Progress 07/01/08 to 06/30/13
Outputs
Target Audience: The study on pathogen virulence and host resistance and resulting translational biotechnology has contributed to efforts to improve disease resistance in crops, particularly rice, by plant pathologists and rice researchers. Comprehensive and well-curated genotypic and phenotypic characteristics of known and novel members of the genera Phytophthora and Fusarium, archived in Phytophthora Database (PD) and Cyber-infrastructure for Fusarium (CiF), respectively, have supported mycologists, plant pathologists, disease diagnosticians, and regulatory agency researchers world-wide in identifying and detecting strains in these two main groups of pathogens. The number of registered PD users is 640 from ~50 countries with ~2,600 visits per month. The CiF averaged ~2,000 visits per month. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? The project provided diverse training opportunities to graduate students and postdoctoral associates in three laboratories (2 graduate students in Geiser lab; 3 graduate students and 3 postdoctoral associates in Kang lab; 4 graduate students and 4 postdoctoral associates in Yang lab) during the past five years. How have the results been disseminated to communities of interest? The Phytophthora Database and Cyber-infrastructure for Fusarium are available via the web. In national and international meetings, the utility and applications of these platforms and new genome editing method have been presented. Research articles describing these platforms and the generation of data archived in them also have been published. What do you plan to do during the next reporting period to accomplish the goals? This is the final report. A new project was started to continue the development of the Phytophthora Database and Cyber-infrastructure for Fusarium and the characterization of fusaria and other plant pathogens.
Impacts
What was accomplished under these goals?
The molecular and biochemical mechanisms of pathogen virulence and host immunity during the rice-fungus interaction have been studied and partially elucidated. Specifically, two families (Nep1-like proteins and zinc finger effectors) of Magnaporthe oryzae effectors were characterized for their delivery mechanisms and potential modes of action in rice cells. A novel mechanism in plant signal transduction was characterized and shown to mediate the cross-talk between the calcium-dependent protein kinase pathway and the mitogen-activated protein kinase pathway. In addition, the RNA-guided genome editing technology has bee adapted to precisely modify rice genome for genetic improvement of agronomic traits. Since rice blast and sheath blight are the two most important diseases in the world. Elucidation of the fungal pathogenesis and host defense mechanisms should aid in the development of novel strategies for controlling rice and other cereal diseases. Accurate identification and phylogenetic analysis of fungal pathogens are critical for understanding the etiology and epidemiology of plant diseases and subsequent regulatory and management responses for disease control. We have utilized a broad approach in developing useful molecular tools to recognize and identify fungal plant pathogens. First and foremost is the characterization of existing fungal culture collection resources using molecular tools to develop a phylogenetic framework for understanding relationships and defining species boundaries, and then in turn developing molecular methods for identification and monitoring of populations. In Phytophthora, working with collaborators F. Martin, M. Coffey, S. Kim and J. Blair, we have utilized isolates in the World Phytophthora Collection, the Pennsylvania Department of Agriculture and laboratories around the world to generate a comprehensive phylogeny of the genus. Data from this and subsequent studied formed the core of Phytophthora Database. In the last year, the first comprehensive phylogeny of the genus Fusarium and a proposal for a phylogenetic circumscription of the genus were published. Cyber-infrastructure for Fusarium supports archiving and sharing of rapidly increasing data in phylogenetics and genomics as well as experience-based knowledge on the genus Fusarium and consists of Fusarium-ID, Fusarium Comparative Genomics Platform (FCGP), and Fusarium Community Platform (FCP). The Fusarium-ID archives phylogenetic marker sequences from most known species along with information associated with characterized isolates and supports strain identification and phylogenetic analyses. The FCGP currently archives five genomes from four species. Besides supporting genome browsing and analysis, the FCGP presents computed characteristics of multiple gene families and functional groups. The FCP is designed to serve as an online community forum for sharing and preserving accumulated experience and knowledge to support future research and education.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Geiser, D. M., Aoki, T., Bacon, C. W., Baker, S. E., Bhattacharyya, M. K., Brandt, M. E., Brown, D. W., Burgess, L. W., Chulze, S., Coleman, J. J., Correll, J. C., Covert, S. F., Crous, P. W., Cuomo, C. W., De Hoog, G. S., Di Pietro, A., Elmer, W. H., Epstein, L., Frandsen, R. J. N., Freeman, S., Glenn, A. E., Gordon, T. R., Hammond-Kosack, K. E., Hanson, L. E., J�menez-Gasco, M. M., Kang, S., Kistler, H. C., Kuldau, G. A., Leslie, J. F., Logrieco, A., Lu, G., Lys�e, E., Ma, L.-J., McCormick, S. P., Migheli, Q., Moretti, A., Munaut, F., ODonnell, K., Pfenning, L., Ploetz, R. C., Proctor, R. H., Rehner, S. A., Robert, V. A.R.G., Rooney, A. P., Salleh, B., Scandiani, M. M., Scauflaire, J., Steenkamp, E., Suga, H., Summerell, B. A., Sutton, D. A., Thrane, U., Trail, F., Diepeningen, A. V., VanEtten, H. D., Viljoen, A., Waalwijk, C., Ward, T. J., Wingfield, M. J., Xu, J.-R., Yang, X.-B., Yli-Mattila, T., and Zhang, N. 2013. One Fungus, One Name: Defining the genus Fusarium in a scientifically robust way that preserves longstanding use. Phytopathology 103: 400-408.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Park, S.-Y., J. Choi, S.-E. Lim, G.-W. Lee, J. Park, Y. Kim, S. Kong, S. Kim, H.-S. Rho, J. Jeon, M.-H. Chi, S. Kim, C. Khang, S. Kang, and Y.-H. Lee. 2013. Global Expression Profiling of Transcription Factor Genes Provides New Insights into Pathogenicity and Stress Responses in the Rice Blast Fungus. PLoS Pathog 9 (6):e1003350.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
ODonnell, K., A. P. Rooney, R. H. Proctor, D. W. Brown, S. P. McCormick, T. J. Ward, R. J. Frandsen, E. Lysoe, S. A. Rehner, T. Aoki, V. A. Robert, P. W. Crous, J. Z. Groenewald, S. Kang, and D. M. Geiser. 2013. Phylogenetic analyses of RPB1 and RPB2 support a middle Cretaceous origin for a clade comprising all agriculturally and medically important fusaria. Fungal Genet Biol 52:20-31.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Yang, D. L., Y. Yang, and Z. He. 2013. Roles of plant hormones and their interplay in rice immunity. Mol Plant 6 (3):675-85.
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Progress 10/01/11 to 09/30/12
Outputs
OUTPUTS: To understand the mode of action of Magnaporthe oryzae zinc finger effectors, a number of rice interacting proteins have been isolated by yeast two-hybrid screening. Preliminary studies suggest that the family of M. oryzae zinc finger effectors target transcription and ubiquitination machineries to suppress basal immunity. In addition, the crosstalk among defense signaling pathways in rice has been further characterized. Antagonistic interactions between jasmonate and gibberellin and between ethylene and abscisic acid were clearly demonstrated in rice and elucidated at the molecular level. Among defense signaling pathways, ethylene biosynthesis and signaling were shown to play a more prominent role in rice disease resistance. Transgenic rice with inducible ethylene production was shown to have enhanced resistance to both rice blast and sheath blight pathogens. Improvement of Phytophthora Database: The online community resource has been updated. Its sequence database now archive sequences of 1-12 phylogenetically informative loci from ~2,600 isolates (representing 130 species). Key morphological and growth characteristics of most newly described and provisional species have been incorporated. Other additions to improve PD functionality include: a) Geographic Information System tools that enable users to visualize the geographic origins of chosen isolates on global-scale maps, b) tool for comparing genetic similarity between isolates via microsatellite markers to support population genetic studies within species, c) comprehensive review of molecular diagnostics tools, relevant references, and the sequence alignments used to develop PCR-based diagnostics tools to support their utilization and new tool development, and d) an online community forum for sharing and preserving experience and knowledge accumulated in the global Phytophthora community. Proposal for unitary use of the name Fusarium: In this proposal, we advocate recognizing the genus Fusarium as the sole name for a group that includes virtually all Fusarium species of importance in plant pathology, mycotoxicology, medicine and basic research. This phylogenetically-guided circumscription will free scientists from any obligation to use other genus names, including teleomorphs, for species nested within this clade, and preserve the application of the name Fusarium in the way it has been used for almost a century. Due to recent changes in the International Code of Nomenclature for algae, fungi and plants, this is an urgent matter that requires community attention. The alternative is to break the longstanding concept of Fusarium into nine or more genera, and remove important taxa such as those in the F. solani species complex from the genus, a move we believe is unnecessary. We present taxonomic and nomenclatural proposals that will preserve established research connections and facilitate communication within and between research communities, and at the same time support strong scientific principles and good taxonomic practice. PARTICIPANTS: Yinong Yang coordinated the work on pathogen virulence and host immunity in the rice-fungus interaction. The experimental work was carried out by graduate students (Wenhua Liu, Emily Helliwell, and Yueying Chen), postdoc (Kabin Xie) and research technologist (Qin Wang). Seogchan Kang coordinated the improvement of Phytophthora database. This work has also involved Frank Martin and Nik Grunwald (USDA-ARS), Gloria Abad (USDA-APHIS), Yilmaz Balci (Univ of Maryland), Mike Coffey (UC-Riverside). The Fusarium phylogenetics study was coordinated by Kerry O'Donnell (USDA-ARS, NCAUR, Peoria), in collaboration with David Geiser and other USDA and academic scientists. The taxonomic proposal was formulated by David Geiser in collaboration with O'Donnell and other scientists. TARGET AUDIENCES: The research on the pathogen virulence and host immunity will be helpful to plant biologists and pathologist who are interested in understanding the molecular mechanisms of host-pathogen interaction and improving strategies for controlling crop diseases. The data and tools in Phytophthora database will better support plant pathologists, disease diagnosticians, and regulatory agency researchers in identifying and detecting Phytophthora. Fusarium is the fourth most commonly used fungal generic name, and it has a large and diverse research community including academic, government and industry scientists and diagnosticians. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Little is known about how fungal effectors target host cellular machineries and modulate infection and pathogenesis. Identification and characterization of host proteins targeted by M. oryzae effectors will help elucidate the molecular mechanism of the fungal pathogenesis and rice disease susceptibility. Further elucidation of signaling crosstalks among different defense pathways at the molecular level allow us to understand the complexity involved in biotic and abiotic stress responses and to identify key elements required for rice disease resistance against specific pathogens under certain environmental conditions. The large estimated diversity of Phytophthora (200-600 species) underscores that our understanding of its ecology and diversity in nature is still limited. To effectively support rapid and accurate identification of pathogenic species, a key step for disease management, we cannot overemphasize the importance of cataloging cultures and associated data that represent the known diversity as references in a readily accessible format. Because Phytophthora pathogens pose a threat to agricultural and environmental systems globally, establishing a mechanism that facilitates international cooperation in documenting the diversity and dynamics of known and novel pathogens becomes extremely critical for mitigating their impact. The Phytophthora Database serves plant pathologists, disease diagnosticians, and regulatory agency researchers in a way similar to what the forensic DNA database does for the federal and state law enforcement agencies. It permits a rapid risk assessment of a newly isolated pathogen and also assists in recognizing patterns of pathogen movement/change. This database now has more than 600 registered users from ~60 different countries and has facilitated the identification and description of new species. The sequence data have also helped the development and validation of new molecular diagnostic tools. To understand the evolution of agriculturally important fusaria and to develop useful tools for diagnosis and epidemiology, we need to be aware of the full spectrum of diversity associated with the genus. In a collaborative effort with scientists at the USDA-ARS NCAUR in Peoria, we inferred a two-locus phylogeny of the genus Fusarium, identifying 20 species complexes within the genus. We also inferred a phylogenetic boundary for the genus and formally proposed that all members within this clade be referred to solely as Fusarium, in concordance with upcoming changes in the International Code of Nomenclature for algae, fungi and plants that end dual nomenclature in fungi. This proposal was designed to preserve the longstanding use of the name Fusarium in the applied sciences in a scientifically robust way, minimizing the potential disruption due to changes in the Code.
Publications
- Helliwell, E. H., Q. Wang, and Y. Yang. 2012. Transgenic rice with inducible ethylene production exhibits broad-spectrum disease resistance to the fungal pathogens Maganporthe oryzae and Rhizhoctonia solani. Plant Biotechnology J. http://dx.doi.org/10.1111/pbi.12004.
- Jia, Y., G. Liu, D. S. Park, F. Correa-Vectoria, and Y. Yang. 2012. Inoculation and scoring methods for rice sheath blight disease. Ed. Y. Yang, Humana Press. In Methods in Molecular Biology: Rice Protocols Vol. 956:257-268.
- Helliwell, E. H. and Y. Yang. 2012. Molecular strategies to improve rice disease resistance. Ed. Y. Yang, Humana Press. In Methods in Molecular Biology: Rice Protocols Vol. 956:285-309.
- Yang, D. L., J. Yao, C. S. Mei, X. H. Xiao-Hong Tong, L. J. Zeng, Q. Li, L. T. Xiao, T. P. Sun, F. Li, X. W. Deng, C. M. Lee, M. Thomashow, Y. Yang, Z. H. He, and S. Y. He. 2012. Plant hormone jasmonate prioritizes defense over growth by interfering with gibberellin signaling cascade. (co-corresponding author). Proc. Natl. Acad. Sci. 109:7152-7153.
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Progress 10/01/10 to 09/30/11
Outputs
OUTPUTS: Two groups of Magnaporthe oryzae effectors were characterized, which include 4 members of the Nep1 (necrosis and ethylene inducing peptide) like protein (MoNLP) family and 8 members of the zinc finger protein family. The MoNLPs appear to act on plant cell membrane and elicit necrotic cell death in both dicot and monocot plants. By contrast, the zinc finger effectors appear to be delivered into host cell via biotrophic interfacial complex. Transient gene expression and stable transgenic analyses reveal that the zinc finger effectors are capable of suppressing programmed cell death and enhancing host susceptibility to M. oryzae infection. We have also identified a motif that is involved in the entry and translocation of the zinc finger effectors into the plant cell. To better understand the mode of action and potential host cellular target(s) of these effectors, the yeast two-hybrid assay was conducted to isolate putative host target proteins. An MoNLP1-interacting rice protein (OsNPI1) has been characterized. The OsNPI1 protein encodes a highly conserved ubiquitin-like protein and is predominantly localized in rice plasma membrane. Suppression of OsNPI1 in rice resulted in lesion mimic phenotype. In addition to studying the M. oryzae effectors, we have identified a novel mechanism which mediates the cross-talk between the calcium-dependent protein kinase pathway and the mitogen-activated protein kinase pathway, both of which are important during the rice defense response. Diversity of saprophytic and pathogenic fusaria in sink drain biofilms: Fusarium is adapted to a wide variety of ecological niches, including indoor plumbing systems. We sampled 471 drains, mostly in bathroom sinks, from 131 buildings in the US. We found that 66% of sinks and 80% of buildings surveyed yielded at least one Fusarium culture. Multilocus sequence typing was used to identify the phylogenetic species and sequence types (STs) of 297 isolates, which revealed that the six most common STs in sinks were identical to the six most frequently associated with human infections. We speculate that the most prevalent STs, by virtue of their ability to form and grow in biofilms, are well adapted to plumbing systems. Characterization of Pathogenesis by F. oxysporum and completion of Cyberinfrastructure for Fusarium (CiF): F. oxysporum causes vascular wilt and root rot diseases in many plant species. We investigated the role of cAMP-dependent protein kinase A of F. oxysporum in growth, morphology, and root attachment, penetration, and pathogenicity in Arabidopsis thaliana. Several experimental tools useful for studying mechanisms of fungal root pathogenesis were also developed. The CiF, consisting of comparative genomics platform (supporting analysis and utilization of sequenced Fusarium genomes), Fusarium-ID (supporting the multigene-based identification of Fusarium isolates), and community-networking platform based on web2.0 tools, was published. PARTICIPANTS: The rice-fungus interaction study was coordinated by Yinong Yang (co-PI). Identification and characterization of fungal effectors and host targets were conducted by Wenhua Liu and Yueying Chen (graduate students). Elucidation of rice defense signaling and characterization of transgenic rice plants were conducted by Kabin Xie (postdoc) and Emily Helliwell (graduate student). Generation of transgenic rice and further characterization of some host target proteins were carried out by Qin Wang (research technologist). The Fusarium sink drain study was coordinated by David Geiser, and performed by PhD student Dylan Short. The work utilized previous data and analyses generated and performed by external collaborators Kerry O'Donnell (USDA-ARS, NCAUR, Peoria) and Ning Zhang (former postdoc in Geiser lab, now at Rutgers). Seogchan Kang and David Geiser coordinated the construction of CiF. The work on the functional characterization of cPKA was mainly conducted by Seogchan Kang and Hye-Seon Kim, a postdoc in Kang's lab. TARGET AUDIENCES: The study on the pathogen virulence and host resistance mechanisms will be helpful to rice researchers and plant pathologists who are interested in improving strategies for controlling crop diseases. The study on sink Fusarium adds to our growing knowledge of the diversity of this important genus, and will have an impact for diagnosticians likely to encounter these fungi in the field. The data and tools in CiF will help plant pathologists, disease diagnosticians, and regulatory agency researchers. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Rice blast and sheath blight are the two most important diseases that negatively impact rice production in the world. Elucidation of the fungal pathogenesis and host defense mechanisms should aid in the development of novel strategies for controlling rice and other cereal diseases. To understand the evolution of agriculturally important fusaria and to develop useful tools for diagnosis and epidemiology, we need to be aware of the full spectrum of diversity associated with the genus. These plumbing and human associated fusaria occur in irrigation systems and may be detected in association with disease outbreaks, even if they are not associated with the disease in question. We hypothesize that these fusaria have undergone specific adaptations that allow them to survive in biofilms, and studying their evolution is bound to reveal insights that are relevant to their roles as plant pathogens and toxin producers. More than 35,000 Fusarium strains isolated from various substrates around the world are accessioned in the Fusarium Research Center (FRC) and the USDA-ARS NRRL Culture Collection. Using this rich strain resource, extensive molecular phylogenetic studies have been conducted, resulting in data covering most agriculturally and/or medically important species complexes. The CiF was built to support the preservation of resulting phylogenetic data and associated cultures in a format that is readily accessible and searchable by members of the global Fusarium research community. Via systematically archiving datasets from multiple areas of research on Fusarium, the CiF will help efficiently leverage new knowledge based on the existing knowledge and support problem solving.
Publications
- Kim, H.-S., S.-Y. Park, S. Lee, E. L. Adams, K. Czymmek, and S. Kang. 2011. Loss of cAMP-dependent protein kinase A affects multiple traits important for root pathogenesis by Fusarium oxysporum. Molecular Plant-Microbe Interactions 24:719-732.
- Park, B., J. Park, K.-C. Cheong, J. Choi, J. Jung, Y.-H. Lee, T. J. Wald, K. O'Donnell, D. M. Geiser, and S. Kang. 2011. Cyber-infrastructure for Fusarium (CiF): Three integrated platforms supporting strain identification, phylogenetics, comparative genomics, and knowledge sharing. Nucleic Acids Research (Database Issue) 39:D640-D646.
- Short, D. P. G., K. O'Donnell, N. Zhang, and D. M. Geiser. 2011. Widespread occurrence of diverse human pathogenic types of the fungus Fusarium detected in bathroom sink drains. Journal of Clinical Microbiology (In Press).
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Progress 10/01/09 to 09/30/10
Outputs
OUTPUTS: 1. Cyberinfrastructure for Fusarium diversity: The fungal genus Fusarium includes many plant and/or animal pathogenic species and produces diverse toxins. Extensive molecular phylogenetic studies, founded on well-preserved culture collections, have established a robust foundation for Fusarium classification and identification. Cyber-infrastructure for Fusarium (CiF; http://www.fusariumdb.org/) was built to support archiving and utilization of resulting phylogenetic data as well as genomics data and consists of Fusarium-ID, Fusarium Comparative Genomics Platform (FCGP), and Fusarium Community Platform (FCP). The Fusarium-ID archives phylogenetic marker sequences from most known species along with information associated with characterized isolates and supports strain identification and phylogenetic analyses. The FCGP currently archives five genomes from four species. Besides supporting genome browsing and analysis, the FCGP presents computed characteristics of multiple gene families and functional groups. The Cart/Favorite function allows users to collect sequences from the Fusarium-ID and the FCGP and analyze them later using multiple tools without requiring repeated copying-and-pasting of sequences. The FCP is designed to serve as a community forum for sharing and preserving accumulated experience and knowledge to support future research and education. 2. Factors mediating pathogenesis in rice blast disease: The Magnaporthe oryzae genome encodes over a thousand of secreted proteins, which are likely critical for the fungal pathogenesis in rice plants. We have characterized two types of M. oryzae effectors, including the four Nep1 (necrosis and ethylene inducing peptide) like proteins (NLP) that elicit host cell death and a family of zing finger proteins that suppress cell death. Unlike other NLPs which were reported to cause cell death only in dicots, MoNLPs are capable of eliciting cell death in both dicot and monocot plants. To better understand the mode of action and potential host cellular target(s) of fungal effectors, MoNLP1 and a zing finger effector were used as baits to screen for interacting rice proteins by the yeast two-hybrid assay. Independent screenings and repeated confirmation tests led to the identification of OsNPI1 (Oryza sativa NLP Interactor1), a highly conserved ubiquitin-like protein. Knockout of the NPI1 orthologue in Arabidopsis T-DNA mutants led to retarded growth and lethal phenotype. Transgenic rice lines with suppression or overexpression of OsNPI1 are being analyzed for altered host response to M. oryzae infection. In addition to M. oryzae effectors, we identified a family of endogenous rice peptide elicitors that involves host resistance responses. We also generated and characterized transgenic rice lines defective in ethylene, abscisic acid, or jasmonic acid biosynthesis or signaling. Transgenic analyses reveal that host resistance to rice blast (M. oryzae) and sheath blight (Rhizoctonia solani) pathogens is positively regulated by ethylene, but negatively modulated by abscisic acid. Jasmonic acid appears to positively regulate rice blast resistance, but negatively regulate sheath blight resistance. PARTICIPANTS: Seogchan Kang and David Geiser coordinated the construction of CiF. Kerry O'Donnell and Todd Ward (USDA-ARS) and Virgilio Balmas and Quirico Migheli (University of Sassari) have collaborated on this work. The rice-pathogen interaction study was coordinated by Yinong Yang (co-PI). Analysis of the fungal effectors and potential host targets were conducted by Zhenyu Liu (postdoc) and Wenhua Liu (graduate student). Elucidation of host defense mechanisms and characterization of transgenic rice plants were conducted by Kabin Xie (postdoc) and Emily Helliwell (graduate student). Dissection of sheath blight resistance was conducted by Junhua Zhang (visiting scientist). Generation of transgenic rice and further characterization of host target proteins were carried out by Qin Wang (research technologist). TARGET AUDIENCES: The phylogenetic framework for Fusarium will help plant pathologists, disease diagnosticians, and regulatory agency researchers. The study on the rice-pathogen interaction and disease resistance mechanisms will be useful to rice researchers and plant pathologists for developing novel strategies for crop disease control. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Cyberinfrastructure for Fusarium diversity: More than 35,000 strains isolated from various substrates around the world are accessioned in the Fusarium Research Center (FRC) and the USDA-ARS NRRL Culture Collection, making this genus the best-preserved fungal group. Using this rich strain resource, extensive molecular phylogenetic studies have been conducted, resulting in data covering most agriculturally and/or medically important species complexes. However, despite these advances, a significant amount of diversity has yet to be explored, and some species complexes are quite poorly characterized phylogenetically. To support and coordinate these tasks, it is essential to archive available phylogenetic data and associated cultures in a format that is readily accessible and searchable by members of the global Fusarium research community. The main motivation for building CiF was to support the archiving and integration of data and knowledge from disparate yet related areas of research on Fusarium through a single integrated platform. Via systematically archiving datasets from multiple areas of research on Fusarium, the CiF aims to efficiently leverage new knowledge and support problem solving. Such data proved useful in our discovery of interesting patterns of diversity in soil fusaria in Sardinia. In the FOSC, we found that certain multilocus haplotypes we had seen elsewhere in the world were also widespread across multiple sites and ecological zones on the island. Superimposed on the distribution of these cosmopolitan haplotypes were haplotypes we had not seen before, that tended to be found only at a single site on the island. We hypothesize that these presumably endemic haplotypes represent native soil saprophytes, and that the cosmopolitan types, most of which had previously been associated with agricultural diseases, were more recent introductions. These endemic soil fusaria are potentially important subjects in studying the evolution of pathogenicity. Factors mediating pathogenesis in rice blast disease: Rice blast and sheath blight are the two most important rice diseases in the world. Understanding the early process of host-pathogen interaction and subsequent defense signaling mechanisms will facilitate the development of novel strategies for controlling rice and other crop diseases.
Publications
- Kang, S., M. A. Mansfield, B. Park, D. M. Geiser, K. L. Ivors, M. D. Coffey, N. Grunwald, F. N. Martin, A. Levesque, and J. E. Blair. 2010. The promise and pitfalls of sequence-based identification of plant pathogenic fungi and oomycetes. Phytopathology 100:732-737.
- Balmas, V., Q. Migheli, B. Schrm, P. Garau, K. O'Donnell, G. Ceccherelli, S. Kang, and D. M. Geiser. 2010. Multilocus phylogenetics show high levels of endemic fusaria inhabiting Sardinian soils (Tyrrhenian Islands). Mycologia 102:803-812.
- Jin, J.-M., S. Lee, J. Lee, S.-R. Baek, J.-C. Kim, S.-H. Yun, S.-Y. Park, S. Kang, and Y.-W. Lee. 2010. Functional characterization and manipulation of the apicidin biosynthetic pathway in Fusarium semitectum. Mol. Microbiology 76:456-466.
- Ma, L.-J., H. C. van der Does, K. A. Borkovich, J. J. Coleman, M.-J. Daboussi, A. Di Pietro, M. Dufresne, M. Freitag, M. Grabherr, B. Henrissat, P. M. Houterman, S. Kang, W.-B. Shim, C. Woloshuk, X. Xie, J.-R. Xu, J. Antonxiw, S. E. Baker, B. H. Bluhm, A. Breakspear, D. W. Brown, R. A. E. Butchko, S. Chapman, R. Coulson, P. M. Coutinho, E. J. G. Danchin, A. Diener, L. R. Gale, D. M. Gardiner, S. Goff, K. E. Hammond-Kosack, K. Hilburn, P. M. Houterman, A. Hua-Van, W. Jonkers, K. Kazan, C. D. Kodira, M. Koehrsen, L. Kumar, Y.-H. Lee, L. Li, J. M. Manners, D. Miranda-Saavedra, M. Mukherjee, G. Park, J. Park, S.-Y. Park, R. H. Proctor, A. Regev, M. C. Ruiz-Roldan, D. Sain, S. Sakthikumar, S. Sykes, D. C. Schwartz, B. G. Turgeon, I. Wapinski, O. Yoder, S. Young, Q. Zeng, S. Zhou, J. Galagan, C. A. Cuomo, H. C. Kistler, and M. Rep. 2010. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium oxysporum. Nature 464:367-373.
- Vleesschauwer, D. D., Y. Yang, C. V. Cruz, and M. Hofte. 2010. Abscisic acid-induced resistance against the brown spot pathogen Cochliobolus miyabeanus in rice involves MAPK-mediated repression of ethylene signaling. Plant Physiology 152:2036-2052.
- Stout, M. J., M. R. Riggio, and Y. Yang. 2009. Direct induced resistance in Oryza sativa to Spodoptera frugiperda. Environ. Entomol. 38(4):1174-1181.
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Progress 10/01/08 to 09/30/09
Outputs
OUTPUTS: Bioinformatic analysis of the genome sequences of Magnaporthe oryzae revealed the presence of over 1000 genes encoding secreted proteins, some of which may function as pathogenesis effectors in rice plants. We have characterized a number of these putative fungal effectors including a small family of four Nep1 (necrosis and ethylene inducing peptide) like proteins (NLPs). Unlike other NLPs that cause cell death only in dicots, M. oryzae NLPs (named as MoNLPs) seem to be capable of eliciting cell death in both dicot and monocot plants. Furthermore, we have isolated a rice protein (MoNPI1) that specifically interacts with MoNLP1 via yeast two-hybrid screening. Expression of MoNPI1 is induced during infection, suggesting that this protein is likely involved in the early process of the rice-M. oryzae interaction. We continued to analyze transgenic rice plants defective in ethylene, abscisic acid, and/or jasmonic acid signaling pathways and to characterize substrates that are phosophorylated by the stress-responsive OsMPK5 kinase. We found that OsMPK5 may act as a negative regulator of ethylene signaling by impinging on signal transduction between OsEIN2 and OsEIL1 in rice. In vitro protein binding and kinase assays revealed that OsMPK5 interacted with and phosphorylated OsEIL1. Transgenic analysis showed that OsEIL1 positively regulated OsERF1 and OsPR5 expression and increased rice disease resistance against M. oryzae. In addition to identifying putative effectors encoded by M. oryzae, we isolated secreted proteins from cultural filtrates of Rhizoctonia solani AG-1 IA, the causal agent of rice sheath blight. These secreted proteins, which were identified using mass spectrometry, may represent putative effectors important for the pathogenicity of this necrotrophic pathogen. We selected 75 isolates of P. capsici and related species from the World Phytophthora Collection to investigate species boundaries among P. capsici and other related species of Phytophthora. Using seven nuclear and four mitochondrial loci, we performed a phylogenetic analysis of isolates previously identified as P. capsici and P. mexicana, as well as P. glovera, P. tropicalis and P. siskiyouensis. Phytophthora capsici and P. mexicana isolates together form a distinct monophyletic group, but there was no support in the multilocus phylogeny for the status of P. mexicana. A novel, highly supported clade of isolates from cacao in Brazil was also resolved, suggesting that these isolates constitute a new species of Phytophthora. There was very strong support for the monophyly of P. glovera, P. tropicalis and P. siskiyouensis. Other isolates showed distant relationships to all other taxa, suggesting that they are single members of currently uncharacterized species. PARTICIPANTS: Yinong Yang coordinated the study of the rice-pathogen interactions. Characterization of the M. oryzae effectors and potential host targets was conducted by Jai Rohila (postdoc), Zhenyu Liu (postdoc), and Wenhua Liu (graduate student). Elucidation of host defense mechanisms and characterization of transgenic rice plants were conducted by Kabin Xie (postdoc), Jianping Chen and Emily Helliwell (graduate students). Qin Wang, a research technologist, was responsible for generating transgenic rice and studying secreted proteins of R. solani. Seogchan Kang and David Geiser coordinated the characterization of the Phytophthora capsici species complex. Michele Mansfield (postdoc) sequenced marker genes for phylogenetic analysis and analyzed the resulting data. Mike Coffey (UC-Riverside), Gloria Abad (USDA-APHIS), and Frank Martin (USDA-ARS) have participated in the characterization of the Phytophthora capsici species complex. TARGET AUDIENCES: The research findings from the study of fungal effectors and rice defense signaling pathways will be useful to rice researchers and plant pathologists for developing novel strategies for crop disease control. The phylogenetic framework for P. capsici and related species will help plant pathologists, disease diagnosticians, and breeders. The phylogenetic marker sequence data will be available through the Phytophthora Database website at www.phytophthoradb.org. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Rice blast and sheath blight are the two most important rice diseases in the world. Identification and characterization of their effectors and host proteins interacting with these effectors are important for understanding the early process of the interaction between rice and these pathogens. Since deploying host disease resistance is one of the most effective and environment-friendly approaches for disease management, elucidation of the defense signaling pathways and their interactions in rice will improve our ability to develop novel strategies for controlling rice and other crop diseases. Phytophthora capsici causes extensive damage worldwide to a considerable number of important agricultural plants, including solanaceous, curcubit, and tropical species. Localized field populations of P. capsici are reported to have considerable morphological and physiological diversity, including resistance to chemical controls, suggesting the presence of distinct populations and/or closely related species. Previous studies provided evidence for subgroups within P. capsici, leading to descriptions of the species P. mexicana and P. tropicalis. The comprehensive phylogenetic analysis based on multiple nuclear and mitochondrial genes established a robust reference framework for identifying P. capsici and related species and monitoring their global distribution.
Publications
- Helliwell, E. E. and Y. Yang. 2009. Systemic signaling in plant defense. In Encyclopedia of Life Sciences. John Wiley and Sons, Ltd. Hoboken, NJ. (In Press).
- Bailey, T. A., X. Zhou, J. Chen, and Y. Yang. 2009. Role of ethylene, abscisic acid and MAP kinase pathways in rice blast disease resistance. In G. Wang and B. Valent, (eds.), Advances in Genetics, Genomics and Control of Rice Blast Disease. Springer Publishing. Heidelberg, Germany. pp. 185-190.
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Progress 10/01/07 to 09/30/08
Outputs
OUTPUTS: We identified several novel Phytophthora species among strains collected from streams and nurseries in Pennsylvania based on the sequences of the internal transcribed spacer (ITS) region of ribosomal RNA-encoding genes. Sequences of seven additional loci were determined to rigorously test whether they should be considered new species and to determine their relationships with known species. The resulting data were deposited to Phytophthora Database (www.phytophthoradb.org). Phenotypic traits of these new species, such as morphology, growth characteristics, and pathogenic characters, were also characterized. Bioinformatic analysis reveals that M. oryzae genome encodes several hundreds of secreted proteins which may facilitate the fungal pathogenesis in rice plants. We have analyzed a dozen of these proteins including a small family of four Nep1 (necrosis and ethylene inducing peptide) like proteins (NLP). Three out of four MoNLPs were capable of eliciting host cell death on tobacco and rice plants. These proteins appear to act as the fungal PAMPs (pathogen-associated molecular patterns) with potential virulence function. In addition, a Xanthomonas-based system is being developed to facilitate the delivery and screening of M. oryzae effectors in rice. To understand the role of a stress-responsive rice mitogen-activated protein kinase (OsMPK5) in mediating rice defense response, more than a dozen of its substrates were identified by phosphorylation screening and bioinformatic analysis. In vivo phosphorylation and functional analysis are being conducted to further elucidate the role of these OsMPK substrates in rice stress signaling. Furthermore, we have generated a series of transgenic rice lines to study the interplay of jasmonic acid, ethylene and abscisic acid signaling pathway during the rice-pathogen interaction. PARTICIPANTS: Seogchan Kang coordinated the identification and characterization of novel Phytophthora species. Sook-Young Park and Michele Mansfield, postdoctoral associates in Kang's lab, conducted phylogenetic analyses with the new species. Bongsoo Park, a graduate student in Kang's lab, curated Phytophthora Database. Yinong Yang coordinated the study of fungal effectors and rice defense response. Jai S. Rohila, a postdoctoral associate, and Wenhua Liu, a graduate student, characterized the fungal effectors. Postdoctoral associates (Gang Ren and Kabin Xie) and graduate students (Jianping Chen and Emily Helliwell) conducted the study of rice defense response. Qin Wang, a research technologist, assisted the research project. TARGET AUDIENCES: The Phytophthora Database supports the identification of Phytophthora by plant pathologists who work on Phytophthora diseases and plant disease diagnosticians. The results generated from the study of fungal effectors and rice defense response will be useful to rice researchers and plant biologists in the U.S. and around the world. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Many novel Phytophthora species have been identified in recent years. This proliferation of newly discovered species is indicative of our limited understanding of the ecology and diversity of Phytophthora in nature. Systematically cataloging what has already been isolated and characterized is essential for future surveys, disease management, and tracking their origins. This catalog stored in Phytophthora Database provides a baseline for accurate identification and risk assessment of new isolates by comparison of genetic/phenotypic similarity. Rice blast and sheath blight are the two most important rice diseases in the world. Identification and characterization of their effectors is critical to the understanding of the fungal pathogenesis and disease occurrence. Since host plant resistance is one of the most effective and environment-friendly approaches for disease management, a better understanding of molecular and biochemical mechanisms underlying host defense responses against fungal infections will facilitate the development of novel strategies for controlling these important diseases.
Publications
- Balci, Y., S. Balci, J.E. Blair, S. Park, S. Kang, and W. MacDonald. 2008. Phytophthora quercetorum sp. nov., a novel species isolated from eastern and north-central US oak forest soils. Mycological Research. 112: 906-916.
- Bailey, T.A., X. Zhou, J. Chen, and Y. Yang. 2008. Towards understanding the signal transduction of rice blast resistance. In Advances in Genetics, Genomics and Control of Rice Blast Disease, Springer. (In Press).
- Blair, J.E., M.D. Coffey, S.-Y. Park, D.M. Geiser, and S. Kang. 2008. A multi-locus phylogeny for Phytophthora utilizing markers derived from complete pathogen genomes. Fungal Genetics & Biology. 45:266-277.
- Park, J., B. Park, N. Veeraraghavan, J.E. Blair, D.M. Geiser, S. Isard, M.A. Mansfield, E. Nikolaeva, S.-Y. Park, J. Russo, S.H. Kim, M. Greene, K.L. Ivors, Y. Balci, M. Peiman, D.C. Erwin, M.D. Coffey, K. Jung, Y.-H. Lee, A. Rossman, D. Farr, E. Cline, N.J. Grunwald, D.G. Luster, J. Schrandt, F. Martin, O.K. Ribeiro, I. Makalowska, and S. Kang. 2008. Phytophthora Database: A forensic database supporting the identification and monitoring of Phytophthora. Plant Disease. 92:966-972.
- Park, D.-S., R.J. Sayler, Y.-G. Hong, M.-H. Nam, and Y. Yang. 2008. A method for inoculation and evaluation of rice sheath blight disease. Plant Disease. 92:25-29.
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