Abstract
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-O)/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.
| Original language | English |
|---|---|
| Pages (from-to) | 122-140 |
| Number of pages | 19 |
| Journal | Plant Journal |
| Volume | 36 |
| Issue number | 1 |
| DOIs | |
| Publication status | Published - Oct 2003 |
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Keywords
- Arabidopsis thaliana
- Framework marker set
- Genotyping
- Mapping
- Single nucleotide polymorphisms (SNPs)
- SNaPshot
ASJC Scopus subject areas
- Plant Science
Cite this
Establishment of a high-efficiency SNP-based framework marker set for Arabidopsis. / Törjék, O.; Berger, D.; Meyer, R. C.; Müssig, C.; Schmid, K. J.; Sörensen, T. Rosleff; Weisshaar, B.; Mitchell-Olds, T.; Altmann, T.
In: Plant Journal, Vol. 36, No. 1, 10.2003, p. 122-140.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Establishment of a high-efficiency SNP-based framework marker set for Arabidopsis
AU - Törjék, O.
AU - Berger, D.
AU - Meyer, R. C.
AU - Müssig, C.
AU - Schmid, K. J.
AU - Sörensen, T. Rosleff
AU - Weisshaar, B.
AU - Mitchell-Olds, T.
AU - Altmann, T.
PY - 2003/10
Y1 - 2003/10
N2 - 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-O)/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.
AB - 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-O)/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.
KW - Arabidopsis thaliana
KW - Framework marker set
KW - Genotyping
KW - Mapping
KW - Single nucleotide polymorphisms (SNPs)
KW - SNaPshot
UR - http://www.scopus.com/inward/record.url?scp=0141907759&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=0141907759&partnerID=8YFLogxK
U2 - 10.1046/j.1365-313X.2003.01861.x
DO - 10.1046/j.1365-313X.2003.01861.x
M3 - Article
C2 - 12974817
AN - SCOPUS:0141907759
VL - 36
SP - 122
EP - 140
JO - Plant Journal
JF - Plant Journal
SN - 0960-7412
IS - 1
ER -