System and method for analysis of plant material for a set of unique exogenous genetic elements

1. A method for identifying in a sample comprising plant DNA,

a plurality of heterologous polynucleotides, wherein each of the heterologous polynucleotides comprises, in the 5′ to 3′ direction, a first nucleotide sequence that is identical between all of the members of the plurality of heterologous polynucleotides; a second nucleotide sequence that is unique among all of the members of the plurality of heterologous polynucleotides; and a third nucleotide sequence that is identical between all of the members of the plurality of heterologous polynucleotides, the method comprising:

contacting the plant DNA in the sample with:

a first oligonucleotide primer that specifically hybridizes to the first nucleotide sequence, and

a second oligonucleotide primer that specifically hybridizes to the third nucleotide sequence;

amplifying in a polymerase chain reaction (PCR) a plurality of amplicons, each containing the second nucleotide sequence that is present in a member of the plurality of heterologous polynucleotides; and

contacting the amplicons with a detectable probe molecule that specifically hybridizes to a binding site in the second nucleotide sequence in a member of the plurality of heterologous polynucleotides, wherein the binding site is selected from the group consisting of SEQ ID NO 1-21 and the complements thereof.

2. The method according to claim 1 , wherein each of the members of the plurality of heterologous polynucleotides comprises a gene in the second nucleotide sequence, and wherein the binding site for the detectable probe molecule is located outside the gene in the second nucleotide sequence of each of the members of the plurality of heterologous polynucleotides.

3. The method according to claim 1 , wherein the detectable probe molecule comprises a fluorophore and a quencher, and wherein specific hybridization of the probe to the binding site in the second nucleotide sequence releases the fluorophore from the quencher in the probe molecule, thereby producing a detectable fluorescence signal.

4. The method according to claim 1 , wherein the amplicons amplified in the PCR reaction are each between about 70 and about 80 nucleotides in length.

5. The method according to claim 1 , wherein the second nucleotide sequence of each of the members of the plurality of heterologous polynucleotides is between about 15 and about 25 nucleotides in length.

6. The method according to claim 1 , wherein at least one of the heterologous polynucleotides consists of, in the 5′ to 3′ direction: the first nucleotide sequence, the second nucleotide sequence, and the third nucleotide sequence.

7. The method according to claim 1 , wherein the steps of the method are performed in an end-point PCR reaction.

8. The method according to claim 1 , wherein the steps of the method are performed in a real-time PCR reaction.

9. The method according to claim 1 , wherein the plant DNA comprises the heterologous polynucleotides in a total amount of at least about 8.33×10 8 % compared to the total amount of DNA in the sample, and a detectable signal is produced by the probe, indicating specific hybridization to the binding site in the second nucleotide sequence.

10. The method according to claim 1 , wherein at least one of the plurality of heterologous polynucleotides comprises an agronomic gene of interest.

11. The method according to claim 1 , wherein contacting the amplicons with the detectable probe molecule does not produce a detectable signal, indicating that the DNA sample does not comprise any of the heterologous polynucleotides.

12. The method according to claim 11 , wherein the heterologous polynucleotides are selected from the group consisting of SEQ ID NOs:22-42 and the complements thereof.