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Nucleic Acids Research Advance Access published online on September 27, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn638
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome

Supat Thongjuea1,2, Vinitchan Ruanjaichon1,2, Richard Bruskiewich3 and Apichart Vanavichit1,*

1RiceGeneDiscovery Unit, Kasetsart University, Kamphangsaen Campus, Nakhon Pathom 73140, 2National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand and 3Crop Research Informatics Laboratory – International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines

*To whom correspondence should be addressed. Tel: 66 34 355 193; Fax: 66 34 355 197; Email: vanavichit{at}gmail.com

Received July 24, 2008. Revised September 10, 2008. Accepted September 15, 2008.

RiceGeneThresher is a public online resource for mining genes underlying genome regions of interest or quantitative trait loci (QTL) in rice genome. It is a compendium of rice genomic resources consisting of genetic markers, genome annotation, expressed sequence tags (ESTs), protein domains, gene ontology, plant stress-responsive genes, metabolic pathways and prediction of protein–protein interactions. RiceGeneThresher system integrates these diverse data sources and provides powerful web-based applications, and flexible tools for delivering customized set of biological data on rice. Its system supports whole-genome gene mining for QTL by querying using DNA marker intervals or genomic loci. RiceGeneThresher provides biologically supported evidences that are essential for targeting groups or networks of genes involved in controlling traits underlying QTL. Users can use it to discover and to assign the most promising candidate genes in preparation for the further gene function validation analysis. The web-based application is freely available at http://rice.kps.ku.ac.th.


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