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  Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana

Clark, R., Schweikert, G., Toomajian, C., Ossowski, S., Zeller, G., Shinn, P., et al. (2007). Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana. Science, 317(5836), 338-342. doi:10.1126/science.1138632.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0013-CC95-4 Version Permalink: http://hdl.handle.net/21.11116/0000-0003-BC81-7
Genre: Journal Article

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 Creators:
Clark, RM1, Author
Schweikert, G1, 2, 3, 4, Author              
Toomajian, C, Author
Ossowski , S1, Author
Zeller, G1, Author
Shinn, P, Author
Warthmann, N1, Author
Hu, TT, Author
Fu, G, Author
Hinds, DA, Author
Chen, H, Author
Frazer, KA, Author
Huson, DH, Author
Schölkopf, B2, 3, Author              
Nordborg, M, Author
Rätsch, G4, Author              
Ecker, JR, 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, ou_1497794              
4Friedrich Miescher Laboratory, Max Planck Society, ou_2575692              

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 Abstract: The genomes of individuals from the same species vary in sequence as a result of different evolutionary processes. To examine the patterns of, and the forces shaping, sequence variation in Arabidopsis thaliana, we performed high-density array resequencing of 20 diverse strains (accessions). More than 1 million nonredundant single-nucleotide polymorphisms (SNPs) were identified at moderate false discovery rates (FDRs), and ~4 of the genome was identified as being highly dissimilar or deleted relative to the reference genome sequence. Patterns of polymorphism are highly nonrandom among gene families, with genes mediating interaction with the biotic environment having exceptional polymorphism levels. At the chromosomal scale, regional variation in polymorphism was readily apparent. A scan for recent selective sweeps revealed several candidate regions, including a notable example in which almost all variation was removed in a 500-kilobase window. Analyzing the polymorphisms we describe in larger sets of accessions will enable a detailed understanding of forces shaping population-wide sequence variation in A. thaliana.

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 Dates: 2007-07
 Publication Status: Published in print
 Pages: -
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 Rev. Method: -
 Identifiers: DOI: 10.1126/science.1138632
BibTex Citekey: 4678
 Degree: -

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Title: Science
  Other : Science
Source Genre: Journal
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Publ. Info: Washington, D.C. : American Association for the Advancement of Science
Pages: - Volume / Issue: 317 (5836) Sequence Number: - Start / End Page: 338 - 342 Identifier: ISSN: 0036-8075
CoNE: https://pure.mpg.de/cone/journals/resource/991042748276600_1