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This article is part of the supplement: Proceedings of the Seventh Annual MCBIOS Conference. Bioinformatics: Systems, Biology, Informatics and Computation

Open Access Proceedings

Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize

Rowena Y Kelley13*, Cathy Gresham2, Jonathan Harper23, Susan M Bridges23, Marilyn L Warburton4, Leigh K Hawkins4, Olga Pechanova1, Bela Peethambaran5, Tibor Pechan6, Dawn S Luthe7, J E Mylroie1, Arunkanth Ankala8, Seval Ozkan9, W B Henry4 and W P Williams4

Author Affiliations

1 Department of Biochemistry and Molecular Biology, Mississippi State University, MS, USA

2 Department of Computer Science and Engineering, Mississippi State University, MS, USA

3 Institute of Digital Biology, Mississippi State University, MS, USA

4 Corn Host Plant Resistance Research Unit, USDA/ARS, Mississippi State, MS, USA

5 Department of Biology, Villanova University, Villanova, PA, USA

6 Life Sciences and Biotechnology Institute, Mississippi Agricultural and Forestry Experiment Station, Mississippi State University, MS, USA

7 Department of Crop and Soil Sciences, The Pennsylvania State University, PA, USA

8 Department of Human Genetics, Emory University of Medicine, GA, USA

9 Department of Plant and Soil Sciences, Mississippi State University, MS, USA

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BMC Bioinformatics 2010, 11(Suppl 6):S25  doi:10.1186/1471-2105-11-S6-S25

Published: 7 October 2010

Abstract

Background

Aspergillus flavus Link:Fr, an opportunistic fungus that produces aflatoxin, is pathogenic to maize and other oilseed crops. Aflatoxin is a potent carcinogen, and its presence markedly reduces the value of grain. Understanding and enhancing host resistance to A. flavus infection and/or subsequent aflatoxin accumulation is generally considered an efficient means of reducing grain losses to aflatoxin. Different proteomic, genomic and genetic studies of maize (Zea mays L.) have generated large data sets with the goal of identifying genes responsible for conferring resistance to A. flavus, or aflatoxin.

Results

In order to maximize the usage of different data sets in new studies, including association mapping, we have constructed a relational database with web interface integrating the results of gene expression, proteomic (both gel-based and shotgun), Quantitative Trait Loci (QTL) genetic mapping studies, and sequence data from the literature to facilitate selection of candidate genes for continued investigation. The Corn Fungal Resistance Associated Sequences Database (CFRAS-DB) (http://agbase.msstate.edu/ webcite) was created with the main goal of identifying genes important to aflatoxin resistance. CFRAS-DB is implemented using MySQL as the relational database management system running on a Linux server, using an Apache web server, and Perl CGI scripts as the web interface. The database and the associated web-based interface allow researchers to examine many lines of evidence (e.g. microarray, proteomics, QTL studies, SNP data) to assess the potential role of a gene or group of genes in the response of different maize lines to A. flavus infection and subsequent production of aflatoxin by the fungus.

Conclusions

CFRAS-DB provides the first opportunity to integrate data pertaining to the problem of A. flavus and aflatoxin resistance in maize in one resource and to support queries across different datasets. The web-based interface gives researchers different query options for mining the database across different types of experiments. The database is publically available at http://agbase.msstate.edu webcite.