Recombination and linkage disequilibrium in Arabidopsis thaliana.
Linkage disequilibrium (LD) is a major aspect of the organization of genetic variation in natural populations. Here we describe the genome-wide pattern of LD in a sample of 19 Arabidopsis thaliana accessions using 341,602 non-singleton SNPs. LD decays within 10 kb on average, considerably faster than previously estimated. Tag SNP selection algorithms and 'hide-the-SNP' simulations suggest that genome-wide association mapping will require only 40%-50% of the observed SNPs, a reduction similar to estimates in a sample of African Americans. An Affymetrix genotyping array containing 250,000 SNPs has been designed based on these results; we demonstrate that it should have more than adequate coverage for genome-wide association mapping. The extent of LD is highly variable, and we find clear evidence of recombination hotspots, which seem to occur preferentially in intergenic regions. LD also reflects the action of selection, and it is more extensive between nonsynonymous polymorphisms than between synonymous polymorphisms.
Kim
Sung
S
Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA.
Plagnol
Vincent
V
Hu
Tina T
TT
Toomajian
Christopher
C
Clark
Richard M
RM
Ossowski
Stephan
S
Ecker
Joseph R
JR
Weigel
Detlef
D
Nordborg
Magnus
M
D017360:Arabidopsis / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods; D032461:Chromosomes, Plant / Q000235:genetics; D018745:Genome, Plant; D005838:Genotype; D006239:Haplotypes; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic