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Plant Physiology 139:619-631 (2005)
© 2005 American Society of Plant Biologists

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Bioinformatics

GERMINATE. A Generic Database for Integrating Genotypic and Phenotypic Information for Plant Genetic Resource Collections1,[w]

Jennifer M. Lee*, Guy F. Davenport2, David Marshall, T.H. Noel Ellis, Michael J. Ambrose, Jo Dicks, Theo J.L. van Hintum and Andrew J. Flavell

Department of Life Sciences, University of Dundee, Dundee DD1 4HN, Scotland, United Kingdom (J.M.L, A.J.F.); John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, United Kingdom (G.F.D., T.H.N.E., M.J.A., J.D.); Scottish Crop Research Institute, Invergowrie DD2 5DA, Scotland, United Kingdom (D.M.); and Centre for Genetic Resources, 6700AA Wageningen, The Netherlands (T.J.L.v.H.)

The extensive germplasm resource collections that are now available for major crop plants and their wild relatives will increasingly provide valuable biological and bioinformatics resources for plant physiologists and geneticists to dissect the molecular basis of key traits and to develop highly adapted plant material to sustain future breeding programs. A key to the efficient deployment of these resources is the development of information systems that will enable the collection and storage of biological information for these plant lines to be integrated with the molecular information that is now becoming available through the use of high-throughput genomics and post-genomics technologies. The GERMINATE database has been designed to hold a diverse variety of data types, ranging from molecular to phenotypic, and to allow querying between such data for any plant species. Data are stored in GERMINATE in a technology-independent manner, such that new technologies can be accommodated in the database as they emerge, without modification of the underlying schema. Users can access data in GERMINATE databases either via a lightweight Perl-CGI Web interface or by the more complex Genomic Diversity and Phenotype Connection software. GERMINATE is released under the GNU General Public License and is available at http://germinate.scri.sari.ac.uk/germinate/.

1 This work was supported by the Biotechnology and Biological Sciences Research Council (grant no. 94/BEP17084) and the Scottish Executive Environment and Rural Affairs Department (grant no. FF00589), as part of the Bioinformatics and E-science program.

2 Present address: International Maize and Wheat Improvement Centre, Apartado postal 6-641, 06600 Mexico DF, Mexico.

[w] The online version of this article contains Web-only data.

www.plantphysiol.org/cgi/doi/10.1104/pp.105.065201.

* Corresponding author; e-mail jennifer.lee{at}scri.ac.uk; fax 441382568587.

Received May 5, 2005; returned for revision July 15, 2005; accepted August 8, 2005.

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