Progress 01/01/03 to 09/30/05
Outputs
The main objectives of this project are (i) to identify genetic markers that can differentiate races/populations within two soybean rust fungi, Phakopsora pachyrhizi and P. meibomiae, through the mining of their genome sequence data, and (ii) to develop a web-based database that will house the genotype and phenotype data from both fungi as well as other pathogens of economic significance. For many pathogens, the identity of a particular isolate at the species level is often not sufficient to predict its traits (virulence, host range, chemical resistance, etc.) because these traits are often variable within pathogen species. Thus, a better understanding of the phenotypic and genetic diversity of soybean rust fungi, and which population/race of a given species is causing a disease in the field is critical for designing successful, long-term disease management strategies. The USDA-ARS Foreign Disease-Weed Science Research (FDWSR) unit at Ft. Detrick and the DOE Joint
Genome Institute are currently sequencing the genomes of both fungi toward the goal of understanding their biology and evolution. In collaboration with Dr. Reid Frederick at USDA/FDWSR, we have searched the available genome sequence data for protein-coding genes that contain highly variable introns and intergenic regions; such regions have been shown to be informative at resolving species boundaries in other fungi. Isolation of genomic DNAs from the collection of P. pachyrhizi and P. meibomiae isolates stored at USDA/FDWSR is currently being conducted. Once their genomics DNA becomes available to us, we will amplify a group of candidate genes from these isolates and sequence to identify informative genes that can differentiate races/populations within each species. We have also identified a large number of microsatellite loci in the P. pachyrhizi genome from analyzing the available genome sequence data. These microsatellite markers can complement our effort to identify/differentiate
different populations/races based on the gene sequence-based markers. In the long run, some of these markers will be used to develop new molecular diagnostic methods. Considering the ability of soybean rust spores to travel long distances, it is critical to detect their presence early so that appropriate measures can be taken to eradicate the pathogen before it has established. For the database, we have established a prototype database (http://fppd.cbio.psu.edu/) with some of the associated computational tools for data analysis and visualization being in place. This database is designed to house data from other fungal pathogens as well.
Impacts
Soybean rust caused by Phakopsora pachyrhizi can inflict serious damage to the soybean crop due to premature defoliation, causing yield reductions ranging from 10 to 80%. A closely related species, P. meibomiae, also causes soybean rust, but is less aggressive than P. pachyrhizi. Although Phakopsora meibomiae was reported in Puerto Rico in 1976 and P. pachyrhizi was reported in Hawaii in 1995, soybean rust has not yet been detected in the continental U.S. until this year. In November of 2004, soybean rust has been detected in a number of Southern states, including Alabama, Arkansas, Florida, Louisiana, Mississippi, Missouri, and Tennessee. A series of September hurricanes probably have brought wind-borne spores from the affected areas in South America. Because early detection and subsequent responses can enhance the probabilities of achieving containment, the development of a tool for rapidly and accurately detecting their presence and specie- and race-identity will be
an essential component in effectively dealing with soybean rust. The volume of taxonomic, phylogenetic, and population genetic analyses of plant pathogenic fungi has increased substantially in recent years. However, complementary efforts to archive and share resulting data have been limited, in part due to the lack of mechanisms and protocols to support such activities. This results in unnecessary fragmentation of community research and duplication of activities. The database we are building will facilitate systematically cataloging such data by the plant pathology community.
Publications
- Geiser, D. M., Jimenez-Gasco, M., Kang, S., Makalowska, I., Veeraraghavan, N., Ward, T.J., Zhang, N., Kuldau, G.A. and O'Donnell, K. 2004. FUSARIUM-ID v.1.0: A DNA sequence database for identifying Fusarium. European J. Plant Pathology 110: 473-479.
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Progress 01/01/03 to 12/31/03
Outputs
Soybean rust caused by Phakopsora pachyrhizi and P. meibomiae can inflict serious damage to the soybean crop. The main objectives of this project are to identify genetic markers that can differentiate races/populations within each species through the use of their genome sequence data and to develop a web-based database that will house the genotype and phenotype data of both fungi. For many pathogens, the identity of a particular isolate at the species level is often not sufficient to predict its traits (virulence, host range, chemical resistance, etc.) because these traits are often variable within pathogen species. Thus, a better understanding of the phenotypic and genetic diversity of soybean rust fungi, and which population/race of a given species is causing a disease in the field is critical for designing successful, long-term disease management strategies. The USDA-ARS Foreign Disease-Weed Science Research (FDWSR) unit at Ft. Detrick and the DOE Joint Genome
Institute are currently sequencing the genomes of both fungi toward the goal of understanding their biology and evolution. In collaboration with Dr. Reid Frederick at USDA/FDWSR, we have searched the available genome sequence data for protein-coding genes that contain highly variable introns and intergenic regions; such regions have been shown to be informative at resolving species boundaries in other fungi. Once the request for Exemption of Selected Biological Agents and Toxins is granted by USDA-APHIS, genomic DNAs from the collection of P. pachyrhizi and P. meibomiae isolates stored at USDA/FDWSR will be obtained. A group of candidate genes identified through the genome sequence search will be amplified by PCR from these isolates and sequenced to identify informative genes that can differentiate races/populations within each species. Some of these genes will also be used to develop new molecular diagnostic methods. Considering the ability of soybean rust spores to travel long
distances, it is critical to detect their presence early so that appropriate measures can be taken to eradicate the pathogen before it has established. Relative to a rather slow start at genotyping soybean rust isolates, we have made a steady progress in developing a database and associated computational tools for storing and searching both genotypes and phenotypes of selected pathogens.
Impacts
Crops and forests in the U.S. are under constant threat from various pathogens, some of which have not yet been established, but have a high likelihood of introduction into the US. Increasing interstate and international commerce is highly conducive for introduction of exotic, non-native pathogens. Soybean rust caused by Phakopsora pachyrhizi can inflict serious damage to the soybean crop due to premature defoliation, causing yield reductions ranging from 10 to 80%. A closely related species, P. meibomiae, also causes soybean rust, but is less aggressive than P. pachyrhizi. Both species have an unusually broad host range, infecting plants in many legume genera. Although P. meibomiae was reported in Puerto Rico in 1976 and P. pachyrhizi was reported in Hawaii in 1995, soybean rust has not yet been detected in the continental U.S. However, it continues to pose a serious threat to the soybean industry in the U.S., because it has been reported in a number of South
American countries, including Brazil, Argentina, and Paraguay, and appears to have been moving to the North through wind-borne spores. Thus, its introduction to major soybean-growing areas in the U.S. in the near future is likely. Because rapid preemptory detection and subsequent responses can enhance the probabilities of achieving containment and eradication, the development of a tool for rapidly and accurately detecting their presence and specie- and race-identity will be an essential component in effectively dealing with soybean rust.
Publications
- Kang, S., Makalowska, I., Frederick, R. and Luster, D. 2003. Plant Pathogen Database: A community resource for archiving and sharing the genetic and phenotypic information of important pathogens. Phytopathology 93:S43.
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