Grant Information
| Knowledge Area | Subject of Investigation | Field of Science | Percent |
|---|---|---|---|
| 216 - Integrated Pest Management Systems | 1460 - Tomato | 1170 - Epidemiology | 34% |
| 216 - Integrated Pest Management Systems | 1131 - Wine grapes | 1170 - Epidemiology | 33% |
| 216 - Integrated Pest Management Systems | 999 - Citrus, general/other | 1170 - Epidemiology | 33% |
The project will develop mathematical models of crop diseases that allow the impacts of those diseases on agricultural sustainability to be studied. For each disease this process involves creating a model specific to that disease which captures its dynamics and impact on crop production. The disease-specific models will be linked to a generic systems model that represents the economic, social and environmental pillars of sustainability. By introducing the simulated effects of diseases from the specific disease models into the generic sustainability model we will be able to examine the relative impacts of different diseases and the mechanisms through which they affect sustainability.
Objective 1 will be achieved by a literature search combined with a virtual workshop convened by the PI to gather the views of a panel of experts in the USA and overseas. The aim of this phase of the research will be to construct a database of examples of impacts of disease on different domains of sustainability. Where possible, quantitative information will be gathered based on reported financial losses. However, we recognize that in many cases only qualitative information will be available. In such cases the panel of experts will be asked to provide opinions as to the extremes and central tendency of the relationships being examined. The consensus of these responses will be used to form subjective probability distributions for the effects.Objective 2 will expand on the definitions of sustainability described above essentially to adapt them specifically to the context of plant disease. The main goals here will be to define appropriate timescales for the survival and simulation models and the appropriate statistical model for the time-course of the instantaneous hazard in the survival models. The first objective will be achieved by elicitation of expert opinion from different stakeholder groups and from collaborators. The second objective will be pursued by combining literature research on the temporal progress of disease, empirical analysis of existing data sets, and by arguments from first principles. Candidate solutions will be tested by evaluation by the panel of experts and adapted in light of suggestions made by them.Objective 3 Once objectives 1 and 2 have been completed, it will be possible to construct simulation models which link plant disease epidemics to the adapted version of SIMOSU. The model will be run using standard numerical simulation methods and a classical sensitivity analysis will be used to examine the response of sustainability to changes in the size of effect assumed for the diseases.Objective 4 will be achieved directly through our choice of simulation software (Simile) which automatically generates a declarative model structure (in Prolog) for each model. The declarative Prolog model can serve as the declarative model in its own right, but we will convert all declarative models to XML code to allow easy interchange with other researchers and interested parties. All declarative models will be made freely available for downloading from the PI's lab website.Objective 5 will develop objective 3 in more detail using case studies from diseases of current interest in the PI's applied research projects with California commodities. The three candidate commodities are salad spinach, processing tomato and wine grape. The diseases of interest are, respectively, downy mildew, spotted wilt virus and leafroll disease. For one or more of these case studies, depending on progress with the preceding objectives, a parameterized version of the model will be used to examine the projected impact of the disease on sustainability under current production conditions.Objective 6 will extend the analysis of objective 5 by examining the potential consequences of changes in production practices (through their expected effects on disease and the variables in SIMOSU) on sustainability. The changes in production practice will be selected to reflect potential impacts of extension efforts or policy changes. These effects will be gathered by discussions with relevant stakeholders in the research.
Target Audience
Progress on various aspects of the project as presented to state and national audiences at various stakeholder and science meetings/conferences. We also reached national and international audiences through publication in peer-reviewed journals. We briefed the USDA-APHIS-MAC for citrus HLB and the USDA-ARS ONP on aspects of the project and developed some aspect of the work into a collaborative project with CDFA to provide research services for pest exclusion of quarantine organisms.
Changes / Problems
Nothing Reported
Training & Professional Development
The project provided training opportunities for one PhD student, in interdisciplinary science and institutional design, one PhD student working on information theory and disease forecasting, and four undergraduate intern researchers working on a range of quantitative projects. In addition one staff researcher acquired new data analysis skills in the construction of hierarchical Bayesian models and the development of social network graphs from interaction data.
Dissemination Streams
Across the the life of the project our approach to dissemination of the results has relied, successfully, on three main approaches. First, we use traditional academic publishing in peer-reviewed journals to make our work available to peer audiences. Second, by the nature of our work much of what we do involves close collaboration with state and federal regulatory and science agencies and we disseminate our research ideas directly to stakeholders by using them in our work on problem solving. Finally we devote considerable time to direct interaction with stakeholders in agriculture and horticulture in our work on problems and, again, the results of our work are put into practice and tested in real time through these interactions.
Next Reporting Steps
Nothing Reported
Target Audience
As a consequence of the COVID-19 situation, we focused activity on writing and publishing papers since opportunities for direct interaction with stakeholders were limited.
Changes / Problems
Nothing Reported
Training & Professional Development
Two PhD students and two undergraduate student interns received training on aspects of model development and data analysis during the reporting period.
Dissemination Streams
Results were disseminated primarily through peer-reviewed publication
Next Reporting Steps
Over the next reporting period we plant to focus attention on objective 6 and develop methods for evaluating decision making at an individual and group level using information theoretic approaches. <br><br>
<br>What was accomplished under these goals? Work during the reporting period focused mainly on objective 1. Our work showed that inducible resistance (which appears to be ubiquitous in plants) is explainable as a bet-hedging strategy for use of scarce resources when plants develop in environments where pathogen attack is not certain. We also showed that shifts in the resistance phenotype in a long-lived perennial species are explainable in terms of induced resistance. Work on evaluation of statistical disease risk models revealed the important properties of three commonly used metrics for measuring model performance. <br><br><b>Publications</b><br>
Target Audience
Progress on various aspects of the project were presented to state and national audiences at various stakeholder and science meetings/conferences. We also reached national and international audiences through publication in peer-reviewed journals.
Changes / Problems
Nothing Reported
Training & Professional Development
One graduate student and two staff members had opportunities to manage projects within the wider program of work and to take responsibility for interaction with our stakeholders.
Dissemination Streams
Our work has been communicated directly to our stakeholders through our participatory approach to science and also through the traditional mechanisms of publication and presentation at meetings. Particularly in the case of our work on citrus HLB, we inform our stakeholders of our activities on their behalf through a regularly updated public website: DATOC.us
Next Reporting Steps
We will continue to work at a range of scales from global to local on key issues where plant pests and diseases threaten the sustainability of crop production. We have just entered into a 2 year agreement with CDFA to provide data analytical support to their pest exclusion branch to improve a range of pest detection and eradication programs. Through Plant Protection Act (Farm Bill) support we will be engaging international collaborators at Cambridge University in the UK to add their modeling capability to the strategic support for HLB response in CA and continuing to build our collaborations with the UC system and with state and federal regulatory agencies to improve plant health. <br><br>
<br>What was accomplished under these goals? Work on the global survey of losses to pests and diseases in major food crops provided the first survey of its kind of crop losses on a global basis. Previous data that were widely cited in support of policy and science recommendations were often based on information submitted by registrants from the pesticide industry from untreated plots in field experiments. While there is no evidence of deliberate malice or efforts to distort the data, such reporting tends to have inherent biases because trials where either no damage occurred or where the applied treatments were not shown to be significantly different from the untreated controls tend not to be reported. In addition such trials do not have true global coverage. Although our method relies on expert judgment we developed methodology to ensure robustness in our estimates. The paper has been cited 88 times in just over a year since publication and has become the de facto standard for crop loss assessment. The team has been requested by the International Society for Plant Pathology to extend our approach to minor crops and forests to develop a global plant health assessment in connection with the UN International Year of Plant Health 2020. At a more local level our work on the California HLB epidemic has demonstrated that real-time epidemiology can be used to provide program support to a phytosanitary program and to improve the sustainability of a key crop commodity in the face of a threatening invasive disease. We documented our approach in a high profile publication and continue to interact with the regulatory program on a daily basis. <br><br><b>Publications</b><br>
Target Audience
Peer scientists, extension advisers, policy and regulatory staff at State and Federal agencies, growers
Changes / Problems
Nothing Reported
Training & Professional Development
A graduate student was trained in the use of software for multi-criteria decision analysis. A staff researcher learned Bayesian model development for statistical analysis.
Dissemination Streams
We have published peer-reviewed articles, policy briefing papers and attended a wide range of industry meetings and workshops.
Next Reporting Steps
We will continue to work on the general theoretical approach and incorporate specific empirical examples. <br><br>
<br>What was accomplished under these goals? The major activity under the project in the last year has been the development of a risk analysis model for risks of citrus HLB spread in California in association with bulk citrus transport. The model was developed to help the Citrus Pest and Disease Prevention Committee (CPDPC) evaluate the need to modify the existing regulations governing covering of bulk loads and pre-shipment mitigations. Our work showed that there was no justification for changing the existing rules. <br><br><b>Publications</b><br>
Target Audience
The target audiences reached during the reporting period include: State and Federal Agency officials responsible for phytosanitary policy and supporting technology development, peer-group scientists working on plant disease epidemiology problems, extension scientists, and agriculture industry stakeholders.
Changes / Problems
Nothing Reported
Training & Professional Development
A graduate student spent 3 months working with USDA-APHIS-PPQ-CHPST staff in Raleigh NC helping to develop plans for new national phytosanitary regulations and processes for seed importation. The student also received training in cognitive map analysis for analyzing complex organizational problems. Two technicians received training in field survey analysis and sample collection for disease surveys in citrus and were then trained to carry out diagnostic laboratory analyses needed to process the samples. Two undergraduate interns and two technicians received training in methods of data analysis and secure data management.
Dissemination Streams
The results have been disseminated by a variety of mechanisms. In some cases we work directly with the target audience and transfer is immediate, such as our work with APHIS on regulatory issues, or our work with CDFA on management of HLB in California. In other cases we contribute to various UC Cooperative Extension efforts and participate in extension meetings and other on-farm activities. We presented work at local, State and national science conferences, we published peer reviewed papers and we also disseminated our work via social media and by giving press interviews.
Next Reporting Steps
We plan to continue with our on-going activities with a switch in emphasis from leafy greens to citrus HLB disease. <br><br>
<br>What was accomplished under these goals? We continued to develop an analysis of threats to the sustainability of fresh-market spinach production in the Western USA, focusing in particular on the regional risk posed by the downy mildew pathogen Peronospora effusa in its annual summer epidemic, and additionally by modeling the long term threat caused by use of contaminated seed. We developed a new evidence-based approach to evaluating the economic trade-offs involved in setting voluntary targets for rejecting seed lots for sale on the basis of P. effusa contamination levels. Since P.effusa is an endemic organism in the USA there is no prospect of federal seed importation regulations being imposed and any action to limit the importation of P.effusa along with seed would need to be operated by the industry through a voluntary self-regulation process. We established a protocol for estimating order-of-magnitude estimates for the epidemic impact arising from contaminated seed. Together with a simple evidence-based approach for calculating seed rejection thresholds, this provides the basis for objective discussion between the seed industry and growers about how to set equitable thresholds for rejecting seed lots, on the basis of balancing potential economic losses on either side of the trading relationship. <br><br><b>Publications</b><br>