Methodology article

Microarray-based method for detection of unknown genetic modifications

Torstein Tengs¹ , Anja B Kristoffersen^2,3 , Knut G Berdal¹ , Tage Thorstensen⁴ , Melinka A Butenko⁴ , Håvard Nesvold^1,3 and Arne Holst-Jensen¹

¹  National Veterinary Institute, Section of Feed and Food Microbiology, PO Box 8156 Dep, 0033 Oslo, Norway

²  National Veterinary Institute, Section of Epidemiology, PO Box 8156 Dep, 0033 Oslo, Norway

³  University of Oslo, Department of Informatics, PO Box 1080, Blindern, 0316 Oslo, Norway

⁴  University of Oslo, Department of Molecular Biosciences, PO Box 1041, Blindern, 0316 Oslo, Norway

author email corresponding author email

BMC Biotechnology 2007, 7:91doi:10.1186/1472-6750-7-91

Published:	18 December 2007

Abstract

Background

Due to the increased use of genetic modifications in crop improvement, there is a need to develop effective methods for the detection of both known and unknown transgene constructs in plants. We have developed a strategy for detection and characterization of unknown genetic modifications and we present a proof of concept for this method using Arabidopsis thaliana and Oryza sativa (rice). The approach relies on direct hybridization of total genomic DNA to high density microarrays designed to have probes tiled throughout a set of reference sequences.

Results

We show that by using arrays with 25 basepair probes covering both strands of a set of 235 vectors (2 million basepairs) we can detect transgene sequences in transformed lines of A. thaliana and rice without prior knowledge about the transformation vectors or the T-DNA constructs used to generate the studied plants.

Conclusion

The approach should allow the user to detect the presence of transgene sequences and get sufficient information for further characterization of unknown genetic constructs in plants. The only requirements are access to a small amount of pure transgene plant material, that the genetic construct in question is above a certain size (here ≥ 140 basepairs) and that parts of the construct shows some degree of sequence similarity with published genetic elements.