Wingen, Luzie U.;Saedler, Heinz;Dekker, Koen - ZIGIA-DB: A Public Database to Access Arabidopsis thaliana Knockout Plants

ECCB 2002 Poster sorted by: Author | Number

Next | Previous poster (in order of the view you have selected)

Title: ZIGIA-DB: A Public Database to Access Arabidopsis thaliana Knockout Plants	P180
Wingen, Luzie U.; Saedler, Heinz; Dekker, Koen wingen@mpiz-koeln.mpg.de Max-Planck Institute for Plant Breeding Research,ZIGIA,Carl-von-Linne-Weg 10,D-50829 Koeln, Germany

Since the sequence of the model plant Arabidopsis thaliana was published in December 2000 by the Arabidopsis Genome Initiative [1] http://www.arabidopsis.org/genome_release.html) new wealth of sequence information.
The genome of Arabidopsis is comparable small, it contains 125 megabases. Nevertheless, because the genes are relative compact and contain only short introns and short regulatory regions,the number of genes encoding proteins is quite high and amounts to 25,000.

The information gained from the Arabidopsis genome sequence is thought to be useful for crop plant research, as the higher plants diverged relative recently in the last 200 million years and are thus thought to contain a partly similiar gene set. Crop plants themselves often have large genomes which are difficult to analyse.

Still the function of most of the 25,000 proteins in Arabidopsis is largely unclear. Sequence comparisons can reveal homologies to other hopefully characterised proteins, but for a majority of proteins the function has to be determined experimentally in vivo. With the genome in hand, the next challenge is the investigation of the roles of individual Arabidopsis proteins.

Clarifying such gene--function relationships on a large scale in the model plant Arabidopsis thaliana is the goal of the ZIGIA project (Center for Functional Genomics in Arabidopsis, http:// www.mpiz-koeln.mpg.de/~zigia/). To fulfill this task, an Arabidopsis knockout population was generated by mutagenising plants with the autonomous maize transposon En-1/Spm. The population currently consists of 11,000 individuals,each carrying 1--20 copies of the transposon. This population is used to study gene--function relationships using forward genetics (screening for plants with predicted differences in phenotype and identifying genes with transposon insertions responsible for the phenotype) or reverse genetics (screening for knockouts in specific genes and analysing the loss-of-function phenotypes of the identified plants).
Several groups at the Max Planck Institute for Plant Breeding Research (MPIZ) and furthermore industrial partners participate in the gene--phenotype discovery. Moreover, ZIGIA also offers to perform screens as a service to the scientific community.

During the project, large amounts of experimental data including sequence data, population genealogy, mutant descriptions, images of phenotypes, gene annotations and results of of our knockout screens were gathered. This massive amount of data is handled by different groups and demands a complex data management infrastructure. This infrastructure is required to support elimination of experimental redundancy, storing results in an easily accessible way and development of powerful tools for querying, nalysing and integrating the data obtained in the project. This structure will make the ZIGIA data a useful resource for future users as the resources generated by ZIGIA may be integrated in the German plant genomics initiative, GABI (http://www.mips.biochem.mpg.de/proj/gabi/), in 2003.

For managing the complex data flow, a relational database was designed containing highly linked tables with the different data classes. The database, named ZIGIA-DB [2] (http://www.bioinfo.de/isb/gcb01/ poster/wingen.html), was implemented as an Oracle database with a web based interface, so that easy data entry and access is possible from different locations and different computer platforms.

Since July 2002 parts of the database are also public available (https:// io.mpiz-koeln.mpg.de/ zigiapublicdb). Scientists world wide have access to the public part of ZIGIA-DB free of charge. They can query the database with their gene of interest for the outcome of our knockout screens. If a candidate plant line ist found, seeds can be obtained from the ZIGIA project. The plant lines putatively carry an En-1/Spm insertion in the gene of interest, and the phenotype of such a knockout plant will be informative for the function of the corresponding gene.

[1] The Arabidopsis Genome Initiative (2000), Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796 - 815.
[2] L. U. Wingen, J. T. Kim, H. Saedler and K. Dekker (2001) ZIGIA-DB: A versatile database for handling complex functional genomic data of Arabidopsis thaliana. Proceedings of the German Conference on Bioinformatics 2001, 234-235.