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The extent of linkage disequilibrium in Arabidopsis thaliana

Abstract

Linkage disequilibrium (LD), the nonrandom occurrence of alleles in haplotypes, has long been of interest to population geneticists. Recently, the rapidly increasing availability of genomic polymorphism data has fueled interest in LD as a tool for fine-scale mapping, in particular for human disease loci1. The chromosomal extent of LD is crucial in this context, because it determines how dense a map must be for associations to be detected and, conversely, limits how finely loci may be mapped2. Arabidopsis thaliana is expected to harbor unusually extensive LD because of its high degree of selfing3. Several polymorphism studies have found very strong LD within individual loci, but also evidence of some recombination4,5,6. Here we investigate the pattern of LD on a genomic scale and show that in global samples, LD decays within approximately 1 cM, or 250 kb. We also show that LD in local populations may be much stronger than that of global populations, presumably as a result of founder events. The combination of a relatively high level of polymorphism and extensive haplotype structure bodes well for developing a genome-wide LD map in A. thaliana.

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Figure 1: LD as a function of distance.
Figure 2: LD as a function of distance for 163 genome-wide SNP markers13.
Figure 3: P values under Fisher's exact test for the genome-wide SNP markers.
Figure 4: LD as a function of genetic distance in local Michigan populations.

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Acknowledgements

C. Dean, U. Johanson and J. Werner provided unpublished data. J. Spiegelman and R. Hufft provided technical assistance.

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Correspondence to Magnus Nordborg.

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Nordborg, M., Borevitz, J., Bergelson, J. et al. The extent of linkage disequilibrium in Arabidopsis thaliana. Nat Genet 30, 190–193 (2002). https://doi.org/10.1038/ng813

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