Modifications of corn transgenic event mon 95379 and methods thereof
The introduction of a recombinant DNA molecule encoding Cry1B.868 or Cry1Da_7 in corn plants addresses the need for novel insect resistance by providing effective protection against Lepidopteran pests, including those resistant to previous traits.
Patent Information
- Application Number
- PCT/US2024/058520
- Authority / Receiving Office
- WO · WO
- Patent Type
- Applications
- Current Assignee / Owner
- Priority Date
- 2023-12-05
- Filing Date
- 2024-12-04
- Publication Date
- 2025-06-12
AI Technical Summary
There is a need for novel transgenic corn events that provide resistance to Lepidopteran insect infestations, including insects that have evolved resistance to existing commercially deployed traits, using modes of action that do not overlap with or resemble previous commercial embodiments.
The development of a recombinant DNA molecule comprising an expression cassette that encodes Cry1B.868 or Cry1Da_7, or specific nucleotide sequences selected from a group of SEQ ID NOs, which confers resistance to Lepidopteran insects by expressing these insecticidal proteins in corn plants.
The modified corn event MON 95379 exhibits resistance to Lepidopteran insect pests such as Fall Armyworm, Corn Earworm, Southwestern Corn Borer, Sugarcane Borer, and Lesser Cornstalk Borer, effectively addressing the issue of insect resistance and providing a novel mode of action.
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Figure US2024058520_12062025_PF_FP_ABST
Abstract
Description
BCS236357 MODIFICATIONS OF CORN TRANSGENIC EVENT MON 95379 AND METHODS THEREOF REFERENCE TO RELATED APPLICATION
[0001] This application claims the priority of U.S. Provisional Appl. Ser. 63 / 606,383, filed December 5, 2023, the entire disclosure of which is incorporated herein by reference. INCORPORATION OF SEQUENCE LISTING
[0002] The sequence listing contained in the file named BCS236357WO_ST26.xml is 305,469 bytes (measured in Microsoft Windows®), was created on September 11, 2024, is filed herewith by electronic submission, and is incorporated by reference. FIELD OF THE INVENTION
[0003] The present invention relates to recombinant DNA molecules present in and / or isolated from a modified corn event MON 95379. The invention also relates to transgenic corn plants, plant parts, seed, cells, and agricultural products containing a modified corn event MON 95379, as well as methods of using the same, and making and detecting the presence of a modified corn event MON 95379. Transgenic corn plants, parts, seeds and cells containing a modified corn event MON 95379 DNA may exhibit resistance to insect infestations in the family Lepidoptera. BACKGROUND
[0004] Corn (zea mays) is an important crop and is a primary food source in many areas of the world. The methods of biotechnology have been applied to corn for improvement of the agronomic traits and quality of the product. One such agronomic trait is insect resistance, which is accomplished through the expression of heterologous insect toxins, also known as transgenes, inserted into the genome of the corn plant.
[0005] The expression of such transgenes in a transgenic plant, plant part, seed or cell may be influenced by many different factors, including the elements used in the cassettes driving transgene expression and the interaction of those elements within a cassette. This is complicated further forBCS236357 a transgenic insertion containing two or more expression cassettes, with each expression cassette having a transgene conferring a separate trait, also known as a multi-gene transgenic event. A commercially useful multi-gene transgenic event requires that each of the transgenes in the transgenic insertion express in the manner necessary for each trait.
[0006] There are a number of different transgenic events in corn that have been described in the art that provide various types of insect resistance, particularly to Lepidopteran species. These transgenic events have been in use commercially in a variety of geographies across the glove for an extended period of time, often have used the same or similar toxins that were in use in earlier deployed transgenic events, and resistance to the expressed toxins in these events by targeted insect pests has been observed in many geographic regions where these have been deployed.
[0007] There is a continuing need in the art to provide novel transgenic events in corn that exhibit resistance to insect infestation, and preferably the novel transgenic events confer resistance to the target insects, including those races that have evolved resistance to the existing commercially deployed traits, using modes of action that are not overlapping with or similar to the modes of action previously deployed in earlier commercial embodiments. The present disclosure provides for modifications of a novel transgenic event that confers resistance to Lepidopteran insect infestations, including Lepidopteran insects that have evolved resistance to commercial embodiments that have been previously deployed. SUMMARY
[0008] In one aspect, the present disclosure provides a recombinant DNA molecule comprising: (a) a first nucleotide sequence (i) comprising an expression cassette that encodes a Cry1B.868 or a Cry1Da_7, or (ii) selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7 and SEQ ID NO: 8; and (b) a second nucleotide sequence that (i) comprises at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 11 or 47, or (b) is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at leastBCS236357 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 11 or 47, or (iii) is selected from the group consisting of SEQ ID NOs: 49-148. In some embodiments, the first nucleotide sequence of the recombinant DNA molecule comprises at least two expression cassettes comprising a first expression cassette and a second expression cassette, wherein the first expression cassette encodes a Cry1B.868 and the second expression cassette encodes a Cry1Da_7 protein. In some embodiments, the recombinant DNA molecule may further comprise (c) a third nucleotide sequence that (i) comprises at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 12 or 48, or (ii) is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 12 or 48, or (iii) is selected from the group consisting of SEQ ID NOs: 149-248. The third nucleotide sequence, in certain embodiments, is selected from the group consisting of SEQ ID NOs: 149-248. The recombinant DNA molecule, in particular embodiments, has a deletion of one or more consecutive nucleotides between the second nucleotide sequence and the third nucleotide sequence relative to SEQ ID NO: 10, 12, or 48. In various embodiments, the second nucleotide sequence is selected from the group consisting of SEQ ID NOs: 49-148. In some embodiments, the recombinant DNA molecule has a deletion of one or more consecutiveBCS236357 nucleotides between the first nucleotide sequence and the second nucleotide sequence relative to SEQ ID NO: 10, 11, or 47.
[0009] In another aspect, the present disclosure provides a recombinant DNA molecule comprising: (a) a first nucleotide sequence (i) comprising an expression cassette that encodes a Cry1B.868 or a Cry1Da_7, or (ii) selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, and SEQ ID NO: 9; and (b) a second nucleotide sequence that (i) comprises at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 12 or 48, or (ii) is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 12 or 48, or (iii) is selected from the group consisting of SEQ ID NOs: 149-248. In some embodiments, the first nucleotide sequence of the recombinant DNA molecule comprises at least two expression cassettes comprising a first expression cassette and a second expression cassette, wherein the first expression cassette encodes a Cry1B.868 and the second expression cassette encodes a Cry1Da_7 protein. In certain embodiment, the second nucleotide sequence is selected from the group consisting of SEQ ID NOs: 149-248. The recombinant DNA molecule, in some embodiments, has a deletion of one or more consecutive nucleotides between the first nucleotide sequence and the second nucleotide sequence relative to SEQ ID NO: 10, 12, or 48. In particular embodiments, the recombinant DNA molecule may further comprise nucleotides 1-862 or 14,181-15,216 of SEQ ID NO: 10.
[0010] In many embodiments, a recombinant DNA molecule of the present disclosure may be comprised in a corn plant, corn plant part, corn plant cell, corn plant seed, corn progeny plant, orBCS236357 commodity or fuel product made from corn and corn plant parts. In some embodiments, a recombinant DNA molecule of the present disclosure may comprise an amplicon diagnostic for the presence of DNA comprising a sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, and SEQ ID NO: 9. A recombinant DNA molecule of the present disclosure, in particular embodiments, is derived from a corn plant, corn plant part, corn seed, processed corn seed, corn plant cell or tissue, animal feed comprising corn, corn oil, corn meal, corn flour, corn flakes, corn bran, food made comprising corn, corn biomass, or fuel products made from corn and corn plant parts.
[0011] In yet another aspect, the present disclosure provides a recombinant DNA molecule comprising a polynucleotide segment of sufficient length to function as a DNA probe that hybridizes specifically under stringent hybridization conditions with a polynucleotide having a sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 47, and SEQ ID NO: 48. In still yet another aspect, the present disclosure provides a pair of DNA molecules that can function as DNA primers when used together in an amplification reaction comprising a first DNA molecule and a second DNA molecule, wherein the first DNA molecule and the second DNA molecule are different, (a) wherein the first DNA molecule is: (i) at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, or at least 99.9% identical or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, or SEQ ID NO: 9, or a complement thereof, or (ii) at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, or at least 99.9% identical or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at leastBCS236357 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 11 or 47, or a complement thereof; and (b) wherein the second DNA molecule is: (i) at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, or at least 99.9% identical or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, or SEQ ID NO: 9, or a complement thereof, or (ii) at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, or at least 99.9% identical or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 11 or 47, or a complement thereof, or (ii) at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, or at least 99.9% identical or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 11 or 47, or a complement thereof, or (iii) at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, or at least 99.9% identical or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 12 or 48, or a complement thereof. In certain embodiments, the first DNA molecule and the second DNA molecule can be used together in an amplification reaction with a sample from a plant, plant part,BCS236357 plant seed, plant cell, food or animal feed, or commodity or fuel product made from a plant or plant part to produce an amplicon diagnostic for the presence of a modified corn event MON 95379 DNA in said sample. The amplicon, in some embodiments, comprises a nucleotide sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 10.
[0012] In one aspect, the present disclosure provides a method of detecting the presence of a DNA segment diagnostic for a modified corn event MON 95379 DNA in a sample, said method comprising: contacting the sample with the DNA molecule that functions as a DNA probe of the present disclosure; subjecting the sample and the DNA molecule to stringent hybridization conditions; and detecting hybridization of the DNA molecule to the DNA segment in the sample, wherein the detection is diagnostic for the presence of the modified corn event MON 95379 DNA in the sample. In another aspect, the present disclosure provides a method of detecting the presence of a DNA segment diagnostic for a modified corn event MON 95379 DNA in a sample, the method comprising: contacting the sample with a pair of DNA molecules capable of functioning as DNA primers when used together in an amplification reaction provided by the present disclosure; performing an amplification reaction sufficient to produce a DNA amplicon; and detecting the presence of the DNA amplicon in the reaction, wherein the presence of the DNA amplicon is diagnostic for the presence of the modified corn event MON 95379 DNA in the sample. In yet another aspect, the present disclosure provides a method of detecting the presence of a DNA segment diagnostic for a modified corn event MON 95379 DNA in a sample, the method comprising performing a sequencing reaction with the sample, wherein the production in the sequencing reaction of a target nucleotide sequence comprising at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, or SEQ ID NO: 9, or a complement thereof, is diagnostic for the modified corn event MON 95379 DNA in the sample. In particular embodiments, the modified corn event MON 95379 is a further modified corn event MON 95379. In yet another embodiment, the present disclosure provides a DNA detection kitBCS236357 comprising: (a) a DNA probe of the present disclosure; and / or (b) a pair of DNA molecules that function as DNA primers as provided by the present disclosure.
[0013] In another aspect, the present disclosure provides a modified corn plant, corn plant part, corn seed, or corn cell comprising a modified corn event MON 95379 or comprising a recombinant DNA molecule as provided herein. In some embodiments, the modified corn plant, corn plant part, corn seed, or corn cell may comprise a recombinant DNA molecule or DNA segment comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 10, or a complement thereof; or a or a recombinant DNA molecule or DNA segment comprising a nucleotide sequence that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9% or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 47, or SEQ ID NO: 48, or a complement thereof. According to present embodiments, the corn plant, corn plant part, corn seed, or corn cell exhibits resistance to Fall Armyworm (Spodoptera frugiperda), Corn Earworm (Helicoverpa zea), Southwestern Corn Borer (Diatraea grandiosella), Surgarcane Borer (Diatraea saccharalis), and / or Lesser Cornstalk Borer (Elasmopalpus lignosellus). In particular embodiments, the corn plant, corn plant part, corn seed, or corn cell is further defined as a progeny plant of any generation of a corn plant comprising a modified corn event MON 95379, or a corn plant part, corn seed, or corn cell derived therefrom. In some embodiments, a recombinant DNA molecule comprises all or part of chromosome 8 of a corn or maize genome, or a DNA segment is present in chromosome 8 of a modified corn plant, corn plant part, corn seed, or corn cell. According to some embodiments, a modified corn event MON 95379 of a modified corn plant, corn plant part, cornBCS236357 seed, or corn cell comprises a genetic modification, mutation or edit, relative to the corn event MON 95379, introduced via a mutagenesis or targeted genome editing technique.
[0014] In yet another aspect, the present disclosure provides a method of producing a progeny corn plant comprising a modified corn event MON 95379 comprising: (a) sexually crossing a first modified corn plant that comprises a modified corn event MON 95379 with itself or a second corn plant; (b) collecting one or more seeds produced from said cross; (c) growing said seed to produce one or more progeny plants; and (d) selecting at least a first progeny plant or seed comprising a modified corn event MON 95379. The present disclosure, in additional embodiments, provides a hybrid modified corn plant or seed comprising a modified corn event MON 95379 produced by the methods described herein. In a further embodiment, the method described herein further comprises: (e) collecting seed from said at least first progeny plant comprising a modified corn event MON 95379. In some embodiments, the hybrid modified corn plan or seed of claim 39, wherein the modified corn event MON 95379 is a further modified corn event MON 95379.
[0015] Aspects of the present disclosure provide a nonliving corn plant material comprising a detectable amount of a recombinant DNA molecule as described herein. In some embodiments, the present disclosure provides microorganisms and commodity products comprising a recombinant DNA molecule of the present disclosure. The microorganism, in a number of embodiments, is a plant cell. In some embodiments, a commodity product is produced from a modified corn plant, corn plant part, corn seed, or corn tissue or cell comprising a modified corn event MON 95379. The modified corn event MON 95379, in certain embodiments, is a further modified corn event MON 95379. Non-limiting examples of commodity products include whole or processed corn seed, animal feed comprising corn, corn oil, corn meal, corn flour, corn flakes, corn bran, corn biomass, and fuel products produced using corn and corn plant parts. In certain aspects, the present disclosure provides a method of producing a commodity product, the method comprising: (a) obtaining a modified corn plant, corn plant part, or corn seed comprising a modified corn event MON 95379; and (b) producing a commodity product from the transgenic corn plant, corn plant part, or corn seed.
[0016] In aspects of the present disclosure, a modified corn event MON 95379 may be a further modified corn event MON 95379.
[0017] In one aspect, the present disclosure provides a corn plant, corn plant part, or corn seed comprising a DNA molecule or segment functional as a template when tested in a DNABCS236357 amplification method to produce an amplicon diagnostic for the presence of a modified corn event MON 95379 DNA.
[0018] In another aspect, the present disclosure provides a method of determining the zygosity of a corn plant, corn plant part, or corn seed comprising a modified corn event MON 95379 comprising: (a) contacting a sample comprising DNA from the corn plant, corn plant part, or corn seed with a pair of DNA molecules that function as DNA primers, as provided by the present disclosure; performing a nucleic acid amplification reaction with the sample and the pair of DNA molecules; and detecting in the nucleic acid amplification reaction a first amplicon diagnostic for a modified corn event MON 95379 and a second amplicon diagnostic for native corn genomic DNA not comprising the modified corn event MON 95379, wherein the presence of only the first amplicon is diagnostic of a corn plant, corn plant part, or corn seed homozygous for the modified corn event MON 95379, and the presence of both the first amplicon and the second amplicon is diagnostic of a corn plant, corn plant part, or corn seed heterozygous for the modified corn event MON 95379. In yet another aspect, the present disclosure provides a method of determining the zygosity of a corn plant, corn plant part, or corn seed comprising a modified corn event MON 95379 and a second primer pair that can produce a second amplicon of a standard genomic sequence known to be single copy and homozygous in the corn plant, corn plant part, or corn seed; contacting the sample with a first probe that specifically hybridizes to the first amplicon and / or all or part of the modified corn event MON 95379, performing a DNA amplification reaction using real-time PCR with the sample and determining the cycle thresholds (Ct values) of the first amplicon and the second amplicon; calculating the difference (ΔCt) between the Ct values of the second amplicon and the first amplicon; and determining the zygosity of the modified corn event MON 95379, wherein a ΔCt of about zero (0) indicates homozygosity of the modified corn event MON 95379 and a ΔCt of about one (1) indicates heterozygosity of the modified corn event MON 95379. In some embodiments, the first and second primer pairs comprise SEQ ID NO: 15 combined with SEQ ID NO: 16, and SEQ ID NO: 18 combined with SEQ ID NO: 19.
[0019] In still yet another aspect, the present disclosure provides a method of determining the zygosity of a corn plant, corn plant part, or corn seed comprising a modified corn event MON 95379 comprising: contacting a sample comprising DNA from the corn plant, corn plant part, or corn seed with a primer pair capable of producing a first amplicon diagnostic for the modified corn event MON 95379 and a second amplicon diagnostic for native corn genomic DNA not comprisingBCS236357 the modified corn event MON 95379; performing a nucleic acid amplification reaction with the sample and the set of primer pairs; and detecting the first amplicon and the second amplicon, wherein the presence of only the first amplicon is diagnostic of a corn plant, corn plant part, or corn seed homozygous for the modified corn event MON 95379, the presence of only the second amplicon is diagnostic of a corn plant, corn plant part, or corn seed homozygous for native corn genomic DNA not comprising the modified corn event MON 95379, and the presence of both the first amplicon and the second amplicon is diagnostic of a corn plant, corn plant part, or corn seed heterozygous for the modified corn event MON 95379. In one aspect, the present disclosure provides a method of determining the zygosity of a corn plant, corn plant part, or corn seed comprising a modified corn event MON 95379 comprising: contacting a sample comprising DNA from the corn plant, corn plant part, or corn seed with a probe set which contains at least a first probe that specifically hybridizes to the modified corn event MON 95379 and at least a second probe that specifically hybridizes to corn genomic DNA that was disrupted by insertion of the heterologous DNA of corn event MON 95379 and is disrupted by the modified corn event MON 95379, wherein the second probe does not hybridize to the modified corn event MON 95379 DNA; and hybridizing the probe set with the sample under stringent hybridization conditions, wherein detecting hybridization of only the first probe under the hybridization conditions is diagnostic for a corn plant, corn plant part, or corn seed homozygous for the modified corn event MON 95379. The probe set, in particular embodiments, comprises SEQ ID NO: 17 and SEQ ID NO: 20. In some embodiments, the modified corn event MON 95379 is a further modified corn event MON 95379.
[0020] Aspects of the present disclosure provide a population of transgenic corn plants, wherein each transgenic corn plant comprises a modified corn event MON 95379. In some embodiments, the population of corn plants has increased resistance to Lepidopteran insect pest species on average relative to a population of control corn plants lacking the modified corn event MON 95379. The modified corn event MON 95379, in additional embodiments, is a further modified corn event MON 95379. In particular embodiments, the population of corn plants has an increased resistance to a Lepidopteran insect pest species on average relative to a population of control corn plants lacking the modified corn event MON 95379.
[0021] In some aspect, the present disclosure provides a method of modifying a corn plant, the method comprising: (a) introducing a site-specific nuclease or a recombinant DNA constructBCS236357 comprising an expression cassette encoding a site-specific nuclease into at least one cell of an explant of a corn plant comprising corn event MON 95379, or a plant part thereof, to produce a modified corn event MON 95379 via a targeted genome editing technique; and (b) developing or regenerating a modified corn plant from the explant, wherein the modified corn plant comprises the modified corn event MON 95379. The modified corn event MON 95379, in additional embodiments, is a further modified corn event MON 95379. Non-limiting examples site-specific nucleases include a zinc-finger nuclease (ZFN), a meganuclease, an RNA-guided endonuclease, a TALE-endonuclease (TALEN), a recombinase, and a transposase. In some embodiments, the site- specific nuclease is an RNA-guided endonuclease or a CRISPR / Cas nuclease. The introducing step (a), in particular embodiments, comprises introducing the recombinant DNA construct into the at least one cell of the explant, wherein the recombinant DNA construct further comprises an expression cassette encoding a first guide RNA (gRNA). The recombinant DNA construct, in additional embodiments, further comprises an expression cassette encoding a second guide RNA (gRNA). The introducing step (a), in certain embodiments, further comprises introducing a first guide RNA (gRNA) or a second recombinant DNA construct comprising an expression cassette encoding a first guide RNA (gRNA) into the at least one cell of the explant. The introducing step (a), in some embodiments, comprises introducing at least two guide RNAs (gRNAs) comprising the first gRNA and a second gRNA into the at least one cell of the explant. In a number of embodiments, the second recombinant DNA construct further comprises an expression cassette encoding a second guide RNA (gRNA). The introducing step (a), in many embodiments, comprises introducing a first gRNA and second recombinant DNA construct comprising an expression cassette encoding a second guide RNA (gRNA) into the at least one cell of the explant. In some embodiments, the site-specific nuclease has a first target site in the genome of the corn plant at or near corn event MON 95379. In particular embodiments, the site-specific nuclease has a second target site in the genome of the corn plant at or near corn event MON 95379. The introducing step (a), in certain embodiments, comprises introducing a second site-specific nuclease or a recombinant DNA construct comprising an expression cassette encoding a second site-specific nuclease into at least one cell of the explant, and wherein the second site-specific nuclease has a second target site in the genome of the corn plant at or near corn event MON 95379. In some embodiments, the first gRNA has a first target site in a flanking DNA sequence, 5´ flank, 3´ flank, junction sequence, or insertion sequence of corn event MON 95379, or a complement thereof. InBCS236357 particular embodiments, the first gRNA has a first target site comprising a target sequence that is: (i) at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9% or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 11 or 47, or a complement thereof; or (ii) at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9% or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides SEQ ID NO: 12 or 48, or a complement thereof;; or (iii) at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9% or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, or SEQ ID NO: 9, or a complement thereof. In some embodiments, the first gRNA has a second target site comprising a target sequence that is: (i) at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9% or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 11 or 47, or a complement thereof; or (ii) at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, atBCS236357 least 99.6%, at least 99.7%, at least 99.8%, at least 99.9% or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 12 or 48, or a complement thereof; or (iii) at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9% or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, or SEQ ID NO: 9, or a complement thereof. In certain embodiments, (i) the first gRNA has a first target site comprising a target sequence that is: (1) at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9% or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 11 or 47, or a complement thereof; or (2) at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9% or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 12 or 48, or a complement thereof; or (3) at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9% or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50BCS236357 consecutive nucleotides of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, or SEQ ID NO: 9, or a complement thereof; and (ii) the second gRNA has a second target site comprising a target sequence that is: (ii) wherein the second gRNA has a second target site comprising a target sequence that is: (1) at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9% or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 11 or 47, or a complement thereof; or (2) at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9% or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 12 or 48, or a complement thereof; or (3) at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9% or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, or SEQ ID NO: 9, or a complement thereof. In some embodiments, the modified corn event MON 95379 comprises a deletion or excision of intervening genomic DNA between the first target site and the second target site, relative to the corn event MON 95379. In certain embodiments, the methods of the present disclosure may further comprise selecting the modified corn plant comprising the modified corn event MON 95379, and sexually crossing the modified corn plant with itself or a second corn plant to produce one or more modified progeny corn plants.BCS236357
[0022] Aspect of the present disclosure provide a method of introducing a target site into a corn plant, the method comprising: (a) introducing a cognate target site into the corn event MON 95379 locus of at least one cell of a corn plant or corn plant part comprising the corn event MON 95379 or an explant thereof via a targeted genome editing technique, wherein the cognate target site is identical or similar to an originator target site for a site-specific nuclease present in the corn event MON 95379 locus, and (b) developing or regenerating a modified corn plant comprising a modified corn event MON 95379 comprising the cognate target site. In some embodiments, the methods of the present disclosure may further comprise: (c) introducing a site-specific nuclease or a recombinant DNA construct comprising an expression cassette encoding a site-specific nuclease into at least one cell of an explant of a corn plant comprising the modified corn event MON 95379 or a plant part thereof, to produce a further modified corn event MON 95379 via a targeted genome editing technique, wherein the target site of the site-specific nuclease includes the cognate target site and the originator target site; and (d) developing or regenerating a second modified corn plant comprising the further modified corn event MON 95379.
[0023] In certain aspects, the present disclosure provides a method of introducing a target site into a corn plant, the method comprising: (a) introducing a cognate target site into the corn event MON 95379 locus of at least one cell of a corn plant or corn plant part comprising the corn event MON 95379 or an explant thereof via a targeted genome editing technique to produce a modified corn event MON 95379 comprising the cognate target site, wherein the cognate target site is identical or similar to an originator target site for a site-specific nuclease present in the corn event MON 95379 locus, and (b) introducing a site-specific nuclease or a recombinant DNA construct comprising an expression cassette encoding a site-specific nuclease into at least one cell of an explant of a modified corn plant comprising the modified corn event MON 95379, or a plant part thereof, to produce a further modified corn event MON 95379 via a targeted genome editing technique, wherein the target site of the site-specific nuclease includes the cognate target site and the originator target site; and (c) developing or regenerating a second modified corn plant comprising the further modified corn event MON 95379. In some embodiments, the further modified corn event MON 95379 of the second modified corn plant comprises a deletion or excision of intervening genomic DNA between the originator target site and the cognate target site, relative to the corn event MON 95379 or modified corn event MON 95379. In certain embodiments, the methods of the present disclosure may further comprise selecting the secondBCS236357 modified corn plant or a progeny plant of the second modified corn plant comprising the further modified corn event MON 95379, and sexually crossing the second modified corn plant or the progeny plant with itself or another corn plant to produce one or more modified progeny corn plants comprising the further modified corn event MON 95379. In additional embodiments, the modified corn event ZM_BCS216090 is a further modified corn event MON 95379. In some aspects, the present disclosure provides a method of modifying an explant of a corn plant or plant part, the method comprising: introducing a site-specific nuclease or a recombinant DNA construct comprising an expression cassette encoding a site-specific nuclease into at least one cell of an explant of a corn plant or plant part comprising corn event MON 95379 to produce a modified corn event MON 95379 into the at least one cell of the explant. In certain embodiments, the modified corn event MON 95379 is a further modified corn event MON 95379. BRIEF DESCRIPTION OF THE DRAWINGS
[0024] FIG. 1 represents the sequence of corn event MON 95379. Horizontal lines and boxes correspond to the positions of SEQ ID NO: 1 ([1]), SEQ ID NO: 2 ([2]), SEQ ID NO: 3 ([3]), SEQ ID NO: 4 ([4]), SEQ ID NO: 5 ([5]), SEQ ID NO: 6 ([6]), SEQ ID NO: 7 ([7]), SEQ ID NO: 8 ([8]), SEQ ID NO: 9 ([9]), SEQ ID NO: 11 (
[0011] ), and SEQ ID NO: 12 (
[0012] ) relative to SEQ ID NO: 10 (
[0010] ). The horizontal arrows labeled SQ51219 (SEQ ID NO: 15) (
[0015] ), SQ21524 (SEQ ID NO: 16) (
[0016] ), SQ50998 (SEQ ID NO: 21) (
[0021] ), SQ50997 (SEQ ID NO: 22) (
[0022] ), SQ50485 (SEQ ID NO: 24) (
[0024] ) and SQ50484 (SEQ ID NO: 25) (
[0025] ) represent the approximate position of subsets of primers that can be used to detect corn event MON 95379. The horizontal arrows labeled PB10269 (SEQ ID NO: 17) (
[0017] ), PB50340 (SEQ ID NO: 23) (
[0023] ), PB50138 (SEQ ID NO: 26) (
[0026] ) represent the approximate position of a DNA probe that can be used to detect corn event MON 95379. “E” represents an enhancer element, “P” represents a promoter element, “L” represents a leader (5´ UTR) element, “I” represents an intron element, “T” represents a 3´ UTR, “Cry1B.868” represents the Cry1B.868 coding sequence element, “Cry1Da_7” represents the Cry1Da_7 coding sequence element, “LoxP” represents the site at which Cre-recombinase marker excision occurred, leaving behind one of the two LoxP sites after marker excision, and “LB” represents the left T-DNA border.
[0025] FIG.2 is a diagrammatic representation of the T-DNA cassettes before integration to form event MON 95379, after integration, and after Cre-excision. The top horizontal box represents theBCS236357 T-DNA cassette in the plasmid vector used to transform event MON 95379, presented as SEQ ID NO: 13 (
[0013] ) (“T-DNA Before Integration”). The horizontal arrows below
[0013] represent the individual genetic elements comprised within the two transgene cassettes. “LB” represents a T- DNA left border element, “E” represents an enhancer element, “P” represents a promoter element, “L” represents a leader (5´ UTR) element, “I” represents an intron element, “T” represents a 3´ UTR, “Cry1B.868” represents the Cry1B.868 coding sequence element, “Cry1Da_7” represents the Cry1Da_7 coding sequence element, “CP4” represents the CP4 selectable marker, “TS” represented a targeting sequence, “LoxP” represents the site at which Cre-recombinase marker excision occurs, and “RB” represents a T-DNA right border element. The middle horizontal box, “Inserted T-DNA After Integration,” represents the T-DNA cassette integrated into the corn genome after transformation wherein the right T-DNA border (RB) was lost during integration. The bottom horizontal box, “Inserted T-DNA After Cre-Excision,” represents the integrated T- DNA cassette after the CP4 selectable marker cassette was excised, leaving behind one of the two LoxP sites and the LB region.
[0026] FIG.3 is a diagrammatic representation of the breeding process to produce the marker-free corn event MON 95379. R0generation events (“transformants”) are those that are derived from the initial transformation with the binary transformation vector used to generate corn event MON 95379. Subsequent “R” generations (R1, and R2) represent successive generations produced through self-pollination of plants derived from the initial R0transformant that resulted in the corn event MON 95379. The R2transformants which are homozygous for the T-DNA insertion are cross-pollinated with an elite transgenic corn line comprising a transgene cassette for the expression of Cre-recombinase, resulting in an F1 generation, wherein many of the progeny have lost the CP4 selectable marker cassette due to Cre-recombinase excision. Hemizygous T-DNA positive, CP4 negative plants are selected and self-pollinated, resulting in an F2 generation. F2 plants homozygous for the inserted T-DNA allele without the CP4 marker and lacking the Cre- recombinase transgene cassette are selected and self-pollinated giving rise to an F3generation. The F3 generation plants are self-pollinated giving rise to a pure line of F4 Gold Standard Seed.BCS236357 BRIEF DESCRIPTION OF THE SEQUENCES
[0027] SEQ ID NO: 1 is a 50-nucleotide sequence representing the 5´ junction region of corn genomic DNA and the integrated transgenic expression cassette. SEQ ID NO: 1 is found within SEQ ID NO: 10 at nucleotide positions 838-887.
[0028] SEQ ID NO: 2 is a 50-nucleotide sequence representing the 3´ junction region of the integrated transgenic expression cassette and the corn genomic DNA. SEQ ID NO: 2 is found within SEQ ID NO: 10 at nucleotide positions 14,156-14,205.
[0029] SEQ ID NO: 3 is a 100-nucleotide sequence representing the 5´ junction region of corn genomic DNA and the integrated transgenic expression cassette. SEQ ID NO: 3 is found within SEQ ID NO: 10 at nucleotide positions 813-912.
[0030] SEQ ID NO: 4 is a 100-nucleotide sequence representing the 3´ junction region of the integrated transgenic expression cassette and the corn genomic DNA. SEQ ID NO: 4 is found within SEQ ID NO: 10 at nucleotide positions 14,131-14,230.
[0031] SEQ ID NO: 5 is a 200-nucleotide sequence representing the 5´ junction region of corn genomic DNA and the integrated transgenic expression cassette. SEQ ID NO: 5 is found within SEQ ID NO: 10 at nucleotide positions 763-962.
[0032] SEQ ID NO: 6 is a 200-nucleotide sequence representing the 3´ junction region of the integrated transgenic expression cassette and the corn genomic DNA. SEQ ID NO: 6 is found within SEQ ID NO: 10 at nucleotide positions 14,081-14,280.
[0033] SEQ ID NO: 7 is a 1,160-nucleotide sequence representing the 5´ junction region of corn genomic DNA and the integrated transgenic expression cassette. SEQ ID NO: 7 is found within SEQ ID NO: 10 at nucleotide positions 1-1,160.
[0034] SEQ ID NO: 8 is a 1,178-nucleotide sequence representing the 3´ junction region of the integrated transgenic expression cassette and the corn genomic DNA. SEQ ID NO: 8 is found within SEQ ID NO: 10 at nucleotide positions 14,039-15,216.
[0035] SEQ ID NO: 9 is a 13,318-nucleotide sequence corresponding to the transgenic inserted T- DNA of corn event MON 95379.
[0036] SEQ ID NO: 10 is a 15,216-nucleotide sequence corresponding to the contig nucleotide sequence of the 5´ genomic flanking DNA nucleotide sequence, the inserted T-DNA nucleotide sequence in event MON 95379, and the 3´ genomic flanking DNA nucleotide sequence; andBCS236357 includes SEQ ID NO: 11 (nucleotides 1-862), SEQ ID NO: 9 (nucleotides 863-14,180), and SEQ ID NO: 12 (nucleotides 14,181-15,216).
[0037] SEQ ID NO: 11 is an 862-nucleotide sequence representing the 5´-flanking corn genomic DNA up to the inserted T-DNA. SEQ ID NO: 11 is found within SEQ ID NO: 10 at nucleotide positions 1-862.
[0038] SEQ ID NO: 12 is a 1,036-nucleotide sequence representing the 3´-flanking corn genomic DNA after the inserted T-DNA. SEQ ID NO: 12 is found within SEQ ID NO: 10 at nucleotide positions 14,181-15,216.
[0039] SEQ ID NO: 13 is a 18,376-nucleotide sequence representing the transgene cassette comprised within the binary plasmid transformation vector used to transform corn to produce corn event MON 95379.
[0040] SEQ ID NO: 14 is a 35-nucleotide sequence representing the LoxP sites used for Cre- mediated excision and recombination. A remaining LoxP site after marker excision can be found within SEQ ID NO: 10 at nucleotide positions 1,080-1,114.
[0041] SEQ ID NO: 15 is a 20-nucleotide sequence corresponding to a thermal amplification primer referred to as SQ51219 used to identify corn event MON 95379 DNA in a sample, and is identical to the nucleotide sequence corresponding to positions 833-852 of SEQ ID NO: 10.
[0042] SEQ ID NO: 16 is a 30-nucleotide sequence corresponding to a thermal amplification primer referred to as SQ21524 used to identify corn event MON 95379 DNA in a sample, and is identical to the reverse complement of the nucleotide sequence corresponding to positions 905- 934 of SEQ ID NO: 10.
[0043] SEQ ID NO: 17 is a 16-nucleotide sequence corresponding to a probe referred to as PB10269 used to identify corn event MON 95379 DNA in a sample, and is identical to the reverse complement of the nucleotide sequence corresponding to positions 886-901 of SEQ ID NO: 10.
[0044] SEQ ID NO: 18 is a 24-nucleotide sequence corresponding to a thermal amplification primer referred to as SQ20222 used as an internal control for the event and zygosity assay for MON 95379 and hybridizes to a region of the corn genome.
[0045] SEQ ID NO: 19 is a 28-nucleotide sequence corresponding to a thermal amplification primer referred to as SQ20221 used as an internal control for the event and zygosity assay for MON 95379 and hybridizes to a region of the corn genome.BCS236357
[0046] SEQ ID NO: 20 is a 29-nucleotide sequence corresponding to a probe referred to as PB50237 used as an internal control for the event and zygosity assay for MON 95379 and hybridizes to a region of the corn genome.
[0047] SEQ ID NO: 21 is a 20-nucleotide sequence corresponding to a thermal amplification primer referred to as SQ50998 used in the zygosity assay for event MON 95379 and hybridizes to the coding sequence of Cry1B.868 within SEQ ID NO: 10; and is identical to the nucleotide sequence corresponding to positions 2,809-2,828 of SEQ ID NO: 10.
[0048] SEQ ID NO: 22 is a 20-nucleotide sequence corresponding to a thermal amplification primer referred to as SQ50997 used in the zygosity assay for event MON 95379 and hybridizes to the coding sequence of Cry1B.868 within SEQ ID NO: 10; and is identical to the reverse complement of the nucleotide sequence corresponding to positions 2,852-2,871 of SEQ ID NO: 10.
[0049] SEQ ID NO: 23 is an 18-nucleotide sequence corresponding to a probe referred to as PB50340 used in the zygosity assay for event MON 95379 and hybridizes to the coding sequence of Cry1B.868 within SEQ ID NO: 10; and is identical to the reverse complement of the nucleotide sequence corresponding to positions 2,833-2,850 of SEQ ID NO: 10.
[0050] SEQ ID NO: 24 is a 19-nucleotide sequence corresponding to a thermal amplification primer referred to as SQ50485 used in the zygosity assay for event MON 95379 and hybridizes to the coding sequence of Cry1Da_7 within SEQ ID NO: 10; and is identical to the nucleotide sequence corresponding to positions 12,820-12,838 of SEQ ID NO: 10.
[0051] SEQ ID NO: 25 is an 18-nucleotide sequence corresponding to a thermal amplification primer referred to as SQ50484 used in the zygosity assay for event MON 95379 and hybridizes to the coding sequence of Cry1Da_7 within SEQ ID NO: 10; and is identical to the reverse complement of the nucleotide sequence corresponding to positions 12,855-12,872 of SEQ ID NO: 10.
[0052] SEQ ID NO: 26 is a 14-nucleotide sequence corresponding to a probe referred to as PB50138 used in the zygosity assay for event MON 95379 and hybridizes to the coding sequence of Cry1Da_7 within SEQ ID NO: 10; and is identical to the reverse complement of the nucleotide sequence corresponding to positions 12,840-12,853 of SEQ ID NO: 10.
[0053] SEQ ID NO: 27 is a 21-nucleotide sequence corresponding to a thermal amplification primer referred to as PNEGDNA used in the zygosity assay for event MON 95379 and hybridizesBCS236357 to a region of corn genomic DNA which was deleted when the T-DNA used to produce event MON 95379 inserted into the corn genome. An amplicon derived from the combination of primers SQ51219 and PNEGDNA is diagnostic for the wild-type allele lacking the event MON 95379 inserted T-DNA.
[0054] SEQ ID NO: 28 is a 14-nucleotide sequence corresponding to a probe referred to as PRBNEGDNA used in the zygosity assay for event MON 95379 and hybridizes to a region of corn genomic DNA which was deleted when the T-DNA used to produce event MON 95379 inserted into the corn genome.
[0055] SEQ ID NO: 29 is a 27-nucleotide sequence corresponding to an OgRRS, OgRRS_5-1.
[0056] SEQ ID NO: 30 is a 27-nucleotide sequence corresponding to an OgRRS, OgRRS_5-2.
[0057] SEQ ID NO: 31 is a 27-nucleotide sequence corresponding to an OgRRS, OgRRS_In-1.
[0058] SEQ ID NO: 32 is a 27-nucleotide sequence corresponding to an OgRRS, OgRRS_3-1.
[0059] SEQ ID NO: 33 is a 27-nucleotide sequence corresponding to an OgRRS, OgRRS_3-2.
[0060] SEQ ID NO: 34 is a 51-nucleotide sequence corresponding to a gRNA, gRNA_OgRRS_5- 1 comprised of a Cas12a protospacer adjacent motif (PAM) site operably linked to a guide-RNA hybridization site.
[0061] SEQ ID NO: 35 is a 51-nucleotide sequence corresponding to a gRNA, gRNA_OgRRS_5- 2.
[0062] SEQ ID NO: 36 is a 51-nucleotide sequence corresponding to a gRNA, gRNA_OgRRS_In- 1.
[0063] SEQ ID NO: 37 is a 51-nucleotide sequence corresponding to a gRNA, gRNA_OgRRS_3- 1.
[0064] SEQ ID NO: 38 is a 51-nucleotide sequence corresponding to a gRNA, gRNA_OgRRS_3- 2.
[0065] SEQ ID NO: 39 is a sequence of a synthetic DNA coding sequence designed for expression in a plant cell encoding a nuclear targeted LbCas12a CRISPR-associated protein.
[0066] SEQ ID NO: 40 is an amino acid sequence of a nuclear targeted LbCas12a CRISPR- associated protein encoded by SEQ ID NO: 39.
[0067] SEQ ID NO: 41 is a sequence of a synthetic DNA coding sequence designed for expression in a plant cell encoding a nuclear targeted LbCas12a-TYCV CRISPR-associated protein.BCS236357
[0068] SEQ ID NO: 42 is an amino acid sequence of a nuclear targeted LbCas12a-TYCV CRISPR-associated protein encoded by SEQ ID NO: 41.
[0069] SEQ ID NO: 43 is a sequence of a synthetic DNA coding sequence designed for expression in a plant cell encoding a nuclear targeted LbCas12a-TATV CRISPR-associated protein.
[0070] SEQ ID NO: 44 is an amino acid sequence of a nuclear targeted LbCas12a-TATV CRISPR-associated protein encoded by SEQ ID NO: 43.
[0071] SEQ ID NO: 45 is a sequence of a synthetic DNA coding sequence designed for expression in a plant cell encoding a nuclear targeted FnCas12a CRISPR-associated protein.
[0072] SEQ ID NO: 46 is an amino acid sequence of a nuclear targeted FnCas12a CRISPR- associated protein encoded by SEQ ID NO: 45.
[0073] SEQ ID NO: 47 is a 5000-nucleotide sequence representing corn genomic DNA that flanks the transgenic insert at the 5´end of the insert. Nucleotides 4,139-5,000 of SEQ ID NO: 47 are identical to nucleotides 1-862 of SEQ ID NO: 11. Nucleotides 1-4,138 are based on the genomic sequence of the B73 corn cultivar.
[0074] SEQ ID NO: 48 is a 5,000-nucleotide sequence representing corn genomic DNA that flanks the transgenic insert at the 3´ end of the insert. Nucleotides 1-1,036 of SEQ ID NO: 48 are identical to nucleotides 1-1,036 of SEQ ID NO: 12. The remaining nucleotides (1,037-5,000) are based on the genomic sequence of the B73 corn cultivar.
[0075] SEQ ID NOs:49-148 are 50-nucleotide sequence in the 5´ flank genomic sequence of corn event MON 95379.
[0076] SEQ ID NOs:149-248 are 50-nucleotide sequence in the 3´ flank genomic sequence of corn event MON 95379. DETAILED DESCRIPTION
[0077] The present disclosure relates to a transgenic corn event – MON 95379 – that achieves insecticidal control over Lepidopteran pests of corn by expression of Cry1B.868 and Cry1Da_7. Specifically, expression of the Cry1B.868 and Cry1Da_7 insect inhibitory proteins in corn event MON 95379 provides resistance to the Lepidopteran insect pests Fall Armyworm (Spodoptera frugiperda), Corn Earworm (Helicoverpa zea), Southwestern Corn Borer (Diatraea grandiosella), Surgarcane Borer (Diatraea saccharalis), and Lesser Cornstalk Borer (Elasmopalpus lignosellus). Event MON 95379 will meet a great need for control of these insects in the corn market, asBCS236357 chemical insecticides often do not provide adequate control of these insects, or require multiple applications over the growing season, increasing the input of chemical pesticides in the environment and adding cost to the production of corn.
[0078] It should be understood that reference to event MON 95379 is equivalent to reference to event MON95379; they are interchangeable and represent the same transgenic corn event.
[0079] Plant transformation techniques are used to insert foreign DNA (also known as transgenic DNA) randomly into a chromosome of the genome of a cell to produce a genetically engineered cell, also referred to as a “transgenic” or “recombinant” cell. Using this technique, many individual cells are transformed, each resulting in a unique “transgenic event” or “event” due to the random insertion of the foreign DNA into the genome. A transgenic plant is then regenerated from each individual transgenic cell. This results in every cell of the transgenic plant containing the uniquely inserted transgenic event as a stable part of its genome. This transgenic plant can then be used to produce progeny plants, each containing the unique transgenic event.
[0080] Corn event MON 95379 was produced by an Agrobacterium-mediated transformation process of corn immature embryos with a single T-DNA binary system. In this system, an Agrobacterium strain employing one binary plasmid vector with a single T-DNA was utilized. The T-DNA construct comprised two transgene cassettes for the expression of the insect toxin coding sequences encoding Cry1B.868 and Cry1Da_7, and a transgene cassette used for the selection of transformed corn cells using glyphosate selection (CP4). The T-DNA construct is SEQ ID NO: 13, and illustrated in Figure 2 (“T-DNA Before Integration”). During integration, the right T-DNA border was lost as shown in Figure 2 (“Inserted T-DNA After Integration”). The glyphosate selection cassette was flanked on both sides with LoxP recognition sites which are recognized by Cre-recombinase, derived from Enterobacteria phage P1 (Larry Gilbertson (2003) Cre-lox recombination: Cre-active tools for plant biotechnology. TRENDS in Biotechnology, 21:12, 550-555).
[0081] As specifically described herein, corn event MON 95379 was produced by a complex research and development process in which: (1) hundreds of plasmid vector constructs – which varied with respect to the coding sequences for the insecticidal proteins, the coding sequences for the transcriptional regulatory elements, and number and orientation of the cassettes within the constructs – were developed and transformed into corn cells to create thousands of events that were tested and analyzed, resulting in the selection of the construct used to generate event MONBCS236357 95379; (2) hundreds of corn cells were transformed with the construct used to generate event MON 95379, creating a population of transgenic plants in which each plant contained a unique transgenic event that was regenerated and tested; (3) the final event MON 95379 was selected after a rigorous multi-year event selection process involving the testing and analysis of molecular characteristics, efficacy, protein expression, and agronomic properties in a variety of genetic backgrounds; and (4) the glyphosate selection cassette in corn event MON 95379 was removed through in vivo Cre- excision to create a “marker-free” final event MON 95379. Corn event MON 95379 was thus produced and selected as a uniquely superior event useful for broad-scale agronomic purposes.
[0082] The plasmid DNA inserted into the genome of corn event MON 95379 was characterized by detailed molecular analysis. This analysis included: the insert number (number of integration sites within the corn genome), the genomic insert location (the specific site in the corn genome where the insertion occurred), the copy number (the number of copies of the T-DNA within one locus), and the integrity of the transgenic inserted DNA. The detailed molecular analysis demonstrated that the integrated T-DNA containing the Cry1B.868 and Cry1Da_7 expression cassettes remained intact after integration and Cre-excision of the glyphosate (CP4) selection cassette. As used herein, an “expression cassette” or “cassette” or “transgene” is a recombinant DNA molecule or sequence comprising a combination of distinct elements that are to be expressed by a transformed cell. As provided herein, an “expression cassette” or “cassette” or “transgene” includes one or more regulatory element(s) operably linked to the coding or transcribable DNA sequences encoding Cry1B.868 or Cry1Da_7 including the promoter, leader, intron and transcription termination sequences. The “expression cassette” or “cassette” or “transgene” is recombinant and heterologous with respect to the transformed plant cell genome. For purposes of the present disclosure, such an “expression cassette” or “cassette” or “transgene” is a recombinant DNA molecule or sequence that encodes the toxins Cry1B.868 or Cry1Da_7. Table 1 provides a list of the elements contained in SEQ ID NO: 10 after Cre-excision of the CP4 cassette, the DNA sequence that corresponds to corn event MON 95379.BCS236357 Table 1. Description of corn event MON 95379 Position in SEQ ID Element NO: 10 Description . a of e alBCS236357 Position in SEQ ID Element NO: 10 Description
[0083] Corn event MON 95379 is characterized as an insertion into a single locus in the corn genome, resulting in two new loci or junction sequences (e.g., sequences set forth in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, and SEQ ID NO: 8) spanning a portion of the inserted DNA and the corn genomic DNA that are not known to appear naturally in the corn genome or other transgenic corn events – they are unique to event MON 95379. These junction sequences are useful in detecting the presence of the event MON 95379 in corn cells, corn tissue, corn seed, and corn plants or corn plant products, such as corn commodity products. DNA molecular probes and primer pairs are described herein that have been developed for use in identifying the presence of these various junction segments in biological samples containing or suspected of containing corn cells, corn seed, corn plant parts, or corn plant tissue that contain the event MON 95379.
[0084] As used herein, a “corn event MON 95379 locus” refers to the genomic locus of the corn event MON 95379 or a modified corn event MON 95379 or a further modified corn event MON 95379, wherein the corn event MON 95379 locus includes the flanking, junction and insertion sequences of the corn event MON 95379 or the modified corn event MON 95379 or furtherBCS236357 modified corn event MON 95379. A modified corn event MON 95379 or a further modified corn event MON 95379 comprises one or more mutations, edits and / or genetic modifications in the corn event MON 95379 locus, such as one or more mutations, edits and / or genetic modifications in a flanking, junction and / or insertion sequence(s) of the corn event MON 95379 locus, relative to the corn event MON 95379.
[0085] According to present embodiments, a modified corn event MON 95379 and methods of making a modified corn event MON 95379 are provided. As is described further herein, various mutagenesis or targeted genome editing techniques and related tools are known and could be made or engineered to permit genetic modification or mutation of the transgenic insert, junction and / or the flanking genomic DNA of corn event MON 95379, such as by deletion, insertion, transposition, inversion, and / or substitution of nucleic acid sequence(s), and / or by insertion or introduction of a guide RNA target site or a cognate target site or CgRRS, and the transgenic event as modified may still be uniquely characterized by the presence of heterologous DNA and / or one or more sequences of the insertion, junction(s) and / or flanking sequence(s) described herein at the same position or location in the genome previously occupied by the unmodified corn event MON 95379 relative to flanking portions or sequences of the native corn genome. According to present embodiments, a modified transgenic event derived from corn event MON 95379 may comprise all or part of the insertion sequence and / or transgene cassette of corn event MON 95379, one or more of the junction sequence(s) of corn event MON 95379, and / or one or more flanking sequence(s) of corn event MON 95379 as described herein.
[0086] As used herein, a “modified corn event MON 95379” refers to any genomic DNA or sequence of the corn event MON 95379 locus comprising one or more mutations, edits or genetic modifications relative to the genomic DNA or sequence of the corn event MON 95379, wherein such mutations or edits are introduced or made by a mutagenesis or targeted genome editing technique of a corn plant, plant part, tissue or cell comprising the corn event MON 95379. A “modified corn event MON 95379” includes, as a type of modified corn event MON 95379, a “further modified corn event MON 95379” made by first inserting a target site or cognate target site or CgRRS into the corn event MON 95379 locus and then further modifying the corn event MON 95379 locus as described herein. For clarity, a “modified corn event MON 95379” includes genomic DNA or sequences of the corn event MON 95379 locus comprising one or more mutations, edits or genetic modifications relative to the genomic DNA or sequence of the cornBCS236357 event MON 95379, wherein such mutations or edits are introduced or made by a mutagenesis or targeted genome editing technique of a corn plant, plant part, tissue or cell comprising the corn event MON 95379, wherein such modified corn event MON 95379 is not a further modified corn event MON 95379. Methods and techniques of mutagenesis are known in the art and include, for example, chemical mutagenesis (i.e., treatment with a chemical mutagen, such as an azide, hydroxylamine, nitrous acid, acridine, nucleotide base analog, or alkylating agent – e.g., EMS (ethylmethane sulfonate), MNU (N-methyl-N-nitrosourea), etc.), physical mutagenesis (e.g., gamma rays, X-rays, UV, ion beam, other forms of radiation, etc.), and insertional mutagenesis (e.g., transposon or T-DNA insertion). As used herein, a “modified corn plant” refers to a corn or maize plant comprising a modified corn event MON 95379 or a further modified corn event MON 95379. Thus, a modified corn plant part, plant seed, plant tissue, or plant cell comprising a modified corn event MON 95379 or a further modified corn event MON 95379 that is derived, taken or descended from a modified corn plant and / or created by genetic modification, mutation or editing of the transgenic insert, junction and / or the flanking genomic DNA of corn event MON 95379 in a corn plant part, plant seed, plant tissue, or plant cell using a mutagenesis or targeted genome editing technique.
[0087] As used herein, a “target site” for genome editing refers to the location of a polynucleotide sequence within a plant genome, which may be within or near corn event MON 95379, that is bound and cleaved by a site-specific nuclease introducing a double stranded break (or single- stranded nick) into the nucleic acid backbone of the polynucleotide sequence and / or its complementary DNA strand. A target site may comprise at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 29, or at least 30 consecutive nucleotides. A “target site” for a RNA-guided nuclease may comprise the sequence of either complementary strand of a double-stranded nucleic acid (DNA) molecule or chromosome at the target site that is bound or hybridized to a guide RNA of a ribonucleoprotein complex comprising the RNA-guided nuclease. A site-specific nuclease may bind to a target site, such as via a non-coding guide RNA (e.g., without being limiting, a CRISPR RNA (crRNA) or a single- guide RNA (sgRNA) as described further below). A non-coding guide RNA (gRNA) provided herein may be complementary to a target site (e.g., complementary to either strand of a double- stranded nucleic acid molecule or chromosome at the target site). It will be appreciated that perfectBCS236357 identity or complementarity may not be required for a non-coding guide RNA to bind or hybridize to a target site. For example, at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, or at least 8 mismatches (or more) between a target site and a non-coding RNA may be tolerated. A “target site” also refers to the location of a polynucleotide sequence within a plant genome, which may be within or near corn event MON 95379 or a modified corn event MON 95379, that is bound and cleaved by another site-specific nuclease that may not be guided by a non-coding RNA molecule, such as a meganuclease, zinc finger nuclease (ZFN), or a transcription activator- like effector nuclease (TALEN), to introduce a double stranded break (or single-stranded nick) into the polynucleotide sequence and / or its complementary DNA strand. As used herein, a “target region” or a “targeted region” refers to a polynucleotide sequence or region that is flanked by two or more target sites. Without being limiting, in some embodiments a target region may be subjected to a mutation, deletion, insertion or inversion. As used herein, “flanked” when used to describe a target region of a polynucleotide sequence or molecule, refers to two or more target sites of the polynucleotide sequence or molecule surrounding the target region, with one target site on each side of the target region.
[0088] As used herein, a “donor molecule”, “donor template”, or “donor template molecule” (collectively a “donor template”), which may be a recombinant DNA donor template, is defined as a nucleic acid molecule having a nucleic acid template or insertion sequence for site-directed, targeted insertion or recombination into the genome of a plant cell via repair of a nick or double- stranded DNA break in the genome of a plant cell. For example, a “donor template” may be used for site-directed integration of a guide RNA target site or a cognate target site or CgRRS into a target site within the genome of a plant. A targeted genome editing technique provided herein may comprise the use of one or more, two or more, three or more, four or more, or five or more donor molecules or templates. A “donor template” may be a single-stranded or double-stranded DNA or RNA molecule or plasmid. An “insertion sequence” of a donor template is a sequence designed for targeted insertion into the genome of a plant cell, which may be of any suitable length, such as to include a guide RNA target site or a cognate target site or CgRRS. Such an insertion sequence of a donor template is distinct and different from the transgenic insertion or insert of corn event MON 95379, although they may potentially have sequence(s) in common. A donor template may also have at least one homology sequence or homology arm, such as two homology arms, to direct the integration of a mutation or insertion sequence into a target site within the genome of a plantBCS236357 via homologous recombination, wherein the homology sequence or homology arm(s) are identical or complementary, or have a percent identity or percent complementarity, to a sequence at or near the target site within the genome of the plant. When a donor template comprises homology arm(s) and an insertion sequence, the homology arm(s) will flank or surround the insertion sequence of the donor template.
[0089] As used herein, a “targeted genome editing technique” refers to any method, protocol, or technique that can be used to make a targeted mutation or edit, such as one or more insertions, deletions, substitutions, inversions, transpositions, mutations and / or other genetic modifications at or near a target site in the genome of a plant, and / or a deletion or excision of a target region between two target sites in the genome of a plant, using a site-specific nuclease, such as a meganuclease, a zinc-finger nuclease (ZFN), an RNA-guided endonuclease (e.g., the CRISPR / Cas9 system), a TALE-endonuclease (TALEN), a recombinase, or a transposase. A site-specific nuclease may introduce a double stranded break (or single-stranded nick) into the nucleic acid backbone of the polynucleotide sequence and / or its complementary DNA strand. Following the introduction of the single or double-stranded break or nick or cleavage of DNA at or near the target site(s) by the site- specific nuclease, the genomic sequence can be repaired via a double strand break repair pathway, which may include, for example, non-homologous end-joining (NHEJ), microhomology-mediated end joining (MMEJ), homologous recombination, synthesis-dependent strand annealing (SDSA), single-strand annealing (SSA), or a combination of any thereof, at or near the target site(s). However, if the repair is imperfect, a mutation or edit may be introduced at or near the target site(s), and a target region between two or more target sites may be deleted or excised.
[0090] A “site-specific nuclease” provided herein may be selected from the group consisting of a zinc-finger nuclease (ZFN), a meganuclease, an RNA-guided endonuclease, a TALE- endonuclease (TALEN), a recombinase, a transposase, or any combination thereof. See, e.g., Khandagale, K. et al., “Genome editing for targeted improvement in plants,” Plant Biotechnol Rep 10: 327-343 (2016); and Gaj, T. et al., “ZFN, TALEN and CRISPR / Cas-based methods for genome engineering,” Trends Biotechnol.31(7): 397-405 (2013), the contents and disclosures of which are incorporated herein by reference. A recombinase may be a serine recombinase attached to a DNA recognition motif, a tyrosine recombinase attached to a DNA recognition motif or other recombinase enzyme known in the art. A recombinase or transposase may be a DNA transposase or recombinase attached to a DNA binding domain. A tyrosine recombinase attached to a DNABCS236357 recognition motif may be selected from the group consisting of a Cre recombinase, a Flp recombinase, and a Tnp1 recombinase. According to some embodiments, a Cre recombinase or a Gin recombinase provided herein is tethered to a zinc-finger DNA binding domain. In another embodiment, a serine recombinase attached to a DNA recognition motif provided herein is selected from the group consisting of a PhiC31 integrase, an R4 integrase, and a TP-901 integrase. In another embodiment, a DNA transposase attached to a DNA binding domain provided herein is selected from the group consisting of a TALE-piggyBac and TALE-Mutator.
[0091] According to embodiments of the present disclosure, an RNA-guided endonuclease may be selected from the group consisting of Cas1, Cas1B, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 (also known as Csn1 and Csx12), Cas10, Csy1, Csy2, Csy3, Cse1, Cse2, Csc1, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1, Cmr3, Cmr4, Cmr5, Cmr6, Csb1, Csb2, Csb3, Csx17, Csx14, Csx10, Csx16, CsaX, Csx3, Csx1, Csx15, Csf1, Csf2, Csf3, Csf4, Cas12a, Cpf1, CasX, CasY, and homologs or modified versions thereof, Argonaute (non-limiting examples of Argonaute proteins include Thermus thermophilus Argonaute (TtAgo), Pyrococcus furiosus Argonaute (PfAgo), Natronobacterium gregoryi Argonaute (NgAgo) and homologs or modified versions thereof. According to some embodiments, an RNA-guided endonuclease may be a Cas9 or Cas12a or Cpf1 enzyme.
[0092] In an aspect, a site-specific nuclease provided herein is selected from the group consisting of a zinc-finger nuclease, a meganuclease, an RNA-guided nuclease, a TALE-nuclease, a recombinase, a transposase, or any combination thereof. In another aspect, a site-specific nuclease provided herein is selected from the group consisting of a Cas9 or a Cas12a or Cpf1. In another aspect, a site-specific nuclease provided herein is selected from the group consisting of a Cas1, a Cas1B, a Cas2, a Cas3, a Cas4, a Cas5, a Cas6, a Cas7, a Cas8, a Cas9, a Cas10, a Cas12a, a Csy1, a Csy2, a Csy3, a Cse1, a Cse2, a Csc1, a Csc2, a Csa5, a Csn2, a Csm2, a Csm3, a Csm4, a Csm5, a Csm6, a Cmr1, a Cmr3, a Cmr4, a Cmr5, a Cmr6, a Csb1, a Csb2, a Csb3, a Csx17, a Csx14, a Csx10, a Csx16, a CsaX, a Csx3, a Csx1, a Csx15, a Csf1, a Csf2, a Csf3, a Csf4, a Cpf1, CasX, CasY, a homolog thereof, or a modified version thereof. In another aspect, an RNA-guided nuclease provided herein is selected from the group consisting of a Cas9 or a Cas12a or Cpf1. In another aspect, an RNA guided nuclease provided herein is selected from the group consisting of a Cas1, a Cas1B, a Cas2, a Cas3, a Cas4, a Cas5, a Cas6, a Cas7, a Cas8, a Cas9, a Cas10, a Cas12a, a Csy1, a Csy2, a Csy3, a Cse1, a Cse2, a Csc1, a Csc2, a Csa5, a Csn2, a Csm2, a Csm3,BCS236357 a Csm4, a Csm5, a Csm6, a Cmr1, a Cmr3, a Cmr4, a Cmr5, a Cmr6, a Csb1, a Csb2, a Csb3, a Csx17, a Csx14, a Csx10, a Csx16, a CsaX, a Csx3, a Csx1, a Csx15, a Csf1, a Csf2, a Csf3, a Csf4, a Cpf1, CasX, CasY, a homolog thereof, or a modified version thereof. In another aspect, a method and / or a composition provided herein comprises at least one, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, or at least ten site- specific nucleases. In yet another aspect, a method and / or a composition provided herein comprises at least one, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, or at least ten polynucleotides encoding at least one, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, or at least ten site-specific nucleases.
[0093] For RNA-guided endonucleases, a guide RNA (gRNA) molecule is further provided to direct the endonuclease to a target site in the genome of the plant via base-pairing or hybridization to cause a DSB or nick at or near the target site. The gRNA may be transformed or introduced into a plant cell or tissue (perhaps along with a nuclease, or nuclease-encoding DNA molecule, construct or vector) as a gRNA molecule, or as a recombinant DNA molecule, construct, or vector comprising a polynucleotide or transcribable DNA sequence encoding the guide RNA operably linked to a plant-expressible promoter. As understood in the art, a “guide RNA” may comprise, for example, a CRISPR RNA (crRNA), a single-chain guide RNA (sgRNA), or any other RNA molecule that may guide or direct an endonuclease to a specific target site in the genome. A “single-chain guide RNA” (or “sgRNA”) is a RNA molecule comprising a crRNA covalently linked a tracrRNA by a linker sequence, which may be expressed as a single RNA transcript or molecule. The guide RNA comprises a guide or targeting sequence that is identical or complementary to a target site within the plant genome, such as within or near corn event MON 95379 or a modified corn event MON 95379. A protospacer-adjacent motif (PAM) may be present in the genome immediately adjacent and upstream or downstream of the genomic target site sequence complementary to the targeting sequence of the guide RNA as known in the art. See, e.g., Wu, X. et al., “Target specificity of the CRISPR-Cas9 system,” Quant Biol. 2(2): 59-70 (2014), the content and disclosure of which is incorporated herein by reference. The guide RNA may typically be a non-coding RNA molecule that does not encode a protein. The guide sequence of the guide RNA may be at least 10 nucleotides in length, such as 12-40 nucleotides, 12-30 nucleotides, 12-20 nucleotides, 12-35 nucleotides, 12-30 nucleotides, 15-30 nucleotides, 17-30BCS236357 nucleotides, or 17-25 nucleotides in length, or about 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more nucleotides in length. The guide sequence may be at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, or more consecutive nucleotides of a DNA sequence at the genomic target site. As used herein, the term “consecutive” in reference to a polynucleotide or protein sequence means without deletions or gaps in the sequence.
[0094] In addition to the guide sequence, a guide RNA may further comprise one or more other structural or scaffold sequence(s), which may bind or interact with an RNA-guided endonuclease. Such scaffold or structural sequences may further interact with other RNA molecules (e.g., tracrRNA). Methods and techniques for designing targeting constructs and guide RNAs for genome editing and site-directed integration at a target site within the genome of a plant using an RNA-guided endonuclease are known in the art.
[0095] According to some embodiments, recombinant DNA molecules, constructs and vectors are provided comprising a polynucleotide or transcribable DNA sequence encoding a site-specific nuclease, such as a zinc-finger nuclease (ZFN), a meganuclease, an RNA-guided endonuclease, a TALE-endonuclease (TALEN), a recombinase, or a transposase, wherein the coding sequence is operably linked to a plant expressible promoter. For RNA-guided endonucleases, recombinant DNA molecules, constructs and vectors are further provided comprising a polynucleotide or transcribable DNA sequence encoding a guide RNA, wherein the guide RNA comprises a guide sequence of sufficient length having a percent identity or complementarity to a target site within the genome of a plant. According to some embodiments, recombinant DNA molecules, constructs and vectors are provided comprising a first polynucleotide or transcribable DNA sequence encoding a site-specific nuclease and a second polynucleotide or transcribable DNA sequence encoding one or more gRNAs. According to some embodiments, each polynucleotide or transcribable DNA sequence of a recombinant DNA molecule, construct and vector that encodes a site-specific nuclease and / or a guide RNA may be operably linked to a plant expressible promoter, such as an inducible promoter, a constitutive promoter, a tissue-specific promoter, etc.
[0096] According to some embodiments, recombinant DNA molecules, constructs and vectors are provided comprising a polynucleotide or transcribable DNA sequence encoding a site-specific nuclease, such as a zinc-finger nuclease (ZFN), a meganuclease, an RNA-guided endonuclease, aBCS236357 TALE-endonuclease (TALEN), a recombinase, or a transposase, wherein the coding sequence is operably linked to a plant expressible promoter. For RNA-guided endonucleases, recombinant DNA molecules, constructs and vectors are further provided comprising a polynucleotide or transcribable DNA sequence encoding a guide RNA, wherein the guide RNA comprises a guide sequence of sufficient length having a percent identity or complementarity to a target site within the genome of a plant. According to some embodiments, recombinant DNA molecules, constructs and vectors are provided comprising a first polynucleotide or transcribable DNA sequence encoding a site-specific nuclease and a second polynucleotide or transcribable DNA sequence encoding one or more gRNAs. According to some embodiments, each polynucleotide or transcribable DNA sequence of a recombinant DNA molecule, construct and vector that encodes a site-specific nuclease and / or a guide RNA may be operably linked to a plant expressible promoter, such as an inducible promoter, a constitutive promoter, a tissue-specific promoter, etc.
[0097] According to some embodiments, a recombinant DNA molecule, construct or vector may comprise a first polynucleotide sequence encoding a site-specific nuclease and a second polynucleotide sequence encoding a guide RNA(s) that may be introduced into a plant cell together via plant transformation techniques. Alternatively, two recombinant DNA molecules, constructs or vectors may be provided including a first recombinant DNA molecule, construct or vector and a second DNA molecule, construct or vector that may be introduced into a plant cell together or sequentially via plant transformation techniques, wherein the first recombinant DNA molecule, construct or vector comprises a polynucleotide sequence encoding a site-specific nuclease and the second recombinant DNA molecule, construct or vector comprises a polynucleotide sequence encoding a guide RNA(s). According to some embodiments, a recombinant DNA molecule, construct or vector comprising a polynucleotide sequence encoding a site-specific nuclease may be introduced via plant transformation techniques into a plant cell that already comprises (or is transformed with) a recombinant DNA construct or vector comprising a polynucleotide sequence encoding a guide RNA(s). Alternatively, a recombinant DNA molecule, construct or vector comprising a polynucleotide sequence encoding a guide RNA may be introduced via plant transformation techniques into a plant cell that already comprises (or is transformed with) a recombinant DNA construct or vector comprising a polynucleotide sequence encoding a site- specific nuclease. According to yet further embodiments, a first plant comprising (or transformed with) a recombinant DNA construct or vector comprising a polynucleotide sequence encoding aBCS236357 site-specific nuclease may be crossed with a second plant comprising (or transformed with) a recombinant DNA construct or vector comprising a polynucleotide sequence encoding a guide RNA(s). Such recombinant DNA molecules, constructs or vectors may be transiently transformed into a plant cell or stably transformed or more preferably integrated into the genome of a plant cell.
[0098] In an aspect, molecules or vectors comprising polynucleotides encoding a site-specific nuclease, and optionally one or more, two or more, three or more, or four or more gRNAs are provided to a plant cell by transformation methods known in the art (e.g., without being limiting, particle bombardment, PEG-mediated protoplast transfection or Agrobacterium-mediated transformation). In an aspect, molecules or vectors comprising polynucleotides encoding a Cas9 nuclease, and optionally one or more, two or more, three or more, or four or more gRNAs are provided to a plant cell by transformation methods known in the art (e.g., without being limiting, particle bombardment, PEG-mediated protoplast transfection or Agrobacterium-mediated transformation). In another aspect, vectors comprising polynucleotides encoding a Cas12a and, optionally one or more, two or more, three or more, or four or more crRNAs are provided to a cell by transformation methods known in the art (e.g., without being limiting, viral transfection, particle bombardment, PEG-mediated protoplast transfection or Agrobacterium-mediated transformation).
[0099] Several site-specific nucleases, such as recombinases, zinc finger nucleases (ZFNs), meganucleases, and TALENs, are not RNA-guided and instead rely on their protein structure to determine their target site for causing the DSB or nick, or they are fused, tethered or attached to a DNA-binding protein domain or motif. The protein structure of the site-specific nuclease (or the fused / attached / tethered DNA binding domain) may target the site-specific nuclease to the target site. According to many of these embodiments, non-RNA-guided site-specific nucleases, such as recombinases, zinc finger nucleases (ZFNs), meganucleases, and TALENs, may be designed, engineered and constructed according to known methods to target and bind to a target site in the genome of a plant, to create a DSB or nick at or near such genomic target site or locus. For example, an engineered site-specific nuclease, such as a recombinase, zinc finger nuclease (ZFN), meganuclease, or TALEN, may be designed to target and bind to a genomic target site within the genome of a plant to create a DSB or nick at the genomic target site.
[0100] In an aspect, a targeted genome editing technique described herein may comprise the use of a zinc finger nuclease (ZFN). ZFNs are synthetic proteins consisting of an engineered zincBCS236357 finger DNA-binding domain fused to a cleavage domain (or a cleavage half-domain), which may be derived from a restriction endonuclease (e.g., FokI). The DNA binding domain may be canonical (C2H2) or non-canonical (e.g., C3H or C4). The DNA-binding domain can comprise one or more zinc fingers (e.g., 2, 3, 4, 5, 6, 7, 8, 9 or more zinc fingers) depending on the target site. Multiple zinc fingers in a DNA-binding domain may be separated by linker sequence(s). ZFNs can be designed to cleave almost any stretch of double-stranded DNA by modification of the zinc finger DNA-binding domain. ZFNs form dimers from monomers composed of a non- specific DNA cleavage domain (e.g., derived from the FokI nuclease) fused to a DNA-binding domain comprising a zinc finger array engineered to bind a target site DNA sequence. The DNA- binding domain of a ZFN may typically be composed of 3-4 (or more) zinc-fingers. The amino acids at positions -1, +2, +3, and +6 relative to the start of the zinc finger α-helix, which contribute to site-specific binding to the target site, can be changed and customized to fit specific target sequences. The other amino acids may form a consensus backbone to generate ZFNs with different sequence specificities. Methods and rules for designing ZFNs for targeting and binding to specific target sequences are known in the art. See, e.g., US Patent App. Nos. 2005 / 0064474, 2009 / 0117617, and 2012 / 0142062, the contents and disclosures of which are incorporated herein by reference. The FokI nuclease domain may require dimerization to cleave DNA and therefore two ZFNs with their C-terminal regions are needed to bind opposite DNA strands of the cleavage site (separated by 5-7 bp). The ZFN monomer can cut the target site if the two-ZF-binding sites are palindromic. A ZFN, as used herein, is broad and includes a monomeric ZFN that can cleave double stranded DNA without assistance from another ZFN. The term ZFN may also be used to refer to one or both members of a pair of ZFNs that are engineered to work together to cleave DNA at the same site.
[0101] Without being limited by any scientific theory, because the DNA-binding specificities of zinc finger domains can be re-engineered using one of various methods, customized ZFNs can theoretically be constructed to target nearly any target sequence (e.g., at or near corn event MON 95379 in a plant genome). Publicly available methods for engineering zinc finger domains include Context-dependent Assembly (CoDA), Oligomerized Pool Engineering (OPEN), and Modular Assembly. In an aspect, a method and / or composition provided herein comprises one or more, two or more, three or more, four or more, or five or more ZFNs. In another aspect, a ZFN provided herein is capable of generating a targeted DSB or nick. In an aspect, vectors comprisingBCS236357 polynucleotides encoding one or more, two or more, three or more, four or more, or five or more ZFNs are provided to a cell by transformation methods known in the art (e.g., without being limiting, viral transfection, particle bombardment, PEG-mediated protoplast transfection, or Agrobacterium-mediated transformation). The ZFNs may be introduced as ZFN proteins, as polynucleotides encoding ZFN proteins, and / or as combinations of proteins and protein-encoding polynucleotides.
[0102] In an aspect, a targeted genome editing technique described herein may comprise the use of a meganuclease. Meganucleases, which are commonly identified in microbes, such as the LAGLIDADG family of homing endonucleases, are unique enzymes with high activity and long recognition sequences (> 14 bp) resulting in site-specific digestion of target DNA. Engineered versions of naturally occurring meganucleases typically have extended DNA recognition sequences (for example, 14 to 40 bp). According to some embodiments, a meganuclease may comprise a scaffold or base enzyme selected from the group consisting of I-CreI, I-CeuI, I-MsoI, I-SceI, I-AniI, and I-DmoI. The engineering of meganucleases can be more challenging than ZFNs and TALENs because the DNA recognition and cleavage functions of meganucleases are intertwined in a single domain. Specialized methods of mutagenesis and high-throughput screening have been used to create novel meganuclease variants that recognize unique sequences and possess improved nuclease activity. Thus, a meganuclease may be selected or engineered to bind to a genomic target site or sequence in a plant. In an aspect, a method and / or composition provided herein comprises one or more, two or more, three or more, four or more, or five or more meganucleases. In another aspect, a meganuclease provided herein is capable of generating a targeted DSB. In an aspect, vectors comprising polynucleotides encoding one or more, two or more, three or more, four or more, or five or more meganucleases are provided to a cell by transformation methods known in the art (e.g., without being limiting, viral transfection, particle bombardment, PEG-mediated protoplast transfection or Agrobacterium-mediated transformation).
[0103] In an aspect, a targeted genome editing technique described herein may comprise the use of a transcription activator-like effector nuclease (TALEN). TALENs are artificial restriction enzymes generated by fusing the transcription activator-like effector (TALE) DNA binding domain to a nuclease domain (e.g., FokI). In some aspects, the nuclease is selected from a group consisting of PvuII, MutH, TevI, FokI, AlwI, MlyI, SbfI, SdaI, StsI, CleDORF, Clo051, and Pept071. For FokI nuclease, when each member of a TALEN pair binds to the DNA sites flankingBCS236357 a target site, the FokI monomers dimerize and cause a double-stranded DNA break at the target site. Besides the wild-type FokI cleavage domain, variants of the FokI cleavage domain with mutations have been designed to improve cleavage specificity and cleavage activity. The FokI domain functions as a dimer, requiring two constructs with unique DNA binding domains for sites in the target genome with proper orientation and spacing. Both the number of amino acid residues between the TALEN DNA binding domain and the FokI cleavage domain and the number of bases between the two individual TALEN binding sites are parameters for achieving high levels of activity. The term TALEN, as used herein, is broad and includes a monomeric TALEN that can cleave double stranded DNA without assistance from another TALEN. The term TALEN also refers to one or both members of a pair of TALENs that work together to cleave DNA at the same site.
[0104] Besides the wild-type FokI cleavage domain, variants of the FokI cleavage domain with mutations have been designed to improve cleavage specificity and cleavage activity. The FokI domain functions as a dimer, requiring two constructs with unique DNA binding domains for sites in the target genome with proper orientation and spacing. Both the number of amino acid residues between the TALEN DNA binding domain and the FokI cleavage domain and the number of bases between the two individual TALEN binding sites are parameters for achieving high levels of activity. PvuII, MutH, and TevI cleavage domains are useful alternatives to FokI and FokI variants for use with TALEs. PvuII functions as a highly specific cleavage domain when coupled to a TALE (see Yank et al.2013. PLoS One.8: e82539). MutH is capable of introducing strand-specific nicks in DNA (see Gabsalilow et al. 2013. Nucleic Acids Research. 41: e83). TevI introduces double- stranded breaks in DNA at targeted sites (see Beurdeley et al., 2013. Nature Communications.4: 1762).
[0105] Transcription activator-like effectors (TALEs) can be engineered to bind practically any DNA sequence, such as at or near the genomic locus of corn event MON 95379 in a plant. TALE has a central DNA-binding domain composed of 13-28 repeat monomers of 33-34 amino acids. The amino acids of each monomer are highly conserved, except for hypervariable amino acid residues at positions 12 and 13. The two variable amino acids are called repeat-variable diresidues (RVDs). The amino acid pairs NI, NG, HD, and NN of RVDs preferentially recognize adenine, thymine, cytosine, and guanine / adenine, respectively, and modulation of RVDs can recognize consecutive DNA bases. This simple relationship between amino acid sequence and DNABCS236357 recognition has allowed for the engineering of specific DNA binding domains by selecting a combination of repeat segments containing the appropriate RVDs. The relationship between amino acid sequence and DNA recognition of the TALE binding domain allows for designable proteins. Software programs such as DNA Works can be used to design TALE constructs. Other methods of designing TALE constructs are known to those of skill in the art. See Doyle et al., Nucleic Acids Research (2012) 40: W117-122.; Cermak et al., Nucleic Acids Research (2011). 39:e82; and tale-nt.cac.cornell.edu / about. In an aspect, a method and / or composition provided herein comprises one or more, two or more, three or more, four or more, or five or more TALENs. In another aspect, a TALEN provided herein is capable of generating a targeted DSB. In an aspect, vectors comprising polynucleotides encoding one or more, two or more, three or more, four or more, or five or more TALENs are provided to a cell by transformation methods known in the art (e.g., without being limiting, viral transfection, particle bombardment, PEG-mediated protoplast transfection or Agrobacterium-mediated transformation). See, e.g., US Patent App. Nos. 2011 / 0145940, 2011 / 0301073, and 2013 / 0117869, the contents and disclosures of which are incorporated herein by reference.
[0106] In an aspect, a targeted genome editing technique described herein may comprise the use of a recombinase. In some embodiments, a tyrosine recombinase attached, etc., to a DNA recognition domain or motif may be selected from the group consisting of a Cre recombinase, a Flp recombinase, and a Tnp1 recombinase. In an aspect, a Cre recombinase or a Gin recombinase provided herein may be tethered to a zinc-finger DNA binding domain. The Flp-FRT site-directed recombination system may come from the 2µ plasmid from the baker’s yeast Saccharomyces cerevisiae. In this system, Flp recombinase (flippase) may recombine sequences between flippase recognition target (FRT) sites. FRT sites comprise 34 nucleotides. Flp may bind to the “arms” of the FRT sites (one arm is in reverse orientation) and cleaves the FRT site at either end of an intervening nucleic acid sequence. After cleavage, Flp may recombine nucleic acid sequences between two FRT sites. Cre-lox is a site-directed recombination system derived from the bacteriophage P1 that is similar to the Flp-FRT recombination system. Cre-lox can be used to invert a nucleic acid sequence, delete a nucleic acid sequence, or translocate a nucleic acid sequence. In this system, Cre recombinase may recombine a pair of lox nucleic acid sequences. Lox sites comprise 34 nucleotides, with the first and last 13 nucleotides (arms) being palindromic. During recombination, Cre recombinase protein binds to two lox sites on different nucleic acidsBCS236357 and cleaves at the lox sites. The cleaved nucleic acids are spliced together (reciprocally translocated) and recombination is complete. In another aspect, a lox site provided herein is a loxP, lox 2272, loxN, lox 511, lox 5171, lox71, lox66, M2, M3, M7, or M11 site.
[0107] As used herein, the term “derived” or “derived from” in reference to a particular DNA molecule, amplicon or sequence in relation to a corn cell, corn tissue, corn seed, corn plant, corn plant part and / or corn plant product, such as a corn commodity product, means that the DNA molecule, amplicon or sequence is taken, purified, isolated, or made, directly or indirectly, from such corn cell, corn tissue, corn seed, corn plant, corn plant part and / or corn plant product, such as a corn commodity product, as the case may be. Alternatively, the term “derived” or “derived from” in reference to a corn plant product, such as a corn commodity product, in relation to a corn cell, corn tissue, corn seed, corn plant, and / or corn plant part, means that the corn plant product is taken, purified, isolated, or made, directly or indirectly, from such corn cell, corn tissue, corn seed, corn plant, and / or corn plant part, as the case may be. “Capable of being detected” refers to the ability of a particular DNA molecule, segment or sequence to be detected in a sample, such as by amplification and determining its presence, size or sequence such as by DNA sequence analysis, and / or binding of a probe to the target DNA molecule, segment or sequence.
[0108] A “sample” is intended to refer to any composition comprising or derived from, either directly or indirectly, a biological sample, source or material. The sample may generally comprise corn DNA and / or substantially or completely pure, purified or isolated corn DNA. A “biological sample” contains biological materials, including but not limited to DNA obtained or derived from, either directly or indirectly, the genome of a corn cell(s), corn tissue(s), corn seed(s), corn plant(s), corn plant part(s) and / or corn plant product(s), such as a corn commodity product(s). Such corn cell(s), corn tissue(s), corn seed(s), corn plant(s), corn plant part(s) and / or corn plant product(s), such as a corn commodity product(s), may comprise corn event MON 95379 or a modified corn event MON 95379 or DNA molecule(s) and / or DNA segment(s) comprising corn event MON 95379 or a modified corn event MON 95379. In some embodiments, a sample or biological sample may comprise corn cell(s), corn tissue(s), corn seed(s), corn plant(s), corn plant part(s), and / or corn plant product(s), whose cells or cellular membranes have been fractured (e.g., disrupted or opened) to release the contents of the corn cell(s) including genomic DNA and / or make the contents of the corn cell(s) including genomic DNA accessible or usable for assays or testing. “Directly” refers to directly obtaining DNA by a skilled artisan from the corn genome by fracturing corn cells (orBCS236357 by obtaining samples of corn that contain fractured corn cells) and exposing or using the genomic DNA from corn cells for the purposes of detection. “Indirectly” refers to obtaining by a skilled artisan a target or specific reference DNA (i.e., a novel and unique junction segment(s) described herein as being diagnostic for the presence of the corn event MON 95379 or a modified corn event MON 95379) in a particular sample, by means other than by obtaining directly via fracturing of corn cells or obtaining a sample of corn that contains fractured corn cells. Such indirect means include, but are not limited to, amplification of a DNA segment that contains a DNA sequence targeted by a particular probe(s) and / or primer set(s) designed to bind with specificity to or near the target sequence, or amplification of a DNA segment comprising all or part of a target sequence that can be measured and characterized (e.g., measured by migration or separation from other segments of DNA and / or identification in an effective matrix, such as an agarose or acrylamide gel or the like, or characterized by direct sequence analysis of the amplicon(s), or cloning of the amplicon(s) into a vector(s) and direct sequencing of the inserted amplicon(s) present within such vector(s).
[0109] Detailed molecular analysis demonstrated that event MON 95379 contains a single T-DNA insertion with one copy of each of the Cry1B.868 and Cry1Da_7 expression cassettes. No additional elements from the transformation construct other than portions of the Agrobacterium tumefaciens left border region used for transgenic DNA transfer from the plant transformation plasmid to the corn genome were identified in event MON 95379. Finally, thermal amplification producing specific amplicons diagnostic for the presence of event MON 95379 in a sample and DNA sequence analyses were performed to determine the arbitrarily assigned 5´ and 3´ insert-to- plant genome junctions, confirm the organization of the elements within the insert, and determine the complete DNA sequence of the inserted transgenic DNA (SEQ ID NO: 9). SEQ ID NO: 11 is a sequence representing the eight hundred sixty-two (862) base-pair (bp) 5´ LH244 corn genomic DNA sequence flanking the inserted T-DNA sequence presented as SEQ ID NO: 9. SEQ ID NO: 12 is a sequence representing the one thousand thirty-six (1,036) bp 3´ LH244 corn genomic DNA sequence flanking the inserted T-DNA sequence presented as SEQ ID NO: 9. SEQ ID NO: 7 is a sequence representing the eight hundred sixty-two (862) base-pair (bp) 5´ LH244 corn genomic DNA sequence flanking the inserted T-DNA sequence combined with two hundred ninety-eight (298) bp of inserted T-DNA sequence presented as SEQ ID NO: 9. SEQ ID NO: 8 is a sequence representing one hundred forty-two (142) bp of inserted T-DNA sequence with the one thousandBCS236357 thirty-six (1,036) bp 3´ LH244 corn genomic DNA sequence flanking the inserted T-DNA sequence presented as SEQ ID NO: 9. SEQ ID NO: 10 corresponds to corn event MON 95379 and contains a contiguous sequence (contig) comprising the 5´ LH244 flanking sequence, the transgene insert of event MON 95379, and the 3´ LH244 flanking sequence, and thus contains the insert-to-plant genome junction sequences.
[0110] Unless otherwise noted herein, terms are to be understood according to conventional usage by those of ordinary skill in the relevant art. Definitions of common terms in molecular biology may be found in Rieger et al., Glossary of Genetics: Classical and Molecular, 5thedition, Springer- Verlag: New York, 1991; and Lewin, Genes V, Oxford University Press: New York, 1994, along with other sources known to those of ordinary skill in the art. As used herein, the term “corn” means species belong to the genus Zea, preferably Zea mays and includes all plant varieties that can be bred with corn plants containing event MON 95379, including wild corn species as well as those plants belonging to the genus Zea that permit breeding between species.
[0111] The present invention provides for transgenic plants which have been transformed with a DNA construct that contains expression cassettes expressing toxic amounts of the insecticidal proteins Cry1B.868 and Cry1Da_7. What is meant by toxic amount is an efficacious amount, an insecticidal amount, an insecticidally-effective amount, a target insect suppressive amount, an efficacious pesticidal amount, an amount in the diet of insects in the order of Lepidoptera that is insecticidal, and other similar terms to be understood according to conventional usage by those of ordinary skill in the relevant art. Corn plants transformed according to the methods and with the DNA construct disclosed herein are resistant to Lepidopteran insect pests.
[0112] A transgenic plant is produced by transformation of a plant cell with a recombinant DNA construct that includes the expression cassette(s) and transgene(s) as described herein, which is also heterologous with respect to the plant cell, regeneration of a plant resulting from the insertion of the transgene into the genome of the plant cell, and selection of a particular plant characterized by insertion into a particular genome location and the number of efficacious features of the regenerated transgenic plant. The term “transgenic event” or “event” refers to the inserted transgenic DNA in the plant genome and flanking genomic sequences immediately adjacent to the inserted transgenic DNA in the genome of the transformed plant, but also refers to a DNA molecule comprising the inserted transgenic DNA in the plant genome and flanking genomic sequences. Each event is unique and would be expected to be transferred to progeny plants that receive theBCS236357 transgenic DNA and event through genetic inheritance and / or segregation from a parent as the result of a sexual or self-cross of a first parental line that includes the inserted transgenic DNA and event either with itself or a second parental line that may or may not contain the same transgenic DNA and event. The parental line that includes the inserted transgenic DNA and event may itself be the original transformant or a progeny plant of said original transformant that may have been generated by “selfing” the transformant with itself or crossing the transformant or a progeny plant of the transformant that includes the inserted transgenic DNA and event with another plant. For purposes of the present disclosure, the “event” refers to corn event MON 95379 or a modified corn event MON 95379.
[0113] As used herein, the term “flanking” in reference to a transgenic event refers to the plant genomic sequence(s) immediately adjacent to the transgenic DNA insertion in the genome of a transformed plant, plant part, plant tissue, or plant cell comprising the transgenic event on the 5´ and / or 3´ side(s) or end(s) of the transgenic event insertion (e.g., corn event MON 95379 or a modified corn event MON 95379). Likewise, “flanking DNA”, “flanking sequence” or “flanking DNA sequence” each refers to a length of genomic DNA sequence immediately adjacent to the transgenic DNA insertion in the genome of the transformed plant on the 5´ and / or 3´ side(s) or end(s) of the insertion. A “5´ flank” means the corn genomic DNA sequence adjacent to and upstream (or on the 5´ end) of the transgenic DNA insertion. For example, a “5´ flank” can include the corn genomic DNA sequence immediately adjacent to and upstream (on the 5´ end) of the transgenic insertion, or any corn genomic DNA sequence upstream (on the 5´ end) of the transgenic insertion that is not immediately adjacent to the transgenic insertion but is within about 5000 nucleotides, within about 4000 nucleotides, within about 3000 nucleotides, within about 2000 nucleotides, or within about 1000 nucleotides upstream of the transgenic insertion. Likewise, a “3´ flank” means the corn genomic DNA sequence adjacent to and downstream (or on the 3´ end) of the transgenic insert. For example, a “3´ flank” can include the corn genomic DNA sequence immediately adjacent to and downstream (on the 3´ end) of the transgenic insertion, or any corn genomic DNA sequence downstream (on the 3´ end) of the transgenic insertion that is not immediately adjacent to the transgenic insertion but is within about 5000 nucleotides, within about 4000 nucleotides, within about 3000 nucleotides, within about 2000 nucleotides, or within about 1000 nucleotides downstream of the transgenic insertion.BCS236357
[0114] SEQ ID NOs: 11 and 12 are 862 and 1,036 nucleotide sequences representing corn (Zea mays) genomic DNA that flanks the transgenic insert at the 5´ and 3´ ends of the insert in corn event MON 95379, respectively. SEQ ID NOs: 47 and 48 are 5,000 nucleotide sequences representing corn (Zea mays) genomic DNA that flanks the transgenic insert at the 5´ and 3´ ends of the insert, respectively. Nucleotides 4,139-5,000 of SEQ ID NO: 47 are identical to nucleotides 1-862 of SEQ ID NO: 11. Nucleotides 1-4,138 are based on the genomic sequence of the B73 corn cultivar (Zm-B73-REFERENCE-GRAMENE-4.0, NCBI). Similarly, nucleotides 1-1,036 of SEQ ID NO: 48 are identical to nucleotides 1-1,036 of SEQ ID NO: 12. The remaining nucleotides (1,037-5,000) are based on the genomic sequence of the B73 corn cultivar.
[0115] The present disclosure provides the original transformant plant and progeny of the transformant that include the transgenic DNA and event. Such progeny may be produced by a sexual cross or outcross between plants comprising the same transgenic DNA and event, or between a plant comprising the transgenic DNA and event with another plant, or by any other method known in the art including any cell or tissue culture method, wherein the progeny includes the transgenic DNA and event. Such other plant may be a transgenic plant comprising the same and / or a different transgene or may be a non-transgenic plant, and each parental plant in a cross or outcross may be the same or different germplasm or breeding line. Even after repeated back- crossing to a recurrent parent, the transgenic DNA and event is present in progeny of the cross at the same chromosomal location. Thus, a “transgenic plant” can be the original transformant plant regenerated from the transformed plant cell and comprising the transgenic DNA and event, or a progeny plant of the original transformant plant, which may be separated from the transformant by one or more generations, that retains the transgenic DNA and event at the same specific location and sequence context in the plant’s genome. The transformant or progeny plant may be homozygous or heterozygous for corn event MON 95379 or a modified corn event MON 95379. In addition, a “transgenic plant” can include a plant produced from a transformed plant cell or tissue, or from another transgenic plant or plant part, by or using cell or tissue culture methods known in the art. A “transgenic plant” may comprise a plant having a transgene or transgenic event (including a modified transgenic event) stably inserted in the genome of at least one cell of the plant (i.e., corn event MON 95379 or a modified corn event MON 95379 in at least one cell of the plant), and the plant may be chimeric or non-chimeric with respect to the transgene and / orBCS236357 event or modified event. A transgenic plant is chimeric with respect to a transgene, event, or modified event if not all cells of the plant comprise the transgene, event, or modified event.
[0116] As used herein, the term “recombinant” refers to a non-natural DNA, protein, or combination that would not normally be found in nature, such as a combination of DNA sequences, proteins that would not naturally occur together, and is the result of human intervention. A “recombinant DNA molecule” is a DNA molecule comprising a combination of DNA sequences that would not naturally occur together and is the result of human intervention. Two or more elements of such combination of DNA sequences may be operably linked to one another. For example, a recombinant DNA molecule may comprise a combination of at least two DNA sequences that are heterologous with respect to each other, such as a DNA molecule that comprises a coding or transcribable DNA sequence operably linked to a heterologous promoter and / or other regulatory expression element(s), and / or a plant genomic DNA sequence comprising all or part of a transgene and a heterologous and flanking genomic sequence(s) adjacent to the transgene, and / or a DNA molecule that is artificially synthesized and comprises a polynucleotide sequence that deviates from any polynucleotide sequence that would normally exist in nature. A recombinant DNA molecule may comprise all or part of a junction sequence of the genome of a plant and all or part of the transgene insertion into the genome of the plant, and / or may comprise a recombinant or heterologous DNA fragment of event MON 95379 or a modified corn event MON 95379. An example of a recombinant DNA molecule is a DNA molecule comprising at least one of SEQ ID NOs: 1-10. As used herein, a recombinant plant, plant part, plant cell or plant tissue is a plant, plant part, plant cell or plant tissue that would not normally exist in nature, is the result of human intervention, and contains a transgene incorporated into the genome of the plant, plant part, plant cell or plant tissue. As a result of such genomic insertion, the recombinant plant is something new and distinctly different from any related wild-type or naturally occurring plant, plant part, plant cell or plant tissue. An example of a recombinant plant, plant part, plant cell or plant tissue is a corn or maize plant, plant part, plant cell or plant tissue containing the event MON 95379 or a modified corn event MON 95379.
[0117] As used herein, the term “heterologous” in reference to a combination of two or more DNA sequences or elements means that the two or more DNA sequences or elements do not normally exist together as such combination in nature without human intervention. As used herein, the term “heterologous” in reference to a DNA molecule, construct or sequence in relation to a plant,BCS236357 microorganism, plant cell or plant genome means that the DNA molecule, construct or sequence does not exist in nature as part of such plant, microorganism, plant cell or plant genome, and / or does not exist in the same physical or genomic location, context or orientation as part of such plant, microorganism, plant cell or plant genome in nature, without human intervention.
[0118] The present disclosure provides DNA molecules and fragments and their corresponding DNA sequences. The terms “DNA” and “DNA molecule” as used herein refer to a deoxyribonucleic acid (DNA) molecule. A DNA molecule may be of genomic or synthetic origin and / or comprise a recombinant or heterologous DNA molecule or sequence. A DNA molecule may be described in reference to its 5´ (upstream) end and 3´ (downstream) end. As used herein, the term “DNA sequence” refers to the polynucleotide sequence of the DNA molecule – i.e., the sequence of consecutive nucleotides in the DNA molecule. As used herein in reference to nucleotides of a polynucleotide or DNA sequence or molecule, the terms “consecutive” and “contiguous” are interchangeable and synonymous and refer to the 5´ to 3´ order of nucleotides in a polynucleotide or DNA sequence, strand or molecule without any gap or interruption between them. By convention, DNA sequences of the disclosure and fragments thereof are disclosed with reference to the 5´ to 3´ direction of only one strand of the two, anti-parallel and complementary DNA strands of a DNA molecule. By implication and intent, the complementary sequences of the sequences provided here (i.e., the sequences of the complementary, opposing, or antiparallel strand), also referred to in the art as the reverse complementary or reverse complement sequences, are within the scope of the present disclosure and are expressly intended to be within the potential scope of the subject matter as claimed. A DNA molecule, or a fragment derived therefrom, can also be extracted from plant part(s), plant cell(s) and / or tissue(s) or a homogenate, extract or lysate from plant part(s), plant cell(s) and / or tissue(s), or can be produced as an amplicon from extracted, purified or isolated DNA from plant part(s), plant cell(s) and / or tissue(s), or a homogenate, extract or lysate from plant part(s), plant cell(s) and / or tissue(s), which may further comprise event MON 95379.
[0119] As used herein, the term “fragment” refers to a smaller piece or sequence of a larger or whole DNA molecule or sequence. For example, a fragment of SEQ ID NO: 9 or 10 may include a sequence that is at least about 12 consecutive nucleotides, at least about 13 consecutive nucleotides, at least about 14 consecutive nucleotides, at least about 15 consecutive nucleotides, at least about 16 consecutive nucleotides, at least about 17 consecutive nucleotides, at least aboutBCS236357 18 consecutive nucleotides, at least about 19 consecutive nucleotides, at least about 20 consecutive nucleotides, at least about 21 consecutive nucleotides, at least about 22 consecutive nucleotides, at least about 23 consecutive nucleotides, at least about 24 consecutive nucleotides, at least about 25 consecutive nucleotides, at least about 30 consecutive nucleotides, at least about 35 consecutive nucleotides, at least about 40 consecutive nucleotides, at least about 45 consecutive nucleotides, at least about 50 consecutive nucleotides, at least about 60 consecutive nucleotides, at least about 70 consecutive nucleotides, at least about 80 consecutive nucleotides, at least about 90 consecutive nucleotides, at least about 100 consecutive nucleotides, at least about 200 consecutive nucleotides, at least about 300 consecutive nucleotides, at least about 400 consecutive nucleotides, or at least about 500 consecutive nucleotides of the larger, whole or complete DNA molecule or sequence of SEQ ID NO: 9 or 10.
[0120] According to present embodiments, a fragment of the DNA sequence of the 5´ flank (SEQ ID NO: 11 or SEQ ID NO: 47) or the 3´ flank (SEQ ID NO: 12 or SEQ ID NO: 48) of corn event MON 95379 can comprise at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, or at least 500 consecutive nucleotides of SEQ ID NO: 11 or SEQ ID NO: 47 or SEQ ID NO: 12 or SEQ ID NO: 48. It is possible that different maize germplasms may have differences in their genomic sequences, which may include differences in the flanking sequence(s), 5´ flank and / or 3´ flank of corn event MON 95379. These differences may result from introgression of the corn event MON 95379 or a modified corn event MON 95379 into a different germplasm and / or spontaneous, mutagenic or genome editing changes that occur in a given germplasm or line. According to some embodiments, DNA molecules, constructs or polynucleotides are provided comprising a sequence or flanking sequence, or a 5´ flank or 3´ flank, that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to SEQ ID NO: 11 or 47 or SEQ ID NO: 12 or 48, or a fragment of either thereof. According to some embodiments, DNA molecules, constructs or polynucleotides are provided comprising a sequence or flanking sequence, or a 5´ flank or 3´ flank, that is at least 90%, at least 91%, at least 92%, at least 93%, atBCS236357 least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, or at least 500 consecutive nucleotides of SEQ ID NO: 11 or 47 or SEQ ID NO: 12 or 48.
[0121] As used herein, the term “isolated” in reference to a molecule means that the molecule is at least partially separated from other molecules or sequences that are normally associated with the molecule in its native or natural state. In some embodiments, the term “isolated” refers to a DNA molecule that is at least partially separated from the nucleic acids or polynucleotide or DNA sequence(s) that normally flank and are covalently linked to the sequence of the DNA molecule in its native or natural state. An “isolated” DNA molecule may have a DNA sequence corresponding to a portion of the genome of a plant cell without other genomic DNA sequence(s) that normally flank and are covalently linked to the DNA sequence in nature. Such an “isolated” DNA molecule may comprise all or part of a transgene(s) and / or transgenic event, which may comprise all or part of corn event MON 95379 or a modified corn event MON 95379 or the transgene(s) or expression cassette(s) described herein. Nucleic acid sequences or elements, such as a coding sequence, intron sequence, untranslated leader sequence, promoter sequence, transcriptional termination sequence, and the like, that are naturally found within the DNA of the genome of an organism are not considered to be “isolated” so long as the element is within the genome of the organism and at the location within the genome in which it is naturally found. However, each of these elements, and subparts of these elements, would be “isolated” within the scope of this disclosure so long as the element or subpart is not within the genome of the organism, and at the location within the genome of the organism, in which it is naturally found. An “isolated” DNA molecule may be any recombinant DNA molecule or amplification product or amplicon, and / or may comprise any DNA sequence removed from its natural or biological state and covalently fused to another DNA molecule or sequence with which it is not associated in nature. Such an isolated DNA molecule could be created by the use of biotechnology techniques, such as by making a recombinant DNA or integrating a foreign or heterologous DNA molecule into the chromosome of a cell, plant, orBCS236357 seed. Thus, any DNA molecule comprising a transgenic, recombinant, chimeric or artificial nucleotide sequence, transgene or expression cassette would be considered to be an “isolated” DNA molecule since these sequences are not naturally occurring, regardless of whether the sequence, transgene or expression cassette is present within a plasmid, vector or construct used to transform plant cells, within the genome of a plant, plant part, plant tissue, or plant cell, or is present in detectable amounts in tissues, progeny, biological samples or commodity products derived from a plant, plant part, plant tissue, or plant cell. A recombinant DNA molecule or sequence, or any fragment derived therefrom, comprising all or part of a transgene or junction sequence of corn event would therefore also be considered to be “isolated.” An “isolated” DNA molecule may be extracted or purified from a transgenic plant(s), plant part(s), plant cell(s) and / or tissue(s), or may be present in a homogenate, extract or lysate from any such transgenic plant(s), plant part(s), plant cell(s) and / or tissue(s), or may be produced as an amplicon or amplification product from plant genomic DNA and / or extracted or purified DNA from transgenic plant(s), plant part(s), plant cell(s) and / or tissue(s), or a homogenate, extract or lysate from plant(s), plant part(s), plant cell(s) and / or tissue(s). For the purposes of this disclosure, any transgenic polynucleotide or DNA sequence, i.e., the nucleotide sequence of the DNA inserted into the genome of a plant or bacterium, or present in an extrachromosomal vector, would be considered to be an “isolated” nucleotide or DNA sequence whether it is present within the plasmid or similar structure used to transform the cells, within the genome of the plant or bacterium, or present in detectable amounts in tissues, progeny, biological samples or commodity products derived from the plant or bacterium. An “isolated” DNA molecule is a chemical or biochemical molecule, regardless of whether the molecule is referred to as a nucleic acid, a nucleic acid sequence, a polynucleotide sequence, a DNA sequence, a nucleic acid molecule, a polynucleotide molecule, a DNA molecule, or the like. An “isolated” molecule can provide industrial applicability when present in a plant cell or in a plant genome or when present outside of a plant cell, and therefore, provides and exhibits (and is intended to provide and exhibit) utility regardless of where the molecule is located.
[0122] The phosphodiester bond linkage between one end of a transgenic insert (or insertion) into the genome of a plant and the flanking corn genomic DNA is referred to as a “junction.” In other words, a “junction” is the connection point or covalent linkage of one end of a transgenic insert and the flanking genomic DNA. One junction is found at the 5´ end of the transgenic insertion and the other is found at the 3´ end of the transgenic insert, referred to herein as the 5´ and 3´ junction,BCS236357 respectively. A “junction sequence” refers to a DNA sequence of any length of consecutive nucleotides that spans the 5´ or 3´ junction of a transgenic event in the plant genome. For a “junction sequence” to be specific to a junction between a transgenic event and a flanking genomic sequence, the junction sequence will generally comprise a sufficient number of consecutive nucleotides at one end of the insertion and a sufficient number of consecutive nucleotides of the flanking genomic sequence. According to some embodiments, a “junction sequence” may comprise (i) at least five (5) consecutive nucleotides, at least ten (10) consecutive nucleotides, at least fifteen (15) consecutive nucleotides, at least twenty (20) consecutive nucleotides, or at least thirty (30) consecutive nucleotides at one end of the insertion and (ii) at least five (5) consecutive nucleotides, at least ten (10) consecutive nucleotides, at least fifteen (15) consecutive nucleotides, at least twenty (20) consecutive nucleotides, or at least thirty (30) consecutive nucleotides of flanking genomic DNA sequence, although it is understood that any length of consecutive nucleotides spanning a junction of a transgenic event in a plant genome may be a junction sequence. A variety of junction sequences of corn event MON 95379 can be determined by one of skill in the art using SEQ ID NO: 10. Examples of junction sequences of corn event MON 95379 are provided as SEQ ID NOs: 1-8. FIG.1 illustrates the physical arrangement and locations of the junction sequences, arranged from 5´ to 3´ (left to right), relative to SEQ ID NO: 10. The junction sequence(s) of a modified corn event MON 95379 may be modified, mutated or edited relative to such junction sequence(s) of corn event MON 95379. The junction sequences of corn event MON 95379 or a modified corn event MON 95379 may be present as part of the genome of a corn plant, plant part, plant seed, or plant tissue or cell containing corn event MON 95379 or a modified corn event MON 95379, a DNA molecule containing all or part of corn event MON 95379 or a modified corn event MON 95379, or a microorganism containing corn event MON 95379 or a modified corn event MON 95379. The identification of any one or more of the junction sequences in a DNA molecule or sample from a plant, plant part, plant seed, or plant tissue or cell indicates that the plant, plant part, plant seed, or plant tissue or cell contains or comprises corn event MON 95379 or a modified corn event MON 95379, or the DNA molecule contains or comprises corn event MON 95379 or a modified corn event MON 95379 or was obtained from a corn plant, plant part, plant seed, or plant tissue or cell containing or comprising corn event MON 95379 or a modified corn event MON 95379, and is diagnostic in each case for the presence of corn event MON 95379 or a modified corn event MON 95379.BCS236357
[0123] The junction sequences described herein can be diagnostic for the presence of all or part of corn event MON 95379, or diagnostic for a modified corn event MON 95379 if the junction sequence is unmodified in the modified corn event MON 95379, and / or a DNA molecule comprising all or part of the Cry1B.868 and Cry1Da_7-encoding transgenes, construct or expression cassette described herein. Thus, the identification or detection, directly or indirectly, of one or more of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, and SEQ ID NO: 10 in a sample or DNA molecule derived from a corn plant, corn plant part, corn seed, or corn tissue or cell, or a commodity product from a corn plant, corn plant part, corn seed, or corn tissue or cell, is diagnostic that the corn plant, corn plant part, corn seed, or corn tissue or cell, or a commodity product from a corn plant, corn plant part, corn seed, or corn tissue or cell has or comprises all or part of corn event MON 95379 or a modified corn event MON 95379. The identification or detection, directly or indirectly, of a 5´ junction sequence and a 3´ junction sequence (each as provided or described herein) in a sample or DNA molecule derived from a corn plant, corn plant part, corn seed, or corn tissue or cell, or a commodity product from a corn plant, corn plant part, corn seed, or corn tissue or cell, is diagnostic that the corn plant, corn plant part, corn seed, or corn tissue or cell, or a commodity product from a corn plant, corn plant part, corn seed, or corn tissue or cell has or comprises corn event MON 95379 or a modified corn event MON 95379. The present disclosure thus provides a DNA molecule that contains at least one of the nucleotide sequences provided as SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 10. Any segment of DNA derived from transgenic corn event MON 95379 that is sufficient to include at least one of the sequences provided as SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 10 is within the scope of the present disclosure. In addition, any DNA or polynucleotide molecule or sequence comprising a sequence complementary to any of the sequences described herein is also within the scope of the present disclosure.
[0124] The disclosure provides DNA, polynucleotide or nucleic acid molecules, which may be single or double stranded, that can be used either as primers or probes for detecting the presence of DNA comprising all or part of event MON 95379 or a modified corn event MON 95379 in a sample derived from a corn plant, corn plant part, corn seed, or corn tissue or cell, or a commodityBCS236357 product from a corn plant, corn plant part, corn seed, or corn tissue or cell. Such primers or probes are specific for a target nucleic acid, polynucleotide or DNA sequence and, as such, are useful for the identification of corn event MON 95379 nucleic acid, polynucleotide or DNA sequence, or a nucleic acid, polynucleotide, or DNA sequence of a modified corn event MON 95379, by the methods described herein. A primer or probe can hybridize to a target nucleic acid, polynucleotide or DNA sequence to allow for specific detection or amplification of a nucleic acid, polynucleotide or DNA molecule or sequence that comprises, or is covalently linked and associated with, the target nucleic acid, polynucleotide or DNA sequence. According to present embodiments, the primers and / or probe may be chosen to identify and distinguish detection of a particular transgenic event and not only the presence of a transgene in a plant genome. The target nucleic acid, polynucleotide or DNA molecule or sequence may comprise all or part of corn event MON 95379 or a modified corn event MON 95379, a junction sequence and / or flanking genomic DNA. Probes and primers according to the present disclosure may have (i) complete or 100% sequence complementarity (i.e., 100% complementary) to a target DNA sequence or (ii) incomplete sequence complementarity to a target DNA sequence, such as at least 60% complementary, at least 65% complementary, at least 70% complementary, at least 75% complementary, at least 80% complementary, at least 85% complementary, at least 90% complementary, at least 95% complementary, or at least 99% complementary to the target DNA sequence as long as the probe or primer has sufficient complementarity to the target DNA sequence to hybridize to the target DNA sequence under stringent hybridization conditions that are suitable and necessary for use of the probe or primer in the relevant amplification or detection assay, reaction or method. As understood in the art, the percentage complementarity of a primer or probe may be lower if the length of the primer or probe is longer and depends on the stringency and use.
[0125] A “probe” is a nucleic acid molecule that is complementary to a strand of target nucleic acid and is useful in hybridization methods. A probe may be attached a conventional detectable label or reporter molecule, e.g., a radioactive isotope, ligand, chemiluminescent agent, or enzyme. Such a probe is complementary to a strand of a target nucleic acid and, in the case of the present invention, to a strand of DNA from event MON 95379 a modified corn event MON 95379, whether from an event MON 95379 containing plant or from a plant containing a modified corn event MON 95379, or from a sample that includes event MON 95379 DNA or DNA from a modified corn event MON 95379. Probes according to the present invention include not only deoxyribonucleicBCS236357 or ribonucleic acids, but also polyamides and other probe materials that bind specifically to a target DNA sequence and can be used to detect the presence of that target DNA sequence. Examples of DNA sequences that may be useful as a probe for detecting corn event MON 95379 or a modified corn event MON 95379 are provided as: SEQ ID NO: 17 (PB10269), SEQ ID NO: 23 (PB50340); SEQ ID NO: 26 (PB50138). A “probe” may also be used to bind a template DNA in a sample comprising all or part of a DNA or nucleotide sequence of corn event MON 95379 or a modified corn event MON 95379 to purify the template DNA from the remainder of the sample using purification methods or techniques known in the art, for example, if the probe is bound or can be bound to a substrate or a particle or bead that can be purified or separated. Such a template DNA may comprise all or part of a DNA or nucleotide sequence of corn event MON 95379 or a modified corn event MON 95379, or a portion or fragment thereof, such as a nucleotide sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 10, or a complement thereof.
[0126] A “primer” is typically a DNA molecule that is designed for use in specific annealing or hybridization methods that involve thermal amplification. A pair of primers may be used with template DNA (such as a sample of corn 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 understood in the art, an “amplification product” or “amplicon” is a DNA molecule or segment produced by an amplification reaction. Amplification or amplifying refers to making multiple copies of a target DNA molecule or segment from a template DNA. A single “primer” may also be used to initiate a sequencing reaction to determine a DNA sequence of a template DNA according to sequencing methods known in the art. Such a sequencing reaction may be used to determine the presence or absence of a DNA molecule or nucleotide sequence, or a portion or fragment thereof, from corn event MON 95379 or a modified corn event MON 95379. Such a template DNA may comprise all or part of a DNA or nucleotide sequence of corn event MON 95379 or a modified corn event MON 95379, or a portion or fragment thereof, such as a nucleotide sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO:BCS236357 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 10, or a complement thereof.
[0127] DNA amplification reactions, methods and techniques are known to those skilled in art. DNA amplification can be accomplished by any of the various nucleic acid amplification methods known in the art, including thermal and isothermal amplification methods including the polymerase chain reaction or PCR. Amplification methods are known in the art and are described, inter alia, in U.S. Patent Nos.4,683,195 and 4,683,202 and in PCR Protocols: A Guide to Methods and Applications, ed. Innis et al., Academic Press, San Diego, 1990. PCR amplification methods have been developed to amplify up to 22 kb (kilobase) of genomic DNA and up to 42 kb of bacteriophage DNA (Cheng et al., Proc. Natl. Acad. Sci. USA 91:5695-5699, 1994). These methods as well as other methods known in the art of DNA amplification may be used in the practice of the present invention. Examples of DNA amplification methods include PCR, Recombinase Polymerase Amplification (RPA) (see for example U.S. Pat No.7,485,428), Strand Displacement Amplification (SDA) (see for example, U.S. Pat. Nos. 5,455,166 and 5,470,723), Transcription-Mediated Amplification (TMA) (see for example, Guatelli et al., Proc. Natl. Acad. Sci. USA 87:1874-1878, 1990), Rolling Circle Amplification (RCA) (see for example, Fire and Xu, Proc. Natl. Acad Sci. USA 92:4641-4645, 1995; Lui, et al., J. Am. Chem. Soc.118:1587-1594, 1996; Lizardi, et al., Nature Genetics 19:225-232, 1998; U.S. Pat. Nos.5,714,320 and 6,235,502), Helicase Dependent Amplification (HDA) (see for example Vincent et al., EMBO Reports 5(8): 795-800, 2004; U.S. Pat. No.7,282,328), and Multiple Displacement Amplification (MDA) (see for example Dean et al., Proc. Natl. Acad Sci. USA 99:5261-5266, 2002). A sequence of the heterologous DNA insert and / or flanking genomic DNA sequence from corn event MON 95379 can be verified or tested by amplifying such DNA molecules from corn seed containing event MON 95379 DNA or corn plants grown from the corn seed containing event MON 95379 DNA, using primers derived from the sequences provided herein, followed by standard DNA sequencing of the PCR amplicon or a cloned DNA fragment thereof.
[0128] According to present embodiments, the sequence of an amplicon of an amplification reaction may comprise one or more of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 10, or a fragment thereof. According to present embodiments, the sequence of an ampliconBCS236357 comprises at least one junction sequence or two junction sequences, such as a 5´ junction sequence and / or a 3´ junction sequence for corn event MON 95379 or a modified corn event MON 95379.
[0129] A primer is typically designed to hybridize in a sequence-specific manner to a complementary target DNA strand to form a hybrid between the primer and target DNA strand, and the primer hybridized or bound to the complementary target DNA strand is a point of recognition for a polymerase to begin extension of the primer (i.e., polymerization of additional nucleotides into a lengthening nucleotide molecule) using as a template the target DNA strand. Primer pairs refer to use of two primers binding opposite strands of a double stranded DNA or polynucleotide segment for the purpose of amplifying the polynucleotide or DNA segment between the positions targeted for binding by the individual primers of the primer pair to the original template DNA or an amplicon of the amplification reaction, typically in a thermal cycling amplification reaction or other conventional DNA amplification method. Primer pairs are typically designed to hybridize to different nearby target positions of a template DNA molecule on opposing strands of the template DNA molecule such that the intervening region or sequence between the two primers can be specifically amplified for use or detection through multiple rounds of amplification. Exemplary DNA molecules useful as primers are provided as SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 25 and SEQ ID NO: 27.
[0130] The primer pair SEQ ID NO: 15 and SEQ ID NO: 16 are useful as a first DNA molecule and a second DNA molecule that is different from the first DNA molecule, and both are each of sufficient length of contiguous nucleotides of SEQ ID NO: 10 to function as DNA primers that, when used together in a thermal amplification reaction with template DNA derived from corn event MON 95379, to produce an amplicon diagnostic for corn event MON 95379 DNA in a sample. The primer pair SEQ ID NO: 21 and SEQ ID NO: 22 are useful as a first DNA molecule and a second DNA molecule that is different from the first DNA molecule, and both are each of sufficient length of contiguous nucleotides of SEQ ID NO: 10 to function as DNA primers that, when used together in a thermal amplification reaction with template DNA derived from corn event MON 95379, to produce an amplicon diagnostic for the zygosity of corn event MON 95379 DNA in a sample. The primer pair SEQ ID NO: 24 and SEQ ID NO: 25 are useful as a first DNA molecule and a second DNA molecule that is different from the first DNA molecule, and both are each of sufficient length of contiguous nucleotides of SEQ ID NO: 10 to function as DNA primersBCS236357 that, when used together in a thermal amplification reaction with template DNA derived from corn event MON 95379, to produce an amplicon diagnostic for the zygosity of corn event MON 95379 DNA in a sample. The primer pair SEQ ID NO: 18 and SEQ ID NO: 19 are useful as a first DNA molecule and a second DNA molecule that is different from the first DNA molecule, and both are each of sufficient length of contiguous nucleotides of a locus within the corn genome to function as DNA primers that, when used together in a thermal amplification reaction with template DNA derived from corn event MON 95379, to produce an amplicon that serves as an internal control for both the diagnosis of corn event MON 95379, as well as the zygosity of corn event MON 95379 DNA in a sample.
[0131] According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises at least one of the nucleotide sequences provided as SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 10. According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, or at least 90 consecutive nucleotides of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, or SEQ ID NO: 6. According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that (i) contains or comprises at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of any one of SEQ ID NOs: 1-10, (ii) is at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 nucleotides in length, and (iii) comprises nucleotides 1,000–1,001 and / or 3,733–3,734 of SEQ ID NO: 10.BCS236357
[0132] According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises (i) two expression cassettes that encode the insect pesticidal insect toxins Cry1B.868 and Cry1Da_7, and (ii) a junction sequence. According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises (i) expression cassettes that encodes the pesticidal insect toxins Cry1B.868 and Cry1Da_7, and (ii) a 5´ flank and / or a 3´ flank sequence. The expression cassette may comprise in operable linkage: (a) a promoter sequence (b) a transcribable DNA sequence encoding a pesticidal insect toxins Cry1B.868 or Cry1Da_7 sequence that is toxic to Lepidopteran insect pest species, and (c) a transcription termination or 3´ UTR sequence. The expression cassette may further comprise any of the elements described in Table 1, which may be operably linked.
[0133] According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises (i) an expression cassette that encodes the pesticidal insect toxins Cry1B.868 and Cry1Da_7, and (ii) a polynucleotide sequence comprising one or more of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, or SEQ ID NO: 10. According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises (i) expression cassettes that encodes the pesticidal insect toxins Cry1B.868 and Cry1Da_7, and (ii) a polynucleotide sequence comprising at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of one or more of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, or SEQ ID NO: 10.
[0134] According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises (i) expression cassettes that encodes the pesticidal insect toxins Cry1B.868 and Cry1Da_7, and (ii) a polynucleotide sequence comprising at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, atBCS236357 least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 17 or SEQ ID NO: 19 or SEQ ID NO: 18 or SEQ ID NO: 20. According to some embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises (i) expression cassettes that encodes the pesticidal insect toxins Cry1B.868 and Cry1Da_7, and (ii) a sequence or flanking sequence, or a 5´ flank or 3´ flank, that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to SEQ ID NO: 11 or 47 or SEQ ID NO: 12 or 48, or a fragment of either thereof. According to some embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises (i) expression cassettes that an pesticidal insect toxins Cry1B.868 and Cry1Da_7, and (ii) a sequence or flanking sequence, or a 5´ flank or 3´ flank, that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 11 or 47 or SEQ ID NO: 12 or 48. According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises (i) expression cassettes that encodes the pesticidal insect toxins Cry1B.868 and Cry1Da_7, and (ii) a polynucleotide sequence comprising one or more polynucleotide sequences selected from SEQ ID NOs: 49-148. According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises (i) expression cassettes that encodes the pesticidal insect toxins Cry1B.868 and Cry1Da_7, and (ii) a polynucleotide sequence comprising one or more polynucleotide sequences selected from SEQ ID NOs: 149-248.BCS236357
[0135] According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises (i) expression cassettes that encodes the pesticidal insect toxins Cry1B.868 and Cry1Da_7, (ii) a polynucleotide sequence comprising at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 11 or SEQ ID NO: 47, and (iii) a polynucleotide sequence comprising at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 12 or SEQ ID NO: 48. According to some embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises (i) expression cassettes that encodes the pesticidal insect toxins Cry1B.868 and Cry1Da_7, (ii) a sequence or flanking sequence, or a 5´ flank, that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to SEQ ID NO: 11 or 47, or a fragment of either thereof, and (iii) a sequence or flanking sequence, or a 3´ flank, that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to SEQ ID NO: 12 or 48, or a fragment of either thereof. According to some embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises (i) expression cassettes that encodes the pesticidal insect toxins Cry1B.868 and Cry1Da_7, and (ii) a sequence or flanking sequence, or a 5´ flank, that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to at least 10, at least 11, at least 12, at least 13, at leastBCS236357 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 11 or 47, and (iii) a sequence or flanking sequence, or a 3´ flank, that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 12 or 48. According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises (i) expression cassettes that encodes the pesticidal insect toxins Cry1B.868 and Cry1Da_7, (ii) a polynucleotide sequence comprising one or more polynucleotide sequences selected from SEQ ID NOs: 49-148, and (iii) a polynucleotide sequence comprising one or more polynucleotide sequences selected from SEQ ID NOs: 149-248.
[0136] According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises expression cassettes that encodes the pesticidal insect toxins Cry1B.868 and Cry1Da_7, wherein the DNA molecule, construct, segment, amplicon, fragment or polynucleotide comprises at its 5´ end at least 50 consecutive nucleotides of SEQ ID NO: 11 or 47. According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises expression cassettes that encodes the pesticidal insect toxins Cry1B.868 and Cry1Da_7, wherein the DNA molecule, construct, segment, amplicon, fragment or polynucleotide comprises at its 3´ end at least 50 consecutive nucleotides of SEQ ID NO: 12 or 48. According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises expression cassettes that encodes the pesticidal insect toxins Cry1B.868 and Cry1Da_7, wherein the DNA molecule, construct, segment, amplicon, fragment or polynucleotide comprises at its 5´ end a polynucleotide sequence selected from SEQ ID NOs:BCS236357 49-148. According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises expression cassettes that encodes the pesticidal insect toxins Cry1B.868 and Cry1Da_7, wherein the DNA molecule, construct, segment, amplicon, fragment or polynucleotide comprises at its 3´ end a polynucleotide sequence selected from SEQ ID NOs: 149-248.
[0137] According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises expression cassettes that encodes the pesticidal insect toxins Cry1B.868 and Cry1Da_7, wherein the DNA molecule, construct, segment, amplicon, fragment or polynucleotide comprises at its 5´ end at least 50 consecutive nucleotides of SEQ ID NO: 11 or 47, wherein the DNA molecule, construct, segment, amplicon, fragment or polynucleotide comprises at its 3´ end at least 50 consecutive nucleotides of SEQ ID NO: 12 or 48, wherein the DNA molecule, construct, segment, amplicon, fragment or polynucleotide comprises at its 5´ end a polynucleotide sequence selected from SEQ ID NOs: 49- 148, and / or wherein the DNA molecule, construct, segment, amplicon, fragment or polynucleotide comprises at its 3´ end a polynucleotide sequence selected from SEQ ID NOs: 149-248.
[0138] According to present embodiments, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 11 or SEQ ID NO: 47 at the 5´ end of a DNA molecule, construct, segment, amplicon, fragment or polynucleotide may be immediately adjacent to and upstream (on the 5´ end) of the transgenic insertion, or may not be immediately adjacent to, but further upstream (on the 5´ end) and within about 5000 nucleotides, within about 4000 nucleotides, within about 3000 nucleotides, within about 2000 nucleotides, or within about 1000 nucleotides of the transgenic insertion. According to present embodiments, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 12 or SEQ ID NO: 48 at the 3´ end of a DNA molecule, construct,BCS236357 segment, amplicon, fragment or polynucleotide may be immediately adjacent to and downstream (on the 3´ end) of the transgenic insertion, or may not be immediately adjacent to but further downstream (on the 3´ end) and within about 5000 nucleotides, within about 4000 nucleotides, within about 3000 nucleotides, within about 2000 nucleotides, or within about 1000 nucleotides of the transgenic insertion. Any sequence comprising at least 50 consecutive nucleotides of SEQ ID NO: 11 or SEQ ID NO:47, or at least 50 consecutive nucleotides of SEQ ID NO: 12 or SEQ ID NO: 48 is within the scope of the present disclosure. A DNA molecule, construct, segment, amplicon, fragment or polynucleotide can comprise at the 5´ and / or 3´ end of the construct (i) at least 50 consecutive nucleotides of SEQ ID NO: 11 or SEQ ID NO: 47; and / or (ii) at least 50 consecutive nucleotides of SEQ ID NO: 12 or SEQ ID NO: 48, respectively.
[0139] According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises (i) SEQ ID NO: 9 or a polynucleotide sequence comprising at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 9, and (ii) a junction sequence. According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises (i) SEQ ID NO: 9 or a polynucleotide sequence comprising at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 9, and (ii) a 5´ flank and / or a 3´ flank sequence.
[0140] According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises (i) SEQ ID NO: 9 or a polynucleotide sequence comprising at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, atBCS236357 least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 9, and (ii) a polynucleotide sequence comprising at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 11 or SEQ ID NO: 47 or SEQ ID NO: 12 or SEQ ID NO: 48. According to some embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises (i) SEQ ID NO: 9 or a polynucleotide sequence comprising at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 9, and (ii) a sequence or flanking sequence, or a 5´ flank or 3´ flank, that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to SEQ ID NO: 11 or 47 or SEQ ID NO: 12 or 48, or a fragment of either thereof.
[0141] According to some embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises (i) SEQ ID NO: 9 or a polynucleotide sequence comprising at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 9, and (ii) a sequence or flanking sequence, or a 5´ flank or 3´ flank, that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at leastBCS236357 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 11 or 47 or SEQ ID NO: 12 or 48. According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises (i) SEQ ID NO: 9 or a polynucleotide sequence comprising at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 9, and (ii) a polynucleotide sequence comprising one or more polynucleotide sequences selected from SEQ ID NOs: 49-148.
[0142] According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises (i) SEQ ID NO: 9 or a polynucleotide sequence comprising at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 9, and (ii) a polynucleotide sequence comprising one or more polynucleotide sequences selected from SEQ ID NOs: 149-248.
[0143] According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises (i) SEQ ID NO: 9 or a polynucleotide sequence comprising at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 9, (ii) a polynucleotide sequence comprising at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at leastBCS236357 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 11 or SEQ ID NO: 47, and (iii) a polynucleotide sequence comprising at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 12 or SEQ ID NO: 48. According to some embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises (i) SEQ ID NO: 9 or a polynucleotide sequence comprising at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 9, (ii) a sequence or flanking sequence, or a 5´ flank, that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to SEQ ID NO: 11 or 47, or a fragment of either thereof, and (iii) a sequence or flanking sequence, or a 3´ flank, that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to SEQ ID NO: 12 or 48, or a fragment of either thereof. According to some embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises (i) SEQ ID NO: 9 or a polynucleotide sequence comprising at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides ofBCS236357 SEQ ID NO: 9, and (ii) a sequence or flanking sequence, or a 5´ flank, that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 11 or 47, and (iii) a sequence or flanking sequence, or a 3´ flank, that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 12 or 48.
[0144] According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises (i) SEQ ID NO: 9 or a polynucleotide sequence comprising at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 9, (ii) a polynucleotide sequence comprising one or more polynucleotide sequences selected from SEQ ID NOs: 49-148, and (iii) a polynucleotide sequence comprising one or more polynucleotide sequences selected from SEQ ID NOs: 149-248.
[0145] According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises SEQ ID NO: 9 or a polynucleotide sequence comprising at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at leastBCS236357 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 9, wherein the DNA molecule, construct, segment, amplicon, fragment or polynucleotide comprises at its 5´ end at least 50 consecutive nucleotides of SEQ ID NO: 11 or 47. According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises SEQ ID NO: 9 or a polynucleotide sequence comprising at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 9, wherein the DNA molecule, construct, segment, amplicon, fragment or polynucleotide comprises at its 3´ end at least 50 consecutive nucleotides of SEQ ID NO: 12 or 48. According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises expression cassettes that encodes the pesticidal insect toxins Cry1B.868 and Cry1Da_7, wherein the DNA molecule, construct, segment, amplicon, fragment or polynucleotide comprises at its 5´ end a polynucleotide sequence selected from SEQ ID NOs: 49-148. According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises SEQ ID NO: 9 or a polynucleotide sequence comprising at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 9, wherein the DNA molecule, construct, segment, amplicon, fragment or polynucleotide comprises at its 3´ end a polynucleotide sequence selected from SEQ ID NOs: 149- 248.
[0146] According to present embodiments, a DNA molecule, construct, segment, amplicon, fragment or polynucleotide is provided that contains or comprises SEQ ID NO: 9 or a polynucleotide sequence comprising at least 10, at least 11, at least 12, at least 13, at least 14, atBCS236357 least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 9, wherein the DNA molecule, construct, segment, amplicon, fragment or polynucleotide comprises at its 5´ end at least 50 consecutive nucleotides of SEQ ID NO: 11 or 47, wherein the DNA molecule, construct, segment, amplicon, fragment or polynucleotide comprises at its 3´ end at least 50 consecutive nucleotides of SEQ ID NO: 12 or 48, wherein the DNA molecule, construct, segment, amplicon, fragment or polynucleotide comprises at its 5´ end a polynucleotide sequence selected from SEQ ID NOs: 49-148, and / or wherein the DNA molecule, construct, segment, amplicon, fragment or polynucleotide comprises at its 3´ end a polynucleotide sequence selected from SEQ ID NOs: 149-248.
[0147] According to present embodiments, a corn plant, plant part, plant seed, plant tissue, plant cell or commodity product is provided comprising any DNA molecule, construct, segment, fragment or polynucleotide described herein. A corn plant comprising a construct as described herein may be further characterized as having resistance to Lepidopteran infestation, relative to a non-transgenic control plant.
[0148] To detect the presence or absence of corn event MON 95379 or a modified corn event MON 95379, the target positions and / or the intervening region or sequence of a template DNA molecule may comprise at least one junction sequence and / or at least a portion of the insert of corn event MON 95379 or a modified corn event MON 95379. To detect the absence of corn event MON 95379, the target positions and / or the intervening region or sequence of a template DNA molecule may comprise corn genomic DNA that does not include a junction sequence or any portion of the insert of corn event MON 95379 or a modified corn event MON 95379. Thus, the presence or absence of an amplicon with a primer pair may be diagnostic of the presence or absence, respectively, of corn event MON 95379 or a modified corn event MON 95379 in a DNA molecule or sample, or vice versa. This may also be possible with more than one primer pair. For example, a first primer pair may produce a first amplicon if corn event MON 95379 or a modified corn event MON 95379 is present, and a second primer pair may produce a second amplicon if corn event MON 95379 or a modified corn event MON 95379 is absent or not present. Alternatively, the size of an amplicon produced in an amplification reaction may also be diagnosticBCS236357 of the presence or absence of corn event MON 95379 or a modified corn event MON 95379 in a DNA molecule or sample – e.g., a primer pair may produce a first amplicon of a first size if corn event MON 95379 or a modified corn event MON 95379 is present or a second amplicon of a second size if corn event MON 95379 or a modified corn event MON 95379 is absent and not present; or a first primer pair may produce a first amplicon of a first size if corn event MON 95379 or a modified corn event MON 95379 is present, and a second primer pair may produce a second amplicon of a second size if corn event MON 95379 or a modified corn event MON 95379 is absent or not present. According to some of these embodiments, at least two primer pairs may be used wherein at least one of the primer pairs is used as an internal control and is not associated with corn event MON 95379 or a modified corn event MON 95379.
[0149] According to present embodiments, a primer pair to detect the presence of all or part of corn event MON 95379 or a modified corn event MON 95379 in a DNA molecule or sample comprises a first primer and a second primer, wherein the first primer is complementary to a 5´ flanking genomic DNA sequence and the second primer is complementary to a sequence within the transgenic insert; or wherein the first primer is complementary to a 5´ flanking genomic DNA sequence and the second primer is complementary to a 3´ flanking genomic DNA sequence; or wherein the first primer is complementary to a 3´ flanking genomic DNA sequence and the second primer is complementary to a 5´ flanking genomic DNA sequence; or wherein the first primer is complementary to a sequence within the transgenic insert and the second primer is complementary to a 3´ flanking genomic DNA sequence; or wherein the first primer is complementary to a sequence within the transgenic insert and the second primer is complementary to a 5´ flanking genomic DNA sequence; or wherein the first primer is complementary to a 3´ flanking genomic DNA sequence and the second primer is complementary to a sequence within the transgenic insert. Each reference in this paragraph to a primer complementary to a 5´ flanking genomic DNA sequence, a 3´ flanking genomic DNA sequence, or a sequence within the transgenic insert of corn event MON 95379 or a modified corn event MON 95379 is also intended to potentially include a primer complementary to the reverse complement or opposing strand of the respective 5´ flanking genomic DNA sequence, 3´ flanking genomic DNA sequence, or sequence within the transgenic insert of corn event MON 95379 or a modified corn event MON 95379.
[0150] Examples of DNA molecules that may be useful as primers are provided as SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 18, and SEQ ID NO: 19. The primer pair SEQ ID NO: 15 andBCS236357 SEQ ID NO: 16 can be useful as a first DNA molecule or primer and a second DNA molecule or primer, wherein each primer has sufficient length of consecutive nucleotides of SEQ ID NO: 10 or a sequence complementary to SEQ ID NO: 10 to function as DNA primers that, when used together in an amplification reaction with template DNA derived from corn event MON 95379 or a modified corn event MON 95379, hybridize to opposite strands of the template DNA and produce an amplicon diagnostic for corn event MON 95379 DNA or DNA from a modified corn event MON 95379 in a sample. The primer pair SEQ ID NO: 18 and SEQ ID NO: 19 are useful as a first DNA molecule or primer and a second DNA molecule or primer, wherein each primer has sufficient length of consecutive nucleotides of a locus within the corn genome to function as DNA primers that, when used together in a thermal amplification reaction with template DNA derived from corn event MON 95379 or a modified corn event MON 95379, to produce an amplicon that serves as an internal control for both the diagnosis of corn event MON 95379 or a modified corn event MON 95379, as well as the zygosity of corn event MON 95379 DNA or DNA from a modified corn event MON 95379 in a sample.
[0151] DNA probes and DNA primers are generally eleven (11) polynucleotides or more in length, often eighteen (18) polynucleotides or more, twenty-four (24) polynucleotides or more, or thirty (30) polynucleotides or more. Such probes and primers are selected to be of sufficient length to hybridize specifically to a target sequence under high stringency hybridization conditions. Preferably, probes and primers according to the present invention have complete sequence similarity with the target sequence, although probes differing from the target sequence that retain the ability to hybridize to target sequences may be designed by conventional methods.
[0152] The nucleic acid probes and primers of the present invention hybridize under stringent conditions to a target DNA molecule. Any conventional nucleic acid hybridization or amplification method can be used to identify the presence of DNA from a transgenic plant in a sample. Polynucleic acid molecules also referred to as nucleic acid segments or fragments thereof are capable of specifically hybridizing to other nucleic acid molecules under certain circumstances.
[0153] As used herein, two polynucleic acid molecules are said to be capable of specifically hybridizing to one another if the two molecules are capable of forming an anti-parallel, double- stranded nucleic acid structure. A nucleic acid molecule is said to be the “complement” of another nucleic acid molecule if they exhibit complete complementarity. As used herein, molecules are said to exhibit “complete complementarity” when every nucleotide of one of the molecules isBCS236357 complementary to a nucleotide of the other. Two molecules are said to be “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 molecules are said to be “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. 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). Departures from complete complementarity are therefore permissible, as long as such departures do not completely preclude the capacity of the molecules to form a double-stranded structure. In order for a nucleic acid molecule 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 salt concentrations employed.
[0154] As used herein, a substantially homologous sequence is a nucleic acid sequence that will specifically hybridize to the complement of the nucleic acid sequence to which it is being compared under high stringency conditions. Appropriate stringency conditions that promote DNA hybridization, for example, 6.0 x sodium chloride / sodium citrate (SSC) at about 45°C, followed by a wash of 2.0 x SSC at 50°C, are known to those skilled in the art or can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6. For example, the salt concentration in the wash step can be selected from a low stringency of about 2.0 x SSC at 50°C to a high stringency of about 0.2 x SSC at 50°C. In addition, the temperature in the wash step can be increased from low stringency conditions at room temperature, about 22°C, to high stringency conditions at about 65°C. Both temperature and salt may be varied, or either the temperature or the salt concentration may be held constant while the other variable is changed. In a preferred embodiment, a polynucleic acid of the present invention will specifically hybridize to one or more of the nucleic acid molecules set forth in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, or SEQ ID NO: 10, or complements thereof or fragments thereof under moderately stringent conditions, for example at about 2.0 x SSC and about 65°C. In a particularly preferred embodiment, a nucleic acid of the present invention will specifically hybridize to one or more of the nucleic acid molecules set forth in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, or SEQ IDBCS236357 NO: 10, or complements or fragments thereof under high stringency conditions. In one aspect of the present invention, a preferred marker nucleic acid molecule of the present invention has the nucleic acid sequence set forth in SEQ ID NO: 1, or SEQ ID NO: 2, or SEQ ID NO: 3, or SEQ ID NO: 4, or SEQ ID NO: 5, or SEQ ID NO: 6, or SEQ ID NO: 7, or SEQ ID NO: 8, or SEQ ID NO: 9, or SEQ ID NO: 10, or complements thereof, or fragments thereof. The hybridization of the probe to the target DNA molecule can be detected by any number of methods known to those skilled in the art, these can include, but are not limited to, fluorescent tags, radioactive tags, antibody based tags, and chemiluminescent tags.
[0155] Regarding the amplification of a target nucleic acid sequence (e.g., by PCR) using a particular amplification primer pair, "stringent conditions" are conditions that permit the primer pair to hybridize only to the target nucleic acid sequence to which a primer having the corresponding wild-type sequence (or its complement) would bind and preferably to produce a unique amplification product, the amplicon, in a DNA thermal amplification reaction.
[0156] The term "specific for (a target sequence)" indicates that a probe or primer hybridizes under stringent hybridization conditions only to the target sequence in a sample comprising the target sequence.
[0157] As used herein, “amplified DNA” or “amplicon” refers to the product of polynucleic acid amplification method directed to a target polynucleic acid molecule that is part of a polynucleic acid template. For example, to determine whether a corn plant resulting from a sexual cross contains transgenic plant genomic DNA from a corn plant comprising event MON 95379 of the present invention, DNA that is extracted from a corn plant tissue sample may be subjected to a polynucleic acid amplification method using a primer pair that includes a first primer derived from a genomic DNA sequence in the region flanking the heterologous inserted DNA of event MON 95379 and is elongated by polymerase 5´ to 3´ in the direction of the inserted DNA. The second primer is derived from the heterologous inserted DNA molecule is elongated by the polymerase 5´ to 3´ in the direction of the flanking genomic DNA from which the first primer is derived. The amplicon may range in length from the combined length of the primer pair plus one nucleotide base pair, or plus about fifty nucleotide base pairs, or plus about two hundred-fifty nucleotide base pairs, or plus about four hundred-fifty nucleotide base pairs or more. Alternatively, a primer pair can be derived from genomic sequence on both sides of the inserted heterologous DNA so as to produce an amplicon that includes the entire insert polynucleotide sequence (e.g., a forward primerBCS236357 isolated from the genomic portion on the 5´ end of SEQ ID NO: 10 and a reverse primer isolated from the genomic portion on the 3´ end of SEQ ID NO: 10 that amplifies a DNA molecule comprising the inserted DNA sequence (SEQ ID NO: 9) identified herein in the event MON 95379 genome). A member of a primer pair derived from the plant genomic sequence adjacent to the inserted transgenic DNA is located a distance from the inserted DNA sequence, this distance can range from one nucleotide base pair up to about twenty thousand nucleotide base pairs. The use of the term “amplicon” specifically excludes primer dimers that may be formed in the DNA thermal amplification reaction.
[0158] For practical purposes, one should design primers 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 thermal amplification reactions, allow for 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 detection. 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 established in the art. Any primer pair derived from the combination of SEQ ID NO: 11 and SEQ ID NO: 9 or the combination of SEQ ID NO: 12 and SEQ ID NO: 9 that are useful in a DNA amplification method to produce an amplicon diagnostic for event MON 95379 or a modified event MON 95379, or progeny thereof is an aspect of the present disclosure. Any single isolated DNA polynucleotide primer molecule comprising at least 15 contiguous nucleotides of SEQ ID NO: 11, or its complement that is useful in a DNA amplification method to produce an amplicon diagnostic for event MON 95379 or a modified event MON 95379, or progeny thereof is an aspect of the present disclosure. Any single isolated DNA polynucleotide primer molecule comprising at least 15 contiguous nucleotides of SEQ ID NO: 12, or its complement that is useful in a DNA amplification method to produce an amplicon diagnostic for plants comprising event MON 95379 or a modified event MON 95379, or progeny thereof is an aspect of the present disclosure. Any single isolated DNA polynucleotide primer molecule comprising at least 15 contiguous nucleotides of SEQ ID NO: 9, or its complement that is useful in a DNA amplification method to produce an amplicon diagnostic for event MON 95379 or a modified event MON 95379, or progeny thereof is an aspect of the present disclosure.BCS236357
[0159] Polynucleic acid amplification can be accomplished by any of the various polynucleic acid amplification methods known in the art, including the polymerase chain reaction (PCR). Amplification methods are known in the art and are described, inter alia, in U.S. Patent Nos. 4,683,195 and 4,683,202 and in PCR Protocols: A Guide to Methods and Applications, ed. Innis et al., Academic Press, San Diego, 1990. PCR amplification methods have been developed to amplify up to 22 kb (kilobase) of genomic DNA and up to 42 kb of bacteriophage DNA (Cheng et al., Proc. Natl. Acad. Sci. USA 91:5695-5699, 1994). These methods as well as other methods known in the art of DNA amplification may be used in the practice of the present invention. The sequence of the heterologous DNA insert or flanking genomic DNA sequence from corn event MON 95379 can be verified (and corrected if necessary) by amplifying such DNA molecules from corn seed containing event MON 95379 DNA or corn plants grown from the corn seed containing event MON 95379 DNA deposited with the ATCC having accession No. PTA-125027, using primers derived from the sequences provided herein, followed by standard DNA sequencing of the PCR amplicon or cloned DNA fragments thereof.
[0160] A diagnostic amplicon produced by the methods described herein may be detected by a plurality of techniques known in the art, such as sequencing, restriction mapping, Northern analysis, Southern analysis, or any other suitable polynucleotide or DNA hybridization, blotting, polymerization and / or amplification based approach or technique. One method is Genetic Bit Analysis (Nikiforov et al., Nucleic Acid Res.22:4167-4175, 1994) where a DNA oligonucleotide is designed that overlaps both the adjacent flanking genomic DNA sequence and the inserted DNA sequence – i.e., a junction sequence. The oligonucleotide is immobilized in wells of a microtiter plate. Following PCR of the region of interest (using, for example, one primer in the inserted sequence and one in the adjacent flanking genomic sequence), a single-stranded PCR product can be hybridized to the immobilized oligonucleotide and serve as a template for a single base extension reaction using a DNA polymerase and labeled dideoxynucleotide triphosphates (ddNTPs) specific for the expected next base. Readout may be fluorescent or ELISA-based. A signal indicates presence of the transgene / genomic junction sequence due to successful amplification, hybridization, and single base extension.
[0161] Another method is the Pyrosequencing technique as described by Winge (Innov. Pharma. Tech. 00:18-24, 2000). In this method, an oligonucleotide is designed that overlaps the adjacent genomic DNA and insert DNA junction. The oligonucleotide is hybridized to single-stranded PCRBCS236357 product from the region of interest (one primer in the inserted sequence and one in the flanking genomic sequence) and incubated in the presence of a DNA polymerase, ATP, sulfurylase, luciferase, apyrase, adenosine 5´ phosphosulfate and luciferin. DNTPs are added individually and the incorporation results in a light signal that is measured. A light signal indicates the presence of the transgene / genomic sequence due to successful amplification, hybridization, and single or multi-base extension.
[0162] Fluorescence Polarization as described by Chen, et al., (Genome Res.9:492-498, 1999) is a method that can be used to detect the amplicon of the present invention. Using this method an oligonucleotide is designed that overlaps the genomic flanking and inserted DNA junction. The oligonucleotide is hybridized to single-stranded PCR product from the region of interest (one primer in the inserted DNA and one in the flanking genomic DNA sequence) and incubated in the presence of a DNA polymerase and a fluorescent-labeled ddNTP. Single base extension results in incorporation of the ddNTP. Incorporation can be measured as a change in polarization using a fluorometer. A change in polarization indicates the presence of the transgene / genomic sequence due to successful amplification, hybridization, and single base extension.
[0163] Real-time Polymerase Chain Reaction (PCR) is the ability to monitor the progress of the PCR as it occurs (i.e., in real time). Data is collected throughout the PCR process, rather than at the end of the PCR. In real-time PCR, reactions are characterized by the point in time during cycling when amplification of a target is first detected rather than the amount of target accumulated after a fixed number of cycles. In a real-time PCR assay, a positive reaction is detected by accumulation of a fluorescent signal. The higher the starting copy number of the nucleic acid target, the sooner a significant increase in fluorescence is observed. The cycle threshold (Ct value) is defined as the number of cycles required for the fluorescent signal to cross the threshold (i.e., exceeds background level). Ct levels are inversely proportional to the amount of target nucleic acid in the sample (i.e., the lower the Ct value, the greater the amount of target nucleic acid in the sample).
[0164] TaqMan® (PE Applied Biosystems, Foster City, CA) is described as a method of detecting and quantifying the presence of a DNA sequence using real-time PCR and is fully understood in the instructions provided by the manufacturer. Briefly, a FRET oligonucleotide probe is designed that overlaps the genomic flanking and insert DNA junction. The FRET probe and PCR primers (one primer in the insert DNA sequence and one in the flanking genomic sequence) are cycled inBCS236357 the presence of a thermalstable polymerase and dNTPs. Hybridization of the FRET probe results in cleavage and release of the fluorescent moiety away from the quenching moiety on the FRET probe. A fluorescent signal indicates the presence of the transgene / genomic sequence due to successful amplification and hybridization.
[0165] Other detection methods known in the art may be used. For example, microfluidics (see, e.g., U.S. Patent Publication No.2006 / 068398; U.S. Patent No.6,544,734) provide methods and devices that can be used to separate and amplify DNA samples or molecules. Optical dyes can be used to detect and measure specific DNA molecules (see, e.g., WO / 05017181). Nanotube devices (see, e.g., WO / 06024023) that comprise an electronic sensor for the detection of DNA molecules or nanobeads that bind specific DNA molecules can then be detected.
[0166] DNA detection kits that are based on DNA amplification methods contain DNA primer molecules that hybridize specifically to a target DNA and amplify a diagnostic amplicon under the appropriate reaction conditions. The kit may provide an agarose gel based detection method or any number of methods of detecting the diagnostic amplicon that are known in the art. DNA detection kits can be developed using the compositions disclosed herein and are useful for identification of corn event MON 95379 DNA or DNA from a modified event MON 95379 in a sample and can be applied to methods for breeding corn plants containing event MON 95379 DNA or DNA from a modified event MON 95379. A kit that contains DNA primers that are homologous or complementary to any portion of the corn genomic region as set forth in SEQ ID NO: 10 and to any portion of the inserted transgenic DNA as set forth in SEQ ID NO: 10 is an object of the invention. The DNA molecules can be used in DNA amplification methods (PCR) or as probes in polynucleic acid hybridization methods, i.e., southern analysis, northern analysis. Kits of the invention may optionally also comprise reagents or instructions for performing the detection or diagnostic reactions described herein.
[0167] Probes and primers as provided herein may have complete 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 molecule 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 salt concentrations employed. Any conventional nucleic acid hybridization or amplificationBCS236357 method can be used to identify the presence of transgenic DNA from corn event MON 95379 or a modified corn event MON 95379 in a sample.
[0168] Any number of methods well known to those skilled in the art can be used to isolate and manipulate a DNA molecule, or fragment thereof, disclosed herein, including DNA isolation or thermal amplification or PCR methods. Such DNA molecule or fragment may be inserted or placed into any suitable vector or plasmid or combined with other elements, sequences or fragments using molecular or recombinant techniques.
[0169] The DNA molecules and corresponding nucleotide sequences provided herein are therefore useful for, among other things, identifying corn event MON 95379 or a modified event MON 95379, detecting the presence of DNA derived from the transgenic corn event MON 95379 or a modified event MON 95379 in a sample, and monitoring samples for the presence and / or absence of corn event MON 95379 or a modified event MON 95379 or plant parts derived from corn plants comprising event MON 95379 or a modified event MON 95379.
[0170] Reference herein to “corn” generally is intended to include corn plants, corn plant cells, corn plant tissues, corn seeds, corn plant parts, corn progeny plants, and / or corn commodity products, depending on the context of its use herein, unless otherwise provided. The present disclosure provides corn plants, corn plant cells, corn plant tissues, corn seeds, corn plant parts (such as pollen, ovule, silk, spike, anther, cob, root tissue, stalk tissue, leaf tissue), corn progeny plants, and corn commodity products. These corn plants, corn plant cells, corn plant tissues, corn seeds, corn plant parts, corn progeny plants, and corn commodity products contain a detectable amount of a polynucleotide or DNA molecule or sequence comprising at least one junction sequence and / or heterologous insert sequence of corn event MON 95379 or a modified event MON 95379, such as a polynucleotide or DNA molecule or sequence having or comprising at least one of the sequences provided as SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 10.
[0171] The present disclosure provides corn plants, corn plant cells, corn seeds, corn plant parts (such as pollen, ovule, silk, spike, anther, cob, root tissue, stalk tissue, leaf tissue), corn progeny plants derived from a transgenic corn plant containing event MON 95379 DNA or DNA from a modified event MON 95379. A representative sample of corn seed containing event MON 95379 DNA has been deposited according to the Budapest Treaty with the American Type CultureBCS236357 Collection (ATCC®). The ATCC repository has assigned the Patent Deposit Designation PTA- 125027 to the seed containing event MON 95379 DNA.
[0172] The present disclosure provides a microorganism comprising a DNA molecule having at least one sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 10 present in its genome. A microorganism is intended to include any microscopic cell or organism, whether prokaryote or eukaryote or otherwise, that contains DNA within a genome or chromosome or an extra-chromosomal DNA structure, such as a plasmid or vector, in such microscopic cell. Microscopic cells or organisms include bacteria (prokaryotes) and cells corresponding to higher life forms (eukaryotes) which are beneath the visual range of the average human. 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 molecules that may be used for subsequent scientific research or as industrial products; and (iii) use with modern 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 modern 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 modern microbiology techniques and may exist in an undifferentiated, unicellular state. The transgenic plant cell’s new genetic composition and phenotype is a technical effect created by the integration 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 integrating recombinant DNA into the genome of the cell and then using this cell to derive additional cells possessing the same heterologous DNA; (ii) methods of culturing cells that contain recombinant DNA using modern 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 modern plant tissue cultureBCS236357 techniques with transgenic plant cells to produce transgenic plants or transgenic plant tissue cultures.
[0173] Corn plants of the present disclosure may pass along the event MON 95379 DNA or DNA from a modified event MON 95379, including transgene(s) or cassette(s) inserted in or part of corn event MON 95379 or a modified event MON 95379, to progeny or offspring. As used herein, “progeny” includes any plant, plant cell, seed, and / or regenerable plant part containing the event MON 95379 DNA or DNA from a modified event MON 95379 derived from an ancestor plant and / or comprising a DNA molecule having at least one sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 10. Corn plants, progeny, and seeds may be homozygous or heterozygous for the corn event MON 95379 or a modified event MON 95379 and / or the transgene(s) or cassette(s) of event MON 95379 or a modified event MON 95379. Progeny may be grown from seeds produced by a corn plant comprising or containing corn event MON 95379 or a modified event MON 95379 and / or from seeds produced by a plant fertilized with pollen from a corn plant comprising or containing corn event MON 95379 or a modified event MON 95379 (i.e., fertilized with pollen comprising or containing corn event MON 95379 or a modified event MON 95379).
[0174] Methods for producing corn plants and seeds containing or comprising maize event MON 95379 or a modified event MON 95379 are provided. Corn plants may be bred using any method known in the art, for example, descriptions of breeding methods that are commonly used can be found in WR Fehr, in Breeding Methods for Cultivar Development, Wilcox J. ed., American Society of Agronomy, Madison WI (1987). Corn plants or progeny plants containing or comprising maize event MON 95379 or a modified event MON 95379 may be self-pollinated (also known as “selfing”) to generate a true breeding line of corn plants, i.e., corn plants homozygous for the transgene and event MON 95379 or a modified event MON 95379. Selfing can result in progeny known as an “inbred” that can be used to produce corn inbred lines that are genetically uniform.
[0175] Alternatively, corn plants or progeny plants containing or comprising maize event MON 95379 or a modified event MON 95379 may be out-crossed or cross-pollinated (also known as “crossing”), e.g., bred with another plant having a different germplasm or genotype, to produce a varietal or hybrid seed or plant that may be homozygous or heterozygous for the transgene(s) or cassette(s) and / or event MON 95379 or a modified event MON 95379 depending on whether theBCS236357 other parental plant also comprises or contains the transgene(s) or cassette(s) and / or event MON 95379 or a modified event MON 95379. The other parental plant may be transgenic or non- transgenic for the same and / or different trait, transgene or event. A varietal or hybrid seed or plant of the invention may thus be derived by sexually crossing a first parent that lacks the specific and unique corn event MON 95379 or a modified event MON 95379 with a second parent comprising corn event MON 95379 or a modified event MON 95379, resulting in a hybrid plant or progeny plant containing or comprising the specific and unique corn event MON 95379 or a modified event MON 95379. Each parent can be a hybrid or an inbred / varietal plant, so long as a parent or progeny plant or seed of the cross has or comprises at least one copy of the corn event MON 95379 or a modified event MON 95379 and / or a DNA molecule having or comprising at least one sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 10.
[0176] Sexually crossing one plant with another plant, i.e., cross-pollinating, may be accomplished or facilitated by human intervention, for example: by human hands or other mechanical means under human, computer or automated control collecting the pollen of one plant and contacting this pollen with the style or stigma of a second plant; by human hands and / or human actions or other mechanical means under human, computer or automated control removing, destroying, devitalizing or covering the stamen or anthers of a plant (e.g., by manual intervention or by application of a chemical gametocide) so that natural self-pollination is prevented and cross- pollination would have 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 removing of parts of the flower to allow for placement or contact of foreign pollen on the style or stigma; by selective placement of plants (e.g., intentionally planting plants in pollinating proximity); and / or by application of chemicals to precipitate flowering or to foster receptivity (of the stigma for pollen).
[0177] Two different transgenic plants may thus be crossed to produce hybrid offspring plants, plant parts and / or seeds that contain two independently segregating transgenes or events wherein at least one of those transgenes or events comprises or is contained within corn event MON 95379 or a modified event MON 95379. For example, transgenic plants comprising corn event MON 95379 or a modified event MON 95379 can be crossed with other transgenic corn plants to produce a plant having the characteristics of both transgenic parents. Back-crossing to a parental plant andBCS236357 out-crossing with a non-transgenic plant are also contemplated, as is vegetative propagation. Descriptions of other breeding methods that are commonly used for different traits and crops are known in the art and 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).
[0178] According to some embodiments, progeny plants, plant parts or seeds may be analyzed using diagnostic methods as described herein to select for plants, plant parts or seeds containing or comprising corn or maize event MON 95379 or a modified event MON 95379. Alternatively, progeny plants, plant parts or seeds may be analyzed using diagnostic methods as described herein to select for plants, plant parts or seeds containing or comprising corn or maize event MON 95379 or a modified event MON 95379.
[0179] Corn plants, progeny, seeds, cells and plant parts comprising corn event MON 95379 or a modified corn event MON 95379, and / or one or transgene(s) or cassette(s) of corn event MON 95379 or a modified corn event MON 95379, may also contain one or more additional corn trait(s) or transgenic events, particularly those introduced by crossing a corn plant containing such transgene(s) or cassette(s) and / or corn event MON 95379 or a modified corn event MON 95379 with another corn plant containing the additional trait(s) or transgenic event(s). Such trait(s) or transgenic event(s) include, but are not limited to, increased insect resistance, herbicide tolerance, increased water use efficiency, increased yield performance, increased drought resistance, increased seed quality, improved nutritional quality, hybrid seed production, or disease or fungal resistance. A corn trait may include any transgenic traits or mutant or edited traits or alleles. Mutant traits or alleles of a gene may be created by any mutagenesis technique known in the art, whereas edited traits may be generated by any genome editing technique or method known in the art. Many transgenic events are known to those of skill in the art. For example, a list of such traits is provided by the United States Department of Agriculture’s (USDA) Animal and Plant Health Inspection Service (APHIS) and can be found on their website: www.aphis.usda.gov. Two or more trait(s) and / or transgenic event(s) comprising or including at least one copy of corn event MON 95379 or a modified corn event MON 95379 may thus be combined in a progeny seed or plant by crossing two parent plants each comprising one or more trait(s) or transgenic event(s), collecting the progeny seed, and selecting for progeny seed or plants that contain the two or more trait(s) or transgenic event(s). These steps may be repeated until the desired combination of trait(s) or transgenic event(s) in a progeny plant is achieved. For the present application, the progenyBCS236357 plant will generally comprise corn event MON 95379 or a modified corn event MON 95379. Back-crossing to a parental plant and out-crossing with a non-transgenic plant are also contemplated and is vegetative propagation.
[0180] A plant part is provided that comprises event MON 95379 or a modified corn event MON 95379 and / or is derived from corn plants comprising event MON 95379 or a modified corn event MON 95379. As used herein, a “plant part” refers to any part of a plant which may comprise event MON 95379 or a modified corn event MON 95379 and / or material derived from a corn plant comprising event MON 95379 or a modified corn event MON 95379. Plant parts include, but are not limited to, plant tissue, pollen, ovule, silk, spike, anther, cob, root tissue, stalk tissue, and leaf tissue. Plant parts may be viable, nonviable, regenerable, and / or non-regenerable.
[0181] A commodity product is provided that is derived from one or more corn plants, plant parts, seeds and / or plant tissues comprising event MON 95379 or a modified corn event MON 95379 and that contains a detectable amount of a nucleic acid or DNA molecule, segment or sequence specific for event MON 95379 or a modified corn event MON 95379. As used herein, a “commodity product” refers to any composition or product comprising material derived from one or more corn plants, whole or processed corn seed, one or more plant cells, and / or one or more plant parts containing or comprising the corn event MON 95379 DNA or DNA from a modified corn event MON 95379. Nonviable commodity products include, but are not limited to, nonviable seeds, whole or processed seeds, seed parts, and plant parts; animal feed comprising corn, corn oil, corn meal, corn flour, corn flakes, corn bran, pasta made with corn, corn biomass, and fuel products produced using corn and corn parts. Viable commodity products include, but are not limited to, seeds, plants, and plant cells. The corn plants comprising event MON 95379 or a modified corn event MON 95379 can thus be used to manufacture any commodity product typically acquired from corn. Any such commodity product that is derived from corn plants comprising event MON 95379 or a modified corn event MON 95379 may contain at least a detectable amount of the specific and unique DNA corresponding to corn event MON 95379 or a modified corn event MON 95379, and specifically may contain a detectable amount of a polynucleotide or DNA molecule having or comprising at least one sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 10. Detection of one or more of these polynucleotide or DNA sequences in a sample may be used to determine or diagnose that the sample is taken from a corn plant, cornBCS236357 plant part, corn plant tissue, corn plant cell, and / or corn plant product, such as a corn commodity product, comprising event MON 95379 or a modified corn event MON 95379, or to determine the content or source of a corn plant, corn plant part, corn plant tissue, corn plant cell, and / or corn plant product, such as a corn commodity product. Any standard method of detection for nucleotide molecules may be used, including methods of detection disclosed herein. A commodity product is within the scope of the present disclosure if there is any detectable amount of a DNA molecule having at least one sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 10 contained or comprised in the commodity product.
[0182] The corn plants, corn plant cells, corn seeds, corn plant parts (such as pollen, ovule, silk, spike, anther, cob, root tissue, stalk tissue, leaf tissue), corn progeny plants, 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 corn event MON 95379 or a modified corn event MON 95379 for agricultural purposes, producing progeny comprising corn event MON 95379 or a modified corn event MON 95379 for plant breeding and research purposes, use with microbiological techniques for industrial and research applications, and sale to consumers.
[0183] Methods for producing an insect resistant corn plant comprising the DNA sequences specific and unique to event MON 95379 or a modified corn event MON 95379 of the present disclosure are provided. A progeny corn plant comprising the event MON 95379 or a modified corn event MON 95379 may be produced, for example, by selfing a parent plant or line comprising the event MON 95379 or a modified corn event MON 95379, wherein such parent plant or line is homozygous or hemizygous for the event MON 95379 or a modified corn event MON 95379, or by crossing a first parent plant or line comprising the event MON 95379 or a modified corn event MON 95379, wherein such parent plant or line is homozygous or hemizygous for the event MON 95379 or a modified corn event MON 95379, with a second parent plant or line having a different genotype or germplasm than the first parent line, wherein the second parent plant or line may or may not contain or comprise the event MON 95379 or a modified corn event MON 95379. As described further herein, a modified corn event MON 95379 may contain one or more of the expression cassette(s) or transgene(s) as provided herein, such as one or both of Cry1B.868 and / or Cry1Da_7 expressing transgene cassette(s). According to some embodiments, the transgenic corn plant(s) comprising the event MON 95379 or a modified corn event MON 95379 of the presentBCS236357 disclosure may exhibit resistance to one or more Lepidopteran insect pest species, such as Fall Armyworm (Spodoptera frugiperda), Corn Earworm (Helicoverpa zea), Southwestern Corn Borer (Diatraea grandiosella), Surgarcane Borer (Diatraea saccharalis), and / or Lesser Cornstalk Borer (Elasmopalpus lignosellus), relative to a non-transgenic control plant. Transgenic plants used in these methods may be homozygous or heterozygous for the transgene or event. Progeny plants produced by these methods may be varietal or hybrid plants; may be grown from seeds produced by plants containing corn event MON 95379 or a modified corn event MON 95379 and / or from seeds produced by a plant fertilized with pollen from a plant containing corn event MON 95379 or a modified corn event MON 95379; and may be homozygous or heterozygous for one or more of the transgene(s) described herein and / or the corn event MON 95379 or a modified corn event MON 95379. 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 out-crossed, e.g., bred with another unrelated plant, to produce a varietal or a hybrid seed or plant.
[0184] Methods of detecting the presence of DNA derived from a corn cell, corn tissue, corn seed, or corn plant comprising corn event MON 95379 or a modified corn event MON 95379 in a sample are provided. One method consists of (i) extracting a DNA sample from at least one corn cell, corn tissue, corn seed, or corn plant; (ii) contacting the DNA sample with at least one primer that is capable of producing DNA sequence specific to event MON 95379 DNA or DNA from or a modified corn event MON 95379 under conditions appropriate for DNA sequencing; (iii) performing a DNA sequencing reaction; and then (iv) confirming that the nucleotide sequence comprises a nucleotide sequence specific for event MON 95379 or a modified corn event MON 95379, of the construct comprised therein, such as one selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 10.
[0185] Another method consists of (i) extracting a DNA sample from at least one corn cell, corn tissue, corn seed, or corn plant; (ii) contacting the DNA sample with a primer pair that is capable of producing an amplicon from event MON 95379 DNA or DNA from a modified corn event MON 95379 under conditions appropriate for DNA amplification; (iii) performing a DNA amplification reaction; and then (iv) detecting the amplicon molecule and / or confirming that the nucleotide sequence of the amplicon comprises a nucleotide sequence specific for event MON 95379 or a modified corn event MON 95379, such as one selected from the group consisting ofBCS236357 SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 10. The amplicon should be one that is specific for event MON 95379, such as an amplicon that comprises SEQ ID NO: 1, or SEQ ID NO: 2, or SEQ ID NO: 3, or SEQ ID NO: 4, or SEQ ID NO: 5, or SEQ ID NO: 6, or SEQ ID NO: 7, or SEQ ID NO: 8, or SEQ ID NO: 9, or SEQ ID NO: 10. The detection of a nucleotide sequence specific for event MON 95379 or a modified corn event MON 95379 in the amplicon is determinative and / or diagnostic for the presence of the corn event MON 95379 specific DNA or DNA specific for a modified corn event MON 95379 in the sample. An example of a primer pair that is capable of producing an amplicon from event MON 95379 DNA or DNA from a modified corn event MON 95379 under conditions appropriate for DNA amplification is provided as SEQ ID NO: 15 and SEQ ID NO: 16. Other primer pairs may be readily designed by one of skill in the art and would produce an amplicon comprising SEQ ID NO: 1, or SEQ ID NO: 2, or SEQ ID NO: 3, or SEQ ID NO: 4, or SEQ ID NO: 5, or SEQ ID NO: 6, or SEQ ID NO: 7, or SEQ ID NO: 8 wherein such a primer pair comprises at least one primer within the genomic region flanking the insert and a second primer within the insert.
[0186] Another method of detecting the presence of DNA derived from a corn cell, corn tissue, corn seed, or corn plant comprising corn event MON 95379 or a modified corn event MON 95379 in a sample consists of (i) extracting a DNA sample from at least one corn cell, corn tissue, corn seed, or corn plant; (ii) contacting the DNA sample with a DNA probe specific for event MON 95379 or a modified corn event MON 95379; (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 of a DNA probe that is specific for event MON 95379 or a modified corn event MON 95379 is provided as SEQ ID NO: 17. Other probes may be readily designed by one of skill in the art and would comprise at least one fragment of genomic DNA flanking the insert and at least one fragment of insert DNA such as the sequence provided in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, and SEQ ID NO: 10. Detection of probe hybridization to the DNA sample is diagnostic for the presence of corn event MON 95379 specific DNA or DNA specific for a modified corn event MON 95379 in the sample. Absence of hybridization is alternatively diagnostic of the absence of corn event MON 95379 specific DNA or DNA specific for a modified corn event MON 95379 in the sample.BCS236357
[0187] DNA detection kits are provided that are useful for the identification of corn event MON 95379 DNA or DNA from a modified corn event MON 95379 in a sample and can also be applied to methods for breeding corn plants containing the appropriate event DNA. Such kits may contain DNA primers and / or probe(s) which are specific for corn event MON 95379 or a modified corn event MON 95379. Such DNA primers and / or probe(s) may comprise one or more of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 10. One example of such a kit comprises at least one DNA molecule of sufficient length of continuous nucleotides of SEQ ID NO: 10 to function as a DNA probe useful for detecting the presence and / or absence of DNA derived from transgenic corn plants comprising event MON 95379 or a modified corn event MON 95379 in a sample. The DNA derived from transgenic corn plants comprising event MON 95379 or a modified corn event MON 95379 would comprise a DNA molecule having at least one sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 10. The primers may comprise a primer pair including a first primer and a second primer, wherein at least one of the primers hybridizes to a flanking sequence and the other primer hybridizes to either an insert sequence of event MON 95379 or a modified corn event MON 95379 in the plant genome or the flanking sequence on the opposite side of the insert. The first and second primers hybridize to opposing strands of the corn plant genomic DNA at different spaced apart positions such that an amplification reaction involving the two primers produces an amplicon comprising the primer sequences and the intervening sequence between the two primers. A probe may be chosen to correspond or hybridize to the amplicon produced with a primer pair or set of primers and may comprise all or part of the primer sequence(s) and / or the intervening sequence of the amplicon between the two primers. A DNA molecule that may be used as a DNA probe for determining, detecting, or diagnosing the presence and / or absence of corn event MON 95379 or a modified corn event MON 95379 in a sample is provided as SEQ ID NO: 17. Other probes may be readily designed by one of skill in the art and should comprise at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, at least 30, at least 31, at least 32, at least 33, at least 34, at least 35, at least 36, at least 37, at least 38, at least 39, or at least 40 contiguous nucleotides of SEQ IDBCS236357 NO: 10 and be sufficiently unique to corn event MON 95379 or a modified corn event MON 95379 in order to identify DNA derived from the event.
[0188] 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 corn event MON 95379 or a modified corn event MON 95379 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 molecule having at least one sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 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 corn event MON 95379 specific DNA or DNA specific for a modified corn event MON 95379 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, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, or at least 30 contiguous nucleotides of sequences provided in, but not limited to SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 10, and be sufficiently unique to corn event MON 95379 DNA or DNA from a modified corn event MON 95379 in order to identify DNA derived from the event.
[0189] The kits and detection methods of the invention are useful for, among other things, identifying corn event MON 95379 or a modified corn event MON 95379, selecting plant varieties or hybrids comprising corn event MON 95379 or a modified corn event MON 95379, detecting the presence of DNA derived from the transgenic corn plant comprising event MON 95379 or a modified corn event MON 95379 in a sample, and monitoring samples for the presence and / or absence of corn plants comprising event MON 95379 or a modified corn event MON 95379, or plant parts derived from corn plants comprising event MON 95379 or a modified corn event MON 95379.
[0190] The sequences of the heterologous DNA insert, junction sequences, or flanking sequence from corn event MON 95379 or a modified corn event MON 95379 can be verified (and corrected if necessary) by amplifying such sequences from the event using primers derived from theBCS236357 sequences provided herein followed by standard DNA sequencing of the amplicon or of the cloned DNA.
[0191] Methods of detecting the zygosity of the transgene allele of DNA derived from a corn cell, corn tissue, corn seed, or corn plant comprising corn event MON 95379 or a modified corn event MON 95379 in a sample are provided. One method consists of (i) extracting a DNA sample from at least one corn cell, corn tissue, corn seed, or corn plant; (ii) contacting the DNA sample with a primer pair that is capable of producing a first amplicon diagnostic for event MON 95379 or a modified corn event MON 95379; (iii) contacting the DNA sample with a primer pair that is capable of producing a second amplicon diagnostic for native corn genomic DNA not comprising event MON 95379 or a modified corn event MON 95379; (iv) performing a DNA amplification reaction; and then (v) detecting the amplicons, wherein the presence of only the first amplicon is diagnostic of a homozygous event MON 95379 DNA or DNA from a modified corn event MON 95379 in the sample, and the presence of both the first amplicon and the second amplicon is diagnostic of a corn plant heterozygous for event MON 95379 or a modified corn event MON 95379. An exemplary set of primers pairs are presented as SEQ ID NO: 15 and SEQ ID NO: 16 which produce an amplicon diagnostic for event MON 95379 or a modified corn event MON 95379; and SEQ ID NO: 15 and SEQ ID NO: 27 which produces an amplicon diagnostic for non- inserted wild-type corn genomic DNA not comprising event MON 95379 or a modified corn event MON 95379. A set of probes can also be incorporated into such an amplification method to be used in a real-time PCR format using the primer pair sets described above. An exemplary set of probes are presented as SEQ ID NO: 17 (diagnostic for the amplicon for the event MON 95379 or a modified corn event MON 95379) and SEQ ID NO: 28 (diagnostic for the amplicon for wild- type corn genomic DNA not comprising event MON 95379 or a modified corn event MON 95379).
[0192] Another method for determining zygosity consists of (i) extracting a DNA sample from at least one corn cell, corn tissue, corn seed, or corn plant; (ii) contacting the DNA sample with a probe set which contains at least a first probe that specifically hybridizes to event MON 95379 DNA or DNA from a modified corn event MON 95379 and at least a second probe that specifically hybridizes to corn genomic DNA that was disrupted by insertion of the heterologous DNA of event MON 95379 or a modified corn event MON 95379 and does not hybridize to event MON 95379 DNA or DNA from a modified corn event MON 95379; (iii) hybridizing the probe set with the sample under stringent hybridization conditions, wherein detecting hybridization of only the firstBCS236357 probe under the hybridization conditions is diagnostic for a homozygous allele of event MON 95379 DNA or DNA from a modified corn event MON 95379 in the sample; and wherein detecting hybridization of both the first probe and the second probe under the hybridization conditions is diagnostic for a heterozygous allele of event MON 95379 or a modified corn event MON 95379 in a DNA sample; and wherein detecting hybridization of only the second probe under the hybridization conditions is diagnostic for the absence of corn event MON 95379 DNA or DNA from a modified corn event MON 95379 in the sample.
[0193] Yet another method for determining zygosity consists of (i) extracting a DNA sample from at least one corn cell, corn tissue, corn seed, or corn plant; (ii) contacting the DNA sample with a primer pair that is capable of producing an amplicon from one or more of the toxin coding sequences encoding Cry1B.868 and / or Cry1Da_7 and / or corn event MON 95379 or a modified corn event MON 95379; (iii) contacting the DNA sample with a primer pair that is capable of producing an amplicon of an internal standard known to be single-copy and homozygous in the corn plant; (iv) contacting the DNA sample with a probe set which contains at least a first probe that specifically hybridizes to one or more of the toxin coding sequences encoding Cry1B.868 and / or Cry1Da_7 and / or corn event MON 95379 or a modified corn event MON 95379, and at least a second probe that specifically hybridizes to the internal standard genomic DNA known to be single-copy and homozygous in the corn plant; (v) performing a DNA amplification reaction using real-time PCR and determining the cycle thresholds (Ct values) of the amplicon corresponding to the toxin coding sequence and the single-copy, homozygous internal standard; (vi) calculating the difference (^Ct) between the Ct value of the single-copy, homozygous internal standard amplicon and the Ct value of the toxin coding sequence amplicon; and (vii) determining zygosity, wherein a ^Ct of around zero (0) indicates homozygosity of the inserted T-DNA and a ^Ct of around one (1) indicates heterozygosity of the inserted T-DNA. Heterozygous and homozygous events are differentiated by a ^Ct value unit of approximately one (1). Given the normal variability observed in real-time PCR due to multiple factors such as amplification efficiency and ideal annealing temperatures, the range of “about one (1)” is defined as a ^Ct of 0.75 to 1.25. Primer pairs and probes for the above method for determining zygosity can either amplify and detect amplicons from the Cry1B.868 cassette or coding sequence and internal standard, or amplify and detect amplicons from the Cry1Da_7 cassette or coding sequence and internal standard, or amplify and detect amplicons from a junction sequence and internal standard.BCS236357 Exemplary primer pairs for the detection of the amplicons corresponding to the Cry1B.868 coding sequence and internal standard are presented as SEQ ID NO: 18 combined with SEQ ID NO: 19 (internal standard) and SEQ ID NO: 21 combined with SEQ ID NO: 22 (Cry1B.868). The accompanying exemplary probes are presented as SEQ ID NO: 20 (internal standard) and SEQ ID NO: 23 (Cry1B.868). Exemplary primer pairs for the detection of the amplicons corresponding to the Cry1Da_7 coding sequence and internal standard are presented as SEQ ID NO: 18 combined with SEQ ID NO: 19 (internal standard) and SEQ ID NO: 24 combined with SEQ ID NO: 25 (Cry1Da_7). The accompanying exemplary probes are presented as SEQ ID NO: 20 (internal standard) and SEQ ID NO: 26 (Cry1Da_7).
[0194] According to embodiments of the present disclosure, a transgenic corn plant or plant part, one or more transgenic corn plants or plant parts or a plurality transgenic corn plants or plant parts as provided herein, or an agricultural field or soil in which a transgenic corn plant or plant part, one or more transgenic corn plants or plant parts or a plurality of transgenic corn plants or plant parts as provided herein are planted or grown, can be treated with an agricultural composition comprising one or more active ingredients or other agents, such as, for example and without limitation, an herbicide or one or more herbicides, a fungicide or one or more fungicides, an insecticide or one or more insecticides, a plant growth regulator or plant stimulant or one or more plant growth regulators and / or plant stimulants, and / or a safener or one or more safeners. Provided below are lists of possible or representative compounds for each of these types of actives or agents, and an agricultural composition may comprise one or any combination or multiplicity of these actives, agents or compounds. Such an agricultural composition may be applied, for example, as a foliar, soil or in-furrow treatment, as a pre-emergent, pre-sowing and / or post-emergent treatment, and / or in some cases, may be applied to a transgenic plant part or seed provided herein.
[0195] An agricultural composition may be formulated according to its intended use and application. The appropriate formulation of the agricultural composition may be chosen to have different physicochemical parameters, components and stabilities of the respective compound(s). Possible types of formulations for an agricultural composition can include, for example: wettable powders (WP), water-soluble powders (SP), water-soluble concentrates, emulsifiable concentrates (EC), emulsions (EW), such as oil-in-water and water-in-oil emulsions, sprayable solutions, suspension concentrates (SC), dispersions based on oil or water, oil-miscible solutions, capsule suspensions (CS), dusting products (DP), dressings, granules for scattering and soil application,BCS236357 granules (GR) in the form of microgranules, spray granules, absorption and adsorption granules, water-dispersible granules (WG), water-soluble granules (SG), ULV formulations, microcapsules and waxes. If appropriate, some agricultural compositions of a pesticidal compound or one or more pesticidal compounds might be formulated and used as a seed coating applied to a plant part or seed as provided herein.
[0196] Plants, progeny, plant parts, plant seeds, plant tissues, and plant cells may contain or comprise one or more additional desirable trait(s). Such desirable traits may be transgenic traits, native traits, or traits produced by other methods, such as genome editing, base editing, prime editing or other conventional mutagenesis methods. Such desirable trait(s) may provide an agronomic, agricultural or commodity benefit to a plant, plant part, plant seed or plant product. Desirable traits may be combined with corn event MON 95379 or a modified corn event MON 95379 by, for example, crossing a corn plant comprising corn event MON 95379 or a modified corn event MON 95379 with another corn plant containing the additional trait(s). Alternatively, a trait may be created by mutagenesis, editing or site-directed integration of or into a plant, plant part or plant cell comprising corn event MON 95379 or a modified corn event MON 95379. Such traits may include, but are not limited to, increased insect resistance, increased water use efficiency, increased nitrogen use efficiency, increased yield performance, increased drought resistance, increased disease resistance, increased seed quality, improved nutritional quality, hybrid seed production, and / or increase herbicide tolerance, in which the trait is measured with respect to a corn plant lacking such transgenic trait. For example, the MON 95379 event or a modified corn event MON 95379 could be stacked by breeding or introgression with another event(s), or a combination of events, known in the art including, but not limited to: ^ MON00603 (also known as NK603 or MON603; Roundup Ready™ 2 Maize for herbicide tolerance; deposited as ATCC PTA-2478 and described in US Patent Application Publication No. 2007 / 292854 and US Patent No. 6,825,400, the entire contents and disclosure of each of which are incorporated herein by reference), ^ MON89034 (YieldGard™ VT Pro™ for insect resistance; deposited as ATCC PTA-7455 and described in PCT Publication No. WO2007 / 140256 and US Patent Application Publication No. US2008 / 260932, the entire contents and disclosure of each of which are incorporated herein by reference),BCS236357 ^ MON88017 (YieldGard™ VT™ Rootworm™ RR2 for herbicide tolerance and insect resistance; deposited as PTA-5582 and described in US Patent Application Publication No. 2008 / 028482 and PCT Publication No. WO2005 / 059103, the entire contents and disclosure of each of which are incorporated herein by reference), ^ MON87427 (Roundup Ready™ Maize for herbicide tolerance, deposited as ATCC PTA- 7899, described in US Patent No. 8,618,358 and PCT Publication No. WO2011 / 062904, the entire contents and disclosure of each of which are incorporated herein by reference), ^ MON87411 (for insect resistance; deposited as ATCC No. PTA-12669 and described in US Patent No.10,316,330 and PCT Publication No. WO2013 / 169923, the entire contents and disclosure of each of which are incorporated herein by reference), ^ MON87429 (for herbicide tolerance; deposited as ATCC PTA-124635 and described in US Patent No.10,920,239 and PCT Publication No. WO2019 / 152316, the entire contents and disclosure of each of which are incorporated herein by reference), ^ MON87460 (Genuity® DroughtGard™ for abiotic stress tolerance; deposited as ATCC No. PTA-8910 and described in PCT Publication No. WO2009 / 111263 and US Patent Application Publication No. 2011 / 0138504, the entire contents and disclosure of each of which are incorporated herein by reference), ^ MON87419 (for herbicide tolerance; deposited as ATCC PTA-120860 and described in US Patent No.11,098,321 and PCT Publication WO2015 / 142571, the entire contents and disclosure of each of which are incorporated herein by reference), ^ MON95275 (for insect resistance, deposited as ATCC PTA-126049 and described in US Patent Application Publication No. US2021 / 332380 and PCT Publication No. WO2021 / 216571, the entire contents and disclosure of each of which are incorporated herein by reference). ^ MON00810 (for insect resistance; also known as MON810; described in US Patent Application Publication No.2002 / 102582, the entire contents and disclosure of which are incorporated herein by reference), ^ MON00021 (also known as GA21; Roundup Ready™ Maize, Agrisure™GT for herbicide tolerance, deposited as ATCC 209033 and described in US Patent Application Publication No. 2005 / 086719 and PCT Publication No. WO1998 / 044140, the entire contents and disclosure of each of which are incorporated herein by reference),BCS236357 ^ MON832 (Roundup Ready™ Maize for herbicide tolerance), ^ MON863 (YieldGard™ Rootworm RW, MaxGard™ for insect resistance; deposited as ATCC PTA-2605 and described in PCT Publication No. WO2004 / 011601 and US Patent Application Publication No. 2006 / 095986, the entire contents and disclosure of each of which are incorporated herein by reference), ^ AGV-PY203-4 (GraINzyme Phytase for modified product quality), ^ ACS-ZM004-3 (Starlink™ Maize for herbicide tolerance and insect resistance), ^ ACS-ZM001-9 (InVigor™ Maize for pollination control system), ^ ACS-ZM005-4 (InVigor™ Maize for pollination control system), ^ ACS-ZM002-1 (Liberty Link™ Maize for herbicide tolerance), ^ ACS-ZM003-2 (Liberty Link™ Maize for herbicide tolerance), ^ DAS-40278-9 (Enlist™ Maize for herbicide tolerance, deposited as ATCC No. PTA- 10244 and described in US Patent No. 11,098,322 and PCT Publication No. WO2011 / 022469), ^ DAS-01507-1 (also known as TC1507; Herculex™ I, Herculex™ CB for herbicide tolerance and insect resistance; described in US Patent Application Publication No. 2005039226 and PCT Publication No WO2004 / 099447), ^ DAS-59122-7 (Herculex™ RW for herbicide tolerance and insect resistance; described in US Patent Application Publication No.2006 / 070139), ^ DKB-89614-9 (Bt Xtra™ Maize for herbicide tolerance and insect resistance), ^ DP-32138-1 (32138 SPT maintainer for pollination control system; deposited as ATCC No. PTA-9158 and described in US Patent Application Publication No.2009 / 0210970 and PCT Publication No. WO2009 / 103049), ^ DP-098140-6 (Optimum™ GAT™ for herbicide tolerance; deposited as ATCC No. PTA- 8296 and described in US Patent Application Publication No. 2009 / 137395 and PCT Publication No. WO2008 / 112019), ^ MIR162 (Agrisure™ Viptera for insect resistance; deposited as ATCC No. PTA-6188 and described in US Patent Application Publication No.2009 / 300784 and PCT Publication No. WO2007 / 142840),BCS236357 ^ MIR604 (Agrisure™ RW for insect resistance, described in US Patent Application Publication No.2008 / 167456 and PCT Publication No. WO2005 / 103301), ^ REN-00038-3 (also known as LY038; Mavera™ Maize for modified product quality; deposited as ATCC No. PTA-5623 and described in PCT Publication No. WO2005 / 061720 and US Patent No. 7,615,621, the entire contents and disclosure of each of which are incorporated herein by reference), ^ SYN-E3272-5 (Enogen™ for modified product quality, described in US Patent No. 7,635,799 and PCT Application Publication No. WO2006 / 098952), ^ SYN-05307-1 (Agrisure® Duracade™ for insect resistance; deposited as ATCC No. PTA- 9561 and described in PCT Publication No. WO2010 / 077816 and US Patent No. US10,100,371), ^ Bt10 (for herbicide tolerance and insect resistance), ^ SYN-BT011-1 (Agrisure™ CB / LL for herbicide tolerance and insect resistance), ^ SYN-EV176-9 (NaturGard KnockOut™, Maximizer™ for herbicide tolerance and insect resistance), ^ MON89034 x DAS-01507-1 x MON603 x MIR162 x DAS-40278-9 (Power Core™ x MIR162 x Enlist™ for herbicide tolerance and insect resistance), ^ DAS-01507-1 x DAS-59122-7 (Herculex XTRA™ for herbicide tolerance and insect resistance), ^ DAS-01507-1 x DAS-59122-7 x MON603 (Herculex XTRA™ RR for herbicide tolerance and insect resistance), ^ DAS-01507-1 x MON603 (Herculex™ I RR for herbicide tolerance and insect resistance), ^ DAS-59122-7 x MON603 (Herculex™ RW Roundup Ready™ 2 for herbicide tolerance and insect resistance), ^ DAS-01507-1 × DAS-59122-7 × MON00810 × MIR604 x MON603 (Optimum™ Intrasect Xtreme for herbicide tolerance and insect resistance), ^ DAS-01507-1 x DAS-59122-7 x MON810 x MON603 (Optimum™ Intrasect XTRA for herbicide tolerance and insect resistance), ^ DAS-01507-1 x MIR604 x MON603 (Optimum™ TRIsect for herbicide tolerance and insect resistance),BCS236357 ^ DAS-01507-1 x MON810 x MON603 (Optimum™ Intrasect for herbicide tolerance and insect resistance), ^ MON00021 x MON810 (Roundup Ready™ YieldGard™ Maize for herbicide tolerance and insect resistance), ^ MON810 x MON88017 (YieldGard™ VT Triple for herbicide tolerance and insect resistance), ^ MON863 x MON810 (YieldGard™ Plus for insect resistance), ^ MON603 x MON810 x MON863 (YieldGard™ Plus with RR for herbicide tolerance and insect resistance), ^ MON863 x MON603 (YieldGard™ RW + RR for herbicide tolerance and insect resistance), ^ MON87427 x MON89034 x DAS-01507-1 x MON87411 x DAS-59122-7 x DAS-40278- 9 (SmartStax™ Pro x Enlist™ for herbicide tolerance and insect resistance), ^ MON89034 x MON88017 (Genuity® VT Triple Pro™ for herbicide tolerance and insect resistance), ^ MON89034 x MON603 (Genuity® VT Double Pro™ for herbicide tolerance and insect resistance), ^ MON89034 x DAS-01507-1 x MON88017 x DAS-59122-7 (Genuity® SmartStax™ for herbicide tolerance and insect resistance), ^ MON89034 x DAS-01507-1 x MON603 (Power Core™ for herbicide tolerance and insect resistance), ^ MON603 x MON810 (YieldGard™ CB + RR for herbicide tolerance and insect resistance), ^ MON603 x ACS-ZM003-2 (Roundup Ready™ Liberty Link™ Maize for herbicide tolerance), ^ ACS-ZM003-2 x MON810 (Liberty Link™ Yieldgard™ Maize for herbicide tolerance and insect resistance), ^ REN-00038-3 x MON810 (Mavera™ YieldGard™ Maize for insect resistance and modified product quality), ^ SYN-05307-1 x MIR604 x SYN-BT011-1 x DAS-01507-1 x MON00021 (Agrisure® Duracade™ 5122 for herbicide tolerance and insect resistance),BCS236357 ^ SYN-05307-1 x MIR604 x SYN-BT011-1 x DAS-01507-1 x MON00021 x MIR162 (Agrisure® Duracade™ 5222 for herbicide tolerance and insect resistance), ^ SYN-BT011-1 x DAS-59122-7 x MIR604 x DAS-01507-1 x MON00021 (Agrisure® 3122 for herbicide tolerance and insect resistance), ^ SYN-BT011-1 x MON00021 (Agrisure™ GT / CB / LL for herbicide tolerance and insect resistance), ^ SYN-BT011-1 x MIR162 (Agrisure® Viptera™ 2100 for herbicide tolerance and insect resistance), ^ SYN-BT011-1 x MIR162 x MON00021 (Agrisure® Viptera™ 3110 for herbicide tolerance and insect resistance), ^ SYN-BT011-1 x MIR162 x MIR604 (Agrisure® Viptera™ 3100 for herbicide tolerance and insect resistance), ^ SYN-BT011-1 x MIR162 x DAS-01507-1 x MON00021 (Agrisure® Viptera™ 3220 for herbicide tolerance and insect resistance), ^ SYN-BT011-1 x MIR604 (Agrisure™ CB / LL / RW for herbicide tolerance and insect resistance), ^ SYN-BT011-1 x MIR604 x MON00021 (Agrisure™ 3000GT for herbicide tolerance and insect resistance), and / or ^ MIR604 x MON00021 (Agrisure™ GT / RW for herbicide tolerance and insect resistance). DEPOSIT INFORMATION
[0197] A deposit of a representative sample of corn seed containing event MON 95379 was made on April 20, 2018 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, and assigned ATCC Accession No. PTA-125027. EXAMPLES
[0198] The following Examples are included to more fully describe the invention. Summarized are the construction and testing of one hundred and twenty-five (125) constructs, the production of about ten thousand seven hundred and eighty-five (10,785) events (both proof of concept andBCS236357 commercial), and the analysis of hundreds of thousands of individual plants over six (6) years through the rigorous molecular, agronomic, and field testing required for the creation and selection of corn event MON 95379.
[0199] The Examples demonstrate 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 have 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 present disclosure, appreciate that many changes can be made in the specific embodiments that are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention. EXAMPLE 1 Expression Cassette Testing, Construct Design, Plant Testing and Construct Selection
[0200] Transgene expression in plants is influenced by numerous different factors. The right combination of insecticidal proteins and different expression elements driving expression in plants, while not resulting in off-phenotypes, must be found. Further, beyond the expression elements themselves and their combination and orientation in a cassette, the expression of transgenes in plants is known to be influenced by chromosomal insertion position, perhaps due to chromatin structure (e.g., heterochromatin) or the proximity of transcriptional regulation elements (e.g., enhancers) close to the integration site (Kurt Weising et al., (1988) Foreign genes in plants: transfer, structure, expression and applications. Annu. Rev. Genet.22: 421-77). For example, it has been observed in plants and in other organisms that there may be wide variation in the levels of expression of an introduced gene from the same construct among events with different chromosomal insertion positions. Different chromosomal insertion positions may also produce differences in spatial or temporal patterns of expression, that may not correspond to the patterns expected from transcriptional regulatory elements present in the introduced gene construct.
[0201] For these reasons, it is often necessary to create and screen a large number of constructs and transformation events in order to identify a construct, and then an event, which demonstrates optimal expression of the introduced genes of interest, while also not producing agronomic or phenotypic off-types.BCS236357
[0202] For these reasons, the development of a transgenic corn plant comprising insecticidal proteins that were active against Lepidopterans without any negative effects on agronomics, yield, or stacking viability required extensive research, development, and analysis. Specifically, over a six (6) year period, approximately ten thousand, seven hundred eight-five (10,785) proof of concept and commercial transgenic events derived from one hundred twenty-five (125) different plasmid vector constructs were developed, tested, and analyzed.
[0203] This Example describes the design and testing in corn plants of one hundred and twenty five (125) different constructs to identify the preferred construct for event creation. Each construct varied with respect to the coding sequences for the insecticidal proteins and the transcriptional regulatory elements. Testing was done to select the best construct for use in expressing the insecticidal proteins in plants. Each construct had a unique configuration, varying by expression cassette composition (both insecticidal proteins and expression elements), orientation, and whether or not proteins were targeted to the chloroplast.
[0204] In an initial proof of concept and developmental stage, one hundred seventeen (117) constructs comprising different combinations of twenty-six (26) distinct promoters, twenty-six (26) distinct introns, and ten (10) distinct insect toxin coding sequences, were used to generate approximately six thousand (6,000) transformed events. After initial molecular characterization for the presence of the transgene(s), five thousand fifty-two (5,052) single and double-copy transformed corn events were selected for further characterization and efficacy testing. These events were evaluated for phenotypic or agronomic off-types, the level of expression of the insect toxin proteins, and efficacy against selected Lepidopteran insect pest species. The resulting efficacy and protein expression data, along with any information regarding phenotypic and agronomic off-types was used to eliminate inefficacious proteins, expression elements and combinations, and was used to design a smaller number of binary commercial transformation plasmid constructs to be used in the next phase of development.
[0205] In the next phase of development, eight (8) new constructs were created. These constructs comprised combinations of two (2) to four (4) insect toxin transgene expression cassettes in different orientations (convergent or divergent). These eight (8) constructs were used to generate a total of five thousand seven hundred thirty-three (5,733) transformed events (also referred to as “transformants”). After shoot formation in culture, a subset of the transformed events were selected based upon visual characteristics and early molecular analysis. A total of eight hundredBCS236357 twenty-three (823) transformed events were selected and transplanted to pots and grown for further study.
[0206] The resulting R0generation transformed events were analyzed for efficacy against selected Lepidopteran species, toxin protein expression, plant health, seed return, and phenotypic and agronomic off-types. The R0 generation events were also characterized molecularly to ensure cassette intactness and proper insertion in the corn genome. Many of the events were dropped from testing due to failure to pass the agronomic analysis and molecular characterization testing. In addition, one (1) of the eight (8) constructs was dropped from further study at this R0 stage because it produced events with off-phenotypes. In addition to these agronomic problems, later mode of action (“MOA”) studies conducted demonstrated that an insect toxin protein contained in this construct demonstrated an overlapping MOA to a commercially-available protein.
[0207] Mode of Action studies were conducted on one of the insect proteins common to four (4) of the eight (8) constructs. These studies demonstrated that this insect protein had an overlapping MOA to a commercially-available protein. Proteins that demonstrate an analogous or overlapping MOA to a currently utilized commercial insecticidal protein are not desirable because of resistance development, which could render a protein with a similar MOA ineffective against insect populations. As such, these four (4) constructs, and the events arising therefrom, were dropped. As noted previously, one (1) of the four (4) dropped constructs also produced events with off- phenotypes at the R0stage.
[0208] In the next stage of development, one hundred fifty (150) events derived from the remaining four (4) constructs were further evaluated at the F1 (heterozygous hybrid) / R1 (homozygous inbred) and R2generation for efficacy, seed return and segregation, phenotypic and agronomic off-types, and further molecular characterization. Two (2) constructs from the remaining four (4) constructs were dropped from further study in this stage for failure to meet one or more of the criteria for advancement, leaving events derived from (2) constructs for further evaluation.
[0209] Seventy-seven (77) events, forty-one (41) derived from the construct used to generate event MON 95379 (“Construct MON95”) and thirty-six (36) events derived from the other construct (“Construct 1”), were evaluated as R2inbreds and F1hybrids for efficacy, seed return and segregation, phenotypic and agronomic off-types and further molecular characterization. BasedBCS236357 upon the results of these evaluations, events associated with Construct 1 were de-prioritized, shelved and stored.
[0210] Thus, numerous rounds of testing and comparison of various constructs revealed that the transgene cassette provided as SEQ ID NO: 13, Construct MON95, was the best option for efficacy against the Lepidopteran pest species Fall Armyworm (FAW, Spodoptera frugiperda), Corn Earworm (CEW, Helicoverpa zea), Southwestern Corn Borer (SWCB, Diatraea grandiosella), Surgarcane Borer (SCB, Diatraea saccharalis), and Lesser Cornstalk Borer (LSCB, Elasmopalpus lignosellus), with the best molecular characterization and agronomic performance.
[0211] Table 2 illustrates the number of transformed events derived (“Plugged”), the number of transformed events selected for growth as R0 events (“Transplanted”), and the points at which each respective construct was dropped in the evaluation, research and development process that led to the selection of Construct MON95. Table 2. Event construct selection. Construct Plugged Transplanted DroppedBCS236357 EXAMPLE 2 Field Trials, Molecular Testing and Event Selection
[0212] This Example describes the molecular characterization, analysis, and testing in field trials of events created with Construct MON95 in multiple locations over several years, which lead to the selection of the final event, MON 95379.
[0213] Table 3 illustrates the process used to select the final event, MON 95379. At the commercial transformation R0 screen, two hundred ten (210) R0 transformed events from Construct MON95 were derived and selected for growth. Of the initial two hundred ten (210) selected R0transformed events, one hundred forty-seven events (147) were dropped due to concerns regarding efficacy, protein expression, seed return and plant health, or molecular characterization. This left sixty-three (63) events for assay and testing in the next stage of development, the F1 Screen and the R1 Nursery stage. In this stage, eleven (11) events were dropped due to efficacy concerns in the greenhouse testing. Another three (3) events were dropped because of insufficient return of seed from the nursery and / or segregation analysis of the resulting seed. Finally, another five (5) events were removed due to issues discovered in molecular characterization and three (3) events were removed due to issues discovered in molecular southern analysis, leaving forty-one (41) events for assay in the next generation. At the R2 / F1 stage of testing, two (2) of the remaining forty-one (41) events were dropped due to issues discovered in further molecular southern characterization, leaving thirty-nine (39) events.
[0214] The remaining thirty-nine (39) events were advanced in two different concurrent parallel testing stages: 1) further field trials; and 2) Cre-excision of the selection cassette and the production of gold standard seed. Events were dropped in each of these concurrent parallel testing stages.
[0215] During Cre-excision, eleven (11) events were dropped due to issues discovered in molecular characterization after cre-excision of the glyphosate selection cassette. Further, another six (6) events were dropped due to issues discovered in molecular characterization during gold standard seed production.
[0216] During the concurrent field testing, based on data collected from the 2016 U.S. Field Trails, another four (4) events were dropped due to efficacy concerns and another twelve (12) events were dropped due to agronomic concerns. Then, based on data collected from the Brazil Field Trials, another event was dropped due to efficacy concerns. Next, bioinformatic analysis conducted during the 2017 U.S. Field Trials resulted in the removal of another three (3) events from furtherBCS236357 testing, leaving two events: Event 1 and MON 95379. After further analysis of the agronomics of the events from multiple field trials in the U.S., Brazil, Argentina and Puerto Rico, event MON 95379 was selected as the event for commercialization because it ranked higher than Event 1 when all the characteristics of molecular characterization, protein expression, efficacy and agronomics of each event were compared. Table 3. MON 95379 event selection. Events RemaininBCS236357 expression, efficacy and agronomics from multiple fieldEXAMPLE 3 Cre-excision of the Glyphosate Selection Cassette in Corn Event MON 95379
[0217] This Example describes the removal of the glyphosate selection cassette from corn event MON 95379 through in vivo Cre-excision. The glyphosate selection cassette was used to select transformed events. By removal of the selection cassette, a “marker-free” event was created wherein only the insecticidal protein expression cassettes remained in the final event.
[0218] Figure 3 illustrates the breeding process used to generate the marker-free event MON 95379 corn event. Corn variety LH244 immature embryos were transformed using an Agrobacterium-mediated transformation process with Construct MON95 (presented as SEQ ID NO: 13, and illustrated in Figure 2). Construct MON95 comprises three (3) expression cassettes: two (2) expression cassettes for the expression of the insecticidal proteins Cry1B.868 and Cry1Da_7, and a single cassette used for the selection of transformed plant cells using glyphosate selection. The selection cassette was flanked on both sides with LoxP Cre-recombinase recognition sites.
[0219] After transformation, the R0 transformants were self-pollinated for two (2) generations, during which time many events were removed based upon various assays such as efficacy, protein expression, seed return and plant health, and molecular characterization. By the R2generation, thirty-nine (39) events remained from the initial two hundred ten (210) events. The thirty-nine (39) homozygous R2 generation events were bred with an elite line of transformed corn plants expressing Cre-recombinase enzyme, derived from Enterobacteria phage P1.
[0220] This stage in which R2generation events were bred with plants expressing Cre- recombinase is identified as “Cre Cross”. Specifically in this stage, de-tasseled (female) R2 generation plants homozygous for SEQ ID NO: 13 were cross-pollinated with transgenic corn plants (male) homozygous for a transgene cassette used for expression of Cre-recombinase enzyme. The Cre-recombinase expressing male donor pollen germinates after landing on the silk tissue of the female plant comprising SEQ ID NO: 13. Once the pollen tube enters the embryoBCS236357 sac, the pollen tube ruptures, setting free the two sperms of the Cre-recombinase expressing male donor. The nucleus of one sperm fuses with the egg nucleus, forming the zygote. The other sperm nucleus fuses with one of the two polar nuclei which in turn fuses with the other polar nucleus, thereby establishing the primary endosperm nucleus.
[0221] Thus, in using the Cre-recombinase expressing plant as the male pollen donor, both the embryo and endosperm of the resulting cross will express Cre-recombinase as the cells divide and develop and become a corn kernel (i.e., seed). The Cre-recombinase binds to inverted repeats in the LoxP site and catalyzes a crossover in an eight-base pair spacer region of the two LoxP sites that flank the expression cassette, resulting in the excision of the marker cassette with one LoxP site remaining in the integrated T-DNA due to recombination (see Figure 2, “Inserted T-DNA After Cre-Excision”).
[0222] The F1 progeny resulting from the Cre Cross were selected for the absence of the CP4 selection cassette and allowed to self-pollinate. Through this process, the two alleles – the Cre- recombinase allele and the allele for the T-DNA used to generate event MON 95379 – segregate in the resulting F2 population, resulting in progeny homozygous or heterozygous for one or both alleles.
[0223] The F2progeny which demonstrated the absence of the Cre-recombinase allele and homozygosity for SEQ ID NO: 9, the transgenic inserted T-DNA after Cre-excision, were selected. These selected F2progeny were self-pollinated, giving rise to an F3generation homozygous for SEQ ID NO: 9.
[0224] A further self-pollination resulted in F3 progeny seed (F4 seed) which were assayed for purity, and were designated as “Gold Standard Seed.” F4 was the first generation of gold standard seed.
[0225] Excision of the glyphosate selection marker cassette did not affect the expression of Cry1B.868 and Cry1Da_7. Removing the glyphosate selection cassette from corn event MON 95379 through Cre-excision provided a transgenic corn event which is resistant to Lepidopteran pests without adding tolerance to glyphosate in the final event. This “marker-free” event assures flexibility when building corn breeding stacks with other corn transgenic events to provide a multiplicity of products incorporating event MON 95379 and allowing multiple options for providing additional traits in the final breeding stacks.BCS236357 EXAMPLE 4 Corn Event MON 95379 Demonstrates Resistance to the Lepidopteran Insect Pests Fall Armyworm, Corn Earworm, Southwestern Corn Borer, Sugarcane Borer
[0226] This Example describes the activity of the MON 95379 event against Lepidopteran insect pests. The insect toxin proteins Cry1B.868 and Cry1Da_7, when expressed together in corn event MON 95379, provide resistant to Fall Armyworm (Spodoptera frugiperda), Corn Earworm (Helicoverpa zea), Southwestern Corn Borer (Diatraea grandiosella), and Surgarcane Borer (Diatraea saccharalis).
[0227] After transformation and insertion of Construct MON95, forty-one (41) R0events were selected for bioassay using leaf discs. Bioassays using plant leaf disks were performed analogous to those described in U.S. Patent No.8,344,207. A non-transformed LH244 corn plant was used to obtain tissue to be used as a negative control. Plates comprising wells with one insect per leaf disc in each well were incubated for three (3) days. After three (3) days, the plates were examined. If at least fifty percent (50%) of the leaf disc in the negative controls was consumed, measurements were taken of the transgenic event leaf discs. If less than fifty percent (50%) of the leaf discs in the negative controls had not yet been consumed, the insects were allowed to continue feeding until the fifty percent (50%) target was achieved. Measurements of leaf damage (“leaf damage ratings” or “LDR”) and mortality were taken for each well. An average of each measure was determined. The leaf damage ratings ranged from one (1) to eleven (11) and reflect a percentage of the consumed leaf disc. Table 4 shows the leaf damage rating scale used for the R0leaf disc assays. On this rating scale, the negative controls will always have an LDR of at least 10. Table 4. Leaf Damage Ratings (LDR) scale for R0leaf disc assays. Amount ofBCS236357 Amount of Leaf Damage feeding
[0228] Table 5 shows the meaone (41) events transformed with Construct MON95, including the MON 95379 event. As can be seen in Table 5, expression of the two insecticidal proteins, Cry1B.868 and Cry1Da_7, provided resistance to Fall Armyworm (FAW), Corn Earworm (CEW), and Southwestern Corn Borer (SWCB). The LDRs for the negative controls were between 10 and 11. The FAW and SWCB consumed only approximately five percent (5%) of the event MON 95379 leaf disc in comparison to the negative controls which consumed at least fifty percent (50%) of the leaf disc. With respect to CEW, only approximately 6.25% of the leaf discs were consumed in comparison to the negative controls which consumed at least fifty percent (50%) of the leaf disc. In addition, one hundred percent (100%) of the FAW and CEW were killed after consuming the event MON 95379 containing leaf discs. Table 5. Mean Leaf Damage Rating (LDR) scores and Mean Mortality for R0plants expressing Cry1B.868 and Cry1Da_7. FAW CEW SWCBBCS236357 FAW CEW SWCB Event Mean Mean MeanBCS236357 FAW CEW SWCB Event Mean Mean Mean
[0229] The forty-one (41 c 93IDI3 variety plants. F1heterozygous progeny plants were selected that comprised Construct MON95. Around five (5) F1plants for each event were artificially infested in a greenhouse for each insect pest species. With respect to FAW, approximately forty (40) neonates were used to infest each F1 plant in the V6 to V8 stage whorl. With respect to SWCB, approximately thirty (30) neonates were used to infest the F1plant in the V6 to V10 stage whorl. Measures of leaf damage for FAW and SWCB were taken approximately fourteen (14) days after infestation. Tables 6 and 7 show the damage rating scales used to assess the leaf damage. Table 6. Leaf damage rating scale for corn plants infested with FAW. Leaf Damage R ti (LDR) D i ti nBCS236357 Leaf Damage Rating (LDR) Description rl m ntTable 7. Leaf damage rating scale for corn plants infested with SWCB. Leaf Damage Rating (LDR) Description
[0230] The SWCB infested F1plants were also assessed for the length of stalk boring caused by SWCB. To determine the length of stalk boring, corn stalks of the corn plants were broken at approximately eye level and the top portion was used to inspect for boring damage. The stalks were split using a double handled knife and the length of the tunnel bored out by SWCB wasBCS236357 measured in centimeters (cm). In these experiments, the tunnel length was capped at ten centimeters (10 cm).
[0231] In addition, five (5) F1plants for each event were also infested with CEW to measure the amount of damage caused by CEW to the corn ear. Approximately forty (40) CEW nymphs were used to infest each plant and were placed on the green silks of R1 stage plants. Twenty-one (21) days after infestation, the developing ears were examined, and the damage was recorded as cm2ear damage.
[0232] Table 8 shows the mean leaf damage ratings for the F1 events infested with FAW and SWCB, the stalk boring lengths caused by SWCB, and the ear damage caused by CEW, wherein “NT” indicates not tested. Table 8. Mean leaf damage ratings of F1transgenic corn plants infested with FAW and SWCB, stalk boring lengths caused by SWCB, and ear damage caused by CEW. CEW SWCB ear e e)BCS236357 CEW SWCB ear e e)BCS236357
[0233] As can be seen in Table 8, leaf damage to corn event MON 95379 was minimal for both FAW and SWCB when compared to the negative controls. Essentially, once the insects started to feed on the event MON 95379 F1leaf, expression of the Cry1B.868 and Cry1Da_7 insecticidal proteins in the corn leaves containing event MON 95379 caused the insect to cease consuming the leaf. SWCB tunneling was not observed in event MON 95379 while the negative controls showed extensive tunneling. With respect to CEW ear damage, the damage to the ear was much less compared to the negative control, and was comparable to the ear damage observed in several commercially-available transgenic corn events. Infestation of the magnitude used in the F1 assays was much higher than what is usually seen in nature. The F1assays demonstrated that corn event MON 95379 provides superior control of FAW, SWCB, and CEW.
[0234] In the summer of 2016, the F1 progeny from the remaining thirty-nine (39) events after R2 / F1 described in Example 2 / Table 3 were assayed for resistance to FAW, CEW, and SWCB in field experiments using artificial infestation. Multiple locations were used to assay resistance.
[0235] FAW resistance was assayed in three (3) locations: Jerseyville, IL; Thomasboro, IL; and Union City, TN. In each location, each event was assayed in three (3) field plots using one (1) row per plot and thirty (30) seeds per row. Forty (40) FAW neonates were used to infest each plant twice, at the early and mid-whorl stage (V4 and V7 vegetative stage). Leaf feeding damage ratings were assessed using the scale as provided in Table 6.
[0236] SWCB resistance was assayed in three (3) locations: one (1) in Jonesboro, AR and two (2) in Union City, TN. In each location, each event was assayed in three (3) field plots using one (1) row per plot and thirty (30) seeds per row. Thirty (30) SWCB neonates were used to infest each plant at the mid-whorl stage (V7-V8). At the time of fifty percent (50%) pollen shed, the plants were infested again with thirty (30) SWCB neonates per plant. Stalk tunneling damage was assessed as previously described.
[0237] CEW resistance was assayed in five (5) locations: Jerseyville, IL, Jonesboro, AR, Monmouth, IL, Thomasboro, IL, and Union City, TN. In each location, each event was assayed in three (3) field plots using one (1) row per plot and thirty (30) seeds per row. Plants were infested when the silks were fresh and green, and some ear formation had started (R1 through R3 stage). CEW egg strips were used for infestation. Each strip contained approximately forty (40) eggs. One (1) strip was placed between the ear and stalk of each plant, with the eggs facing ear and close to the silks. Evaluation of ear damage was determined twenty-one (21) to twenty-eight (28) daysBCS236357 after infestations. By this time, the insect has progressed from larval to pupal stage. Damage to the ears was measured as previously described.
[0238] For FAW and SWCB, data from all three (3) locations was used. For CEW, due to various field conditions, only data from Jonesboro, AR could be used. Table 9 shows the mean FAW leaf damage ratings, the SWCB tunnel lengths, and the CEW ear damage measurements for each of the tested events and the negative control. Table 9. Mean FAW leaf damage ratings, SWCB tunnel length, and CEW ear damage for 2016 field efficacy trials. SWCB CEW Tunnel Ear eBCS236357 SWCB CEW Tunnel Ear Event e
[0239] As demonstrated, p excellent control of FAW, SWCB, and CEW when compared to the negative control. The level of infestation in these assays was much higher than what would normally be encountered in the field under natural conditions, demonstrating the superior performance of event MON 95379 under high insect pressure.
[0240] During concurrent field trials and Cre-excision of the selection cassette and the production of Gold Standard Seed, further characterization of the events was performed. As a result of extensive molecular characterization, efficacy, expression, and agronomic studies, events wereBCS236357 dropped from testing, leaving two (2) events: Event 1 and MON 95379. Event 1 was de-prioritized based on observed yield drag in agronomic studies, leaving event MON 95379 for advancement.
[0241] During the 2016 to 2017 growing season in Argentina, event MON 95379 was assayed for resistance to FAW, CEW, and SCB in temperate and subtropical regions under natural infestation conditions. FAW leaf damage ratings were determined for event MON 95379 grown in the sub- tropical region of Argentina using the scale provided in Table 6. SCB tunneling data was obtained for event MON 95379 from two (2) locations in the temperate region of Argentina. CEW ear damage data was obtained for event MON 95379 from two (2) locations in the temperate region and three (3) locations in the subtropical regions of Argentina. Table 11 shows the mean FAW leaf damage ratings, SCB tunnel length, and CEW ear damage under natural infestation conditions for event MON 95379 and a negative control during the 2016-2017 Argentina growing seasons. Table 10. Mean FAW leaf damage ratings, SCB tunnel length, and CEW ear damage for 2016-2017 Argentina field efficacy trials. CEW Ear FAW SCB Tunnel Damage
[0242] As can be seen in Table 10, event MON 95379 provided resistance to FAW, SCB, and CEW when compared to the negative control under natural infestation conditions in Argentina.
[0243] Event MON 95379 was also evaluated for resistance against FAW resistant to a commercially-available corn event (MON89034, which expresses Cry1a.105 and Cry2Ab2) over three (3) growing seasons in Puerto Rico (January 2016, July 2016, and January 2017). Table 11 shows the mean leaf damage ratings based upon the scale presented in Table 6 for each of the three (3) growing seasons compared with event MON89034 and the negative control.BCS236357 Table 11. Mean leaf damage ratings for event MON 95379 and event MON89034 naturally- infested with event MON89034-resistant FAW. Jan July Jan Event 2016 2016 2017
[0244] As can be seen in Table 11, corn event MON 95379 demonstrated resistance to event MON89034-resistant FAW under high natural pressure relative to the negative control.
[0245] In the summer of 2017, event MON 95379 was evaluated for resistance against FAW, SWCB, and CEW in the United States using methods similar to that described for the summer of 2016. FAW resistance was assayed at three (3) locations: Jerseyville, IL; Thomasboro, IL; and Monmouth, IL. In each location, each event was assayed in three (3) field plots using one (1) row per plot and thirty (30) seeds per row. Forty (40) FAW neonates were used to infest each plant two times. The first infestation occurred around V5 stage. The second infestation for plants in Monmouth, IL and Jerseyville, IL occurred around V8 stage. Due to a low hatch rate and poor weather, a second infestation was not possible in Thomasboro, IL. FAW leaf feeding damage ratings were assessed using the scale as provided in Table 6.
[0246] SWCB resistance was assayed at three (3) locations, one (1) in Jonesboro, AR and two (2) in Union City, IL. In each location, each event was assayed in three (3) field plots using one (1) row per plot and thirty (30) seeds per row. Thirty (30) SWCB neonates were used to infest each plant two times. Under normal conditions, the first infest is performed at the mid-whorl stage (V7- V8) in half of the row, but infestation was delayed about a week. Regardless, strong insect pressure was established. At the time of fifty percent (50%) pollen shed the second half of the row of plants were infested with thirty (30) SWCB neonates per plant. Stalk tunneling damage was assessed as previously described.
[0247] CEW resistance was assayed at six (6) locations: Jerseyville, IL, Jonesboro, AR, Paragould, AR, Monmouth, IL, and two locations in Union City, TN. In each location, each event was assayed in three (3) field plots using one (1) row per plot and thirty (30) seeds per row. Due to a shortage of insects, infestations in Monmouth, IL and Jerseyville, IL were infested two (2) to three (3)BCS236357 weeks later than when silks are fresh and green. In Monmouth, approximately twenty-two (22) neonates were used to infest each plant. In Jerseyville, IL, twenty-three (23) to twenty-four (24) neonates were used to infest partially opened corn ears. In Jonesboro, AR, one (1) of the three (3) rows received approximately thirty (30) neonates per plant, and the other two (2) rows received sixteen (16) to (18) neonates per plant. In Paragould, AR, all three (3) rows received approximately thirty (30) neonates per plant. Infestation was delayed in the two locations of Union City, TN due to insect availability. Both locations received eighteen (18) neonates per plant. Evaluation of ear damage was determined twenty-one (21) to twenty-eight (28) days after infestations. Damage to the ears was expressed as previously described. Artificial infestations were conducted on both marker and marker-free event MON 95379 plants. In addition, assays were also conducted using the natural insect pressure at the locations for the marker-containing event MON 95379 plants. Tables 12 and 13 show the FAW leaf damage ratings, SWCB tunnel lengths, and the CEW ear damage for marker-containing and marker-free event MON 95379 plants. Table 12. Mean FAW leaf damage ratings, SWCB tunnel length, and CEW ear damage for event MON 95379 plants before Cre-excision of the selection marker under conditions of artificial and natural infestation. Before Cre-excision of CP4 Marker l onBCS236357 Table 13. Mean FAW leaf damage ratings, SWCB tunnel length, and CEW ear damage for marker-free event MON 95379 plants under artificial infestation. After Cre-excision of CP4 Marker SWCB l n
[0248] As can beistance against FAW, SWCB, and CEW under artificial (marker and marker-free) and natural (marker-free) infestation conditions.
[0249] In 2018, a hybrid cross of event MON 95379 with event MON89034 was assayed for resistance to FAW in a Brazil field trial under natural infestation conditions. The field trial was conducted in Santa Helena de Goiás, State of Goiás. In this location there are FAW populations resistant to the transgenic corn event MON89034. Transgenic corn plants corresponding to the cross of events MON 95379 x MON89034, event MON89034, and a conventional corn plant (negative control) were planted. At V6 stage, leaf damage rating scores were determined for sixty (60) plants corresponding to the cross of events MON 95379 x MON89034, thirty (30) plants corresponding to event MON89034, and thirty (30) negative controls using the scale presented in Table 6. In addition, the number of FAW neonates, larvae greater than two millimeters (2mm) and less than or equal to 1.5 centimeters, and larvae greater than 1.5 centimeters were recorded for each plant. Table 14 shows the mean leaf damage ratings for the cross of events MON 95379 x MON89034, event MON89034, and the negative control, along with the numbers of neonates and larvae observed on the corn plants.BCS236357 Table 14. Mean FAW leaf damage rating and number of neonates and larvae from Brazil, 2018 field trials for the cross of events MON 95379 x MON89034, event MON89034 and negative control. FAW Larvae >2 mm Larvae >1.5 Event (LDR) Neonates and ≤1.5 cm cm
[0250] 4 provided resistance to FAW under natural infestation conditions relative to the negative control. The cross of events MON 95379 x MON89034 also performed better than event MON89034 under conditions where event MON89034-resistant FAW are within the population of FAW. With respect to neonates and larvae, none were observed on the plants corresponding to the cross of events MON 95379 x MON89034. Neonates and larvae between two (2) millimeters and one and a half (1.5) centimeters were observed on event MON89034 plants. The negative control plants were observed to have even more larvae than event MON89034 plants, and had larvae that had grown greater than 1.5 centimeters. EXAMPLE 5 Assay of Activity of Corn Event MON 95379 against Lesser Cornstalk Borer
[0251] This Example describes the assay of activity of transgenic corn event MON 95379 against the Lepidopteran insect pest, Lesser Cornstalk Borer (LSCB, Elasmopalpus lignosellus).
[0252] Event MON 95379 was grown in a greenhouse along with negative control plants and infested with LSCB neonates. Ten (10) event MON 95379 plants and nine (9) negative control plants were grown in individual pots. Nine (9) days after planting, each plant was infested with ten (10) LSCB neonates per plant. Twenty-two (22) days after infestation, the plants were examined and rated for damage using a 0-4 damage rating scale as presented in Table 15.BCS2363...
Claims
BCS236357 What is claimed is:
1. A recombinant DNA molecule comprising: a) a first nucleotide sequence (i) comprising an expression cassette that encodes a Cry1B.868 or Cry1Da_7, and / or (ii) selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7 and SEQ ID NO: 8; and b) a second nucleotide sequence that i. comprises at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 11 or 47, or ii. is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 11 or 47, or iii. is selected from the group consisting of SEQ ID NOs: 49-148.
2. The recombinant DNA molecule of claim 1, further comprising: c) a third nucleotide sequence that i. comprises at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at leastBCS236357 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 12 or 48, or ii. is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 12 or 48, or iii. is selected from the group consisting of SEQ ID NOs: 149-248.
3. The recombinant DNA molecule of claim 2, wherein the third nucleotide sequence is selected from the group consisting of SEQ ID NOs: 149-248.
4. The recombinant DNA molecule of claim 3, wherein the recombinant DNA molecule has a deletion of one or more consecutive nucleotides between the second nucleotide sequence and the third nucleotide sequence relative to SEQ ID NO: 10, 12, or 48.
5. The recombinant DNA molecule of any one of claims 1-4, wherein the second nucleotide sequence is selected from the group consisting of SEQ ID NOs: 49-148.
6. The recombinant DNA molecule of any one of claims 1-5, wherein the recombinant DNA molecule has a deletion of one or more consecutive nucleotides between the first nucleotide sequence and the second nucleotide sequence relative to SEQ ID NO: 10, 11, or 47.
7. A recombinant DNA molecule comprising: a) a first nucleotide sequence (i) comprising an expression cassette that encodes a Cry1B.868 or Cry1Da_7, and / or (ii) selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, and SEQ ID NO: 9; andBCS236357 b) a second nucleotide sequence that i. comprises at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 12 or 48, or ii. is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 12 or 48, or iii. is selected from the group consisting of SEQ ID NOs: 149-248.
8. The recombinant DNA molecule of claim 7, wherein the second nucleotide sequence is selected from the group consisting of SEQ ID NOs: 149-248.
9. The recombinant DNA molecule of claim 7 or 8, wherein the recombinant DNA molecule has a deletion of one or more consecutive nucleotides between the first nucleotide sequence and the second nucleotide sequence relative to SEQ ID NO: 10, 12, or 48.
10. The recombinant DNA molecule of any one of claims 1-6, further comprising nucleotides 1-862 or 14,181-15,216 of SEQ ID NO:
10.
11. The recombinant DNA molecule of any one of claims 1-10, wherein said recombinant DNA molecule is comprised in a corn plant, corn plant part, corn plant cell, corn plant seed, corn progeny plant, or commodity or fuel product made from corn and corn plant parts.BCS236357 12. The recombinant DNA molecule of any one of claims 1-10, wherein said recombinant DNA molecule comprises an amplicon diagnostic for the presence of DNA comprising a sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, and SEQ ID NO:
9.
13. The recombinant DNA molecule comprising a polynucleotide of claims 1-11, wherein the recombinant DNA molecule is derived from a corn plant, corn plant part, corn seed, processed corn seed, corn plant cell or tissue, animal feed comprising corn, corn oil, corn meal, corn flour, corn flakes, corn bran, food made comprising corn, corn biomass, or fuel products made from corn and corn plant parts.
14. A recombinant DNA molecule comprising a polynucleotide segment of sufficient length to function as a DNA probe that hybridizes specifically under stringent hybridization conditions with a polynucleotide having a sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 47, and SEQ ID NO:
48.
15. A pair of DNA molecules that can function as DNA primers when used together in an amplification reaction comprising a first DNA molecule and a second DNA molecule, wherein the first DNA molecule and the second DNA molecule are different, a) wherein the first DNA molecule is: i. at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, or at least 99.9% identical or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, or SEQ ID NO: 9, or a complement thereof, orBCS236357 ii. at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, or at least 99.9% identical or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 11 or 47, or a complement thereof; and b) wherein the second DNA molecule is: i. at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, or at least 99.9% identical or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, or SEQ ID NO: 9, or a complement thereof, or ii. at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, or at least 99.9% identical or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 11 or 47, or a complement thereof, or iii. at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%,BCS236357 at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, or at least 99.9% identical or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 12 or 48, or a complement thereof.
16. The pair of DNA molecules of claim 15, wherein the first DNA molecule and the second DNA molecule can be used together in an amplification reaction with a sample from a plant, plant part, plant seed, plant cell, food or animal feed, or commodity or fuel product made from a plant or plant part to produce an amplicon diagnostic for the presence of a modified corn event MON 95379 DNA in said sample.
17. The pair of DNA molecules of claim 16, wherein the amplicon comprises a nucleotide sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO:
10.
18. The pair of DNA molecules of claim 16 or 17, wherein the modified corn event MON 95379 DNA is a further modified corn event MON 95379 DNA.
19. A method of detecting the presence of a DNA segment diagnostic for a modified corn event MON 95379 DNA in a sample, said method comprising: a) contacting said sample with the DNA molecule of any one of claims 1-14; b) subjecting said sample and said DNA molecule to stringent hybridization conditions; and c) detecting hybridization of said DNA molecule to said DNA segment in said sample, wherein said detection is diagnostic for the presence of said modified corn event MON 95379 DNA in said sample.
20. A method of detecting the presence of a DNA segment diagnostic for a modified corn event MON 95379 DNA in a sample, said method comprising: a) contacting said sample with the pair of DNA molecules of any one of claims 15- 18; b) performing an amplification reaction sufficient to produce a DNA amplicon; andBCS236357 c) detecting the presence of said DNA amplicon in said reaction, wherein the presence of said DNA amplicon is diagnostic for the presence of said modified corn event MON 95379 DNA in said sample.
21. A method of detecting the presence of a DNA segment diagnostic for a modified corn event MON 95379 DNA in a sample, said method comprising performing a sequencing reaction with the sample, wherein the production in the sequencing reaction of a target nucleotide sequence comprising at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, or SEQ ID NO: 9, or a complement thereof, is diagnostic for the modified corn event MON 95379 DNA in the sample.
22. The method of claim 19, 20, or 21, wherein the modified corn event MON 95379 is a further modified corn event MON 95379.
23. A modified corn plant, corn plant part, corn seed, or corn cell comprising a modified corn event MON 95379 or the recombinant DNA molecule of any one of claims 1-14.
24. The modified corn plant, corn plant part, corn seed, or corn cell of claim 23 comprising: a) the recombinant DNA molecule of any one of claims 1-14; or b) a recombinant DNA molecule or segment comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 10, or a complement thereof; or c) a recombinant DNA molecule or segment comprising a nucleotide sequence that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9% or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, atBCS236357 least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 1,000, at least 1,500, or at least 2,000 consecutive nucleotides of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 47, or SEQ ID NO: 48, or a complement thereof.
25. The modified corn plant, corn plant part, corn seed, or corn cell of claim 23 or 24, wherein the corn plant, corn plant part, corn seed, or corn cell is further defined as a progeny plant of any generation of a corn plant comprising a modified corn event MON 95379, or a corn plant part, corn seed, or corn cell derived therefrom.
26. The modified corn plant, corn plant part, corn seed, or corn cell of any of claims 23-25, wherein the corn plant, corn plant part, corn seed, or corn cell exhibits resistance to a Lepidopteran insect pest species and / or comprises an expression cassette that encodes a Cry1B.868 or Cry1Da_7 protein.
27. The modified corn plant of claims 23-26, wherein the corn plant exhibits resistance to Fall Armyworm (Spodoptera frugiperda), Corn Earworm (Helicoverpa zea), Southwestern Corn Borer (Diatraea grandiosella), Surgarcane Borer (Diatraea saccharalis), and / or Lesser Cornstalk Borer (Elasmopalpus lignosellus).
28. The modified corn plant, corn plant part, corn seed, or corn cell of any of claims 23-27, wherein the recombinant DNA molecule is chromosome 8 of the modified corn plant, corn plant part, corn seed, or corn cell, or the DNA segment is present in chromosome 8 of the modified corn plant, corn plant part, corn seed, or corn cell.
29. The modified corn plant, corn plant part, corn seed, or corn cell of any one of claims 23- 28, wherein the modified corn event MON 95379 is a further modified corn event MON 95379.
30. The modified corn plant, corn plant part, corn seed, or corn cell of claim 23, wherein the modified corn event MON 95379 of the modified corn plant, corn plant part, corn seed, or corn cell comprises a genetic modification, mutation or edit, relative to the corn event MON 95379, introduced via a targeted genome editing technique.
31. A DNA detection kit comprising: a) the recombinant DNA molecule of claim 14; andBCS236357 b) the pair of DNA molecules of any one of claims 15-17.
32. A method of producing a progeny corn plant comprising a modified corn event MON 95379 comprising: a) sexually crossing a first modified corn plant that comprises a modified corn event MON 95379 with itself or a second corn plant; b) collecting one or more seeds produced from said cross; c) growing said seed to produce one or more progeny plants; and d) selecting at least a first progeny plant or seed comprising a modified corn event MON 95379.
33. The method of claim 32, wherein the modified corn event MON95275 is a further modified corn event MON 95379.
34. The method of claims 25 or 26, further comprising: e) collecting seed from said at least first progeny plant comprising a modified corn event MON 95379.
35. A hybrid modified corn plant or seed comprising a modified corn event MON 95379 produced by the method of any one of claims 32-34.
36. The hybrid modified corn plan or seed of claim 35, wherein the modified corn event MON 95379 is a further modified corn event MON 95379.
37. A nonliving corn plant material comprising a detectable amount of the recombinant DNA molecule of any one of claims 1-14.
38. A microorganism comprising the recombinant DNA molecule of any one of claims 1-14.
39. The microorganism of claim 38, wherein the microorganism is a plant cell.
40. A commodity product comprising the recombinant DNA molecule of any one of claims 1- 14.
41. The commodity product of claim 40, wherein said commodity product is produced from a modified corn plant, corn plant part, corn seed, or corn tissue or cell comprising a modified corn event MON 95379.
42. The commodity product of claims 40 or 41, further selected from the group consisting of whole or processed corn seed, animal feed comprising corn, corn oil, corn meal, corn flour, corn flakes, corn bran, corn biomass, and fuel products produced using corn and corn plant parts.BCS236357 43. The commodity product of any one of claims 40-42, wherein the modified corn event MON 95379 is a further modified corn event MON 95379.
44. A method of producing a commodity product, said method comprising: a) obtaining a modified corn plant, corn plant part, or corn seed comprising a modified corn event MON 95379; and b) producing a commodity product from the transgenic corn plant, corn plant part, or corn seed.
45. A corn plant, corn plant part, or corn seed comprising a DNA molecule or segment functional as a template when tested in a DNA amplification method to produce an amplicon diagnostic for the presence of a modified corn event MON 95379 DNA.
46. A method of determining the zygosity of a corn plant, corn plant part, or corn seed comprising a modified corn event MON 95379 comprising: a) contacting a sample comprising DNA from the corn plant, corn plant part, or corn seed with the pair of DNA molecules of claim 15; b) performing a nucleic acid amplification reaction with the sample and the pair of DNA molecules; and c) detecting in the nucleic acid amplification reaction a first amplicon diagnostic for a modified corn event MON 95379 and a second amplicon diagnostic for native corn genomic DNA not comprising the modified corn event MON 95379, wherein the presence of only the first amplicon is diagnostic of a corn plant, corn plant part, or corn seed homozygous for the modified corn event MON 95379, and the presence of both the first amplicon and the second amplicon is diagnostic of a corn plant, corn plant part, or corn seed heterozygous for the modified corn event MON 95379.
47. A method of determining the zygosity of a corn plant, corn plant part, or corn seed comprising a modified corn event MON 95379 comprising: a) contacting a sample comprising DNA from the corn plant, corn plant part, or corn seed with a first primer pair that can produce a first amplicon of all or part of the modified corn event MON 95379 and a second primer pair that can produce a second amplicon of a standard genomic sequence known to be single copy and homozygous in the corn plant, corn plant part, or corn seed;BCS236357 b) contacting the sample with a first probe that specifically hybridizes to the first amplicon and / or all or part of the modified corn event MON 95379, and a second probe that specifically hybridizes to the standard genomic sequence; c) performing a DNA amplification reaction using real-time PCR with the sample and determining the cycle thresholds (Ct values) of the first amplicon and the second amplicon; d) calculating the difference (ΔCt) between the Ct values of the second amplicon and the first amplicon; and e) determining the zygosity of the modified corn event MON 95379, wherein a ΔCt of about zero (0) indicates homozygosity of the modified corn event MON 95379 and a ΔCt of about one (1) indicates heterozygosity of the modified corn event MON 95379.
48. The method of claim 46 or 47, wherein the first and second primer pairs comprise SEQ ID NO: 15 combined with SEQ ID NO: 16, and SEQ ID NO: 18 combined with SEQ ID NO:
19.
49. A method of determining the zygosity of a corn plant, corn plant part, or corn seed comprising a modified corn event MON 95379 comprising: a) contacting a sample comprising DNA from the corn plant, corn plant part, or corn seed with a primer pair capable of producing a first amplicon diagnostic for the modified corn event MON 95379 and a second amplicon diagnostic for native corn genomic DNA not comprising the modified corn event MON 95379; b) performing a nucleic acid amplification reaction with the sample and the set of primer pairs; and c) detecting the first amplicon and the second amplicon, wherein the presence of only the first amplicon is diagnostic of a corn plant, corn plant part, or corn seed homozygous for the modified corn event MON 95379, the presence of only the second amplicon is diagnostic of a corn plant, corn plant part, or corn seed homozygous for native corn genomic DNA not comprising the modified corn event MON 95379, and the presence of both the first amplicon and the second amplicon is diagnostic of a corn plant, corn plant part, or corn seed heterozygous for the modified corn event MON 95379.BCS236357 50. A method for determining the zygosity of a corn plant, corn plant part, or corn seed comprising a modified corn event MON 95379 comprising: a) contacting a sample comprising DNA from the corn plant, corn plant part, or corn seed with a probe set which contains at least a first probe that specifically hybridizes to the modified corn event MON 95379 and at least a second probe that specifically hybridizes to corn genomic DNA that was disrupted by insertion of the heterologous DNA of corn event MON 95379 and is disrupted by the modified corn event MON 95379 DNA, wherein the second probe does not hybridize to the modified corn event MON 95379 DNA; and b) hybridizing the probe set with the sample under stringent hybridization conditions, wherein detecting hybridization of only the first probe under the hybridization conditions is diagnostic for a corn plant, corn plant part, or corn seed homozygous for the modified corn event MON 95379, and wherein detecting hybridization of both the first probe and the second probe under the hybridization conditions is diagnostic for a corn plant, corn plant part, or corn seed heterozygous for the modified corn event MON 95379.
51. The method of claim 50, wherein the probe set comprises SEQ ID NO: 17 and SEQ ID NO:
20.
52. The method of any one of claims 46-51, wherein the modified corn event MON95275 is a further modified corn event MON 95379.
53. A population of transgenic corn plants, wherein each transgenic corn plant of the population comprises a modified corn event MON 95379.
54. The population of claim 53, wherein each transgenic corn plant of the population exhibits resistance to a Lepidopteran insect pest species.
55. The population of transgenic corn plants of claim 53 or 54, wherein the modified corn event MON 95379 is a further modified corn event MON 95379.
56. A method of modifying a corn plant, the method comprising: a) introducing a site-specific nuclease or a recombinant DNA construct comprising an expression cassette encoding a site-specific nuclease into at least one cell of an explant of a corn plant comprising corn event MON 95379, or a plant part thereof, to produce a modified corn event MON 95379 via a genome editing technique; andBCS236357 b) developing or regenerating a modified corn plant from the explant, wherein the modified corn plant comprises the modified corn event MON 95379.
57. The method of claim 56, wherein the site-specific nuclease is a zinc-finger nuclease (ZFN), a meganuclease, an RNA-guided endonuclease, a TALE-endonuclease (TALEN), a recombinase, or a transposase.
58. The method of claim 56 or 57, wherein the site-specific nuclease is an RNA-guided endonuclease or a CRISPR / Cas nuclease.
59. The method of claim 58, wherein the introducing step (a) comprises introducing the recombinant DNA construct into the at least one cell of the explant, and wherein the recombinant DNA construct further comprises an expression cassette encoding a first guide RNA (gRNA).
60. The method of claim 59, wherein the recombinant DNA construct further comprises an expression cassette encoding a second guide RNA (gRNA).
61. The method of claim 58, wherein the introducing step (a) further comprises introducing a first guide RNA (gRNA) or a second recombinant DNA construct comprising an expression cassette encoding a first guide RNA (gRNA) into the at least one cell of the explant.
62. The method of claim 61, wherein the introducing step (a) comprises introducing at least two guide RNAs (gRNAs) comprising the first gRNA and a second gRNA into the at least one cell of the explant.
63. The method of claim 61, wherein the second recombinant DNA construct further comprises an expression cassette encoding a second guide RNA (gRNA).
64. The method of claim 61, wherein the introducing step (a) comprises introducing a first gRNA and second recombinant DNA construct comprising an expression cassette encoding a second guide RNA (gRNA) into the at least one cell of the explant.
65. The method of any one of claims 56-64, wherein the site-specific nuclease has a first target site in the genome of the corn plant at or near corn event MON 95379.
66. The method of claim 65, wherein the site-specific nuclease has a second target site in the genome of the corn plant at or near corn event MON 95379.
67. The method of any one of claims 56-66, wherein the introducing step (a) comprises introducing a second site-specific nuclease or a recombinant DNA construct comprising anBCS236357 expression cassette encoding a second site-specific nuclease into at least one cell of the explant, and wherein the second site-specific nuclease has a second target site in the genome of the corn plant at or near corn event MON 95379.
68. The method of any one of claims 59-64, wherein the first gRNA has a first target site in a flanking DNA sequence, 5´ flank, 3´ flank, junction sequence, or insertion sequence of corn event MON 95379, or a complement thereof.
69. The method of any one of claims 59-64 and 68, wherein the first gRNA has a first target site comprising a target sequence that is: i. at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9% or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 11 or 47, or a complement thereof; or ii. at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9% or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 12 or 48, or a complement thereof; or iii. at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9% or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, atBCS236357 least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, or SEQ ID NO: 9, or a complement thereof.
70. The method of claim 69, wherein the first gRNA has a second target site comprising a target sequence that is: i. at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9% or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 11 or 47, or a complement thereof; or ii. at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9% or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 12 or 48, or a complement thereof; or iii. at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9% or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at leastBCS236357 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, or SEQ ID NO: 9, or a complement thereof.
71. The method of any one of claims 59-64 and 68-70, i. wherein the first gRNA has a first target site comprising a target sequence that is:
1. at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9% or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 11 or 47, or a complement thereof; or 2. at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9% or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 12 or 48, or a complement thereof; or 3. at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9% or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, atBCS236357 least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, or SEQ ID NO: 9, or a complement thereof; and ii. wherein the second gRNA has a second target site comprising a target sequence that is:
1. at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9% or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 11 or 47, or a complement thereof; or 2. at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9% or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 12 or 48, or a complement thereof; or 3. at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9% or 100% identical to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, atBCS236357 least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive nucleotides of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, or SEQ ID NO: 9, or a complement thereof.
72. The method of any one of claims 66, 67, 70, or 71, wherein the modified corn event MON 95379 comprises a deletion or excision of intervening genomic DNA between the first target site and the second target site, relative to the corn event MON 95379.
73. The method of any one of claims 56-72, further comprising: c) selecting the modified corn plant comprising the modified corn event MON 95379; and d) sexually crossing the modified corn plant with itself or a second corn plant to produce one or more modified progeny corn plants.
74. A method of introducing a target site into a corn plant, the method comprising: a) introducing a cognate target site into the corn event MON 95379 locus of at least one cell of a corn plant or corn plant part comprising the corn event MON 95379 or an explant thereof via a targeted genome editing technique, wherein the cognate target site is identical or similar to an originator target site for a site-specific nuclease present in the corn event MON 95379 locus; and b) developing or regenerating a modified corn plant comprising a modified corn event MON 95379 comprising the cognate target site.
75. The method of claim 74, further comprising: c) introducing a site-specific nuclease or a recombinant DNA construct comprising an expression cassette encoding a site-specific nuclease into at least one cell of an explant of a corn plant comprising the modified corn event MON 95379 or a plant part thereof, to produce a further modified corn event MON 95379 via a targeted genome editing technique, wherein the target site of the site-specific nuclease includes the cognate target site and the originator target site; and d) developing or regenerating a second modified corn plant comprising the further modified corn event MON 95379.BCS236357 76. A method of introducing a target site into a corn plant, the method comprising: a) introducing a cognate target site into the corn event MON 95379 locus of at least one cell of a corn plant or corn plant part comprising the corn event MON 95379 or an explant thereof via a targeted genome editing technique to produce a modified corn event MON 95379 comprising the cognate target site, wherein the cognate target site is identical or similar to an originator target site for a site-specific nuclease present in the corn event MON 95379 locus, and b) introducing a site-specific nuclease or a recombinant DNA construct comprising an expression cassette encoding a site-specific nuclease into at least one cell of an explant of a modified corn plant comprising the modified corn event MON 95379, or a plant part thereof, to produce a further modified corn event MON 95379 via a targeted genome editing technique, wherein the target site of the site-specific nuclease includes the cognate target site and the originator target site; and c) developing or regenerating a second modified corn plant comprising the further modified corn event MON 95379.
77. The method of claim 75 or 76, wherein the further modified corn event MON 95379 of the second modified corn plant comprises a deletion or excision of intervening genomic DNA between the originator target site and the cognate target site, relative to the corn event MON 95379 or modified corn event MON 95379.
78. The method of claim 75-77, further comprising: selecting the second modified corn plant or a progeny plant of the second modified corn plant comprising the further modified corn event MON 95379, and sexually crossing the second modified corn plant or the progeny plant with itself or another corn plant to produce one or more modified progeny corn plants comprising the further modified corn event MON 95379.
79. The method of claim 74 or 76, wherein the modified corn event MON 95379 is a further modified corn event MON 95379.
80. A method of producing a progeny corn plant comprising a modified corn event MON 95379 comprising: a) sexually crossing a first modified corn plant that comprises a modified corn event MON 95379 with itself or a second corn plant;BCS236357 b) collecting one or more seeds produced from said cross; c) growing said seed to produce one or more progeny plants; and d) selecting at least a first progeny plant or seed comprising a modified corn event MON 95379.
81. A method of modifying an explant of a corn plant or plant part, the method comprising: introducing a site-specific nuclease or a recombinant DNA construct comprising an expression cassette encoding a site-specific nuclease into at least one cell of an explant of a corn plant or plant part comprising corn event MON 95379 to produce a modified corn event MON 95379 into the at least one cell of the explant.
82. The method of claim 81, wherein the modified corn event MON 95379 is a further modified corn event MON 95379.
Citation Information
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Corn transgenic event mon 95379 and methods for detection and uses thereof
WO2020028172A1