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J. Exp. Bot. 60, 1409-25. A strong effect of growth medium and organ type on the identification of QTLs for phytate and mineral concentrations in three Arabidopsis thaliana RIL populations. 2009

Ghandilyan, A., Ilk, N., Hanhart, C., Mbengue, M., Barboza, L., Schat, H., Koornneef, M., El-Lithy, M., Vreugdenhil, D., Reymond, M. and Aarts, M.G.

Notes: Mineral accumulation was studied in Arabidopsis thaliana comparing loci involved with growing in soil versus hydroponics. An F2 population derived from a cross between Landsberg erecta (Ler; maternal parent) and Eringsboda-1 (Eri-1; paternal parent) was propagated by single seed descent for nine successive generations in soil.
The flower buds of three plants per line were collected, and the DNA extracted using the Wizard® Magnetic 96 DNA Plant System and used for genotyping with 90 amplified fragment length polymorphism PCR (AFLP) and 39 single sequence length polymorphisms (SSLP) markers to build a genetic map of quantitative trait loci (QTL). (4136)

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Mol. Ecol. 15, 1405–1418. Distribution of genetic variation within and among local populations of Arabidopsis thaliana over its species range. 2006

Bakker, E.G., Stahl, E.A., Toomajian, C., Nordborg, M., Kreitman, M. and Bergelson, J.

Notes: Variation in five microsatellite loci and five SNPs covering all Arabidopsis thaliana chromosomes was examined using samples from four individuals from each of 37 local populations, including North America, England, Eastern and Western Europe, Asia, and a selection of ecotypes. Genomic DNA was extracted from leaf tissue using the Wizard® Magnetic 96 DNA Plant System and a GenoGrinder® instrument then used for amplification with the 10 loci chosen. (3427)

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Genetics 172, 1867–1876. New Arabidopsis recombinant inbred line populations genotyped using SNPWave and their use for mapping flowering-time quantitative trait loci. 2006

el-Lithy, M.E., Bentsink, L., Hanhart, C.J., Ruys, G.J., Rovito, D., Broekhof, J.L., van der Poel, H.J., van Eijk, M.J., Vreugdenhil, D. and Koornneef, M.

Notes: To examine the flowering time for three new Arabidopsis thaliana recombinant inbred lines (RIL), genomic DNA was isolated from leaves of 92 Arabidopsis accessions and from flower buds of the three RILs using the Wizard® Magnetic 96 DNA Plant System. The purified DNA was used for single sequence length polymorphisms (SSLPs) genotyping. (3417)

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BMC Plant Biol. 5, 23. A fully automatable enzymatic method for DNA extraction from plant tissues. 2005

Manen, J.F., Sinitsyna, O., Aeschbach, L., Markov, A.V. and Sinitsyn, A.

Notes: To demonstrate that enzymatic digestion of plant material prior to genomic DNA isolation could work as well as mechanical disruption, 5mm leaf punches from 48 randomly chosen species were placed in a multiwell plate and digested overnight with a mix of different carbohydrases. Using the Wizard® Magnetic 96 DNA Plant System, the genomic DNA was isolated and one fourth of the isolated DNA was loaded onto an agarose gel. Since some isolated genomic DNA showed signs of degradation, both leaves and seeds were digested for various lengths of time (1–3 hours for most species) to find the optimal digestion time. The Wizard® Magnetic 96 DNA Plant System was compared to CTAB methods for genomic DNA isolation from the digested plant material, and agarose gel analysis indicated that both methods isolated similar amounts of DNA. (3426)

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Plant J. 35(2), 273-283. Gene trapping of the Arabidopsis genome with a firefly luciferase reporter. 2003

Yamamoto, Y.Y., Tsuhara, Y., Gohda, K., Suzuki, K. and Matsui, M.

Notes: These researchers used luciferase-containing T-DNA insertions in Arabidopsis thaliana for gene trapping. Luciferase was chosen because its transient expresion allowed temporal expression studies. Several insertion vectors were constructed and found to have different insertion frequencies.  Vectors containing the luc+  gene had substantially higher insertion rates than native luciferase vectors. Luciferase activity was measured in vivo with a CCD camera or, for longer term studies, with an automated scintillation counter sampling every 15-25 minutes over one week. The application of IRES sites in gene trapping experiments was also investigated using firefly and Renilla luciferases. The Dual-Luciferase® Reporter Assay System was used to monitor luciferase activity in vitro.  Finally, to sequence the T-DNA insertion sites, genomic DNA was isolated from T2 seedlings using the Wizard® Magnetic 96 DNA Plant System and was subsequently amplified and sequenced.  (2787)

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Plant J. 36(3), 421-429. Sequence database of 1172 T-DNA insertion sites in Arabidopsis activation-tagging lines that showed phenotypes in T1 generation. 2003

Ichikawa, T., Nakazawa, M., Kawashima, M., Muto, S., Gohda, K., Suzuki, K., Ishikawa, A., Kobayashi, H., Yoshizumi, T., Tsumoto, Y., Tsuhara, Y., Iizumi, H., Goto, Y. and Matsui, M.

Notes: To find gain-of-function mutants in Arabidopsis, T-DNA insertions were screened for visible phenotypes. 1172 plants were found to have gain-of-function insertions. To map the insertion site of the T-DNA, genomic DNA was isolated on an automated workstation (Tecan Genesis®) using the Wizard® Magnetic 96 DNA Plant System The original plasmid was then isolated from the genomic DNA after digestion and transformation into bacteria. The plasmid was sequenced to determine the site of insertion. (2788)

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