Progress 03/01/11 to 02/28/17
Outputs
Target Audience: The target audience are potato and tomato growers throughout the United States, educators, crop protection consultants, and researchers. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?During the past year, six graduate students and 2 postdoctoral worked on the project, along with one undergraduate. Theyreceived training in plant disease diagnostics, phylogenetics, genetics, genomics, bioinformatics, molecular plant sciences, and computer programming. How have the results been disseminated to communities of interest?Our group published eleven referreed papers in scientific journals during the past year. In addition, presentations were made at the American Phytopathological Society in Tampa Florida; at the Oomycete Molecular Genetics Conference in Pacific Grove, California; the Fungal Genetics Conference in Pacific Grove, California; and the Molecular Plant-Microbe Interaction Congress in Portland, Oregon. In addition, software to call single-nucleotide polymorphisms or related genetic variants was developed and placed on a public database, Github. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
IMPACT This project continued to focus on short and long-term solutions to late blight. Managing disease requires monitoring the pathogen (since some strains are more or less aggressive, or require the use of different fungicides), understanding how the pathogen (P. infestans) changes its characteristics, learning how the pathogen moves, and testing solutions for plant-based resistance. In the past year, we monitored a shift in the pathogen towards more fungicide-resistant lineages, developed new assays for identifying the pathogen and identifying its characteristics; this will help growers choose the most effective management solution. We also showed that new strains of the pathogen migrate from Mexico, which will help predict future threats. Sources of resistance in wild potato were also identified. Resources for molecular studies of the pathogen were improved by developing a new genome sequence and more accurately predicting the structure and thus function of the pathogen's genes. SPECIFIC RESULTS 1. Monitoring pathogen populations. For 2016, a total of 54 reports were confirmed for late blight throughout the US. Genotyping indicated that they represented lineages US8, US11, US23, and US24. Among genotyped lineages, approximately 44% were collected from potato and 56% were collected from tomato. As in previous years, collections were primarily US23, but the fraction of US8 increased significantly. Most US23 isolates collected from the eastern coast of the US, while other lineages were detected in the western US. 2. Addressing origins and relationships between US lineages. We tested for phylogenetic relationships among U.S. lineages using a population of 31 whole-genome sequences, including dominant U.S. clonal lineages and global strains. We also analyzed ancestry of the mitochondrial genome and nuclear loci. We found support for a shared ancestry among lineages US11 and US18 from the mitochondrial genome and one nuclear haplotype. The other haplotype assorted independently, indicating independent ancestry. We found no support for emergence of any other of the lineages from a common ancestor in the US; instead, each clonal lineage seemed to emerge via migration from a sexual population, potentially located in central Mexico. All lineages, except US23, show greater allelic diversity with Mexico, suggesting that migration route. The findings suggest multiple introductions led to the population structure in the US over the past three decades. We also examined relationships between herbarium specimens of P. infestans and recent isolates. The same unique SSR multilocus genotype, FAM-1, caused the historic outbreaks. FAM-1 grouped with the oldest specimens collected in Colombia and Central America, and was distinct from more recent aggressive lineages in the US. The US1 lineage formed a mid-20th century group. Other modern US lineages and the oldest Mexican lineages formed a group with recent Mexican lineages, suggesting a Mexican origin. A survey of mitochondrial haplotypes in global herbarium specimens documented the more frequent occurrence of the HERB-1 (type Ia) mitochondrial haplotype in archival collections. FAM-1 lineage survived for almost 100 years in the US, was widespread, and was displaced in the mid-20th century by US1 lineage and then by other new lineages from Mexico. 3. Understanding phenotypes at a genomic level. We used high-throughput sequencing to infer chromosomal ploidy, copy number variation, and gene deletions in P. infestans. Our results support the hypothesis that populations at the center of origin of P. infestans are mostly sexual and diploid, and clonal lineages elsewhere in the world are mostly triploid. We also find presence-absence polymorphism of genes in the gene-sparse, effector enriched regions of the genome. These results add to our understanding of P. infestans epidemics as consisting not only of novel genotypes but of massively restructured genomes. Also in support of this goal, we created software to facilitate variant analysis. Functions to read and write VCF files into the r language, extract data, plot summary statistics, and visualize other parameters of the data were implemented.In support of the goal of understanding pathogenicity at a genomic level, and to develop diagnostic tools, we improved the genome assembly of P. infestans. Compared to the prior assembly (from 2009), approximately 20Mb of gaps were filled, the number of contigs were reduced by more than 10-fold, new genes were identified, and linkage analysis was performed that scaffolds the assembly into 14 pseudochromosomes. Using those maps along with SNP analysis, the region determining metalaxyl resistance was identified. Multiple loci were found to determine aggressiveness and sporulation intensity. Transcriptional regulators that control the expression of effectors needed to establish infection were also purified. 4. Improved diagnostics. Validation of a LAMP-based assay for the detection of P. infestans continued. This included testing the sensitivity and specificity of the assay. The assay was found to be specific to P. infestans after testing against other Phytophthora species that infect potato and tomato, and other pathogens. In addition, a consistently positive detection of P. infestans DNA was measured at 1 pg/μl. This represents a 10-fold increase in sensitivity over the conventional PCR assays. The assay was paired with a mobile device consisting of a tablet and a case for holding and reading samples, allowing field deployment. Informative SNPs from the genome analyses were used to develop high resolution melt (HRM) assays and locked nucleic acid (LNA) probes to differentiate lineage US23 from three other U.S. lineages. Three primer pairs targeting SNPs were capable of separating lineage US-23 from lineages US8, US11, and US24 using HRM analysis. Additionally, two LNA probes were designed to target a portion of the P. infestans genome containing two SNPs diagnostic for US23. A single multiplex quantitative polymerase chain reaction assay containing both differentially labeled LNA probes differentiated individuals belonging to lineage US-23 from those belonging to US8, US11, and US24. Antibodies apparently specific to P. infestans were identified. Candidates identified bioinformatically (using refined gene models and screened for expression by RNA-seq analysis of different developmental stages) were used to generate antibodies to P. infestans-specific peptides or recombinant proteins. Two candidates yielded antisera that reacted to P. infestans, but not Phytophthora capsici, potato, or tomato. 5. Potential transgenic solutions. One goal of the project was to determine if resistance to late blight could be achieved by overexpressing pathogen detection genes generically referred to as PRRs. More than 10 additional tomato lines for heterogeneous expression of the Nicotiana benthamiana LRK1 (NbLRK1) gene. None of the lines showed significant over-expression of LRK1. Instead, experiments focused on a transgenic line (35S::NbLRK1) previously generated. While over-expression of LRK1 in tomato conferred resistance to one specific P. infestans isolate, US10, no difference was observed using isolates from lineages US23, US24 and US25. 6. Conventional resistance. A screen of 126 wild diploid Solanum accessions from the Commonwealth Potato Collection (CPC) with P. infestans isolates identified resistances in nine wild species. Effector-omics, allele mining, and a sequencing method called RenSeq (which we developed to focus on resistance genes) were utilized to investigate resistance in Solanum okadae accessions. Combined with transient expression assays and assays with multiple P. infestans isolates, the presence of a novel resistance gene was confirmed. The Ren-seq data has provided the means to speed its introgression into commercial germplasm.
Publications
- Type:
Book Chapters
Status:
Published
Year Published:
2016
Citation:
Fry WE: Phytophthora infestans: New Tools (and Old Ones) Lead to New Understanding and Precision Management. Annual Review of Phytopathology, Vol 54. 2016;54:529-547.
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Ah-Fong AMV, Kim KS, Judelson HS: RNA-seq of life stages of the oomycete Phytophthora infestans reveals dynamic changes in metabolic, signal transduction, and pathogenesis genes and a major role for calcium signaling in development. BMC Genomics. 2017;18:198.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Hansen ZR, Everts KL, Fry WE, Gevens AJ, Grunwald NJ, Gugino BK, Johnson DA, Johnson SB, Judelson HS, Knaus BJ, et al: Genetic Variation within Clonal Lineages of Phytophthora infestans Revealed through Genotyping-By-Sequencing, and Implications for Late Blight Epidemiology. Plos One. 2016;11:e0165690.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Hansen ZR, Knaus BJ, Tabima JF, Press CM, Judelson HS, Grunwald NJ, Smart CD: SNP-Based Differentiation of Phytophthora infestans Clonal Lineages Using Locked Nucleic Acid Probes and High-Resolution Melt Analysis. Plant Disease. 2016;100:1297-1306.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Hansen ZR, Knaus BJ, Tabima JF, Press CM, Judelson HS, Grunwald NJ, Smart CD: Loop-mediated isothermal amplification for detection of the tomato and potato late blight pathogen, Phytophthora infestans. Journal of Applied Microbiology. 2016;120:1010-1020.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Knaus BJ, Tabima JF, Davis CE, Judelson HS, Grunwald NJ: Genomic Analyses of Dominant US Clonal Lineages of Phytophthora infestans Reveals a Shared Common Ancestry for Clonal Lineages US11 and US18 and a Lack of Recently Shared Ancestry Among All Other US Lineages. Phytopathology. 2016;106:1393-1403.
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Liu YX, Langemeier MR, Small IM, Joseph L, Fry WE: Risk Management Strategies using Precision Agriculture Technology to Manage Potato Late Blight. Agronomy Journal. 2017;109:562-575.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Saville AC, Martin MD, Ristaino JB: Historic Late Blight Outbreaks Caused by a Widespread Dominant Lineage of Phytophthora infestans (Mont.) de Bary. Plos One. 2016;11:e0168381.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Van Weymers PS, Baker K, Chen X, Harrower B, Cooke DE, Gilroy EM, Birch PR, Thilliez GJ, Lees AK, Lynott JS, et al: Utilizing "Omic" Technologies to Identify and Prioritize Novel Sources of Resistance to the Oomycete Pathogen Phytophthora infestans in Potato Germplasm Collections. Front Plant Sci. 2016;7:672.
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Wang, J., Larsen, M. M., Garay-Serrano, E., Gregorio-Cipriano, R., Rodr�guez-Alvarado, G., Gr�nwald, N. J., Fernandez-Pavia, S. P., and Goss, E. M. Metapopulation structure in the potato late blight pathogen at the Mexico center of origin. Mol Ecol. 2017;26:10911107.
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Knaus, B. J., and Gr�nwald, N. J. VcfR: a package to manipulate and visualize VCF data in R. Molecular Ecology Resources 2017;17:44-53.
|
Progress 03/01/15 to 02/29/16
Outputs
Target Audience:The primary target audience are potato and tomato growers throughout the United States, educators, and crop protection consultants. Researchers (pathologists and plant breeders) are a secondary target. The project is populated by extension personnel that reach the main areas of the country that are at risk of late blight, who interact with both large and small growers, organic and conventional growers, etc. Undergraduates are an additional target audience, as there is an educational component of the project that gives research experiences to undergraduates. Changes/Problems:It was necessary to divert resources to improving the P. infestans genome sequence, in order to support the genetic mapping, isolate diversity, and complex trait analysis components of the project. What opportunities for training and professional development has the project provided?Undergraduate summer research. We hosted 12 undergraduates this summer. Each worked for about 10 weeks on projects related to late blight or other oomycete diseases. In mid-summer, the students participated in a web symposium. Students prepared an abstract booklet which was shared among the participants, the faculty mentors introduced themselves to the students and described their group's roles in the overall project, the students gave presentations describing their research activities, and the long-term career plans of the students were discussed. We have tracked the outcomes of the prior students in the program. Of those who have graduated from college, 43% are in graduate school in a "relevant" field (plant biology/plant pathology/microbiology), 20% are in graduate school in another field (such as molecular biology), 10% are in medical school, and 24% have lab-based jobs. Graduate student and postdoctoral training: Ten graduate students and 3 postdoctorals worked on the project during the past year, and received training in plant disease diagnostics, phylogenetics, molecular genetics, genomics and bioinformatics, molecular plant sciences, and computer programming. How have the results been disseminated to communities of interest?Extension education activities. About 38 presentations were made to growers and other stakeholders during the year, and five articles focusing on late blight management were written for extension or trade publications. Extension personnel outside our project were also trained to monitor for late blight and to submit samples for phenotypic and genotypic analysis. Growers were reminded to notify their local extension educator, members of our group, and/or the USAblight website about outbreaks. Over the past five years, our extension team members have given about 300 talks, written about 200 articles, had over 40 blog posts/year, hosted at least 6 webinars and made two videos. Field Days/Demonstration Plots. The public (and breeding companies) were invited to view tests of the Ph2/Ph3 tomato lines developed by this project. These were held at four locations in the eastern US. Website. USABlight.org continued to process disease reports, send alerts, and house a large amount of management information including videos on scouting and identifying other diseases that are similar to late blight. Traffic to the web site was similar with the patterns seen in the previous years. There were a total of 24,906 visits to USABlight.org in 2015, with 53,505 pageviews. Traffic to the website peaked in July. A total of 118 confirmed reports of Late Blight were placed on the map hosted on the web site. The disease reports triggered 7,721 disease alerts to subscribers; the number of subscribers increased by 90 over the past year to a total of 438. Genotype information from 135 samples collected at sites of disease outbreak were also provided to stakeholders through the website. Although support for extension activities by this grant will end this year, the collaborative network established by this project will persist. Lines of communication and other resources developed by the project will help the extension members to continue to disseminate information to stakeholders. What do you plan to do during the next reporting period to accomplish the goals?Work during the next year will focus on the following activities: 1. Characterization of fungicide resistance. Analysis of this trait will continue, using an improved P. infestans genome assembly that contains longer contigs, fewer gaps, and more accurate gene models. After validation of the assembly and SNP mapping, candidate genes will be identified by linkage analysis and functional testing. 2. Tests of pattern recognition receptors (PRR). This will ocntinue using an expanded number of transgenic tomato lines. 3. Studies of late blight resistance gene Ph2. This effort will continue using a sequencing-based method that identifies genomic regions that cosegregates with the gene. 4. Complex traits and diversity within P. infestans. This will continue using a combination of genome and targeted sequencing, and mapping of traits, from US lineages of P. infestans and from a GWAS association study based on Mexican isolates. 5. Antibodies specific to P. infestans. New targets for diagnostic antibodies will be tested.
Impacts
What was accomplished under these goals?
IMPACT The project has provided useful tools for controlling late blight. These include an alert system to help growers schedule fungicide applications, a system for reporting isolates to a web site to help growers know when the pathogen is nearby, a Decision Support System tool to increase the efficiency of fungicide use, a system for obtaining genotype and phenotype data for strains of the pathogen to help indicate the best control strategy, improved methods for detecting the pathogen, and cultivars with enhanced resistance. The project has also established a network of extension personnel that will outlive the project and continue to allow improved management of late blight. In total, this project has contributed to increased food security and made potato and tomato production more sustainable. ACCOMPLISHMENTS 1. Scouting for late blight and reporting outbreaks. This activity, largely involving our extension participants, continued to identify occurrences of late blight. Reports were provided to the USAblight.org web site, and plant material collected for genotyping. Reports submitted to USABlight.org from others were moderated to ensure their accuracy; 118 of 154 reports during 2015 were confirmed to be late blight. 2. Extension research. This included field trials and fungicide tests. Much of the latter was integrated into a coordinated test of the Decision Support System (see below). Several groups also tested technologies for detecting the pathogen, which led to new LAMP assays and primer sets capable of distinguishing different lineages of the pathogen. 3. Decision Support System. This management tool can be accessed through USAblight.org. Tests were performed on conventional potato, conventional tomato, and organic tomato in field experiments in WI, MD, FL, NC, WA and NY. This is the second year of evaluation. For 2015 , thresholds for fungicides applied to moderately susceptible cultivars were more conservative than before, using thresholds from simulations. In general, the DSS used fungicide effectively (less disease) and more efficiently (better disease suppression per unit fungicide) than the weekly schedule. The DSS is being modified to incorporate irrigation effects, which can alter the microclimate in a field. To obtain data for this, relative humidity, leaf wetness and temperature were measured within potato canopies and their effects on late blight development estimated in commercial fields under sprinkler irrigation. Programming for these enhancements were completed. Progress was also made towards adding a disease forecast for early blight into the DSS. Tests of leaf wetness sensors as an input for the DSS were performed. An RH threshold of 93% seemed optimal for use in disease models to reflect saturation. 4. Improving grower communication. A survey indicated that growers were motivated to share/not share information about late blight on their farms by economic concerns for business loss, cooperative concerns for reciprocation and information receiver's trustworthiness, and normative concerns derived from a sense of shared responsibility, reciprocity, and community cohesiveness. Surveys were also conducted to gauge the effectiveness of USAblight.org, and identify directions for improvement. The most popular functions are the late blight map, genotype information for strains, and contextual details surrounding an outbreaks (host crop, etc.). Also of value were email alerts, management techniques, and information on levels of resistance to fungicides. Areas for improvement include providing more information on the size and severity of outbreaks, more information about how to use the DSS, and the development of a separate page with information for home gardeners. 5. Isolate characterization. 158 samples from 20 states were received. Microsatellite genotype data was generated and provided quickly to all senders. US-8 was detected once, US-11 four times, US-22 once, and US-23 83 times. This continues the trend seen in prior years where the dominance of US-23 increased, while US-8 and US-11 persisted (mainly in the western US). Since US-23 is mefenoxam-sensitive, this information helps inform management decisions for growers. Two new genotypes were detected, one being very resistant to mefenoxam. Isolates were also examined by whole-genome and reduced representation (GBS) sequencing to reveal indicate relationships between and within lineages. Variation within gene families, including RxLR effectors, provided novel insights into dynamics in clonal and sexual populations. Sexually diverse populations from Mexico were also obtained for GWAS analysis. 6. Mefenoxam resistance gene. A polymerase subunit gene identified by others as being a possible cause of resistance could not be confirmed by our association and linkage analysis studies. Instead, by mapping SNPs in a cross we identified a different location for the gene. The analysis could not be completed, however, due to gaps and errors in the existing P. infestans genome assembly. A new assembly was thus generated using newer technologies. Based on preliminary analyses, the new assembly seems to be 100 times better in terms of contig number and includes more of the genome. Following validation of the assembly, SNP mapping will resume. 7. Identification AvrPh2 and AvrPh3. Following up on our development of a transient expression system and the analysis of sequencing data from diverse isolates, a library of effectors were tested for phenotype against the Ph2 and Ph3 R genes. Effector recognition studies identified five AvrPh3 candidates. Co-infiltration studies using Ph3 and "boost of pathogenicity" assays identified two effectors representing AvrPh3. 8. Economic assessment. Comparisons of risk-adjusted net returns for DSS and 7-day fungicide application recommendations were made for potatoes in 59 locations under worst-case and randomly selected start date scenarios. The former represents high blight risk production areas. The DSS recommendations were preferred to the 7-day recommendations in most locations and for most susceptible, moderately susceptible, and moderately resistant cultivars. Depending on producer risk aversion level, the difference risk-adjusted net returns between DSS and 7-day fungicide application recommendations for the worst-case scenario ranged from $305-544, or $30-85 for the random selected start date scenario, for susceptible cultivars. The DSS recommended spray schedule was also more effective rather than a calendar spray schedule. 9. Plant-based solutions: Breeding for resistance. Activities in 2015 included the identification of plants homozygous for Ph-2 & Ph-3 to serve as parents for breeding, and development of 58 hybrids using 11 late blight resistant parents crossed to 13 susceptible inbreds (some including resistance to TSWV, TYLCV, or Fusarium). Field testing at four sites indicated that the Ph-2 & Ph-3 lines showed superior disease resistance. Tests also gathered information on yield, performance in sensory panels, and sugars and acidity. Primers specific to Ph3 were identified to aid marker-assisted selection, and progress was made towards identifying Ph2 candidates. 10. New plant resistance sources. Following the screening of a germplasm collection, several promising sources of resistance were characterized. The most promising came from the wild potato S. verrucosum. The resistance appears to be novel and genetic mapping has delimited the R gene to a 7 Mb region. 11. Transgenic plant solutions. Tests of PRR genes as sources of resistance to late blight continued. Several genes were identified from tomato and other sources, and over-expressed in tomato and potato. Preliminary tests indicated that resistance was enhanced in tomato by several of these genes. Results from potato, however, were not as promising. Tests with expanded numbers of transgenic plants are needed to confirm these results.
Publications
- Type:
Journal Articles
Status:
Awaiting Publication
Year Published:
2016
Citation:
Hansen, Z., Knaus, B., Tabima, J., Press, C., Judelson, H.S., Grunwald, N. and Smart, C. (2016) SNP-based differentiation of Phytophthora infestans clonal lineages using locked nucleic acid probes and high resolution melt analysis. Plant Dissease, in press.
- Type:
Journal Articles
Status:
Awaiting Publication
Year Published:
2016
Citation:
Hansen, Z., Knaus, B., Tabima, J., Press, C., Judelson, H., Grunwald, N. and Smart, C. (2016) Loop-Mediated Isothermal Amplification (LAMP) for Detection of the Tomato and Potato Late Blight Pathogen Phytophthora infestans. Journal of Applied Microbiology, in press.
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Matson, M.E.H., Small, I.M., Fry, W.E. and Judelson, H.S. (2015) Metalaxyl Resistance in Phytophthora infestans: Assessing Role of RPA190 Gene and Diversity Within Clonal Lineages. Phytopathology, 105, 1594-1600.
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Small, I. M., L. Joseph and W. E. Fry (2015). Development and implementation of the BlightPro Decision Support System for potato and tomato late blight management. Computers and Electronics in Agriculture. http://dx.doi.org/10.1016/j.compag.2015.05.010
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Small, I. M., L. Joseph and W. E. Fry (2015). Evaluation of the BlightPro Decision Support System for Management of Potato Late Blight Using Computer Simulation and Field Validation. Phytopathology 107, 1545-1554.
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Fry, W.E., Birch, P.R.J., Judelson, H.S., Grunwald, N.J., Danies, G., Everts, K.L., Gevens, A.J., Gugion, B.K., Johnson, D.A., Johnson, S.B., McGrath, M.T., Myers, K.L., Ristaino, J.B., Roberts, P.D., Secor G., and Smart, C.D. 2015. Five reasons to consider Phytophthora infestans a re-emerging pathogen. Phytopathology 105:966-981.
- Type:
Journal Articles
Status:
Awaiting Publication
Year Published:
2016
Citation:
Ristaino, J. B. and Pfister, D. 2016. What a painfully interesting subject: Charles Darwins studies of potato late blight. Bioscience 62, in press.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Johnson, D.A., and Cummings, T.F. 2016. In-canopy environment of sprinkler irrigated potato fields as a factor for late blight management in the semiarid environment of the Columbia Basin. Am. J. Potato Res. 93:in press DOI 10.1007/s12230-016-9500-1
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Progress 03/01/14 to 02/28/15
Outputs
Target Audience: The primary target audience are potato and tomato growers throughout the United States, educators, and crop protection consultants. Researchers (pathologists and plant breeders) are a secondary target. The project is populated by extension personnel that reach the main areas of the country that are at risk of late blight, who interact with both large and small growers, organic and conventional growers, etc. There is also an educational component of the project that gives research experiences to undergraduates. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? Undergraduate summer research.We hosted a total of 11 undergraduates and one high school student affiliated with our project. Each student worked for about 10 weeks on projects related to late blight or other oomycete diseases. Titles of their projects were: "Indirect germination of US lineages ofPhytophthora infestans", "Rapid diagnostic and detection strategies for management of tomato late blight", "Assisting growers to manage late blight", "Isothermal Amplification assay for detectingP. infestans", "Test of the Cornell DSS for management of late blight", "PhenotypingPhytophthora syringae", "Computational analysis of clonal lineages in mixed mating type populations", "Metabolic strategies of oomycete pathogens of potato", "Manipulation of PRR genes in tomato and potato", "Phytophthora-inducible PRR genes from tomato", and "CharacterizingPhytophthora infestansin Wisconsin." In mid-summer, the students participated in a web symposium. Students prepared an abstract booklet which was shared among the participants, the faculty mentors introduced themselves to the students and described their group's roles in the overall project, and the students gave presentations describing their research activities and long-term career plans. North American Late Blight Symposium.This 1.5 day meeting was held in August in Minneapolis, MN, just before the joint meeting of the American and Canadian Phytopathological Societies. There were 92 attendees. Eleven domestic graduate students and postdoctorals were provided with travel awards. How have the results been disseminated to communities of interest? Extension education activities.About 80 presentations were made to growers and other stakeholders during the year. In addition, three webinars were conducted, a Spanish version of our late blight scouting video was completed, and a new video on "Late Blight Imitators" was completed. Forty articles focusing on late blight management were written, and either new or expanded late blight email user lists were developed. A webinar entitled "Late blight of potato and tomato; recent occurrences and management experiences" was held that attracted 314 attendees. The Extension co-PDs also used the Decision Support System as well as other tools to know when to deliver information on late blight risk to growers. Growers were also reminded to notify their local extension educator, members of our group, and/or the website about outbreaks. Other extension personnel were also trained to monitor for late blight and to submit samples for phenotypic and genotypic analysis. Website. USABlight.org continues to process disease reports, send alerts, and houses a large amount of management information including videos on scouting and identifying other diseases that are similar to late blight. The plan is also to post fungicide and variety trial data. Traffic to the web site was consistent with the patterns seen in the previous 2 years, although traffic in late August and September was higher, perhaps because disease reports continued into September. There were a total of 238 confirmed reports of Late Blight and 25,750 visits to USABlight.org in 2014. What do you plan to do during the next reporting period to accomplish the goals? We will: 1. Continue to collect and characterize isolates of P. infestans from the USA. 2. Continue to collect and characterize isolates of P. infestans from Mexico. 3. Continue to improve our web site and DSS system. 4. Test the DSS at multiple locations nationwide 5. Conduct educational activities related to managing late blight. 6. Provide training to undergraduates through a summer research program. 7. Test new rapid detection methods for P. infestans. 8. Perform economic assessments of grower needs.? 9. Identify and improve options for plant resistance based on traditional genetics and transgenic solutions.
Impacts
What was accomplished under these goals?
IMPACT The project has already provided useful tools to growers and extension personnel for controlling the devastating late blight disease. This includes a disease alert system (to help growers schedule fungicide applications), a system for reporting isolates to a national web site (to help growers know when the pathogen is in their area), a decision support system (to increase the efficiency of fungicide use), and a system for obtaining genotype and phenotype data for the strains of the pathogen that are causing outbreaks (to help indicate the best control strategy). We have also established a network of extension personnel that work together to improve late blight management and grower education on a nationwide basis. In development are several additional tools for managing late blight. These include tomato varieties with enhanced resistance to the disease. Solutions for increasing resistance in potato are also underway. Also in progress is an economic assessment to evaluate the impact of the management tools, which should be useful for educating stakeholders on improved management strategies. ACCOMPLISHMENTS 1. Scouting for late blight. Team members continued to report outbreaks of late blight to the USAblight.org site and submit samples for genotyping. Team members supplied about 160 samples from 23 states and one Canadian province to the Fry lab for genotyping. The Extension members were also responsible for moderating reports submitted to the USABlight web site and ensuring all reports are accurately determined to be (or not to be) late blight. 2. Extension research. Members of our group also conducted field trials of tomato cultivars, potato cultivars, and fungicide tests. Much of the latter was integrated into a coordinated test of the Decision Support System at ten sites. Several groups also tested detection technologies, including a spore trap method. Two groups also worked on developing several different types of diagnostic DNA assays. 3. Improving grower communication. Data collection for the grower survey obtained responses from growers who met the following criteria: (1) grew 1 or more acres of potatoes or tomatoes, and (2) made decisions for their potato or tomato crop. Findings include that 40% had been infected by late blight; growers feel a strong sense of community with nearby farmers; and overall neighbors were the most trusted sources of information, followed by extension. 4. Decision Support System (DSS). Comprehensive tests were performed on conventional potato at five locations, conventional tomato at five locations, and organic tomato at two sites. The DSS was usually beneficial in terms of disease suppression and economics (less fungicide applications). A new algorithm for the DSS was developed that forecasts the favorability of weather conditions for sporulation and release at the source, survival of sporangia in transit, and subsequent infection of host tissue at the target site. 5. Isolate characterization. 160 samples were received and microsatellite genotype data was quickly provided to all senders. US-23 was dominant in 2014, representing 127 of 157 late blight samples (several turned out not to be late blight). US-8 was detected twice, US-24 five times, and novel genotypes at least six times. Several groups worked together to develop DNA tests that do not use microsatellite data to assign lineages, using markers specific for the US-8, US-11, and US-23 were developed. Fungicide sensitivity testing continued on isolates obtained in 2013 and 2014. Neither the introduction nor development of insensitivity to mefenoxam in current US populations during the period was observed. Genotyping efforts analyzed the evolutionary relationships among US genotypes based on multilocus sequencing of nuclear and mtDNA genes, and microsatellite analysis. Phylogenetic analyses including maximum likelihood, haplotype mapping, and coalescent analyses have been conducted.Interestingly, US-1 shared many alleles with US-22, US-23, and US-24; all of these are mostly mefenoxam-sensitive. GBS was also used to gain a better idea of the variability within a clonal lineage. 6. Development of new diagnostic tools: P. infestans-specific antibodies. For one target, we previously obtained monoclonals but these did not detect the native protein. This year, we obtained polyclonals against two peptides obtained from four rabbits. Each recognized peptides in ELISA assays, but disappointingly no signal was obtained against whole protein. Antibodies against other candidates are in production. 7. Development of new diagnostic tools: Mefenoxam resistance. The goal here was to develop a DNA test to predict the sensitivity of P. infestans strains to this fungicide. Intriguing, the genetics of insensitivity is complex. There appears to be two "major genes" plus multiple minor genes. Interestingly, the US-23 and US-24 lineages were diverseand seem to be polyploids. Another interesting observation was that sensitive isolates may be able to temporarily "acquire" resistance to mefenoxam after being exposed to the compound. Gene expression studies identified several up-regulated genes that might contribute to such resistance, including two ABC transporters. 8. Development of new diagnostic tools: Identification AvrPh2 and AvrPh3. Following up on our development of a transient expression system using potato virus X delivery via Agrobacterium tumefaciens, a library of effectors were tested for phenotype. Effector recognition studies have identified four AvrPh3 candidates. 9. Economic assessment. Examinations were made of net returns from multiple control scenarios. Comparisons were made for potatoes in U.S. locations under the assumption that late blight was detected early in the growing season. For each cultivar and location, the number of fungicide applications, disease severity, yield loss due to disease severity, and risk adjusted net returns were compared, with the analysis including susceptible, moderately susceptible, and moderately resistant cultivars. Depending on the assumed producer risk aversion level, the difference in the risk-adjusted net returns ranged from $308 to $534 per acre for susceptible cultivars depending on the control schema that was selected. 10. Plant-based solutions: Breeding for resistance. Twenty-three Ph2 and Ph3 tomato hybrids were tested in fall 2014 and five were selected for harvesting in our hybrid evaluation trial. Two performed very well for marketable yield and ranked in the top 6 of a 46 entry trial. Seedling bioassays were conducted that verified all our selections for resistance using molecular markers. In potato, extensive characterizations were performed of potential sources of resistance using wild diploid Solanum. Accessions were screened with core effectors. Several of the new sources of resistance were found to consistently perform well and are being mapped. 11. Plant-based solutions: Transgenic solutions. Prior data suggested that silencing a core defense gene increased resistance to P. infestans, in controlled greenhouse and growth chamber studies. The opposite occurred when the gene was silenced in potato. The experiment was repeated under field conditions. Several lines had minor enhancement of resistance to late blight, but not through the entire season. Other potential defense genes were tested in transgenic tomato and potato lines. Tomato lines exhibited resistance, whereas a potato line displayed only partial resistance. Further tests are in progress.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Childers, R., Danies, G., Myers, K., Fei, Z., Small, I.M. and Fry, W. E. 2015. Acquired resistance to mefenoxam in sensitive isolates of Phytophthora infestans, Phytopathology, 105:342-9
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Hansen, Z.R., Small, I.M., Mutschler-Chu, M., Fry, W.E., and Smart, C.D. 2014 Differential susceptibility of thirty nine tomato varieties to Phytophthora infestans clonal lineage US-23. Plant Disease, 98, 1666-1670
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Chapman S, Stevens LJ, Boevink PC, Engelhardt S, Alexander CJ, et al. (2014) Detection of the Virulent Form of AVR3a from Phytophthora infestans following Artificial Evolution of Potato Resistance Gene R3a. PLoS ONE 9(10): e110158. doi:10.1371/journal.pone.0110158
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Kamoun, S., Furzer, O., Jones, J.D.G, Judelson, H.S., Shad Ali, G., Dalio, R. J. D., Guha Roy, S., Schena, L., Zampounis, A., Panabi�res, F., Cahill, D., Ruocco, M., Figueiredo, A., Chen, X.R., Hulvey, J., Stam, R., Lamour, K., Gijzen, M., Tyler, B.M., Gr�nwald, N.J., T�r, M., Shahid Mukhtar, M., Tome, D., Van den Ackerveken, G., McDowell, J., Daayf, F., Fry, W. E., Lindqvist-Kreuze, H., Meijer, H. J. G., Petre, B., Ristaino, J., Yoshida, K., Birch, P., and Govers, F. The Top 10 oomycete pathogens in molecular plant pathology. Molecular Plant Pathology. 2015. DOI: 10.1111/mpp.12190.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
McComas, K., Besley, J., & Steinhardt, J. (2014). Factors influencing U.S. consumer support for genetic modification to prevent crop disease. Appetite, 78C, 8-14.
- Type:
Journal Articles
Status:
Awaiting Publication
Year Published:
2015
Citation:
Saville, A., Graham, K., Gr�nwald, N., Myers, K., Fry, W. and Ristaino, J. B. 2015. Fungicide sensitivity of US genotypes of Phytophthora infestans (Mont.) de Bary to six oomycete-targeted compounds. Plant Disease http://dx.doi.org/10.1094/PDIS-05-14-0452-RE.
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Progress 02/28/13 to 02/27/14
Outputs
Target Audience: The primary target audience are potato and tomato growers throughout the United States, educators, and crop protection consultants. Researchers (pathologists and plant breeders) are a secondary target. The project is populated by extension personnel that reach the main areas of the country that are at risk of late blight, who interact with both large and small growers, organic and conventional growers, etc. There is also an educational component of the project that gives research experiences to undergraduates. Changes/Problems: Strategies for improving progress on economic assessments are under consideration. What opportunities for training and professional development has the project provided? During the summer, eight co-PDs hosted a total of 10 undergraduate researchers for 10 weeks each. Each student received a stipend, and depending on their location, housing or a housing allowance. Their research topics were related to late blight, other aspects ofPhytophthorabiology or pathology, or plant resistance mechanisms. The topics were "Sensitivity of recent genotypes ofPhytophthora infestansto oomycete-targeted compounds", "InvestigatingPhytophthora infestansrace, virulence and detection strategies", "Mefenoxam sensitivity of strain US-23 ofPhytophthora infestansin the United States", "The relationship ofPhytophthora ramorumlineages and fungicide resistance", "Functions of homeobox and Mads-box transcription factors inPhytophthora infestans", "Identification ofPhytophthora infestanslineages through genetic markers", "Silencing theNAC1gene to determine its role in disease resistance, and "Cloning and characterization ofPhytophthora-induciblePRRgenes from tomato." All students had independent projects, but to build "team spirit" and educate the students about each others' work, a web-based meeting was held in mid-July. Each prepared an abstract describing their project, spoke about their work to the other participants and faculty mentors, answered questions, and described their career goals. In addition,training was provided to 10 graduate students, and 5 postdoctorals directly associated with the project. In addition, our extension personnel provided training to crop protection professionals (consultants, advisors) throughworkshops, training videos, and webinars; topics included identifying and managing late blight, and use of the Decision Support System tool. How have the results been disseminated to communities of interest? Extension education and field trials. The extension team presented 53 talks (either all or part of which covered late blight) to growers, extension educators, consultants, and home gardeners, and wrote 28 extension articles. Team members also held two TV appearances, and developed a late blight scouting video which is available on USAblight.org and YouTube. A Spanish version of the video is nearing completion. The tri-fold brochure about late blight produced in 2012 was distributed to additional users, and a Spanish version was completed. Other activities included six field trials of cultivars and/or fungicides (NY, FL, NC, ND, PA and WI). For example, one involved a test of 40 tomato varieties and was replicated in two locations (upstate NY and Long Island, NY); the results indicated that varieties containing Ph2 and Ph3 had the highest resistance. The utility of using a roto-rod spore trap to evaluate disease likelihood was also evaluated. Training in Decision Support System.Users in 21 states have expressed interest in the DSS. Much effort was devoted to illustrating the new features to older users, and introducing the system to new users. Several evaluations of the DSS were conducted, including a carefully controlled stress test (inoculum present) in Pennsylvania, a test with an extension agent in upstate NY who evaluated the DSS on 4000 acres of potatoes and tomatoes, and tests at the Mountain Horticultural Crops Research and Extension Center in NC and University of Maryland Lower Eastern Shore Research and Education Center (although no disease occurred at the latter). Results of these trials are now being evaluated. What do you plan to do during the next reporting period to accomplish the goals? We will: 1. Continue to collect and characterize isolates of P. infestans from the USA. 2. Continue to collect and characterize isolates of P. infestans from Mexico, emphasizing sites nearer to the Toluca Valley to maximize diversity. 3. Continue to improve our web site and DSS system. 4. Test the DSS at multiple locations nationwide 5. Conduct educational activities related to managing late blight. 6. Provide training to undergraduates through a summer research program. 7. Run a North American Late Blight Symposium in the summer. 8. Conduct large-scale surveys for improving grower communication. 9. Test new rapid detection methods for P. infestans. 10. Assess baseline sensitivities to fungicides and the molecular basis of fungicide insensitivity. 11. Perform economic assessments of grower needs. Identify and improve options for plant resistance based on traditional genetics and transgenic solutions.
Impacts
What was accomplished under these goals?
Scouting fields for late blight. Infected material was collected and DNA was recovered from 153 samples for analysis. Web site. The USAblight.org website has continued to function, with 15,792 unique visitors. The number of states making disease reports expanded, with information coming from 131 counties in 21 states. Improving grower communication. In year two, preliminary interviews were held with 23 growers across 6 states which yielded information about their previous experience with late blight. That information was processed and used during Year Three to finalize questions for the grower survey. NASS will conduct the full survey in 2014. Decision Support System. Several revisions and enhancements were developed over the past year. One is a mobile app for smart phones that allows reports to be developed using location-specific historical and weather forecast data, and to input fungicide data. A feature has also been developed to enable a single advisor (extension or commercial) provide summary data for a series of locations. These join other new inputs that allow users to select potato and tomato cultivars with varying degrees of susceptibility to late blight, and different fungicides. Additional data on cultivar susceptibilities and fungicide efficacies were obtained to help calibrate the DSS. The feasibility of adding additional weather inputs to the DSS was appraised. An earlier plan to add more detailed weather modeling was judged to be impractical due to the computing requirements needed to cover the needed geographic area. Instead, a project was initiated to evaluate the use of leaf wetness sensors and their relationship to co-located humidity sensors, with a goal of improving the ability to estimate leaf wetness from standard weather station data. Tests have begun using leaf wetness sensors Isolate characterization. Genotyping. Seasonwide, 153 samples were received for analysis. The vast majority, 98%, were US23. Also received was one US7 (FL), one US8 (PA) and one US24 (ME). Interestingly, one potato and two tomato samples were diseased by Phytophthora nicotianae. Within US23, there was microsatellite diversity at locus D13, even though the isolates were the same based on RFLP DNA probe RG57. Genotyping of most isolates during 2013 was completed within 24-48 hrs of receipt, with results posted to the sender by email and to USAblight.org. Typically samples were received sporadically during the season (0-4 per day), which reduces the efficiency of the process. A curious population of isolates from 2010 and 2011 from upstate NY was also evaluated in some detail. Eleven genotypes were identified using mitochondrial, SSR, allozyme, and RFLP markers, and mating type. Both A1 and A2 types were present, with the data suggestive of the existence of progeny with US22 being one parent. Using genome sequences generated by this project for US1, US8, US22 and US23, single nucleotide polymorphisms (SNPs) are being detected to match SNPs to genotype and phenotype, study the evolutionary history of the lineages, and develop DNA assays to more rapidly distinguish the lineages. Genotyping by sequencing (GBS) runs are also being performed in support of developing these diagnostic assays. Pathogenicity: Several traits were studied in eight US8, 34 US22, 7 US23 and 9 US24 isolates. US22 and US23 are pathogenic on both potatoes and tomatoes, but US23 appears to be the more aggressive of the two lineages. US24 as well as US8 are primarily potato pathogens. Interestingly, US24 releases zoospores much more rapidly than do US23 and US22. Whether variation in pathogenicity occurred within lineages was assessed using US22. DNA markers revealed the existence of a variant (Var1) in US22. Still being analyzed are isolates from Mexico. Fungicide response. Sensitivity to mefenoxam was assessed on 206 isolates in the four lineages. In general, US8 was resistant, US22 and US23 were sensitive, and US24 was generally sensitive. Differences in mefenoxam sensitivity between years, for each clonal lineage, were analyzed using a standard least square model. For US8, US22 and US23 mefenoxam sensitivity did not vary significantly among the years studied. However, US24 isolates from 2011 were less sensitive than those from 2010. Assays of five other fungicides against the P. infestans lineages have been completed. Development of new diagnostic tools. Diagnostic antibodies. Candidates peptides were screened and two monoclonal lines obtained in late summer. In ELISA, both detected the synthetic peptide but neither reacted with proteins from P. infestans (from artificial cultures and extracts of infected plants). Negative results were observed in Western blots.. Additional targets are being evaluated. Mefenoxam resistance. Two approaches are being pursued. One involved checking candidate genes for changes associated with resistance. The second strategy involves SNP detection in segregating crosses. In addition, a High Resolution Melt (HRM) assay was developed to distinguish genotypes of the top candidate gene. AvrPh2 and AvrPh3. Seeds from five pairs of tomato lines isogenic for Ph2 and Ph3 were obtained and plants were propagated in the glasshouse to produce more seed for experimentation. Also, tests were performed to identify the best methods for transiently expressing effectors in these plants. So far, two effectors yielded reproducible and specific hypersensitive responses (necrosis) in the Ph3 line, but not in the Ph2 line or susceptible cultivar, indicating that these two effectors could be the product of the AvrPh3 gene. A further 10 effectors produced HRs in either the Ph2 or the Ph3 lines. Economic assessment. The focus is on developing a stochastic, dynamic model of the late blight Decision Support System (DSS), which aims at introducing economic decisions into the DSS. Current analyses are focusing on potato. Tomato breeding for Resistance. Following up on crosses made during the second year of the project, additional rounds of backcrossing were completed. A new effort was started to improve the crossing strategy. The goal is to identify markers closer to Ph2 and Ph3 than those currently in service. Meanwhile, a computational study was performed of the Rpi-Ph2 and Rpi-Ph3 loci using the latest potato and tomato genome models. Transgenic solutions: CRT1. Intriguingly, silencing raised susceptibility to late blight in potato but increased resistance in tomato. No effect was seen in tomato against root knot nematode, in potato against the cyst nematode, against aphids in Nicotiana benthamiana, or against potato virus Y in potato. In potato inoculated with leafroll virus using aphids, no difference was observed in virus titer. Transgenic solutions: PRRs. Multiple transgenic tomato and potato lines were established that express the N. benthamiana LRK1 gene or Arabidopsis PEPR1 and are now being tested. Several approaches are also being used to identify tomato PRRs. In addition, forty Arabidopsis T-DNA knockout lines with insertions in putative PRR genes were obtained and are now being tested against PAMPs. 14 Phytophthora-inducible putative PRR genes from tomato were cloned and are being tested. Finding durable R genes. The goal is to identify "durable" sources of resistance from wild potato by screening germplasm collections with P. infestans isolates, and identify (and clone) R genes that interact with Avr genes that occur widely throughout P. infestans. This project is partially funded by European agencies. Progress: To find durable R genes, more than 220 diploid wild potato accessions from the CPC were screened. More than 30 good sources of resistance were identified. The identification of 'core' effectors is also ongoing using microarrays, RNAseq, and genome sequencing to identify those present and expressed in every P. infestans genotype. More than 60 were identified.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Danies, G., I. M. Small, K. Myers, R. Childers and W. E. Fry (2013). "Phenotypic Characterization of Recent Clonal Lineages of Phytophthora infestans in the United States." Plant Disease 97:873-881
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
McGrath, M. T., Menasha, S. R., and LaMarsh, K. A. 2013. Evaluation of late blight resistant tomato cultivars and experimental hybrids on Long Island, NY, 2012. Plant Disease Management Reports 7:V021.
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Progress 02/29/12 to 02/27/13
Outputs
Target Audience: The primary target audience are potato and tomato growers throughout the United States, educators, and crop protection consultants. Researchers (pathologists and plant breeders) are a secondary target. The project is populated by extension personnel that reach the main areas of the country that are at risk of late blight, who interact with both large and small growers, organic and conventional growers, etc. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? Training was provided to 10 graduate students, 12 undergraduates, and 5 postdoctorals directly associated with the project. In addition, our extension personnel provided training to crop protection professionals (consultants, advisors) through workshops, training videos, and webinars; topics included identifying and managing late blight, and use of the Decision Support System tool. How have the results been disseminated to communities of interest? Our extension team presented over 65 talks to growers, extension educators, consultants, and home gardeners, and wrote 54 extension articles. In addition, we produced a tri-fold brochure about late blight, and distributed 20,630 copies to stakeholders. Team members also held 1 webinar, had 1 TV and 1 radio appearance, and made about 40 posts on various blogs. Our web site provided information to the public on identifying and managing late blight. An analysis of the IP addresses of visitors to the web site indicated that many were not from commercial potato and tomato growing areas and likely represent the general public. What do you plan to do during the next reporting period to accomplish the goals? We will: 1. Continue to collect and characterize isolates of P. infestans from the USA. 2. Continue to collect and characterize isolates of P. infestans from Mexico, emphasizing sites nearer to the Toluca Valley to maximize diversity. 3. Continue to improve our web site and DSS system. 4. Generate additional educational materials related to managing late blight. 5. Provide training to undergraduates through a summer research program. 6. Complete our analyses of consumer attitudes to GMOs and shift resources to surveys for improving grower communication. 7. Continue to enhance and test the Decision Support System. 8. Test new rapid detection methods for P. infestans. 9. Assess baseline sensitivities to fungicides and the molecular basis of fungicide insensitivity. 10. Perform economic assessments of grower needs. 11. Identify and improve options for plant resistance based on traditional genetics and transgenic solutions.
Impacts
What was accomplished under these goals?
1. Scouting fields. The goal is to obtain isolates of P. infestans for genotyping and phenotyping studies, to inform management tools. Progress: Late blight was reported in over 12 states this year. Infected plant material, or P. infestans isolated from plants, were collected; more than 200 samples were obtained during the growing season from 12 states, in addition to Mexico. 2. Web site. The goal is to develop a web-based system for reporting outbreaks and alerting stakeholders. Progress: The prototype website was enhanced by improving links between sample submissions and disease reports, and adding a table of current genotypes and their characteristics. Changes were also made to system code to minimize malicious attacks. A system for web-based moderation of disease reports was also developed. Improvements in the disease management section and links to state extension pages were created. A total of 312 reports were recorded in 2012, of which 255 were confirmed to be late blight. We also monitored visits to the web site. 16,755 unique visitors were recorded, with 91% from the USA and 13% from mobile accounts. 3. Improving grower communication. The goal is to optimize strategies for communicating with growers. Progress: Growers across several states were interviewed, including tomato and potato growers, large and small producers, and organic and conventional operations. Data were obtained about the grower’s previous experience with late blight; their use of communication technologies for information seeking and sharing; and their trust and credibility assessment of information sources. Anonymity, ease of information sharing, and interpersonal connections were perceived to be important for disseminating information on late blight. 4. Extension education and field trials. Progress: The extension team presented 67 talks to growers, extension educators, consultants, and home gardeners, and wrote 54 extension articles. A tri-fold brochure about late blight was produced and distributed to stakeholders. Team members also held webinars, had TV and radio appearances, made about posts on blogs, and developed computer programs. A video on late blight is also in production and field trials were performed testing the relative resistance/tolerance of tomato varieties in two locations, and fungicide efficacy on stored tubers and field plants. 5. Decision Support System (DSS). The goal is to deploy and improve a DSS for growers and other stakeholders. Progress: Several revisions were made to the DSS. One enables users to receive email alerts based on weather (historical and forecast), host resistance, and fungicide effect. Also, a simplified alert system for Simcast and Blitecast was deployed, to allow alerts to be visible on a phone. The DSS was also enhanced to include additional fungicides. Data in support of these changes were obtained from field experiments, and the effectiveness of the DSS was evaluated based on data from several sites. A training webinar was held for co-PDs and others. The possibility of enhancing the DSS further with weather inputs was explored. Other experiments related to the DSS involved testing how fungicides should be integrated with the use of the RB R gene. At an international field site we studied the performance of RB hybrid clones against late blight and the number of fungicide sprays required. Fungicide tests showed that one, two, or three sprays progressively reduced foliar blight and increased yield, and lower dosages also reduced infection and raised yield. 6. Isolate characterization. The main objective is to monitor traits of P. infestans populations to inform growers, assess how well microsatellites predict phenotype, and characterize phenotypes for refining the DSS. Progress: Isolates were tested throughout the season and data reported rapidly to the provider. About 1% were US8, 1% US22, 4% US11, 4% US24, and 92% US23. In general, US8 isolates were mefenoxam-resistant, US22 and US23 sensitive, and US24 fairly sensitive. Tests of isolates against other fungicides are in progress. Tests of other biological characteristics of isolates identified variation in zoospore release rates and pathogenicity. 7. New diagnostic tools. The goals are to develop antibody tests to rapidly diagnose infections, and DNA-based tests for traits important for disease management. Progress: Putative P. infestans-specific epitopes were identified and used to order monoclonal antibodies, which should be delivered in the middle of year 3. Progress was also made in characterizing the basis of fungicide resistance. DNA-based tests against candidate genes indicated a strong correlation between a certain SNP and insensitivity, based on surveys of USA and international isolates. Diversity in resistance mechanisms was evident and is being pursued genetically using mapping populations. Steps towards developing a DNA assay to predict the reaction of P. infestans isolates to resistance genes were achieved, with progress reported towards cloning the pathogen avirulence genes based on functional testing of candidate effectors in plant germplasm. 8. Economic assessment. The overall goal is to assess the impact of the tools being developed in the project. Progress: A literature review conducted. 9. Resistance breeding. The goal is to breed R genes for tomato into commercially acceptable cultivars, and identify useful genes for potato. Progress: A fourth round of backcrossing in tomato was successfully completed for several R genes. For each recurrent parent, three plants were identified that were heterozygous for each R gene. New DNA-based marker development was necessary for some genotypes. In potato, screening of wild accessions is proceeding, and potentially useful R gene sources were identified. Genome sequencing identified the effector complement of US isolates of P. infestans, including "core effectors" for plant-based screening. 10. Transgenic solutions: Goals were to study the role of a gene shown to mediate defense involving R genes and Pattern Recognition Receptors, and implement strategies for identifying new Pattern Recognition Receptors (PRR). Progress: Gene silencing and overexpression studies demonstrated the role of the cloned gene in plant defense against late blight, in both potato and tomato. However, there were differences between the species. Results also suggested that our gene acts in pathways distinct from some of the known R genes. A patent application covering the gene was filed. For PRRs, genetics and yeast two-hybrid studies were performed to address the interaction between known PAMPs and PRR genes. Additional PAMPs were identified from P. infestans as a prerequisite to identifying the plant interactors. 11. Perception of biotechnology. The goal to address factors that influence consumer decisions to purchase genetically engineered plants. Progress: Results from the 2011 national survey were analyzed. Sampling was narrowed to consumers, or people who made most of the decisions at the grocery store. The results suggested that contextualizing ag biotech in relation to late blight mattered little. More important was the perceived fairness of those making decisions about ag biotech. Overall, the results argue for the importance of considering how scientists’ behaviors and actions are perceived alongside individuals’ perceptions about the risks of ag biotech. 12. Undergraduate education. During the summer, seven co-PD labs hosted a total of 11 undergraduates. Each worked for about 10 weeks on projects related to Phytophthora. Examples of topics included: measuring fungicide resistance, testing effectiveness of the DSS, developing plasmids for expressing transgenes in P. infestans, scouting for late blight, etc. Students also participated in a web-based conference in which they discussed their individual projects and learned about how their work fit into our plan for developing sustainable solutions for late blight.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2012
Citation:
1. Fry, W. E., McGrath, M. T., Seaman, A., Zitter, T. A., McLeod, A., Danies, G., Small, I. M., Myers, K., Everts, K., Gevens, A. J., Gugino, B., Johnson, S. B., Judelson, H., Ristaino, J. B., Roberts, P., B. Secor, G., Seebold, K. W., Jr., Snover-Clift, K. L., Wyenandt, A., Grunwald, N. J., Smart, C. D. 2012. The 2009 Late Blight Pandemic in Eastern USA- causes and results. Plant Dis. 96: 296-306.
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Progress 03/01/11 to 02/28/12
Outputs
OUTPUTS: To obtain information about outbreaks of late blight, a network was developed involving members of the project and unfunded collaborators. The network was also used to obtain over 140 isolates (from Connecticut, Maine, Maryland, Minnesota, New Hampshire, New York, North Dakota, Pennsylvania, Virginia, Wisconsin) for genotype and phenotype analysis. Microsatellite DNA markers provided information about pathogen lineages, with results usually returned to providers within 1-2 days. About 90% of genotypes matched lineages found in previous years; the remainder appear to be novel. Isolates were also tested for phenotyped such as aggressiveness, resistance to fungicides, etc. To study fungicide resistance over a longer timeframe, isolates from the past three years were examined for sensitivities to seven fungicides. Field plots of potato were also established in Chapingo, Mexico (where populations of P. infestans are very diverse) to obtain additional isolates, many of which were characterized for traits including lesion growth, sporulation, host preference, fungicide resistance, and the parameters for spore germination. To disseminate information to stakeholders about outbreaks, a website (USAblight.org) was established. Enhancements added over the year included email alerts, a system to confirm/deny reports, and links to other content including a Decision Support System (DSS). The DSS was made available to co-PDs and then to a broader audience, and its predictive algorithms enhanced in anticipation of incorporating pathogen lineage data. Our extension members provided information about late blight to stakeholders though newsletters, fact sheets, oral presentations, weekly blog posts, training sessions for farm agents/horticultural agents, etc. Research activities in support of disease management included steps towards DNA and antibody-based diagnostic tools. Targets for antibodies were developed using proteomics, and genetic analyses plus sequencing used to develop markers for trait-specific DNA assays. Progress was also made in developing tomato cultivars with improved resistance characteristics, through two cycles of backcrossing. Detached leaf and small plant disease screens are starting to teste selected BC2 plants to measure linkage of DNA markers to resistance genes, which will be used to select plants for more crosses. Several approaches for transgenic resistance were also assessed, including overexpression and silencing studies of genes that play roles in mediating defense, involving both traditional resistance genes and pattern recognition receptors. This entailed characterizing genes from other species, identifying orthologs from tomato and potato, and then testing their function in transgenic tomato and potato. A national survey of consumers was also conducted to address factors that influence their decisions to purchase genetically engineered plants, including tradeoffs between transgenics and fungicide use. Data were gathered to assess the economic impact of the tools and resources being developed in the project. Finally, undergraduates were provided with experience in our research and extension laboratories. PARTICIPANTS: Overall management of the project was provided by the PD and co-PDs Howard Judelson (UC-Riverside), William Fry (Cornell University), and Christine Smart (also Cornell). Other co-PDs included Niklaus Grunwald of USDA-ARS, Corvallis; Fangming Xiao, University of Idaho; Paul Birch and Ingo Hein, James Hutton Institute, Scotland; Jean Ristaino and Ryan Boyles, North Carolina State Univ; John Scott and Pamela Roberts, University of Florida; Kenneth Seebold, University of Kentucky; Hector Lozoya, Univ. Autonoma Chapingo, Mexico; Thomas Girke, Thomas Univ. of Cal-Riverside; Geri Gay, Margaret McGrath, and Katherine McComas, Cornell University; Daniel Klessig, Boyce Thompson Inst.; Steven Johnson, University of Maine; Alexandra Stone, Oregon State University; Beth Gugino, Pennsylvania State Univ.; Amanda Gevens, University of Wisconsin; Katheryne Everts, University of Maryland; John Besley, Univ. of South Carolina; and Brent Gloy, Purdue University. Working in their groups were graduate students (Matt Tancos, Victoria Ferguson, Maria Holdcroft, Nayely Robledo-Trejo, Anna Seidl, Amilcar Sanchez Perez, Joseph Steinhardt, Giovanna Danies, Joanna Kud, and Ian Small), postdoctoral scientists (Sam Hutton, Sarah Smith, Patricia Manosalva, Xinwei Chen, Carol Davis, Laetitia Poidevin), undergraduates (nathan Martin, Chris Gamill, Ian Brasted, Deepthika Ennamuri, Richard Childers, Kiersten Bekoscke, Caleb Pearce, Corley Gibbs, Michelle Ploch, Apolonio Huerta, Jonathan Blahut, Arianne Fricke) and techicians/other professional staff (Brian Harrower, Kevin Myers, Jose Diaz, Abby Seaman, Mark Brooks, John McGuire, Dolly Cummings, Laura Joseph, Amanda Saville, Erica Lassiter, Viviana Rivera-Varas). The students and postdoctorals were exposed to training in plant pathology, molecular genetics, computer programming, social science research, and similar activities. A range of training events were also provided to others through the grant. Prominent among these were 43 extension talks focused on late blight. These reached approximately 3094 growers and educators. TARGET AUDIENCES: The primary target audience are potato and tomato growers throughout the United States, educators, and crop protection consultants. These were reached through 43 extension talks that focused on management of the late blight diseases. In addition, printed materials were distributed through a variety of venues to other growers and a web site (USAblight.org) was developed that provides stakeholders with information about the locations of late blight epidemics, links to information that provides advice on detecting and managing the disease, and links to extension personnel throughout the country that can aid stakeholders. A second audience are crop consultants and extension personnel/farm advisors that also work with growers, and home gardeners. Through the web site and printed materials are activities are designed to not only contact people within states with co-PDs funded by the grant, but also nationwide. An additional target audience are undergraduates interested in agriculture and the plant sciences, who were engaged by our project's summer research internship program. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
Outcomes included the development of breeding material for tomato resistant to late blight; release of a system for disseminating information to growers on a nationwide basis about how to recognize late blight and where in the country the disease is occurring; release and enhancement of a Decision Support System for improving disease management and enhancing the efficient use of crop protection chemicals; collection of baseline fungicide resistance levels of isolates; characterization of genetic diversity of pathogen strains throughout the United States; identification of gene and protein targets for diagnostic assays useful for growers and other stakeholders; publication of instructional materials for stakeholders; education of growers through extension activities; identification of genes useful for transgenic approaches for late blight resistance; assessment of the public's perceptions towards biotechnology; and training of undergraduate students in science and more specifically in plant pathology. Impacts of these activities include better control of late blight; reduced use of fungicides, to both improve the profitability of potato and tomato production and reduce chemical discharges to the environment; and greater food security. The undergraduate research program will lead to a better-educated public and hopefully pursuit of careers in plant pathology and/or plant science by many of the participants. One specific example of an impact of our disease reporting and isolate characterization activities is our network's ability to track the point source of inoculum for a major outbreak in New York (a garden center marketing affected plants, or a nearby garden where their material was planted). Targeting the source helped to arrest the outbreak, and led to improvements in greenhouse management. To help improve the outcomes and impacts of the project, a year-end meeting was held with representatives of grower, crop consultant, agribusiness, commodity group, and university researcher communities who provided feedback and suggestions.
Publications
- Everts, K.L., 2012. Selected Fungicides and Bactericides Labeled for Greenhouse Use. In Commercial Vegetable Production Recommendations, 2012. University of Maryland Extension Publication (in cooperation with the University of Delaware; the Pennsylvania State University; Rutgers, The State University of New Jersey; Virginia Polytechnic Institute and State University; and West Virginia University. Jordan, S.A., Dobbs, J., Clark, R., Cleveland, K.M., Gevens, A.J. 2012. Evaluation of fungicides for control of late blight in potato in storage, 2010-2011. Plant Disease Management Reports 6:V093. Online publication. doi: 10.1094/PDMR06. Gevens, A.J., Sanchez Perez, A., Seidl, A.C. 2012. Updates on late blight for 2011 and management in 2012. University of Wisconsin Extension-Wisconsin Potato & Vegetable Growers Association Grower Education Conference. Holiday Inn Hotel & Conference Center. Educational Conference Proceedings. (Online Proceedings). Gevens, A.J., S.A. Jordan, A.C. Seidl, A. Sanchez Perez. 2012. 2011 Updates on Tomato and Potato Late Blight and Cucurbit Downy Mildew. Wisconsin Crop Management Conference. Alliance Energy Center. Madison, WI. Volume 51 (Online Proceedings). Gevens, A. J. 2012. Vegetable Disease Updates. University of Wisconsin Extension. Wisconsin Crop Manager. March-Present. Contributor of 8 articles, to date. Editor 2011-current. Online newsletter. Gevens, A. J. 2011. Vegetable Disease Updates. University of Wisconsin Extension. Wisconsin Crop Manager. February-Present. 18 articles. Online newsletter. Bussan, A.J., Colquhoun, J.B., Cullen, E.M., Davis, V.M., Gevens, A.J., Groves, R.L., Heider, D.J., Ruark, M.D. 2011. Commercial Vegetable Production in Wisconsin, 2012. University of Wisconsin Cooperative Extension Publication A3422. Gevens, A.J., Seidl, A.C., Sanchez Perez, A. 2011. Late blight in review. Badger Beat - Common Tater. McGrath, M. T. 2012. Nine Key Steps To Managing Late Blight In Tomatoes. IPM video. Growing Produce.com. Gugino, B.K. 2012. Tomato disease update: Looking back and then forward to 2012. 2012 Mid-Atlantic Fruit and Vegetable Convention Proceedings, PA Vegetable Growers Association, Richfield, PA. Pp. 124-126. Gugino, B.K. 2012. Update on potato diseases. 2012 Mid-Atlantic Fruit and Vegetable Convention Proceedings, PA Vegetable Growers Association, Richfield, PA. Pp. 97-99. Johnson, S. B. 2012. Potato Late Blight Manager Smartphone application. Android Code 2 Version 1.2 available at: https://market.android.com/detailsid=com.mcteam.PotatoProgram&featur e=search_result#t=W251bGwsMSwyLDEsImNvbS5tY3RlYW0uUG90YXRvUHJvZ3JhbS Jd
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