Establishment of a high-efficiency SNP-based framework marker set for Arabidopsis
Article first published online: 15 SEP 2003
The Plant Journal
Volume 36, Issue 1, pages 122–140, October 2003
How to Cite
Törjék, O., Berger, D., Meyer, R. C., Müssig, C., Schmid, K. J., Rosleff Sörensen, T., Weisshaar, B., Mitchell-Olds, T. and Altmann, T. (2003), Establishment of a high-efficiency SNP-based framework marker set for Arabidopsis. The Plant Journal, 36: 122–140. doi: 10.1046/j.1365-313X.2003.01861.x
- Issue published online: 15 SEP 2003
- Article first published online: 15 SEP 2003
- Received 13 May 2003; revised 18 July 2003; accepted 24 July 2003.
- single nucleotide polymorphisms (SNPs);
- Arabidopsis thaliana;
- framework marker set
The major goal of this project was the establishment of a tool for rapid mapping of new mutations and genotyping in Arabidopsis consisting of at least 100 evenly spaced framework markers. We assembled a single nucleotide polymorphism (SNP)-based marker set consisting of 112 polymorphic sites with average spacing of 1.15 Mbp derived from an SNP database that we recently developed. This information was used to set up efficient SNP detection reactions based on multiplexed primer extension assays. The 112 Columbia (Col-0)/C24 framework markers were used to assemble 18 multiplexed SNaPshot assays with which up to eight separate loci can be genotyped in a single-tube/single-capillary format. In addition, for 110 framework markers matrix-assisted laser desorption/ionization time of flight (MALDI-ToF) assays have been established for high throughput analyses. We demonstrated the usefulness and the robustness of both procedures of this tool by genotyping 48 BC3F1 individuals created between the accessions Col-0 and C24. Subsets of 10–62 of the established markers discriminate between various combinations of the accessions Col-0, C24, Landsberg erecta (Ler), Cape Verdi Islands (Cvi) and Niederzenz (Nd). Using a subset of 17 evenly distributed and established SNP markers that are also polymorphic between Ler and Col-0, we were able to rapidly map a mutant gene (tbr1) to an interval of 2.3 Mbp in an Ler (tbr1) × Col-0 cross.