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An Inventory of Sequence Polymorphisms For Arabidopsis

2006

Talk

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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.

Author(s): Clark, R. and Ossowski, S. and Schweikert, G. and Rätsch, G. and Shinn, P. and Zeller, G. and Warthmann, N. and Fu, G. and Hinds, D. and Chen, H. and Frazer, K. and Huson, D. and Schölkopf, B. and Nordborg, M. and Ecker, J. and Weigel, D.
Year: 2006
Month: April
Day: 0

Department(s): Empirical Inference
Bibtex Type: Talk (talk)

Digital: 0
Event Name: 17th International Conference on Arabidopsis Research
Event Place: Madison, Wisc., USA
Language: en
Organization: Max-Planck-Gesellschaft
School: Biologische Kybernetik

BibTex

@talk{3951,
  title = {An Inventory of Sequence Polymorphisms For Arabidopsis},
  author = {Clark, R. and Ossowski, S. and Schweikert, G. and R{\"a}tsch, G. and Shinn, P. and Zeller, G. and Warthmann, N. and Fu, G. and Hinds, D. and Chen, H. and Frazer, K. and Huson, D. and Sch{\"o}lkopf, B. and Nordborg, M. and Ecker, J. and Weigel, D.},
  organization = {Max-Planck-Gesellschaft},
  school = {Biologische Kybernetik},
  month = apr,
  year = {2006},
  month_numeric = {4}
}