Establishment of a high-efficiency SNP-based framework marker set for Arabidopsis.

Journal Article (Journal Article)

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) x Col-0 cross.

Full Text

Duke Authors

Cited Authors

  • Törjék, O; Berger, D; Meyer, RC; Müssig, C; Schmid, KJ; Rosleff Sörensen, T; Weisshaar, B; Mitchell-Olds, T; Altmann, T

Published Date

  • October 1, 2003

Published In

Volume / Issue

  • 36 / 1

Start / End Page

  • 122 - 140

PubMed ID

  • 12974817

Electronic International Standard Serial Number (EISSN)

  • 1365-313X

International Standard Serial Number (ISSN)

  • 0960-7412

Digital Object Identifier (DOI)

  • 10.1046/j.1365-313x.2003.01861.x


  • eng