Grantee Research Project Results
Final Report: Reducing Fungicide Usage for Potato Production by Unraveling Tuber and Foliage Defense Mechanisms Against the Late Blight Pathogen Phytophthora Infestans
EPA Grant Number: SU834316Title: Reducing Fungicide Usage for Potato Production by Unraveling Tuber and Foliage Defense Mechanisms Against the Late Blight Pathogen Phytophthora Infestans
Investigators: Bradeen, James M.
Institution: University of Minnesota
EPA Project Officer: Page, Angela
Phase: I
Project Period: August 15, 2009 through August 14, 2010
Project Amount: $9,996
RFA: P3 Awards: A National Student Design Competition for Sustainability Focusing on People, Prosperity and the Planet (2009) RFA Text | Recipients Lists
Research Category: Pollution Prevention/Sustainable Development , P3 Challenge Area - Sustainable and Healthy Communities , P3 Awards , Sustainable and Healthy Communities
Objective:
Potato ranks among the world's most important food crops and is an especially promising food for developing countries. Late blight disease results in multi-billion dollar yield losses and the application of millions of tons of fungicides each year. Chemical-dependent potato farming carries high production and environmental costs. One of the most economical and environmentally sound ways to reduce fungicide usage is deployment of late blight resistance genes. We have a long research history of working with RB, a foliar late blight resistance gene from a wild potato species. As we move towards large-scale deployment of the RB gene in India and other parts of the world, its impact on both foliar and tuber late blight disease must be considered.This project utilizes “next generation,” high-throughput RNA sequencing to identify plant genes involved in resistance to late blight in foliage and tubers. Our research will enhance basic understanding in the plant sciences and will assist researchers in developing specific deployment strategies for RB in a no- or reduced-fungicide production setting.
This project encompasses a series of experiments aimed at testing the following hypotheses:
- Hypothesis 1: Different organs of potato (e.g., foliage vs. tubers) use the same or similar defense mechanisms against the late blight pathogen P. infestans.
- Hypothesis 2: Differences in disease phenotypes in different organs within the same genotype are due to differences in timing of defense initiation.
- Hypothesis 3: High resistance gene transcript levels lead to earlier initiation of defense mechanisms in all plant organs.
Summary/Accomplishments (Outputs/Outcomes):
- More than 215 million RNA sequences from potato tubers infected with P. infestans were generated. This represents a >1,300-fold increase in data generation relative to our previous expectation of 160,000 sequence reads. This increase was achieved by capitalizing upon emerging next generation sequencing technology (Illumina Solexa).
- Bioinformatic comparison of tuber and foliar datasets from potato reveal that while many of the same genes are activated in both tissues when P. infestans attacks, overall defense response mechanisms in leaves and tubers might be substantially different. These analyses are ongoing.
- We have identified a large set of genes that are responsive in the potato tuber to attack by P. infestans. These genes constitute candidates for genes involved in resistance mechanisms in the tuber.
- Although this project focused on potato gene transcription, application of newer sequencing technologies allowed us to simultaneously develop a large dataset of genes transcribed in the pathogen as well. Some of these genes may be critical in defining a microbe’s ability to attack certain plant genotypes. Future analyses of these genes may reveal new disease control strategies. These genes also may be utilized in future studies as molecular markers to quantify late blight disease development.
Conclusions:
The foliar late blight resistance gene RB, the most-promising genetic resource for reducing fungicide usage for potato production, can also be utilized to reduce incidence of tuber late blight disease. This finding has worldwide significance as RB is likely to be deployed on a large scale. Most immediately, RB will be deployed in India, the third largest potato producing nation, beginning in 2012.
- Our study reveals basic strategies used by plants to defend against plant pathogens and suggests that defense mechanisms can be modulated in different plant tissues. This research has yielded large plant and pathogen datasets for downstream analyses.
- Our research is among the first to utilize next generation sequencing technologies to study plant-microbe interactions and, to our knowledge, is the very first to study the potato tuber-P. infestans interaction transcriptome. Our research provides a roadmap for other plant scientists. Importantly, the methodologies we tested and employed in this study can be capitalized upon to further refine our understanding of potato-P. infestans interactions, yielding strategies for resistance gene deployment in a no- or reduced-fungicide production setting (see Phase II proposal).
Proposed Phase II Objectives and Strategies:
Objective: Our Phase II research is designed to translate phenotypic and molecular analyses of potato-P. infestans interactions into disease forecasting models that will yield recommendations of reduced fungicide usage for potato production. Building on observations from previous research, including our Phase I project, our Phase II experiments will explicitly test the following hypotheses:
- Hypothesis 1: The age of a ‘Russet Burbank’ potato tuber influences the degree to which the late blight resistance gene RB imparts tuber blight resistance. These differences in disease resistance are due to delayed onset of resistance mechanisms in older tubers post infection rather than fundamental changes in genetic pathways triggered.
- Hypothesis 2: Both potato age and genetic background (cultivar) influence late blight disease resistance levels in the foliage. Differences in disease resistance are due to changes in a plant’s response time and/or intensity to pathogen attack.
- Hypothesis 3: Late blight forecasting models can be modified to incorporate both potato plant age and cultivar as factors in predicting the risk of late blight infection. Incorporating age and cultivar into forecasting models will result in recommendations of a reduced number of fungicide applications.
Strategies: Both phenotypic and molecular experiments will be conducted in Phase II by a team of graduate and undergraduate student reseachers. Phenotypic assays aimed at understanding how plant age and genetic background impact a potato’s level of resistance to P. infestans will be conducted using whole plant greenhouse assays and laboratory-based detached leaf assays. In total, plants of seven potato backgrounds and five ages will be surveyed. Molecular assays will include the application of next generation sequencing (Illumina Solexa) tested and employed during Phase I to further refine our understanding of potato-P. infestans interactions in both the tuber and the foliage. In total, 32 sequence datasets (a total of ~840 million sequence reads) will be generated and analyzed using established (Phase I) bioinformatics pipelines. Sequencing efforts will be supported in Phase II by quantitative RT-PCR of specific genes shown through sequence analyses to be involved in regulating defense responses. Knowledge gained from phenotypic and molecular assays will be translated into applied potato production by modifying existing late blight disease forecasting models to incorporate potato genetic background and age as factors in determining when a potato farmer should apply fungicides. A simulated test using climatic data from previous growing seasons will be used to assess the degree to which fungicide usage can be reduced using the modified disease forecasting models.
References:
Journal Articles:
No journal articles submitted with this report: View all 2 publications for this projectSupplemental Keywords:
Next-generation sequencing, Potato, Late blight, Fungicide usage, Disease Monitoring, 454 sequencing, pyrosequencing, transcriptomics, plant-pathogen interactomeRelevant Websites:
The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Conclusions drawn by the principal investigators have not been reviewed by the Agency.