The pattern of polymorphism in Arabidopsis thaliana

Magnus Nordborg, Tina T. Hu, Yoko Ishino, Jinal Jhaveri, Christopher Toomajian, Honggang Zheng, Erica Bakker, Peter Calabrese, Jean Gladstone, Rana Goyal, Mattias Jakobsson, Sung Kim, Yuri Morozov, Badri Padhukasahasram, Vincent Plagnol, Noah A. Rosenberg, Chitiksha Shah, Jeffrey D. Wall, Jue Wang, Keyan ZhaoTheodore Kalbfleisch, Vincent Schulz, Martin Kreitman, Joy Bergelson

Research output: Contribution to journalArticlepeer-review


We resequenced 876 short fragments in a sample of 96 individuals of Arabidopsis thaliana that included stock center accessions as well as a hierarchical sample from natural populations. Although A. thaliana is a selfing weed, the pattern of polymorphism in general agrees with what is expected for a widely distributed, sexually reproducing species. Linkage disequilibrium decays rapidly, within 50 kb. Variation is shared worldwide, although population structure and isolation by distance are evident. The data fail to fit standard neutral models in several ways. There is a genome-wide excess of rare alleles, at least partially due to selection. There is too much variation between genomic regions in the level of polymorphism. The local level of polymorphism is negatively correlated with gene density and positively correlated with segmental duplications. Because the data do not fit theoretical null distributions, attempts to infer natural selection from polymorphism data will require genome-wide surveys of polymorphism in order to identify anomalous regions. Despite this, our data support the utility of A. thaliana as a model for evolutionary functional genomics.

Original languageEnglish (US)
Article numbere196
Pages (from-to)1289-1299
Number of pages11
JournalPLoS biology
Issue number7
StatePublished - Jul 2005

ASJC Scopus subject areas

  • General Neuroscience
  • General Biochemistry, Genetics and Molecular Biology
  • General Immunology and Microbiology
  • General Agricultural and Biological Sciences


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