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.
Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA.
Sung
S
Kim
Vincent
V
Plagnol
Tina T
TT
Hu
Christopher
C
Toomajian
Richard M
RM
Clark
Stephan
S
Ossowski
Joseph R
JR
Ecker
Detlef
D
Weigel
Magnus
M
Nordborg
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