Development, timeline and output of GABI-Kat 


Since January 2015, some people from the "Plant Genome Research" group at Bielefeld University (Weisshaar lab) try to keep the GABI-Kat community service alive. However, due to lack of hands and time, we are slower than before.

The figures below illustrate the output that was generated by GABI-Kat until 2014. Scroll down to read about GABI-Kat history.

Figure 1: Progress of donation of confirmed CDSi alleles to NASC


The green dotted line represents the number of genes for which CDSi hit predictions are available in the GABI-Kat collection. Donation to NASC started in 2005. The gray dashed line illustrates the number of lines, which would have been available at NASC if the donation would have started directly at the begin of the GABI-Kat project.


Figure 2: No of finally resolved insertion predictions



In this graph the number of insertion site predictions is shown for which a final result of the confirmation process was generated. This means that the confirmation attempt was either successful or failed and the insertion is not addressed anymore. 

GABI-Kat was initiated at the Max-Planck-Institute of Plant Breeding Research (Cologne, Germany) in the year 1999 and the work started in June 2000. The initial PI's were Bernd Weisshaar, Koen Dekker, Bernd Reiss and Heinz Saedler. Funding was provided by BMBF/PTJ through the GABI programme. By building on experience from the ZIGIA project (which centred on transposons for insertional mutagenesis in A. thaliana, see Dekker et al., 2003; BIOTECHNOLOGIA 4:9-31 - note that the Journal is not published anymore, the link leads to PUB), selection, growth and leaf harvest for DNA extraction from about 90,000 single T-DNA-transformed lines was completed around February 2006. Within GABI-2, the project was continued to moderately increase the number of lines to be analysed (within GABI-1 it was 70,000), to further improve the quality of the mutant population, and to continue to serve the Arabidopsis community with providing confirmed insertion lines.

At the end of December 2006, the project was moved from MPIZ Cologne to Bielefeld University (Chair of Genome Research, Bernd Weisshaar) where GABI-Kat-II (or GKat) started on the 1st of January 2007. At the same time, the project was extended until December 2008. The main focus of this extension was to transfer more lines to NASC, and to confirm all lines that contain insertions in genes that are not hit in other populations.

At the end of 2008, there was first a continuation of the running grant until June 2009, and then an extension of the project until June 2011. The goal was to confirm additional lines and transfer them to NASC. In parallel, the community service continued and the FST collection was re-annotated with new data from TAIR.

In 2011, there was first a continuation of the running grant until December 2011, and then an extension of the project until June 2014. New FSTs that had been generated from low-coverage parts of the collection and re-annotation according to TAIR10 of all existing FSTs allowed to extend the number of predicted insertions. The community service and donation to NASC continued.

In March 2014, the GABI-Kat grant was extended to the end of December 2014. Although we got very nice support from quite some users, and also strong support from ABRC and NASC, the grant was not renewed or extended. Anyway, we thank BMBF/PtJ for many years (many more than usual for a "normal" project) of very helpful support!