Microarray Analysis of Soybean Treated With Fusarium Toxin and Development of a Soybean Gene Expression Database
Li, Min
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Permalink
https://hdl.handle.net/2142/85034
Description
Title
Microarray Analysis of Soybean Treated With Fusarium Toxin and Development of a Soybean Gene Expression Database
Author(s)
Li, Min
Issue Date
2007
Doctoral Committee Chair(s)
Clough, Steven J.
Department of Study
Crop Sciences
Discipline
Crop Sciences
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
Biology, Bioinformatics
Language
eng
Abstract
Sudden death syndrome (SDS) of soybean is a devastating disease caused by the soilborne fungus Fusarium solani sp. glycines (Fsg) that limits maximum yield potential. SDS is of increasing concern in the United States because it continues to spread into important soybean production areas. Yield losses range from 15% to over 80%. Identification and study of the soybean genes controlling the biochemical/cellular processes that condition SDS disease resistance can bring closer to understanding the basic mechanisms of defense responses. Based on gene expression profiles among three soybean varieties, PI567.374 (highly resistant), Williams 82 (intermediate) and Essex (highly susceptible), which were treated with Fsg cell-free filtrate, a total of 1869 differentially expressed genes were identified upon toxin treatment, representing approximately 20% of the 9216 probe sets used in this study. Cross comparisons of the profiles from different experiments allowed identification of four SDS resistance genes that appear to be induced specifically in P1567.374, and another four genes induced commonly between the two resistant varieties. Further functional annotations based on sequence homology suggested that these eight genes might encode proteins involved in cell wall modification, detoxification, defense response, primary metabolism and membrane transport. To perform expression profile comparisons across experiments, and to handle the large volumes of microarray expression data, an expression database equipped with analysis tools was constructed and a gene information database was developed to store and retrieve fundamental information on genes present on soybean cDNA microarray, such as Genbank IDs, Tentative Consensus (TC) information, annotations. In addition, a BLAST server was developed to allow users to find soybean homologs for their sequences of interest. The functions and utility of the online database were demonstrated by analysis and comparison of expression data from our SDS study and those from other soybean microarray studies. The overall clustering result indicates that the resistance response to Fsg filtrate is most similar to incompatible P. syringae inoculation, less similar to compatible P. syringae inoculation, and distant to herbicide and Rhizobium treatments, suggesting that plants employ shared defense mechanisms against plant pathogen infection.
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