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The genomic pattern of linkage disequilibrium in Arabidopsis thaliana

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Clark,  R
Department Molecular Biology, Max Planck Institute for Developmental Biology, Max Planck Society;

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Weigel,  D       
Department Molecular Biology, Max Planck Institute for Developmental Biology, Max Planck Society;

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http://www.arabidopsisresearch.org/images/ICAR/17th_ICAR_2006_conference_book.pdf
(Abstract)

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Citation

Hu, T., Kim, S., Plagnol, V., Toomajian, C., Clark, R., Lister, C., et al. (2006). The genomic pattern of linkage disequilibrium in Arabidopsis thaliana. Poster presented at 17th International Conference on Arabidopsis Research (ICAR 2006), Madison, WI, USA.


Cite as: https://hdl.handle.net/21.11116/0000-000C-B353-C
Abstract
We describe the pattern of linkage disequilibrium in 20 inbred accessions of Arabidopsis thaliana, using a dense set of over 250,000 non-singleton single nucleotide polymorphisms (SNPs) generated using Perlegen whole-genome re-sequencing oligonucleotide tiling arrays. Linkage disequilibrium decays rapidly (within 10kb) in general, but varies greatly across the genome and is strongly correlated with direct estimates of recombination. On a finer scale, we find that linkage disequilibrium appears to be higher within rather than between genes, indicating that recombination may be suppressed in genes. However, the decay of linkage disequilibrium is also slower for nonsynonymous as compared to synonymous polymorphisms, demonstrating the effect of selection.