Prototype oligo array for direct transgene detection

Abstract

We have developed an oligonucleotide microarray for detecting transgenic sequences in unamplified DNA. It consists of 390 probes, 27-33 bases long, targeting 100 sequences found in 6 commercial biotech crops. The probes were specific to conserved promoter/terminator sequences, genes for specific traits, selection markers and eventspecific sequences. A double-filtering strategy was used to design the probes and hybridizations were performed using an optimized catanionic solvent. Using this system, we were able to identify an unauthorized TT51-1 rice line (GenBank EU880444) containing previously undisclosed transgenic elements. Transgenic sequences copy numbers were determined by southern-blot analysis and sequence expression was confirmed by reverse-transcription PCR and sequencing. Analysis of 5% and 10% (w/w) transgenic rice and soybean samples showed that reliable detection depended on the copy numbers of target sequences and probe specificity. Our system detected multiple-copy inserts in 5% TT51-1 rice samples but not single-copy inserts in 10% GTS 40-3-2 soybean samples.