted for use across multiple commodities.

Output: Year 1

  • Assess simplified DNA extractions and lateral flow technology or other point-of-use tech for one common pathogen in a single commodity group.

Year 2

  • Assess simplified DNA extractions and lateral flow technology for one common pathogen in each participating commodity group

Year 5

  • Diversify point-of-use tech and become a leading source of this tech for the agricultural community

Anticipated Impact:

Rapid in-field diagnostics that can be used by personnel in the agricultural community with little or no laboratory experience. Results from these tests may be used to provide fine-scale inputs for regional models or perhaps individual growers.

Goal #4

Lead in-person training for graduate students, postdoctoral researchers, and other visiting scholars in molecular diagnostic techniques.

Milestones/Performance Expectations:

  • Develop a short workshop or training program for interested scholars that is related to basic skills needed for molecular-based diagnostics.

Performance Measures:

  • Opportunity for shared learning of protocol standardization (SOP development) techniques for pathogen detection.
  • Focused laboratory training for scientists to develop pathogen tests that align with the RAC area of interest

Output: Year 1

Discuss or survey the areas of interest or gaps in molecular-based techniques from each research group

Year 2

  • Begin and complete workshop and lesson development on the identified gaps or areas of interest and invite 1-2 trainees for the first of a 2-3-day workshop?

Year 5

  • Become a center for training in molecular-based diagnostics (laboratory and in-field diagnostic technology) for scholars that participate in the NPMTI.

Anticipated Impact:

Increased skill development in molecular techniques among NPMTI members that will improve pathogen test development and validations.