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  An Inventory of Sequence Polymorphisms For Arabidopsis

Clark, R., Ossowski S, Schweikert, G., Rätsch, G., Shinn P, Zeller G, Warthmann N, Fu G, Hinds D, Chen H, Frazer K, Huson D, Schölkopf, B., Nordborg M, Ecker, J., & Weigel, D. (2006). An Inventory of Sequence Polymorphisms For Arabidopsis. Talk presented at 17th International Conference on Arabidopsis Research. Madison, Wisc., USA.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0013-D249-5 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0013-D24A-3
Genre: Talk

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 Creators:
Clark, R, Author
Ossowski S, Schweikert, G1, Author              
Rätsch, G1, Author              
Shinn P, Zeller G, Warthmann N, Fu G, Hinds D, Chen H, Frazer K, Huson D, Schölkopf, B1, Author              
Nordborg M, Ecker, J, Author
Weigel, D, Author
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1Department Empirical Inference, Max Planck Institute for Biological Cybernetics, Max Planck Society, escidoc:1497795              

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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 ~ 0.03 (average of 1 SNP for every 216 bp of the genome). A heuristic algorithm predicted in addition ~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: 2006-04
 Publication Status: Published in print
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 Identifiers: BibTex Citekey: 3951
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Title: 17th International Conference on Arabidopsis Research
Place of Event: Madison, Wisc., USA
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