Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana

Karl J. Schmid, Thomas Rosleff Sörensen, Ralf Stracke, O. Törjék, Thomas Altmann, Tom Mitchell-Olds, Bernd Weisshaar

Research output: Contribution to journalArticle

161 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)1250-1257
Number of pages8
JournalGenome Research
Volume13
Issue number6 A
DOIs
Publication statusPublished - Jun 1 2003

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Nucleotide Mapping
Arabidopsis
Single Nucleotide Polymorphism
Sequence Tagged Sites
Genome
Expressed Sequence Tags
Gene Library
Chromosome Mapping
Quantitative Trait Loci
Genetic Markers
Internet
Open Reading Frames
Organism Cloning

ASJC Scopus subject areas

  • Genetics

Cite this

Schmid, K. J., Sörensen, T. R., Stracke, R., Törjék, O., Altmann, T., Mitchell-Olds, T., & Weisshaar, B. (2003). Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana. Genome Research, 13(6 A), 1250-1257. https://doi.org/10.1101/gr.728603

Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana. / Schmid, Karl J.; Sörensen, Thomas Rosleff; Stracke, Ralf; Törjék, O.; Altmann, Thomas; Mitchell-Olds, Tom; Weisshaar, Bernd.

In: Genome Research, Vol. 13, No. 6 A, 01.06.2003, p. 1250-1257.

Research output: Contribution to journalArticle

Schmid, KJ, Sörensen, TR, Stracke, R, Törjék, O, Altmann, T, Mitchell-Olds, T & Weisshaar, B 2003, 'Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana', Genome Research, vol. 13, no. 6 A, pp. 1250-1257. https://doi.org/10.1101/gr.728603
Schmid, Karl J. ; Sörensen, Thomas Rosleff ; Stracke, Ralf ; Törjék, O. ; Altmann, Thomas ; Mitchell-Olds, Tom ; Weisshaar, Bernd. / Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana. In: Genome Research. 2003 ; Vol. 13, No. 6 A. pp. 1250-1257.
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