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The Pattern of Polymorphism in Arabidopsis thaliana

Author

Listed:
  • 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 Zhao
  • Theodore Kalbfleisch
  • Vincent Schulz
  • Martin Kreitman
  • Joy Bergelson

Abstract

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. A systematic global survey of genomic DNA sequence polymorphism in Arabidopsis thaliana reveals that standard genetic tests for selection do not apply to this species but supports its status as a model organism.

Suggested Citation

  • 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 , 2005. "The Pattern of Polymorphism in Arabidopsis thaliana," PLOS Biology, Public Library of Science, vol. 3(7), pages 1-1, May.
  • Handle: RePEc:plo:pbio00:0030196
    DOI: 10.1371/journal.pbio.0030196
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    References listed on IDEAS

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    1. Joshua M Akey & Michael A Eberle & Mark J Rieder & Christopher S Carlson & Mark D Shriver & Deborah A Nickerson & Leonid Kruglyak, 2004. "Population History and Natural Selection Shape Patterns of Genetic Variation in 132 Genes," PLOS Biology, Public Library of Science, vol. 2(10), pages 1-1, September.
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    1. Qichao Lian & Victor Solier & Birgit Walkemeier & Stéphanie Durand & Bruno Huettel & Korbinian Schneeberger & Raphael Mercier, 2022. "The megabase-scale crossover landscape is largely independent of sequence divergence," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    2. Christina L Richards & Ulises Rosas & Joshua Banta & Naeha Bhambhra & Michael D Purugganan, 2012. "Genome-Wide Patterns of Arabidopsis Gene Expression in Nature," PLOS Genetics, Public Library of Science, vol. 8(4), pages 1-14, April.
    3. Yuankun Yang & Christina E. Steidele & Clemens Rössner & Birgit Löffelhardt & Dagmar Kolb & Thomas Leisen & Weiguo Zhang & Christina Ludwig & Georg Felix & Michael F. Seidl & Annette Becker & Thorsten, 2023. "Convergent evolution of plant pattern recognition receptors sensing cysteine-rich patterns from three microbial kingdoms," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    4. Maja Szymanska-Lejman & Wojciech Dziegielewski & Julia Dluzewska & Nadia Kbiri & Anna Bieluszewska & R. Scott Poethig & Piotr A. Ziolkowski, 2023. "The effect of DNA polymorphisms and natural variation on crossover hotspot activity in Arabidopsis hybrids," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    5. Li Fan & Katja Fröhlich & Eric Melzer & Rory N. Pruitt & Isabell Albert & Lisha Zhang & Anna Joe & Chenlei Hua & Yanyue Song & Markus Albert & Sang-Tae Kim & Detlef Weigel & Cyril Zipfel & Eunyoung Ch, 2022. "Genotyping-by-sequencing-based identification of Arabidopsis pattern recognition receptor RLP32 recognizing proteobacterial translation initiation factor IF1," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    6. Nagylaki, Thomas, 2011. "The influence of partial panmixia on neutral models of spatial variation," Theoretical Population Biology, Elsevier, vol. 79(1), pages 19-38.
    7. Eriksson, A. & Mahjani, B. & Mehlig, B., 2009. "Sequential Markov coalescent algorithms for population models with demographic structure," Theoretical Population Biology, Elsevier, vol. 76(2), pages 84-91.

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