Nature Genetics
30, 190 - 193 (2002)
Published online: 7 January 2002; | doi:10.1038/ng813
The extent of linkage disequilibrium in Arabidopsis thalianaMagnus Nordborg1, Justin O. Borevitz2, Joy Bergelson3, Charles C. Berry4, Joanne Chory2, 5, Jenny Hagenblad6, Martin Kreitman3, Julin N. Maloof2, Tina Noyes7, Peter J. Oefner7, Eli A. Stahl3
& Detlef Weigel2, 81
Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA. 2
Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA. 3
Department of Ecology & Evolution, University of Chicago, Chicago, Illinois, USA. 4
Department of Family & Preventive Medicine, University of California, San Diego, La Jolla, California, USA. 5
The Howard Hughes Medical Institute, La Jolla, California, USA. 6
Department of Genetics, Lund University, Lund, Sweden. 7
Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA. 8
Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.
Correspondence should be addressed to Magnus Nordborg magnus@usc.eduLinkage 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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