Abstract:
: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.
journal_name
Nat Genetjournal_title
Nature geneticsauthors
Kim S,Plagnol V,Hu TT,Toomajian C,Clark RM,Ossowski S,Ecker JR,Weigel D,Nordborg Mdoi
10.1038/ng2115subject
Has Abstractpub_date
2007-09-01 00:00:00pages
1151-5issue
9eissn
1061-4036issn
1546-1718pii
ng2115journal_volume
39pub_type
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