The extent of linkage disequilibrium in Arabidopsis thaliana.
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.
Nordborg
Magnus
M
Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA.
Borevitz
Justin O
JO
Bergelson
Joy
J
Berry
Charles C
CC
Chory
Joanne
J
Hagenblad
Jenny
J
Kreitman
Martin
M
Maloof
Julin N
JN
Noyes
Tina
T
Oefner
Peter J
PJ
Stahl
Eli A
EA
Weigel
Detlef
D
D017360:Arabidopsis / Q000235:genetics*; D002874:Chromosome Mapping; D018745:Genome, Plant; D006239:Haplotypes; D006801:Humans; D007178:Inbreeding; D015810:Linkage Disequilibrium; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide