Microarray-based method for detection of unknown genetic modifications.
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.


CONCLUSIONS
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.
Tengs
Torstein
T
National Veterinary Institute, Section of Feed and Food Microbiology, PO Box 8156 Dep, 0033 Oslo, Norway. torstein.tengs@vetinst.no
Kristoffersen
Anja B
AB
Berdal
Knut G
KG
Thorstensen
Tage
T
Butenko
Melinka A
MA
Nesvold
Håvard
H
Holst-Jensen
Arne
A
D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods; D004252:DNA Mutational Analysis / Q000379:methods*; D015342:DNA Probes / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics*; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012275:Oryza / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
D015342:DNA Probes; D018744:DNA, Plant