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United States Department of Agriculture

Agricultural Research Service

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Research Project: Comparative Genomic Systems for Molecular Detection and Control of Toxigenic Fusarium

Location: Bacterial Foodborne Pathogens & Mycology Research Unit

2012 Annual Report


1a.Objectives (from AD-416):
The overall goal of this project is to contribute to the effective control of toxigenic Fusarium, especially those responsible for FHB of small grain cereals, in order to enhance food safety and crop production in the U.S. and around the world. The proposed project is designed to produce a robust evolutionary framework for understanding the genetic and phenotypic diversity, geographic distribution and population biology of toxigenic fusaria, and will result in novel technologies for the rapid detection, identification and control of toxigenic fusarial pathogens of critical importance to food safety and food security. This framework will also support and facilitate work by the global Fusarium research community. The specific objectives are: Objective 1: characterize the genetic diversity and mycotoxin potential of Fusarium head blight and other fusarial pathogens, develop novel pathogen detection technologies, and expand web-accessible informational database to facilitate the rapid and accurate identification of toxigenic fusaria via the Internet. Objective 2: Determine the global population structure of F. graminearum and identify genetic variation associated with population-level difference in growth, reproduction, and toxin accumulation phenotypes as a means to improve pathogen modeling and surveillance. Objective 3: Characterize the mechanisms that drive the diversification and adaptive evolution of virulence genes in Fusarium genomes as well as host defense genes involved in immunogenicity and disease response.


1b.Approach (from AD-416):
Toxins produced by plant-pathogenic Fusarium pose a significant threat to food safety and place a major burden on the world’s agricultural economy. The primary objectives of the proposed research are to:.
1)Characterize the genetic diversity and mycotoxin potential of Fusarium head blight (FHB) and other fusarial pathogens, develop novel pathogen detection technologies, and expand web-accessible informational databases to facilitate the rapid and accurate identification of toxigenic fusaria via the Internet,.
2)Determine the global population structure of F. graminearum and identify genetic variation associated with population-level differences in growth, reproduction, and toxin accumulation phenotypes as a means to improve pathogen modeling and surveillance, and.
3)Characterize the mechanisms that drive the diversification and adaptive evolution of virulence genes in Fusarium genomes as well as host defense genes involved in immunogenicity and disease response. These complementary objectives are directed at developing robust pathogen control strategies through elucidating the evolution, population structure, phenotypic diversity, host range, geographic distribution and adaptive potential of toxigenic fusaria. In addition, the planned research will produce enhanced methods for identification and characterization (e.g. toxin type, toxin accumulation potential, and host preference) of Fusarium responsible for mycotoxin contamination of cereals and other food. The information and molecular tools developed as a result of this project will address the needs of small grain cereal producers, food and feed processors, the U.S. Department of Agriculture (USDA) Federal Grain Inspection Service (FGIS), the USDA Animal and Plant Health Inspection Service (APHIS), and the Food and Drug Administration (FDA).


3.Progress Report:
This research is directed at developing robust Fusarium head blight cereal pathogen control strategies and enhanced methods for identification and characterization of species responsible for mycotoxin contamination of cereals and other food. In order to facilitate accurate identification of toxigenic and pathogenic fusaria via the Internet, we expanded the DNA sequence-based informational databases Fusarium-ID (http://isolate.fusariumdb.org) and Fusarium MLST (http://www.cbs.knaw.nl/fusarium) to include data on the phylogenetic spectrum of fusaria. In addition, genes responsible for the production of several toxins were identified in the unpublished whole genome sequences of two Fusarium species that cause diseases of plants, and the phylogenetic distribution of toxin genes and gene clusters was mapped on the first robust molecular phylogeny of Fusarium. This research provides a framework for determining toxin potential across the genus. In order to develop an understanding of agriculturally-significant variation within Fusarium head blight (FHB) pathogen populations in the United States and around the world, we produced an initial assessment of their diversity and evolutionary relationships within and between FHB populations from five continents. In order to generate a more complete picture of global FHB diversity, we sequenced large regions of the genomes of strains representing FHB populations from around the globe. These data are being used to identify recent and potential future movement of FHB pathogen populations and to detect introductions of invasive pathogen populations. These data will also be used to identify regions of the genome that are responsible for observed differences in growth, toxin production, and aggressiveness in order to improve disease modeling, detection, and control strategies. In addition, we completed an initial survey of FHB pathogens collected from wheat in the Midwestern United States, and initiated studies of diverse FHB populations in France and Brazil in order to evaluate host-preference and assess the potential threat posed by FHB species and populations from outside the United States. Finally, we conducted an analysis of the growth and toxin production characteristics for a series of FHB populations collected from across Canada in order to determine why an introduced FHB population has been so successful in western Canada. This information will be analyzed in order to provide novel insights into disease control strategies aimed at reducing the spread of an invasive, and highly toxigenic, FHB pathogen population in the United States and Canada. To improve our capacity to conduct comparative genomic analyses of Fusarium, we have established a next-generation sequencing facility at NCAUR. An Ion Proton semiconductor sequencing system has been acquired for sequencing fungal genomes and transcriptomes, and for resequencing large fragments of the Fusarium genome across populations. In order to facilitate analysis and storage of the data generated from this sequencer, we are installing a computational cluster, an 80 terabyte network attached storage server, and genome analysis software.


4.Accomplishments
1. Enabling rapid identification of toxigenic and pathogenic Fusarium species. Fusarium species rank among the most economically destructive plant pathogens and mycotoxigenic fungi, posing a constant threat to plant and animal health, and food safety. ARS scientists in the Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agricultural Utilization Research, Peoria, IL, in collaboration with agricultural scientists in Denmark, Israel, Japan, The Netherlands, and Norway, determined that DNA sequence data could be used to accurately type agriculturally important pathogens and help predict toxin potential. In addition, the researchers identified genes responsible for the production of several toxins injurious to humans and plants in the whole genome sequence of two phytopathogenic Fusarium species. Lastly, the DNA sequence data have been incorporated into Fusarium-ID (http://isolate.fusariumdb.org, at the Pennsylvania State University, Philadelphia, PA, and Fusarium MLST (http://www.cbs.knaw.nl/fusarium) at the Centraalbureau voor Schimmelcultures (CBS-KNAW) Biodiversity Center, Utrecht, The Netherlands, two web-accessible sites dedicated to promoting DNA sequence-based identifications of pathogenic and toxigenic fusaria via the Internet. The two websites promote agricultural biosecurity worldwide by facilitating global molecular surveillance of pathogenic fusaria and by enabling plant quarantine officials, plant breeders, and plant pathologists to accurately detect and identify these pathogens for the first time.


Review Publications
Sarver, B.A., Ward, T.J., Gale, L.R., Broz, K.L., Kistler, H.C., Aoki, T., Nicholson, P., Carter, J., O Donnell, K. 2011. Novel fusarium head blight pathogens from Nepal and Louisiana revealed by multilocus genealogical concordance. Fungal Genetics and Biology. 48(12):1077-1152.

Lee, S., Ward, T.J., Siletzky, R.M., Kathariou, S. 2012. Two novel type II restriction-modification (RM) systems occupying genomically equivalent locations on the chromosomes of Listeria monocytogenes strains. Applied and Environmental Microbiology. 78(8):2623-2630.

Lee, S., Ward, T.J., Siletzky, R.M., Kathariou, S., Graves, L., Sperry, K., Wolf, L. 2012. Atypical Listeria monocytogenes Serotype 4b strains harboring a lineage II-specific gene cassette. Applied and Environmental Microbiology. 78(3):660-667.

O Donnell, K., Humber, R.A., Geiser, D.M., Kang, S., Park, B., Robert, V.A., Crous, P.W., Johnston, P.R., Aoki, T., Rooney, A.P., Rehner, S.A. 2011. Phylogenetic diversity of insecticolous fusaria inferred from multilocus DNA sequence data and their molecular identification via FUSARIUM-ID and Fusarium MLST. Mycologia. 104(2):427-445.

Last Modified: 8/21/2014
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