OA16563A

OA16563A - Cotton transgenic event MON 88701 and methods of use thereof.

Info

Publication number: OA16563A
Application number: OA1201300401
Authority: OA
Inventors: Ronald J. Brinker; Wen C. Burns; Paul C. C. Feng; John A. Kendig; Sherry Leclere; Jennifer Lynn; MALVEN Marianne LUTKE
Original assignee: Monsanto Technology Llc
Priority date: 2011-03-30
Filing date: 2012-03-13
Publication date: 2015-10-22

Abstract

The invention provides cotton event MON 88701, and plants, plant cells, seeds, plant parts, and commodity products comprising event MON 88701. The invention also provides polynucleotides specific for event MON 88701 and plants, plant cells, seeds, plant parts, and commodity products comprising polynucleotides specific for event MON 88701. The invention also provides methods related to event MON 88701.

Description

COTTON TRANSGENIC EVENT MON 88701 AND METHODS

OFUSETHEREOF

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of United States Provisional Application No. 61/469,118, filed on March 30, 2011, herein incorporated by reference in its entirety.

INCORPORATION OF SEQUENCE LISTING

The sequence listing contained in the file named “MONS302WO.txt”, which is 21 kilobytes (size as measured in Microsoft Windows®) and was created on March 9, 2012, is fïled herewith by electronic submission and is incorporated by reference herein.

FIELD OF THE INVENTION

The invention relates to transgenic Gossypium hirsutum event MON 88701. The event exhibits tolérance to dicamba and glufosinate herbicides. The invention also relates to plants, plant parts, plant seeds, plant cells, agricultural products, and methods related to event MON 88701 and provides nucléotide molécules that are unique to the event and were created in connection with the insertion of transgenic DNA into the genome of a Gossypium hirsutum plant.

BACKGROUND OF THE INVENTION

Cotton (Gossypium hirsutum) is an important crop in many areas of the world, and the methods of biotechnology hâve been applied to this crop in order to produce cotton with désirable traits. One such désirable trait is herbicide tolérance. The expression of an herbicide tolérance transgene in a plant can confier the désirable trait of herbicide tolérance on the plant, but expression of the transgene may be influenced by the chromosomal location and the genomic resuit of the transgene insertion. For example, it has been observed in plants that there often is variation in the level and pattern of transgene expression among individual events that differ in the chromosomal insertion site of the transgene but are otherwise identical. There may also be undesirable and/or désirable phenotypic or agronomie différences between events. Because of this, it is often necessary to produce and analyze a large number

I

F of individual plant transformation events in order to select an event having both the désirable trait and the optimal phenotypic and agricultural characteristics necessary to make it suitable for commercial purposes. Such sélection often requires greenhouse and field trials with many events over multiple years, in multiple locations, and under 5 a variety of conditions so that a significant amount of agronomie, phenotypic, and molecular data may be collected. The resulting data and observations must then be analyzed by teams of scientists and agronomists with the goal of selecting a commercially suitable event. Such an event, once selected, may then be used for introgressîng the désirable trait into other genetic backgrounds using plant breeding 10 methods, and thus producing a number of different crop varieties that contain the désirable trait and are suitably adapted to spécifie local growing conditions.

SUMMARY OFTHE INVENTION

The invention provides transgenic cotton plants comprising event

MON 88701, which exhibit commercially acceptable tolérance to applications of 15 dicamba and glufosinate herbicides, having a représentative seed sample deposited with the American Type Culture Collection (ATCC®) under Patent Deposit Désignation PTA-11754. The invention also provides novel DNA molécules related to cotton event MON 88701 and methods of using these molécules. The invention also provides seeds, progeny, plant parts, cells, and commodity products of cotton 20 plants comprising event MON 88701. The invention also provides methods of using cotton event MON 88701 and methods of producing cotton tolérant to both dicamba and glufosinate herbicides.

The invention provides recombinant DNA molécules related to cotton event MON 88701. These recombinant DNA molécules may comprise nucléotide 25 molécules having a nucléotide sequence representing a région of the genomic DNA flanking the transgene insertion, and/or a région of the transgene insertion, and/or a contîguous sequence of any of these régions such as a région of the junction between the transgene insertion and flanking genomic DNA of cotton event MON 88701. The invention also provides DNA molécules useful as primers and probes diagnostic for 30 cotton event MON 88701 and amplîcons diagnostic for the presence of cotton event MON 88701. Cotton plants, plant cells, plant parts, commodity products, progeny, and seeds comprising these molécules are also disclosed.

I

The invention provides methods, compositions, and kits useful for detecting the presence and/or absence of DNA derived from cotton event MON 88701 and thus the presence and/or absence of the event. The invention provides a method for détection of MON 88701 by contacting a sample comprising DNA with a primer set 5 that when used in a nucleic acid amplification reaction with genomic DNA from a cotton plant or seed comprising event MON 88701 produces an amplified DNA diagnostic for cotton event MON 88701, performing a nucleic acid amplification reaction thereby producing the amplified DNA, and detecting the presence and/or absence of the amplified DNA. The invention also provides a method for détection of 10 MON 88701 by contacting a sample comprising DNA with a probe that when used în a hybridization reaction with DNA from cotton event MON 88701 hybridizes to a DNA molécule spécifie for cotton event MON 88701, performing a hybridization reaction, and detecting the hybridization of the probe to the DNA molécule. Kits comprising the methods and compositions of the invention useful for detecting the 15 presence of DNA derived from cotton event MON 88701 are also provided.

The invention provides a cotton plant, seed, plant cell, progeny plant, plant part, or commodity product derived from a plant, plant cell, or seed comprising cotton event MON 88701. The invention also provides a cotton plant, seed, plant cell, progeny plant, plant part, or commodity product comprising a recombinant DNA 20 molécule having a nucléotide sequence selected from the group consisting of SEQ ID NO: 1-10, and compléments and fragments thereof. The invention also provides a cotton plant, seed, plant cell, progeny plant, plant part, or commodity product derived from the plant or seed comprising cotton event MON 88701 and comprising a recombinant DNA molécule that produces an amplified DNA molécule comprising a 25 sequence selected from SEQ ID NO: 1-10 in a DNA amplification method.

The invention provides a method for controliing weeds in a field by planting cotton plants comprising event MON 88701 and then applying an effective dose of dicamba, glufosinate, or both dicamba and glufosinate herbicides capable of controliing the weeds without injuring the cotton event MON 88701 containing 30 plants. The invention also provides a method for controliing weeds in a field by applying an effective dose of at least dicamba, glufosinate, or dicamba and glufosinate herbicides to control weeds in a field and then planting cotton plants comprising event MON 88701 in the field. The invention also provides a method for producing cotton seed or lint essentially free of weed seeds by planting seeds of a dicamba and f

glufosinate tolérant cotton plants comprising MON 88701 in a field, applying to the field a post-emergence effective dose of at least dicamba, glufosinate, or dicamba and glufosinate herbicides sufficient to kill the weed species, and harvesting seed or lint from the field.

The invention provides methods of producing a cotton plant and/or seed that tolérâtes application of dicamba and glufosinate herbicides by sexually crossing a cotton event MON 88701 containing plant comprising a sequence selected from SEQ ID NO: 1-10 with a second cotton plant, thereby producing seed, growing the seed to produce progeny plants, treating the progeny plants with dicamba and/or glufosinate, 10 and selecting a progeny plant that is tolérant to both dicamba and glufosinate. The methods may also include selfing the selected progeny plant to produce a plurality of second génération progeny plants and selecting from these a dicamba and glufosinate tolérant plant. The methods may also include sexually crossing the selected progeny plant with another cotton plant to produce seed, growing the seed to produce a second 15 génération of progeny plants, treating the second génération of progeny plants with dicamba and/or glufosinate, and selecting a second génération progeny plant that is tolérant to dicamba and glufosinate. The invention provides methods of producing a cotton plant and/or seed that tolérâtes application of dicamba and glufosinate herbicides by selfing a dicamba and glufosinate tolérant cotton plant comprising event 20 MON 88701 comprising a sequence selected from SEQ ID NO: 1-10, thereby producing seed, growing the seed to produce progeny plants, treating the progeny plants with dicamba and/or glufosinate; and selecting a progeny plant that is tolérant to dicamba and glufosinate. The invention provides methods of determining the zygosity of a cotton event MON 88701 containing plant or seed comprising 25 contacting a cotton DNA sample with a primer set comprising SEQ ID NO: 11, 12, and 14 and a probe set comprising SEQ ID NO: 13 and 15; then performing a nucleic acid amplification reaction with the sample, primer set, and probe set; then detecting în the nucleic acid amplification reaction a first fluorescent signal that is diagnostic for event MON 88701 and a second fluorescent signal different from the first 30 fluorescent signal and that is diagnostic for native cotton genomic DNA corresponding to the location of insertion of the event MON 88701 transgene; and analyzing the presence and/or absence of the first fluorescent signal and the second fluorescent signal in the nucleic acid amplification reaction, wherein the presence of both fluorescent signais indicates the sample is heterozygous for event MON 88701 and the presence of only the first fluorescent signal indicates the sample is homozygous for event MON 88701. The invention also provides a cotton plant, seed, plant cell, or plant part comprising dicamba and glufosinate tolérance genes mapped on chromosome A08 at the map position of 19.3 cM and bordered by NG0207927 at the map position of 18.6 cM on left and by NG0207529 at the map position of 20.0 cM on right, and methods of using the same. The foregoing and other aspects of the invention will become more apparent from the following detailed description.

BRIEF DESCRIPTION OF THE DRAWINGS

Figure 1 illustrâtes the organization of the transgenic insert in the genome of a cotton plant comprising event MON 88701. [A] corresponds to the relative position of SEQ ID NO: 1; [A’] corresponds to the relative position of SEQ ID NO: 3; [A”] corresponds to the relative position of SEQ ID NO: 5; [B] corresponds to the relative position of SEQ ID NO: 2; [B’J corresponds to the relative position of SEQ ID NO: 4; [B”] corresponds to the relative position of SEQ ID NO: 6; [C] corresponds to the relative position of SEQ ID NO: 7; [D] corresponds to the relative position of SEQ ID NO: 8; [E] corresponds to the relative position of SEQ ID NO: 9; [F] corresponds to the relative position of SEQ ID NO: 10; SQ21654 and SQ23205 correspond to the relative position of primers used to identify cotton event MON 88701.

Figure 2 shows two years of agronomie yield field trial data reported as pounds of seedeotton per acre.

Figure 3 shows first year yield field trial data reported as pounds of seedeotton per acre.

Figure 4 shows second year yield field trial data reported as pounds of seedeotton per acre with increasing amounts of either dicamba (4.A.) or glufosinate (4.B.) herbicide.

Figure 5 shows percentage of necrotic spotting occurring with increasing amounts of either dicamba (5.A.) or glufosinate (5.B.) herbicide.

Figure 6 shows yield field trial data as pounds of seedeotton per acre of the spray regimen for event MON 88701.

Figure 7 shows plants comprising event MON 88701 versus nontransgenic Coker 130 plants sprayed with dicamba and glufosinate in the field. Herbicide applications were 1 lb dicamba (2X) at pre; 1 lb glufosinate (2X) at 2-leaf; 1 lb dicamba at 5-leaf; and 1 lb glufosinate at 8 leaf. —

BRIEF DESCRIPTION OF THE SEQUENCES

SEQ ID NO: 1 is a twenty nucléotide sequence representing the 5’ junction région of cotton genomic DNA and the integrated transgenic expression cassette. SEQ ID NO: 1 is positioned in SEQ ID NO: 10 at nucléotide position 1117-1136.

SEQ ID NO: 2 is a twenty nucléotide sequence representing the 3’ junction région of cotton genomic DNA and the integrated transgenic expression cassette. SEQ ID NO: 2 is positioned in SEQ ID NO: 10 at nucléotide position 5222-5241.

SEQ ID NO: 3 is a sixty nucléotide sequence representing the 5’ junction région of cotton genomic DNA and the integrated transgenic expression cassette.

SEQ ID NO: 4 is a sixty nucléotide sequence representing the 3’ junction région of cotton genomic DNA and the integrated transgenic expression cassette.

SEQ ID NO: 5 is a one-hundred nucléotide sequence representing the 5’ junction région of cotton genomic DNA and the integrated transgenic expression cassette.

SEQ ID NO: 6 is a one-hundred nucléotide sequence representing the 3’ junction région of cotton genomic DNA and the integrated transgenic expression cassette.

SEQ ID NO: 7 is the 5’ sequence flanking the inserted DNA of MON 88701 up to and including a portion of integrated transgenic expression cassette.

SEQ ID NO: 8 is the 3’ sequence flanking the inserted DNA of MON 88701 up to and including a portion of integrated transgenic expression cassette.

SEQ ID NO: 9 is the sequence of the integrated transgenic expression cassette.

SEQ ID NO: 10 is the contiguous nucléotide sequence of the 5’ sequence 25 flanking the inserted DNA (SEQ ID NO: 7), the integrated transgenic expression cassette (SEQ ID NO: 9), and the 3’ sequence flanking the inserted DNA (SEQ ID NO: 8). SEQ ID NO: 10 includes SEQ ID NO: 1 -9.

SEQ ID NO: 11 is the sequence of a primer referred to as Primer SQ21654 and used to identify cotton event MON 88701. It is complimentary to the inserted 30 expression cassette at the région close to the 3’ transgene insertion border, A PCR amplicon produced from a TAQMAN® (PE Applied Biosystems, Foster City, CA) assay using the combination of primers SQ21654 and SQ23205 (SEQ ID NO: 12) is a positive resuit for the presence of the event MON 88701. This primer set may also be used to identity a MON 88701 event in a zygosity assay.

SEQ ID NO: 12 is the sequence of a primer referred to as Primer SQ23205 and used to identify cotton event MON 88701. It is complimentary to a 3’ région flanking the inserted expression cassette and close to the transgene DNA insertion border. A PCR amplicon produced from a TAQMAN® (PE Applied Biosystems, Foster City, CA) assay using the combination of primers SQ21654 (SEQ ID NO: 11) and SQ23205 is a positive resuit for the presence of the event MON 88701. This is also the primer used to identify MON 88701 event and wild-type with a zygosity assay.

SEQ ID NO: 13 is the sequence of a probe referred to as Probe PB 10280 and used to identify cotton event MON 88701. It is complimentary to a région of the inserted expression cassette and adjacent to the 3’ junction of the genomic DNA, This probe is a 6-FAM™-labeled synthetic oligonucleotide. Release of a fluorescent signal in an amplification reaction using primers SQ21654 and SQ23205 (SEQ ID NO: 11-12) in combination with 6-FAM™-labeled probe PB 10280 is diagnostic of event MON 88701 in a TAQMAN® assay. PB 10280 is also the probe used to identify a MON 88701 event in a zygosity assay.

SEQ ID NO: 14 is the sequence of a primer referred to as Primer SQ23901 and used to identify a cotton wild-type allele in a MON 88701 zygosity assay.

SEQ ID NO: 15 is the sequence of a VIC ™-labeled probe referred to as Probe PB 10631 and used to identify a cotton wild-type allele in a MON 88701 zygosity assay.

DETAILED DESCRIPTION

The following définitions and methods are provided to better define the invention and to guide those of ordinary skill in the art in the practice of the invention. Unless otherwise noted, terms are to be understood according to conventional usage by those of ordinary skill in the relevant art.

The invention provides a transgenic cotton event MON 88701 that exhibits commercially acceptable tolérance to applications of dicamba and glufosinate herbicides. The event comprises a single insertion of transgenic DNA into the chromosome/genome of the cotton germplasm. An “event” is produced by: (i) transformation of a plant cell with a nucleic acid construct that includes a transgene of interest, (ii) régénération of a population of plants resulting from the insertion of the transgene into the genome of the plant, and (iii) sélection of a particular plant characterized by insertion of the transgene into a particular location in the plant’s genome.

The term “event” refers to a DNA molécule comprising the inserted DNA and the flanking cotton genomie DNA îmmediately adjacent to either side of the inserted DNA. This DNA molécule is created by the act of inserting the transgenic DNA into the genome of the cotton plant, i.e., by the act of transformation. This DNA molécule therefore comprises a nucléotide sequence that is both spécifie to the event and that is 10 unique to the genome of the cotton plant into which the transgenic DNA has been inserted, in that this nucléotide sequence contains both the sequence of a particular région of cotton genomie DNA and of the transgenic DNA insert. The arrangement of the inserted DNA in cotton event MON 88701 in relation to the surrounding cotton plant genome DNA is therefore spécifie and unique for cotton event MON 88701.

This DNA molécule is also an intégral part of the cotton chromosome of event MON 88701 containing plants and as such is static in the plant and may be passed on to progeny of the plant.

The présent invention also provides the original transformant that includes the transgene inserted into the particular location in the plant’s genome and progeny of 20 the transformant that include the transgene inserted into the particular location in the plant’s genome. Such progeny may be produced by a sexual outeross between the transformant, or its progeny, and another plant. Such other plant may be a transgenic plant comprising the same or different transgene and/or a nontransgenic plant, such as one from a different variety. Even after repeated back-crossing to a récurrent parent, 25 the inserted DNA and flanking DNA from the transformed parent is présent in the progeny of the cross at the same genomie location.

As used herein, the term “cotton” means Gossypium hirsulum and includes ail plant varieties that can be bred with cotton, including wild cotton species as well as those plants belonging to Gossypium that permit breeding between species.

Event MON 88701 comprises an integrated transgenic expression cassette that confers tolérance to applications of dicamba and glufosinate herbicides to the cotton plant. “Dicamba” refers to 3,6-dichloro-2-methoxybenzoic acid. Dicamba is a synthetic auxin herbicide useful for controlling broadleaf weeds. Cotton plants were transformed with a gene (dmo) from Stenotrophomonas maltophilia encoding y/— dicamba mono-oxygenase (DMO). DMO is an enzyme that catalyzes the deactivation of dicamba via an O-demethylation reaction to the nonherbicidal compound 3,5dichlorosalicylic acid. “Glufosînate” refers to 2-amino-4(hydroxymethylphosphinyl)butanoic acid. Glufosînate is an organophosporus herbicide useful for controlling a broad spectrum of annual and perennial grass and broadleaf weeds. Cotton plants were transformed with a Bialaphos Résistance gene (bar) from Streptomyces hygroscopicus encoding phosphinothricin acetyl transferase (PAT). PAT is an enzyme that catalyzes acétylation and thus inactivation of glufosînate.

As used herein, the term “recombinant” refers to a form of DNA and/or protein and/or an organism that would not normally be found in nature and as such was created by human intervention. Such human intervention may produce a recombinant DNA molécule and/or a recombinant plant. As used herein, a “recombinant DNA molécule” is a DNA molécule comprising a combination of DNA molécules that would not naturally occur together and is the resuit of human intervention, e.g., a DNA molécule that is comprised of a combination of at least two DNA molécules heterologous to each other, and/or a DNA molécule that is artificially synthesized and comprises a polynucleotide sequence that deviates from the polynucleotide sequence that would normally exist in nature, and/or a DNA molécule that comprises a transgene artificially incorporated into a host cell’s genomic DNA and the associated flanking DNA of the host cell’s genome. An example of a recombinant DNA molécule is a DNA molécule described herein resulting from the insertion of the transgene into the cotton genomic DNA, which may ultimately resuit in the expression of a recombinant RNA and/or protein molécule in that organism. As used herein, a “recombinant plant” is a plant that would not normally exist in nature, is the resuit of human intervention, and contains a transgene and/or heterologous DNA molécule incorporated into its genome. As a resuit of such genomic alteration, the recombinant plant is distinctly different from the related wildtype plant. An example of a recombinant plant is a cotton plant described herein as comprising event MON 88701.

As used herein, the term “transgene” refers to a nucléotide molécule artificially incorporated into a host cell’s genome. Such transgene may be heterologous to the host cell. The term “transgenic plant” refers to a plant comprising such a transgene.

As used herein, the term “heterologous” refers to a first molécule not normally found in combination with a second molécule in nature. For example, a molécule may be derived from a first species and inserted into the genome of a second species. The molécule would thus be heterologous to the host and artificially incorporated into a host cell’s genome.

As used herein, the term “chimeric” refers to a single DNA molécule produced by fusing a first DNA molécule to a second DNA molécule, where neither first nor second DNA molécule would normally be found in that configuration, i.e., fused to the other. The chimeric DNA molécule is thus a new DNA molécule not otherwise normally found in nature.

The invention provides DNA molécules and their correspondîng nucléotide sequences. As used herein, the term “DNA”, “DNA molécule”, “nucléotide molécule” refers to a DNA molécule of genomic or synthetic origin, i.e., a polymer of deoxyribonucleotide bases or a polynucleotide molécule, read from the 5’ (upstream) end to the 3’ (downstream) end. As used herein, the term “DNA sequence”, “nucléotide sequence” or “polynucleotide sequence” refers to the nucléotide sequence of a DNA molécule. The nomenclature used herein is that required by Title 37 of the United States Code of Fédéral Régulations § 1.822 and set forth in the tables in WIPO Standard ST.25 (1998), Appendix 2, Tables l and 3. By convention, the nucléotide sequences of the invention provided as SEQ ID NOs: l-ΊΟ and fragments thereof are disclosed with reference to only one strand of the two complementary nucléotide sequence strands. By implication, the complementary sequences (i.e. the sequences of the complementary strand), also referred to in the art as the reverse complementary sequences, are within the scope of the invention and are expressly intended to be within the scope of the subject matter claimed.

The nucléotide sequence correspondîng to the complété nucléotide sequence of the inserted transgenic DNA and substantial segments of the cotton genome DNA flanking either end of the inserted transgenic DNA is provided herein as SEQ ID NO: 10. A subsection of this is the inserted transgenic DNA provided as SEQ ID NO: 9. The nucléotide sequence of the cotton genome DNA physically linked by phosphodiester bond linkage to and therefore flanking the 5’ end of the inserted transgenic DNA is set forth as shown in Figure l and provided as SEQ ID NO: 1,3,5, and 7. The nucléotide sequence of the cotton genome DNA physically linked by phosphodiester bond linkage to and therefore flanking the 3’ end of the inserted transgenic DNA is set forth as shown in Figure l and provided as SEQ ID NO: 2, 4, 6, and 8.

The cotton event MON 88701 further comprises two régions, one spanning the 5’ location and one spanning the 3’ location where the transgenic DNA is inserted into the genomic DNA, referred to herein as the 5’ and 3’ junction, respectively. A “junction sequence” or “junction région” refers to the DNA sequence and/or corresponding DNA molécule that spans the inserted transgenic DNA and the adjacent flanking genomic DNA. The junction sequences may be arbitrarily represented by the nucleotîde sequences provided as SEQ ID NO: l and SEQ ID NO: 2, each representing 10 nucléotides of the flanking genomic DNA adjacent to and contiguous with 10 nucléotides of insert DNA. Alternatively, the junction sequences may be arbitrarily represented by the two 60 nucleotîde sequences provided as SEQ ID NO: 3 and SEQ ID NO: 4, each representing 30 nucléotides of the flanking genomic DNA adjacent to and contiguous with 30 nucléotides of insert DNA. Alternatively, the junction sequences may be arbitrarily represented by the two 100 nucleotîde sequences provided as SEQ ID NO: 5 and SEQ ID NO: 6, each representing 50 nucléotides of the flanking genomic DNA adjacent to and contiguous with 50 nucléotides of insert DNA. These nucléotides are connected by phosphodiester linkage and in cotton event MON 88701 are présent as part of the genome. The identification of one or more of SEQ ID NO: 1-10 in a sample derived from a cotton plant, seed, or plant part is determinative that the DNA was obtained from cotton event MON 88701 and is diagnostic for the presence in a sample of DNA from cotton event MON 88701. The invention thus provîdes a DNA molécule that contains at least one of the nucleotîde sequences provided as SEQ ID NO: 1-10. Any segment of DNA derived from transgenic cotton event MON 88701 that is sufficient to include at least one of the sequences provided as provided as SEQ ID NO: 1-10 is within the scope of the invention. In addition, any polynucleotide comprising a sequence complementary to any of the sequences described within this paragraph is within the scope of the invention. Figure 1 illustrâtes the physical arrangement of SEQ ID NO: 1-9 relative to SEQ ID NO: 10 arranged from 5’ to 3’.

The invention provides exemplary DNA molécules that can be used either as primers or probes for diagnosing the presence of DNA derived from a cotton plant comprising event MON 88701 in a sample. Such primers or probes are spécifie for a target nucleic acid sequence and as such are useful for the identification of cotton event MON 88701 nucleic acid sequence by the methods of the invention described herein.

A “primer” is typically a highly purified, isolated polynucleotide that is designed for use in spécifie anneaiing or hybridization methods that involve thermal amplification. A pair of primers may be used with template DNA, such as a sample of cotton genomic DNA, in a thermal amplification, such as polymerase chain reaction (PCR), to produce an amplicon, where the amplicon produced from such reaction would have a DNA sequence corresponding to sequence of the template DNA located between the two sites where the primers hybridized to the template. As used herein, an “amplicon” is a piece or fragment of DNA that has been synthesized using amplification techniques. An amplicon of the invention comprises at least one of the sequences provided as provided as SEQ ID NO: l-ΊΟ. A primer is typically designed to hybridize to a complementary target DNA strand to form a hybrid between the primer and the target DNA strand, and the presence of the primer is a point of récognition by a polymerase to begîn extension of the primer (i.e., polymerization of additional nucléotides into a lengthening nucléotide molécule) using as a template the target DNA strand. Primer pairs, as used in the invention, are intended to refer to use of two primers binding opposite strands of a double stranded nucléotide segment for the purpose of amplifying linearly the polynucleotide segment between the positions targeted for binding by the individual members of the primer pair, typically in a thermal amplification reaction or other conventional nucleic-acid amplification methods. Exemplary DNA molécules useful as primers are provided as SEQ ID NO: 11-12. The primer pair provided as SEQ ID NO: 11 and SEQ ID NO: 12 are useful as a first DNA molécule and a second DNA molécule that is different from the first DNA molécule, and both are each of sufficient length of contiguous nucléotides of SEQ ID NO: 10 to function as DNA primers that, when used together in a thermal amplification reaction with template DNA derived from cotton event MON 88701, to produce an amplicon diagnostic for cotton event MON 88701 DNA in a sample.

A “probe” is an isolated nucleic acid that is complementary to a strand of a target nucleic acid. Probes according to the invention include not only deoxyribonucleic or ribonucleic acids but also polyamides and other probe materials that bind specifically to a target DNA sequence and the détection of such binding can be useful in diagnosing, discriminating, determining, or confirming the presence of that target DNA sequence in a particular sample. A probe may be attached to a conventional détectable label or reporter molécule, e.g., a radioactive isotope, ligand, chemiluminescent agent, or enzyme. An exemplary DNA molécule useful as a probe is provided as SEQ ID NO: 13.

Probes and primers according to the invention may hâve complété sequence identity with the target sequence, although primers and probes differing from the target sequence that retain the ability to hybridize preferentially to target sequences may be designed by conventional methods. In order for a nucleic acid molécule to serve as a primer or probe it need only be sufficiently complementary in sequence to be able to form a stable double-stranded structure under the particular solvent and sait concentrations employed. Any conventional nucleic acid hybridization or amplification method can be used to identify the presence of transgenic DNA from cotton event MON 88701 in a sample. Probes and primers are generally at least about 11 nucléotides, at least about 18 nucléotides, at least about 24 nucléotides, or at least about 30 nucléotides or more in length. Such probes and primers hybridize specifically to a target DNA sequence under stringent hybridization conditions. Conventional stringency conditions are described by Sambrook et al., 1989, and by Haymes et al., In: Nucleic Acid Hybridization, A Practical Approach, IRL Press, Washington, DC (1985). As used herein, two nucleic acid molécules are capable of specifically hybridizîng to one another if the two molécules are capable of forming an anti-parallel, double-stranded nucleic acid structure. A nucleic acid molécule is the “complément” of another nucleic acid molécule if they exhibit complété complementarity. As used herein, two molécules exhibit “complété complementarity” if when aligned every nucléotide of the first molécule is complementary to every nucléotide of the second molécule. Two molécules are “minimally complementary” if they can hybridize to one another with sufficient stability to permit them to remain annealed to one another under at least conventional “low-stringency” conditions. Similarly, the molécules are “complementary” if they can hybridize to one another with sufficient stability to permit them to remain annealed to one another under conventional “high-stringency” conditions. Departures from complété complementarity are therefore permissible, as long as such departures do not completely preclude the capacity of the molécules to form a double-stranded structure.

As used herein, the term “isolated” refers to at least partially separating a thy— molécule from other molécules normally associated with it in its native or natural state. In one embodiment, the term “isolated” refers to a DNA molécule that is at least partially separated from the nucleic acids which normally flank the DNA molécule in its native or natural state. Thus, DNA molécules fused to regulatory or coding sequences with which they are not normally associated, for example as the resuit of recombinant techniques, are considered isolated herein. Such molécules are considered isolated even when integrated into the chromosome of a host cell or présent in a nucleic acid solution with other DNA molécules.

Any number of methods well known to those skilled in the art can be used to isolate and manipulate a DNA molécule, or fragment thereof, disclosed in the invention. For example, PCR (polymerase chain reaction) technology can be used to amplify a particular starting DNA molécule and/or to produce variants of the original molécule. DNA molécules, or fragment thereof, can also be obtained by other techniques such as by directly synthesizing the fragment by chemical means, as is commonly practiced by using an automated oligonucleotide synthesizer.

The DNA molécules and corresponding nucléotide sequences provided herein are therefore useful for, among other things, identifying cotton event MON 88701, selecting plant varieties or hybrids comprising cotton event MON 88701, detecting the presence of DNA derived from the transgenic cotton event MON 88701 in a sample, and monitoring samples for the presence and/or absence of cotton event MON 88701 or plant parts derived from cotton plants comprising event MON 88701.

The invention provides cotton plants, progeny, seeds, plant cells, plant parts (such as pollen, ovule, pod, flower tissue, root tissue, stem tissue, and leaf tissue), and commodity products. These plants, progeny, seeds, plant cells, plant parts, and commodity products contain a détectable amount of a polynucleotide of the invention,

i.e., such as a polynucleotide having at least one of the sequences provided as SEQ ID NO: 1-10. Plants, progeny, seeds, plant cells, and plant parts of the invention may also contain one or more additional transgenes. Such transgene may be any nucléotide sequence encoding a protein or RNA molécule conferring a désirable trait including but not limited to increased insect résistance, increased water use efficiency, increased yield performance, increased drought résistance, increased seed quality, improved nutritional quality, and/or increased herbicide tolérance, in which the désirable trait is measured with respect to a cotton plant lacking such additional transgene.

The invention provides cotton plants, progeny, seeds, plant cells, and plant part such as pollen, ovule, pod, flower, root or stem tissue, and leaves derived from a transgenic cotton plant comprising event MON 88701. A représentative sample of cotton seed comprising event MON 88701 has been deposited according to the Budapest Treaty with the American Type Culture Collection (ATCC®). The ATCC reposîtory has assigned the Patent Deposit Désignation PTA-11754 to the event MON 88701 comprising seed.

The invention provides a microorganism comprising a DNA molécule having at least one sequence selected from SEQ ID NO: 1-10 présent in its genome. An example of such a microorganism is a transgenic plant cell. Microorganisms, such as a plant cell of the invention, are useful in many industrial applications, including but not limited to: (i) use as research tool for scientific inquiry or industrial research; (ii) use in culture for producing endogenous or recombinant carbohydrate, lipid, nucleic acid, or protein products or small molécules that may be used for subséquent scientific research or as industrial products; and (iii) use with modem plant tissue culture techniques to produce transgenic plants or plant tissue cultures that may then be used for agricultural research or production. The production and use of microorganisms such as transgenic plant cells utilizes modem microbiological techniques and human intervention to produce a man-made, unique microorganism. In this process, recombinant DNA is inserted into a plant cell’s genome to create a transgenic plant cell that is separate and unique from naturally occurring plant cells. This transgenic plant cell can then be cultured much like bacteria and yeast cells using modem microbiology techniques and may exist in an undifferentiated, unicellular state. The new plant cell’s genetic composition and phenotype is a technical effect created by the intégration of the heterologous DNA into the genome of the cell. Another aspect of the invention is a method of using a microorganism of the invention. Methods of using microorganisms of the invention, such as transgenic plant cells, include (i) methods of producing transgenic cells by integratîng recombinant DNA into the genome of the cell and then using this cell to dérivé additional cells possessing the same heterologous DNA; (ii) methods of culturing cells that contain recombinant DNA using modem microbiology techniques; (iii) methods of producing and purifying endogenous or recombinant carbohydrate, lipid, nucleic acid, or protein products from cultured cells; and (iv) methods of using modem plant tissue culture — techniques with transgenic plant cells to produce transgenic plants or transgenic plant tissue cultures.

Plants of the invention may pass along the event DNA, including the transgene, to progeny. As used herein, “progeny” includes any plant, seed, plant cell, and/or regenerable plant part comprising the event DNA derived from an ancestor plant and/or comprising a DNA molécule having at least one sequence selected from SEQ ID NO: l-10. Plants, progeny, and seeds may be homozygous or heterozygous for the transgene. Progeny may be grown from seeds produced by a cotton event MON 88701 containing plant and/or from seeds produced by a plant fertilized with pollen from a cotton event MON 88701 containing plant.

Progeny plants may be self-pollinated (also known as “selfing”) to generate a true breeding line of plants, i.e., plants homozygous for the transgene. Selfing of appropriate progeny can produce plants that are homozygous for both added, exogenous genes.

Altematively, progeny plants may be outcrossed, e.g., bred with another unrelated plant, to produce a varietal or a hybrid seed or plant. The other unrelated plant may be transgenic or nontransgenic. A varietal or hybrid seed or plant of the invention may thus be derived by crossing a first parent that lacks the spécifie and unique DNA of the cotton event MON 88701 with a second parent comprising cotton event MON 88701, resulting in a hybrid comprising the spécifie and unique DNA of the cotton event MON 88701. Each parent can be a hybrid or an inbred/varietal, so long as the cross or breeding results in a plant or seed of the invention, i.e., a seed having at least one allele containing the DNA of cotton event MON 88701 and/or a DNA molécule having at least one sequence selected from SEQ ID NO: 1-10. Two different transgenic plants may thus be crossed to produce hybrid offspring that contain two independently segregating, added, exogenous genes. For example, the MON 88701 containing dicamba and glufosinate tolérant cotton can be crossed with other transgenic cotton plants to produce a plant having the characteristics of both transgenic parents. One example of this would be a cross of MON 88701 containing dicamba and glufosinate tolérant cotton with a plant having one or more additional traits such as herbicide tolérance (e.g. cotton event MON 1445 or cotton event MON 88913) and/or insect control (e.g. cotton event MON 15985, MON 757, or MON 531), resulting in a progeny plant or seed that is tolérant to dicamba and glufosinate and has at least one or more additional traits. Back-crossing to a parental plant and out-crossing with a non-transgenic plant are also contemplated, as is végétative propagation. Descriptions of other breeding methods that are commonly used for different traits and crops can be found in one of several references, e.g., Fehr, in Breeding Methods for Cultivar Development, Wilcox J. ed., American Society of Agronomy, Madison WI (1987),

The invention provides a plant part that is derived from cotton plants comprising event MON 88701. As used herein, a “plant part” refers to any part of a plant which is comprised of material derived from a cotton plant comprising event MON 88701. Plant parts include but are not limited to pollen, ovule, pod, flower, root or stem tissue, fibers, and leaves. Plant parts may be viable, nonviable, regenerable, and/or nonregenerable.

The invention provides a commodity product that is derived from cotton plants comprising event MON 88701. As used herein, a “commodity product” refers to any composition or product which is comprised of material derived from a cotton event MON 88701 containing plant, seed, plant cell, or plant part. Commodity products may be sold to consumers and may be viable or nonviable. Nonviable commodity products include but are not limited to nonviable seeds; processed seeds, seed parts, and plant parts; lint; seeds and plant parts processed for feed or food, oil, fiber, paper, biomasses, and fuel products. Viable commodity products include but are not limited to seeds, plants, and plant cells. The cotton plants comprising event MON 88701 can thus be used to manufacture any commodity product typically acquired from cotton. Any such commodity product that is derived from cotton plants comprising event MON 88701 may contain at least a détectable amount of the spécifie and unique DNA corresponding to cotton event MON 88701, and specifically may contain a détectable amount of a polynucleotide comprising a DNA molécule having at least one sequence selected from SEQ ID NO: 1-10. Any standard method of détection for nucléotide molécules may be used, including methods of détection disclosed herein. A commodity product is within the scope of the invention if there is any détectable amount of a DNA molécule having at least one sequence selected from SEQ ID NO: 1-10 in the commodity product.

The plants, progeny, seeds, plant cells, plant parts (such as pollen, ovule, pod, flower, root or stem tissue, and leaves), and commodity products of the invention are therefore useful for, among other things, growing plants for the purpose of producing seed and/or plant parts comprising cotton event MON 88701 for agricultural purposes, producing progeny comprising cotton event MON 88701 for plant breeding and research purposes, use with microbiological techniques for industrial and research applications, and sale to consumers.

The invention provides methods for controlling weeds and methods for producing plants using dicamba and glufosinate herbicides and cotton event MON 88701. A method for controlling weeds in a field is provided and consists of planting cotton event MON 88701 containing varietal or hybrid plants in a field and applying a herbicidally effective dose of dicamba or glufosinate or dicamba and glufosinate to the field for the purpose of controlling weeds in the field without injuring the MON 88701 containing plants. Such application of dicamba or glufosinate or dicamba and glufosinate herbicides may be pre-emergence, i.e., any time after MON 88701 containing seed is planted and before MON 88701 containing plants emerge, or post-emergence, i.e., any time after MON 88701 containing plants emerge. Another method for controlling weeds in a field is also provided and consists of applying an effective dose of dicamba or glufosinate or dicamba and glufosinate herbicides to control weeds in a field and then planting cotton plants comprising event MON 88701 in the field. Such application of dicamba or glufosinate or dicamba and glufosinate herbicides would be pre-planting, i.e., before MON 88701 containing seed is planted, and could be done any time pre-planting including, but not limited to, about 14 days pre-planting to about 1 day pre-planting. The invention also provides a method for producing cotton seed or lint essentially free of weed seeds by planting seeds of a dicamba and glufosinate tolérant cotton plants comprising MON 88701 in a field, applying a post-emergence effective dose of dicamba or glufosinate or dicamba and glufosinate herbicides sufficient to kîll the weed to the field, and harvestîng seed or lint from the field. A herbicidally effective dose of dicamba for use in the field should consist of a range from about 0.005 pounds per acre to about 16 pounds per acre of dicamba over a growing season. In one embodiment, a total of about 0.5 pounds per acre to about 2 pounds per acre of dicamba is applied over a growing season. Multiple applications of dicamba may be used over a growing season, for example, two applications (such as a pre-planting application and a post-emergence application or a pre-emergence application and a post-emergence application) or three applications (such as a pre-planting application, a pre-emergence application, and a post-emergence application). A herbicidally effective dose of glufosinate for use in the field should consist of a range from about 0.005 pounds per acre to about 16 pounds per acre of glufosinate over a growing season. In one embodiment, a total of about 0.5 pounds per acre to about l .59 pounds per acre of glufosinate is applied over a growing season. Multiple applications of glufosinate may be used over a growing season, for example, two applications (such as a pre-planting application and a postemergence application or a pre-emergence application and a post-emergence application) or three applications (such as a pre-planting application, a pre-emergence application, and a post-emergence application or three post-emergence applications).

Methods for producing an herbicide tolérant cotton plant comprising the DNA sequences spécifie and unique to event MON 88701 of the invention are provided. Transgenic plants used in these methods may be homozygous or heterozygous for the transgene. Progeny plants produced by these methods may be varietal or hybrid plants; may be grown from seeds produced by a cotton event MON 88701 containing plant and/or from seeds produced by a plant fertilized with pollen from a cotton event MON 88701 containing plant; and may be homozygous or heterozygous for the transgene. Progeny plants may be subsequently self-pollinated to generate a true breeding line of plants, i.e., plants homozygous for the transgene, or alternatively may be outerossed, e.g., bred with another unrelated plant, to produce a varietal or a hybrid seed or plant.

A cotton plant that tolérâtes application of dicamba and glufosinate herbicides may be produced by sexually crossing an event MON 88701 containing plant comprising a DNA molécule having at least one sequence selected from SEQ ID NO: 1-10 with another cotton plant and thereby producing seed, which is then grown into progeny plants. These progeny plants may then be treated with dicamba and/or glufosinate herbicides to select for progeny plants that are tolérant to dicamba and glufosinate herbicides. Alternatively, these progeny plants may be analyzed using diagnostic methods to select for progeny plants that contain the event MON 88701 DNA. The other plant used in the crossing may or may not be tolérant to dicamba and glufosinate herbicides and may or may not be transgenic. The progeny plant and/or seed produced may be varietal or hybrid seed. In practicîng this method, the step of sexually crossing one plant with another plant, i.e., cross-pollinating, may be accomplished or facilitated by human intervention, for example: by human hands collecting the pollen of one plant and contacting this pollen with the style or stigma of a second plant; by human hands and/or actions removing, destroying, or covering the stamen or anthers of a plant (e.g., by detasseling or by application of a chemîcal gametocide) so that natural self-pollination is prevented and cross-pollination would hâve to take place in order for fertilization to occur; by human placement of pollinating insects in a position for “directed pollination” (e.g., by placing beehives in orchards or fields or by caging plants with pollinating insects); by human opening or 5 removing of parts of the flower to allow for placement or contact of foreign pollen on the style or stigma (e.g., in soy which naturally has flowers that hinder or prevent cross-pollination, making them naturally obligate self-pollinators without human intervention); by sélective placement of plants (e.g., intentionally planting plants in pollinating proximity); and/or by application of chemicals to precipitate flowering or 10 to foster receptivity (of the stigma for pollen).

A cotton plant that tolérâtes application of dicamba and glufosinate herbicides may be produced by selfing an event MON 88701 containing plant comprising a DNA molécule having at least one sequence selected from SEQ ID NO: l-ΊΟ and thereby producing seed, which is then grown into progeny plants. These progeny 15 plants may then be treated with dicamba and glufosinate herbicides to select for progeny plants that are tolérant to dicamba and glufosinate herbicides. Alternatively, these progeny plants may be analyzed using diagnostic methods to select for progeny plants that contain the event MON 88701 DNA. In practicing this method, the step of sexually crossing one plant with itself, i.e., self-pollinating or selfing, may be 20 accomplished or facîlitated by human intervention, for example: by human hands collecting the pollen of the plant and contacting this pollen with the style or stigma of the same plant and then optionally preventing further fertilization of the plant; by human hands and/or actions removing, destroying, or covering the stamen or anthers of other nearby plants (e.g., by detasseling or by application of a chemical 25 gametocide) so that natural cross-pollination is prevented and self-pollination would hâve to take place in order for fertilization to occur; by human placement of pollinating insects in a position for “directed pollination” (e.g., by caging a plant alone with pollinating insects); by human manipulation of the flower or its parts to allow for self-pollination; by sélective placement of plants (e.g., intentionally planting 30 plants beyond pollinating proximity); and/or by application of chemicals to precipitate flowering or to foster receptivity (of the stigma for pollen).

Progeny cotton plants and seeds encompassed by these methods and produced by using these methods will be distinct from other cotton plants, for example because the progeny cotton plants and seeds: are recombinant and as such created by human intervention; are dicamba and glufosinate herbicide tolérant; contain at least one allele that consists of the transgene DNA of the invention; and/or contain a détectable amount of a DNA molécule comprising at least one sequence selected from SEQ ID NO: 1-10. A seed may be selected from an indivîdual progeny plant, and so long as the seed comprises a DNA molécule having at least one sequence selected from SEQ ID NO: 1-10, it will be within the scope ofthe invention.

In practicing the invention, two different transgenic plants can be crossed to produce hybrid offspring that contain two independently segregating heterologous genes. Selfing of appropriate progeny can produce plants that are homozygous for both genes. Back-crossing to a parental plant and out-crossing with a non-transgenic plant are also contemplated, as is végétative propagation. Descriptions of other methods that are commonly used for different traits and crops can be found in one of several references, e.g., Fehr, in Breeding Methods for Cultivar Development, Wilcox J. ed., American Society of Agronomy, Madison WI (1987).

The plants and seeds used in the methods disclosed herein may also contain one or more additional transgenes. Such transgene may be any nucléotide sequence encoding a protein or RNA molécule conferring a désirable trait including but not limited to increased insect résistance, increased water use efficiency, increased yield performance, increased drought résistance, increased seed quality, improved nutritional quality, and/or increased herbicide tolérance, in which the désirable trait is measured with respect to a cotton plant lacking such additional transgene.

The methods of the invention are therefore useful for, among other things, controlling weeds in a field while growing plants for the purpose of producing seed and/or plant parts comprising cotton event MON 88701 for agricultural or research purposes, selecting for progeny comprising cotton event MON 88701 for plant breeding or research purposes, and producing progeny plants and seeds comprising cotton event MON 88701.

The plants, progeny, seeds, plant cells, plant parts (such as pollen, ovule, pod, flower, root or stem tissue, and leaves), and commodity products of the invention may be evaluated for DNA composition, gene expression, and/or protein expression. Such évaluation may be done by using any standard method such as PCR, northem blotting, southem analysis, western blotting, immuno-precipitation, and EL1SA or by using the methods of détection and/or the détection kits provided herein. ---21

Methods of detecting the presence of DNA derived from a cotton cell, tissue, seed, or plant comprising cotton event MON 88701 in a sample are provided. One method consists of (i) extracting a DNA sample from at least one cotton cell, tissue, seed, or plant, (ii) contacting the DNA sample with at least one primer that is capable of producing DNA sequence spécifie to event MON 88701 DNA under conditions appropriate for DNA sequencing, (iii) performing a DNA sequencîng reaction, and then (iv) confirming that the nucléotide sequence comprises a nucléotide sequence spécifie for event MON 88701, such as one selected from the group consisting of SEQ ID NO: 1-10. Another method consists of (i) extracting a DNA sample from at least one cotton cell, tissue, seed, or plant, (ii) contacting the DNA sample with a primer pair that is capable of producing an amplicon from event MON 88701 DNA under conditions appropriate for DNA amplification, (iii) performing a DNA amplification reaction, and then (iv) detecting the amplicon molécule and/or confirming that the nucléotide sequence of the amplicon comprises a nucléotide sequence spécifie for event MON 88701, such as one selected from the group consisting of SEQ ID NO: 1-10. The amplicon should be one that is spécifie for event MON 88701, such as an amplicon that comprises SEQ ID NO: 1 or SEQ ID NO: 2. The détection of a nucléotide sequence spécifie for event MON 88701 in the amplicon is determinative and/or diagnostic for the presence of the cotton event MON 88701 spécifie DNA in the sample. An example of a primer pair that is capable of producing an amplicon from event MON 88701 DNA under conditions appropriate for DNA amplification is provided as SEQ ID NO: 11-12. Other primer pairs may be readily designed by one of skill in the art and would comprise at least one fragment of SEQ ID NO: 10. Another method of detecting the presence of DNA derived from a cotton cell, tissue, seed, or plant comprising cotton event MON 88701 in a sample consists of (i) extracting a DNA sample from at least one cotton cell, tissue, seed, or plant, (ii) contacting the DNA sample with a DNA probe spécifie for event MON 88701 DNA, (iii) allowing the probe and the DNA sample to hybridize under stringent hybridization conditions, and then (iv) detecting hybridization between the probe and the target DNA sample. An example of the sequence a DNA probe that is spécifie for event MON 88701 DNA is provided as SEQ ID NO: 13. Other probes may be readily designed by one of skill in the art and would comprise at least one fragment of SEQ ID NO: 10. Détection of probe hybridization to the DNA sample is diagnostic for the presence of cotton event MON 88701 spécifie DNA in the sample. Absence of yy— hybridization is alternatively diagnostic of the absence of cotton event MON 88701 spécifie DNA in the sample.

DNA détection kits are provided that are useful for the identification of cotton event MON 88701 DNA in a sample and can also be applied to methods for breeding cotton plants containing the appropriate event DNA. Such kits contain DNA primers and/or probes comprising fragments of SEQ ID NO: 1-10. One example of such a kit comprises at least one DNA molécule of sufficient length of contiguous nucléotides of SEQ ID NO: 10 to function as a DNA probe useful for detecting the presence and/or absence of DNA derived from transgenic cotton plants comprising event MON 88701 in a sample. The DNA derived from transgenic cotton plants comprising event MON 88701 would comprise a DNA molécule having at least one sequence selected from SEQ ID NO: 1-10. A DNA molécule sufficient for use as a DNA probe is provided that is useful for determining, detecting, or diagnosing the presence and/or absence of cotton event MON 88701 DNA in a sample is provided as SEQ ID NO: 13. Other probes may be readily designed by one of skill in the art and should comprise at least 15 contiguous nucléotides of SEQ ID NO: 10 and be sufficiently unique to cotton event MON 88701 DNA in order to identify DNA derived from the event. Another type of kit comprises a primer pair useful for producing an amplicon useful for detecting the presence and/or absence of DNA derived from transgenic cotton event MON 88701 in a sample. Such a kit would employ a method comprising contacting a target DNA sample with a primer pair as described herein, then performing a nucleic acid amplification reaction sufficient to produce an amplicon comprising a DNA molécule having at least one sequence selected ffom SEQ ID NO: 1-10, and then detecting the presence and/or absence of the amplicon. Such a method may also include sequencing the amplicon or a fragment thereof, which would be determinative of, i.e. diagnostic for, the presence of the cotton event MON 88701 spécifie DNA in the target DNA sample. Other primer pairs may be readily designed by one of skill in the art and should comprise at least 15 contiguous nucléotides of SEQ ID NO: 10 and be sufficiently unique to cotton event MON 88701 DNA in order to identify DNA derived from the event.

Nucleic-acid amplification can be accomplished by any of the various nucleicacid amplification methods known in the art, including thermal amplification methods. Many techniques are known in the art for detecting, quantifying, and/or sequencing the amplicon produced by these methods. One exemplary technique useful in practicing this invention is TAQMAN® (PE Applied Biosystems, Foster

City, CA).

The kits and détection methods of the invention are useful for, among other things, identifying cotton event MON 88701, selectîng plant varieties or hybrids comprising cotton event MON 88701, detecting the presence of DNA derived from the transgenic cotton plants comprising event MON 88701 in a sample, and monitoring samples for the presence and/or absence of cotton plants comprising event MON 88701 or plant parts derived from cotton plants comprising event MON 88701.

The sequence of the heterologous DNA insert, junction sequences, or flanking sequences from cotton event MON 88701 can be verified (and corrected if necessary) by amplifying such sequences from the event using primers derived from the sequences provided herein followed by standard DNA sequencing of the amplicon or of the cloned DNA.

As used herein, the term “comprising” means “including but not limited to”.

The following examples are included to demonstrate examples of certain preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples that follow represent approaches the inventors hâve found function well in the practice of the invention, and thus can be considered to constitute examples of preferred modes for its practice. However, those of skill in the art should, in light of the présent disclosure, appreciate that many changes can be made in the spécifie embodiments that are disclosed and still obtain a like or similar resuit without departing from the spirit and scope of the invention.

EXAMPLES

Example 1: Transformation of Cotton and MON 88701 event sélection

This example describes the production, analysis, and sélection of event MON 88701. Summarized is the production and analysis of thousands of individual plants over multiple years through the rigorous molecular, phenotypic, and field testing required for the ultimate sélection of the commercial event, the MON 88701 event.

The transgenic dicamba and glufosinate tolérant cotton event MON 88701 was created through yig/Oàactenum-mediated transformation of cotton hypocotyl tissue utilizing a plant transformation vector comprising the expression cassette illustrated in Figure 1. Methods for transforming cotton are known in the art. To produce the

MON 88701 event, Coker 130 cotton material (Asgrow, St Louis, MO) was used for plant transformation. Cotton cells were transformed and regenerated into intact cotton plants. Rooted plants with normal phenotypic characteristics were selected and transferred to soil for growth and further assessment.

R0 plants were transferred to soil and subjected to herbicide screening at IX or 2X field rates (i.e., 0.5 or 1.0 lb/acre active ingrédient) of both dicamba and glufosinate. Subsequently, R0 plants containing only a single T-DNA expression cassette were identified and selected. The T-DNA expression cassette contains the Peanut chlorotic streak virus (PC1SV) promoter with a duplicated enhancer région (PPClSV.FLt-enh); operably linked to a DNA leader derived from RNA transcript of Tobacco etch virus (L-TEV); operably linked to a DNA molécule encoding an Nterminal chloroplast transit peptide from chloroplast transit peptide from 5enolpyruvylshikimate-3-phosphate synthase (EPSPS) from Arabidopsis thaliana (TSCTP2); operably linked to a DNA molécule encoding dicamba mono-oxygenase (DMO) from Stenotrophomonas maltophilia; operably linked to a 3’ UTR DNA molécule derived from the fiber protein E6 gene of sea-island cotton (T-Gb.E6-3b); operably linked to the promoter of the enhanced 35S RNA transcript (with a duplicated enhancer région) from Cauliflower mosaic virus (P-CaMV.35S-enh); operably linked to a DNA leader derived from the 5 untranslated région of the heat shock protein 70 (HSP70) gene from Pétunia x hybrida (L-Ph.DnaK); operably linked to the Bialaphos Résistance gene (bar) gene from Slreptomyces hygroscopicus encoding a phosphinothricin acetyl transferase (PAT) (CR-Sh.bar); operably linked to a 3’ untranslated région from the nopaline synthase (NOS) gene (which directs polyadenylation of mRNA) from Agrobacterium tumefaciens (T-AGRtu.nos).

The MON 88701 event was selected from among approximately 151 individual transgenic events based on its superior combination of phenotypic characteristics (including commercial level tolérance to both dicamba and glufosinate herbicides), molecular characteristics (determined using a comprehensive molecular profile analysis), and haplotype association. Sélection of the MON 88701 event from among the original 151 transgenic events was a multi-year process requiring data analysis at each step. Two waves of transformation events were processed to allow for a larger number of events from which to choose the final commercial event. Table 1 provides a summary of each type of analysis with the number of events selected and advanced for each step of event screening. The Puerto Rico field trial efficacy screen for Wave 2 preceded the first U.S. field trial.

Table l

Event Screening Analysis Step	Wave 1	Wave 2
RO - Transformation Quality Analysis	48	103
RO - Herbicide Efficacy Analysis	26	57
RI - Agronomie Seed Production	9	26
RI - Herbicide Efficacy Analysis	9	23
First U.S. Field Trial	8	10
Preliminary Molecular Analysis	4	19
Puerto Rico Field Trial Efficacy Screen	3	17
Second U.S. Field Trial	2	n/d
Detailed Molecular Analysis	1	6

The original 151 transgenic RO events were analyzed using a combination of analytical techniques (Transformation Quality Analysis încluding TaqMan and/or PCR analysis) and RO Herbicide Efficacy Analysis (herbicide spray). Selected RO event containing plants were then self-fertilized to produce RI seed, and 32 of the events were then advanced for RI Herbicide Efficacy Analysis.

Detailed molecular analysis was completed on events passing agronomie and efficacy field trials. Northem blots were used to confirm that the dmo and bar messenger RNA transcripts were présent in samples prepared from seed of the tested events. Western blot analysis was done to confirm that a single DMO and PAT protein band was présent in samples prepared from leaf tissue of the tested events. Nterminal sequencing of the isolated, purified PAT protein showed the expected amino acid sequence at the N-terminus of the PAT protein. N-terminal sequencing of the isolated, purified DMO protein showed 9 amino acids from the CTP (TS-CTP2) présent at the N-terminus of the DMO protein.

Agronomie field testing consisted of planting paired positive isoline and négative isoline events (containing the transgene cassette and lacking the transgene cassette, respectively) side-by-side with two rows of wild type (non-transgenic) Coker

130 per plot. The plots were maintained weed and insect free using conventional — control programs for the duration of the trial. Data collected included planting date, stand counts, plant height, node number, gross agronomic/phenotypic différences, boll samples, harvest date, and yield. Stand counts for each plot were taken at 10 days after planting (DAP) and again at 20 DAP. Cotylédons that had completely cleared the soil were considered “emerged”. Any différences noted in plant density, i.e. skips, poor germination, loss due to crusting, washouts, etc., were noted. Final stands had 10 plants per meter on average. Plant height measurements were taken at first flower plus two weeks (FF2). Average measurements of plant height (cm) of five plants per plot were recorded. On the same plants used for plant height measurements, the number of nodes were counted (cotylédon is node 0). Any gross agronomie différences were recorded, such as leaf morphology, branching habit, leaf color, time to flowering, fruiting pattern, etc. Boll samples were randomly harvested from 50 first position bolls (seedeotton only) from the middle of the plants (notes 8-12). The boll samples were used to calculate lint fraction and fiber quality. For yield déterminations, plots were defoliated and a boll opener (with ethephon, i.e. PREP) was used prior to harvest. Plots were harvested and recorded as pounds per plot of seedeotton and expressed as pounds per acre of seedeotton. There was no significant yield différence between positive isoline events, the paired négative isoline events, and wild-type Coker 130 cotton for two years of agronomie field trials (Figure 2).

In year 1, efficacy testing was conducted with eight events compared to nontransgenic, wild-type Coker 130. For this testing, paired plots were sprayed with dicamba (Clarity®, BASF, Research Triangle Park, NC) and glufosinate (Ignite®, Bayer CropScience, Research Triangle Park, NC) or left unsprayed. The plots were maintained weed- and insect-free using conventional control programs for the duration of the trial. Ail herbicide treatments are represented as pounds of active ingrédient per acre (Ib/A). For plots that were sprayed, the following applications were conducted: dicamba was applied preemergence at l lb/A followed by glufosinate applied 1.09 lb/A at the 2 node stage, followed by dicamba applied at 1 lb/A at the 5 node stage, followed by glufosinate applied 1.09 lb/A at the 8 node stage, followed by dicamba applied at 1 lb/A at the 12 node stage. Neither dicamba nor glufosinate were applied with surfactants, fertilizer additive, or other adjuvant. Injury ratings were taken at the following stages, which were immediately prior to the next assigned herbicide application: at the 2-node cotton stage, rating activity was taken for percent epînasty (dicamba damage) and percent total injury, with focus on epinasty; at the 5-node stage, rating activity was taken for percent epinasty, percent bum or necrosis (glufosinate injury) and percent total injury, with focus on necrosis; at the 8-node stage, rating activity was taken for percent epinasty, percent bum or necrosis, and percent total injury, with focus on epinasty; at the 12-node stage, rating activity was taken for percent epinasty, percent bum or necrosis and percent total injury, with focus on necrosis; at mid-bloom stage, rating activity was taken for percent epinasty, percent bum or necrosis and percent total injury, with focus on epinasty; and for late bloom stage, rating activity was taken for percent epinasty, percent bum or necrosis and percent total injury. Additional agronomie data were collected in these efficacy field trials including: planting date, stand counts (taken at 7 and 14 DAP), gross agronomic/phenotypic différences, harvest date, and yield. Injury ratings used standard weed science percent scales where 0% equals no crop injury and 100% equals complété crop death. Ratings made for dicamba injury are referred to as epinasty and appears as twisting, growth malformation. Ratings made for glufosinate injury are referred to as bum or necrosis and appears as chlorosis and or necrosis. For yield déterminations, plots were defoliated and a boll opener (with ethephon, i.e. PREP) was used prior to harvest. Plots were harvested and yield recorded as Ibs/plot of seed cotton and expressed as lb/acre of seed cotton. Agronomic/phenotypic différences were notedin fruiting profile as normal or as unusual. There was no significant différence in yield of seed cotton between paired sprayed and unsprayed events compared to unsprayed wild-type Coker 130 (Figure 3). The wild-type Coker 130 did not survive the spray regimen (Figure 7).

In year 2, efficacy testing was conducted with twelve events compared to nontransgenic, wild-type Coker 130. For this testing, paired plots were either sprayed or not sprayed. The plots were maintained weed- and insect-free using conventional control programs for the duration of the trial. For the plots that were sprayed, the following treatment applications were conducted (1) 0.5 lb/A dicamba applied PRE, Early POST, Mid POST and Late POST; (2) 1 lb/A dicamba applied PRE, Early POST, Mid POST and Late POST; (3) 2 lb/A dicamba applied PRE, Early POST, Mid POST and Late POST; (4) 0.5 lb/A glufosinate applied Early POST, Mid POST and Late POST: (5) 1 lb/A glufosinate applied Early POST, Mid POST and Late POST: 6) 2 lb/A glufosinate applied Early POST, Mid POST and Late POST; and 7) Control (unsprayed). Preemergence (PRE) is defined as immediately after cotton planting (within 24 hours); Early POST as 2-node cotton; Mid POST as 8-node cotton; and Late POST as 14 node cotton. For these efficacy field trials, there were three plots composed entirely of wild-type cotton (Coker 130). At each postemergence timing (Early, Mid, Late), one-half of a plot was sprayed with the IX rate (0.5 lb/A) of dicamba and one-half of the same plot was sprayed with the IX rate (0.5 lb/Α) of glufosinate. Each of the three plots received dicamba and glufosinate spray at one of the post-emergence timing spray applications (Early, Mid, Late).

The spray protocol consisted of the herbicides applied at 10 gallons per acre water volume using the following sprayer set up (which is within the standards used for most weed science research). XR TeeJet® extended range fiat spray tips with an 80-degree spray angle were used (TeeJet Technologies, Wheaton, IL). There were 2 nozzles per row (nozzles spaced at 15” for 30” rows, 19” for 38” rows and 20” for 40” rows). Nozzle size depended on sprayer speed and nozzle spacing; however, nozzle size was selected to resuit in a spray pressure of 25 to 35 PSL Boom height was adjusted to allow for 50% spray overlap (which occurs at roughly 30” above the top of the crop).

At each rating time, the following observations were recorded: 1) percent necrosis or bum on the most affected leaves; 2) percent necrosis or bum on a wholeplant basis; 3) epinasty; and 4) any other relevant injury that was observed. Ratings were taken four days after each application and immedîately prior to subséquent applications. The rating schedule time and objective were as follows: 1) 4-7 days after emergence and again immedîately before 2-node spray to check for preemergence effects of dicamba spray; 2) 4 days after the 2-node spray and again immedîately before the 8-node spray to détermine the rating of the 2-node spray; 3); 4 days after the 8-node spray and again immedîately before the 14-node spray to détermine the rating of the 8-node spray 4); 4 days after the 14-node spray and again 10 days after the 14-node spray to détermine the rating of the 14-node spray; and 5) at cutout to détermine the late season rating of the net effect of ail sprays. Injury ratings used standard weed science percent scales where 0% equals no crop injury and 100% equals complété crop death. Ratings made for dicamba injury are referred to as epinasty and appears as twîsting, growth malformation. Ratings made for glufosinate injury are referred to as bum or necrosis and appears as chlorosis and or necrosis. For yield déterminations, plots were defoliated and a boll opener (with ethephon, i.e. PREP) was used prior to harvest. Plots were harvested and recorded as lbs/plot of seedcotton and expressed as lb/acre of seedcotton. Wild-type Coker 130 plants did not survive herbicide spray and therefore no yield was recorded from Coker 130 plots.

As seen in Figure 4.A, yield was nearly équivalent for plants comprising the

MON 88701 event with increasing application rates of dicamba herbicide. As seen in

Figure 4.B, yield was nearly équivalent for plants comprising the MON 88701 event with increasing application rates of glufosînate herbicide. For injury ratings, Figure

5.A shows increased percentage of injury to plants comprising the MON 88701 event with increasing application rates of dicamba. Figure 5.B shows increased percentage of injury to plants comprising the MON 88701 event with increasing application rates of glufosînate.

In year 3, efficacy field testing of event MON 88701 was conducted to study the rate and timing of application of dicamba and/or glufosînate. The plots were maintained weed- and insect-ffee using conventional control programs for the duration of the trial. The treatment and application timing are detailed in Table 2. Neither dicamba nor glufosînate were applied with surfactants, fertilizer additive or other adjuvant. The sprayer protocol was as described for year 2 efficacy field testing. Stand rating, Visual injury ratîng (percent epinasty, percent necrosis), plant height and node number, 50-boll sampling, and yield déterminations were as described for agronomie and efficacy field testing above.

Table 2

Treatment	Rate (lb ai/A)	Application timing
1 to 3 Node	5 to 7 node	10 to 12 node	15 to 18 node
1	0.5	Dicamba	Glufosînate	Dicamba	Glufosînate
2	1	Dicamba	Glufosînate	Dicamba	Glufosînate
3	0.5	Glufosînate	Dicamba	Glufosînate	Dicamba
4	1	Glufosînate	Dicamba	Glufosînate	Dicamba
5	0.25*	Tank Mix	Tank Mix	Tank Mix	Tank Mix
6	0.5*	Tank Mix	Tank Mix	Tank Mix	Tank Mix
7	1*	Tank Mix	Tank Mix	Tank Mix	Tank Mix
8	0.5	Dicamba	Dicamba	Dicamba	Dicamba
9	1	Dicamba	Dicamba	Dicamba	Dicamba
10	0.5	Glufosînate	Glufosînate	Glufosînate	Glufosînate
11	1	Glufosînate	Glufosînate	Glufosînate	Glufosînate

- Control *With tank mixes, the rate is what was used for the individual herbicides:

0.25 = 0.25 lb/Α dicamba + 0.25 lb /A glufosinate

There was a slight yield drag when dicamba and glufosinate were tank mixed and applied at four times in season at l lb/acre each (Figure 6). For ail other treatment regimens, there was no yield loss to plants comprising the MON 88701 event when sprayed with dicamba, glufosinate, or dicamba and glufosinate (Figure 6).

Example 2: Characterization of MON 88701 DNA sequences

This example describes the molecular characterization of the MON 88701 event. The DNA inserted into the genome of cotton plants comprising MON 88701 and the genomie sequence flanking this insertion were characterized by detailed molecular analyses. These analyses included: the insert sequence, the insert number (number of intégration sites within the cotton genome), the copy number (number of copies of transgene DNA within one locus), the integrity of the inserted gene cassette, the flanking sequences, and the association of the insertion with haplotype régions of the cotton genome.

Molecular DNA probes were used that included the intact coding région and its respective regulatory éléments, the promoters, introns, and polyadenylation sequences of the plant expression cassettes. The analysis showed that MON 88701 eontains a single transgene DNA insertion with one copy of the expression cassette. Inverse PCR and DNA sequence analyses were performed to détermine the 5’ and 3’ insert-to-plant genome junctions, confirm the organization of the éléments within the insert (Figure 1), and détermine the complété DNA sequence of the insert in cotton plants comprising event MON 88701 (provided herein as SEQ ID NO: 9). A cotton plant that comprises in its genome the linked transgene genetic éléments shown in Figure 1 and is résistant to dicamba and glufosinate herbicides îs an aspect of the invention.

Sequences flanking the transgene DNA insertion în MON 88701 were determined using inverse PCR as described in Ochman et al., 1990 (PCR Protocols: A guide to Methods and Applications, Academie Press, Inc.) and/or genome walker techniques. Plant genomie DNA was isolated from both Coker 130 and the transgenic cotton lines from tissue grown under standard greenhouse conditions. Approximately —

0.2 gram of young leaf tissue was lyophilized and powdered via the addition of several small steel beads followed by vigorous agitation. Tissue was washed twice with 5 mL of 100% methanol followed by one wash with 5 mL of 50% methanol to remove interfering phenolic compounds. DNA was extracted by the addition of 7 mL of CTAB extraction buffer (100 mM Tris pH 8.0, 1.4 M NaCI, 20 mM EDTA, 2 % w/v hexadecyltri méthylammonium bromide, 1 % w/v polyvinylpyrrolidone, 1% w/v poly(vînylpolypyrrolidone), 0.07% beta-mercaptoethanol, 1 mM DTT). Samples were incubated at 65°C for 45 min to fully lyse cells then, spun for 5 min at 3000g to remove insoluble débris. The supematant was extracted with 7 mL of chloroform isoamyl alcohol 24:1, spun at 3000 g for 5 min to separate phases, and DNA was extracted from the aqueous phase in a fresh tube by the addition of 6 mL of isopropanol. DNA pellets were washed with 6 mL of 70% éthanol to remove any salts, and pellets were allowed to air dry, The DNA pellets were resuspended in 10 mM Tris pH 8.0 containing 0.5 ug/mL DNase-free RNase and incubated at 37°C 1 hour. Following treatment, DNA was quantified using Quant-iT™ PicoGreen® (Molecular Probes, Inc. Eugene, OR). This method can be modified by one skilled in the art to extract DNA from any tissue of cotton. An aliquot of DNA was digested with restriction endonucléases selected based upon restriction analysis of the transgene DNA. After self-Iigation of restriction fragments, PCR was performed using primera designed from the transgene DNA sequence that would amplify sequences extending away from the 5’ and 3’ ends of the transgene DNA. PCR products were separated by agarose gel electrophoresis and purified using a QIAGEN gel purification kit (Qiagen, Valencia, CA). The subséquent DNA products were sequenced directly using standard DNA sequencing protocole. The 5’ flanking sequence which extends into the right border sequence of the expression cassette transgene DNA is presented as SEQ ID NO: 7 ([C], see Figure 1). The 3’ flanking sequence which extends into the left border sequence of the expression cassette transgene DNA is presented as SEQ ID NO: 8 ([D], see Figure 1). The portion of the expression cassette DNA that was fully integrated into the Coker genomic DNA is presented as SEQ ID NO: 9 ([E], see Figure 1).

Isolated DNA molécule sequences were compared to the transgene DNA sequence to identify the flanking sequence and the co-isolated transgene DNA fragment. Confirmation of the presence of the expression cassette was achieved by —

PCR with primers designed based upon the deduced flanking sequence data and the known transgene DNA sequence. The wild-type sequence corresponding to the same région in which the transgene DNA was integrated in the transformed line was isolated using primers designed from the flanking sequences in MON 88701, The 5 PCR reactions were performed using the Phusion® High -Fîdelity PCR Master Mix with HF Buffer (New England Biolabs, Ipswich, MA). The flanking DNA sequences in MON 88701 and the Coker wild-type sequence were analyzed against multiple nucléotide and protein databases. This information was used to examine the relationship of the transgene to the plant genome and to look for the insertion site 10 integrity. The flanking sequence and wild-type sequences were used to design primers for TAQMAN® endpoint assays used to identify the events. Zygosity assays were developed using this information.

The dicamba and glufosinate tolérance transgene cassette was mapped in cotton plants comprising event MON 88701 on chromosome A08 at the map position 15 of 19.3 cM and bordered by NG0207927 at the map position of 18.6 cM on left and by NG0207529 at the map position of 20.0 cM on right.

Example 3: Event spécifie endpoint TAQMAN® assays

This example describes an event spécifie endpoint TAQMAN® thermal 20 amplification method developed to identify event MON 88701 in a sample.

Examples of conditions useful with the event MON 88701 Spécifie Endpoint TAQMAN® method are as follows: Step 1: 18 megohm water adjusted for final volume of 10 μΐ. Step 2: 5.0 μΐ of 2X Universal Master Mix (dNTPs, enzyme, buffer) to a IX final concentration. Step 3: 0.5 μΐ Event Primer-1 (SQ21654) and 25 Event Primer-2 (SQ23205). Mix (resuspended in 18 megohm water to a concentration of 20 uM for each primer) to 1.0 μΜ final concentration (for example in a microcentrifuge tube, the following should be added to achieve 500 μΐ at a final concentration of 20 uM: 100 μΐ of Primer SQ21654 at a concentration of 100 μΜ;

100 μΐ of Primer SQ23205 at a concentration of 100 μΜ; 300 μΐ of 18 megohm 30 water). Step 4: 0.2 μΐ Event 6-FAM™ MGB Probe PB 10280 (resuspended in 18 megohm water to a concentration of 10 μΜ to 0.2 μΜ final concentration. Step 5: 0.5 μΐ Internai Control Primer-1 and Internai Control Primer-2 Mix (resuspended in 18 megohm water to a concentration of 20 μΜ for each primer) to 1.0 μΜ final concentration. Step 6: 0.2 μΐ Internai Control VIC ™ Probe to 0.2 μΜ final concentration (resuspended in 18 megohm water to a concentration of 10 μΜ) Step 7: 3.0 μΐ Extracted DNA (template) for each sample with one each of the foilowing comprising l. Leaf Samples to be analyzed; 2. Négative control (non-transgenic DNA); 3. Négative water control (no template); 4. Positive control MON 88701 DNA. Step 8: Thermocycler Conditions as follows: One Cycle at 50°C for 2 minutes; One Cycle at 95°C for 10 minutes; Ten Cycles of 95°C for 15 seconds then 64°C for 1 minute with -l°C/cycle; Thirty Cycles of 95°C for 15 seconds then 54°C 1 minute, optional additional 10 to 20 cycles (95°C for 15 seconds then 64°C for 1 minute (-l°C/cycle) may provide more distinct population séparation during EndPoint TaqMan® analysis; final cycle of 10°C.

The DNA primers used in the endpoint assay are primers SQ21654 (SEQ ID NO: 11), SQ23205 (SEQ ID NO: 12), and 6-FAM™ labeled probe PB 10280 (SEQ ID NO: 13). 6-FAM is a fluorescent dye product of Applied Biosystems (Foster City, CA) attached to the DNA probe. For TAQMAN® MGB™ probes, the 5’ exonuclease activity of Taq DNA polymerase cleaves the probe from the 5’-end, between the fluorophore and quencher. When hybridized to the target DNA strand, quencher and fluorophore are separated enough to produce a fluorescent signal, thus releasing fluorescence. SQ21654 (SEQ ID NO: 11) and SQ23205 (SEQ ID NO: 12) when used with these reaction methods with PB 10280 (SEQ ID NO: 13) produce a DNA amplicon that is diagnostic for event MON 88701 DNA. The controls for this analysis should include a positive control from cotton containing event MON 88701 DNA, a négative control from non-transgenic cotton, and a négative control that contains no template DNA. Additionally, a control for the PCR reaction includes Internai Control Primers and an Internai Control Probe, spécifie to a single copy gene in the Gossypium genome. One of skill in the art will know how to design primers spécifie to a single copy gene in the Gossypium genome. These assays are optimized for use with either an Applied Biosystems GeneAmp® PCR System 9700 (run at maximum speed) or MJ Research DNA Engine PTC-225 thermal cycler. Other methods and apparatus known to those skilled in the art that produce amplicons that identify the event MON 88701 DNA is within the skill of the art.

R0 plants demonstrating the presence of the expression cassette were allowed to develop into fully mature plants and seed was harvested from these. Probes based on the sequence of the expression cassette were used to détermine copy number of the transgenic expression cassette in the RI plants using a combination of Southem analysis and endpoint TAQMAN®.

A zygosity assay is useful for determining if a plant comprising an event is homozygous for the event DNA; that is comprising the exogenous DNA in the same location on each chromosome of a chromosomal pair; or heterozygous for an event DNA, that is comprising the exogenous DNA on only one chromosome of a chromosomal pair; or is null for the event DNA, that is wildtype. The endpoint TAQMAN® thermal amplification method was also used to develop zygosity assays for event MON 88701. This example describes an event-specific endpoint TAQMAN® thermal amplification method developed to détermine the zygosity of event MON 88701 in a sample. For this assay, a three primer assay was employed wherein primer SQ21654 hybridizes and extends specifically from the 3’ junction of the inserted exogenous DNA and genomic DNA, primer SQ23205 hybridizes and extends specifically from the DNA flanking the 3' side of the inserted exogenous DNA, and primer SQ23901 hybridizes and extends specifically from genomic DNA into which was integrated the inserted exogenous DNA. The three primers are diagnostic for the event. In this example, primer SQ21654 and primer SQ23205 and the 6-FAM™-Iabeled oligonucleotide probe PB 10280 are diagnostic when there is a copy of the inserted exogenous DNA. In this example, SQ23205 and primer SQ23901 and the VIC™-labeled oligonucleotide probe PB 10631 are diagnostic when there is no copy of the inserted exogenous DNA present in the genomic DNA, i.e. wild-type. When the three primers and two probes are mixed together in a PCR reaction with DNA extracted from a plant homozygous for event MON 88701, there is a fluorescent signal only from 6-FAM™-labeled oligonucleotide probe PB 10280 which is indicative of and diagnostic for a plant homozygous for event MON 88701. When the three primers and two probes are mixed together in a PCR reaction with DNA extracted from a plant heterozygous for event MON 88701, there is a fluorescent signal from both the 6-FAM™-labeled oligonucleotide probe PB 10280 and the VIC™-labeled oligonucleotide probe PB 10631 which is indicative of and diagnostic for a plant heterozygous for event MON 88701. When the three primers and two probes are mixed together in a PCR reaction with DNA extracted from a plant which is null for event MON 88701 (i.e. wildtype), there is a fluorescent signal from only the VIC™-labeled oligonucleotide probe PB 10631 which is indicative of and diagnostic for a plant null for event MON 88701, i.e. wild-type. Examples of conditions useful with this method are as follows. Step l : 18 megohm water adjusted for final volume of 10 μΐ. Step 2: 5.0 μΐ of 2X Universal Master Mix (Applied Biosystems cat # 4304437; dNTPs, enzyme, buffer) to a IX final concentration. Step 3: 0.5 μΐ of Zygosity Primers SQ21654; SQ23205 and SQ23901(resuspended in 18 megohm water to a concentration of 20 μΜ for each primer) to a final concentration of l.O μΜ. Step 4: 0.2 μΐ 6-FAM™ Probe PB10280 (resuspended in 18 megohm water to a concentration of 10 μΜ) to 0.2 μΜ final concentration. Step 5: 0.2 μΐ VIC™ Probe PB!0631 (resuspended in 18 megohm water to a concentration of 10 μΜ) to 0.2 μΜ final concentration. Step 6: 3.0 μΙ Extracted DNA (template) for each sample with one each of the following comprising 1. Leaf Samples to be analyzed (45 ng/ul of genomic DNA diluted in water); 2. Négative control (non-transgenic cotton DNA; 5 ng/ul diluted in water); 3. Négative water control (no template; solution in which DNA was resuspended); 4, Positive control MON 88701 genomic DNA from known heterozygous sample (5 ng/ul diluted in water); 5. 4. Positive control MON 88701 genomic DNA from known homozygous sample (5 ng/ul diluted in water). Step 7: Gently mix. Step 8: Thermocycler Conditions when using Applied Biosystems GeneAmp® PCR System 9700 (run at maximum speed) or MJ Research DNA Engine PTC-225 thermal cycler are as follows: One Cycle at 50°C for 2 minutes; one cycle at 95°C for 10 minutes; Ten Cycles of (95°C for 15 seconds then 64°C for 1 minute (-l°C/cycle); Thirty Cycles of (95°C for 15 seconds then 54°C for 1 minute); Optional additional 10 to 20 cycles (95°C for 15 seconds then 64°C for 1 minute (-l°C/cycle) may provide more distinct population séparation during EndPoint TaqMan® analysis; One cycle at 10°C hold.

Example 4: Identification of event MON 88701 in any cotton breeding activity

This example describes how one may identify the MON 88701 event within progeny of any cotton breeding activity. DNA event primer pairs are used to produce an amplicon diagnostic for cotton event MON 88701. An amplicon diagnostic for MON 88701 comprises at least one of the sequences provided as SEQ ID NO: 1-10. Event primer pairs that will produce a diagnostic amplicon for MON 88701 include primer pairs based upon the flanking sequences and the inserted expression cassette. For example, to produce a diagnostic amplicon in which SEQ ID NO: 1 is found, one would design a forward primer based upon the genomic flanking sequence portion of SEQ ID NO: 7 and a reverse primer based upon the inserted expression cassette DNA — sequence with the primera of sufficient length of contiguous nucléotides to specifically hybridize to the event DNA. To produce a diagnostic amplicon in which SEQ ID NO: 2 is found, one would design a forward primer based upon the inserted expression cassette DNA sequence and a reverse primer based upon the genomic 5 flanking sequence portion of SEQ ID NO: 8 with the primera of sufficient length of contiguous nucléotides to specifically hybridize to the event DNA. For practical purposes, one should design primera which produce amplicons of a limited size range, for example, between 100 to 1000 bases. Smaller (shorter polynucleotide length) sized amplicons in general are more reliably produced in PCR reactions, allow for 10 shorter cycle times, and can be easily separated and visualized on agarose gels or adapted for use in endpoint TAQMAN®-like assays. Smaller amplicons can be produced and detected by methods known in the art of DNA amplicon détection. In addition, amplicons produced using the primer pairs can be cloned into vectors, propagated, isolated, and sequenced or can be sequenced directly with methods well 15 established in the art. Any primer pair that is useful in a DNA amplification method to produce an amplicon diagnostic for MON 88701 or plants comprising MONS 88701 or progeny thereof is an aspect of the invention. An example of the amplification conditions for this analysis is illustrated in Example 3.

An analysis for event MON 88701 containing plant tissue sample should include a positive tissue control from a plant comprising event MON 88701, a négative control from a cotton plant that does not contain event MON 88701 (for example, but not limited to Coker), and a négative control that contains no cotton genomic DNA. A primer pair that will amplify an endogenous cotton DNA molécule will serve as an internai control for the DNA amplification conditions. Additional primer sequences can be selected from SEQ ID NO: 10 by those skilled in the art of DNA amplification methods, and conditions selected for the production of an amplicon by the methods shown in Example 3 may differ, but resuit in an amplicon diagnostic for event MON 88701 DNA, DNA détection kits contain at least one DNA primer of sufficient length of contiguous nucléotides derived from SEQ ID NO: 10, that when used in a DNA amplification method produces a diagnostic amplicon for MON 88701 is an aspect of the invention.

A deposit of a représentative sample of cotton seed comprising event MON 88701 has been made according to the Budapest Treaty with the American Type Culture Collection (ATCC) having an address at 10801 University Boulevard, —

Manassas, Virginia USA, Zip Code 20110. The ATCC Patent Deposit Désignation (accession number) for seeds comprising event MON 88701 is PTA-11754 and the date of deposit was March 17, 201l. Access to the deposits will be available during the pendency of the application to the Commissioner of Patents and Trademarks and 5 persons determined by the Commissioner to be entitled thereto upon request. The deposit will be maintained in the depository for a period of 30 years, or 5 years after the last request, or for the effective life of the patent, whichever is longer, and will be replaced as necessary during that period.

Having illustrated and described the principles of the invention, it should be apparent to persons skilled in the art that the invention can be modified in arrangement and detail without departîng from such principles. We claim ail modifications that are within the spirit and scope of the appended claims. —

Claims

1. A recombinant DNA molécule comprising a nucieotide sequence selected from the group consisting of SEQ ID NO: l-ΙΟ, and compléments thereof.

2. The recombinant DNA molécule of claim l formed by the insertion of a heterologous nucleic acid molécule into the genomic DNA of a cotton plant or cell.

3. The recombinant DNA molécule of claim I, wherein said DNA molécule is derived from a transgenic cotton plant comprising event MON 88701, a représentative sample of seed comprising cotton event MON 88701 having been deposited under ATCC Accession No. PTA-l 1754.

4. The recombinant DNA moiecule of claim l, wherein said DNA molécule is in a cotton plant, plant cell, seed, plant part, or commodity product.

5. The recombinant DNA moiecule of claim l, wherein said DNA moiecule is an amplicon diagnostic for the presence of DNA derived from event MON 88701.

6. A DNA probe comprising a nucieotide sequence of sufficient length of contiguous nucléotides of SEQ ID NO: 10, or a complément thereof, to function as a DNA probe that hybridizes under stringent hybridization conditions with a DNA moiecule comprising a nucieotide sequence selected from the group consisting of SEQ ID NO: l-ΙΟ and does not hÿbridize under the stringent hybridization conditions with a DNA moiecule not comprising a nucieotide sequence selected from the group consistingof SEQ ID NO: Î-IO.

7. A pair of DNA molécules comprising a first DNA moiecule and a second DNA moiecule different from the first DNA moiecule, wherein said first and second DNA molécules each comprise a nucieotide sequence of sufficient length of contiguous nucléotides of SEQ ID NO: 10, or a complément thereof, to function as DNA primers when used together in an amplification reaction with DNA derived from event MON 88701 to produce an amplicon diagnostic for cotton event MON 88701 DNA in a sample.

8. A method of detecting the presence of a DNA moiecule derived from a cotton plant comprising event MON 88701 in a sample, said method comprising:

a) contacting said sample with the DNA probe of claim 6;

b) subjecting said sample and said DNA probe to stringent hybridization conditions; and v~·—

c) detecting hybridization of said DNA probe to a DNA molécule in said sample, wherein the hybridization of said DNA probe to said DNA molécule indicates the presence of a DNA molécule derived from cotton event MON 88701 in said sample.

9. A method of detecting the presence of a DNA molécule derived from a cotton plant comprising event MON 88701 in a sample, said method comprising:

a) contacting said sample with the pair of DNA molécules of claim 7;

b) performing an amplification reaction sufficient to produce a DNA amplicon comprising a sequence selected from the group consisting of SEQ ID NO: 110, and compléments thereof; and

c) detecting the presence of said DNA amplicon in said reaction, wherein the presence of said DNA amplicon in said reaction indicates the presence of a DNA molécule derived from a cotton plant comprising event MON 88701 in said sample.

10. A DNA détection kit comprising at least one DNA molécule comprising a nucléotide sequence of sufficient length of contiguous nucléotides of SEQ ID NO: 10, and compléments thereof, to function as a DNA primer or probe spécifie for detecting the presence of DNA derived from a cotton plant comprising event MON 88701, wherein détection of said DNA is diagnostic for the presence of event MON 88701 DNA in a sample.

11. A recombinant cotton plant, seed, cell, or plant part thereof comprising the recombinant DNA molécule of claim 1.

12. The recombinant cotton plant, seed, cell, or plant part thereof of claim 11, wherein said plant, seed, cell, or plant part thereof is tolérant to treatment with dicamba and glufosinate herbicides.

13. The recombinant cotton plant, seed, cell, or plant part thereof of claim 11, the genome of which produces an amplicon comprising a DNA molécule selected from the group consisting of SEQ ID NO: 1-10, and compléments thereof, when tested in a DNA amplification method.

14. A cotton plant, seed, cell or part thereof comprising event MON 88701, a représentative sample of seed comprising event MON 88701 having been deposited under ATCC Accession No. PTA-11754.

15. The cotton plant, seed, cell or part thereof of claim 14, wherein said cotton plant or seed is a hybrid having at least one parent comprising cotton event MON 88701.

16. A nonhving plant material comprising the recombinant DNA molécule of claim 1.

17. A microorganism comprising the recombinant DNA molécule of claim 1.

18. The microorganism of claim 17, wherein said microorganism is a plant cell.

19. A commodity product comprising the recombinant DNA molécule of claim 1.

20. A method for controlling weeds in a field comprising planting cotton plants comprising event MON 88701 in a field and applying an effective dose of dicamba or glufosinate or dicamba and glufosinate herbicide to control weeds in said field without injuring said cotton plants comprising event MON 88701.

21. The method of claim 20, wherein said effective dose of dicamba herbicide is a total of about 0.005 pounds per acre to about 16 pounds per acre of dicamba herbicide over a growing season.

22. The method of claim 20, wherein said effective dose of dicamba herbicide is a total of about 0.5 pounds per acre to about 2 pounds per acre of dicamba herbicide over a growing season.

23. The method of claim 20, wherein said effective dose of glufosinate herbicide is a total of about 0.005 pounds per acre to about 16 pounds per acre of glufosinate herbicide over a growing season.

24. The method of claim 20, wherein said effective dose of glufosinate herbicide is a total of about 0.5 pounds per acre to about 1.59 pounds per acre of glufosinate herbicide over a growing season.

25. A method for controlling weeds in a field comprising applying an effective dose of dicamba or glufosinate or dicamba and glufosinate herbicide to control weeds in a field and then planting cotton plants comprising event MON 88701 in said field.

26. The method of claim 25, wherein said effective dose of dicamba herbicide is from about 0.005 pounds to about 16 pounds per acre and said planting cotton plants comprising event MON 88701 is within 14 days of said applying the effective dose of dicamba herbicide.

27. A method for producing cotton seed or lint essentially free of weed seeds, said method comprising:

a) planting seeds comprising cotton event MON 88701 in a field; '

b) applying an effective dose of a dicamba or glufosinate or dicamba and glufosinate herbicide to said field to kill weeds in said field without injuring cotton plants comprising event MON 88701 ; and

c) harvesting cotton seed or lint from said field.

28. A method of producing a cotton plant that tolérâtes application of dicamba and glufosinate herbicide comprising:

a) sexually crossing a transgenic cotton plant comprising event MON 88701 comprising a nucléotide molécule having a nucléotide sequence selected from the group consisting of SEQ ID NO: l-8, and compléments thereof, with a second cotton plant;

b) collecting the seed produced from said cross;

c) growing said seed to produce a plurality of progeny plants;

d) treating said plurality of progeny plants with dicamba or glufosinate or dicamba and glufosinate; and

e) selecting a progeny plant that is tolérant to dicamba and glufosinate.

29. A method of producing a cotton plant that tolérâtes application of dicamba and glufosinate herbicide comprising:

a) selfing a transgenic cotton plant comprising event MON 88701 comprising a nucléotide molécule having a nucléotide sequence selected from the group consisting of SEQ ID NO: l-8, and compléments thereof;

b) collecting the seed produced from said selfing;

c) growing said seed to produce a plurality of progeny plants;

e) selecting a progeny plant that is tolérant to dicamba and glufosinate.

30. A method of determining the zygosity of a cotton plant or seed comprising event MON 88701 comprising:

a) contacting a sample comprising cotton DNA with a primer set and a probe set that

i) when used together in a nucleic acid amplification reaction with event MON 88701 DNA, produces a first amplicon that is diagnostic for event MON 88701; and ii) when used together in a nucleic acid amplification reaction with cotton genomic DNA other than event MON 88701 DNA, produces a second amplicon that is diagnostic native cotton genomic DNA other than event

MON 88701;

b) performing a nucleic acid amplification reaction with said sample, primer set, and probe set;

c) detecting in said nucleic acid amplification reaction a first fluorescent signal that is diagnostic for event MON 88701 and a second fluorescent signal different from said first fluorescent signal and diagnostic for native cotton genomic DNA corresponding to the location of insertion of the event MON 88701 transgene; and

d) analyzing the presence or absence of said first fluorescent signal and said second fluorescent signal in said nucleic acid amplification reaction, wherein the presence of both fluorescent signais indicates said sample is heterozygous for event MON 88701 and the presence of only said first fluorescent signal indicates said sample is homozygous for event MON 88701.

31. The method of claim 30, wherein the primer set comprises SEQ ID NO: 11, SEQ ID NO: 12 and SEQ ID NO: 14.

32. The method of claim 30, wherein the probe set comprises SEQ ID NO: 13 and SEQ IDNO: 15.

33. A cotton haplotype région comprising event MON 88701 and mapped on chromosome A08 at the map position of 19.3 cM and bordered by NG0207927 at the map position of 18.6 cM on left and by NG0207529 at the map position of 20.0 cM on right.