75 Integrating Membrane Transport with Male Gametophyte ... - TAIR

373 An Inventory of Common Sequence Polymorphisms for Arabidopsis
Richard Clark 1 , Stephan Ossowski 1 , Gabriele Schweikert 1, 2 , Georg Zeller 3 , Paul Shinn 4 , Gunnar Raetsch 5 , Norman
Warthmann 1 , Glenn Fu 6 , David Hinds 6 , Huaming Cheng 4 , Kelly Frazer 6 , Chris Toomajian 7 , Tina Hu 7 , Daniel Huson 3 ,
Bernhard Schoelkopf 2 , Magnus Nordborg 7 , Joseph Ecker 4 , Detlef Weigel 1
1
Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 37-
39, Tuebingen, Germany, 2 Max Planck Institute for Biological Cybernetics, Spemannstrasse 38, Tuebingen,
Germany, 3 Center for Bioinformatics Tuebingen, Tuebingen University, Tuebingen, Germany , 4 Genomic
Analysis Laboratory, The Salk Institute, 10010 North Torrey Pines Road, La Jolla, CA, USA, 5 Friedrich
Miescher Laboratory of the Max Planck Society, Max Planck, Spemannstrasse 35, Tuebingen, Germany,
6
Perlegen Sciences, 2021 Stierlin Court, Mountain View, CA, USA, 7 Molecular and Computational Biology,
University of Southern California, Los Angeles, CA, USA
We have used high-density oligonucleotide arrays to identify common sequence variation in 20 wild strains of
Arabidopsis thaliana that were chosen for maximal genetic diversity. The entire 119 Mb reference genome was tiled on
the arrays, which were hybridized with whole genome, isothermally amplified DNA to minimize ascertainment biases.
Using two approaches, a model based algorithm, and a newly developed machine learning method using Support Vector
Machines, we identified over 550,000 single nucleotide polymorphisms (SNPs) with a false discovery rate of ~ 0.03
(an average of 1 SNP for every 216 bp in the genome). A heuristic algorithm also predicted ~700 highly polymorphic
or deleted regions in each accession. Nearly 700 SNP or deletion polymorphisms predicted to cause major functional
effects (e.g., premature stop codons, or deletion of coding sequence) were validated by traditional methods. Using this
data set, we provide the first systematic description of the types of genes that harbor major effect polymorphisms in
natural populations at moderate allele frequencies. The data also provide an unprecedented resource for the study of
genetic variation in an experimentally tractable, multicellular reference organism.
374 The GABI-Kat Arabidopsis thaliana T-DNA Mutagenised Population for Flanking Sequence
Tag-Based Reverse Genetics: 2006 Update
Mario Rosso, Yong Li, Prisca Viehoever, Bernd Weisshaar
Bielefeld University
The GABI-Kat population of T-DNA mutagenised Arabidopsis thaliana lines with sequence-characterised insertion
sites is used extensively for efficient progress in plant functional genomics. T-DNA insertion mutants were created in the
accession Columbia (Col-0). DNA from leaves of T1 plants was extracted and used for the production of flanking sequence
tag (FST) data. About 107,500 FSTs were submitted to EMBL/GenBank/DDBJ and are also available from the GABI-Kat
website (http://www.gabi-kat.de). This website also gives access to information about which mutant allele was present in
which line, and about the predicted location of the insertion site relative to the given gene. Recent studies indicate that
insertion sites appeared significantly more frequent in regions before transcription start and after poly(A)-addition sites
of predicted genes. Also, a "restriction site bias" was detected that explains for a fraction of the untagged genes why they
are not covered with FST-indexed mutants (Li, Rosso, Ulker and Weisshaar, Genomics 2006, in press).
In addition to serving the community with confirmed insertion mutants, we have started to transfer the most relevant
GABI-Kat lines to the Nottingham Arabidopsis Stock Centre (NASC; http://www.arabidopsis.info/). This was made
possible by an agreement between the funding partners of GABI and the Max-Planck-Society (MPG) who announced
in June 2005 that GABI-Kat lines will become freely available to the international research community. As of March
2006, 2,282 sets of T3 seed that represent one confirmed line each have been delivered to NASC. These about 2,300 sets
consist of more that 34,500 individual seed stocks which include in most cases a homozygous stock for a given insertion
allele. The number of GABI-Kat lines available from NASC will continue to grow.