Recombination and linkage disequilibrium in Arabidopsis thaliana Export

@article{citeulike:1607997, 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.}, author = {Kim, Sung and Plagnol, Vincent and Hu, Tina T. and Toomajian, Christopher and Clark, Richard M. and Ossowski, Stephan and Ecker, Joseph R. and Weigel, Detlef and Nordborg, Magnus}, citeulike-article-id = {1607997}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/ng2115}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/ng2115}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/17676040}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=17676040}, day = {05}, doi = {10.1038/ng2115}, issn = {1061-4036}, journal = {Nature Genetics}, keywords = {arabidopsis, ld}, month = {August}, number = {9}, pages = {1151--1155}, posted-at = {2009-09-23 17:50:08}, priority = {2}, publisher = {Nature Publishing Group}, title = {Recombination and linkage disequilibrium in Arabidopsis thaliana}, url = {http://dx.doi.org/10.1038/ng2115}, volume = {39}, year = {2007} }

TY - JOUR ID - citeulike:1607997 L3 - citeulike-article-id:1607997 N2 - 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. IS - 9 JF - Nature Genetics SN - 1061-4036 EP - 1155 TI - Recombination and linkage disequilibrium in Arabidopsis thaliana PB - Nature Publishing Group VL - 39 SP - 1151 KW - arabidopsis KW - ld AU - Kim, Sung AU - Plagnol, Vincent AU - Hu, Tina AU - Toomajian, Christopher AU - Clark, Richard AU - Ossowski, Stephan AU - Ecker, Joseph AU - Weigel, Detlef AU - Nordborg, Magnus PY - 2007/08/05/ UR - http://dx.doi.org/10.1038/ng2115 ER -