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United States Department of Agriculture

Agricultural Research Service

Title: Development of a Fusarium graminearum Affymetrix Genechip for Profiling Fungal Gene Expression in Vitro and in Planta

item Guldener, Ulrich
item Seong, Kye-yong
item Boddu, Jayanand
item Cho, Seungho
item Trail, Frances
item Xu, Jin-rong
item Adam, Gerhard
item Mewes, Hans-werner
item Muehlbauer, Gary
item Kistler, H - Corby

Submitted to: Fungal Genetics and Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/19/2006
Publication Date: 3/13/2006
Citation: Guldener, U., Seong, K., Boddu, J., Cho, S., Trail, F., Xu, J., Adam, G., Mewes, H., Muehlbauer, G.J., Kistler, H.C. 2006. Development of a Fusarium graminearum Affymetrix GeneChip for Profiling Fungal Gene Expression in Vitro and in Planta. Fungal Genetics and Biology. 43:316-325.

Interpretive Summary: Fusarium head blight disease, caused by the fungus Fusarium graminearum, is an extremely destructive disease on all varieties of wheat and barley. Further knowledge of the genetic basis for how the fungus causes disease may give clues for alternative approaches to disease management and control. In this work we describe the design and construction of a DNA microarray based on the genome sequence of F. graminearum. Microarrays allow us to study how genes are turned on and off during developmental processes such as reproduction and plant infection. From these resources we hope to identify novel genes or gene regulation patterns that may be critical for pathogenicity in the fungus and thus may be targets for novel disease control measures. This information will be useful to other scientists engaged in research to improve disease management on small grain crops. Microarray data from this report are freely available on the Internet and thus accessible to scientists in both the public and private sectors. Additionally, based on the work described here, other researchers may purchase microarrays from private sector distributors or make their own, based on information available on the Internet.

Technical Abstract: Recently the genome sequences of several filamentous fungi have become available, providing the opportunity for large-scale functional analysis including genome wide expression analysis. We report the design and validation of the first Affymetrix GeneChip microarray based on the entire genome of a filamentous fungus, the ascomycetous plant pathogen Fusarium graminearum. To maximize the likelihood of representing all putative genes (~14,000) on the array, two distinct sets of automatically predicted gene calls were used and integrated into the Fusarium graminearum Genome DataBase (Güldener et al. 2005). From these gene sets, a subset of calls was manually annotated and a non-redundant extract of all calls together with additional EST sequences and controls were submitted for GeneChip design. Experiments conducted to test the performance of the Fusarium graminearum GeneChip indicated that experimental signal variation was low for both technical and biological replications. Hybridization experiments using genomic DNA demonstrated the usefulness of the F. graminearum GeneChip for experimentation with F. graminearum and at least four additional pathogenic Fusarium species. Differential transcript accumulation was detected using the F. graminearum GeneChip with treatments derived from the fungus grown in culture under three nutritional regimes and in comparison with fungal growth in infected barley. The ability to detect fungal genes in planta is surprisingly sensitive even without efforts to enrich for fungal transcripts. The Plant Expression Database (PLEXdb, will be used as a public repository for raw and normalized expression data from the F. graminearum GeneChip. The F. graminearum GeneChip will help to accelerate exploration of the pathogen – host interaction pathways that may involve interactions between pathogenicity genes in the fungus and disease response pathways in the plant.

Last Modified: 08/22/2017
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