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Recombination and linkage disequilibrium in Arabidopsis thaliana

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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Figure 1: Decay of LD.
Figure 2: Recombination rate variation on chromosome 1 (centromere excluded).
Figure 3: The decay of LD across strong hotspots in two 70 kb regions.
Figure 4: Evidence of purifying selection on different types of sites.

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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.

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Authors

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.

Corresponding author

Correspondence to Magnus Nordborg.

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The authors declare no competing financial interests.

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Supplementary Figures 1–5, Supplementary Table 1, Supplementary Methods (PDF 1475 kb)

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Kim, S., Plagnol, V., Hu, T. et al. Recombination and linkage disequilibrium in Arabidopsis thaliana. Nat Genet 39, 1151–1155 (2007). https://doi.org/10.1038/ng2115

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