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  An Inventory of Common Sequence Polymorphisms for Arabidopsis

Clark, R., Ossowski, S., Schweikert, G., Zeller, G., Shinn, P., Raetsch, G., et al. (2006). An Inventory of Common Sequence Polymorphisms for Arabidopsis. Poster presented at 17th International Conference on Arabidopsis Research (ICAR 2006), Madison, WI, USA.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0004-C764-B Version Permalink: http://hdl.handle.net/21.11116/0000-0004-C765-A
Genre: Poster

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 Creators:
Clark, R1, Author
Ossowski, S1, Author
Schweikert, G1, 2, 3, Author              
Zeller, G, Author              
Shinn , P, Author
Raetsch, G4, Author              
Warthmann, N1, Author
Fu, G, Author
Hinds, D, Author
Cheng, H, Author
Frazer, K, Author
Toomajian, C, Author
Hu, T, Author
Huson, D, Author
Schölkopf, B2, 3, Author              
Nordborg, M, Author
Ecker, J, Author
Weigel, D1, Author              
Affiliations:
1Max Planck Institute for Developmental Biology, Max Planck Society, Max-Planck-Ring 5, 72076 Tübingen, DE, ou_2421691              
2Department Empirical Inference, Max Planck Institute for Biological Cybernetics, Max Planck Society, ou_1497795              
3Max Planck Institute for Biological Cybernetics, Max Planck Society, Spemannstrasse 38, 72076 Tübingen, DE, ou_1497794              
4Friedrich Miescher Laboratory, Max Planck Society, ou_2575692              

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 Abstract: We have used high-density oligonucleotide arrays to characterize common sequence variation in 20 wild strains of Arabidopsis thaliana that were chosen for maximal genetic diversity. Both strands of each possible SNP of the 119 Mb reference genome were represented on the arrays, which were hybridized with whole genome, isothermally amplified DNA to minimize ascertainment biases. Using two complementary approaches, a model based algorithm, and a newly developed machine learning method, we identified over 550,000 SNPs with a false discovery rate of \verb=~= 0.03 (average of 1 SNP for every 216 bp of the genome). A heuristic algorithm predicted in addition \verb=~=700 highly polymorphic or deleted regions per accession. Over 700 predicted polymorphisms with major functional effects (e.g., premature stop codons, or deletions of coding sequence) were validated by dideoxy sequencing. 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 model organism.

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 Dates: 2006-07
 Publication Status: Published online
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Title: 17th International Conference on Arabidopsis Research (ICAR 2006)
Place of Event: Madison, WI, USA
Start-/End Date: 2006-06-28 - 2006-07-02

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Title: 17th International Conference on Arabidopsis Research (ICAR 2006)
Source Genre: Proceedings
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Pages: - Volume / Issue: - Sequence Number: 373 Start / End Page: 187 Identifier: -