Progress 03/01/09 to 02/28/13
Outputs
OUTPUTS: PCR-based diagnostic tools for identifying new Pgt races. Development of the diagnostic assay for the Ug99 race group has been completed. Stage-1 assay is designed to identify members of the of the Ug99 race group of P. graminis f. sp. tritici. This assay has been extensively tested, using more than 500 samples, with an accuracy rate of over 99%. This assay has been tested in four outside laboratories, including an APHIS-PPQ-CPHST lab, and the resulting data are consistent across platforms and sites. In addition, this assay has been deployed in one lab in Africa. Further testing by CPHST is required, prior to deployment to NPDN labs. Refinement of the stage-2 assay has been completed and is composed of panel of 15 SNP markers. Stage-2 assay has been tested with over 200 samples and has shown to be able to predict race phenotypes within the Ug99 race group with an accuracy of better than 99%. In addition, stage-2 assay is able to identify false positives from the stage-1 assay. This assay is in the process of being tested in an outside laboratory. Work will continue with CPHST to certify the stage-1 assay and arrange training and deployment to NPDN labs. Operational early warning system for WSR based on aerobiological modeling and spore collection. The IAMS model is configured for near-real time forecasting of wheat stem, stripe and leaf rust and has been used by PSU graduate students in Plant Biology during the 2012 for forecasting projects. In addition, two undergraduate students in the PSU Department of Meteorology were trained in 2012 to make ensemble forecasts of the risk of wheat rust spread. These forecasts were incorporated into the Field Crops Rust Forecast Bulletin that was distributed to Extension specialists during the 2012 growing season. Online IT products and management guidelines for growers based on observations, model results & commentaries. Cereal Disease IT platform software tools for entering observations and commentary on WSR and other cereal diseases into a national database was integrated into the Industry Pest Information Platform for Extension and Education in 2012. PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: To sustain our preparations for the incursion of new races of Ug99 into the U.S. beyond the period of the grant, we have integrated the Cereal Rust Information System into the new Industry Pest Information Platform for Extension and Education. This action, unanticipate at the time we wrote the grant proposal, will enable the IT structure that we built to support cereal disease monitoring, modeling, and communications to continue. Partners from industry have pledged to support iPiPE.
Impacts
Rapid identification of new Pgt races. Government and university scientists now have a diagnostic assay for the Ug99 race group in lieu of an incursion of TTKSK, TTKSF, TTKSP, TTTSK and PTKSK into the U.S. The stage 1 assay is completed, tested, and shared with APHIS-PPQ-CPHST. A stage 2 assay able to identify false positives from the stage-1 assay will be ready to deploy shortly. Operational early warning system for WSR. Output from the IAMS wheat stem rust model is now being used on a daily basis during growing season to assess the risk of infection from aerial transport of rust spores from southern to northern latitudes in North America. The system has been integrated into the Industry Pest Information Platform for Extension and Education (iPiPE) and will be sustained into the future by agricultural industry partners. Online IT products and management guidelines for growers based on observations, model results and commentaries. Government scientists, university Extension specialists, industry agents and crop consultants are using the IT tools and management guides develop as part of the Cereal Rust Information Platform to monitor and interpret distributions of wheat rust and other pests. The tools have been integrated into the iPiPE so as to be sustained by industry partners.
Publications
- Pan, Y, S.A. Isard, and M. Chamecki. 2012. Dispersion of heavy particles emitted from area sources in the unstable atmospheric boundary layer. Boundary Layer Meterorology 146: 235-256.
- Chamecki, M., N.S. Dufault, and S.A. Isard, 2012. Atmospheric dispersion of wheat rust spores: a new theoretical framework to interpret field data and estimate downwind dispersion. Journal of Applied Meteorology and Climatology 51: 672-685.
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Progress 03/01/10 to 02/28/11
Outputs
OUTPUTS: PCR-based diagnostic tools for identifying new Pgt races in infected plant tissue and spores. Continued progress has been made on the development of qPCR assay for the detection of Ug99 and related Pgt races. This Ug99 race group currently consists of 5 related races; TTKSK, TTKSF, TTKST, TTKSP, TTTSK and PTKSK. A core set of 5 primer/probes have been developed and tested with an extensive collection of Pgt isolates, including approximately 200 collections from Africa. This core set is able to distinguish Ug99 race group from all other isolates tested. All isolates of the Ug99 race group are positive for all five of these assays, while non-Ug99 race group Pgt isolates test positive for no more than 3 of the 5 assays in this core set. Additional markers continue to be developed. Operational early warning system for WSR based on aerobiological modeling and spore collection. The IAMS model was configured for near-real time forecasting of wheat stem, stripe and leaf rust during the 2011 growing season. Two additional undergraduate meteorology students at PSU were trained to make ensemble forecasts of the risk of wheat rust spread. Monitoring, reporting, and managing protocols and guidelines for WSR. The third Cereal Rust workshop for wheat extension pathologists was held on 14-15 Oct 2010 in St. Paul. The discussion focused on: 1) survey and monitoring, 2) communication and information technology, 3) development of a communications plan, 4) diagnostic tests, 5) barberry survey, 6) management strategies involving fungicides, and 7) management strategies involving host resistance. Online IT products and management guidelines for growers based on observations, model results & commentaries. Cereal Disease IT platform software tools for entering observations and commentary on WSR and other cereal diseases into a national database was modified to accommodate needs expressed by Extension specialists who had used the system in 2010. An "Express" website was constructed to speed the entry process for Extension specialist commentary. PARTICIPANTS: Scott A. Isard, Professor of Aerobiology, Departments of Plant Pathology and Meteorology, Penn State University (PSU); Marcelo Chamecki, Assistant Professor, Department of Meteorology, PSU; Nicholas Dufault, Post-doc, Department of Plant Pathology, PSU; Simone Gleicher, Karen Bunavage, and Katelyn Johnson undergraduate students, PSU; Les Szabo, Research Geneticist, USDA-ARS-CDL; Jo Anne Crouch, Post-doc, USDA-ARS-CDL; Carrie Lapaire Harmon, Southern Plant Diagnostic Network; Sarah Hambleton, Agriculture and Agri-Food Canada; Erick DeWolf, Associate Professor, Department of Plant Pathology, KSU; Joseph Russo, Senior Researcher, ZedX Inc. Three additional undergraduate students in the Department of Meteorology at PSU were trained to make forecasts of risk of rust spore movement in the air. TARGET AUDIENCES: National Plant Diagnostic Staff - provided diagnostic kits and training for identifying new races of wheat stem rust; Wheat Extension pathologists - provided training for use of Cereal Rust Information System to report observations of wheat rusts; PSU meteorology undergraduate students - provided training on using models and data to make forecasts of aerial movement of rust spores; PSU undergraduate students - provided field experience related to measuring the flux of rust spores from wheat canopies. PROJECT MODIFICATIONS: We asked for and received a no-cost extension of the grant period to continue our work on developing and deploying rapid diagnosic tools for identifying new races of wheat stem rust.
Impacts
Knowledge on how to rapidly detect new Pgt races with PCR methods. A preliminary set of primers/probes was sent to two diagnostic laboratories (Carrie Lapaire Harmon, SPDN; Sarah Hambleton, Agriculture and Agri-Food Canada) for testing. Both of these laboratories were able to replicate the results obtained at the CDL. Adoption by State Specialists of online procedures for monitoring, commenting, and reporting wheat diseases in support of the Cereal Rust IT platform (CRIP). Extension specialists from the wheat producing states are using the CRIP in 2011 to comment on presence and severity of WSR (races currently present in the U.S.) as well as barley leaf rust, oat crown rust, oat stem rust, wheat leaf rust and stripe rust. Operational early warning system for WSR based on monitoring and aerobiological modeling. Extension specialists receive near real-time information on the geographic distribution of leaf, stripe and stem rust through CRIP maps and a biweekly assessment of the risk of stem, stripe, and leaf rust spread through the Wheat Rust Forecast Bulletin. This information is used by the Extension specialists to create management guidelines for growers.
Publications
- No publications reported this period
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Progress 03/01/09 to 02/28/10
Outputs
OUTPUTS: PCR-based diagnostic tools for identifying new Pgt races in infected plant tissue and spores - Dr. Crouch was hired to fill the Postdoctoral position and is working with Dr. Szabo on the development of molecular assays for rapid identification of Ug99 and related Pgt isolates. A SNP data set based on Illumina genome sequence data for Ug99 (race TTKSK), the three variants within this lineage (races TTKST, TTTSK and TTKSF), an isolate from Yemen (race TRTTF) and 2 U.S. isolates (races SCCLC and DFBJC) has been used to develop primers and probe marker sets. About 50 real-time primer/probes sets (using TaqMan probes) have been developed and tested. Seven primer/probe sets passed the initial screen and now have been tested using a set of approximately 150 Pgt isolates. Operational early warning system for WSR based on aerobiological modeling and spore collection - The IAMS model was developed and is operational for WSR. It will be deployed as soon as Ug99 is identified in the Western Hemisphere. HYSPLIT aerobiology models for tracking rusts have been incorporated into the Cereal Disease IT platform. Monitoring, reporting, and managing protocols and guidelines for WSR. Extension materials for identifying WSR have been developed and distributed - The Cereal Disease IT platform for reporting WSR (as well as barley leaf rust, oat crown rust, oat stem rust, wheat leaf rust and stripe rust) has been developed and is currently operated by ZedX in partnership with the CDL. Online IT products and management guidelines for growers based on observations, model results & commentaries - New software tools for entering observations and other relevant information on WSR and other cereal diseases into a national database, making commentary, running trajectory models, and displaying maps are currently available to Extension Specialists on the Cereal Disease IT platform. Students who understand interactions of biological and meteorological factors that govern pest movement and how to use this knowledge for agro-ecosystem management - In fall 2008, Dr. Isard taught the proposed graduate-level aerobiology course in the Ecology Program at Penn State. A second graduate level aerobiology field methods course will be taught by Drs Isard and Chamecki at Penn State during summer 2010. Germplasm with improved WSR resistance - The breeding programs at LSU and TAM are participating in marker-assisted selection for rapid improvement of effective stem rust resistance. PARTICIPANTS: Scott A. Isard (PD, PSU) - adapted Integrated Aerobiology Modeling System (IAMS) to wheat rust and analyzed model output, organized Advisory Committee meeting, designed Cereal Disease Information Platform (CDIP) website, trained Extension Specialists to use website, and taught graduate level aerobiology course. Julie Golod (PSU) - helped design tools for the CDIP. Les Szabo (PI) and Joanne Crouch (USDA ARS CDL)worked to develope diagnostics for new Pgt races and analyzed rain samples for wheat rust spores. Mark Hughes (USDA ARS CDL) worked to design and deploy CDIP website. Joe Russo (PI, ZedX Inc) helped design and directed building of CDIP website and helped modify IAMS for wheat rust. Brian Holderman and Ed Weaver (ZedX Inc) - programmers who wrote computer code for CDIP website. Jeff Grimm (ZedX Inc) - programmer who modified and ran IAMS. Erick DeWolf (PI, KSU) - organized and chaired workshop for Great Plains Small Grains Extension Specialist to plan monitoring program and learn to use CDIP website. TARGET AUDIENCES: To date, Small Grains Extension Specialists from Great Plains states have been the target audience for project outcomes. This group of about 10 individuals attended a workshop in January 2010 to learn to use the Cereal Disease Information Platform and is currently reporting wheat diseases and contributing commentary to the website on a regular basis. Six PSU graduate students who participated in the Ecological Aerobiology Course at PSU now better understand interactions of biological and meteorological factors that govern pest movements and how to use this knowledge for agro-ecosystem management. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
Knowledge on how to rapidly detect new Pgt races with PCR methods - The 7 primer/probe sets are able to distinguish the Ug99 lineage from all North American Pgt isolates and most international isolates. In this collection there are four Pgt isolates (three from North Africa and one from Central Europe) that give the same profile, as isolates of the Ug99 lineage. Additional primer/probe sets are being designed and tested to increase the specificity. Improved knowledge of WSR aerobiology - The modified IAMS model was used for evaluating the risk of aerial transport of wheat stem rust spores from potential off-shore source regions to the Western Hemisphere. We concluded that the risk of aerial transport by natural means of Ug99 to the Western Hemisphere is very low. The implication of this finding is that the most likely route by which Ug99 will enter the Western Hemisphere, if it does, is by human-mediated transport. Simulations were conducted using the major wheat producing areas of Mexico as the source of stem rust spores. These results indicated that potential opportunities for transport of stem rust spores from these areas to wheat growing areas in the southern and central U.S. are relatively common. This implies that Ug99 would likely spread through the air into wheat producing regions of the U.S. within a few years if it was introduced into Mexico. Adoption by State Specialists of online procedures for monitoring, commenting, and reporting wheat diseases in support of the Cereal Disease IT platform - Many extension specialists from Great Plains states (those trained at the Feb workshop) are using the Cereal Disease IT platform in 2010 to report and comment on WSR (races currently present in the U.S.) as well as barley leaf rust, oat crown rust, oat stem rust, wheat leaf rust and stripe rust.
Publications
- No publications reported this period
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