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The extent of linkage disequilibrium in Arabidopsis thaliana

Nordborg, M; Borevitz, JO; Bergelson, J; Berry, CC; Chory, J; Hagenblad, Jenny LU ; Kreitman, M; Maloof, JN; Noyes, T and Oefner, PJ, et al. (2002) In Nature Genetics 30(2). p.190-193
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 loci(1). 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(2). Arabidopsis thaliana is expected to harbor unusually extensive LD because of its high degree of selfing(3). Several polymorphism studies have found very strong LD within individual loci, but also evidence of some recombination(4-6). Here we... (More)
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(1). 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(2). Arabidopsis thaliana is expected to harbor unusually extensive LD because of its high degree of selfing(3). Several polymorphism studies have found very strong LD within individual loci, but also evidence of some recombination(4-6). 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. (Less)
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publishing date
type
Contribution to journal
publication status
published
subject
in
Nature Genetics
volume
30
issue
2
pages
190 - 193
publisher
Nature Publishing Group
external identifiers
  • pmid:11780140
  • wos:000173708700020
  • scopus:0036479020
ISSN
1546-1718
DOI
10.1038/ng813
language
English
LU publication?
yes
id
937e4590-5e12-4fe2-8209-04f3ab1bbb27 (old id 343737)
date added to LUP
2007-11-16 14:53:55
date last changed
2017-11-05 04:28:15
@article{937e4590-5e12-4fe2-8209-04f3ab1bbb27,
  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 loci(1). 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(2). Arabidopsis thaliana is expected to harbor unusually extensive LD because of its high degree of selfing(3). Several polymorphism studies have found very strong LD within individual loci, but also evidence of some recombination(4-6). 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.},
  author       = {Nordborg, M and Borevitz, JO and Bergelson, J and Berry, CC and Chory, J and Hagenblad, Jenny and Kreitman, M and Maloof, JN and Noyes, T and Oefner, PJ and Stahl, EA and Weigel, D},
  issn         = {1546-1718},
  language     = {eng},
  number       = {2},
  pages        = {190--193},
  publisher    = {Nature Publishing Group},
  series       = {Nature Genetics},
  title        = {The extent of linkage disequilibrium in Arabidopsis thaliana},
  url          = {http://dx.doi.org/10.1038/ng813},
  volume       = {30},
  year         = {2002},
}