The extent of linkage disequilibrium in Arabidopsis thaliana

Magnus Nordborg, Justin O. Borevitz, Joy Bergelson, Charles C. Berry, Joanne Chory, Jenny Hagenblad, Martin Kreitman, Julin N. Maloof, Tina Noyes, Peter J. Oefner, Eli A. Stahl, Detlef Weigel

Research output: Contribution to journalArticlepeer-review

375 Scopus citations


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 loci. 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 mapped. Arabidopsis thaliana is expected to harbor unusually extensive LD because of its high degree of selfing. Several polymorphism studies have found very strong LD within individual loci, but also evidence of some recombination. 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.

Original languageEnglish
Pages (from-to)190-193
Number of pages4
JournalNature Genetics
Issue number2
StatePublished - Feb 2002
Externally publishedYes


Dive into the research topics of 'The extent of linkage disequilibrium in Arabidopsis thaliana'. Together they form a unique fingerprint.

Cite this