ARS | Publication request: Microarray analysis: Uses and Limitations

Submitted to: HortScience
Publication Type: Abstract Only
Publication Acceptance Date: February 25, 2007
Publication Date: June 1, 2007
Citation: Wechter, W.P., Levi, A., Kluepfel, D.A., Gonzalez, E.T., Presting, G. 2007. Microarray Analysis: Uses and Limitations. HortScience. 42:477.

Technical Abstract: The use of microarray technology has exploded in resent years. All areas of biological research have found application for this powerful platform. From human disease studies to microbial detection systems, a plethora of uses for this technology are currently in place with new uses being developed continuously. Although an extremely powerful technology, certain limitations do exist. These limitations include sensitivity, false discovery, and cost. Some current uses of microarrays in agriculture include gene expression studies, microbial identification, transcription factor profiling and comparative genome sequencing. Several projects in our laboratory utilize high-density microarrays. In one of these studies, we are investigating the global, genetic regulation of a biocontrol bacterium during interaction with a host plant’s rhizosphere. This study has identified more than 300 up-regulated and down-regulated genes that are appear to be modulated in/by the rhizosphere. Transposon-based gene-knock out studies and quantitative-PCR have confirmed the microarray results for several of these genes. In a second study, we have used a bioinformatics-based approach to develop microarrays for use in identifying targeted soil-borne bacteria. This proof of concept approach allowed us to identify specific bacteria at levels of less than 1,000 cells/gram of soil using high-density photolithography arrays.