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Patent Analysis of

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

Updated Time 12 June 2019

Patent Registration Data

Publication Number

US10017828

Application Number

US14/204957

Application Date

11 March 2014

Publication Date

10 July 2018

Current Assignee

DOW AGROSCIENCES LLC

Original Assignee (Applicant)

DOW AGROSCIENCES LLC

International Classification

C12Q1/68,C12Q1/6816,C12Q1/6895,C12P19/34

Cooperative Classification

C12Q1/6895,C12Q1/6816,C12Q2563/179

Inventor

DAVIES, JOHN P.,LEE, WARREN S.,REDDY, VAKA S.,LIU, XING LIANG,GAMPALA, SATYALINGA S.

Patent Images

This patent contains figures and images illustrating the invention and its embodiment.

US10017828 System analysis 1 US10017828 System analysis 2 US10017828 System analysis 3
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Abstract

This disclosure concerns a system and method for detecting heterologous DNA in plant materials.

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Claims

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 8.33×108% 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.

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Claim Tree

  • 1
    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
    • 3. The method according to claim 1, wherein
      • the detectable probe molecule comprises
    • 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
    • 10. The method according to claim 1, wherein
      • at least one of the plurality of heterologous polynucleotides comprises
    • 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
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Description

FIELD OF THE DISCLOSURE

The present disclosure relates to plant biotechnology. Embodiments of the disclosure relate to the use of unique exogenous genetic elements in a system and method for detecting and tracking transgenic events through production and commercialization of genetically modified plants and products produced therefrom.

BACKGROUND

A genetically modified organism (GMO), such as a genetically-modified plant, is defined at least one transformation event that usually involves the insertion of a heterologous gene construct into the recipient organism. The heterologous gene construct is typically composed of several elements, including at least a gene of interest and regulatory regions for exerting control of gene expression. In addition, the construct may be flanked by DNA sequences from the cloning vector. The majority of genetically-modified plants have been transformed with constructs containing the Cauliflower Mosaic Virus (CaMV) 35S promoter (P-35S) and/or the CaMV 35S terminator (T-35S), or the Agrobacterium tumefaciens nopaline synthase terminator (T-Nos). The most commonly used cloning vectors are derived from pBR322, containing a gene coding for resistance to ampicillin (bla) antibiotics, and vectors containing a gene coding for resistance to neomycin/kanamycin (nptll) antibiotics.

Detection of GMOs may be desired for many reasons. For example, qualitative detection may be used to identify unauthorized GMO material or use of such material. Further, detection may be desired to identify safe or unsafe material, or for the certification of purity of identity-preserved material. Quantitative detection may be used to comply with legal or contractually-agreed thresholds of GMO contamination (e.g., when products of high purity are desired as in the case of organic farming or seed lot certification). Detection may also play a role in safety assessment and risk management by allowing tracing of the GMO material. In many of the foregoing applications, high sensitivity is required for the detection method.

The development of effective analytical methods for transgene detection and identification of GMOs that reduce time and associated costs of analysis has been an extremely active area of research for many years. Morriset et al. (2008) Eur. Food Res. Technol. 227:1287-97. Yet, no adequate strategy has been devised that provides adequate detection capabilities for the many heterologous gene constructs and transformation events currently in use. DNA is the analyte of choice for the routine laboratory detection and quantification of GMOs since it can be effectively detected after extraction from seed, feed or even highly processed food samples.

Preferred current transgene detection methods detect event-specific elements (e.g., transgene sequences) in transgenic plants. Since most of the generic genetic elements integrated in a transgenic event (e.g., promoter, reporter gene, terminator) are frequently used in multiple vectors, tracking specific events by these genetic elements becomes challenging.

Because of the sensitivity desired for detection assays, DNA is typically first amplified by polymerase chain reaction (PCR) from the sample in such an assay. PCR-based GMO detection methods can be Classified according to their level of specificity. Each category corresponds to the identity of the DNA that is amplified in the PCR reaction: (1) screening targets; (2) gene-specific targets; (3) construct-specific targets; and (4) event-specific targets.

The first category of PCR methods (i.e., amplifying screening targets, for example, the P-35S, T-35S, T-Nos, bla, and ornptll genetic elements) have wide applications for detecting transformed material. Matsuoka et al. (2002) J. Agric. Food Chem. 93:35-8. However, these methods cannot be used to identify the GMO, since the presence of the presence of GMO-derived DNA does not necessarily follow from the presence of the screening target. For example, the source of P-35S or T-35S may be naturally-occurring CaMV. Wolf et al. (2000) Eur. Food Res. Technol. 210:367-72.

The second category of PCR methods (i.e., amplifying a gene of interest, for example, the CryIA gene) are more specific than the first category of methods. Vaitilingom et al. (1999) J. Agric. Food Chem. 47:5261-6. There is greater diversity among the genes of interest than among the available (and commonly used) promoters and terminators, and normally a positive signal for the amplification of a specific transgene implies that GM-derived DNA is present in the sample. However, these methods cannot distinguish between different GMOs that may comprise the same gene of interest, such as an herbicide resistance gene. This failing will become more problematic in the future, as common transgenes are stacked together with others in particular combinations that are characteristic of specific GMOs.

The third category of PCR methods targets (i.e., amplifying a junction between adjacent elements of the heterologous gene construct, for example, between the promoter and the gene of interest) provides the only unique signature of a transformation event, within the limitations of present day technology. Zimmerman et al. (1998) Lebensm.-Wiss u Technol. 31: 664-7. Unfortunately, even event-specific methods have their limitations. For example, when two GMOs are crossed (e.g., two different GM maize, such as T25 and Mon810), the resulting hybrid offspring may contain signatures of both events and will therefore be indistinguishable from its two parents in a PCR test. A further onerous limitation of these detection methods is that a specific primer pair is required for each GMO to identify. Moreover, information regarding the construct insertion site is necessary to design primers and conduct the detection assay, which makes detection of uncharacterized GMOs impossible.

New approaches adhere to a general strategy including the selection of an optimal set of different detection methods to search for and identify particular GMOs present in a sample. Querci et al. (2010) Anal. Bioanal. Chem. 396:1991-2002. Recently, a database providing information on optimal detection methods for particular GMOs, and including specific DNA sequences of inserted and flanking elements in many of the GMOs, was provided. Dong et al. (2008) BMC Bioinformatics 9:260. The database is to be updated and increased as new GMOs are introduced and detection methods investigated as a collective task for entities involved in the detection of GMOs. This database is expected to be a useful tool for analytical laboratories performing GMO testing.

In the future, however, GMO detection according to this conventional wisdom will become prohibitively expensive, due to increasing numbers of approved GMO plants, each of which will have its own optimal detection method. Furthermore, it is increasingly common to combine multiple agronomic traits in a single GMO (“gene stacking”). Taverniers et al. (2008) Environ. Biosafety Res. 7:197-218. Gene stacking introduces a difficult challenge to GMO detection. With the exception of testing of single seeds or tissue derived from individual plants, no existing detection method can adequately discriminate between the combined presence of material from two or more single trait GMOs, and single stacked GMOs. Akiyama et al. (2005) J. Agric. Food Chem. 55:5942-7; Holst-Jensen et al. (2006) J. Agric. Food Chem. 54:2799-809; Taverniers et al. (2008), supra.

In recent years, DNA-based detection methods including microarray/chip and multiplex PCRs were explored for the potential for increasing detection assay sensitivity and output, and for identifying stacked GMOs. See, e.g., Tengs et al. (2007) BMC Biotechnol. 7:91. For example, Peano et al. (2005) Anal. Biochem. 346:90-100 and Prins et al. (2008) BMC Genomics 9:584 reported an approach combining a transgene specific ligation reaction, PCR amplification of the ligated oligonucleotide, hybridization, and microarray detection. Multiple oligonucleotide tags immobilized on the microarray surface that targeted the amplified ligation products were used to provide multiplex capabilities in this approach. Such detection methods and multiplexing tools represent the approaches currently used to develop GMO detection methods that address the expectation that sensitive detection will be required in the future from complicated samples containing a diverse plurality of events.

BRIEF SUMMARY OF THE DISCLOSURE

Described herein is a system providing a single highly-specific and highly-sensitive PCR-based detection assay for determining the presence of a plurality of unique transgenic events. In some embodiments, the system and method thereof does not require any information regarding the integration site of the transgenic event to perform the method. In some examples, a single pair of oligonucleotide primers (a universal primer pair) may be utilized to amplify polynucleotides from many different exogenous constructs that may then be specifically detected via a single assay. Embodiments herein utilize unique nucleotide sequences (within a set of vectors) that may have similar thermodynamic properties, which sequences (referred to in some places herein as “unique exogenous genetic elements” or “UGEs”) are uniquely associated with a particular transgene and may be detected in substantially the same assay as other such unique nucleotides within the set of vectors. Systems and methods herein may provide a single means to detect/screen for multiple transgenes, thus reducing the overall number of detection assays required for adventitious presence testing.

Some embodiments provide methods for identifying a heterologous nucleic acid in a plant or plant material (e.g., seed), wherein the heterologous nucleic acid comprises a 5′ polynucleotide, a UGE, and a 3′ polynucleotide. In particular embodiments, such a method comprises providing a sample comprising DNA from the plant or plant material; contacting the DNA with a pair of oligonucleotide primers that specifically hybridize to the 5′ and 3′ polynucleotides; amplifying an amplicon comprising the 5′ polynucleotide, the UGE, and the 3′ polynucleotide; and detecting the UGE using a specific probe (e.g., in a fluorescence-based PCR assay, such as a hydrolysis probe assay). In particular embodiments, such a method comprises detecting the UGE by sequencing the amplified fragments comprising the 5′ polynucleotide, the UGE, and the 3′ polynucleotide. As demonstrated by the several Examples herein, methods according to particular embodiments provide surprising specificity that is unprecedented in a generalizable GMO detection method.

Some embodiments provide systems for detecting at least one heterologous nucleic acid in a plant or plant material. Some systems comprise a set of vectors each comprising a heterologous nucleic acid containing a 5′ polynucleotide, a UGE, and a 3′ polynucleotide, wherein the 5′ polynucleotide and 3′ polynucleotide are universal (i.e., common to all) in the vector set, and wherein the UGE of each of the vectors is unique to the set. Some systems may comprise a universal forward primer oligonucleotide that specifically hybridizes to the 5′ polynucleotide, and a universal reverse primer oligonucleotide that specifically hybridizes to the 3′ polynucleotide. Particular systems may comprise a set of probe molecules, wherein each of the probe molecules specifically hybridizes to only one of the UGEs in the vector set.

Systems and methods herein may be used to identify the presence of a vast number of transgenic events in GMO plants, including those with stacked transgenes, with a previously unavailable level of specificity and generalizability. In some examples, systems and methods herein obviate the need to independently develop detection assays for different events and combine disparate detection methods to obtain good GMO coverage, which can be a prohibitively expensive strategy.

Multiple genes of interest may be introduced into plant transformation vectors comprising UGEs and universal primer sites, and transgenic plants may be obtained using these vectors. Thereby, multiple genes may be transformed and tracked in transgenic plants using a single UGE-specific detection assay. Transgenic plants transformed with these constructs may be tested using a bulked segregate analysis approach that significantly reduces the number of assays required to identify the transgenic plants for further uses, compared to previously available techniques. Further, systems and methods herein may aid commercial advancement decisions in trait introgression programs by facilitating analysis of field samples for the presence of intended traits, as well as the absence of unintended traits (adventitious presence).

The foregoing and other features will become more apparent from the following detailed description of several embodiments, which proceeds with reference to the accompanying figures.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 includes a schematic presentation of a sequence alignment between six exemplary UGE-containing polynucleotides (SEQ ID NOs:55-60), from plasmids pEPP1135-pEPP1140, respectively. F-Primer and R-Primer represent universal forward and reverse PCR primers.

FIG. 2 includes detection results from UGE-specific PCR assays. UGE-specific plasmid DNA were used as the positive controls (shown in circles) and non-transgenic corn DNA and no template control samples were used as negative controls. Samples were run in triplicates.

FIG. 3 includes detection results showing that extremely low concentrations of target UGE DNA can be detected using hydrolysis probes designed to specifically hybridize thereto. Template (plasmid DNA) concentrations ranging from 0.0000001 ng to 1 ng were tested (shown from left to right orientation) in end-point PCRs. No-template control was included to test the non-specificity (marked in circle).

FIG. 4 includes detection results of a plasmid comprising a target UGE (SEQ ID NO:3) in a non-transgenic corn genomic DNA background using a fluorescence-based hydrolysis PCR assay. Melting curve analysis and cycle number for target and internal control crossing points (Cp) are presented.

FIG. 5 includes detection results of a plasmid comprising a target UGE (SEQ ID NO:8) in a non-transgenic corn genomic DNA background using a fluorescence-based hydrolysis PCR assay. Melting curve analysis and cycle number for target and internal control crossing points (Cp) are presented.

FIG. 6 includes a schematic showing a UGE cloning strategy. In the schematic, “PTU” represents a Plant Transformation Unit and “ZP” represents the amplicon comprising the UGE. “LB” and “RB” represent Left and Right borders of T-DNA, respectively.

FIG. 7 includes a schematic showing an example of a UGE cloning strategy for agronomic trait projects. This example illustrates that a UGE was cloned between a selectable marker (OsAct1-AAD1-ZmLip) and the agronomic gene of interest.

FIG. 8 includes data showing detection of UGE sequences in T1 transgenic corn seed. Positive controls: Plasmid DNA containing the UGE sequences; Negative controls: Non-transgenic corn genomic DNA; 8A: Transgenic corn seed containing UGE2; 8B: Transgenic corn seed containing UGE3.

FIG. 9 includes data showing detection of a UGE sequence (UGE3) in homozygous transgenic corn seed samples. Negative controls—Non-transgenic corn DNA; Positive controls—ZCZ0000003 plasmid DNA; Samples—Transgenic T2 corn seed DNA expressing UGE3 (pDAB108526, pDAB108527, pDAB108528; 6 different seed sources were used as listed in Table 9).

FIG. 10 includes data showing the sensitivity of UGE detection from transgenic maize (UGE3). Negative controls—Non-transgenic corn DNA; Positive controls—ZCZ0000003 plasmid DNA Samples—Dilutions of transgenic T2 corn seed DNA (pDAB108526—Source ID # ZQ11LQ199088.0016.016).

FIG. 11 includes data demonstrating the detection of a UGE in a spiked transgenic seed sample with a hydrolysis probe PCR Assay. Negative controls—Non-transgenic corn DNA; Positive controls—1% genomic DNA; Samples—36 DNA samples from spiked corn seed (1 transgenic seed in 99 non-transgenic seed)—12 biological replicates and 3 technical replicates.

SEQUENCE LISTING

The nucleic acid sequences listed in the accompanying sequence listing are shown using standard letter abbreviations for nucleotide bases, as defined in 37 C.F.R. § 1.822. Only one strand of each nucleic acid sequence is shown, but the complementary strand is understood to be included by any reference to the displayed strand. In the accompanying sequence listing:

SEQ ID NOs:1-21 show exemplary oligonucleotide probes designed to specifically hybridize to (identical) UGE polynucleotides (“UGE1”-“UGE21,” respectively)

SEQ ID NOs:22-42 show amplicons (“Amplicons 1-21”), each comprising an exemplary UGE and 5′ and 3′ binding sites for universal PCR Forward and Reverse primers.

SEQ ID NOs:43-46 show primers useful in certain UGE fluorescence-based PCR assays to generate amplicons for UGE detection via a hydrolysis probe assay.

SEQ ID NO:47 shows a maize invertase gene that may be used as a positive control in particular embodiments to validate PCR and hydrolysis probe reaction conditions.

SEQ ID NO:48 shows a maize ZSSIIb gene that may be used as a positive control in particular embodiments to validate PCR and hydrolysis probe reaction conditions.

SEQ ID NOs:49-50 show primers useful for amplifying a portion of a maize invertase gene.

SEQ ID NO:51 shows a probe oligonucleotide that may be used to detect a maize invertase gene.

SEQ ID NOs:52-53 show primers useful for amplifying a portion of a maize ZSSIIb gene.

SEQ ID NO:54 shows a probe oligonucleotide that may be used to detect a maize ZSSIIb gene.

SEQ ID NOs:55-60 show UGE-containing polynucleotides from members of a set of plant transformation vectors (pEPP1135-pEPP1140).

DETAILED DESCRIPTION

I. Overview of Several Embodiments

Sensitive and reliable detection methods are necessary for monitoring genetically modified organisms (GMO). Existing DNA detection methods are geared towards targeting the screening elements, plant-specific elements, or event-specific elements in transgenic plants. Described herein is the use of unique, synthetic non-coding synthetic DNA sequences (UGEs) that, when incorporated into plant transformation vectors, may assist in monitoring transgenic plants by serving as targets for robust universal assay development. Several UGE sequences have been tested for the ease of fluorescence-based assay development and their utility in monitoring the transgenic plants was demonstrated. Constructs comprising a UGE flanked by universal primer sites were introduced into plant transformation vectors, and specific hydrolysis probe detection assays were shown to rapidly track each transformation vector.

II. Abbreviations

ABC-transporter ATP-binding cassette transporter

AP adventitious presence

BHQ2 Black Hole Quencher™-2

FAM 6-carboxy fluorescein amidite

FET fluorescent energy transfer

HEX hexachloro-fluorescein

MGBNFQ Minor Groove Binder Non-Fluorescent Quencher

PCR polymerase chain reaction

UGE unique exogenous genetic element

III. Terms

Adventitious Presence: As used herein, “Adventitious Presence” (AP) refers to the unintentional and incidental commingling of trace amounts of transgenic material in a sample of plant material. Adventitious presence may be exemplified, for example, by the presence of trace amounts of transgenic material in a sample believed to be wholly comprised of non-transgenic material, or may be exemplified by the presence trace amounts of transgenic material of one type in a sample of material believed to be wholly comprised of transgenic material of a different type.

Backcrossing: Backcrossing methods may be used to introduce a nucleic acid sequence into plants. The backcrossing technique has been widely used for decades to introduce new traits into plants. Jensen, N., Ed. Plant Breeding Methodology, John Wiley & Sons, Inc., 1988. In a typical backcross protocol, the original variety of interest (recurrent parent) is crossed to a second variety (non-recurrent parent) that carries a gene of interest to be transferred. The resulting progeny from this cross are then crossed again to the recurrent parent, and the process is repeated until a plant is obtained wherein essentially all of the desired morphological and physiological characteristics of the recurrent plant are recovered in the converted plant, in addition to the transferred gene from the non-recurrent parent.

Isolated: An “isolated” biological component (such as a nucleic acid or protein) has been substantially separated, produced apart from, or purified away from other biological components in the cell of the organism in which the component naturally occurs (i.e., other chromosomal and extra-chromosomal DNA and RNA, and proteins), while effecting a chemical or functional change in the component (e.g., a nucleic acid may be isolated from a chromosome by breaking chemical bonds connecting the nucleic acid to the remaining DNA in the chromosome). Nucleic acid molecules and proteins that have been “isolated” include nucleic acid molecules and proteins purified by standard purification methods. The term also embraces nucleic acids and proteins prepared by recombinant expression in a host cell, as well as chemically-synthesized nucleic acid molecules, proteins, and peptides.

Nucleic acid molecule: As used herein, the term “nucleic acid molecule” may refer to a polymeric form of nucleotides, which may include both sense and anti-sense strands of RNA, cDNA, genomic DNA, and synthetic forms and mixed polymers of the above. A nucleotide may refer to a ribonucleotide, deoxyribonucleotide, or a modified form of either type of nucleotide. A “nucleic acid molecule,” as used herein, is synonymous with “nucleic acid” and “polynucleotide.” A nucleic acid molecule is usually at least 10 bases in length, unless otherwise specified. The term includes single- and double-stranded forms of DNA. A nucleic acid molecule can include either or both naturally occurring and modified nucleotides linked together by naturally occurring and/or non-naturally occurring nucleotide linkages.

Nucleic acid molecules may be modified chemically or biochemically, or may contain non-natural or derivatized nucleotide bases, as will be readily appreciated by those of skill in the art. Such modifications include, for example, labels, methylation, substitution of one or more of the naturally occurring nucleotides with an analog, internucleotide modifications (e.g., uncharged linkages: for example, methyl phosphonates, phosphotriesters, phosphoramidates, carbamates, etc.; charged linkages: for example, phosphorothioates, phosphorodithioates, etc.; pendent moieties: for example, peptides; intercalators: for example, acridine, psoralen, etc.; chelators; alkylators; and modified linkages: for example, alpha anomeric nucleic acids, etc.). The term “nucleic acid molecule” also includes any topological conformation, including single-stranded, double-stranded, partially duplexed, triplexed, hairpinned, circular, and padlocked conformations.

Exogenous: The term “exogenous,” as applied to nucleic acids (e.g., polynucleotides, DNA, RNA, and genes) herein, refers to one or more nucleic acid(s) that are not normally present within their specific environment or context. For example, if a host cell is transformed with a nucleic acid that does not occur in the untransformed host cell in nature, then that nucleic acid is exogenous to the host cell. The term exogenous, as used herein, also refers to one or more nucleic acid(s) that are identical in sequence to a nucleic acid already present in a host cell, but that are located in a different cellular or genomic context than the nucleic acid with the same sequence already present in the host cell. For example, a nucleic acid that is integrated in the genome of the host cell in a different location than a nucleic acid with the same sequence is normally integrated in the genome of the host cell is exogenous to the host cell. Furthermore, a nucleic acid (e.g., a DNA molecule) that is present in a plasmid or vector in the host cell is exogenous to the host cell when a nucleic acid with the same sequence is only normally present in the genome of the host cell.

Heterologous: The term “heterologous,” as applied to nucleic acids (e.g., polynucleotides, DNA, RNA, and genes) herein, means of different origin. For example, if a host cell is transformed with a nucleic acid that does not occur in the untransformed host cell in nature, then that nucleic acid is heterologous (and exogenous) to the host cell. Furthermore, different elements (e.g., promoter, enhancer, coding sequence, terminator, etc.) of a transforming nucleic acid may be heterologous to one another and/or to the transformed host. The term heterologous, as used herein, may also be applied to one or more nucleic acid(s) that are identical in sequence to a nucleic acid already present in a host cell, but that are now linked to different additional sequences and/or are present at a different copy number, etc.

Sequence identity: The term “sequence identity” or “identity,” as used herein, in the context of two nucleic acid or polypeptide sequences, may refer to the residues in the two sequences that are the same when aligned for maximum correspondence over a specified comparison window.

As used herein, the term “percentage of sequence identity” may refer to the value determined by comparing two optimally aligned sequences (e.g., nucleic acid sequences, and amino acid sequences) over a comparison window, wherein the portion of the sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleotide or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the comparison window, and multiplying the result by 100 to yield the percentage of sequence identity.

Methods for aligning sequences for comparison are well-known in the art. Various programs and alignment algorithms are described in, for example: Smith and Waterman (1981) Adv. Appl. Math. 2:482; Needleman and Wunsch (1970) J. Mol. Biol. 48:443; Pearson and Lipman (1988) Proc. Natl. Acad. Sci. U.S.A. 85:2444; Higgins and Sharp (1988) Gene 73:237-44; Higgins and Sharp (1989) CABIOS 5:151-3; Corpet et al. (1988) Nucleic Acids Res. 16:10881-90; Huang et al. (1992) Comp. Appl. Biosci. 8:155-65; Pearson et al. (1994) Methods Mol. Biol. 24:307-31; Tatiana et al. (1999) FEMS Microbiol. Lett. 174:247-50. A detailed consideration of sequence alignment methods and homology calculations can be found in, e.g., Altschul et al. (1990) J. Mol. Biol. 215:403-10.

The National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST™; Altschul et al. (1990)) is available from several sources, including the National Center for Biotechnology Information (Bethesda, Md.), and on the internet, for use in connection with several sequence analysis programs. A description of how to determine sequence identity using this program is available on the internet under the “help” section for BLAST™. For comparisons of nucleic acid sequences, the “Blast 2 sequences” function of the BLAST™ (Blastn) program may be employed using the default parameters. Nucleic acid sequences with even greater similarity to the reference sequences will show increasing percentage identity when assessed by this method.

As used herein, the term “substantially identical” may refer to nucleotide sequences that are more than 85% identical. For example, a substantially identical nucleotide sequence may be at least 85.5%; at least 86%; at least 87%; at least 88%; at least 89%; at least 90%; at least 91%; at least 92%; at least 93%; at least 94%; at least 95%; at least 96%; at least 97%; at least 98%; at least 99%; or at least 99.5% identical to the reference sequence.

Probe: In some embodiments, the presence of a particular nucleic acid (e.g., a UGE) in a sample may be detected through the use of a nucleic acid probe. A probe may be a DNA molecule or an RNA molecule. A probe may contain all or a portion of the nucleotide sequence of the particular nucleic acid, and may optionally further contain at least one additional nucleotide sequence and/or label(s).

An oligonucleotide probe sequence may be prepared synthetically or by cloning. Suitable cloning vectors are well-known to those of skill in the art. An oligonucleotide probe may be labeled or unlabeled. A wide variety of techniques exist for labeling nucleic acid molecules, including, for example and without limitation: Radiolabeling by nick translation; random priming; tailing with terminal deoxytransferase; etc., where the nucleotides employed are labeled, for example, with radioactive 32P. Other labels which may be used include, for example and without limitation: Fluorophores (e.g., alone or with a quencher); enzymes; enzyme substrates; enzyme cofactors; enzyme inhibitors; etc. Alternatively, the use of a label that provides a detectable signal, by itself or in conjunction with other reactive agents, may be replaced by ligands to which receptors bind, where the receptors are labeled (for example, by the above-indicated labels) to provide detectable signals, either by themselves, or in conjunction with other reagents. See, e.g., Leary et al. (1983) Proc. Natl. Acad. Sci. USA 80:4045-9.

A probe may also be a nucleic acid molecule that is “specifically hybridizable” or “specifically complementary” to the particular nucleic acid to be detected (i.e., the target). “Specifically hybridizable” and “specifically complementary” are terms that indicate a sufficient degree of complementarity such that stable and specific binding occurs between the probe and the target. A nucleic acid molecule need not be 100% complementary to its target sequence to be specifically hybridizable. A nucleic acid molecule is specifically hybridizable when there is a sufficient degree of complementarity to avoid non-specific binding of the nucleic acid to non-target sequences under conditions where specific binding is desired, for example, under stringent hybridization conditions.

Hybridization conditions resulting in particular degrees of stringency will vary depending upon the nature of the hybridization method of choice and the composition and length of the hybridizing nucleic acid sequences. Generally, the temperature of hybridization and the ionic strength (especially the Na+ and/or Mg++ concentration) of the hybridization buffer will determine the stringency of hybridization, though wash times also influence stringency. Calculations regarding hybridization conditions required for attaining particular degrees of stringency are known to those of ordinary skill in the art, and are discussed, for example, in Sambrook et al. (ed.) Molecular Cloning: A Laboratory Manual, 2nd ed., vol. 1-3, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989, chapters 9 and 11; and Hames and Higgins (eds.) Nucleic Acid Hybridization, IRL Press, Oxford, 1985. Further detailed instruction and guidance with regard to the hybridization of nucleic acids may be found, for example, in Tijssen, “Overview of principles of hybridization and the strategy of nucleic acid probe assays,” in Laboratory Techniques in Biochemistry and Molecular Biology-Hybridization with Nucleic Acid Probes, Part I, Chapter 2, Elsevier, N.Y., 1993; and Ausubel et al., Eds., Current Protocols in Molecular Biology, Chapter 2, Greene Publishing and Wiley-Interscience, NY, 1995.

As used herein, “stringent conditions” encompass conditions under which hybridization will only occur if there is less than 25% mismatch between the hybridization molecule and the DNA target. “Stringent conditions” include further particular levels of stringency. Thus, as used herein, “moderate stringency” conditions are those under which molecules with more than 25% sequence mismatch will not hybridize; conditions of “medium stringency” are those under which molecules with more than 15% mismatch will not hybridize; and conditions of “high stringency” are those under which sequences with more than 10% mismatch will not hybridize. Conditions of “very high stringency” are those under which sequences with more than 6% mismatch will not hybridize.

In particular embodiments, stringent conditions are hybridization at 65° C. in 6× saline-sodium citrate (SSC) buffer, 5×Denhardt's solution, 0.5% SDS, and 100 μg sheared salmon testes DNA, followed by 15-30 minute sequential washes at 65° C. in 2×SSC buffer and 0.5% SDS, followed by 1×SSC buffer and 0.5% SDS, and finally 0.2×SSC buffer and 0.5% SDS.

Operably linked: A first nucleic acid sequence is operably linked with a second nucleic acid sequence when the first nucleic acid sequence is in a functional relationship with the second nucleic acid sequence. For instance, a promoter is operably linked with a coding sequence when the promoter affects the transcription or expression of the coding sequence. When recombinantly produced, operably linked nucleic acid sequences are generally contiguous and, where necessary to join two protein-coding regions, in the same reading frame. However, elements need not be contiguous to be operably linked.

Promoter: A region of DNA that generally is located upstream (towards the 5′ region of a gene) that is needed for transcription. Promoters permit the proper activation or repression of the gene which they control. A promoter contains specific sequences that are recognized by transcription factors. These factors bind to the promoter DNA sequences and result in the recruitment of RNA polymerase, the enzyme that synthesizes the RNA from the coding region of the gene. In some embodiments, tissue-specific promoters are used. A tissue-specific promoter is a DNA sequence that directs a higher level of transcription of an associated gene in the tissue for which the promoter is specific relative to the other tissues of the organism. Examples of tissue-specific promoters include tapetum-specific promoters; anther-specific promoters; pollen-specific promoters (See, e.g., U.S. Pat. No. 7,141,424, and International PCT Publication No. WO 99/042587); ovule-specific promoters; (See, e.g., U.S. Patent Application No. 2001/047525 A1); fruit-specific promoters (See, e.g., U.S. Pat. Nos. 4,943,674, and 5,753,475); and seed-specific promoters (See, e.g., U.S. Pat. Nos. 5,420,034, and 5,608,152). In some embodiments, developmental stage-specific promoters are also used, e.g., a promoter active at a later stage in development.

Transformed: A virus or vector “transforms” or “transduces” a cell when it transfers nucleic acid molecules into the cell. A cell is “transformed” by a nucleic acid molecule transduced into the cell when the nucleic acid molecule becomes stably replicated by the cell, either by incorporation of the nucleic acid molecule into the cellular genome or by episomal replication. As used herein, the term “transformation” encompasses all techniques by which a nucleic acid molecule can be introduced into such a cell. Examples include, but are not limited to, transfection with viral vectors, transformation with plasmid vectors, electroporation (Fromm et al. (1986) Nature 319:791-3), lipofection (Feigner et al. (1987) Proc. Natl. Acad. Sci. USA 84:7413-7), microinjection (Mueller et al. (1978) Cell 15:579-85), Agrobacterium-mediated transfer (Fraley et al. (1983) Proc. Natl. Acad. Sci. USA 80:4803-7), direct DNA uptake, and microprojectile bombardment (Klein et al. (1987) Nature 327:70).

Transgene: An exogenous nucleic acid sequence. In one example, a transgene is a gene sequence (e.g., a herbicide-resistance gene), a gene encoding an industrially or pharmaceutically useful compound, or a gene encoding a desirable agricultural trait. In yet another example, the transgene is an antisense nucleic acid sequence, wherein expression of the antisense nucleic acid sequence inhibits expression of a target nucleic acid sequence. A transgene may contain regulatory sequences operably linked to the transgene (e.g., a promoter).

Vector: As used herein, the term “vector” refers to a polynucleotide or other molecule that is capable of transferring at least one nucleic acid segment(s) into a cell. A vector may optionally comprise components/elements that mediate vector maintenance and/or enable its intended use (e.g., sequences necessary for replication, genes imparting drug or antibiotic resistance, a multiple cloning site, and/or operably linked promoter/enhancer elements that enable the expression of a cloned gene). Vectors may be derived, for example, from plasmids, bacteriophages, or plant or animal viruses. A “cloning vector,”“shuttle vector,” or “subcloning vector” generally comprises operably linked elements to facilitate cloning or subcloning steps (e.g., a multiple cloning site containing multiple restriction endonuclease sites).

Expression Vector: The term “expression vector,” as used herein, refers to a vector comprising operably linked polynucleotide sequences that may facilitate expression of a coding sequence in a particular host organism. For example, a bacterial expression vector may facilitate expression of a coding sequence in a bacterium. Likewise, a plant expression vector may facilitate expression of a coding sequence in a plant cell. Polynucleotide sequences that facilitate expression in prokaryotes may include, for example and without limitation, a promoter; an operator; and a ribosome binding site. Eukaryotic expression vectors (e.g., a plant expression vector) may comprise, for example, promoters; enhancers; termination signals; and polyadenylation signals (and other sequences) that are generally different from those used in prokaryotic expression vectors.

Trait or phenotype: The terms “trait” and “phenotype” are used interchangeably herein. For the purposes of the present disclosure, traits of particular interest include agronomically important traits, as may be expressed, for example, in a crop plant.

Unique exogenous genetic element (UGE): UGEs are unique, synthetic DNA sequences that when incorporated into plant transformation vectors, serve as targets for DNA detection assays. First, a single unique pre-validated UGE is introduced into a plant transformation vector. Second, the UGE-containing plant transformation vector is used for cloning multiple genes driven by the same promoter. UGE-specific fluorescence-based PCR assays are rapidly developed to track each transformation vector with relative ease. Transgenic plants derived from these constructs can be tested using a bulked segregate analysis approach to reduce the number of assays significantly.

IV. Unique Exogenous Genetic Elements

Embodiments herein include unique, synthetic non-coding synthetic DNA sequences (referred to herein as “Unique exogenous Genetic Elements,” or “UGEs”) that may be used to develop a universal method for the UGE-specific detection of nucleic acids. UGEs may be designed such that all of those in a set have similar thermodynamic properties as oligonucleotides in a hybridization assay. Within a set of nucleic acids, for example, for introduction into an organism, a set of distinct/unique UGEs may be included with a further nucleic acid(s) of interest in the nucleic acids of the set, to identify in a specifically identifiable fashion constructs from a particular company or laboratory, constructs containing certain classes of genes or genetic elements, and/or GMOs (e.g., plants) comprising such constructs.

In some embodiments, the UGEs are unique identification markers that are flanked and amplified by common primers, universal to the set, such that nucleic acids comprising the UGEs may be universally and specifically identified, for example, by DNA sequence analysis, hybridization, and fluorescence-based PCR analysis. In some examples, heterologous nucleic acids comprising UGEs in a GMO may be identified using a fluorescence-based real-time PCR method with unique quenchable fluorescently-labeled probes (e.g., a hydrolysis probe) that specifically hybridize to the UGEs. For example, the UGE oligonucleotides themselves may be incorporated in a labeled probe molecule. Universal PCR primers and UGEs may provide highly specific and highly efficient amplification and fluorescence-based detection in a single assay for a complicated GMO material comprising many different transgenes. In some examples, heterologous nucleic acids comprising a UGE in a GMO may be identified by sequencing an amplified DNA fragment that is flanked by the universal primers, so as to determine the identity of the UGE present in the sample.

Fluorescence-coupled PCR is utilized as a detection assay in particular embodiments. Such PCR-based assays are known in the art. U.S. Pat. Nos. 5,210,015 and 5,487,972. For example, particular embodiments utilize a PCR reaction involving three oligonucleotides: a forward primer; a reverse primer; and a fluorogenic probe. The fluorogenic probe may comprise, for example and without limitation, an oligonucleotide labeled at the 5′ end with a reporter fluorescent dye (e.g., FAM and HEX), and labeled at the 3′ end with a quencher dye (e.g., MGBNFQ and BHQ2). In such exemplary probe molecules, excitation of the reporter fluorescent dye at a specific wavelength (488 nm) will not lead to fluorescence, due to FET suppression as a result of spatial proximity to the quencher dye. During a hydrolysis probe PCR assay, the probe with the primers initially hybridizes to the target DNA. In the extension phase, the probe positioned between the primers contacts the polymerase and is hydrolyzed through its exonuclease activity. Probe hydrolysis releases the fluorescent reporter from the FET suppression, and the reporter fluorescence increases with each PCR cycle in accordance with the accumulation of PCR product.

In some embodiments, a UGE is designed to have a length sufficient to provide adequate sequence diversity within the set comprising the UGE, such that oligonucleotide probes may be designed to specifically hybridize to each of the UGEs in the set. For example, a UGE may be designed to be, for example and without limitation: more than about 10; more than about 15; more than about 20; more than about 25; between about 10 and about 25; between about 15 and about 25; between about 10 and about 20; and between about 15 and about 20 nucleotides in length. In particular embodiments, a UGE is selected from the group consisting of UGE1-UGE21 (SEQ ID NOs:1-21).

In some embodiments, a UGE may be comprised in an amplifiable nucleic acid (an amplicon) that also comprises flanking universal primers. In some examples, the flanking universal primers may be directly adjacent to the UGE; i.e., not separated by any further nucleotide sequence. An amplicon comprising a UGE and flanking universal primers may be of sufficient length to be amplifiable in a PCR reaction. For example and without limitation, such an amplicon may be less than about 150; less than about 130; less than about 110; less than about 100; less than about 90; less than about 85; less than about 80; between about 60 and about 100; between about 60 and about 90; between about 60 and about 80; between about 70 and about 100; between about 70 and about 90; and between about 70 and about 80 nucleotides in length. In particular embodiments, an amplicon comprising a UGE and flanking primer sites is selected from the group consisting of Amplicons 1-21 (SEQ ID NOs:22-42).

In some embodiments, a UGE (e.g., in an amplicon also comprising flanking universal primers) may, for example, be comprised in a vector system including, for example and without limitation, a linear plasmid, and a closed circular plasmid. In particular examples, the vector may be an expression vector. Amplicons comprising UGEs according to particular embodiments may, for example, be inserted into a vector, such that the nucleic acid sequence is operably linked to one or more regulatory sequences. Many vectors are available for this purpose, and selection of the particular vector may depend, for example, on the size of the nucleic acid to be inserted into the vector, the particular host cell to be transformed with the vector, and/or the amount of the fusion protein that is desired to be expressed. A vector typically contains various components, the identity of which depend on a function of the vector (e.g., amplification of DNA and expression of DNA), and the particular host cell(s) with which the vector is compatible.

Some embodiments may include a plant transformation vector that comprises a UGE flanked by universal primer sites, and a gene of interest that is operatively linked to at least one regulatory sequence. The gene of interest may be expressed, under the control of the regulatory sequence(s), in a plant cell, tissue, or organism to produce the fusion protein. Such a regulatory sequence may be a promoter sequence that functions in a host plant cell.

Promoters suitable for use in nucleic acid molecules according to some embodiments include those that are inducible, viral, synthetic, or constitutive, all of which are well known in the art. Non-limiting examples of promoters that may be useful in embodiments of the invention are provided by: U.S. Pat. No. 6,437,217 (maize RS81 promoter); U.S. Pat. No. 5,641,876 (rice actin promoter); U.S. Pat. No. 6,426,446 (maize RS324 promoter); U.S. Pat. No. 6,429,362 (maize PR-1 promoter); U.S. Pat. No. 6,232,526 (maize A3 promoter); U.S. Pat. No. 6,177,611 (constitutive maize promoters); U.S. Pat. Nos. 5,322,938, 5,352,605, 5,359,142, and 5,530,196 (35S promoter); U.S. Pat. No. 6,433,252 (maize L3 oleosin promoter); U.S. Pat. No. 6,429,357 (rice actin 2 promoter, and rice actin 2 intron); U.S. Pat. No. 6,294,714 (light-inducible promoters); U.S. Pat. No. 6,140,078 (salt-inducible promoters); U.S. Pat. No. 6,252,138 (pathogen-inducible promoters); U.S. Pat. No. 6,175,060 (phosphorous deficiency-inducible promoters); U.S. Pat. No. 6,388,170 (bidirectional promoters); U.S. Pat. No. 6,635,806 (gamma-coixin promoter); and U.S. patent application Ser. No. 09/757,089 (maize chloroplast aldolase promoter).

Additional exemplary promoters include the nopaline synthase (NOS) promoter (Ebert et al. (1987) Proc. Natl. Acad. Sci. USA 84(16):5745-9); the octopine synthase (OCS) promoter (which is carried on tumor-inducing plasmids of Agrobacterium tumefaciens); the caulimovirus promoters such as the cauliflower mosaic virus (CaMV) 19S promoter (Lawton et al. (1987) Plant Mol. Biol. 9:315-24); the CaMV 35S promoter (Odell et al. (1985) Nature 313:810-2; the figwort mosaic virus 35S-promoter (Walker et al. (1987) Proc. Natl. Acad. Sci. USA 84(19):6624-8); the sucrose synthase promoter (Yang and Russell (1990) Proc. Natl. Acad. Sci. USA 87:4144-8); the R gene complex promoter (Chandler et al. (1989) Plant Cell 1:1175-83); the chlorophyll a/b binding protein gene promoter; CaMV35S (U.S. Pat. Nos. 5,322,938, 5,352,605, 5,359,142, and 5,530,196); FMV35S (U.S. Pat. Nos. 6,051,753, and 5,378,619); a PC1SV promoter (U.S. Pat. No. 5,850,019); the SCP1 promoter (U.S. Pat. No. 6,677,503); and AGRtu.nos promoters (GenBank Accession No. V00087; Depicker et al. (1982) J. Mol. Appl. Genet. 1:561-73; Bevan et al. (1983) Nature 304:184-7).

In particular embodiments, nucleic acid molecules of the invention may comprise a tissue-specific promoter. A tissue-specific promoter is a nucleotide sequence that directs a higher level of transcription of an operably linked nucleotide sequence in the tissue for which the promoter is specific, relative to the other tissues of the organism. Examples of tissue-specific promoters include, without limitation: tapetum-specific promoters; anther-specific promoters; pollen-specific promoters (See, e.g., U.S. Pat. No. 7,141,424, and International PCT Publication No. WO 99/042587); ovule-specific promoters; (See, e.g., U.S. Patent Application No. 2001/047525 A1); fruit-specific promoters (See, e.g., U.S. Pat. Nos. 4,943,674, and 5,753,475); and seed-specific promoters (See, e.g., U.S. Pat. Nos. 5,420,034, and 5,608,152). In some embodiments, a developmental stage-specific promoter (e.g., a promoter active at a later stage in development) may be used in a composition or method of the invention.

Additional regulatory sequences that may in some embodiments be operably linked to a nucleic acid molecule include 5′ UTRs located between a promoter sequence and a coding sequence that function as a translation leader sequence. The translation leader sequence is present in the fully-processed mRNA, and it may affect processing of the primary transcript, and/or RNA stability. Examples of translation leader sequences include maize and petunia heat shock protein leaders (U.S. Pat. No. 5,362,865), plant virus coat protein leaders, plant rubisco leaders, and others. See, e.g., Turner and Foster (1995) Molecular Biotech. 3(3):225-36. Non-limiting examples of 5′ UTRs are provided by: GmHsp (U.S. Pat. No. 5,659,122); PhDnaK (U.S. Pat. No. 5,362,865); AtAnt1; TEV (Carrington and Freed (1990) J. Virol. 64:1590-7); and AGRtunos (GenBank Accession No. V00087; and Bevan et al. (1983), supra).

Additional regulatory sequences that may in some embodiments be operably linked to a nucleic acid molecule also include 3′ non-translated sequences, 3′ transcription termination regions, or poly-adenylation regions. These are genetic elements located downstream of a nucleotide sequence, and include polynucleotides that provide polyadenylation signal, and/or other regulatory signals capable of affecting transcription or mRNA processing. The polyadenylation signal functions in plants to cause the addition of polyadenylate nucleotides to the 3′ end of the mRNA precursor. The polyadenylation sequence can be derived from a variety of plant genes, or from T-DNA genes. A non-limiting example of a 3′ transcription termination region is the nopaline synthase 3′ region (nos 3′; Fraley et al. (1983) Proc. Natl. Acad. Sci. USA 80:4803-7). An example of the use of different 3′ nontranslated regions is provided in Ingelbrecht et al. (1989) Plant Cell 1:671-80. Non-limiting examples of polyadenylation signals include one from a Pisum sativum RbcS2 gene (Ps.RbcS2-E9; Coruzzi et al. (1984) EMBO J. 3:1671-9) and AGRtu.nos (GenBank Accession No. E01312).

Additional information regarding regulatory sequences that may be useful in particular embodiments is described, for example, in Goeddel (1990) “Gene Expression Technology,” Methods Enzymol. 185, Academic Press, San Diego, Calif.

A recombinant nucleic acid molecule or vector of the present invention may comprise a selectable marker that confers a selectable phenotype on a transformed cell, such as a plant cell. Selectable markers may also be used to select for plants or plant cells that comprise a nucleic acid molecule of the invention. The marker may encode biocide resistance, antibiotic resistance (e.g., kanamycin, Geneticin (G418), bleomycin, and hygromycin), or herbicide resistance (e.g., glyphosate). Examples of selectable markers include, but are not limited to: a neo gene that confers kanamycin resistance and can be selected for using, e.g., kanamycin and G418; a bar gene that confers bialaphos resistance; a mutant EPSP synthase gene that confers glyphosate resistance; a nitrilase gene that confers resistance to bromoxynil; a mutant acetolactate synthase gene (ALS) that confers imidazolinone or sulfonylurea resistance; and a methotrexate-resistant DHFR gene. Multiple selectable markers are available that confer resistance to chemical agents including, for example and without limitation, ampicillin; bleomycin; chloramphenicol; gentamycin; hygromycin; kanamycin; lincomycin; methotrexate; phosphinothricin; puromycin; spectinomycin; rifampicin; streptomycin; and tetracycline. Examples of such selectable markers are illustrated in, e.g., U.S. Pat. Nos. 5,550,318; 5,633,435; 5,780,708 and 6,118,047.

A nucleic acid molecule or vector of the present invention may also or alternatively include a screenable marker. Screenable markers may be used to monitor expression. Exemplary screenable markers include a β-glucuronidase or uidA gene (GUS) which encodes an enzyme for which various chromogenic substrates are known (Jefferson et al. (1987) Plant Mol. Biol. Rep. 5:387-405); an R-locus gene, which encodes a product that regulates the production of anthocyanin pigments (red color) in plant tissues (Dellaporta et al. (1988) “Molecular cloning of the maize R-nj allele by transposon tagging with Ac.” In 18th Stadler Genetics Symposium, P. Gustafson and R. Appels, eds., Plenum, N.Y. (pp. 263-82); a β-lactamase gene (Sutcliffe et al. (1978) Proc. Natl. Acad. Sci. USA 75:3737-41); a gene which encodes an enzyme for which various chromogenic substrates are known (e.g., PADAC, a chromogenic cephalosporin); a luciferase gene (Ow et al. (1986) Science 234:856-9); a xylE gene that encodes a catechol dioxygenase that converts chromogenic catechols (Zukowski et al. (1983) Gene 46(2-3):247-55); an amylase gene (Ikatu et al. (1990) Bio/Technol. 8:241-2); a tyrosinase gene which encodes an enzyme capable of oxidizing tyrosine to DOPA and dopaquinone, which in turn condenses to melanin (Katz et al. (1983) J. Gen. Microbiol. 129:2703-14); and an α-galactosidase.

Suitable methods for transformation of host cells include any method by which DNA can be introduced into a cell, for example and without limitation: by transformation of protoplasts (See, e.g., U.S. Pat. No. 5,508,184); by desiccation/inhibition-mediated DNA uptake (See, e.g., Potrykus et al. (1985) Mol. Gen. Genet. 199:183-8); by electroporation (See, e.g., U.S. Pat. No. 5,384,253); by agitation with silicon carbide fibers (See, e.g., U.S. Pat. Nos. 5,302,523 and 5,464,765); by Agrobacterium-mediated transformation (See, e.g., U.S. Pat. Nos. 5,563,055, 5,591,616, 5,693,512, 5,824,877, 5,981,840, and 6,384,301); and by acceleration of DNA-coated particles (See, e.g., U.S. Pat. Nos. 5,015,580, 5,550,318, 5,538,880, 6,160,208, 6,399,861, and 6,403,865). Through the application of techniques such as these, the cells of virtually any species may be stably transformed. In some embodiments, transforming DNA is integrated into the genome of the host cell. In the case of multicellular species, transgenic cells may be regenerated into a transgenic organism. Any of these techniques may be used to produce a transgenic plant, for example, comprising one or more nucleic acid sequences of the invention in the genome of the transgenic plant.

The most widely-utilized method for introducing an expression vector into plants is based on the natural transformation system of Agrobacterium. A. tumefaciens and A. rhizogenes are plant pathogenic soil bacteria that genetically transform plant cells. The Ti and Ri plasmids of A. tumefaciens and A. rhizogenes, respectively, carry genes responsible for genetic transformation of the plant. The Ti(tumor-inducing)-plasmids contain a large segment, known as T-DNA, which is transferred to transformed plants. Another segment of the Ti plasmid, the vir region, is responsible for T-DNA transfer. The T-DNA region is bordered by left-hand and right-hand borders that are each composed of terminal repeated nucleotide sequences. In some modified binary vectors, the tumor-inducing genes have been deleted, and the functions of the vir region are utilized to transfer foreign DNA bordered by the T-DNA border sequences. The T-region may also contain, for example, a selectable marker for efficient recovery of transgenic plants and cells, and a multiple cloning site for inserting sequences for transfer such as a nucleic acid encoding a fusion protein of the invention.

Thus, in some embodiments, a plant transformation vector is derived from a Ti plasmid of A. tumefaciens (See, e.g., U.S. Pat. Nos. 4,536,475, 4,693,977, 4,886,937, and 5,501,967; and European Patent EP 0 122 791) or a R, plasmid of A. rhizogenes. Additional plant transformation vectors include, for example and without limitation, those described by Herrera-Estrella et al. (1983) Nature 303:209-13; Bevan et al. (1983), supra; Klee et al. (1985) Bio/Technol. 3:637-42; and in European Patent EP 0 120 516, and those derived from any of the foregoing. Other bacteria, such as Sinorhizobium, Rhizobium, and Mesorhizobium that naturally interact with plants can be modified to mediate gene transfer to a number of diverse plants. These plant-associated symbiotic bacteria can be made competent for gene transfer by acquisition of both a disarmed Ti plasmid and a suitable binary vector.

After providing exogenous DNA to recipient cells, transformed cells are generally identified for further culturing and plant regeneration. In order to improve the ability to identify transformed cells, one may desire to employ a selectable or screenable marker gene, as previously set forth, with the vector used to generate the transformant. In the case where a selectable marker is used, transformed cells are identified within the potentially transformed cell population by exposing the cells to a selective agent or agents. In the case where a screenable marker is used, cells may be screened for the desired marker gene trait.

Cells that survive the exposure to the selective agent, or cells that have been scored positive in a screening assay, may be cultured in media that supports regeneration of plants. In some embodiments, any suitable plant tissue culture media (e.g., MS and N6 media) may be modified by including further substances, such as growth regulators. Tissue may be maintained on a basic media with growth regulators until sufficient tissue is available to begin plant regeneration efforts, or following repeated rounds of manual selection, until the morphology of the tissue is suitable for regeneration (e.g., at least 2 weeks), then transferred to media conducive to shoot formation. Cultures are transferred periodically until sufficient shoot formation has occurred. Once shoots are formed, they are transferred to media conducive to root formation. Once sufficient roots are formed, plants can be transferred to soil for further growth and maturity.

A transgenic plant formed using Agrobacterium-dependent transformation methods typically contains a single recombinant DNA sequence inserted into one chromosome. The single recombinant DNA sequence is referred to as a “transgenic event” or “integration event.” Such transgenic plants are heterozygous for the inserted DNA sequence. In some embodiments, a transgenic plant homozygous with respect to a transgene may be obtained by sexually mating (selfing) an independent segregant transgenic plant that contains a single exogenous gene sequence to itself, for example, an F0 plant, to produce F1 seed. One fourth of the F1 seed produced will be homozygous with respect to the transgene. Germinating F1 seed results in plants that can be tested for heterozygosity, typically using a SNP assay or a thermal amplification assay that allows for the distinction between heterozygotes and homozygotes (i.e., a zygosity assay).

In addition to direct transformation of a plant or plant cell with a nucleic acid molecule of the invention, transgenic plants may be prepared in some embodiments by crossing a first plant having at least one transgenic event with a second plant lacking such an event. For example, a nucleic acid molecule comprising a UGE may be introduced into a first plant line that is amenable to transformation, to produce a transgenic plant, which transgenic plant may be crossed with a second plant line to introgress the nucleic acid molecule comprising the UGE into the second plant line.

In some embodiments herein, any GMO may be analyzed. In particular embodiments, the GMO is a genetically-modified plant. A plant material sample that is analyzed using particular systems and methods herein may be any substance that can comprise different and multiple exogenous nucleic acids, for example and without limitation, exogenous nucleic acids that are specific to a genetically modified plant, or having a genetically modified plant origin. In some examples, a sample may be a food, a food ingredient, a food additive, and/or a solid or liquid extract that could comprise material from a GMO. In some examples, nucleic acids may be extracted from the plant material sample prior to analysis.

Genetically modified plants may be a dicot or monocot plant species. Non-limiting examples of plant cells from dicotyledonous plants that may be analyzed according to specific embodiments the invention include: alfalfa; beans; Brassica; broccoli; cabbage; canola; carrot; cauliflower; celery; Chinese cabbage; cotton; cucumber; eggplant; lettuce; melon; pea; pepper; peanut; potato; pumpkin; radish; rapeseed; spinach; soybean; squash; sugarbeet; sunflower; tobacco; tomato; and watermelon. Non-limiting examples of plant cells from monocotyledonous plants that may be transformed according to specific embodiments the invention include: maize; onion; rice; sorghum; wheat; rye; millet; sugarcane; oat; triticale; switchgrass; and turfgrass.

The following examples are provided to illustrate certain particular features and/or embodiments. The examples should not be construed to limit the disclosure to the particular features or embodiments exemplified.

EXAMPLES

Example 1: Design and Construction of Vectors Comprising Unique Genetic Elements for Transgenic Plant Production

Unique, synthetic genetic elements (UGEs) comprising random nucleotide sequences of 15-25 bp were generated using a macro in the Excel® (MICROSOFT) application. A random number series was generated of the desired length comprising digits 1 through 4. Each digit was matched to a specified nucleotide base (e.g., 1=A; 2=C; 3=G; and 4=T) to generate a polynucleotide that was then synthesized by a commercial vendor for cloning manipulations.

The UGEs were each incorporated into a 70-80 bp longer sequence (referred to herein as an amplicon) comprising flanking sequences for binding of universal PCR Forward and Reverse primers. 21 UGEs and 21 related amplicons (each comprising a UGE sequence and flanking universal primer binding sites) were designed and were synthesized into high copy plasmids by a commercial vendor (DNA 2.0; Menlo Park, Calif.). Table 1 lists the sequences of 21 UGEs and the corresponding amplicons.


TABLE 1
Sequences of UGEs and of amplicons comprising a specific 
UGE (underlined) and universal primer binding sites
UGE
No.
UGE Sequence
Amplicon Sequence
 1
TTCAATTCTGGA
TGCAGGTCAATCCCATTGCTTTTGTTCAATTCTGGAAATC
AATCC
CTCTCTGCGATCGCTTCTCGAGGTCATTCATATGCTTG
(SEQ ID NO: 1)
(SEQ ID NO: 22)
 2
AACAAAGGCCCC
TGCAGGTCAATCCCATTGCTTTTGAACAAAGGCCCCAATC
AATC
TCTCTGCGATCGCTTCTCGAGGTCATTCATATGCTTG
(SEQ ID NO: 2)
(SEQ ID NO: 23)
 3
CACCTACCCACC
TGCAGGTCAATCCCATTGCTTTTGCACCTACCCACCCTAC
CTACT
TTCTCTGCGATCGCTTCTCGAGGTCATTCATATGCTTG
(SEQ ID NO: 3)
(SEQ ID NO: 24)
 4
CGTTATCCCGCA
TGCAGGTCAATCCCATTGCTTTTGCGTTATCCCGCATAGT
TAGTAG
AGTCTCTGCGATCGCTTCTCGAGGTCATTCATATGCTTG
(SEQ ID NO: 4)
(SEQ ID NO: 25)
 5
ATTGGTTTGGTG
TGCAGGTCAATCCCATTGCTTTTGATTGGTTTGGTGGTGA
GTGAGAT
GATTCTCTGCGATCGCTTCTCGAGGTCATTCATATGCTTG
(SEQ ID NO: 5)
(SEQ ID NO: 26)
 6
ACGTATCACAGC
TGCAGGTCAATCCCATTGCTTTTGACGTATCACAGCTCCT
TCCTAG
AGTCTCTGCGATCGCTTCTCGAGGTCATTCATATGCTTG
(SEQ ID NO: 6)
(SEQ ID NO: 27)
 7
TTAGTATTGGCA
GGCGCCCGGTATTTGTTAAAAGCGGCTACTTAGTATTGGC
GCAGACC
AGCAGACCTAGTCAAGACGAGCAGTCCGAAGCGATCGC
(SEQ ID NO: 7)
(SEQ ID NO: 28)
 8
CCAATAAGACTG
GGCGCCCGGTATTTGTTAAAAGCGGCCAATAAGACTGAAG
AAGTTGAC
TTGACTAGTCAAGACGAGCAGTCCGAAGCGATCGC
(SEQ ID NO: 8)
(SEQ ID NO: 29)
 9
CTACCTCGATCG
GGCGCCCGGTATTTGTTAAAAGCGGCTACCTCGATCGCCC
CCCATA
ATATAGTCAAGACGAGCAGTCCGAAGCGATCGC
(SEQ ID NO: 9)
(SEQ ID NO: 30)
10
TGTTAGGCTACG
GGCGCCCGGTATTTGTTAAAAGCGGTGTTAGGCTACGATA
ATAGGGTT
GGGTTTAGTCAAGACGAGCAGTCCGAAGCGATCGC
(SEQ ID NO: 10)
(SEQ ID NO: 31)
11
TACGCGCTTCAT
GGCGCCCGGTATTTGTTAAAAGCGGTACGCGCTTCATCCT
CCTA
ATAGTCAAGACGAGCAGTCCGAAGCGATCGC
(SEQ ID NO: 11)
(SEQ ID NO: 32)
12
CGACTCATCAAA
GGCGCCCGGTATTTGTTAAAAGCGGCGACTCATCAAACAC
CACGATT
GATTTAGTCAAGACGAGCAGTCCGAAGCGATCGC
(SEQ ID NO: 12)
(SEQ ID NO: 33)
13
ACAATTCTCACT
GGCGCCCGGTATTTGTTAAAAGCGGACAATTCTCACTTTC
TTCGTCTAT
GTCTATTAGTCAAGACGAGCAGTCCGAAGCGATCGC
(SEQ ID NO: 13)
(SEQ ID NO: 34)
14
CACCCGCATCAT
GGCGCCCGGTATTTGTTAAAAGCGGCACCCGCATCATGTA
GTAGA
GATAGTCAAGACGAGCAGTCCGAAGCGATCGC
(SEQ ID NO: 14)
(SEQ ID NO: 35)
15
CTCGTACGCGTG
GGCGCCCGGTATTTGTTAAAAGCGGCTCGTACGCGTGGAA
GAAA
ATAGTCAAGACGAGCAGTCCGAAGCGATCGC
(SEQ ID NO: 15)
(SEQ ID NO: 36)
16
TTAGTCAAAGAC
GGCGCCCGGTATTTGTTAAAAGCGGTTAGTCAAAGACGCC
GCCCGATT
CGATTTAGTCAAGACGAGCAGTCCGAAGCGATCGC
(SEQ ID NO: 16)
(SEQ ID NO: 37)
17
TATTCGCATCTG
GGCGCCCGGTATTTGTTAAAAGCGGTATTCGCATCTGGGC
GGCGAT
GATTAGTCAAGACGAGCAGTCCGAAGCGATCGC
(SEQ ID NO: 17)
(SEQ ID NO: 38)
18
TCCTGAACTTCT
GGCGCCCGGTATTTGTTAAAAGCGGTCCTGAACTTCTACA
ACATAGCT
TAGCTTAGTCAAGACGAGCAGTCCGAAGCGATCGC
(SEQ ID NO: 18)
(SEQ ID NO: 39)
19
ACTGCCAGTTAG
GGCGCCCGGTATTTGTTAAAAGCGGACTGCCAGTTAGCTG
CTGC
CTAGTCAAGACGAGCAGTCCGAAGCGATCGC
(SEQ ID NO: 19)
(SEQ ID NO: 40)
20
TCAGTCGCAACT
GGCGCCCGGTATTTGTTAAAAGCGGTCAGTCGCAACTAGC
AGCGAA
GAATAGTCAAGACGAGCAGTCCGAAGCGATCGC
(SEQ ID NO: 20)
(SEQ ID NO: 41)
21
CGATAGCTTTCG
GGCGCCCGGTATTTGTTAAAAGCGGCGATAGCTTTCGAAG
AAGTACT
TACTTAGTCAAGACGAGCAGTCCGAAGCGATCGC
(SEQ ID NO: 21)
(SEQ ID NO: 42)

Sets of modified high copy plant transformation vectors were constructed by cloning a selected amplicon fragment comprising a UGE, unique to the set, into NarIII and AsiSI sites of a progenitor plant transformation vector (an Agrobacterium binary vector). The amplicon fragments were commonly positioned between the promoter region of a gene designed to serve as a plant selectable marker (e.g., a herbicide tolerance gene) and the (oppositely-oriented) promoter region of a first gene of interest. Often, other genes of interest were also included between the T-DNA borders.

Example 2: Maize Genomic DNA Extraction

Genomic DNA from single maize seed samples was extracted using a modified FastID™ method (FastID™ Genomic DNA 96-well Extraction Kit; GENETIC ID, Fairfield, Iowa). Seed samples were ground using ⅜ inch stainless steel balls in 4 mL polycarbonate vials (OPS Diagnostics LLC, Lebanon, N.J.) on a GENO/GRINDER™ 2010 (SPEX SAMPLEPREP, Metuchen, N.J.) for 2 minutes at 1500 rpm. 1 mL lysis buffer containing Proteinase K (FastID™ Genomic DNA Kit) was added to the single seed ground powder, and the slurry was further homogenized for 20 seconds at 1500 rpm. Vials were centrifuged for 3 minutes at 1450×g and 200 μL supernatant was transferred to KINGFISHER™ 96 well Deep Well plates (Thermo Fisher Scientific Inc., Indianapolis, Ind.) containing binding buffer with magnetic beads (MAGATTRACT™ Suspension G; Qiagen).

Alternatively, in experiments wherein the bulk ground powder was destined for Adventitious Presence testing, 600 μL lysis buffer was added, and the slurry was homogenized for 5 minutes at 1360 rpm on the GENO/GRINDER™ 2010. The samples were spun down for 5 minutes at 6800×g, and 200 μL supernatant was transferred to KINGFISHER™ plates containing the binding buffer with magnetic beads.

In both instances (single seed and bulk ground seed), DNA bound to the magnetic beads was washed and eluted using a KINGFISHER™ automatic DNA extraction platform. DNA was eluted in 200 μL 1×TE buffer (10 mM Tris HCL, 1 mM EDTA, pH 8.0), and was stored at 4° C. until further use. Extracted DNA was quantified using a QUANT-IT™ PICO GREEN DNA assay kit (MOLECULAR PROBES; Invitrogen, Carlsbad, Calif.), and buffer was added to a final concentration of 10 ng/μL.

Example 3: Production of Transgenic Maize Plants

Immature embryos were isolated from ears of Zea mays inbred line B104 when the embryos were about 1.8 to 2.4 mm in length. The embryos were incubated with an Agrobacterium suspension containing acetosyringone and the surfactant, BREAK THRU™ S-233 at an Optical Density of 1.0 for 20 to 30 minutes, and then placed on co-cultivation medium, oriented scutellum-up.

The co-cultivation step was continued for 3 to 4 days, then the embryos were transferred onto plant tissue culture medium containing antibiotics for 7 days to suppress Agrobacterium growth and initiate callus formation. Calli were moved to medium containing an appropriate selection agent to suppress growth of non-transformed tissue for 3 weeks, and then were placed on selection medium containing plant growth hormones for 7 days to induce somatic embryo germination. After one week of exposure to the plant growth hormone medium, calli were placed on a plant regeneration medium with selection.

Plants typically formed within 1 to 2 weeks after being transferred to the plant regeneration medium, and as plantlets developed, they were moved to plant growth medium. 10-15 mg leaf tissue from each plant were sampled for hydrolysis probe PCR analysis of the selectable marker gene (AAD1; U.S. Pat. No. 7,838,733) one week before 30 to 40 low-copy-number events (i.e., 1 to 3 copies of the selectable marker gene) per construct were transferred to the greenhouse for transplantation and growth in greenhouse. All T0 events were de-tasseled and pollinated with B104 pollen for T1 seed production. T1 and T2 plants were self-pollinated to produce homozygous seeds.

Example 4: Detection of Unique Genetic Elements Comprised in a Vector Set

Individual UGEs in plasmid DNA containing the UGE amplicons were detected using a PCR method with a unique hydrolysis oligonucleotide probe. Universal primers were used in the PCR assays for amplification and detection of UGEs from different groups of constructs. Universal primers used to amplify the amplicons listed in Table 1 are described in Table 2. Quenchable fluorescence-based PCR hydrolysis probes were designed to be specifically hybridizable to target UGEs, and were labeled with FAM fluorescence reporter dye (MGBNFQ as quencher). Hydrolysis probe oligonucleotides comprised a nucleotide sequence identical to the UGE to be detected.

Pre-validation of UGEs was carried out by testing serial dilutions of UGE-containing plasmid DNA by themselves, and non-transgenic corn genomic DNA spiked with varying concentrations of UGE-containing plasmid DNA. Thus, primers and hydrolysis probes were also designed to amplify and specifically hybridize to target corn internal controls, ZSSIIb (SEQ ID NO:48) and Invertase (SEQ ID NO:47). Table 3. These control probes were labeled with HEX fluorescence reporter dye (BHQ2 as quencher). Primers and probes were obtained from Applied BioSystems (Carlsbad, Calif.) or Integrated DNA Technologies (Coralville, Iowa). PCR reagents were obtained from Qiagen (Valencia, Calif.).


TABLE 2
Primer pairs and sequences of PCR primers  
used to amplify fragments comprising UGEs  
for hydrolysis probe assays.
Alternative
Used to
Universal
Detect
Primer Sets
Primer Sequence
UGE Nos.
Forward
TGCAGGTCAATCCCATTGC 
1-6
Primer
(SEQ ID NO: 43)
Reverse
CAAGCATATGAATGACCTCGAGAA 
Primer
(SEQ ID NO: 44)
Forward
CGCCCGGTATTTGTTAAAAGC 
7-21
Primer
(SEQ ID NO: 45)
Reverse
CTTCGGACTGCTCGTCTTGAC 
Primer
(SEQ ID NO: 46)


TABLE 3
PCR primer and probe sequences used to 
detect maize internal control genes.
Invertase
Forward Primer
TGGCGGACGACGACTTGT
(SEQ ID NO: 49)
Reverse Primer
AAAGTTTGGAGGCTGCCGT
(SEQ ID NO: 50)
Probe
CGAGCAGACCGCCGTGTACTTCTACC
Oligonucleotide
(SEQ ID NO: 51)
ZSSIIb
Forward Primer
CTCCCAATCCTTTGACATCTGC
(SEQ ID NO: 52)
Reverse Primer
TCGATTTCTCTCTTGGTGACAGG
(SEQ ID NO: 53)
Probe
AGCAAAGTCAGAGCGCTGCAATGCA
Oligonucleotide
(SEQ ID NO: 54)

Validation by Hydrolysis Probe PCR assays demonstrated that individual UGEs were detected with high accuracy, specificity, and efficiency. End-point and real-time PCR techniques were utilized to detect UGEs from plasmids and corn genomic DNA, according to the conditions in Tables 4-5. Biplex PCR assays (TAQMAN®) were performed to detect both the target (UGE) as well as the internal control (Invertase or ZSSIIb).


TABLE 4
Components of the PCR reaction.
Stock
Reagent
Final
Concen-
Volume
Concen-
Component
tration
(μL)
tration
PCR Buffer (with 10 mM MgCl2)
10x
1.5
1.25x
MgCl2
25
mM
1.5
3.125
mM
dNTP mix (10 mM; 2.5 mM
10
mM
1.2
1
mM
each dNTP)
UGE Target-Forward Primer
20
μM
0.3
0.5
μM
UGE Target-Reverse Primer
20
μM
0.3
0.5
μM
UGE Target-FAM-Probe
10
μM
0.06
0.05
μM
Internal Control-Forward
20
μM
0.1
0.167
μM
Primer*
Internal Control-Reverse
20
μM
0.1
0.167
μM
Primer*
Internal Control-HEX-Probe*
10
μM
0.06
0.05
μM
HOTSTART ™ Taq Polymerase
5 U/μL
0.1
0.042 U/μL
Water**
6.78
Total
12 μL
Volume
*As appropriate; included in experiments containing maize genomic DNA.
**As appropriate to adjust total volume to 12 μL

After PCR mixes were made (Table 4), 7 μL of mix (for a 384-well plate) or 12 μL of mix (for a 96-well plate) were transferred into each well, and 3 μL of DNA sample (up to 30 ng/reaction) were added. The PCR plates were sealed with a FLEXISEAL™ membrane, and the reactions were run in a thermocycler.

Different PCR conditions were utilized to detect UGEs in plasmid samples (Table 5a), when the UGE plasmids were spiked into genomic DNA prepared from non-transgenic maize (Table 5b), or when UGEs were assayed in genomic DNA prepared from transgenic maize (Table 5c). In experiments wherein the UGE plasmids were spiked into maize genomic DNA, and when UGEs were assayed in transgenic maize DNA, biplex hydrolysis probe PCR assays were carried out to detect both the UGE and the maize internal control (reference) genes (invertase or ZSSIIb). For end-point PCR reactions, either a C1000 thermocycler (BIORAD) or a PE9700 thermocycler (PERKIN ELMER) was used. For real-time PCR reactions, a LIGHTCYCLER® II thermocycler (ROCHE) was used.


TABLE 5
PCR Reaction Parameters.
Step
Temp. (° C.)
Time
No. Cycles
5a. End-point hydrolysis probe PCR program for detection of
UGEs in plasmid DNAs
Activation
95
 15 min
1
Denaturation
95
30 sec
40
Annealing
52
30 sec
Extension
72
30 sec
Terminal Extension
72
5 min
1
Cooling
4
Hold
1
5b. Real-time hydrolysis probe PCR program for detection of
UGEs in plasmids spiked into non-transgenic maize genomic DNA
Activation
95
 15 min
1
Denaturation
95
30 sec
50
Annealing
52
30 sec
Extension
72
30 sec
Terminal Extension
72
5 min
1
Cooling
4
Hold
1
5c. End-point hydrolysis probe PCR program for detection of
UGEs in transgenic maize genomic DNA
Activation
95
 15 min
1
Denaturation
95
30 sec
40
Annealing
60
30 sec
Extension
72
30 sec
Terminal Extension
72
5 min
1
Cooling
4
Hold
1

Completed PCR plates were read on a PHERASTAR™ FS fluorescence plate reader (BMG LABTECH; Cary, N.C.).

Amplicons comprising one of six UGEs (Table 1; UGE1-UGE6) were synthesized and cloned into high copy number plasmids, and appropriate plasmid DNAs (i.e. pEPP1135 to pEPP1140; corresponding to UGE1-UGE6, respectively) were used for testing PCR amplification and detection efficiency, specificity, and sensitivity in the end-point PCR reactions. Sequences of polynucleotides comprising the six UGEs and flanking elements were aligned in Vector NTI to show the differences in nucleotide sequence. FIG. 1.

Specificity of UGE Detection

Hydrolysis probes (labeled with FAM fluorescent dye) targeting the six UGEs were tested against each of the UGE plasmid DNAs (pEPP1135-pEPP1140). Each designed hydrolysis probe targeting one of the six different UGEs specifically amplified the target UGE (marked with circles), and no non-specific amplification/cross-reactivity was seen from other probes. FIG. 2. The hydrolysis probes were shown to distinguish between all six different UGE-containing cassettes in plasmid DNA (pEPP1135-pEPP1140). Probes were also tested against no template control and negative control corn DNA to rule out any non-specific binding. FIG. 2.

Sensitivity of UGE Detection

Using appropriate UGE template/hydrolysis probe combinations for each of the UGE-containing plasmids, hydrolysis probe assay end-point PCR reactions were performed to determine the level of method sensitivity. Plasmid DNA containing the UGEs was used as template for PCR amplification. Concentrations ranging from 0.0000001 ng to 1 ng plasmid DNA were tested. Results showed that very low concentrations of UGE-containing template DNA can be detected with all the hydrolysis probes. FIG. 3. Probes were also tested against no template control and negative control corn DNA to rule out any non-specific binding. FIG. 3.

Example 5: Specific and Sensitive Detection of Unique Genetic Elements in Maize DNA Detection of UGE DNA in Non-Transgenic Maize Genomic DNA

UGEs (UGE2, UGE3, and UGE7-UGE21) were detected by real-time hydrolysis probe PCR when spiked into a background of maize genomic DNA. Dilutions ranging from 0.0000001 ng to 1 ng were tested. Real-time PCRs were performed using the LIGHTCYCLER™ II thermocycler. Melting curves were analyzed and mean Cp values were calculated for each target DNA dilution. Detection limits determined for each of the UGEs tested are listed in Table 6. Examples of individual assays (detection of UGE3 and UGE4) are shown in FIG. 4 and FIG. 5, respectively. These PCR results demonstrated the feasibility of detecting UGEs with high sensitivity, which suggests that UGEs can provide a novel tool to detect plant transformation constructs.


TABLE 6
Limits of detection for UGEs when spiked into non-transgenic maize
genomic DNA. “Lowest Amount Detected” represents the limit
of detection for each UGE in a hydrolysis probe real-time PCR assay.
UGE No.
Lowest Amount Detected (ng)
2
0.0001
3
0.00001
7
0.0000001
8
0.0000001
9
0.0000001
10
0.0000001
11
0.000001
12
0.0000001
13
0.0000001
14
0.000001
15
0.0000001
16
0.000001
17
0.000001
18
0.0000001
19
0.000001
20
0.0000001
21
0.000001

Detection of UGEs in Genomic DNA from Seeds of Transgenic Maize Plants.

UGE amplicons were further cloned into plant transformation vectors following the strategy described in FIGS. 6-7. Twelve amplicons comprising a UGE were used in 366 plant expression vectors carrying different genes of interest, and nearly 8,000 transgenic events were generated. Table 7.


TABLE 7
Amplicons comprising a UGE incorporated
into plant transformation vectors.
Number of
Number of T1
UGE No.
Constructs
Events with Seeds
1
25
1127
2
26
594
3
20
711
4
23
1048
5
25
997
6
24
939
7
72
538
8
25
922
9
25
800
10
27
150
11
61
12
13
Total
366
7826

Genomic DNA isolated from seeds of heterozygous T1 transgenic events obtained by transformation with constructs that contained UGE2 and UGE3 were used for testing UGE detection (seed sources are listed in Table 8). Genomic DNA was isolated as described earlier. The concentration of the genomic DNA was adjusted to 10 ng/μL, and a total of 30 ng genomic DNA was used for each PCR reaction. Non-transgenic corn seed DNA was used as a negative control.


TABLE 8
Materials used for UGE detections in genomic DNA prepared
from seeds of heterozygous transgenic maize plants.
UGE No.
Seed ID
Event ID
Transforming Plasmid
2
ZT00274311
ZX17897-0859190
pDAB106476
2
ZT00276232
ZX18037-0867761
pDAB106479
2
ZT00328210
ZX18758-0889569
pDAB106529
3
ZT00305360
ZX20077-0912363
pDAB108323
4
ZT00328418
ZX19537-0906115
pDAB108526
4
ZT00297283
ZX19538-0905769
pDAB108527

UGE-specific end-point hydrolysis probe PCR assays were run, and the results were analyzed as a function of normalized fluorescence vs. sample number. FIG. 8. The results showed a sensitive amplification and detection of target UGE sequences from transgenic samples and no amplification from non-transgenic corn samples, thereby demonstrating the specificity of the detection method.

Example 6: Use of Unique Genetic Elements for Adventitious Presence Testing

To test the use of UGEs for adventitious presence detection, T2 homozygous seeds were obtained from transgenic plants produced by transformation with constructs containing UGE3 (seed sources listed in Table 9). In total, 35 homozygous transgenic seeds per event were chosen and genomic DNA was isolated.


TABLE 9
Identities of materials used for UGE3 detection in genomic DNA
prepared from seeds of homozygous T2 transgenic maize plants.
Pedigree
Source ID
B104/
ZQ11LQ199088.0016.016
pDAB108526{ZX19537}0906118.001-B
B104/
ZQ11LQ199111.0092.092
pDAB108526{ZX19537}0906133.001-B
B104/
ZQ11LQ199735.2436.2436
pDAB108527{ZX19538}0907077.001-B
B104/
ZQ11LQ199785.2620.2620
pDAB108527{ZX19698}0907681.001-B
B104/
ZQ11LQ199807.2688.2688
pDAB108528{ZX19737}0908226.001-B
B104/
ZQ11LQ199831.2740.2740
pDAB108528{ZX19737}0908230.001-B

UGE-specific end-point hydrolysis probe PCR assays were run, and the results were analyzed as described in Example 5. The results showed clear amplification of target UGE3 sequences from the homozygous transgenic samples and positive control samples, and no amplification from non-transgenic maize samples (negative controls). FIG. 9.

Samples of maize genomic DNA prepared from 35 homozygous seeds of transgenic Source ID No. ZQ11LQ199088.0016.016 (Table 9) were pooled and serial dilutions (100%, 10%, 1%, 0.5% and 0.1% transgenic DNA) were generated using non-transgenic maize genomic DNA as the background (diluent). Six replicates of each transgenic DNA dilution were run in end-point hydrolysis probe PCR assays (40 cycles).

Results were analyzed as a function of relative fluorescence vs. sample number. FIG. 10. Measured relative fluorescence from all of the dilutions was detected. No non-specific amplification was observed from negative samples (no template control and non-transgenic DNA controls). These results demonstrate that UGEs can be detected in genomic DNA prepared from transgenic maize seeds with extremely high sensitivity and accuracy.

Pools of 100 seed are typically tested for adventitious presence, which requires a suitable detection method to identify a single contaminating transgenic seed among 99 non-transgenic seeds, which equals a 1% sensitivity requirement. A single transgenic T2 corn seed (pDAB108526—Source ID # ZQ11LQ199088.0016.016) containing a UGE (UGE3) was spiked into a pool of 99 non-transgenic corn seeds. Isolated DNA from the seed pool was tested using the end-point hydrolysis probe PCR. Results demonstrated that contaminating seed can be easily detected using the UGE-specific assay (FIG. 11), further strengthening the argument that UGEs can be used for AP testing, and for monitoring transgenic events.

<160> NUMBER OF SEQ ID NOS: 60

<210> SEQ ID NO: 1

<211> LENGTH: 17

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Unique specifically detectable nucleotide

sequence (UGE1)

<400> SEQENCE: 1

ttcaattctg gaaatcc 17

<210> SEQ ID NO: 2

<211> LENGTH: 16

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Unique specifically detectable nucleotide

sequence (UGE2)

<400> SEQENCE: 2

aacaaaggcc ccaatc 16

<210> SEQ ID NO: 3

<211> LENGTH: 17

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Unique specifically detectable nucleotide

sequence (UGE3)

<400> SEQENCE: 3

cacctaccca ccctact 17

<210> SEQ ID NO: 4

<211> LENGTH: 18

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Unique specifically detectable nucleotide

sequence (UGE4)

<400> SEQENCE: 4

cgttatcccg catagtag 18

<210> SEQ ID NO: 5

<211> LENGTH: 19

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Unique specifically detectable nucleotide

sequence (UGE5)

<400> SEQENCE: 5

attggtttgg tggtgagat 19

<210> SEQ ID NO: 6

<211> LENGTH: 18

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Unique specifically detectable nucleotide

sequence (UGE6)

<400> SEQENCE: 6

acgtatcaca gctcctag 18

<210> SEQ ID NO: 7

<211> LENGTH: 19

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Unique specifically detectable nucleotide

sequence (UGE7)

<400> SEQENCE: 7

ttagtattgg cagcagacc 19

<210> SEQ ID NO: 8

<211> LENGTH: 20

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Unique specifically detectable nucleotide

sequence (UGE8)

<400> SEQENCE: 8

ccaataagac tgaagttgac 20

<210> SEQ ID NO: 9

<211> LENGTH: 18

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Unique specifically detectable nucleotide

sequence (UGE9)

<400> SEQENCE: 9

ctacctcgat cgcccata 18

<210> SEQ ID NO: 10

<211> LENGTH: 20

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Unique specifically detectable nucleotide

sequence (UGE10)

<400> SEQENCE: 10

tgttaggcta cgatagggtt 20

<210> SEQ ID NO: 11

<211> LENGTH: 16

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Unique specifically detectable nucleotide

sequence (UGE11)

<400> SEQENCE: 11

tacgcgcttc atccta 16

<210> SEQ ID NO: 12

<211> LENGTH: 19

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Unique specifically detectable nucleotide

sequence (UGE12)

<400> SEQENCE: 12

cgactcatca aacacgatt 19

<210> SEQ ID NO: 13

<211> LENGTH: 21

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Unique specifically detectable nucleotide

sequence (UGE13)

<400> SEQENCE: 13

acaattctca ctttcgtcta t 21

<210> SEQ ID NO: 14

<211> LENGTH: 17

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Unique specifically detectable nucleotide

sequence (UGE14)

<400> SEQENCE: 14

cacccgcatc atgtaga 17

<210> SEQ ID NO: 15

<211> LENGTH: 16

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Unique specifically detectable nucleotide

sequence (UGE15)

<400> SEQENCE: 15

ctcgtacgcg tggaaa 16

<210> SEQ ID NO: 16

<211> LENGTH: 20

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Unique specifically detectable nucleotide

sequence (UGE16)

<400> SEQENCE: 16

ttagtcaaag acgcccgatt 20

<210> SEQ ID NO: 17

<211> LENGTH: 18

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Unique specifically detectable nucleotide

sequence (UGE17)

<400> SEQENCE: 17

tattcgcatc tgggcgat 18

<210> SEQ ID NO: 18

<211> LENGTH: 20

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Unique specifically detectable nucleotide

sequence (UGE18)

<400> SEQENCE: 18

tcctgaactt ctacatagct 20

<210> SEQ ID NO: 19

<211> LENGTH: 16

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Unique specifically detectable nucleotide

sequence (UGE19)

<400> SEQENCE: 19

actgccagtt agctgc 16

<210> SEQ ID NO: 20

<211> LENGTH: 18

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Unique specifically detectable nucleotide

sequence (UGE20)

<400> SEQENCE: 20

tcagtcgcaa ctagcgaa 18

<210> SEQ ID NO: 21

<211> LENGTH: 19

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Unique specifically detectable nucleotide

sequence (UGE21)

<400> SEQENCE: 21

cgatagcttt cgaagtact 19

<210> SEQ ID NO: 22

<211> LENGTH: 78

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Amplicon 1

<400> SEQENCE: 22

tgcaggtcaa tcccattgct tttgttcaat tctggaaatc ctctctgcga tcgcttctcg 60

aggtcattca tatgcttg 78

<210> SEQ ID NO: 23

<211> LENGTH: 77

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Amplicon 2

<400> SEQENCE: 23

tgcaggtcaa tcccattgct tttgaacaaa ggccccaatc tctctgcgat cgcttctcga 60

ggtcattcat atgcttg 77

<210> SEQ ID NO: 24

<211> LENGTH: 78

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Amplicon 3

<400> SEQENCE: 24

tgcaggtcaa tcccattgct tttgcaccta cccaccctac ttctctgcga tcgcttctcg 60

aggtcattca tatgcttg 78

<210> SEQ ID NO: 25

<211> LENGTH: 79

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Amplicon 4

<400> SEQENCE: 25

tgcaggtcaa tcccattgct tttgcgttat cccgcatagt agtctctgcg atcgcttctc 60

gaggtcattc atatgcttg 79

<210> SEQ ID NO: 26

<211> LENGTH: 80

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Amplicon 5

<400> SEQENCE: 26

tgcaggtcaa tcccattgct tttgattggt ttggtggtga gattctctgc gatcgcttct 60

cgaggtcatt catatgcttg 80

<210> SEQ ID NO: 27

<211> LENGTH: 79

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Amplicon 6

<400> SEQENCE: 27

tgcaggtcaa tcccattgct tttgacgtat cacagctcct agtctctgcg atcgcttctc 60

gaggtcattc atatgcttg 79

<210> SEQ ID NO: 28

<211> LENGTH: 78

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Amplicon 7

<400> SEQENCE: 28

ggcgcccggt atttgttaaa agcggctact tagtattggc agcagaccta gtcaagacga 60

gcagtccgaa gcgatcgc 78

<210> SEQ ID NO: 29

<211> LENGTH: 75

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Amplicon 8

<400> SEQENCE: 29

ggcgcccggt atttgttaaa agcggccaat aagactgaag ttgactagtc aagacgagca 60

gtccgaagcg atcgc 75

<210> SEQ ID NO: 30

<211> LENGTH: 73

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Amplicon 9

<400> SEQENCE: 30

ggcgcccggt atttgttaaa agcggctacc tcgatcgccc atatagtcaa gacgagcagt 60

ccgaagcgat cgc 73

<210> SEQ ID NO: 31

<211> LENGTH: 75

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Amplicon 10

<400> SEQENCE: 31

ggcgcccggt atttgttaaa agcggtgtta ggctacgata gggtttagtc aagacgagca 60

gtccgaagcg atcgc 75

<210> SEQ ID NO: 32

<211> LENGTH: 71

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Amplicon 11

<400> SEQENCE: 32

ggcgcccggt atttgttaaa agcggtacgc gcttcatcct atagtcaaga cgagcagtcc 60

gaagcgatcg c 71

<210> SEQ ID NO: 33

<211> LENGTH: 74

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Amplicon 12

<400> SEQENCE: 33

ggcgcccggt atttgttaaa agcggcgact catcaaacac gatttagtca agacgagcag 60

tccgaagcga tcgc 74

<210> SEQ ID NO: 34

<211> LENGTH: 76

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Amplicon 13

<400> SEQENCE: 34

ggcgcccggt atttgttaaa agcggacaat tctcactttc gtctattagt caagacgagc 60

agtccgaagc gatcgc 76

<210> SEQ ID NO: 35

<211> LENGTH: 72

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Amplicon 14

<400> SEQENCE: 35

ggcgcccggt atttgttaaa agcggcaccc gcatcatgta gatagtcaag acgagcagtc 60

cgaagcgatc gc 72

<210> SEQ ID NO: 36

<211> LENGTH: 71

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Amplicon 15

<400> SEQENCE: 36

ggcgcccggt atttgttaaa agcggctcgt acgcgtggaa atagtcaaga cgagcagtcc 60

gaagcgatcg c 71

<210> SEQ ID NO: 37

<211> LENGTH: 75

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Amplicon 16

<400> SEQENCE: 37

ggcgcccggt atttgttaaa agcggttagt caaagacgcc cgatttagtc aagacgagca 60

gtccgaagcg atcgc 75

<210> SEQ ID NO: 38

<211> LENGTH: 73

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Amplicon 17

<400> SEQENCE: 38

ggcgcccggt atttgttaaa agcggtattc gcatctgggc gattagtcaa gacgagcagt 60

ccgaagcgat cgc 73

<210> SEQ ID NO: 39

<211> LENGTH: 75

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Amplicon 18

<400> SEQENCE: 39

ggcgcccggt atttgttaaa agcggtcctg aacttctaca tagcttagtc aagacgagca 60

gtccgaagcg atcgc 75

<210> SEQ ID NO: 40

<211> LENGTH: 71

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Amplicon 19

<400> SEQENCE: 40

ggcgcccggt atttgttaaa agcggactgc cagttagctg ctagtcaaga cgagcagtcc 60

gaagcgatcg c 71

<210> SEQ ID NO: 41

<211> LENGTH: 73

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Amplicon 20

<400> SEQENCE: 41

ggcgcccggt atttgttaaa agcggtcagt cgcaactagc gaatagtcaa gacgagcagt 60

ccgaagcgat cgc 73

<210> SEQ ID NO: 42

<211> LENGTH: 74

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Amplicon 21

<400> SEQENCE: 42

ggcgcccggt atttgttaaa agcggcgata gctttcgaag tacttagtca agacgagcag 60

tccgaagcga tcgc 74

<210> SEQ ID NO: 43

<211> LENGTH: 19

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Universal forward primer

<400> SEQENCE: 43

tgcaggtcaa tcccattgc 19

<210> SEQ ID NO: 44

<211> LENGTH: 24

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Universal reverse primer

<400> SEQENCE: 44

caagcatatg aatgacctcg agaa 24

<210> SEQ ID NO: 45

<211> LENGTH: 21

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Universal forward primer

<400> SEQENCE: 45

cgcccggtat ttgttaaaag c 21

<210> SEQ ID NO: 46

<211> LENGTH: 21

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Universal reverse primer

<400> SEQENCE: 46

cttcggactg ctcgtcttga c 21

<210> SEQ ID NO: 47

<211> LENGTH: 4233

<212> TYPE: DNA

<213> ORGANISM: Zea mays

<400> SEQENCE: 47

agcctggtgt ttccggagga gacagacatg atccctgccg ttgctgatcc gacgacgctg 60

gacggcgggg gcgcgcgcag gccgttgctc ccggagacgg accctcgggg gcgtgctgcc 120

gccggcgccg agcagaagcg gccgccggct acgccgaccg ttctcaccgc cgtcgtctcc 180

gccgtgctcc tgctcgtcct cgtggcggtc acagtcctcg cgtcgcagca cgtcgacggg 240

caggctgggg gcgttcccgc gggcgaagat gccgtcgtcg tcgaggtggc cgcctcccgt 300

ggcgtggctg agggcgtgtc ggagaagtcc acggccccgc tcctcggctc cggcgcgctc 360

caggacttct cctggaccaa cgcgatgctg gcgtggcagc gcacggcgtt ccacttccag 420

ccccccaaga actggatgaa cggttagttg gacccgtcgc catcggtgac gacgcgcgga 480

tcgttttttt cttttttcct ctcgttctgg ctctaacttg gttccgcgtt tctgtcacgg 540

acgcctcgtg cacatggcga tacccgatcc gccggccgcg tatatctatc tacctcgacc 600

ggcttctcca gatccgaacg gtaagttgtt ggctccgata cgatcgatca catgtgagct 660

cggcatgctg cttttctgcg cgtgcatgcg gctcctagca ttccacgtcc acgggtcgtg 720

acatcaatgc acgatataat cgtatcggta cagagatatt gtcccatcag ctgctagctt 780

tcgcgtattg atgtcgtgac attttgcacg caggtccgct gtatcacaag ggctggtacc 840

acctcttcta ccagtggaac ccggactccg cggtatgggg caacatcacc tggggccacg 900

ccgtctcgcg cgacctcctc cactggctgc acctaccgct ggccatggtg cccgatcacc 960

cgtacgacgc caacggcgtc tggtccgggt cggcgacgcg cctgcccgac ggccggatcg 1020

tcatgctcta cacgggctcc acggcggagt cgtcggcgca ggtgcagaac ctcgcggagc 1080

cggccgacgc gtccgacccg ctgctgcggg agtgggtcaa gtcggacgcc aacccggtgc 1140

tggtgccgcc gccgggcatc gggccgacgg acttccgcga cccgacgacg gcgtgtcgga 1200

cgccggccgg caacgacacg gcgtggcggg tcgccatcgg gtccaaggac cgggaccacg 1260

cggggctggc gctggtgtac cggacggagg acttcgtgcg gtacgacccg gcgccggcgc 1320

tgatgcacgc cgtgccgggc accggcatgt gggagtgcgt ggacttctac ccggtggccg 1380

cgggatcagg cgccgcggcg ggcagcgggg acgggctgga gacgtccgcg gcgccgggac 1440

ccggggtgaa gcacgtgctc aaggctagcc tcgacgacga caagcacgac tactacgcga 1500

tcggcaccta cgacccggcg acggacacct ggacccccga cagcgcggag gacgacgtcg 1560

ggatcggcct ccggtacgac tatggcaagt actacgcgtc gaagaccttc tacgaccccg 1620

tccttcgccg gcgggtgctc tgggggtggg tcggcgagac cgacagcgag cgcgcggaca 1680

tcctcaaggg ctgggcatcc gtgcaggtac gtctcagggt ttgaggctag catggcttca 1740

atcttgctgg catcgaatca ttaatgggca gatattataa cttgataatc tgggttggtt 1800

gtgtgtggtg gggatggtga cacacgcgcg gtaataatgt agctaagctg gttaaggatg 1860

agtaatgggg ttgcgtataa acgacagctc tgctaccatt acttctgaca cccgattgaa 1920

ggagacaaca gtaggggtag ccggtagggt tcgtcgactt gccttttctt ttttcctttg 1980

ttttgttgtg gatcgtccaa cacaaggaaa ataggatcat ccaacaaaca tggaagtaat 2040

cccgtaaaac atttctcaag gaaccatcta gctagacgag cgtggcatga tccatgcatg 2100

cacaaacact agataggtct ctgcagctgt gatgttcctt tacatatacc accgtccaaa 2160

ctgaatccgg tctgaaaatt gttcaagcag agaggccccg atcctcacac ctgtacacgt 2220

ccctgtacgc gccgtcgtgg tctcccgtga tcctgccccg tcccctccac gcggccacgc 2280

ctgctgcagc gctctgtaca agcgtgcacc acgtgagaat ttccgtctac tcgagcctag 2340

tagttagacg ggaaaacgag aggaagcgca cggtccaagc acaacacttt gcgcgggccc 2400

gtgacttgtc tccggttggc tgagggcgcg cgacagagat gtatggcgcc gcggcgtgtc 2460

ttgtgtcttg tcttgcctat acaccgtagt cagagactgt gtcaaagccg tccaacgaca 2520

atgagctagg aaacgggttg gagagctggg ttcttgcctt gcctcctgtg atgtctttgc 2580

cttgcatagg gggcgcagta tgtagctttg cgttttactt cacgccaaag gatactgctg 2640

atcgtgaatt attattatta tatatatatc gaatatcgat ttcgtcgctc tcgtggggtt 2700

ttattttcca gactcaaact tttcaaaagg cctgtgtttt agttcttttc ttccaattga 2760

gtaggcaagg cgtgtgagtg tgaccaacgc atgcatggat atcgtggtag actggtagag 2820

ctgtcgttac cagcgcgatg cttgtatatg tttgcagtat tttcaaatga atgtctcagc 2880

tagcgtacag ttgaccaagt cgacgtggag ggcgcacaac agacctctga cattattcac 2940

ttttttttta ccatgccgtg cacgtgcagt caatccccag gacggtcctc ctggacacga 3000

agacgggcag caacctgctc cagtggccgg tggtggaggt ggagaacctc cggatgagcg 3060

gcaagagctt cgacggcgtc gcgctggacc gcggatccgt cgtgcccctc gacgtcggca 3120

aggcgacgca ggtgacgccg cacgcagcct gctgcagcga acgaactcgc gcgttgccgg 3180

cccgcggcca gctgacttag tttctctggc tgatcgaccg tgtgcctgcg tgcgtgcagt 3240

tggacatcga ggctgtgttc gaggtggacg cgtcggacgc ggcgggcgtc acggaggccg 3300

acgtgacgtt caactgcagc accagcgcag gcgcggcggg ccggggcctg ctcggcccgt 3360

tcggccttct cgtgctggcg gacgacgact tgtccgagca gaccgccgtg tacttctacc 3420

tgctcaaggg cacggacggc agcctccaaa ctttcttctg ccaagacgag ctcaggtatg 3480

tatgttatga cttatgacca tgcatgcatg cgcatttctt agctaggctg tgaagcttct 3540

tgttgagttg tttcacagat gcttaccgtc tgctttgttt cgtatttcga ctaggcatcc 3600

aaggcgaacg atctggttaa gagagtatac gggagcttgg tccctgtgct agatggggag 3660

aatctctcgg tcagaatact ggtaagtttt tacagcgcca gccatgcatg tgttggccag 3720

ccagctgctg gtactttgga cactcgttct tctcgcactg ctcattattg cttctgatct 3780

ggatgcacta caaattgaag gttgaccact ccatcgtgga gagctttgct caaggcggga 3840

ggacgtgcat cacgtcgcga gtgtacccca cacgagccat ctacgactcc gcccgcgtct 3900

tcctcttcaa caacgccaca catgctcacg tcaaagcaaa atccgtcaag atctggcagc 3960

tcaactccgc ctacatccgg ccatatccgg caacgacgac ttctctatga ctaaattaag 4020

tgacggacag ataggcgata ttgcatactt gcatcatgaa ctcatttgta caacagtgat 4080

tgtttaattt atttgctgcc ttccttatcc ttcttgtgaa actatatggt acacacatgt 4140

atcattaggt ctagtagtgt tgttgcaaag acacttagac accagaggtt ccaggagtat 4200

cagagataag gtataagagg gagcagggag cag 4233

<210> SEQ ID NO: 48

<211> LENGTH: 2480

<212> TYPE: DNA

<213> ORGANISM: Zea mays

<400> SEQENCE: 48

gcggccgcct ggtaggcgct ggtacaagcg gaagcagcag tagcgtgagg catccccatg 60

ccgggggcaa tctcttcctc gtcgtcggct tttctcctcc ccgtcgcgtc ctcctcgccg 120

cggcgcaggc ggggcagtgt gggtgctgct ctgcgctcgt acggctacag cggcgcggag 180

ctgcggttgc attgggcgcg gcggggcccg cctcaggatg gagcggcgtc ggtacgcgcc 240

gcagcggcac cggccggggg cgaaagcgag gaggcagcga agagctcctc ctcgtcccag 300

gcgggcgctg ttcagggcag cacggccaag gctgtggatt ctgcttcacc tcccaatcct 360

ttgacatctg ctccgaagca aagtcagagc gctgcaatgc aaaacggaac gagtgggggc 420

agcagcgcga gcaccgccgc gccggtgtcc ggacccaaag ctgatcatcc atcagctcct 480

gtcaccaaga gagaaatcga tgccagtgcg gtgaagccag agcccgcagg tgatgatgct 540

agaccggtgg aaagcatagg catcgctgaa ccggtggatg ctaaggctga tgcagctccg 600

gctacagatg cggcggcgag tgctccttat gacagggagg ataatgaacc tggccctttg 660

gctgggccta atgtgatgaa cgtcgtcgtg gtggcttctg aatgtgctcc tttctgcaag 720

acaggtggcc ttggagatgt cgtgggtgct ttgcctaagg ctctggcgag gagaggacac 780

cgtgttatgg tcgtgatacc aagatatgga gagtatgccg aagcccggga tttaggtgta 840

aggagacgtt acaaggtagc tggacaggat tcagaagtta cttattttca ctcttacatt 900

gatggagttg attttgtatt cgtagaagcc cctcccttcc ggcaccggca caataatatt 960

tatgggggag aaagattgga tattttgaag cgcatgattt tgttctgcaa ggccgctgtt 1020

gaggttccat ggtatgctcc atgtggcggt actgtctatg gtgatggcaa cttagttttc 1080

attgctaatg attggcatac cgcacttctg cctgtctatc taaaggccta ttaccgggac 1140

aatggtttga tgcagtatgc tcgctctgtg cttgtgatac acaacattgc tcatcagggt 1200

cgtggccctg tagacgactt cgtcaatttt gacttgcctg aacactacat cgaccacttc 1260

aaactgtatg acaacattgg tggggatcac agcaacgttt ttgctgcggg gctgaagacg 1320

gcagaccggg tggtgaccgt tagcaatggc tacatgtggg agctgaagac ttcggaaggc 1380

gggtggggcc tccacgacat cataaaccag aacgactgga agctgcaggg catcgtgaac 1440

ggcatcgaca tgagcgagtg gaaccccgct gtggacgtgc acctccactc cgacgactac 1500

accaactaca cgttcgagac gctggacacc ggcaagcggc agtgcaaggc cgccctgcag 1560

cggcagctgg gcctgcaggt ccgcgacgac gtgccactga tcgggttcat cgggcggctg 1620

gaccaccaga agggcgtgga catcatcgcc gacgcgatcc actggatcgc ggggcaggac 1680

gtgcagctcg tgatgctggg caccgggcgg gccgacctgg aggacatgct gcggcggttc 1740

gagtcggagc acagcgacaa ggtgcgcgcg tgggtggggt tctcggtgcc cctggcgcac 1800

cgcatcacgg cgggcgcgga catcctgctg atgccgtcgc ggttcgagcc gtgcgggctg 1860

aaccagctct acgccatggc gtacgggacc gtgcccgtgg tgcacgccgt gggggggctc 1920

cgggacacgg tggcgccgtt cgacccgttc aacgacaccg ggctcgggtg gacgttcgac 1980

cgcgcggagg cgaaccggat gatcgacgcg ctctcgcact gcctcaccac gtaccggaac 2040

tacaaggaga gctggcgcgc ctgcagggcg cgcggcatgg ccgaggacct cagctgggac 2100

cacgccgccg tgctgtatga ggacgtgctc gtcaaggcga agtaccagtg gtgagcgaat 2160

taattggcga cgcgacgccg ctcctgtcgc aggacctgga cgttatttag aaggctcttc 2220

tccctggcgg ctttgatgcg tgcgtcgcat ttgcgccggg cggacgggcg acggtggttg 2280

gcctaccgcc tacgtcggct gcgtgccctg ggaatttggg cgggcacgat gatgccactg 2340

ggcaccgggc gcggggtagt atgatatgaa accgacggcg atggagatga ggcgcatggc 2400

attttcccac tgataaatgg ggagttgtat gctactttaa tatcgccact cctgttagta 2460

tttatattga tggcggccgc 2480

<210> SEQ ID NO: 49

<211> LENGTH: 18

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Forward invertase primer

<400> SEQENCE: 49

tggcggacga cgacttgt 18

<210> SEQ ID NO: 50

<211> LENGTH: 19

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Reverse invertase primer

<400> SEQENCE: 50

aaagtttgga ggctgccgt 19

<210> SEQ ID NO: 51

<211> LENGTH: 26

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Invertase probe oligonucleotide

<400> SEQENCE: 51

cgagcagacc gccgtgtact tctacc 26

<210> SEQ ID NO: 52

<211> LENGTH: 22

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Forward ZSSIIb primer

<400> SEQENCE: 52

ctcccaatcc tttgacatct gc 22

<210> SEQ ID NO: 53

<211> LENGTH: 23

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Reverse ZSSIIb primer

<400> SEQENCE: 53

tcgatttctc tcttggtgac agg 23

<210> SEQ ID NO: 54

<211> LENGTH: 25

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: ZSSIIb probe oligonucleotide

<400> SEQENCE: 54

agcaaagtca gagcgctgca atgca 25

<210> SEQ ID NO: 55

<211> LENGTH: 84

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Polynucleotide comprising unique genetic

element and flanking universal primer sites

<400> SEQENCE: 55

ggcgcctgca ggtcaatccc attgcttttg ttcaattctg gaaatcctct ctgcgatcgc 60

ttctcgaggt cattcatatg cttg 84

<210> SEQ ID NO: 56

<211> LENGTH: 86

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Polynucleotide comprising unique genetic

element and flanking universal primer sites

<400> SEQENCE: 56

ggcgcctgca ggtcaatccc attgcttttg attggtttgg tggtgagatt ctctgcgatc 60

gcttctcgag gtcattcata tgcttg 86

<210> SEQ ID NO: 57

<211> LENGTH: 83

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Polynucleotide comprising unique genetic

element and flanking universal primer sites

<400> SEQENCE: 57

ggcgcctgca ggtcaatccc attgcttttg aacaaaggcc ccaatctctc tgcgatcgct 60

tctcgaggtc attcatatgc ttg 83

<210> SEQ ID NO: 58

<211> LENGTH: 84

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Polynucleotide comprising unique genetic

element and flanking universal primer sites

<400> SEQENCE: 58

ggcgcctgca ggtcaatccc attgcttttg cacctaccca ccctacttct ctgcgatcgc 60

ttctcgaggt cattcatatg cttg 84

<210> SEQ ID NO: 59

<211> LENGTH: 85

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Polynucleotide comprising unique genetic

element and flanking universal primer sites

<400> SEQENCE: 59

ggcgcctgca ggtcaatccc attgcttttg cgttatcccg catagtagtc tctgcgatcg 60

cttctcgagg tcattcatat gcttg 85

<210> SEQ ID NO: 60

<211> LENGTH: 85

<212> TYPE: DNA

<213> ORGANISM: Artificial Sequence

<220> FEATURE:

<223> OTHER INFORMATION: Polynucleotide comprising unique genetic

element and flanking universal primer sites

<400> SEQENCE: 60

ggcgcctgca ggtcaatccc attgcttttg acgtatcaca gctcctagtc tctgcgatcg 60

cttctcgagg tcattcatat gcttg 85

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Patent Valuation

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20.05/100 Score

Market Attractiveness

It shows from an IP point of view how many competitors are active and innovations are made in the different technical fields of the company. On a company level, the market attractiveness is often also an indicator of how diversified a company is. Here we look into the commercial relevance of the market.

66.0/100 Score

Market Coverage

It shows the sizes of the market that is covered with the IP and in how many countries the IP guarantees protection. It reflects a market size that is potentially addressable with the invented technology/formulation with a legal protection which also includes a freedom to operate. Here we look into the size of the impacted market.

70.91/100 Score

Technology Quality

It shows the degree of innovation that can be derived from a company’s IP. Here we look into ease of detection, ability to design around and significance of the patented feature to the product/service.

78.0/100 Score

Assignee Score

It takes the R&D behavior of the company itself into account that results in IP. During the invention phase, larger companies are considered to assign a higher R&D budget on a certain technology field, these companies have a better influence on their market, on what is marketable and what might lead to a standard.

20.95/100 Score

Legal Score

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Citation

Patents Cited in This Cited by
Title Current Assignee Application Date Publication Date
Methods and kits for detecting genetically modified organism (GMO) ASIAGEN CORPORATION 08 June 2005 14 December 2006
Identification and/or quantification method of nucleotide sequence(s) elements specific of genetically modified plants on arrays EPPENDORF ARRAY TECHNOLOGIES S.A. 23 April 2009 24 September 2009
Test kit and method for quantitatively detecting genetically modified DNA in foodstuff by means of fluorescence-coupled PCR BIOINSIDE GMBH 03 August 2001 07 August 2003
Fluorescent primer system for detection of nucleic acids (Q priming) TEMASEK LIFE SCIENCES LABORATORY LIMITED 05 December 2006 21 June 2011
Germplasm containing an identifier nucleotide sequence and method for identifying germplasm FFR COOPERATIVE, INC. 20 August 1998 24 December 2002
See full citation <>

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