GABI-Kat SimpleSearch: new features of the Arabidopsis thaliana T-DNA mutant database

Abstract

T-DNA insertion mutants are very valuable for reverse genetics in Arabidopsis thaliana. Several projects have generated large sequence-indexed collections of T-DNA insertion lines, of which GABI-Kat is the second largest resource worldwide. User access to the collection and its Flanking Sequence Tags (FSTs) is provided by the front end SimpleSearch (http://www.GABI-Kat.de). Several significant improvements have been implemented recently. The database now relies on the TAIRv10 genome sequence and annotation dataset. All FSTs have been newly mapped using an optimized procedure that leads to improved accuracy of insertion site predictions. A fraction of the collection with weak FST yield was re-analysed by generating new FSTs. Along with newly found predictions for older sequences about 20 000 new FSTs were included in the database. Information about groups of FSTs pointing to the same insertion site that is found in several lines but is real only in a single line are included, and many problematic FST-to-line links have been corrected using new wet-lab data. SimpleSearch currently contains data from ∼71 000 lines with predicted insertions covering 62.5% of the 27 206 nuclear protein coding genes, and offers insertion allele-specific data from 9545 confirmed lines that are available from the Nottingham Arabidopsis Stock Centre.

The plant‐specific CDKB 1‐ CYCB 1 complex mediates homologous recombination repair in Arabidopsis

“…cycb1;1 and cycb1;2 T‐DNA insertion lines were isolated from the Koncz collection (Rios et al , 2002). T‐DNA insertion line cycb1;3 (pst15850) was obtained from the RIKEN collection (Yokohama, Japan) and cycb1;4 from the GABI‐KAT collection (Bielefeld, Germany) (Kleinboelting et al , 2012). The ku70 (Riha et al , 2002), wee1 (De Schutter et al , 2007), and rad51 (Li et al , 2004) mutants were described previously.…”

Natural variation in arsenate tolerance identifies an arsenate reductase in Arabidopsis thaliana

“…36), respectively, were used for QTL mapping for As(V) tolerance as estimated by the RGR assay (Supplementary Data 2,3). The At2g21045 T-DNA mutant (GK-868F11) that bears an insertion in the second exon was obtained from the GABI-Kat 37 . Homozygous knockout plants were selected by PCR using the T-DNA-specific primer 5 0 -ATAATAACGCTGC GGACATCTACATTTT-3 0 and the At2g21045-specific primer 5 0 -AAATGTTCA TCTTTCTTGCAAACC-3 0 .…”

“…Homozygous knockout plants were selected by PCR using the T-DNA-specific primer 5 0 -ATAATAACGCTGC GGACATCTACATTTT-3 0 and the At2g21045-specific primer 5 0 -AAATGTTCA TCTTTCTTGCAAACC-3 0 . The At5g03455 T-DNA mutant (GK-772G06) 37 with an insertion in AtACR2 and its overexpression line were used. Both lines were kindly provided by Professor Francis Dennis, Cardiff University (Wales, UK).…”

Genome-Wide Association Mapping of Fertility Reduction upon Heat Stress Reveals Developmental Stage-Specific QTLs in Arabidopsis thaliana

“…FRI-sf2 (CS6209) can also be obtained from the ABRC Stock Center. In addition, the following SALK T-DNA insertion mutants (Alonso et al, 2003) and GABI-Kat T-DNA insertion mutants (Kleinboelting et al, 2012) were obtained from NASC: qul2-2 (SALK_065604c), AT2G03505 (GABI_745A07), AT2G03490 (SALK_125910), mips3-2 (SALK_120131c; Donahue et al, 2010), and AT5G10200 (SALK_040912c). Seeds of the mutants qul1-1 and qul1-1 qul2-1 were kindly provided by L. Østergaard (Fuentes et al, 2010).…”