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Recombination and linkage disequilibrium in Arabidopsis thaliana

Nature Genetics volume 39, pages 11511155 (2007) | Download Citation

Abstract

Linkage disequilibrium (LD) is a major aspect of the organization of genetic variation in natural populations. Here we describe the genome-wide pattern of LD in a sample of 19 Arabidopsis thaliana accessions using 341,602 non-singleton SNPs. LD decays within 10 kb on average, considerably faster than previously estimated. Tag SNP selection algorithms and 'hide-the-SNP' simulations suggest that genome-wide association mapping will require only 40%–50% of the observed SNPs, a reduction similar to estimates in a sample of African Americans. An Affymetrix genotyping array containing 250,000 SNPs has been designed based on these results; we demonstrate that it should have more than adequate coverage for genome-wide association mapping. The extent of LD is highly variable, and we find clear evidence of recombination hotspots, which seem to occur preferentially in intergenic regions. LD also reflects the action of selection, and it is more extensive between nonsynonymous polymorphisms than between synonymous polymorphisms.

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Acknowledgements

Support was provided by grants from the US National Institutes of Health (HG002790 to M. Waterman, GM62932 to D.W. and a postdoctoral fellowship to C.T.) and the US National Science Foundation (DEB-0115062 to M.N.) and by funds from the Max Planck Society. D.W. is a director of the Max Planck Institute.

Author information

Author notes

    • Sung Kim
    • , Vincent Plagnol
    • , Tina T Hu
    •  & Christopher Toomajian

    These authors contributed equally to this work.

Affiliations

  1. Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA.

    • Sung Kim
    • , Vincent Plagnol
    • , Tina T Hu
    • , Christopher Toomajian
    •  & Magnus Nordborg
  2. Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 OXY, UK.

    • Vincent Plagnol
  3. Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.

    • Richard M Clark
    • , Stephan Ossowski
    •  & Detlef Weigel
  4. Salk Institute Genome Analysis Laboratory, and The Salk Institute for Biological Studies, La Jolla, California 92037, USA.

    • Joseph R Ecker
  5. Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.

    • Joseph R Ecker
    •  & Detlef Weigel

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Contributions

S.K., V.P., T.T.H. and C.T. carried out all the population genetics analyses and assisted with writing the paper. R.M.C. and S.O. analyzed the raw array data. J.R.E. and D.W. directed the array resequencing project. M.N. directed the population genetics analyses and wrote the paper. All authors commented on and revised the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Magnus Nordborg.

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DOI

https://doi.org/10.1038/ng2115

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