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

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 s...

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Autores principales: Kelley, Rowena Y, Gresham, Cathy, Harper, Jonathan, Bridges, Susan M, Warburton, Marilyn L, Hawkins, Leigh K, Pechanova, Olga, Peethambaran, Bela, Pechan, Tibor, Luthe, Dawn S, Mylroie, J E, Ankala, Arunkanth, Ozkan, Seval, Henry, W B, Williams, W P
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3026372/
https://www.ncbi.nlm.nih.gov/pubmed/20946609
http://dx.doi.org/10.1186/1471-2105-11-S6-S25
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author Kelley, Rowena Y
Gresham, Cathy
Harper, Jonathan
Bridges, Susan M
Warburton, Marilyn L
Hawkins, Leigh K
Pechanova, Olga
Peethambaran, Bela
Pechan, Tibor
Luthe, Dawn S
Mylroie, J E
Ankala, Arunkanth
Ozkan, Seval
Henry, W B
Williams, W P
author_facet Kelley, Rowena Y
Gresham, Cathy
Harper, Jonathan
Bridges, Susan M
Warburton, Marilyn L
Hawkins, Leigh K
Pechanova, Olga
Peethambaran, Bela
Pechan, Tibor
Luthe, Dawn S
Mylroie, J E
Ankala, Arunkanth
Ozkan, Seval
Henry, W B
Williams, W P
author_sort Kelley, Rowena Y
collection PubMed
description 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/) 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.
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spelling pubmed-30263722011-01-26 Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize Kelley, Rowena Y Gresham, Cathy Harper, Jonathan Bridges, Susan M Warburton, Marilyn L Hawkins, Leigh K Pechanova, Olga Peethambaran, Bela Pechan, Tibor Luthe, Dawn S Mylroie, J E Ankala, Arunkanth Ozkan, Seval Henry, W B Williams, W P BMC Bioinformatics Proceedings 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/) 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. BioMed Central 2010-10-07 /pmc/articles/PMC3026372/ /pubmed/20946609 http://dx.doi.org/10.1186/1471-2105-11-S6-S25 Text en Copyright ©2010 Kelley et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Proceedings
Kelley, Rowena Y
Gresham, Cathy
Harper, Jonathan
Bridges, Susan M
Warburton, Marilyn L
Hawkins, Leigh K
Pechanova, Olga
Peethambaran, Bela
Pechan, Tibor
Luthe, Dawn S
Mylroie, J E
Ankala, Arunkanth
Ozkan, Seval
Henry, W B
Williams, W P
Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize
title Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize
title_full Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize
title_fullStr Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize
title_full_unstemmed Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize
title_short Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize
title_sort integrated database for identifying candidate genes for aspergillus flavus resistance in maize
topic Proceedings
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3026372/
https://www.ncbi.nlm.nih.gov/pubmed/20946609
http://dx.doi.org/10.1186/1471-2105-11-S6-S25
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