RT Journal
A1 Schmid, Karl J.
A1 Sörensen, Thomas Rosleff
A1 Stracke, Ralf
A1 Törjék, Ottó
A1 Altmann, Thomas
A1 Mitchell-Olds, Tom
A1 Weisshaar, Bernd
T1 Large-Scale Identification and Analysis of Genome-Wide Single-Nucleotide  Polymorphisms for Mapping in Arabidopsis thaliana
JF Genome Research 
JO Genome Research 
YR 2003 
FD June 01 
VO 13 
IS 6a 
SP 1250 
OP 1257 
DO 10.1101/gr.728603 
UL http://genome.cshlp.org/content/13/6a/1250.abstract 
AB Genetic markers such as single nucleotide polymorphisms (SNPs) are  essential tools for positional cloning, association, or quantitative trait  locus mapping and the determination of genetic relationships between  individuals. We identified and characterized a genome-wide set of SNP markers  by generating 10,706 expressed sequence tags (ESTs) from cDNA libraries  derived from 6 different accessions, and by analysis of 606 sequence tagged  sites (STS) from up to 12 accessions of the model flowering plant  Arabidopsis thaliana. The cDNA libraries for EST sequencing were made  from individuals that were stressed by various means to enrich for transcripts  from genes expressed under such conditions. SNPs discovered in these sequences  may be useful markers for mapping genes involved in interactions with the  biotic and abiotic environment. The STS loci are distributed randomly over the  genome. By comparison with the Col-0 genome sequence, we identified a total of  8051 SNPs and 637 insertion/deletion polymorphisms (InDel). Analysis of  STS-derived SNPs shows that most SNPs are rare, but that it is possible to  identify intermediate frequency framework markers that can be used for genetic  mapping in many different combinations of accessions. A substantial proportion  of SNPs located in ORFs caused a change of the encoded amino acid. A  comparison of the density of our SNP markers among accessions in both the EST  and STS datasets, revealed that Cvi-0 is the most divergent accession from  Col-0 among the 12 accessions studied. All of these markers are freely  available via the internet.