US20130047297A1 - Polynucleotide molecules for gene regulation in plants - Google Patents

Polynucleotide molecules for gene regulation in plants Download PDF

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US20130047297A1
US20130047297A1 US13/583,302 US201113583302A US2013047297A1 US 20130047297 A1 US20130047297 A1 US 20130047297A1 US 201113583302 A US201113583302 A US 201113583302A US 2013047297 A1 US2013047297 A1 US 2013047297A1
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plant
endogenous gene
sequence
polynucleotide
polynucleotides
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Robert D. Sammons
Sergey Ivashuta
Hong Liu
Dafu Wang
Paul C.C. Feng
Andrei Y. Kouranov
Scott E. Andersen
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Monsanto Technology LLC
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    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01N—PRESERVATION OF BODIES OF HUMANS OR ANIMALS OR PLANTS OR PARTS THEREOF; BIOCIDES, e.g. AS DISINFECTANTS, AS PESTICIDES OR AS HERBICIDES; PEST REPELLANTS OR ATTRACTANTS; PLANT GROWTH REGULATORS
    • A01N63/00—Biocides, pest repellants or attractants, or plant growth regulators containing microorganisms, viruses, microbial fungi, animals or substances produced by, or obtained from, microorganisms, viruses, microbial fungi or animals, e.g. enzymes or fermentates
    • A01N63/60—Isolated nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C12N15/1137—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing against enzymes
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01N—PRESERVATION OF BODIES OF HUMANS OR ANIMALS OR PLANTS OR PARTS THEREOF; BIOCIDES, e.g. AS DISINFECTANTS, AS PESTICIDES OR AS HERBICIDES; PEST REPELLANTS OR ATTRACTANTS; PLANT GROWTH REGULATORS
    • A01N57/00—Biocides, pest repellants or attractants, or plant growth regulators containing organic phosphorus compounds
    • A01N57/10—Biocides, pest repellants or attractants, or plant growth regulators containing organic phosphorus compounds having phosphorus-to-oxygen bonds or phosphorus-to-sulfur bonds
    • A01N57/16—Biocides, pest repellants or attractants, or plant growth regulators containing organic phosphorus compounds having phosphorus-to-oxygen bonds or phosphorus-to-sulfur bonds containing heterocyclic radicals
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8201—Methods for introducing genetic material into plant cells, e.g. DNA, RNA, stable or transient incorporation, tissue culture methods adapted for transformation
    • C12N15/8206—Methods for introducing genetic material into plant cells, e.g. DNA, RNA, stable or transient incorporation, tissue culture methods adapted for transformation by physical or chemical, i.e. non-biological, means, e.g. electroporation, PEG mediated
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8201—Methods for introducing genetic material into plant cells, e.g. DNA, RNA, stable or transient incorporation, tissue culture methods adapted for transformation
    • C12N15/8206—Methods for introducing genetic material into plant cells, e.g. DNA, RNA, stable or transient incorporation, tissue culture methods adapted for transformation by physical or chemical, i.e. non-biological, means, e.g. electroporation, PEG mediated
    • C12N15/8207—Methods for introducing genetic material into plant cells, e.g. DNA, RNA, stable or transient incorporation, tissue culture methods adapted for transformation by physical or chemical, i.e. non-biological, means, e.g. electroporation, PEG mediated by mechanical means, e.g. microinjection, particle bombardment, silicon whiskers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8216—Methods for controlling, regulating or enhancing expression of transgenes in plant cells
    • C12N15/8218—Antisense, co-suppression, viral induced gene silencing [VIGS], post-transcriptional induced gene silencing [PTGS]

Definitions

  • polynucleotide molecules for regulating genes in plants and methods of making and using such molecules.
  • Herbicide-resistant weeds are identified with a variety of modes of action. Resistance resulting from selection for multiple copies of genes producing herbicide targetted proteins in pigweed is reported by Gaines et al. (2010) Proc. Natl. Acad. Sci. USA, 107(3):1029-1034. Resistance resulting from mutations in genes producing herbicide targetted proteins in goosegrass, prickly lettuce, and ryegrass are reported by Baerson et al. (2002) Plant Physiol., 129(3):1265-1275; Preston et al. (2006) Pesticide Biochem.
  • This invention provides polynucleotide molecules and methods for regulating genes in plants, e. g., by providing RNA for systemic regulation of genes.
  • Various aspects of the invention provide polynucleotide molecules and methods for regulating endogenous genes and transgenes in a plant cell and polynucleotide molecules.
  • the polynucleotides, compositions, and methods disclosed herein are useful for regulating endogenous genes of a plant pest or pathogen.
  • the polynucleotide molecules are provided in compositions that can permeate or be absorbed into living plant tissue to initiate systemic gene silencing of endogenous genes or transgenes, or of their transcribed RNA.
  • polynucleotide molecules ultimately provide to a plant, or allow the production in cells in a plant, RNA that is capable of hybridizing under physiological conditions in a plant cell to RNA transcribed from a target endogenous gene or target transgene in the plant cell, thereby effecting regulation of the target gene, e. g., silencing or suppression of the target gene.
  • polynucleotide molecules disclosed herein are useful also for ultimately providing to a plant, or allowing the production in cells of a plant, RNA that is capable of hybridizing under physiological conditions to RNA transcribed from a target gene in a cell of an invertebrate pest or of a viral pathogen of the plant, thereby effecting regulation of the target gene, e. g., silencing or suppression of the target gene.
  • the silencing or suppression of the target gene leads to the upregulation of another gene that is itself affected or regulated by the target gene's expression.
  • compositions and methods of this invention are believed to operate through one or more of the several natural cellular pathways involved in RNA-mediated gene suppression as generally described in reviews by Brodersen and Voinnet (2006), Trends Genetics, 22:268-280; Tomari and Zamore (2005) Genes & Dev., 19:517-529; Vaucheret (2006) Genes Dev., 20:759-771; Meins et al. (2005) Annu. Rev. Cell Dev. Biol., 21:297-318; and Jones-Rhoades et al. (2006) Annu. Rev. Plant Biol., 57:19-53.
  • RNA-mediated gene suppression generally involves a double-stranded RNA (dsRNA) intermediate that is formed intramolecularly within a single RNA molecule or intermolecularly between two RNA molecules.
  • This longer dsRNA intermediate is processed by a ribonuclease of the RNase III family (Dicer or Dicer-like ribonuclease) to one or more shorter double-stranded RNAs, one strand of which is incorporated into the RNA-induced silencing complex (“RISC”).
  • RISC RNA-induced silencing complex
  • siRNA pathway involves the cleavage of a longer double-stranded RNA intermediate to small interfering RNAs (“siRNAs”).
  • siRNAs The size of siRNAs is believed to range from about 19 to about 25 base pairs, but the most common classes of siRNAs in plants include those containing 21 base pairs or 24 base pairs. See, Hamilton et al. (2002) EMBO J., 21:4671-4679.
  • oligonucleotide means a polynucleotide molecule having a length of 18-25 nucleotides, similar to the size of processed small RNA molecules in gene silencing mechanisms.
  • compositions for inducing systemic silencing of a target gene in a plant including (a) an agent for conditioning of a plant to permeation by polynucleotides and (b) polynucleotide molecules; and, herbicidal treatment with compositions including (a) an agent for conditioning of a plant to permeation by polynucleotide molecules, (b) polynucleotide molecules.
  • these compositions can include a non-nucleotide herbicide.
  • the invention provides methods for: controlling herbicide-resistant volunteer plants; investigating reverse genetics by modulating an endogenous gene in a plant by applying onto tissue of a growing plant a composition for providing single-stranded RNA molecules in a plant cell for systemic regulation of genes; inducing systemic silencing of a target gene including topical application of polynucleotides to a plant; inducing systemic silencing of a target gene in a plant by (a) conditioning of a plant to permeation by polynucleotides and (b) topically applying polynucleotides to the plant; investigating reverse genetics by modulating an endogenous gene in a plant by topically applying onto a living plant a topically applied composition including polynucleotide molecules and an agent for conditioning of a plant to permeation by such polynucleotide molecules.
  • the invention provides a plant with exogenous DNA or RNA for suppressing an endogenous gene, where the exogenous DNA is not integrated into a chromosome of the plant, the exogenous RNA is not transcribed from DNA integrated into a chromosome of the plant, and the endogenous gene is suppressed by topical application of a polynucleotide to the plant.
  • FIG. 1 presents SEQ ID NO:1, a nucleotide sequence encoding Palmer amaranth EPSPS.
  • FIG. 2 presents SEQ ID NO:3 which is a nucleotide sequence of a synthesized Pol III gene.
  • FIG. 3 illustrates the morbidity of Palmer amaranth plants treated with a dsRNA.
  • FIG. 3A depicts the plants 7 days after the glyphosate treatment.
  • FIG. 3B depicts surfactant-treated plants that were treated with the long dsRNA solution followed by glyphosate treatment after 72 hours.
  • FIG. 3C depicts surfactant-treated plants that were treated with the short dsRNA solution followed by glyphosate treatment after 72 hours.
  • FIG. 4 illustrates the bleaching in Nicotiana benthamiana plants treated with a dsRNA composition.
  • FIG. 5 presents SEQ ID NO:2 which is a nucleotide sequence of a Nicotiana benthamiana phytoene desaturase.
  • FIG. 6 illustrates 5′-Alexa Fluor 488-labelled anti-sense ssDNA oligonucleotides (SEQ ID NO:15) permeating glyphosate-resistant Palmer amaranth leaves as described in Example 9.
  • FIG. 7 depicts results of EPSPS mRNA measured in glyphosate-resistant Palmer amaranth leaves treated with anti-sense ssDNA oligonucleotides for EPSPS as described in Example 9. Bars represent replicate experiments for each of treatments #1-#4 (indicated by the numbers enclosed in circles and referring to Table 2) and for controls (leaves permeated with anti-sense ssDNA oligonucleotides for a barley seed protein, SEQ ID NO:14, treated with or without glyphosate).
  • FIG. 8 depicts results of EPSPS protein measured in glyphosate-resistant Palmer amaranth leaves topically treated with anti-sense ssDNA oligonucleotides for EPSPS as described in Example 9; treatments are indicated by the numbers enclosed in circles and refer to Table 2.
  • FIG. 9 depicts results of shikimate accumulation measured in glyphosate-resistant Palmer amaranth leaves treated with anti-sense ssDNA oligonucleotides for EPSPS in two experiments as described in Example 9; treatments are indicated by the numbers enclosed in circles and refer to Table 2.
  • FIG. 10 depicts the nucleotide sequence of a Nicotiana benthamiana phytoene desaturase (SEQ ID NO:2).
  • FIG. 11 schematically depicts the location of the sequences of assayed oligonucleotides and polynucleotides (see Table 3) in relation to the phytoene synthase sequence (SEQ ID NO:16) as described in Example 10.
  • FIG. 12A illustrates apical leaf bleaching in Nicotiana benthamiana plants topically treated with buffer (“Control”), a 200-mer dsRNA polynucleotide with an RNA sequence corresponding to the segment consisting of nucleotides 914-1113 of SEQ ID NO:2 (“200 nt dsRNA”), and a combination of single-stranded DNA oligonucleotides and polynucleotides (SEQ ID NOs:16, 17, 20, 21, 24, 25, and 26) (“ssDNA oligos”) as described in Example 10.
  • Control a 200-mer dsRNA polynucleotide with an RNA sequence corresponding to the segment consisting of nucleotides 914-1113 of SEQ ID NO:2
  • 200 nt dsRNA 200 nt dsRNA
  • ssDNA oligos a combination of single-stranded DNA oligonucleotides and polynucleotides
  • RNA isolated from Nicotiana benthamiana plants treated with buffer (control), the 200-mer dsRNA polynucleotide, and the ssDNA oligonucleotides are also shown.
  • FIG. 13 illustrates apical leaf bleaching in Nicotiana benthamiana plants topically treated in duplicate with various combinations of polynucleotides or oligonucleotides (numbers refer to the treatments listed in Table 4) as described in Example 10. The control (Treatment 13 in Table 4) plants are not shown.
  • FIG. 14 illustrates apical leaf bleaching in Nicotiana benthamiana plants topically treated with the polynucleotides listed in Table 5 as described in Example 10.
  • FIG. 15 illustrates apical leaf bleaching observed in Nicotiana benthamiana plants after topical treatment with the PDS 21-mer anti-sense ssDNA (SEQ ID NO:34, “21 nt PDS anti-sense”) or with previously assayed PDS anti-sense 22-mer oligonucleotides without a T7 promoter (SEQ ID NOs:22 and 23) (“PDS anti-sense”). Little or no visible bleaching of apical leaves was observed after topical treatment with the buffer only or after topical treatment with PDS 21-mer sense ssDNA (SEQ ID NO:36, “21 nt PDS sense”) as described in Example 10.
  • PDS 21-mer anti-sense ssDNA SEQ ID NO:34, “21 nt PDS anti-sense”
  • PDS anti-sense previously assayed PDS anti-sense 22-mer oligonucleotides without a T7 promoter
  • FIG. 16 illustrates an alignment of the Palmer amaranth and Nicotiana benthamiana PDS DNA sequences showing about 71% identity (1252/1762) as described in Example 11.
  • FIG. 17 illustrates apical leaf bleaching observed in Palmer amaranth plants topically treated with 678 by or 198 by Palmer PDS dsRNA but not in Palmer amaranth plants topically treated with a 260 base pair dsRNA of corn root worm gene as described in Example 11.
  • FIG. 18A illustrates bleaching of apical leaves, stems, and flowers of Nicotiana benthamiana plants topically treated first with a surfactant solution and then with an ssDNA PDS oligonucleotide to induce systemic silencing of phytoene desaturase as described in Example 12.
  • FIG. 18B illustrates bleaching of apical leaves, stems, and flowers of Nicotiana benthamiana plants topically treated with an ssDNA PDS oligonucleotide to induce systemic silencing of phytoene desaturase, with or without conditioning with a surfactant solution, as described in Example 12.
  • FIG. 19 illustrates results of assays on different glyphosate-resistant Palmer amaranth lines (3 plants per replicate) treated with the conditions listed in Table 6, as described in Example 13. Photographs were taken at 7 days after glyphosate treatment (experiments 1-6) or at 9 days after glyphosate treatment (experiments 7-9).
  • FIG. 20 illustrates location of two small RNAs identified as abundant in EPSPS dsRNA-treated Palmer amaranth plants and which are shown as italicized underlined nucleotides at positions 564-588 and 743-767 of the full-length EPSPS (SEQ ID NO:40), as described in Example 14.
  • the EPSPS sequence also shows the location of the four oligonucleotide-size “short” EPSPS dsRNA molecules (underlined, non-italicized text) and the three “long” double-stranded RNA polynucleotides (bolded text as described in Example 1.
  • FIG. 21A illustrates results of treating Palmer amaranth plants with surfactant followed by dsRNA at one of three application amounts, followed by herbicide, as described in Example 17.
  • FIG. 21B illustrates results of assay 1 carried out on glyphosate-resistant Palmer amaranth grown from field-collected seeds as described in Example 17; plants are shown at 8 days and 30 days after treatment with herbicide.
  • FIG. 22 illustrates results obtained from treating Palmer amaranth with tallowamine surfactant and ammonium sulfate or with transfection reagents, as described in Example 18.
  • FIG. 23 illustrates results of treating glyphosate-resistant Palmer amaranth plants with either EPSPS dsRNAs or EPSPS DNA/RNA hybrids, as described in Example 19.
  • FIG. 24 illustrates results of treating glyphosate-resistant Palmer amaranth plants with either EPSPS dsRNA or EPSPS ssDNA polynucleotides, as described in Example 20.
  • the upper photography was taken at 8 days after herbicide spray and the lower (bar) graph presents the results as a glyphosate injury (GI) scored 8 days after herbicide spray.
  • GI glyphosate injury
  • FIG. 25A illustrates twelve dsRNA polynucleotides corresponding to DNA segments of approximately 250 by each covering in a tiling manner the full coding sequence and part of the 5′ and 3′ untranslated regions of the Palmer EPSPS gene, as described in Example 21; the four oligonucleotide-size “short” EPSPS dsRNA molecules as described in Example 1 and FIG. 1 are located in the tiling segments 2, 3, 4, and 8 respectively, and are shown as light grey bars within those segments.
  • FIG. 25B and FIG. 25C illustrates results of treating glyphosate-resistant Palmer amaranth plants with dsRNAs designed from these tiling segments or the four “short” dsRNA molecules or buffer.
  • FIG. 26 illustrates results of treating glyphosate-resistant Palmer amaranth plants with glyphosate followed by spraying with 1% Silwet L-77 followed by application of EPSPS dsRNA in buffer containing 2% ammonium sulfate, as described in Example 22.
  • Untreated (“UT”) control plants were treated only with the 1% Silwet L-77 spray but not with herbicide or dsRNA. Plants were photographed and rated at 16 days after treatment.
  • FIG. 27 illustrates results of treating a field population of high copy number glyphosate-resistant Palmer amaranth with a composition containing a 20 ⁇ or 100 ⁇ amount of EPSPS dsRNA polynucleotides, surfactant, ammonium sulfate, and herbicide or with a composition containing, surfactant, ammonium sulfate, and herbicide, as described in Example 23. For each treatment, two replicate 1 foot by 5 foot plots were treated.
  • FIG. 28 depicts the progression of bleaching and death of the lettuce plants treated with 1 nanomole ssDNA per plant at (from top to bottom) 37, 46, and 60 days after treatment, as described in Example 24.
  • FIG. 29A illustrates systemic silencing in lettuce plants evidenced by bleaching observed at 4 or 12 days after topical treatment with polynucleotides, as described in Example 24.
  • FIG. 29B depicts the systemic silencing evidenced by bleaching observed at 4 after topical treatment with the four individual anti-sense ssDNAs (“HL287”, SEQ ID NO:43; “HL288”, SEQ ID NO:44; “HL289”, SEQ ID NO:45; and “HL290”, SEQ ID NO:46) or with a mixture of all four.
  • FIG. 30 illustrates bleaching of leaves (right top panel) and flowers (right middle panel) of tomato plants treated with tomato phytoene desaturase polynucleotides, as described in Example 25.
  • FIG. 30 also illustrates the stunting of the tomato plants treated with PDS polynucleotides (lower panel).
  • FIG. 31 illustrates enhancement of glyphosate herbicidal activity in low-copy number Palmer amaranth of the EPSPS polynucleotides by TIF polynucleotides and that the TIF polynucleotides have herbicidal activity on their own, as described in Example 26.
  • EPSPS polynucleotides “1, 3, 4” refer to “short” dsRNAs having an anti-sense strand that is capable of hybridizing to the mRNA transcribed from the Palmer amaranth EPSPS gene (SEQ ID NO:1) at positions 14-38 (short dsRNA-1), 345-369 (short dsRNA-3), and 1105-1129 (short dsRNA-4), respectively as indicated by underlined nucleotides in FIG. 1 (see Example 1).
  • EPSPS “5” refers to IDT [5] (SEQ ID NOS:91-92 as described in Table 11).
  • FIG. 32 illustrates enhancement of glyphosate herbicidal activity in high-copy number Palmer amaranth of the EPSPS polynucleotides by TIF polynucleotides and that the TIF polynucleotides have herbicidal activity on their own, as described in Example 26.
  • EPSPS polynucleotides “1, 3, 4” refer to “short” dsRNAs having an anti-sense strand that is capable of hybridizing to the mRNA transcribed from the Palmer amaranth EPSPS gene (SEQ ID NO:1) at positions 14-38 (short dsRNA-1), 345-369 (short dsRNA-3), and 1105-1129 (short dsRNA-4), respectively as indicated by underlined nucleotides in FIG. 1 (see Example 1).
  • EPSPS “5” refers to IDT [5] (SEQ ID NOS:91-92 as described in Table 11).
  • FIG. 33 illustrates the herbicidal effect on Palmer amaranth after treatment with the indicated combinations of non-polynucleotide herbicides and polynucleotides, as described in Example 28.
  • FIG. 34 illustrates an alignment of the Nicotiana benthamiana PDS locus 1 promoter (SEQ ID NO:319) and PDS locus 2 promoter (SEQ ID NO:320), as described in Example 30.
  • FIG. 35 schematically illustrates the Nicotiana benthamiana PDS locus 1 and locus 2 promoters and the regions targetted by mixtures of polynucleotides, as described in Example 30.
  • FIG. 36 illustrates the effect on plant height in Nicotiana benthamiana in plants treated with a PDS anti-sense polynucleotide ( FIG. 36A ), EPSPS anti-sense polynucleotides ( FIG. 36B ), or RuBisCO anti-sense polynucleotides ( FIG. 36C ), as described in Example 33.
  • FIG. 37 illustrates the effect on Zea mays (Gaspe) monocot plants by topical treatment with dsRNA polynucleotides (“EPSPS DNA oligo”) targetting the endogenous EPSPS gene, or with buffer alone as a control, as described in Example 34.
  • EPSPS DNA oligo dsRNA polynucleotides
  • FIG. 38 illustrates the effect of varying glyphos ate counter-ions on herbicidal activity on glyphosate-resistant Palmer amaranth plants, as described in Example 35.
  • FIG. 39 illustrates the effect of the polyamines spermine (“SPM”) and spermidine (“SPMD”) or ammonium sulfate (“AMS”) on glyphosate-resistant Palmer amaranth containing 33, 36, or 57 copies of EPSPS, as described in Example 35.
  • SPM polyamines spermine
  • SPMD spermidine
  • AMS ammonium sulfate
  • fb 4 ⁇ WM means “followed by treatment with glyphosate (3360 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide)”.
  • nucleic acid sequences in the text of this specification are given, when read from left to right, in the 5′ to 3′ direction. Nucleic acid sequences may be provided as DNA or as RNA, as specified; disclosure of one necessarily defines the other, as is known to one of ordinary skill in the art. Where a term is provided in the singular, the inventors also contemplate aspects of the invention described by the plural of that term.
  • non-transcribable polynucleotides is meant that the polynucleotides do not comprise a complete polymerase II transcription unit.
  • solution refers to homogeneous mixtures and non-homogeneous mixtures such as suspensions, colloids, micelles, and emulsions.
  • polynucleotide refers to a nucleic acid molecule containing multiple nucleotides and generally refers both to “oligonucleotides” (a polynucleotide molecule of 18-25 nucleotides in length) and polynucleotides of 26 or more nucleotides.
  • oligonucleotides a polynucleotide molecule of 18-25 nucleotides in length
  • Embodiments of this invention include compositions including oligonucleotides having a length of 18-25 nucleotides (e. g., 18-mers, 19-mers, 20-mers, 21-mers, 22-mers, 23-mers, 24-mers, or 25-mers), or medium-length polynucleotides having a length of 26 or more nucleotides (e.
  • a polynucleotide is double-stranded, its length can be similarly described in terms of base pairs.
  • Polynucleotide compositions used in the various embodiments of this invention include compositions including oligonucleotides or polynucleotides or a mixture of both, including RNA or DNA or RNA/DNA hybrids or chemically modified oligonucleotides or polynucleotides or a mixture thereof.
  • the polynucleotide may be a combination of ribonucleotides and deoxyribonucleotides, e.
  • the polynucleotide includes non-canonical nucleotides such as inosine, thiouridine, or pseudouridine.
  • the polynucleotide includes chemically modified nucleotides. Examples of chemically modified oligonucleotides or polynucleotides are well known in the art; see, e. g., Verma and Eckstein (1998) Annu.
  • oligonucleotide or polynucleotide can be partially or completely modified with phosphorothioate, phosphorodithioate, or methylphosphonate internucleotide linkage modifications, modified nucleoside bases or modified sugars can be used in oligonucleotide or polynucleotide synthesis, and oligonucleotides or polynucleotides can be labelled with a fluorescent moiety (e. g., fluorescein or rhodamine) or other label (e. g., biotin).
  • a fluorescent moiety e. g., fluorescein or rhodamine
  • other label e. g., biotin
  • the polynucleotides can be single- or double-stranded RNA or single- or double-stranded DNA or double-stranded DNA/RNA hybrids or modified analogues thereof, and can be of oligonucleotide lengths or longer.
  • the polynucleotides that provide single-stranded RNA in the plant cell are selected from the group consisting of (a) a single-stranded RNA molecule, (b) a single-stranded RNA molecule that self-hybridizes to form a double-stranded RNA molecule, (c) a double-stranded RNA molecule, (d) a single-stranded DNA molecule, (e) a single-stranded DNA molecule that self-hybridizes to form a double-stranded DNA molecule, and (f) a single-stranded DNA molecule including a modified Pol III gene that is transcribed to an RNA molecule, (g) a double-stranded DNA molecule, (h) a double-stranded DNA molecule including a modified Pol III gene that is transcribed to an RNA molecule, (i) a double-stranded, hybridized RNA/DNA molecule, or
  • these polynucleotides include chemically modified nucleotides or non-canonical nucleotides.
  • the polynucleotides include double-stranded DNA formed by intramolecular hybridization, double-stranded DNA formed by intermolecular hybridization, double-stranded RNA formed by intramolecular hybridization, or double-stranded RNA formed by intermolecular hybridization.
  • the polynucleotides include single-stranded DNA or single-stranded RNA that self-hybridizes to form a hairpin structure having an at least partially double-stranded structure including at least one segment that will hybridize under physiological conditions in the cell to RNA transcribed from the gene targetted for suppression. Not intending to be bound by any mechanism, it is believed that such polynucleotides are or will produce single-stranded RNA with at least one segment that will hybridize under physiological conditions in a cell to RNA transcribed from the gene targetted for suppression.
  • the polynucleotides further includes a promoter, generally a promoter functional in a plant, e. g., a pol II promoter, a pol III promoter, a pol IV promoter, or a pol V promoter.
  • the polynucleotide compositions are formulated with counter-ions or other molecules that are known to associate with nucleic acid molecules, e. g., tetraalkyl ammonium ions, trialkyl ammonium ions, sulfonium ions, lithium ions, and polyamines such as spermine, spermidine, or putrescine.
  • the polynucleotide compositions are formulated with a non-polynucleotide herbicide (e. g., the chemical herbicides disclosed herein in the section headed “Herbicide-Tolerance Proteins”) or with a transferring agent or permeability-enhancing agent (see the section headed “Permeability-Enhancing Agents and Treatments”).
  • the polynucleotides are designed to induce systemic regulation or suppression of an endogenous gene in a plant and are designed to have a sequence essentially identical or essentially complementary to the sequence (which can be coding sequence or non-coding sequence) of an endogenous gene of a plant or to the sequence of RNA transcribed from an endogenous gene of a plant.
  • sequence essentially identical or essentially complementary is meant that the polynucleotides (or at least one strand of a double-stranded polynucleotide) are designed to hybridize under physiological conditions in cells of the plant to the endogenous gene or to RNA transcribed from the endogenous gene to effect regulation or suppression of the endogenous gene.
  • Embodiments of single-stranded polynucleotides functional in this invention have sequence complementarity that need not be 100% but is at least sufficient to permit hybridization to RNA transcribed from the target gene to form a duplex under physiological conditions in a plant cell to permit cleavage by a gene silencing mechanism.
  • the segment is designed to be essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target gene or messenger RNA transcribed from the target gene.
  • essentially identical is meant having 100% sequence identity or at least about 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% sequence identity when compared to the sequence of 18 or more contiguous nucleotides in either the target gene or RNA transcribed from the target gene; by “essentially complementary” is meant having 100% sequence complementarity or at least about 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% sequence complementarity when compared to the sequence of 18 or more contiguous nucleotides in either the target gene or RNA transcribed from the target gene.
  • polynucleotide molecules are designed to have 100% sequence identity with or complementarity to one allele of a given target gene (e. g., coding or non-coding sequence of a gene for an herbicide-tolerance protein, an herbicide-deactivating protein, a stress-response gene, or an essential gene); in other embodiments the polynucleotide molecules are designed to have 100% sequence identity with or complementarity to multiple alleles of a given target gene.
  • a given target gene e. coding or non-coding sequence of a gene for an herbicide-tolerance protein, an herbicide-deactivating protein, a stress-response gene, or an essential gene
  • the polynucleotides are modified RNA polymerase III genes, e. g., genes that transcribe 7SL signal recognition particle RNA or U6 spliceosomal RNA (Pol III genes) or polynucleotides containing a functional Pol III promoter sequence.
  • the polynucleotides are modified Pol III genes containing sense and anti-sense DNA corresponding to RNA of the targetted gene identified for regulation replacing the DNA sequence originally transcribed by the Pol III gene.
  • the polynucleotides useful in this invention typically effect regulation or modulation (e. g., suppression) of gene expression during a period during the life of the treated plant of at least 1 week or longer and typically in systemic fashion. For instance, within days of treating a plant leaf with a polynucleotide composition of this invention, primary and transitive siRNAs can be detected in other leaves lateral to and above the treated leaf and in apical tissue.
  • kits from Ambion have DNA ligated on the 5′ end that encodes a bacterial T7 polymerase promoter that makes RNA strands that can be assembled into a dsRNA.
  • dsRNA molecules can be produced from expression cassettes in bacterial cells that have regulated or deficient RNase III enzyme activity.
  • Long polynucleotide molecules can also be assembled from multiple RNA or DNA fragments.
  • design parameters such as Reynolds score and Tuschl rules are known in the art and are used in selecting polynucleotide sequences effective in gene silencing.
  • random design or empirical selection of polynucleotide sequences is used in selecting polynucleotide sequences effective in gene silencing.
  • sequence of a polynucleotide is screened against the genomic DNA of the intended plant to minimize unintentional silencing of other genes.
  • polynucleotide compositions of this invention are useful in compositions, such as solutions of polynucleotide molecules, at low concentrations, alone or in combination with other components (e. g., surfactants, salts, and non-polynucleotide herbicides) either in the same solution or in separately applied solutions. While there is no upper limit on the concentrations and dosages of polynucleotide molecules that can useful in the methods of this invention, lower effective concentrations and dosages will generally be sought for efficiency. The concentrations can be adjusted in consideration of the volume of spray applied to plant leaves.
  • a useful treatment for herbaceous plants using 25-mer oligonucleotide molecules is about 1 nanomole of oligonucleotide molecules per plant, e. g., from about 0.05 to 1 nanomole per plant.
  • Other embodiments for herbaceous plants include useful ranges of about 0.05 to about 100 nanomoles, or about 0.1 to about 20 nanomoles, or about 1 nanomole to about 10 nanomoles of polynucleotides per plant. Very large plants, trees, or vines may require correspondingly larger amounts of polynucleotides. When using long dsRNA molecules that can be processed into multiple oligonucleotides, lower concentrations can be used.
  • the factor 1 ⁇ when applied to oligonucleotide molecules is arbitrarily used to denote a treatment of 0.8 nanomoles of polynucleotide molecule per plant; 10 ⁇ , 8 nanomoles of polynucleotide molecule per plant; and 100 ⁇ , 80 nanomoles of polynucleotide molecule per plant,
  • a treatment of 0.8 nanomoles of polynucleotide molecule per plant 10 ⁇ , 8 nanomoles of polynucleotide molecule per plant
  • 100 ⁇ , 80 nanomoles of polynucleotide molecule per plant For example, in example 23 plants were treated with an aqueous solution comprising a 100 ⁇ treatment of EPSPS dsRNA (264 micrograms or 80 nanomoles) per plant.
  • This invention provides polynucleotide molecules for providing single-stranded RNA for systemic regulation of genes in a plant cell. More specifically, the invention also provides compositions and methods for inducing systemic regulation (e. g., systemic suppression or silencing) of a target gene in a plant by topical application to the plant of a polynucleotide molecule with a segment in a nucleotide sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target gene or RNA transcribed from the target gene, whereby the composition permeates the interior of the plant and induces systemic regulation of the target gene by the action of single-stranded RNA that hybridizes to the transcribed RNA, e. g., messenger RNA.
  • the polynucleotide molecule can be one or more polynucleotide molecules with a single such segment, multiples of such a segment, multiple different such segments, or combination thereof.
  • compositions and methods of this invention can comprise transferring agents or permeability-enhancing agents and treatments to condition the surface of plant tissue, e. g., leaves, stems, roots, flowers, or fruits, to permeation by the polynucleotide molecules into plant cells.
  • the transfer of polynucleotides into plant cells can be facilitated by the prior or contemporaneous application of a polynucleotide-transferring agent to the plant tissue.
  • the transferring agent is applied subsequent to the application of the polynucleotide composition.
  • the polynucleotide transferring agent enables a pathway for polynucleotides through cuticle wax barriers, stomata and/or cell wall or membrane barriers and into plant cells.
  • Suitable agents to facilitate transfer of the composition into a plant cell include agents that increase permeability of the exterior of the plant or that increase permeability of plant cells to oligonucleotides or polynucleotides. Such agents to facilitate transfer of the composition into a plant cell include a chemical agent, or a physical agent, or combinations thereof.
  • Chemical agents for conditioning includes (a) surfactants, (b) an organic solvents or an aqueous solutions or aqueous mixtures of organic solvents, (c) oxidizing agents, (e) acids, (f) bases, (g) oils, (h) enzymes, or combinations thereof.
  • Embodiments of the method can optionally include an incubation step, a neutralization step (e.
  • agents or treatments for conditioning of a plant to permeation by polynucleotides include emulsions, reverse emulsions, liposomes, and other micellar-like compositions.
  • agents or treatments for conditioning of a plant to permeation by polynucleotides include counter-ions or other molecules that are known to associate with nucleic acid molecules, e.
  • Organic solvents useful in conditioning a plant to permeation by polynucleotides include DMSO, DMF, pyridine, N-pyrrolidine, hexamethylphosphoramide, acetonitrile, dioxane, polypropylene glycol, other solvents miscible with water or that will dissolve phosphonucleotides in non-aqueous systems (such as is used in synthetic reactions).
  • Naturally derived or synthetic oils with or without surfactants or emulsifiers can be used, e.
  • plant-sourced oils such as those listed in the 9 th Compendium of Herbicide Adjuvants, publicly available on line at www.herbicide.adjuvants.com
  • crop oils e. g., paraffinic oils, polyol fatty acid esters, or oils with short-chain molecules modified with amides or polyamines such as polyethyleneimine or N-pyrrolidine.
  • Such agents for conditioning of a plant to permeation by polynucleotides are applied to the plant by any convenient method, e.g., spraying or coating with a powder, emulsion, suspension, or solution; similarly, the polynucleotide molecules are applied to the plant by any convenient method, e. g., spraying or wiping a solution, emulsion, or suspension.
  • useful surfactants include sodium or lithium salts of fatty acids (such as tallow or tallowamines or phospholipids) and organosilicone surfactants.
  • organosilicone surfactants include organosilicone surfactants including nonionic organosilicone surfactants, e. g., trisiloxane ethoxylate surfactants or a silicone polyether copolymer such as a copolymer of polyalkylene oxide modified heptamethyl trisiloxane and allyloxypolypropylene glycol methylether (commercially available as Silwet® L-77 surfactant having CAS Number 27306-78-1 and EPA Number: CAL.REG.NO.
  • Silwet L-77 surfactant When Silwet L-77 surfactant is used as a pre-spray treatment of plant leaves or other surfaces, concentrations in the range of about 0.015 to about 2 percent by weight (wt %) (e.
  • Useful physical agents can include (a) abrasives such as carborundum, corundum, sand, calcite, pumice, garnet, and the like, (b) nanoparticles such as carbon nanotubes or (c) a physical force.
  • abrasives such as carborundum, corundum, sand, calcite, pumice, garnet, and the like
  • nanoparticles such as carbon nanotubes or (c) a physical force.
  • Carbon nanotubes are disclosed by Kam et al. (2004) J. Am. Chem. Soc., 126 (22):6850-6851, Liu et al. (2009) Nano Lett., 9(3):1007-1010, and Khodakovskaya et al. (2009) ACS Nano, 3(10):3221-3227.
  • Physical force agents can include heating, chilling, the application of positive pressure, or ultrasound treatment.
  • Embodiments of the method can optionally include an incubation step, a neutralization step (e. g., to neutralize an acid, base, or oxidizing agent, or to inactivate an enzyme), a rinsing step, or combinations thereof.
  • the methods of the invention can further include the application of other agents which will have enhanced effect due to the silencing of certain genes. For example, when a polynucleotide is designed to regulate genes that provide herbicide resistance, the subsequent application of the herbicide can have a dramatic effect on herbicide efficacy.
  • Agents for laboratory conditioning of a plant to permeation by polynucleotides include, e. g., application of a chemical agent, enzymatic treatment, heating or chilling, treatment with positive or negative pressure, or ultrasound treatment.
  • Agents for conditioning plants in a field include chemical agents such as surfactants and salts.
  • compositions and methods of the invention are useful for modulating the expression of an endogenous or transgenic target gene in a plant cell.
  • a target gene includes coding (protein-coding or translatable) sequence, non-coding (non-translatable) sequence, or both coding and non-coding sequence.
  • Compositions of the invention can include polynucleotides and oligonucleotides designed to target multiple genes, or multiple segments of one or more genes.
  • the target gene can include multiple consecutive segments of a target gene, multiple non-consecutive segments of a target gene, multiple alleles of a target gene, or multiple target genes from one or more species.
  • Examples of target genes include endogenous plant genes and transgenes expressed in plant cells.
  • Other examples of target genes include endogenous genes of plant viral pathogens or endogenous genes of invertebrate plant pests.
  • Target genes can include genes encoding herbicide-tolerance proteins, non-coding sequences including regulatory RNAs, and essential genes, which are genes necessary for sustaining cellular life or to support reproduction of an organism.
  • Embodiments of essential genes include genes involved in DNA or RNA replication, gene transcription, RNA-mediated gene regulation, protein synthesis, energy production, and cell division.
  • One example of a compendium of essential genes is described in Zhang et al. (2004) Nucleic Acids Res., 32:D271-D272, and is available at tubic.tju. edu.cn/deg/; version DEG 5.4 lists 777 essential genes for Arabidopsis thaliana.
  • Target genes can include genes encoding transcription factors and genes encoding enzymes involved in the biosynthesis or catabolism of molecules in plants such as, but not limited to, amino acids, fatty acids and other lipids, sugars and other carbohydrates, biological polymers, and secondary metabolites including alkaloids, terpenoids, polyketides, non-ribosomal peptides, and secondary metabolites of mixed biosynthetic origin.
  • TIF translation initiation factor
  • RuBisCO ribulose-1,5-bisphosphate carboxylase oxygenase
  • Target genes can include genes encoding transcription factors and genes encoding enzymes involved in the biosynthesis or catabolism of molecules in plants such as, but not limited to, amino acids, fatty acids and other lipids, sugars and other carbohydrates, biological polymers, and secondary metabolites including alkaloids, terpenoids, polyketides, non-ribosomal peptides, and secondary metabolites of mixed biosynthetic origin.
  • Single-stranded RNA molecules of this invention can be provided directly to the plant cell as RNA or provided indirectly, e. g., where a polynucleotide molecule in the treatment composition causes in cells of a plant the production of the single-stranded RNA that is capable of hybridizing to the target gene's transcript.
  • compositions of polynucleotide molecules further include one or more permeability enhancing agents to facilitate transfer of the polynucleotide molecules into a plant cell, such as agents for conditioning of a plant to permeation by polynucleotides.
  • methods include one or more applications of the polynucleotide composition and one or more applications of a permeability-enhancing agent for conditioning of a plant to permeation by polynucleotides.
  • the agent for conditioning to permeation is an organosilicone surfactant
  • embodiments of the polynucleotide molecules are double-stranded RNA oligonucleotides, single-stranded RNA oligonucleotides, double-stranded RNA polynucleotides, single-stranded RNA polynucleotides, double-stranded DNA oligonucleotides, single-stranded DNA oligonucleotides, double-stranded DNA polynucleotides, single-stranded DNA polynucleotides, chemically modified RNA or DNA oligonucleotides or polynucleotides or mixtures thereof.
  • An aspect of the invention provides a method for inducing systemic silencing of a target gene in a plant including (a) conditioning of a plant to permeation by polynucleotides and (b) topical application of polynucleotide molecules to the plant, where the polynucleotide molecules include at least one segment of 18 or more contiguous nucleotides cloned from or otherwise identified from the target gene in either anti-sense or sense orientation, whereby the polynucleotide molecules permeate the interior of the plant and induce systemic silencing of the target gene.
  • the conditioning and polynucleotide application can be performed separately or in a single step.
  • the conditioning can precede or can follow the polynucleotide application within minutes, hours, or days. In some embodiments more than one conditioning step or more than one polynucleotide molecule application can be performed on the same plant.
  • the segment can be cloned or identified from (a) coding (i. e., protein-encoding), (b) non-coding, or (c) both coding and non-coding parts of the target gene. Non-coding parts include DNA (or the RNA encoded by the DNA) encoding RNA regulatory sequences (e.
  • RNAs having structural or enzymatic function e. g., ribozymes, ribosomal RNAs, t-RNAs, aptamers, and riboswitches.
  • the target gene is (a) an endogenous gene of the plant, (b) an endogenous gene of a viral pathogen of the plant, (c) an endogenous gene of an invertebrate pest of the plant, (d) an endogenous gene of a symbiont of an invertebrate pest of the plant, or (e) an man-made gene inserted into a transgenic plant.
  • the target gene is endogenous to a plant
  • the target gene (a) is an endogenous gene of the plant that is essential for maintaining the growth or life of the plant, (b) encodes a protein that provides herbicide resistance to the plant, or (c) transcribes to an RNA regulatory molecule.
  • the conditioning includes application of a chemical agent, abrasion, wounding, enzymatic treatment, heating or chilling, treatment with positive or negative pressure, ultrasound treatment, or combinations thereof.
  • the conditioning includes application of a surfactant, such as organosilicone surfactants, e.
  • the conditioning includes application of (a) a surfactant, (b) an organic solvent or an aqueous solution or aqueous mixture of an organic solvent, (c) a polypropylene glycol or an aqueous solution or aqueous mixture of polypropylene glycol, (d) nanoparticles, (e) an oxidizing agent, (f) an acid or a base, or (g) an oil, or of a combination thereof.
  • Embodiments of the method can optionally include an incubation step, a neutralization step (e. g., to neutralize an acid, base, or oxidizing agent, or to inactivate an enzyme), a rinsing step, or combinations thereof.
  • a neutralization step e. g., to neutralize an acid, base, or oxidizing agent, or to inactivate an enzyme
  • a rinsing step or combinations thereof.
  • compositions for inducing systemic silencing of a target gene in a plant including (a) an agent for conditioning of a plant to permeation by polynucleotides and (b) polynucleotide molecules with at least one segment of 18 or more contiguous nucleotides essentially identical or complementary to the sequence of nucleotides of the target gene in either anti-sense or sense orientation.
  • Such compositions can be used for the various methods disclosed herein including methods for investigating reverse genetics by modulating an endogenous gene in a plant, and as herbicidal compositions for the disclosed methods of weed control and volunteer plant control.
  • Another aspect of the invention provides a plant including exogenous DNA or RNA for suppressing an endogenous gene, wherein the exogenous DNA is not integrated into a chromosome of the plant and the exogenous RNA is not transcribed from DNA integrated into a chromosome of the plant, and wherein the endogenous gene is suppressed by topical application of a polynucleotide to the plant.
  • the exogenous DNA or RNA can be designed for suppressing an endogenous plant gene involved in responding to a pest or pathogen to provide control of plant pests or diseases.
  • Such plant can be grown from seed or produced by a cutting, cloning, or grafting process (i. e., a plant not grown from a seed).
  • Such plant is a row crop plant, a fruit, a vegetable, a tree, or an ornamental plant.
  • the plant is a row crop plant (e. g., corn, soybean, cotton, canola, sugar beet, alfalfa, sugarcane, rice, and wheat), or is a vegetable (e. g., tomato, sweet pepper, hot pepper, melon, watermelon, cucumber, eggplant, cauliflower, broccoli, lettuce, spinach, onion, peas, carrots, sweet corn, Chinese cabbage, leek, fennel, pumpkin, squash or gourd, radish, Brussels sprouts, tomatillo, garden beans, dry beans, or okra), or is an culinary plant (e.
  • a plant produced by a cutting, cloning, or grafting process include fruit trees and plants including citrus, apples, avocados, tomatoes, eggplant, cucumber, melons, watermelons, and grapes as well as various ornamental plants.
  • the invention provides a method for investigating reverse genetics by regulating or modulating an endogenous target gene in a plant; such method includes applying onto tissue of a growing plant a composition for providing (directly or indirectly) single-stranded RNA of this invention for systemic regulation of genes in a plant cell.
  • messenger RNA encoding a protein or regulatory RNA gene is targetted by a polynucleotide of the invention, effecting modulation of the gene during a period of at least 1 week during the life of the plant, e. g., to identify traits that can be imparted by topical application of polynucleotides.
  • the method can further include additional steps, e.
  • exposing the plant to an array of compounds to identify herbicide interactions or exposing the plant to abiotic stress (e. g., water deficit stress, nutrient deficit stress, heat stress, cold stress, salinity stress) or to biotic treatments (e. g., challenge with an insect or nematode pest or with a viral, fungal, or bacterial pathogen or exposure to a chemical compound or biological treatment) to identify responses by the plant to the stress or treatment.
  • abiotic stress e. g., water deficit stress, nutrient deficit stress, heat stress, cold stress, salinity stress
  • biotic treatments e. g., challenge with an insect or nematode pest or with a viral, fungal, or bacterial pathogen or exposure to a chemical compound or biological treatment
  • libraries of plants with a variety of transiently silenced genes are screened against libraries of compounds (e.
  • herbicides g., herbicides, phytohormones, endogenous or exogenous defense elicitors such as salicylic acid or hatpins, deficiencies of molecules providing a plant nutrient such as nitrogen, phosphorous, potassium, sulfur, calcium, magnesium, iron, and zinc) to identify interactions with such compounds.
  • phytohormones such as salicylic acid or hatpins
  • deficiencies of molecules providing a plant nutrient such as nitrogen, phosphorous, potassium, sulfur, calcium, magnesium, iron, and zinc
  • plants useful in such screens include Amaranthus palmeri and Nicotiana benthamiana.
  • this method can be used to silence a transgene being expressed in a plant, thus providing a negative control that is an event-independent measurement of a transgene's contribution to plant performance or effect on a trait Imparting a negative control effect may require multiple successive treatments with the polynucleotide molecules of this invention during the life cycle of a plant.
  • compositions and methods of the invention are also useful for transiently silencing one or more genes in a growing plant cell or whole plant to effect a desired phenotype in response to culture conditions, environmental or abiotic or biotic stress, or change in market demand during the growing season or in the post-harvest environment.
  • compositions and methods of the invention are useful for transiently suppressing a biosynthetic or catabolic gene in order to produce a plant or plant product with a desired phenotype, such as a desired nutritional composition of a crop plant product, e.
  • compositions and methods of the invention are useful for transiently suppressing an RNA regulatory molecule such as a microRNA (miRNA) or an endogenous miRNA decoy such as an endogenous miRNA, miRNA precursor, or miRNA decoy as disclosed in US Patent Application Publication 2009/0070898 which is incorporated herein by reference.
  • miRNA microRNA
  • Embodiments of the invention are useful for suppressing an endogenous plant gene involved in responding to a pest or pathogen, thus providing control of plant pests or diseases.
  • the polynucleotides, compositions, and delivery methods disclosed herein are further useful in suppressing an endogenous target gene of an invertebrate pest of a plant, e. g., lepidopteran or coleopteran pests which can ingest RNA from the plant, thus providing control of plant pests or pest-induced diseases, e. g., by use of a topical spray for crop plants, vegetables, or fruit trees with DNA or RNA molecules targeting an invertebrate essential gene or a gene of a symbiont of the invertebrate pest.
  • the polynucleotides, compositions, and delivery methods disclosed herein are further useful in providing control of a viral pathogen, e. g., by use of a topical anti-viral spray for crop plants, vegetables, or fruit trees with DNA or RNA molecules targeting a viral gene.
  • An aspect of the invention provides a liquid herbicidal composition
  • a liquid herbicidal composition comprising polynucleotide molecules as a plant lethal agent which provides at least one species of single-stranded RNA which can hybridize under physiological conditions in a plant cell to RNA transcribed from endogenous gene(s) in the plant cell.
  • the target gene encodes a protein that provides tolerance to an herbicide or encodes a gene essential for maintaining the growth or life of the plant.
  • the liquid herbicidal composition can further include permeability-enhancing agents, non-nucleotide herbicides, or combinations thereof and can be used in a multi-step treatment with the non-nucleotide herbicide and/or the permeability-enhancing agents applied separately.
  • An embodiment of the liquid herbicidal composition is a liquid including an organosilicone surfactant as permeability-enhancing agent and oligonucleotides or polynucleotides as plant lethal agent which provide to cells of the plant single-stranded RNA capable of hybridizing under physiological conditions in the plant cells to RNA transcribed from a target gene in the plant cell to effect silencing of the target gene.
  • a liquid herbicidal composition effective against glyphosate-resistant plants includes an organosilicone surfactant such as Silwet® L-77 surfactant and polynucleotide molecules for providing single-stranded RNA capable of hybridizing under physiological conditions in the plant cells to the RNA transcript of an endogenous or transgenic EPSPS gene encoding an EPSPS protein that provides tolerance to glyphosate
  • an organosilicone surfactant such as Silwet® L-77 surfactant
  • polynucleotide molecules for providing single-stranded RNA capable of hybridizing under physiological conditions in the plant cells to the RNA transcript of an endogenous or transgenic EPSPS gene encoding an EPSPS protein that provides tolerance to glyphosate
  • the polynucleotide molecule can function as a plant lethal agent, i.e., a nucleotide herbicide.
  • These herbicidal compositions including polynucleotide molecules can be adapted for topical coating
  • An aspect of the invention provides a composition adapted for topical coating onto leaves or other surfaces of a living plant including a permeability-enhancing agent, e.g., a surfactant such as an organosilicone surfactant, and oligonucleotides or polynucleotides that provide (directly or indirectly) single-stranded RNA that can hybridize under physiological conditions in a plant cell to RNA transcribed from an endogenous plant gene in the cell.
  • the endogenous plant gene is an endogenous plant gene encoding a protein that provides herbicide tolerance to herbicides such as glyphosate, dicamba, or sulfonylurea. Examples of such proteins that provide herbicide tolerance are disclosed below in the section “Herbicide-Tolerance Proteins”.
  • Another aspect of the invention provides a method for controlling herbicide-resistant volunteer plants growing in a field of herbicide-resistant crop plants including applying onto the leaves or other surface of the volunteer plants a composition that provides to, or allows the production in, cells of the volunteer plants a single-stranded RNA molecule that is capable of hybridizing under physiological conditions in cells of the volunteer plants to RNA that is transcribed from an endogenous gene in the cells, wherein the endogenous gene (i) is an essential gene for maintaining the growth or life of the volunteer plant, (ii) encodes a protein that provides herbicide resistance to the volunteer plant, or (iii) transcribes to an RNA regulatory agent (e.
  • the composition that provides to, or allows the production in, cells of the volunteer plants a single-stranded RNA molecule that is capable of hybridizing under physiological conditions in cells of the volunteer plants to RNA that is transcribed from an endogenous gene in the cells includes at least one polynucleotide molecule selected from the group consisting of (a) a single-stranded RNA molecule, (b) a single-stranded RNA molecule that self-hybridizes to form a double-stranded RNA molecule, (c) a double-stranded RNA molecule, (d) a single-stranded DNA molecule, (e) a single-stranded DNA molecule that self-hybridizes to form a double-stranded DNA molecule, and (f) a polynucleotide molecule selected from the group consisting of (a) a single-stranded RNA molecule, (b) a single-stranded RNA molecule that self-hybrid
  • compositions and methods of the invention are useful in controlling herbicide-tolerant (resistant) weeds or volunteer herbicide-tolerant (resistant) transgenic plants that may be growing in crop fields, e. g., a field of herbicide-resistant crop plants such as corn, soybean, cotton, canola, sugar beet, alfalfa, sugarcane, rice, wheat, as well as fruit and vegetable crops.
  • a field of herbicide-resistant crop plants such as corn, soybean, cotton, canola, sugar beet, alfalfa, sugarcane, rice, wheat, as well as fruit and vegetable crops.
  • the weed or the volunteer plant is pigweed (e.
  • the endogenous gene encodes a protein that provides herbicide tolerance; examples of such proteins are disclosed herein in the section “Herbicide-Tolerance Proteins”.
  • single-stranded RNA selectively suppresses a gene in a specific plant species but not in others, to permit selective control of that plant species.
  • a non-selective, single-stranded RNA molecule suppresses a common gene in multiple plant species, permitting broader control across a group or taxon of plants.
  • the method further includes applying onto the weed or volunteer plant a quantity of non-nucleotide herbicide (e.
  • glyphosate, dicamba, glufosinate or sulfonylurea for which the protein targetted by an RNA molecule provides resistance allowing dual modes of action through reducing production of the target protein by action of the RNA molecule and inhibiting the function of protein that is produced by action of the non-nucleotide herbicide; the herbicide can be applied in a separate (earlier or later) step from, or together with, the nucleotide composition.
  • Applying a polynucleotide composition concurrently with, or followed by, application of a conventional non-nucleotide herbicide in some cases provides weed or volunteer plant control with synergistic effect (i. e., where the combined effect is greater than the sum of effects of the treatments made separately).
  • Natural (non-transgenic) and transgenic plants exhibiting herbicide tolerance often have a gene that encodes a protein that is responsible for the herbicide tolerance, e. g., a transgene that provides the tolerance, a mutated endogenous gene that provides the tolerance or multiple copies of an endogenous gene that is normally targetted by an herbicide.
  • a strategy for control of such plants is to apply an agent that suppresses, or at least reduces the expression of, the gene encoding the protein that imparts herbicide tolerance.
  • Examples of a protein that provides tolerance to an herbicide include e.
  • EPSPS 5-enolpyruvylshikimate-3-phosphate synthase
  • GOX glyphosate oxidoreductase
  • GAT glyphosate-N-acetyl transferase
  • dicamba monooxygenase a phosphinothricin acetyltransferase
  • 2,2-dichloropropionic acid dehalogenase an acetohydroxyacid synthase, an acetolactate synthase, a haloarylnitrilase
  • EPSPS 5-enolpyruvylshikimate-3-phosphate synthase
  • nucleic acids encoding proteins conferring tolerance to herbicides include 5-enolpyruvylshikimate-3-phosphate synthases (EPSPS; see, e. g., U.S. Pat. Nos. 5,627,061, 5,633,435 RE39247, 6,040,497, and 5,094,945, and PCT International Application Publications WO04074443 and WO04009761), glyphosate oxidoreductase (GOX; U.S. Pat. No. 5,463,175), glyphosate decarboxylase (PCT International Application Publication WO05003362, U.S. Pat. No. 7,405,347, and U.S.
  • EPSPS 5-enolpyruvylshikimate-3-phosphate synthases
  • GOX glyphosate oxidoreductase
  • PCT International Application Publication WO05003362 U.S. Pat. No. 7,405,347, and U.
  • glyphosate-N-acetyl transferase (GAT; U.S. Pat. No. 7,714,188) conferring tolerance to glyphosate; dicamba monooxygenase conferring tolerance to auxin-like herbicides such as dicamba (U.S. Pat. No. 7,105,724); phosphinothricin acetyltransferase (pat or bar) conferring tolerance to phosphinothricin or glufosinate (U.S. Pat. No.
  • dihydrodipicolinic acid synthase for conferring to tolerance to aminoethyl cysteine (PCT International Application Publication WO8911789); phytoene desaturase (crtI) for conferring tolerance to pyridazinone herbicides such as norflurazon (Japan Patent JP06343473); hydroxyphenylpyruvate dioxygenase, a 4-hydroxyphenylacetic acid oxidase and a 4-hydroxyphenylacetic 1-hydrolase (U.S. Pat. No. 7,304,209) for conferring tolerance to cyclopropylisoxazole herbicides such as isoxaflutole (U.S. Pat. No.
  • protoporphyrinogen oxidase I protox
  • protoporphyrinogen oxidase inhibitors U.S. Pat. No. 5,939,602
  • aryloxyalkanoate dioxygenase AAD-1
  • a serine hydroxymethyltransferase US Patent Application Publication 2008/0155716
  • a glufosinate-tolerant glutamine synthase US Patent Application Publication 2009/0018016.
  • herbicides examples include phenoxy auxins (such as 2,4-D and dichlorprop), pyridyloxy auxins (such as fluroxypyr and triclopyr), aryloxyphenoxypropionates (AOPP) acetyl-coenzyme A carboxylase (ACCase) inhibitors (such as haloxyfop, quizalofop, and diclofop), and 5-substituted phenoxyacetate protoporphyrinogen oxidase IX inhibitors (such as pyraflufen and flumiclorac).
  • phenoxy auxins such as 2,4-D and dichlorprop
  • pyridyloxy auxins such as fluroxypyr and triclopyr
  • AOPP aryloxyphenoxypropionates
  • nucleotide sequences of the nucleic acids encoding herbicide-tolerance proteins and the sequences of the herbicide-tolerance proteins, as disclosed in the U.S. patent and patent application publications cited in this paragraph are incorporated herein by reference.
  • aspects of this invention provide polynucleotides and methods that directly or indirectly provide to a plant cell RNAs that hybridize to RNA encoding such herbicide-tolerance proteins at a level to be lethal to the plant or at least at a level to reduce herbicide tolerance. Due to the sequence degeneracy of the DNA encoding herbicide-tolerance proteins it is possible to design a polynucleotide for use in this invention that is specifically effective in a particular plant. Due to conservation of domains of DNA among a multitude of plants it is possible to design a polynucleotide for use in this invention that is effective across a variety of plants.
  • the polynucleotide is admixed with the corresponding herbicide to potentiate the activity of the herbicide by providing improved herbicidal activity.
  • the polynucleotide is utilized separately from the herbicide but in combination with an application of the herbicide as a pre- or post-treatment.
  • the organosilicone surfactant is advantageously combined with the herbicide and the polynucleotide or is combined with one or the other when the compositions are applied in a sequential manner. Plants in a greenhouse setting can be treated using a track sprayer or laboratory sprayer with a 11001XR spray nozzle to deliver the sample solution at a determined rate (e. g., 140 L/ha) at 0.25 MPa pressure.
  • the treatment solution can be applied with a CO 2 pressurized backpack sprayer calibrated to deliver the appropriate rate of the composition with a 11015 flat fan spray nozzle with a customized single nozzle assembly (to minimize waste) at a spray pressure of 0.25 MPa; the single nozzle sprayer provides an effective spray swath of 60 cm above the canopy of 3 to 12 inch tall growing plants.
  • a method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene.
  • a method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene in plant cells other than those topically coated.
  • a method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene systemically in at least one plant organ.
  • a method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the polynucleotide composition induces suppression of the target endogenous gene.
  • a method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the polynucleotide composition effects a desired phenotype in the growing plant or plant organ.
  • a method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the polynucleotide composition suppresses expression of an enzyme, a structural protein or a plant regulatory protein in the growing plants or plant organs.
  • a method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the polynucleotide composition is a plant lethal agent.
  • a method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the target endogenous gene encodes a protein that interacts with an herbicide.
  • a method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the target endogenous gene is selected from the group consisting of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), an acetohydroxyacid synthase or an acetolactate synthase (ALS), an acetyl-coenzyme A carboxylase (ACCase),
  • a method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the target endogenous gene encodes a protein essential for maintaining the growth of the growing plants.
  • a method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the target endogenous gene is selected from the group consisting of RuBisCO, Translation Initiation Factor, and phytoene desaturase.
  • a method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the target endogenous gene encodes a protein that provides tolerance to an herbicide.
  • a method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the target endogenous gene encodes a mutant acetolactate synthase enzyme that confers resistance to sulfonylurea and imidazolinone herbicides or a mutant ACCase that confers resistance to aryloxyphenoxy propionate herbicides.
  • a method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the polynucleotide composition further includes a second polynucleotide, the second polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides of a second target endogenous gene or messenger RNA transcribed from the second target endogenous gene.
  • XV A method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the polynucleotide composition further includes a second polynucleotide, the second polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides of a second target endogenous gene or messenger RNA transcribed from the second target endogenous gene,
  • XVI A method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the target endogenous gene is non-coding sequence, coding sequence, or a combination of non-coding sequence and coding sequence.
  • a method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the polynucleotide composition is coated onto an organ of the growing plants.
  • a method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the polynucleotide composition is coated onto a leaf, stem, seed, fruit, or flower of the growing plants.
  • a method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the polynucleotide composition further includes a second polynucleotide, the second polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides of a different segment of the target endogenous gene or messenger RNA transcribed from the target endogen
  • XX A method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the growing plants are in an open field or in a greenhouse.
  • XXI A method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the polynucleotides are not integrated into the chromosome of the growing plants.
  • XXII A method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the transferring agent is selected from the group consisting of a surfactant and a salt.
  • a method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the transferring agent is selected from the group consisting of an organosilicone surfactant and a salt.
  • XXIV A method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the transferring agent is selected from the group consisting of a silicone polyether copolymer organosilicone surfactant and a salt.
  • XXV A method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the transferring agent is selected from the group consisting of a silicone polyether copolymer organosilicone surfactant and a salt, wherein the silicone polyether copolymer is a copolymer of polyalkylene oxide modified heptamethyl trisiloxane and allyloxypolypropylene glycol methyl
  • XXVI A method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the transferring agent is selected from the group consisting of a surfactant and salt, wherein the salt is an organic or an inorganic salt.
  • a method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the transferring agent is selected from the group consisting of a surfactant, an organic ammonium salt, and an inorganic ammonium salt.
  • a method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the transferring agent is selected from the group consisting of a surfactant and ammonium sulfate.
  • XXIX A method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the transferring agent is selected from the group consisting of a surfactant and a salt and further includes a humectant or a chelating agent.
  • XXX A method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the polynucleotide composition is coated onto the growing plants or plant organs by a spray apparatus.
  • XXXI A method for regulating expression of a target endogenous gene in growing plants or plant organs including topically coating onto the growing plants or plant organs a polynucleotide composition comprised of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene and an effective amount of a transferring agent to permit the at least one polynucleotide to permeate the interior of the growing plants, whereby the at least one polynucleotide regulates the expression of the target endogenous gene, wherein the polynucleotide is selected from the group consisting of ssDNA, dsDNA, ssRNA, dsRNA and RNA/DNA hybrids.
  • a method for potentiating activity of an herbicide in growing plants including (a) topically coating onto the surface of the growing plants a polynucleotide composition, included of at least one polynucleotide having sequence essentially identical to, or or essentially complementary to, a sequence of 18 or more contiguous nucleotides of a essentially complementary to, a sequence of 18 or more contiguous nucleotides in an endogenous gene of the plant, wherein the endogenous gene expresses a protein that interacts with an herbicide, and an effective amount of a transferring agent to permit the polynucleotides to permeate the interior of the growing plants, and (b) applying the herbicide to the growing plants; whereby the at least one polynucleotide permeates the interior of the growing plants and induces suppression of the endogenous gene, thereby potentiating activity of the herbicide in the growing plants.
  • a method for potentiating activity of an herbicide in growing plants including (a) topically coating onto the surface of the growing plants a polynucleotide composition, included of at least one polynucleotide having sequence essentially identical to, or or essentially complementary to, a sequence of 18 or more contiguous nucleotides of a essentially complementary to, a sequence of 18 or more contiguous nucleotides in an endogenous gene of the plant, wherein the endogenous gene expresses a protein that interacts with an herbicide, and an effective amount of a transferring agent to permit the polynucleotides to permeate the interior of the growing plants, and (b) applying the herbicide to the growing plants; whereby the at least one polynucleotide permeates the interior of the growing plants and induces suppression of the endogenous gene, thereby potentiating activity of the herbicide in the growing plants, wherein the endogenous gene expresses a protein that is a herbicide target gene
  • (XXXIV) A method for potentiating activity of an herbicide in growing plants including (a) topically coating onto the surface of the growing plants a polynucleotide composition, included of at least one polynucleotide having sequence essentially identical to, or or essentially complementary to, a sequence of 18 or more contiguous nucleotides of a essentially complementary to, a sequence of 18 or more contiguous nucleotides in an endogenous gene of the plant, wherein the endogenous gene expresses a protein that interacts with an herbicide, and an effective amount of a transferring agent to permit the polynucleotides to permeate the interior of the growing plants, and (b) applying the herbicide to the growing plants; whereby the at least one polynucleotide permeates the interior of the growing plants and induces suppression of the endogenous gene, thereby potentiating activity of the herbicide in the growing plants, wherein the endogenous gene expresses a protein that is a herbicide target
  • (XXXV) A method for potentiating activity of an herbicide in growing plants including (a) topically coating onto the surface of the growing plants a polynucleotide composition, included of at least one polynucleotide having sequence essentially identical to, or or essentially complementary to, a sequence of 18 or more contiguous nucleotides of a essentially complementary to, a sequence of 18 or more contiguous nucleotides in an endogenous gene of the plant, wherein the endogenous gene expresses a protein that interacts with an herbicide, and an effective amount of a transferring agent to permit the polynucleotides to permeate the interior of the growing plants, and (b) applying the herbicide to the growing plants; whereby the at least one polynucleotide permeates the interior of the growing plants and induces suppression of the endogenous gene, thereby potentiating activity of the herbicide in the growing plants, wherein the polynucleotide composition and the herbicide are applied separately or in
  • a method for potentiating activity of an herbicide in growing plants including (a) topically coating onto the surface of the growing plants a polynucleotide composition, included of at least one polynucleotide having sequence essentially identical to, or or essentially complementary to, a sequence of 18 or more contiguous nucleotides of a essentially complementary to, a sequence of 18 or more contiguous nucleotides in an endogenous gene of the plant, wherein the endogenous gene expresses a protein that interacts with an herbicide, and an effective amount of a transferring agent to permit the polynucleotides to permeate the interior of the growing plants, and (b) applying the herbicide to the growing plants; whereby the at least one polynucleotide permeates the interior of the growing plants and induces suppression of the endogenous gene, thereby potentiating activity of the herbicide in the growing plants, wherein the polynucleotide is selected from the group consisting of ss
  • a method for potentiating activity of an herbicide in growing plants including (a) topically coating onto the surface of the growing plants a polynucleotide composition, included of at least one polynucleotide having sequence essentially identical to, or or essentially complementary to, a sequence of 18 or more contiguous nucleotides of a essentially complementary to, a sequence of 18 or more contiguous nucleotides in an endogenous gene of the plant, wherein the endogenous gene expresses a protein that interacts with an herbicide, and an effective amount of a transferring agent to permit the polynucleotides to permeate the interior of the growing plants, and (b) applying the herbicide to the growing plants; whereby the at least one polynucleotide permeates the interior of the growing plants and induces suppression of the endogenous gene, thereby potentiating activity of the herbicide in the growing plants, wherein the polynucleotide composition further includes a second polynucle
  • a method for potentiating activity of an herbicide in growing plants including (a) topically coating onto the surface of the growing plants a polynucleotide composition, included of at least one polynucleotide having sequence essentially identical to, or or essentially complementary to, a sequence of 18 or more contiguous nucleotides of a essentially complementary to, a sequence of 18 or more contiguous nucleotides in an endogenous gene of the plant, wherein the endogenous gene expresses a protein that interacts with an herbicide, and an effective amount of a transferring agent to permit the polynucleotides to permeate the interior of the growing plants, and (b) applying the herbicide to the growing plants; whereby the at least one polynucleotide permeates the interior of the growing plants and induces suppression of the endogenous gene, thereby potentiating activity of the herbicide in the growing plants, wherein the polynucleotide composition further includes a plurality of polyn
  • a method for potentiating activity of an herbicide in growing plants including (a) topically coating onto the surface of the growing plants a polynucleotide composition, included of at least one polynucleotide having sequence essentially identical to, or or essentially complementary to, a sequence of 18 or more contiguous nucleotides of a essentially complementary to, a sequence of 18 or more contiguous nucleotides in an endogenous gene of the plant, wherein the endogenous gene expresses a protein that interacts with an herbicide, and an effective amount of a transferring agent to permit the polynucleotides to permeate the interior of the growing plants, and (b) applying the herbicide to the growing plants; whereby the at least one polynucleotide permeates the interior of the growing plants and induces suppression of the endogenous gene, thereby potentiating activity of the herbicide in the growing plants, wherein the transferring agent is selected from the group consisting of a surfactant and
  • (XL) A method for potentiating activity of an herbicide in growing plants including (a) topically coating onto the surface of the growing plants a polynucleotide composition, included of at least one polynucleotide having sequence essentially identical to, or or essentially complementary to, a sequence of 18 or more contiguous nucleotides of a essentially complementary to, a sequence of 18 or more contiguous nucleotides in an endogenous gene of the plant, wherein the endogenous gene expresses a protein that interacts with an herbicide, and an effective amount of a transferring agent to permit the polynucleotides to permeate the interior of the growing plants, and (b) applying the herbicide to the growing plants; whereby the at least one polynucleotide permeates the interior of the growing plants and induces suppression of the endogenous gene, thereby potentiating activity of the herbicide in the growing plants, wherein the transferring agent is selected from the group consisting of an organosilicone surfact
  • a method for potentiating activity of an herbicide in growing plants including (a) topically coating onto the surface of the growing plants a polynucleotide composition, included of at least one polynucleotide having sequence essentially identical to, or or essentially complementary to, a sequence of 18 or more contiguous nucleotides of a essentially complementary to, a sequence of 18 or more contiguous nucleotides in an endogenous gene of the plant, wherein the endogenous gene expresses a protein that interacts with an herbicide, and an effective amount of a transferring agent to permit the polynucleotides to permeate the interior of the growing plants, and (b) applying the herbicide to the growing plants; whereby the at least one polynucleotide permeates the interior of the growing plants and induces suppression of the endogenous gene, thereby potentiating activity of the herbicide in the growing plants, wherein the transferring agent is selected from the group consisting of a silicone polyether copolymer
  • a method for potentiating activity of an herbicide in growing plants including (a) topically coating onto the surface of the growing plants a polynucleotide composition, included of at least one polynucleotide having sequence essentially identical to, or or essentially complementary to, a sequence of 18 or more contiguous nucleotides of a essentially complementary to, a sequence of 18 or more contiguous nucleotides in an endogenous gene of the plant, wherein the endogenous gene expresses a protein that interacts with an herbicide, and an effective amount of a transferring agent to permit the polynucleotides to permeate the interior of the growing plants, and (b) applying the herbicide to the growing plants; whereby the at least one polynucleotide permeates the interior of the growing plants and induces suppression of the endogenous gene, thereby potentiating activity of the herbicide in the growing plants, wherein the transferring agent is selected from the group consisting of a silicone polyether copoly
  • a method for potentiating activity of an herbicide in growing plants including (a) topically coating onto the surface of the growing plants a polynucleotide composition, included of at least one polynucleotide having sequence essentially identical to, or or essentially complementary to, a sequence of 18 or more contiguous nucleotides of a essentially complementary to, a sequence of 18 or more contiguous nucleotides in an endogenous gene of the plant, wherein the endogenous gene expresses a protein that interacts with an herbicide, and an effective amount of a transferring agent to permit the polynucleotides to permeate the interior of the growing plants, and (b) applying the herbicide to the growing plants; whereby the at least one polynucleotide permeates the interior of the growing plants and induces suppression of the endogenous gene, thereby potentiating activity of the herbicide in the growing plants, wherein the transferring agent is selected from the group consisting of a surfactant and a
  • a method for potentiating activity of an herbicide in growing plants including (a) topically coating onto the surface of the growing plants a polynucleotide composition, included of at least one polynucleotide having sequence essentially identical to, or or essentially complementary to, a sequence of 18 or more contiguous nucleotides of a essentially complementary to, a sequence of 18 or more contiguous nucleotides in an endogenous gene of the plant, wherein the endogenous gene expresses a protein that interacts with an herbicide, and an effective amount of a transferring agent to permit the polynucleotides to permeate the interior of the growing plants, and (b) applying the herbicide to the growing plants; whereby the at least one polynucleotide permeates the interior of the growing plants and induces suppression of the endogenous gene, thereby potentiating activity of the herbicide in the growing plants, wherein the transferring agent is selected from the group consisting of a surfactant, an organic solvent, or organic
  • (XLV) A method for potentiating activity of an herbicide in growing plants including (a) topically coating onto the surface of the growing plants a polynucleotide composition, included of at least one polynucleotide having sequence essentially identical to, or or essentially complementary to, a sequence of 18 or more contiguous nucleotides of a essentially complementary to, a sequence of 18 or more contiguous nucleotides in an endogenous gene of the plant, wherein the endogenous gene expresses a protein that interacts with an herbicide, and an effective amount of a transferring agent to permit the polynucleotides to permeate the interior of the growing plants, and (b) applying the herbicide to the growing plants; whereby the at least one polynucleotide permeates the interior of the growing plants and induces suppression of the endogenous gene, thereby potentiating activity of the herbicide in the growing plants, wherein the transferring agent is selected from the group consisting of a surfactant and ammoni
  • XLVI A method for potentiating activity of an herbicide in growing plants including (a) topically coating onto the surface of the growing plants a polynucleotide composition, included of at least one polynucleotide having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides of a essentially complementary to, a sequence of 18 or more contiguous nucleotides in an endogenous gene of the plant, wherein the endogenous gene expresses a protein that interacts with an herbicide, and an effective amount of a transferring agent to permit the polynucleotides to permeate the interior of the growing plants, and (b) applying the herbicide to the growing plants; whereby the at least one polynucleotide permeates the interior of the growing plants and induces suppression of the endogenous gene, thereby potentiating activity of the herbicide in the growing plants, wherein the transferring agent is selected from the group consisting of a surfactant and a salt
  • XLVII In a liquid, herbicidal composition adapted for topical coating onto the exterior surface of growing plants including surfactant and at least one plant lethal agent, the improvement wherein the plant lethal agent includes polynucleotides having a sequence essentially identical or complementary to sequence of a plant gene or sequence of the plant gene's transcribed RNA, the polynucleotides effecting systemic production of small RNAs that hybridize to a probe for the plant gene.
  • composition including a non-polynucleotide herbicide, the improvement wherein the composition further includes polynucleotides having a sequence essentially identical or complementary to sequence of a plant gene or sequence of the plant gene's transcribed RNA.
  • composition consisting essentially of (a) a solution of non-transcribable double-stranded DNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the double-stranded DNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the double-stranded DNA polynucleotides from the surface of the plant into cells of the plant.
  • composition consisting essentially of (a) a solution of non-transcribable double-stranded DNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the double-stranded DNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the double-stranded DNA polynucleotides from the surface of the plant into cells of the plant, wherein the transferring agent is selected from the group consisting of a surfactant and a salt.
  • a composition consisting essentially of (a) a solution of non-transcribable double-stranded DNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the double-stranded DNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the double-stranded DNA polynucleotides from the surface of the plant into cells of the plant, wherein the transferring agent is selected from the group consisting of an organosilicone surfactant and an inorganic salt.
  • a composition consisting essentially of (a) a solution of non-transcribable double-stranded DNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the double-stranded DNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the double-stranded DNA polynucleotides from the surface of the plant into cells of the plant, wherein the transferring agent is selected from the group consisting of a silicone polyether copolymer organosilicone surfactant and an inorganic salt.
  • composition consisting essentially of (a) a solution of non-transcribable double-stranded DNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the double-stranded DNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the double-stranded DNA polynucleotides from the surface of the plant into cells of the plant, wherein the transferring agent is selected from the group consisting of a silicone polyether copolymer organosilicone surfactant and an inorganic salt, wherein the silicone polyether copolymer is a copolymer of polyalkylene oxide modified heptamethyl trisiloxane and allyloxypol
  • composition consisting essentially of (a) a solution of non-transcribable double-stranded DNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the double-stranded DNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the double-stranded DNA polynucleotides from the surface of the plant into cells of the plant, further including a non-polynucleotide herbicidal molecule.
  • LV A composition consisting essentially of (a) a solution of non-transcribable double-stranded DNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the double-stranded DNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the double-stranded DNA polynucleotides from the surface of the plant into cells of the plant, wherein the plant gene encodes a protein that provides herbicide tolerance and is a 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), an acetohydroxyacid synthase or an acetolactate synthase (ALS), an acetyl-coenzyme A
  • (LVI) A composition consisting essentially of (a) a solution of non-transcribable single-stranded DNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the single-stranded DNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the single-stranded DNA polynucleotides from the surface of the plant into cells of the plant.
  • (LVII) A composition consisting essentially of (a) a solution of non-transcribable single-stranded DNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the single-stranded DNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the single-stranded DNA polynucleotides from the surface of the plant into cells of the plant, wherein the transferring agent is selected from the group consisting of a surfactant and a salt.
  • (LVIII) A composition consisting essentially of (a) a solution of non-transcribable single-stranded DNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the single-stranded DNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the single-stranded DNA polynucleotides from the surface of the plant into cells of the plant, wherein the transferring agent is selected from the group consisting of an organosilicone surfactant and an inorganic salt.
  • a composition consisting essentially of (a) a solution of non-transcribable single-stranded DNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the single-stranded DNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the single-stranded DNA polynucleotides from the surface of the plant into cells of the plant, wherein the transferring agent is selected from the group consisting of an silicone polyether copolymer organosilicone surfactant and an inorganic salt.
  • composition consisting essentially of (a) a solution of non-transcribable single-stranded DNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the single-stranded DNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the single-stranded DNA polynucleotides from the surface of the plant into cells of the plant, wherein the transferring agent is selected from the group consisting of an silicone polyether copolymer organosilicone surfactant and an inorganic salt, wherein the silicone polyether copolymer is a copolymer of polyalkylene oxide modified heptamethyl trisiloxane and allyloxypoly
  • composition consisting essentially of (a) a solution of non-transcribable single-stranded DNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the single-stranded DNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the single-stranded DNA polynucleotides from the surface of the plant into cells of the plant, further including a non-polynucleotide herbicidal molecule.
  • composition consisting essentially of (a) a solution of non-transcribable single-stranded DNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the single-stranded DNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the single-stranded DNA polynucleotides from the surface of the plant into cells of the plant, wherein the plant gene encodes a protein that provides herbicide tolerance and is a 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), an acetohydroxyacid synthase or an acetolactate synthase (ALS), an acetyl-coen
  • EPSPS 5-
  • composition consisting essentially of (a) a solution of non-transcribable double-stranded RNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the double-stranded RNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the double-stranded RNA polynucleotides from the surface of the plant into cells of the plant.
  • composition consisting essentially of (a) a solution of non-transcribable double-stranded RNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the double-stranded RNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the double-stranded RNA polynucleotides from the surface of the plant into cells of the plant, wherein the transferring agent is selected from the group consisting of a surfactant and a salt.
  • composition consisting essentially of (a) a solution of non-transcribable double-stranded RNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the double-stranded RNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the double-stranded RNA polynucleotides from the surface of the plant into cells of the plant, wherein the transferring agent is selected from the group consisting of an organosilicone surfactant and an inorganic salt.
  • composition consisting essentially of (a) a solution of non-transcribable double-stranded RNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the double-stranded RNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the double-stranded RNA polynucleotides from the surface of the plant into cells of the plant, wherein the transferring agent is selected from the group consisting of a silicone polyether copolymer organosilicone surfactant and an inorganic salt.
  • composition consisting essentially of (a) a solution of non-transcribable double-stranded RNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the double-stranded RNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the double-stranded RNA polynucleotides from the surface of the plant into cells of the plant, wherein the transferring agent is selected from the group consisting of a silicone polyether copolymer organosilicone surfactant and an inorganic salt, wherein the silicone polyether copolymer is a copolymer of polyalkylene oxide modified heptamethyl trisiloxane and
  • composition consisting essentially of (a) a solution of non-transcribable double-stranded RNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the double-stranded RNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the double-stranded RNA polynucleotides from the surface of the plant into cells of the plant, further including a non-polynucleotide herbicidal molecule.
  • composition consisting essentially of (a) a solution of non-transcribable double-stranded RNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the double-stranded RNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the double-stranded RNA polynucleotides from the surface of the plant into cells of the plant, wherein the plant gene encodes a protein that provides herbicide tolerance and is a 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), an acetohydroxyacid synthase or an acetolactate synthase (ALS), an acetyl
  • EPSPS 5-
  • composition consisting essentially of (a) a solution of non-transcribable single-stranded RNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the single-stranded RNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the single-stranded RNA polynucleotides from the surface of the plant into cells of the plant.
  • composition consisting essentially of (a) a solution of non-transcribable single-stranded RNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the single-stranded RNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the single-stranded RNA polynucleotides from the surface of the plant into cells of the plant, wherein the transferring agent is selected from the group consisting of a surfactant and a salt.
  • composition consisting essentially of (a) a solution of non-transcribable single-stranded RNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the single-stranded RNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the single-stranded RNA polynucleotides from the surface of the plant into cells of the plant, wherein the transferring agent is selected from the group consisting of an organosilicone surfactant and an inorganic salt.
  • composition consisting essentially of (a) a solution of non-transcribable single-stranded RNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the single-stranded RNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the single-stranded RNA polynucleotides from the surface of the plant into cells of the plant, wherein the transferring agent is selected from the group consisting of an silicone polyether copolymer organosilicone surfactant and an inorganic salt.
  • composition consisting essentially of (a) a solution of non-transcribable single-stranded RNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the single-stranded RNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the single-stranded RNA polynucleotides from the surface of the plant into cells of the plant, wherein the transferring agent is selected from the group consisting of an silicone polyether copolymer organosilicone surfactant and an inorganic salt, wherein the silicone polyether copolymer is a copolymer of polyalkylene oxide modified heptamethyl trisiloxane and
  • composition consisting essentially of (a) a solution of non-transcribable single-stranded RNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the single-stranded RNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the single-stranded RNA polynucleotides from the surface of the plant into cells of the plant, further including a non-polynucleotide herbicidal molecule.
  • composition consisting essentially of (a) a solution of non-transcribable single-stranded RNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the single-stranded RNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the single-stranded RNA polynucleotides from the surface of the plant into cells of the plant, wherein the plant gene encodes a protein that provides herbicide tolerance and is a 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), an acetohydroxyacid synthase or an acetolactate synthase (ALS), an acetyl
  • EPSPS 5-
  • composition consisting essentially of (a) a solution of non-transcribable double-stranded DNA/RNA hybrid polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the double-stranded DNA/RNA hybrid polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the double-stranded DNA/RNA hybrid polynucleotides from the surface of the plant into cells of the plant.
  • composition consisting essentially of (a) a solution of non-transcribable double-stranded DNA/RNA hybrid polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the double-stranded DNA/RNA hybrid polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the double-stranded DNA/RNA hybrid polynucleotides from the surface of the plant into cells of the plant, wherein the transferring agent is selected from the group consisting of a surfactant and a salt.
  • composition consisting essentially of (a) a solution of non-transcribable double-stranded DNA/RNA hybrid polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the double-stranded DNA/RNA hybrid polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the double-stranded DNA/RNA hybrid polynucleotides from the surface of the plant into cells of the plant, wherein the transferring agent is selected from the group consisting of an organosilicone surfactant and an inorganic salt.
  • composition consisting essentially of (a) a solution of non-transcribable double-stranded DNA/RNA hybrid polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the double-stranded DNA/RNA hybrid polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the double-stranded DNA/RNA hybrid polynucleotides from the surface of the plant into cells of the plant, wherein the transferring agent is selected from the group consisting of an silicone polyether copolymer organosilicone surfactant and an inorganic salt.
  • composition consisting essentially of (a) a solution of non-transcribable double-stranded DNA/RNA hybrid polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the double-stranded DNA/RNA hybrid polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the double-stranded DNA/RNA hybrid polynucleotides from the surface of the plant into cells of the plant, wherein the transferring agent is selected from the group consisting of an silicone polyether copolymer organosilicone surfactant and an inorganic salt, wherein the silicone polyether copolymer is a copolymer of polyalkylene oxide modified heptamethyl tri
  • composition consisting essentially of (a) a solution of non-transcribable double-stranded DNA/RNA hybrid polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the double-stranded DNA/RNA hybrid polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the double-stranded DNA/RNA hybrid polynucleotides from the surface of the plant into cells of the plant, further including a non-polynucleotide herbicidal molecule.
  • composition consisting essentially of (a) a solution of non-transcribable double-stranded DNA/RNA hybrid polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the double-stranded DNA/RNA hybrid polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the double-stranded DNA/RNA hybrid polynucleotides from the surface of the plant into cells of the plant, wherein the plant gene encodes a protein that provides herbicide tolerance and is a 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), an acetohydroxyacid synthase or an acetolactate synthase (ALS
  • (LXXXIV) A method for selectively controlling targeted herbicide-resistant volunteer plants growing in a field of herbicide-resistant crop plants including applying onto the leaves of the volunteer plants a composition including polynucleotide oligomers that provides in cells of the volunteer plants systemic, single-stranded RNA that is capable of hybridizing under physiological conditions in cells of the volunteer plants to messenger RNA that is transcribed from an endogenous gene that (i) is an essential gene for maintaining the growth or life of the volunteer plant, (ii) encodes a protein that provides herbicide resistance to the volunteer plant, or (iii) transcribes to an RNA regulatory agent.
  • (LXXXV) A method for selectively controlling targeted herbicide-resistant volunteer plants growing in a field of herbicide-resistant crop plants including applying onto the leaves of the volunteer plants a composition including polynucleotide oligomers that provides in cells of the volunteer plants systemic, single-stranded RNA that is capable of hybridizing under physiological conditions in cells of the volunteer plants to messenger RNA that is transcribed from an endogenous gene that (i) is an essential gene for maintaining the growth or life of the volunteer plant, (ii) encodes a protein that provides herbicide resistance to the volunteer plant, or (iii) transcribes to an RNA regulatory agent, wherein the composition includes a surfactant and oligomers selected from the group consisting of single-stranded RNA, double-stranded RNA, single-stranded DNA, double-stranded DNA, and double-stranded, hybridized RNA/DNA, wherein the oligomers having a sequence essentially identical or complementary to messenger RNA of the endogenous gene; and where
  • a method for selectively controlling targeted herbicide-resistant volunteer plants growing in a field of herbicide-resistant crop plants including applying onto the leaves of the volunteer plants a composition including polynucleotide oligomers that provides in cells of the volunteer plants systemic, single-stranded RNA that is capable of hybridizing under physiological conditions in cells of the volunteer plants to messenger RNA that is transcribed from an endogenous gene that (i) is an essential gene for maintaining the growth or life of the volunteer plant, (ii) encodes a protein that provides herbicide resistance to the volunteer plant, or (iii) transcribes to an RNA regulatory agent, wherein the volunteer plant is pigweed, velvetleaf, waterhemp, prickly lettuce, dandelion, alfalfa, corn, soybean, canola, cotton, sugar beet, sugarcane, wheat, rice, or a vegetable.
  • a method for selectively controlling targeted herbicide-resistant volunteer plants growing in a field of herbicide-resistant crop plants including applying onto the leaves of the volunteer plants a composition including polynucleotide oligomers that provides in cells of the volunteer plants systemic, single-stranded RNA that is capable of hybridizing under physiological conditions in cells of the volunteer plants to messenger RNA that is transcribed from an endogenous gene that (i) is an essential gene for maintaining the growth or life of the volunteer plant, (ii) encodes a protein that provides herbicide resistance to the volunteer plant, or (iii) transcribes to an RNA regulatory agent, wherein the crop plants are corn, soybean, cotton, canola, sugar beet, alfalfa, sugarcane, rice, wheat, or fruit or vegetable crops.
  • a method for selectively controlling targeted herbicide-resistant volunteer plants growing in a field of herbicide-resistant crop plants including applying onto the leaves of the volunteer plants a composition including polynucleotide oligomers that provides in cells of the volunteer plants systemic, single-stranded RNA that is capable of hybridizing under physiological conditions in cells of the volunteer plants to messenger RNA that is transcribed from an endogenous gene that (i) is an essential gene for maintaining the growth or life of the volunteer plant, (ii) encodes a protein that provides herbicide resistance to the volunteer plant, or (iii) transcribes to an RNA regulatory agent, wherein the endogenous gene encodes a protein that provides herbicide resistance to the volunteer plant and the protein is a 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), an acetohydroxyacid synthase or an acetolactate synthase (ALS), an acetyl-coenzyme A carboxylase (ACCas
  • EPSPS 5-en
  • (LXXXIX) A method for selectively controlling targeted herbicide-resistant volunteer plants growing in a field of herbicide-resistant crop plants including applying onto the leaves of the volunteer plants a composition including polynucleotide oligomers that provides in cells of the volunteer plants systemic, single-stranded RNA that is capable of hybridizing under physiological conditions in cells of the volunteer plants to messenger RNA that is transcribed from an endogenous gene that (i) is an essential gene for maintaining the growth or life of the volunteer plant, (ii) encodes a protein that provides herbicide resistance to the volunteer plant, or (iii) transcribes to an RNA regulatory agent, wherein the endogenous gene encodes a protein that provides herbicide resistance to the volunteer plant and the protein is a 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), an acetohydroxyacid synthase or an acetolactate synthase (ALS), an acetyl-coenzyme A carboxylase (ACCa
  • (XC) A method for investigating reverse genetics by modulating an endogenous target gene in a plant, the method including applying onto tissue of a growing plant: (1) a composition consisting essentially of (a) a solution of non-transcribable double-stranded DNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the double-stranded DNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the double-stranded DNA polynucleotides from the surface of the plant into cells of the plant; or (2) a composition consisting essentially of (a) a solution of non-transcribable single-stranded DNA polynucleotides having a sequence essentially identical
  • XCI A method for investigating reverse genetics by modulating an endogenous target gene in a plant, the method including applying onto tissue of a growing plant: (1) a composition consisting essentially of (a) a solution of non-transcribable double-stranded DNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the double-stranded DNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the double-stranded DNA polynucleotides from the surface of the plant into cells of the plant; or (2) a composition consisting essentially of (a) a solution of non-transcribable single-stranded DNA polynucleotides having a sequence essentially identical or
  • XCII A method for investigating reverse genetics by modulating an endogenous target gene in a plant, the method including applying onto tissue of a growing plant: (1) a composition consisting essentially of (a) a solution of non-transcribable double-stranded DNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the double-stranded DNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the double-stranded DNA polynucleotides from the surface of the plant into cells of the plant; or (2) a composition consisting essentially of (a) a solution of non-transcribable single-stranded DNA polynucleotides having a sequence essentially identical
  • (XCIII) A method for investigating reverse genetics by modulating an endogenous target gene in a plant, the method including applying onto tissue of a growing plant: (1) a composition consisting essentially of (a) a solution of non-transcribable double-stranded DNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the double-stranded DNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the double-stranded DNA polynucleotides from the surface of the plant into cells of the plant; or (2) a composition consisting essentially of (a) a solution of non-transcribable single-stranded DNA polynucleotides having a sequence essentially
  • XCIV A method for investigating reverse genetics by modulating an endogenous gene in a plant, the method including topically applying onto tissue of a living plant: (1) a composition consisting essentially of (a) a solution of non-transcribable double-stranded DNA polynucleotides having a sequence essentially identical or complementary to the sequence of an endogenous gene of a plant or to the sequence of RNA transcribed from the endogenous gene; wherein the double-stranded DNA polynucleotides are capable of hybridizing under physiological conditions in cells of the plant to the endogenous gene or to the RNA transcribed from the endogenous gene to effect silencing of the endogenous gene; and (b) transferring agent effective for facilitating transfer of the double-stranded DNA polynucleotides from the surface of the plant into cells of the plant; or (2) a composition consisting essentially of (a) a solution of non-transcribable single-stranded DNA polynucleotides having a sequence essentially
  • XCV An herbicidal composition including an aqueous solution of (a) an agent for conditioning of a plant to permeation by polynucleotide oligomers, and (b) polynucleotide oligomers including at least one polynucleotide strand including at least one segment of 18 or more contiguous nucleotides of an endogenous gene of the plant in either anti-sense or sense orientation, wherein the endogenous gene encodes a protein that provides to the plant resistance to a chemical herbicide or is an essential gene.
  • An herbicidal composition including an aqueous solution of (a) an agent for conditioning of a plant to permeation by polynucleotide oligomers, and (b) polynucleotide oligomers including at least one polynucleotide strand including at least one segment of 18 or more contiguous nucleotides of an endogenous gene of the plant in either anti-sense or sense orientation, wherein the endogenous gene encodes a protein that provides to the plant resistance to a chemical herbicide or is an essential gene, further including a chemical herbicide.
  • An herbicidal composition including an aqueous solution of (a) an agent for conditioning of a plant to permeation by polynucleotide oligomers, and (b) polynucleotide oligomers including at least one polynucleotide strand including at least one segment of 18 or more contiguous nucleotides of an endogenous gene of the plant in either anti-sense or sense orientation, wherein the endogenous gene encodes a protein that provides to the plant resistance to a chemical herbicide or is an essential gene, further including a chemical herbicide, including a glyphosate, dicamba, phosphinothricin, bromoxynil, ioxynil, or chlorsulfuron herbicide compounds.
  • An herbicidal composition including an aqueous solution of (a) an agent for conditioning of a plant to permeation by polynucleotide oligomers, and (b) polynucleotide oligomers including at least one polynucleotide strand including at least one segment of 18 or more contiguous nucleotides of an endogenous gene of the plant in either anti-sense or sense orientation, wherein the endogenous gene encodes a protein that provides to the plant resistance to a chemical herbicide or is an essential gene, further including a chemical herbicide, including a glyphosate compound, a silicone polyether copolymer surfactant and polynucleotide oligomers.
  • XCIX A plant including exogenous DNA or RNA for suppressing an endogenous gene, wherein the exogenous DNA is not integrated into a chromosome of the plant and the exogenous RNA is not transcribed from DNA integrated into a chromosome of the plant, and wherein the endogenous gene is suppressed by topical application of a polynucleotide to the plant after the plant has emerged from a seed.
  • C A method to deliver a polynucleotide to the interior of a plant cell by topical application of the polynucleotide to the exterior of the plant cell, the method including combining the polynucleotide with an organosilicone surfactant.
  • (CI) A method to deliver a polynucleotide to the interior of a plant cell by topical application of the polynucleotide to the exterior of the plant cell, the method including combining the polynucleotide with an organosilicone surfactant, wherein the organosilicone surfactant is a silicone polyether copolymer.
  • a method to deliver a polynucleotide to the interior of a plant cell by topical application of the polynucleotide to the exterior of the plant cell including combining the polynucleotide with an organosilicone surfactant, wherein the organosilicone surfactant is a silicone polyether copolymer, wherein the silicone polyether copolymer is a copolymer of polyalkylene oxide modified heptamethyl trisiloxane and allyloxypolypropylene glycol methylether.
  • CIII A method to deliver a polynucleotide to the interior of a plant cell by topical application of the polynucleotide to the exterior of the plant cell, the method including combining the polynucleotide with an organosilicone surfactant and an organic or an inorganic salt.
  • CIV A method to deliver a polynucleotide to the interior of a plant cell by topical application of the polynucleotide to the exterior of the plant cell, the method including combining the polynucleotide with an organosilicone surfactant and an organic or an inorganic salt, wherein the salt is an ammonium salt.
  • CV A method to deliver a polynucleotide to the interior of a plant cell by topical application of the polynucleotide to the exterior of the plant cell, the method including combining the polynucleotide with an organosilicone surfactant and an organic or an inorganic salt, wherein the salt is an ammonium salt, wherein the ammonium salt is ammonium sulfate.
  • CVI A method to deliver a polynucleotide to the interior of a plant cell by topical application of the polynucleotide to the exterior of the plant cell, the method including combining the polynucleotide with an organosilicone surfactant, wherein the polynucleotide composition is coated onto the growing plants or plant organs by a spray apparatus.
  • Genotypes of glyphosate-resistant Palmer amaranth were identified as having multiple copies, e. g., from 4 to more than 100 copies, of the gene encoding 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) which is targetted by the glyphosate compounds in herbicide treatments.
  • EPSPS 5-enolpyruvylshikimate-3-phosphate synthase
  • oligonucleotide-size “short” dsRNA molecules were designed with an anti-sense strand that is capable of hybridizing to the mRNA transcribed from the Palmer amaranth EPSPS gene at positions 14-38 (short dsRNA-1), positions 153-177 (short dsRNA-2), 345-369 (short dsRNA-3), and 1105-1129 (short dsRNA-4), as indicated by underlined nucleotides in FIG. 1 .
  • the four designed short dsRNAs were purchased from Integrated DNA Technologies (IDT); the dsRNAs had a two nucleotide overhang at the 3′ end of the anti-sense strand, and had two deoxynucleotides as the terminal nucleotides at the 3′ end of the sense strand.
  • RNA polynucleotides were designed with one strand that is capable of hybridizing to the mRNA transcribed from the Palmer amaranth EPSPS gene at positions 16-170 (long dsRNA-1), 451-722 (long dsRNA-2), and 1109-1328 (long dsRNA-3) as indicted by the bolded nucleotides in FIG. 1 .
  • the three designed long dsRNAs were made using an Ambion MEGAscript® RNAi Kit, Cat. No. 1626.
  • Vegetative clones of glyphosate-resistant Palmer amaranth with 16 copies of the endogenous gene encoding EPSPS were grown in 3.5 inch square pots with SunGro® Redi-earth seedling mix containing 3.5 kg/cubic meter Osmocote® 14-14-14 fertilizer in a greenhouse with 14-hour photoperiod and a daytime temperature of 30 degrees centigrade and night temperature of 20 degrees centigrade; the plants were watered with deionized water as necessary.
  • a pretreatment surfactant solution for leaf dip was prepared by diluting Silwet L-77 brand organosilicone surfactant with distilled water to 0.1% (v/v).
  • a pretreatment 5% (w/v) carborundum solution was prepared by mixing 2 g carborundum (400 grit) in 40 ml distilled water.
  • a treatment buffer solution was prepared with 10 mM sodium phosphate and 0.01% (v/v) Silwet L-77 organosilicone surfactant in DEPC water (Omega Bio-Tek) and adjusted to pH 6.8.
  • a short dsRNA solution was prepared with equimolar amounts of each of the four short dsRNAs (identified above) in treatment buffer solution at a concentration of 0.005 nanomoles of each short dsRNA per microliter.
  • a long dsRNA solution was prepared with equimolar amounts of each of the three long dsRNAs in treatment buffer at a concentration of 0.0006 nanomoles of each of long dsRNA per microliter.
  • a mixed (short/long) dsRNA solution was prepared with 0.005 nanomoles of each of the four short dsRNAs and 0.0006 nanomoles of each of the three long dsRNAs per microliter.
  • Vegetative clones of glyphosate-resistant Palmer amaranth with 16 copies of the endogenous gene encoding EPSPS were pre-treated with carborundum solution or surfactant solution to condition the leaves to transfer or permeation of dsRNA.
  • carborundum solution pre-treatment leaf abrasion was effected by gently rubbing 0.5 ml of the carborundum solution on the upper surface of a leaf, rinsing with water and blotting dry.
  • surfactant solution pre-treatment four, fully-expanded, mature source leaves were dipped in the surfactant solution and allowed to dry.
  • the conditioned leaves were treated with either buffer solution (as a control) or 40 microliters of a dsRNA solution (applying 10 microliters of dsRNA solution on each of 4 leaves per plant).
  • Treatment with the short dsRNA solution applied about 0.8 nanomoles of short dsRNA molecules (0.2 nanomoles of each short dsRNA) to each treated plant.
  • Treatment with the long dsRNA solution applied about 0.072 nanomoles of long dsRNA molecules (0.024 nanomoles of each long dsRNA) to each treated plant.
  • Treatment with the mixed (short/long) dsRNA solution applied about 0.8 nanomoles of the short dsRNA molecules and about 0.072 nanomoles of the long dsRNA molecules to each treated plant. Except for controls, all plants were sprayed with a glyphosate herbicide solution (1682 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide) immediately, 48, or 72 hours after dsRNA treatment and evaluated at least after 7 days post-glyphos ate treatment.
  • a glyphosate herbicide solution (1682 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide
  • This example illustrates the utility of the polynucleotide molecules of this invention for improving the control of glyphosate herbicide-sensitive weeds.
  • the mixed (short/long) dsRNA solutions prepared in Example 1 were applied to glyphosate-sensitive velvetleaf plants (a total of 40 microliters applied to two leaves) that had been pre-treated with the surfactant solution used in Example 1. Control plants were treated with buffer only following pre-treatment with the surfactant solution. 48 hours after dsRNA treatment the plants were treated with glyphosate herbicide solution (53 g acid equivalent per hectare of Roundup® WeatherMAX® brand glyphosate herbicide).
  • This example illustrates the utility of the polynucleotide molecules of this invention for controlling weeds in transgenic glyphosate-resistant crops.
  • Transgenic alfalfa, canola, corn, cotton, rice, soybean, sugarcane, sugar beet, and wheat plants having recombinant DNA for expressing a bacterial EPSPS see U.S. Pat. No.
  • RE39,247 for a description of glyphosate-resistant “class II” EPSPS genes are treated with (a) the surfactant solution used in Example 1, (b) the mixed (short/long) dsRNA solution prepared in Example 1, and (c) glyphosate herbicide solution (1682 g acid equivalence per hectare Roundup® WeatherMAX®) 48 hours after dsRNA treatment. After 30 days all transgenic glyphosate-resistant crop plants survive and exhibit no stunting.
  • This example illustrates the utility of the polynucleotide molecules of the invention as herbicidal agents.
  • Two dsRNA polynucleotide molecules were designed to target overlapping segments of mRNA encoding phytoene desaturase in tobacco ( Nicotiana benthamiana ).
  • a dsRNA targeting a 192 nt length (shown in bold in FIG. 5 ) and a 685 nt length (shown in underline in FIG. 5 ) of the mRNA were made using an Ambion® MEGAscript® kit. Separate dsRNA solutions were prepared.
  • Tobacco plant leaves were pretreated with surfactant solution prepared as in Example 1 and then treated with either one of the dsRNA solutions applying about 0.6 micromoles of dsRNA per plant.
  • On day 9 after dsRNA treatment phytoene desaturase silencing was apparent from visible leaf bleaching on apical leaves; see FIG. 4 .
  • At 15 days after treatment with dsRNA one half of the treated plants appeared to be dead and the other half of the plants had most of the above ground tissues bleached.
  • Northern blot analysis indicates the presence of siRNAs corresponding to the dsRNAs used in treatment.
  • dsRNA oligonucleotide molecules are designed to target RNA encoding EPSPS for each of the following plants: ragweed ( Ambrosia artemisiifolia ), giant ragweed ( Ambrosia trifida ), Johnsongrass ( Sorghum halepense ), hairy fleabane ( Conzya bonariensis ), sourgrass ( Digitaria insularis ), liverseedgrass ( Urochloa panicoides ), euphorbia ( Euphorbia heterophylla ), junglerice ( Echinochloa colona ), lambsquarters ( Chenopodium album ), green foxtail ( Setaria viridis ), foxtail millet ( Setaria italic ), barnyard grass ( Echinochloa crus - galli ), crabgrass ( Digitaria sanguinalis ), cocklebur ( Xanth), ragweed ( Ambrosia artemisiifolia ), giant ragweed ( Ambro
  • dsRNA oligonucleotide molecules are designed to target RNA encoding acetolactate synthase and phytoene desaturase for each of the plants listed in Example 5. Plant leaves are pretreated with surfactant solution prepared as in Example 1 and treated with dsRNA solutions at a treatment of about 1 nanomole per plant. After 15 days treated plants are dead, dying, or stunted.
  • Example 4 further illustrates the utility of the polynucleotide molecules of the invention as herbicidal agents.
  • the method of Example 4 is repeated to provide short dsRNA oligonucleotides that are designed to target RNA encoding each of the following proteins in Palmer amaranth: a 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), an acetyl-coenzyme A carboxylase, a dihydropteroate synthase, a protoporphyrin IX oxygenase, a hydroxyphenylpyruvate dioxygenase, a glutamine synthase, D1 protein, a translation initiation factor (TIF), a ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO), and a DNA-dependent ATPase (ddATPase).
  • EPSPS 5-enolpyruvylshikimate-3-phosphate synthase
  • Leaves of separate glyphosate-resistant Palmer amaranth plants are treated with the surfactant solution prepared as in Example 1 and separately each of the dsRNA oligonucleotide molecules in the manner of Example 1 at a treatment of 1 nanomole of dsRNA per plant. After 30 days the treated plants are dead, dying, or stunted.
  • a synthetic Pol III gene is created using elements from an Arabidopsis thaliana U6 snRNA gene to provide a dsDNA molecule with two copies of RGCCCR elements (bold and underlined), an upstream sequence element (USE) having the sequence “TCCCACATCG” (SEQ ID NO:4, bold and underlined), a TATA box (bold and underlined), a “G” nucleotide (bold and underlined), anti-sense DNA (italics) corresponding to a bacterial DNA encoding an EPSPS protein (see U.S. Pat.
  • a solution of 0.1 wt % Silwet L-77 brand organosilicone surfactant and a solution of multiple copies of the dsDNA molecule are sprayed onto leaves of volunteer glyphosate-resistant corn plants growing in a field of glyphosate-resistant soybean plants, followed 7 days later by treatment with Roundup WeatherMAX® brand glyphosate herbicide. 15 days later the corn plants are dead and the soybean plants are fostering; control glyphosate-resistant corn plants treated only with surfactant and glyphosate herbicide are thriving.
  • polynucleotide molecules were applied to and permeated into plant tissue thereby inducing systemic regulation, i. e., silencing, of a target gene (an endogenous EPSPS). More specifically, a composition including single-stranded DNA (ssDNA) oligonucleotides suppressed the expression of an endogenous EPSPS in glyphosate-tolerant Palmer amaranth ( Amaranthus palmeri ).
  • ssDNA single-stranded DNA
  • the anti-sense ssDNA oligonucleotides were designed using IDT SciTools software (available at idtdna.com/Scitools/Applications/Anti-sense/Anti-sense.aspx).
  • the oligonucleotides included four ssDNA oligonucleotides anti-sense to Amaranthus palmeri EPSPS (SEQ ID NOs:8, 9, 10, and 11), two chemically modified (phosphorothioate modified) ssDNA oligonucleotides anti-sense to Amaranthus palmeri EPSPS (SEQ ID NOs:12 and 13), a control ssDNA oligonucleotide anti-sense to a control gene, barley ( Hordeum vulgare ) seed protein, GenBank ID X97636 (SEQ ID NO:14), and a chemically modified (5′-labelled with Alexa Fluor 488 from Invitrogen) ssDNA oligonucleotide anti-sense to Amaranthus palmeri EPSPS (SEQ ID NO:15), as indicated in Table 1.
  • Anti-sense ssDNA oligonucleotides SEQ Name ID NO: Sequence (5′ to 3′) Note Anti-sense_PO1 8 ACCCTCCACGACTGCCCTTT Anti-sense_P02 9 GTTTCCTTCACTCTCCAGC Anti-sense_PO3 10 GTAGCTTGAGCCATTATTGT Anti-sense_PO4 11 GTTGATGGTAGTAGCTTGAG Anti-sense_PS1 12 ACCCTCCACGACTGCCCTTT phosphorothioate modification of the three 5′-terminal and three 3′-terminal nucleotides Anti-sense_PS2 13 GTTTCCTTCACTCTCCAGC phosphorothioate modification of the three 5′-terminal and three 3′-terminal nucleotides Anti-sense_ck 14 AAGCGGTTGAGCACTGAA Control sequence, barley seed protein, GenBank ID X97636 Anti-sense_PO1_488 15 ACCCTCCACGACTGCCCTTT 5′-labelled
  • Oligonucleotide uptake was demonstrated with the fluorescently labelled ssDNA oligonucleotides (SEQ ID NO:15) confirming that ssDNA oligonucleotides permeated the leaf tissue.
  • Petioles of detached leaves of glyphosate-resistant Palmer amaranth were placed in 200 mM sucrose solution with fluorescently labelled ssDNA oligonucleotides (SEQ ID NO:15).
  • Leaf images were taken by Bio-Rad PharosFX imager equipped with a 488 nm laser from 4 h up to 48 h after uptake through petiole. Leaves incubated with 200 mM sucrose alone served as control.
  • EPSPS suppression was demonstrated with detached leaves of glyphosate-resistant Palmer amaranth using the petiole uptake technique. Petioles of detached leaves of glyphosate-resistant Palmer amaranth were placed in 200 mM sucrose solution with oligonucleotides according to the treatments listed in Table 2. Control leaves were permeated with the anti-sense control (SEQ ID NO:14), and additionally treated with or without 50 micrograms/mL glyphosate. EPSPS mRNA, EPSPS protein, and shikimate levels were measured after 48 h incubation.
  • EPSPS mRNA total leaf RNA was isolated and quantitative real-time RT-PCR was performed to compare EPSPS mRNA levels.
  • total leaf soluble protein was isolated, separated by SDS-PAGE, and EPSPS protein levels measured by Western blot using antibodies against maize EPSPS_TIPA.
  • This example illustrates an aspect of the invention.
  • growing plants were treated with a topically applied composition for inducing systemic silencing of a target gene in a plant including (a) an agent for conditioning of a plant to permeation by polynucleotides and (b) polynucleotides including at least one polynucleotide strand including at least one segment of 18 or more contiguous nucleotides of the target gene in either anti-sense or sense orientation.
  • tobacco plants were treated with (a) a topically applied surfactant solution for conditioning of the plant to permeation by polynucleotides and (b) a composition including topically applied DNA oligonucleotides or polynucleotides having at least one strand including at least one segment of 18 or more contiguous nucleotides of the target gene in either anti-sense or sense orientation, whereby systemic regulation or suppression of the target gene (a phytoene desaturase, “PDS”) was achieved.
  • PDS phytoene desaturase
  • the target gene used was a Nicotiana benthamiana phytoene desaturase (SEQ ID NO:2), shown in FIG. 10 ; the segment consisting of nucleotides 421-1120 of SEQ ID NO:2 (underlined text in FIG. 10 ) was used to design a 700-mer dsRNA polynucleotide (“PDS 700-mer”) and the segment consisting of nucleotides 914-1113 of SEQ ID NO:2 (bolded underlined text in FIG. 10 ) was used to design a 200-mer dsRNA polynucleotide (“PDS 200-mer”). Sequences of other polynucleotides or oligonucleotides used in the treatments are listed in Table 3.
  • FIG. 10 The target gene used was a Nicotiana benthamiana phytoene desaturase (SEQ ID NO:2), shown in FIG. 10 ; the segment consisting of nucleotides 421-1120 of SEQ ID NO:2 (underlined text in
  • FIG. 11 schematically depicts the location of the sequences of these oligonucleotides and polynucleotides in relation to the phytoene synthase (SEQ ID NO:2) sequence.
  • Non-plant sequences obtained from corn rootworm (“CRW”), SEQ ID NOs:27, 28, 29, and 30 were used as non-homologous controls.
  • FIG. 12A illustrates results of an assay where a 200-mer dsRNA polynucleotide with an RNA sequence corresponding to the “PDS 200-mer” segment (nucleotides 914-1113 of SEQ ID NO:2) and a combination of single-stranded DNA oligonucleotides and polynucleotides (SEQ ID NOs:16, 17, 20, 21, 24, 25, and 26) were separately applied to tobacco plants.
  • the 200-mer dsRNA polynucleotide was applied at a concentration of 0.6 microM. Bleaching of apical leaves was observed after topical treatment with the polynucleotides and oligonucleotides, indicating systemic regulation or suppression of the target phytoene desaturase gene.
  • FIG. 12B illustrates results of northern blot analysis of RNA isolated from Nicotiana benthamiana plants treated with buffer (control), the 200-mer dsRNA polynucleotide, and the ssDNA oligonucleotides. Also shown is RNA isolated from plants that had been stressed by being kept at 4 degrees Celsius and in the dark overnight prior to treatment with the 200-mer dsRNA polynucleotides.
  • FIG. 13 illustrates phenotypes observed at day 12 after treatment in another assay of the effect from twelve combinations of polynucleotides or oligonucleotides (see Table 4).
  • Table 4 also lists observations of visible bleaching of the plants at day 5 after treatment and the results of chlorophyll measurements taken at days 7 and 12 after treatment. Chlorophyll measurements are an indication of suppression of the target gene phytoene desaturase, and measurements were taken at 6 spots on the apical area, focussing on visibly bleached leaves or (in plants without visible bleaching) on leaves in equivalent locations on the plants; lower chlorophyll measurement values indicate suppression of phytoene desaturase.
  • anti-sense oligonucleotides with the T7 promoter as well as anti-sense oligonucleotides without the T7 promoter (treatment 8) both provided strong bleaching, indicating strong systemic regulation of the target phytoene desaturase gene.
  • Table 5 shows six polynucleotides: a 40-mer segment (“PDS 40-mer sense ssDNA”, SEQ ID NO:31) consisting of the 5′-most 40 nucleotides of the “PDS 700-mer” (nucleotides 1081-1120 of SEQ ID NO:2), and four anti-sense single-stranded DNA polynucleotides and one sense single-stranded DNA polynucleotide synthesized based on the “PDS 40-mer sense ssDNA” sequence (SEQ ID NO:31).
  • FIG. 14 illustrates results of topical treatment of tobacco plants with the polynucleotides and oligonucleotides.
  • PDS 700-mer dsRNA 700-mer dsRNA polynucleotide
  • PDS T7 anti-sense previously assayed PDS anti-sense 22-mer oligonucleotides with a T7 promoter
  • PDS anti-sense 22-mer oligonucleotides without a T7 promoter SEQ ID NOs:22 and 23
  • results of another assay are shown in FIG. 15 , strong bleaching of apical leaves indicating systemic regulation or suppression of the target gene phytoene desaturase was observed after topical treatment with the PDS 21-mer anti-sense ssDNA (SEQ ID NO:34, “21 nt PDS anti-sense”) or with previously assayed PDS anti-sense 22-mer oligonucleotides without a T7 promoter (SEQ ID NOs:22 and 23) (“PDS anti-sense”). Little or no visible bleaching of apical leaves was observed after topical treatment with the buffer only (“control: buffer”), or after topical treatment with PDS 21-mer sense ssDNA (SEQ ID NO:36, “21 nt PDS sense”).
  • This example illustrates treatment of growing plants with a topically applied composition for inducing systemic silencing of a target gene in a plant including (a) an agent for conditioning of a plant to permeation by polynucleotides and (b) polynucleotides including at least one polynucleotide strand including at least one segment of 18 or more contiguous nucleotides of the target gene in either anti-sense or sense orientation. More specifically, this example demonstrates the target specificity (sequence specificity) of the polynucleotides.
  • Nicotiana benthamiana phytoene desaturase has the sequence ATGCCCCAAATCGGACTTGTATCTGCTGTTAATTTGAGAGTCCAAGGTAATTCAGCTTATCTTTGGA GCTCGAGGTCTTCGTTGGGAACTGAAAGTCAAGATGTTTGCTTGCAAAGGAATTTGTTATGTTTTG GTAGTAGCGACTCCATGGGGCATAAGTTAAGGATTCGTACTCCAAGTGCCACGACCCGAAGATTG ACAAAGGACTTTAATCCTTTAAAGGTAGTCTGCATTGATTATCCAAGACCAGCTAGACAATACA GTTAACTATTTGGAGGCGGCGTTATTATCATCATCATCGTTTCGTACTTCCTCACGCCCAACTAAACCAT TGGAGATTGTTATTGCTGGTGCAGGTTTGGGTGGTTTGTCTACAGCAAAATATCTGGCAGATGCTG GTCACAAACCGATATTGCTGGAG GCAAGAGATGTCCTAGGTGGGAAGGTAGCTGCATGGAAAGAT GATGATGGAGATTGGTACGAGACTGGGT
  • This example describes use of a topically applied composition including at least one polynucleotide strand including at least one segment of 18 or more contiguous nucleotides of a target gene in either anti-sense or sense orientation to induce systemic silencing of a target gene in a plant. More specifically this example demonstrates using a single treatment with a phytoene desaturase (PDS) oligonucleotide to induce systemic silencing in different plant organs including leaves, stems, and flowers.
  • PDS phytoene desaturase
  • Nicotiana benthamiana Four-week old tobacco ( Nicotiana benthamiana ) plants were used in all treatments. Two fully expanded leaves (one cotyledon, one true leaf) were conditioned by dipping into freshly made surfactant solution (0.1% Silwet L-77 in double-distilled water) for a few seconds and allowed to dry for 15-30 minutes.
  • surfactant solution 0.1% Silwet L-77 in double-distilled water
  • ssDNA 22-mer oligonucleotide with the sequence GGCAGTACAATTAAAGGAGATG (SEQ ID NO:39), corresponding to the nucleotides at positions 1099-1120 of Nicotiana benthamiana phytoene desaturase (SEQ ID NO:2) was applied as a 25 micromolar solution in 0.01% Silwet L-77 in 5 millimolar sodium phosphate buffer, pH 6.8 to the top surface of each conditioned leaf for a total of 40 microliters (1 nanomole oligonucleotide) per plant. Control plants were treated with the Silwet solution without the DNA oligonucleotide. Plants were observed for bleaching 3 days post-treatment. Apical leaves, stems, and flowers of plants treated with the ssDNA oligonucleotide all displayed bleaching indicating systemic silencing of PDS ( FIG. 18A ).
  • tobacco plants were conditioned by dipping in 0.1% Silwet L-77 in double-distilled water, allowed to dry for 15-30 minutes, and treated with the PDS ssDNA 22-mer (SEQ ID NO:39) applied as a 25 micromolar solution in 0.01% Silwet L-77 in 5 millimolar sodium phosphate buffer, pH 6.8 to the top surface of each conditioned leaf for a total of 40 microliters (1 nanomole oligonucleotide) per plant.
  • PDS ssDNA 22-mer SEQ ID NO:39
  • This example illustrates methods and topically applied compositions for inducing systemic silencing including the use of agents for conditioning of a plant to permeation by polynucleotides. More specifically, this example describes use of polynucleotides of the invention to control herbicide-resistant Palmer amaranth.
  • EPSPS 5-enolpyruvylshikimate-3-phosphate synthase
  • dsRNA designed to silence EPSPS followed by treatment with glyphosate
  • EPSPS 5-enolpyruvylshikimate-3-phosphate synthase
  • Palmer amaranth plants having high copy numbers of EPSPS i. e., 30 or more copies of EPSPS
  • glyphosate resistant high-copy Palmer amaranth using treatments similar to those described in Example 1 but where either dose of dsRNA was increased up to ten-fold (i.
  • Step 1 EPSPS Palmer EPSPS dsRNA amaranth Copy Experiment relative dsRNA delivery line number number concentration vehicle Step 2 Step 3* R31 35 1 10X 0.1% tallowamine 1% Silwet L-77 4x WeatherMAX surfactant + 10% (48 h) glycerol 2 10X 2% ammonium 1% Silwet L-77 4x WeatherMAX sulfate + 0.1% (48 h) tallowamine surfactant + 10% glycerol 3 Buffer only 2% ammonium 1% Silwet L-77 4x WeatherMAX (control) sulfate + 0.1% (48 h) tallowamine surfactant + 10% glycerol Step 2 Palmer EPSPS EPSPS dsRNA dsRNA amaranth Copy Experiment relative delivery line number number Step 1 concentration vehicle Step 3* R34 57 4 — 10X 1% Silwet L-77 + 4x WeatherMAX 2% (48 h) ammonium sulfate
  • This example illustrates methods and topically applied compositions for inducing systemic silencing including the use of agents for conditioning of a plant to permeation by polynucleotides.
  • RNAs identified through small RNA sequencing were found to be abundant in and unique to Palmer amaranth plants that had been treated with four oligonucleotide-size “short” EPSPS dsRNA molecules as described in Example 1. These two small RNAs were respectively mapped to nucleotide positions 743-764 and 566-585 of the full-length EPSPS having the sequence shown in FIG. 20 (SEQ ID NO:40).
  • short dsRNA-5 25 nucleotide long oligonucleotide-size “short” dsRNA molecules were designed with an anti-sense strand that is capable of hybridizing to the mRNA transcribed from the Palmer amaranth EPSPS gene at nucleotide positions 743-767 (“short dsRNA-5”) and 564-588 (“short dsRNA-6”), as indicated by the italicized underlined nucleotides in SEQ ID NO:40 shown in FIG.
  • This example illustrates methods and topically applied compositions for inducing systemic silencing including the use of agents for conditioning of a plant to permeation by polynucleotides. More specifically, this example describes use of salicylic acid and polynucleotides.
  • Salicylic acid induces virus resistance in tobacco; see, e. g., Chivasa et al. (1997) Plant Cell, 19:547-557. Glyphosate-resistant Palmer amaranth plants having 49 or 63 copies EPSPS were pretreated with 15 millimolar SA.
  • a solution of the four oligonucleotide-size “short” EPSPS dsRNA molecules (described in Example 1) was applied by hand at 1, 5, or 24 hours after treatment with SA, followed 72 hours later by spraying with glyphosate (1682 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide). No improvement of the effects of the dsRNAs and glyphosate activity (estimated by observing plant growth measured as plant height) was observed for any of the SA treatments at 7 days after glyphosate treatment.
  • This example illustrates methods and topically applied compositions for inducing systemic silencing including the use of agents for conditioning of a plant to permeation by polynucleotides. More specifically, this example describes variations in the order and timing of application of polynucleotides and surfactant solution.
  • This example illustrates methods and topically applied compositions for inducing systemic silencing including the use of agents for conditioning of a plant to permeation by polynucleotides. More specifically, this example describes application of polynucleotides of the invention by low-volume spray and the use of a silicone surfactant and ammonium sulfate.
  • dsRNA a solution of the four oligonucleotide-size “short” EPSPS dsRNA molecules described in Example 1
  • glyphosate 1682 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide
  • the dsRNA solution contained equal amounts of the four oligonucleotide-size “short” EPSPS dsRNA molecules described in Example 1 in buffer at a “4 ⁇ ” dose (3.2 nanomoles per plant); the buffer consisted of 10 millimolar sodium phosphate and 0.01% (v/v) Silwet L-77 organosilicone surfactant in diethylpyrocarbonate (DEPC) water (Omega Bio-Tek) and adjusted to pH 6.8; and herbicide was a glyphosate herbicide applied at 840 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide at a rate of 159 liters/acre. Results are provided in Table 7.
  • Assays 1 and 2 These assays were carried out on glyphosate-resistant Palmer amaranth grown from seeds obtained from a soil sample from a farm location with known glyphosate-resistant Palmer amaranth stands. For assay 1, ten plants per treatment were treated as follows: (1) spraying 1% Silwet L-77; (2) spraying 2 milliliters of the dsRNA solution; and (3) spraying glyphosate. For assay 2, eighteen plants per treatment were treated using the same procedure as in assay 1.
  • Assay 3 This assay compared treatments applied at different developmental stages and used seedlings grown from Palmer amaranth seeds from a Macon County, Ga. site and selected for glyphosate resistance.
  • the buffer included 2% ammonium sulfate. Twelve small (3-leaf stage) or twelve large (5-leaf stage) seedlings per treatment were treated as follows: (1) spraying 1% Silwet L-77; (2) spraying 2 milliliters of the dsRNA solution; and (3) spraying glyphosate. This treatment provided better control (killed more plants) on small seedlings as compared to the larger seedlings.
  • the dsRNA treatment killed or stunted more glyphosate-resistant plants than treatment with buffer and herbicide achieved, although at 16 days after treatment not all dsRNA-treated plants were killed.
  • Assays 4 and 5 These assays used Palmer amaranth plants grown from seeds in soil from a Pemiscot, Mo. farm.
  • the buffer included 2% ammonium sulfate. Eleven small (3-leaf stage) seedlings per treatment were treated as follows: (1) spraying 1% Silwet L-77; (2) spraying 2 milliliters of the dsRNA solution; and (3) spraying glyphosate. For assay 5, twelve plants per treatment were treated using the same procedure as in assay 4.
  • Assay 6 This assay used Palmer amaranth plants grown from seeds in soil from the “Ivy2” farm. The buffer included 2% ammonium sulfate. Eighteen small (3-leaf stage) seedlings per treatment were treated as follows: (1) spraying 1% Silwet L-77; (2) applying 2 milliliters of the dsRNA solution, either by hand or by spraying; and (3) spraying glyphosate. In this assay the method of application (hand drop or spraying) provided similar results.
  • Assay 7 This assay used 3- to 4-leaf stage Palmer amaranth seedlings grown from F3 seeds selected for glyphosate resistance and more resistant to glyphosate than plants in assays 1-6.
  • the buffer included 2% ammonium sulfate. Eighteen plants per treatment were treated as follows: (1) spraying 1% Silwet L-77; (2) spraying 2 milliliters of the dsRNA solution; and (3) spraying glyphosate.
  • This example illustrates methods and topically applied compositions for inducing systemic silencing including the use of agents for conditioning of a plant to permeation by polynucleotides.
  • the dsRNA solution contained equal amounts of the four oligonucleotide-size “short” EPSPS dsRNA molecules described in Example 1 at a “10 ⁇ ” dose (8 nanomoles per plant) in a solution containing either 0.2% tallowamine surfactant and 2% ammonium sulfate (identified in FIG.
  • tallowamine/AMS transfection reagents
  • transfection reagents (a) a polyamine (JetPRIMETM, Polyplus-transfection SA, Illkirch, France), (b) a magnetic nanoparticle (SilenceMag, OZ Biosciences, Marseille, France), (c) a peptide (N-TERTM Nanoparticle, Sigma-Aldrich, St. Louis, Mo.), (d) a lipid (siPORTTM NeoFXTM, Ambion, Foster City, Calif.), or (e) a cationic lipid/polymer (TransIT®, Mirus Bio, Madison, Wis.).
  • Plants were treated as follows: (1) hand-applying dsRNA solution; (2) spraying 1% Silwet L-77; and (3) spraying with glyphosate applied at 840 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide at a rate of 159 liters/acre.
  • This protocol when used with dsRNA in the tallowamine surfactant/ammonium sulfate solution kills glyphosate-resistant Palmer amaranth having 35 copies EPSPS. Results are depicted in FIG. 22 .
  • compositions including topically applied polynucleotides for inducing systemic silencing in a plant More specifically, this example describes use of different types of polynucleotides for inducing systemic silencing.
  • Sense single-stranded DNAs ssDNAs
  • ssRNAs anti-sense single-stranded RNAs corresponding to the Palmer amaranth EPSPS gene at positions 14-38, positions 153-177, 345-369, and 1105-1129 (indicated by underlined nucleotides in FIG. 1 ) were purchased from Integrated DNA Technologies.
  • the sense ssDNAs and anti-sense ssRNAs were annealed by heating equal moles of mixed ssDNAs and ssRNAs at 95 degrees Celsius for 5 minutes and slowly cooled over 1.5-2 hours to room temperature to yield the DNA/RNA hybrids.
  • 16-copy glyphosate-resistant Palmer amaranth plants were used in the assays which used this procedure: (1) spraying 1% Silwet L-77; (2) hand-applying on four mature leaves of each plant a total of 0.8 nanomoles of either the Palmer EPSPS dsRNAs (as described in Example 1) or of the Palmer EPSPS DNA/RNA hybrids; and (3) spraying with glyphosate applied at 840 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide at a rate of 159 liters/acre.
  • Results are depicted in FIG. 23 . Seven days after the herbicide spraying, 4 out of 6 dsRNA-treated plants were dead and the remaining 2 were dying, whereas plants sprayed with the DNA/RNA hybrid were stunted in growth (glyphosate injury) compared to the control.
  • compositions including topically applied polynucleotides for inducing systemic silencing in a plant More specifically, this example describes use of different types of polynucleotides for inducing systemic silencing.
  • This example illustrates methods using compositions including topically applied polynucleotides for inducing systemic silencing in a plant. More specifically, this example describes selection of a polynucleotide sequence for inducing systemic silencing in a plant.
  • dsRNAs of approximately 250 by each and having one strand of the dsRNA corresponding to the EPSPS tiled DNA sequences of SEQ ID NOS:41-52 (Table 8) were designed to cover in a tiling fashion the full coding sequence and part of the 5′ and 3′ untranslated regions of the Palmer amaranth EPSPS gene, as depicted in FIG. 25A .
  • the four oligonucleotide-size “short” EPSPS dsRNA molecules as described in Example 1 and FIG. 1 are located in the tiling segments 2, 3, 4, and 8 respectively, and are shown as light grey bars within those segments.
  • the polynucleotides were synthesized in vitro transcription using a pBR322 vector with the EPSPS polynucleotides inserted at EcoRI and BamHI cloning sites; plasmid DNA was isolated with Qiagen Maxi prep kits and digested with EcoRI and BamHI restriction enzymes. The digested DNA solution was used in the treatment of the plants without further purification.
  • Glyphosate-resistant Palmer amaranth plants having 16 copies of EPSPS were treated as follows: spraying with 1% Silwet L-77; (2) hand application of a dsRNA solution (containing polynucleotides selected from the twelve tiling segments or the four “short” dsRNA molecules described in Example 1 at the rate of 0.01 nanomole DNA/plant) or buffer as a control; and (3) 48 hours later spraying with glyphosate applied at 840 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide at a rate of 159 liters/acre. Above-ground height of the treated plants was observed 11 days after herbicide treatment; plants that were dead or dying were assigned a height of zero. Results are depicted in FIGS.
  • the dsRNA polynucleotides combinations showing the greatest efficacy in this assay included the four “short” dsRNA molecules described in Example 1, the combination of tiling segments 2, 5, 8, and 11, and the combination of tiling segments 7, 8, and 9.
  • compositions including topically applied polynucleotides for inducing systemic silencing in a plant. More specifically, this example describes topical application of polynucleotides following application of herbicide to a plant.
  • glyphosate-resistant Palmer amaranth plants having 16 copies of EPSPS were sprayed with glyphos ate applied at 840 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide at a rate of 159 liters/acre.
  • the plants were treated by spraying with 1% Silwet L-77.
  • the plants were treated by hand application of either 0.8 nanomoles (“1 ⁇ ”) per plant of the four oligonucleotide-size “short” EPSPS dsRNA molecules as described in Example 1 in buffer containing 2% ammonium sulfate or buffer containing 2% ammonium sulfate.
  • This example illustrates methods using compositions including topically applied polynucleotides for inducing systemic silencing in a plant. More specifically, this example describes a single-step topical application of a single composition including polynucleotides, surfactant, and herbicide for controlling herbicide-resistant weeds.
  • This assay was carried out on a field population of glyphosate-resistant Palmer amaranth plants that were known to have very high copy numbers of EPSPS (plants from this study site have been reported to have from 5 to more than 160 copies of EPSPS by Gaines et al. (2010) Proc. Natl. Acad. Sci. USA, 107:1029-1034).
  • the polynucleotides used in this assay were an equimolar mixture of the four oligonucleotide-size “short” EPSPS dsRNA molecules as described in Example 1.
  • Results are depicted in FIG. 27 . Treating the plants with only glyphosate (applied at 1682 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide at a rate of 159 liters/acre) in a solution that also contained Silwet L-77 and ammonium sulfate resulted in about 70% control (death of plants).
  • the one-step treatment using a composition containing the 20 ⁇ EPSPS dsRNA polynucleotides, surfactant, ammonium sulfate, and herbicide resulted in about 80-85% control of the glyphosate-resistant Palmer amaranth, which is the approximate control rate obtained by spraying with glyphosate applied at 6720 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide at a rate of 159 liters/acre (i. e., at 8 times the standard application rate of about 840 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide at a rate of 159 liters/acre).
  • the one-step treatment using a composition containing the 100 ⁇ EPSPS dsRNA polynucleotides, surfactant, ammonium sulfate, and herbicide resulted in about 90-95% control of the glyphosate-resistant Palmer amaranth, which is the approximate control rate obtained by spraying with glyphosate applied at 13440 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide at a rate of 159 liters/acre (i. e., at 16 times the standard application rate of about 840 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide at a rate of 159 liters/acre).
  • This example illustrates a method for inducing systemic regulation of a target gene in a vegetable plant by topical application to the vegetable of a polynucleotide molecule including a segment with a nucleotide sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target gene or RNA transcribed from the target gene, whereby the molecule permeates the interior of the vegetable plant and induces systemic regulation of the target gene.
  • growing vegetable plants were treated with a topically applied composition for inducing systemic silencing of a target gene in a vegetable or fruit crop plant including (a) an agent for conditioning of a plant to permeation by polynucleotides and (b) polynucleotides including at least one polynucleotide strand including at least one segment of 18 or more contiguous nucleotides of the target gene in either anti-sense or sense orientation.
  • this example demonstrates the use of topically applied polynucleotides to induce systemic silencing of a phytoene desaturase (PDS) gene in a vegetable crop plant, i. e., lettuce ( Lactuca sativa ).
  • PDS phytoene desaturase
  • Polynucleotide single-stranded DNAs of 21-45 nucleotides in length with the following sequences were synthesized: taatacgactcactatagggtttggagcttacccaaATGtac (“HL286”, sense orientation, SEQ ID NO:54), taatacgactcactatagggaggccacgtcagcatttcattgttc (“HL287”, anti-sense orientation, SEQ ID NO:55), ccattcaATGgtgcaggtaaaac (“HL288”, anti-sense orientation, SEQ ID NO:56), catagaATGctccttccactg (“HL289”, anti-sense orientation, SEQ ID NO:57), and caaataaattttgtacatttgggtaagctccaa (“HL290”, anti-sense orientation, SEQ ID NO:58).
  • An ssDNA solution was made with an equal mixture of
  • FIG. 28 depicts the progression of bleaching and death of the lettuce plants treated with 1 nanomole ssDNA per plant at (from top to bottom) 37, 46, and 60 days after treatment.
  • FIG. 29A depicts the systemic silencing evidenced by bleaching observed at 4 or 12 days after topical treatment with the polynucleotides.
  • FIG. 29B depicts the systemic silencing evidenced by bleaching observed at 4 after topical treatment with the anti-sense ssDNAs.
  • This example illustrates an aspect of the invention.
  • growing plants were treated with a topically applied composition for inducing systemic silencing of a target gene in a plant including (a) an agent for conditioning of a plant to permeation by polynucleotides and (b) polynucleotides including at least one polynucleotide strand including at least one segment of 18 or more contiguous nucleotides of the target gene in either anti-sense or sense orientation.
  • PDS phytoene desaturase
  • Tomato PDS has the sequence
  • a 2.5 micromolar dsRNA solution was made with the 201 nucleotide dsRNA polynucleotide (SEQ ID NO:60) in 0.01% Silwet L-77 in 5 millimolar sodium phosphate buffer, pH 6.8.
  • FIG. 30 depicts the systemic silencing of the target gene PDS as evidenced by bleaching of the dsRNA-treated plants 30 days after topical treatment. The dsRNA-treated plants were severely stunted, compared to control plants.
  • This example illustrates an improvement to herbicidal compositions adapted for topical coating onto the exterior surface of a growing plant
  • the plant lethal agent includes polynucleotides having a sequence essentially identical or complementary to sequences of one or more plant genes or sequence of transcribed DNA from the plant genes.
  • the polynucleotides effect systemic suppression of the plant gene in plant organs or tissues other than those that received the topical polynucleotide application.
  • this example illustrates an herbicidal composition adapted for topical coating onto the exterior surface of a growing plant comprising surfactant and at least one plant lethal agent including combinations of polynucleotides having sequence targeting the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene, a transcription initiation factor (TIF), and DNA-dependent ATPase (ddATPase) in Palmer amaranth.
  • EPSPS 5-enolpyruvylshikimate-3-phosphate synthase
  • TEZ transcription initiation factor
  • ddATPase DNA-dependent ATPase
  • the herbicidal composition includes at least one of the following 21-base-pair double-stranded RNA polynucleotides:
  • nDsRNA1 sense strand (SEQ ID NO: 63) CUACCAUCAACAAUGGUCC and anti-sense strand (SEQ ID NO: 64) GGACACCAUUGUUGAUGGUAG (2)
  • nDsRNA3 sense strand (SEQ ID NO: 65) GUCGACAACUUGCUGUAUAGU and anti-sense strand (SEQ ID NO: 66) ACUAUACAGCAAGUUGUCGAC
  • nDsRNA4 sense strand (SEQ ID NO: 67) GGUCACCUGGACAGAGAAUAG and anti-sense strand (SEQ ID NO: 68) CUAUUCUCUGUCCAGGUGACC (4)
  • nDsNA5 sense strand (SEQ ID NO: 69) AAUGCCAGAUGUUGCUAUGAC and anti-sense strand (SEQ ID NO: 70) GUCAUAGCAACAUCUGGCAUU
  • the herbicidal composition includes a mixture of all four of the above dsRNA polynucleotides having SEQ ID NOS: 63-70.
  • the herbicidal composition includes single-stranded DNA polynucleotides with deoxyribonucleotide sequences corresponding to one or more of the dsRNA sequences SEQ ID NOS: 63-70.
  • the herbicidal composition includes RNA/DNA hybrids with nucleotide sequences corresponding to one or more of the dsRNA sequences SEQ ID NOS: 63-70.
  • the herbicidal composition includes dsRNA polynucleotides where the 2′ hydroxyls are methylated for stability.
  • the herbicidal composition includes a surfactant such as Silwet L-77 (or other effective surfactants such as those provided in Example 36).
  • the herbicidal composition can include one or more additives such as a salt, chelating agent, or a humectant (such as those provided in Example 35) to improve herbicidal performance, e. g., by enhancing transfer of the polynucleotide into the interior of the plant, enhancing efficacy of the polynucleotides, or potentiating the herbicidal activity of the non-polynucleotide herbicide.
  • the herbicidal composition includes polynucleotides designed to regulate multiple genes in the plant.
  • the herbicidal composition includes polynucleotides having sequence essentially identical or complementary to the sequence of a second gene or to the sequence of RNA transcribed from the second gene, wherein the regulation of the second gene provides a synergistic enhancement of the herbicidal activity of the composition.
  • the herbicidal composition includes polynucleotides having sequence essentially identical or complementary to the sequence of the endogenous Palmer amaranth 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene or to the sequence of RNA transcribed from the endogenous EPSPS gene as well as polynucleotides having sequence essentially identical or complementary to the sequence of the endogenous Palmer translation initiation factor (TIF) gene or to the sequence of RNA transcribed from the endogenous TIF gene.
  • Translation initiation factor (TIF) is a nuclear-encoded chloroplast protein that is essential for initiating protein synthesis and is expressed throughout a plant.
  • TIF sequences were identified from Palmer amaranth ( Amaranthus palmeri ); one TIF gene was identified to have the sequence of SEQ ID NO:71. Examples of polynucleotides for suppression of this TIF gene in Amaranthus palmeri are listed in Table 10.
  • the herbicidal composition includes a mixture of at least two of the above EPSPS dsRNA polynucleotides having SEQ ID NOS: 63-70 and also at least one polynucleotide having sequence essentially identical or complementary to the sequence of the endogenous Palmer translation initiation factor (TIF) gene or to the sequence of RNA transcribed from the endogenous TIF gene, such as those provided in Table 10.
  • TIF Palmer translation initiation factor
  • the herbicidal composition includes a mixture of the four EPSPS dsRNA polynucleotides having SEQ ID NOS: 63-70 and a 160 base-pair TIF double-stranded RNA polynucleotide having the sense sequence of UUCGAGUAAUGGGAAAUUGGAUAAUGUAGAGGAGAGGAAGAAGGUUAUUGAU UCAUUGGAUGAGGUAUUAGAAAAGGCCGAGAGAUUAGAAACGGCGAACUUAC AAGCAGAUAAUAGAAAGGAUAGCACAAAUGUAAAUAAACCGUCUCCGAGUGU AAGU (SEQ ID NO.
  • the polynucleotides are designed to regulate multiple target genes, resulting in a synergistic effect on herbicide activity.
  • a synergistic effect on herbicide activity was obtained by treatment of a plant with polynucleotides designed to suppress a translation initiation factor (TIF) and 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) followed by treatment with the non-polynucleotide herbicide glyphosate.
  • TEZ translation initiation factor
  • EPSPS 5-enolpyruvylshikimate-3-phosphate synthase
  • polynucleotides listed in Table 11 were produced by synthesis or by in vitro transcription.
  • ddATPase Palmer/DNA-dependent A Sense: ATPase (ddATPase) dsRNA GAUCACAAAUUUGCCGGUUUAUGAUCAAAUACGGAACAUAAGACA (168-mer) synthesized via GAUACACUUGAACACCAUGAUUCGCAUUGGGGGUGUGGUUACUCG in vitro T7 transcription UCGUUCUGGAGUAUUCCCUCAGUUGAUGCAGGUGAAGUAUGACUG CAAUAAAUGUGGGGCUAUCCUGGGUCCCUUUUU (SEQ ID NO.
  • Protocol 1 Apply mixture of polynucleotides in 1% Silwet L-77, 2% ammonium sulfate in 10 (1-step hand) millimolar sodium phosphate buffer, pH 6.8 (or control buffer solution of 1% Silwet L-77, 2% ammonium sulfate in 10 millimolar sodium phosphate buffer, pH 6.8) by hand pipetting 2. 48 or 72 hours later, spray glyphosate (“2X Wmax” or 1682 g acid equivalent per hectare of Roundup ® WeatherMAX ® brand herbicide) by regular sprayer (10 gallons/acre) 2 1.
  • 2X Wmax or 1682 g acid equivalent per hectare of Roundup ® WeatherMAX ® brand herbicide
  • spray glyphosate (“2X Wmax” or 1682 g acid equivalent per hectare of Roundup ® WeatherMAX ® brand herbicide) by regular sprayer (10 gallons/acre) 5 Spray mixture of polynucleotides in 1% Silwet L-77, 2% ammonium sulfate in 10 millimolar (tank mix) sodium phosphate buffer, pH 6.8 containing glyphosate at 1682 g acid equivalent per hectare of Roundup ® WeatherMAX ® brand herbicide (or control buffer solution of 1% Silwet L-77, 2% ammonium sulfate in 10 millimolar sodium phosphate buffer, pH 6.8 containing glyphosate at 1682 g acid equivalent per hectare of Roundup ® WeatherMAX ® brand herbicide) by Milli sprayer.
  • Double-stranded 25-mer RNA polynucleotide sequences for suppression of the TIF gene in Amaranthus palmeri were designed as listed in Table 14.
  • TIF_dsRNA1 antisense 115 5′-UUUUCUAAUACCUCAUCCAAUGAAU-3′ sense: 116 5′-AUUCAUUGGAUGAGGUAUUAGAAAA-3′
  • TIF_dsRNA2 antisense 117 5′-UAUCUGCUUGUAAGUUCGCCGUUUC-3′ sense: 118 5′-GAAACGGCGAACUUACAAGCAGAUA-3′
  • TIF_dsRNA3 antisense 119 5′-GGAGACGGUUUAUUUACAUUUGUGC-3′ sense: 120 5′-GCACAAAUGUAAAUAAACCGUCUCC-3′
  • TIF_dsRNA4 antisense 121 5′-UAUUUACAGGUUUACCAUUGGUUGA-3′ sense: 122 5′-UCAACCAAUGGUAAACCUGUAAAUA-3′
  • TIF 25-mer dsRNA polynucleotides were tested on both high (112) copy and low (16) copy EPSPS glyphosate-resistant Palmer amaranth.
  • High-copy plants were treated with a mixture of 4 short EPSPS dsRNAs (short dsRNA-1, short dsRNA-3, short dsRNA-4, as described in Example 1 and IDT [5] (SEQ ID NOS:91-92 as described in Table 11) at 11.5 grams/acre and one individual TIF dsRNA at 5.8 grams/acre, or with each individual TIF 25-mer dsRNA at 5.8 grams/acre; polynucleotide solutions were formulated in 10 millimolar sodium phosphate buffer (pH 6.8) containing 2% ammonium sulfate and 1% Silwet L-77. Thirty minutes after polynucleotide treatment, plants were either sprayed with glyphosate (1682 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide) or not.
  • glyphosate (1682 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide
  • Results are depicted in FIGS. 31 and 32 and show that the TIF polynucleotides enhance the activity of the EPSPS polynucleotides and that the TIF polynucleotides have herbicidal activity on their own.
  • aspects of the invention include polynucleotide compositions and methods of use for potentiating the activity of a non-polynucleotide herbicide in a plant.
  • a polynucleotide composition designed to regulate an herbicide target gene, or an herbicide deactivation gene, or a stress response gene, or a combination of such target genes is applied to a weed or to a volunteer plant, concurrently or followed or preceded by application of a non-polynucleotide herbicide (typically a conventional chemical herbicide), resulting in potentiation of the activity of the non-polynucleotide herbicide.
  • a non-polynucleotide herbicide typically a conventional chemical herbicide
  • a polynucleotide composition with a non-polynucleotide herbicide provides a synergistic effect, i. e., the herbicidal effect of the combination is greater than the sum of the herbicidal effect of the polynucleotide composition and the herbicidal effect of the non-polynucleotide herbicide.
  • Target gene glyphosate 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) Lactofen, flumioxazin, etc protoporphyrinogen oxidase (PPO) Mesotrione, isoxaflutole 4-hydroxyphenyl-pyruvate-dioxygenase (HPPD) Quizalofop, clethodim acetyl coenzyme A carboxylase (ACCase) Norflurazone, clomazone phytoene desaturase (PDS) glufosinate glutamine synthase (GS) Rimsulfuron, chlorsulfuron acetolactate synthase (ALS) Atrazine, diuron, D1 protein of photosystem II (PSII) bromoxynil, metribuzin Dinitroaniline, tubulin pendimethalin Dichlobenil, isoxaben Cellu
  • EPSPS glyphosate 5-eno
  • Target gene herbicide deactivation gene
  • Acetochlor glutathione S-transferase (GST) metolachlor
  • GST glutathione S-transferase
  • This example illustrates a method for inducing systemic regulation of a target endogenous gene in a growing plant including topically coating onto leaves of the growing plant polynucleotides having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either the target endogenous gene or messenger RNA transcribed from the target endogenous gene, whereby the polynucleotides permeate the interior of the growing plant and induce systemic regulation of the target endogenous gene.
  • Double-stranded RNA or anti-sense ssDNA polynucleotides were designed for the herbicide targetted genes 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), phytoene desaturase (PDS), protoporphyrin IX oxygenase (PPO), phenylalanine ammonia lyase (PAL), hydroxyphenylpyruvate dioxygenase (HPPD), acetyl-coenzyme A carboxylase (ACCase), acetolactate synthase (ALS), and glutamine synthase (GS).
  • EPSPS 5-enolpyruvylshikimate-3-phosphate synthase
  • PDS phytoene desaturase
  • PPO protoporphyrin IX oxygenase
  • PAL phenylalanine ammonia lyase
  • HPPD hydroxyphenylpyruvate dioxygenase
  • PPO_OLIGO5 21 CAGCAATGGCGGTAGGTAACA 129
  • PPO_OLIGO6 21 GCAATTGCCCGAATCCTTTTA 130
  • PPO_OLIGO7 21 TAGCTCAATATCAAGGTCCTA
  • PPO_OLIGO8 21 TCATAAGCACCCTCTATACAC
  • PAL PAL_OLIGO1 21 TTCTTAACCTCGTCGAGATG
  • HPPD_OLIGO5 21 CGATGTAAGGAATTTGGTAAA 145
  • HPPD_OLIGO6 21 CGAGGGGATTGCAGCAGAAGA 146
  • HPPD_OLIGO7 21 GTAGGAGAATACGGTGAAGTA 147
  • HPPD_OLIGO8 21 GACCCCAAGAAAATCGTCTGC 148
  • ACCase ACCA_OLIGO1 20 GTCTTACAAGGGTTCTCAA 149
  • Topical anti-sense ACCA_OLIGO2 21 ATCTATGTTCACCTCCCTGTG 150 DNA caused ACCA_OLIGO3 21 ATAAACCATTAGCTTTCCCGG 151 stunting of plant ACCA_OLIGO4 21 TTTATTGGAACAAGCGGAGTT 152 growth.
  • ACCA_OLI005 21 TATAGCACCACTTCCCGATAG 153 ACCA_OLIGO6 21 GCACCACGAGGATCACAAGAA 154 ACCA_OLIGO7 21 CCACCCGAGAAACCTCTCCAA 155 ACCA_OLIGO8 21 CAGTCTTGACGAGTGATTCCT 156 ALS ALS-OLIGO1 22 GTTCTTCAGGGCTAAATCGGGA 157 No significant ALS-OLIGO2 22 GTTCAAGAGCTTCAACGAGAAC 158 phenotype ALS-OLIGO3 22 ATACAAACTCCAACGCGTCCAG 159 ALS-OLIGO4 22 CTCTTGGAAAGCATCAGTACCA 160 ALS-OLIGO5 22 CTAGAAAGATACCCACCCAATT 161 ALS-OLIGO6 22 ACTAGAATTCAAACACCCACCC 162 ALS-OLIGO7 22 TTTCTGCTCATTCAACTCCTCC 163 ALS-OLIGO8 22 TATGTATGCCCGGTTAGCTT 164 GS GS
  • ssDNA polynucleotides that target the enzymes 4-hydroxyphenylpyruvate (HPPD) and protoporphyrinogen oxidase (PPO), and a transcription initiation factor (TIF), and their effect on the herbicide activity when used in combination with the herbicides mesotrione, fomesafen, and atrazine in Palmer amaranth was investigated.
  • HPPD 4-hydroxyphenylpyruvate
  • PPO protoporphyrinogen oxidase
  • TEZ transcription initiation factor
  • the polynucleotides used in this experiment were 8 HPPD anti-sense ssDNA oligonucleotides (SEQ ID NOS:141-148), 8 PPO anti-sense oligonucleotides (SEQ ID NOS:125-132), and 8 TIF anti-sense ssDNA oligonucleotides (SEQ ID NOS:75-82, see Example 26).
  • Glyphosate-sensitive Palmer amaranth Amaranthus palmeri ) plants were grown in 4-inch square pots with Sun Gro® Redi-Earth seedling mix containing 3.5 kg/cubic meter Osmocote® 14-14-14 fertilizer in a greenhouse with 14 h photoperiod and a daytime temperature of 30 degrees Celsius and night temperature of 20 degrees Celsius. The plants were sub-irrigated as necessary.
  • Plants at 10 to 15 cm height were pre-treated manually with 40 microliters (4 fully expanded mature leaves were treated with 10 microliters of solution per leaf on each plant) of a buffer-surfactant solution (as a control; 0.5% Silwet L-77 and 2% ammonium sulfate), or a buffer-surfactant-ssDNA polynucleotide mixture of the anti-sense oligonucleotides targetting HPPD, PPO, or TIF. Some plants were left untreated and were used as controls.
  • a buffer-surfactant solution as a control; 0.5% Silwet L-77 and 2% ammonium sulfate
  • a buffer-surfactant-ssDNA polynucleotide mixture of the anti-sense oligonucleotides targetting HPPD, PPO, or TIF Some plants were left untreated and were used as controls.
  • a low rate of each herbicide (mesotrione: 13 g per acre, equivalent to 1 ⁇ 8 of the recommended field rate; fomesafen: 16 g per acre, equivalent to 1/22 of the recommended field rate; and atrazine: 170 g per acre, equivalent to 1 ⁇ 8 of the recommended field rate,) was used to be able to detect any improvement of herbicide activity by the oligonucleotide mixture.
  • Plant height was determined at four days after herbicide treatment. Data were collected from one experiment with four replications per treatment. Results (expressed as Palmer amaranth plant height as affected by the buffer-surfactant solution, ssDNA, and herbicide treatment combinations) are presented in Table 19 and FIG. 33 . Plants treated with HPPD anti-sense ssDNA oligonucleotides, PPO anti-sense ssDNA oligonucleotides, and TIF anti-sense ssDNA oligonucleotides showed growth stunting, measuring 125, 153, and 115 mm, respectively, while the plants treated with buffer-surfactant (control) measured 185 mm ( FIG. 33 ).
  • HPPD anti-sense ssDNA oligonucleotides Treatment with HPPD anti-sense ssDNA oligonucleotides, PPO anti-sense ssDNA oligonucleotides, and TIF anti-sense ssDNA oligonucleotides respectively caused a 32%, 18%, and 38% growth reduction relative to the buffer-surfactant control.
  • This example illustrates tested sequences of double-stranded RNA polynucleotides designed for different essential genes to ascertain the effect of the tested sequence on observable phenotype.
  • the tested polynucleotides and resulting phenotype observations are listed in Table 20.
  • Sequence ID NO Phenotype Translation sense 160 UUCGAGUAAUGGGAAAUUGGAUAAUGUA 73 Topical dsRNA initiation GAGGAGAGGAAGAAGGUUAUUGAUUCAU caused stunting of factor (TIF) UGGAUGAGGUAUUAGAAAAGGCCGAGAG plant growth.
  • protease 14 UGCCAUUAGAAGCUUGCCUAGCUAGCUA (UBP) CUCAGCUCCGGAGGAGGUGAUGGACUUC UACAGCACUGCAUUGAAGGCAAAGGCAA CUGCUACAAA anti- 150 UUUGUAGCAGUUGCCUUUGCCUUCAAUG 184 sense CAGUGCUGUAGAAGUCCAUCACCUCCUC CGGAGCUGAGUAGCUAGCUAGGCAAGCU UCUAAUGGCACCCUUGGGCGAACUACUU CACUAGCAUCAAUAUCCUUUCCUUCAGC AUCAGCUUCA Serine sense 155 ACACCUGCCCUAACAUCUCGGGGUUUUC 185 No significant hydroxy- UCGAAGAAGAUUUGUUAAAGUGGCCGA phenotype.
  • This example illustrates polynucleotides which are designed to target a particular low sequence homology region and are useful e. g., for selecting a specific allele of a target gene or a gene of a specific species.
  • Polynucleotides designed to target non-coding sequence are useful in regulating non-coding RNAs that are involved in gene regulations, e. g., regulating non-coding RNAs that are processed to siRNAs in an RNAi-regulated pathway.
  • the promoter sequence used in this alignment is the one with the most 5′ transcription start site.
  • the Nicotiana benthamiana PDS1 and PDS2 genes were found to have low sequence homology in the promoter region but high sequence homology in the coding region.
  • Polynucleotides designed to target different parts of the PDS 1 and PDS2 promoters are listed in Table 21.
  • polynucleotides (1 nanomole/plant of each applied polynucleotide) as listed in Table 21 and illustrated in FIG. 35 were tested on 4-week-old Nicotiana benthamiana plants using a procedure similar to that described in Example 12.
  • Polynucleotide solutions were prepared in 0.01% (v/v) Silwet L-77 and 2% (w/v) ammonium sulfate in 5 millimolar sodium phosphate, pH 6.8.
  • Two fully expanded leaves per plant were dipped into 0.1% Silwet L-77 solution freshly made with ddH2O for a few seconds, and allowed to dry. About 30 minutes later, 20 microliters of polynucleotide solution was applied to each of the two pre-treated leaves.
  • Positive control plants were similarly treated with a DNA oligonucleotide targetting a conserved segment of the coding region of PDS 1 and PDS2; negative control plants were similarly treated with a DNA oligonucleotide designed to silence green fluorescent protein (GFP).
  • GFP green fluorescent protein
  • All six combinations of polynucleotides designed to target the PDS 1 or PDS2 promoter regions induced systemic silencing in the treated plants as evidenced by bleaching.
  • Treatment with either dsRNA or dsDNA polynucleotides of approximately 200 by and targetting the PDS1 or PDS2 promoter regions also induced systemic silencing in the treated plants as evidenced by bleaching.
  • This example illustrates a polynucleotide sequence that regulates gene expression in more than one plant species.
  • Two highly conserved regions in EPSPS sequences from different weed species were identified and shown as the “Region 1” and “Region 2” sequences in Table 23.
  • Table 24 lists 21-, 22-, 24-, 35-, 45-, and 55-mer dsRNA polynucleotide sequences designed based on the EPSPS consensus sequence for region 2,
  • the EPSPS consensus dsRNA polynucleotides were synthesized by in vitro transcription and topically applied as crude RNA preparations. Glyphosate-resistant weeds (16-copy Palmer amaranth and horseweed) were treated with the six individual (21-, 22-, 24-, 35-, 45-, 55-mer) consensus dsRNAs; non-glyphosate-resistant weeds (waterhemp, sicklepod, crabgrass, morning glory, lambsquarter, Euphorbia) were treated with the three individual shorter (21-, 22-, 24-mer) consensus dsRNAs.
  • glyphosate-resistant plants were treated with glyphosate (1682 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide) and non-glyphosate-resistant plants were treated with glyphos ate (105 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide).
  • glyphosate 1682 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide
  • glyphos ate 105 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide.
  • All six EPSPS region 2 consensus dsRNA polynucleotides were found to give 100% control (killed plants) of glyphosate-resistant Palmer amaranth; control Palmer amaranth plants treated with glyphosate alone were not killed.
  • the three shorter (21-, 22-, 24-mer) EPSPS region 2 consensus dsRNA polynucleotides tested individually were found to give 95%, 80% and 65% control (combining killed and injured plants), respectively, of waterhemp; waterhemp plants treated with glyphosate alone gave about 40% control (combining killed and injured plants); and a mixture of all three shorter (21-, 22-, 24-mer) consensus dsRNA polynucleotides gave about the same control as glyphosate alone.
  • the EPSPS region 2 consensus dsRNA polynucleotides did not cause an observable effect on the other weed species (horseweed, sicklepod, crabgrass, morning glory, lambsquarter, euphorbia) tested.
  • This example illustrates use of a topical polynucleotide treatment for transiently silencing a gene in a plant to effect a desired phenotype.
  • Silencing polyphenol oxidase in plant tissues inhibits browning of cut or damaged plant tissues, a valuable trait for fruits and vegetables where resistance to browning is a desirable trait.
  • Anti-sense DNA oligonucleotides with the sequences shown in Table 25 were designed to target three polyphenol oxidase genes (PPO1, PPO2, and PPO3) from lettuce; the underlined text indicates T7 sequence that was included in the anti-sense polynucleotides.
  • Three-week old lettuce plants (variety SVR3603 L4) were treated as follows. Two source leaves (leaves that are older and are ⁇ 60% of their mature size) on each plant were pre-treated with 0.1% (v/v) Silwet-L-77 and allowed to dry ( ⁇ 15 minutes).
  • Control plants were treated either with an unrelated polynucleotide HH02-05 (anti-sense to phytoene desaturase) or with buffer (0.01% (v/v) Silwet L-77 and 2% (w/v) ammonium sulfate in 5 millimolar sodium phosphate, pH 6.8) alone.
  • untreated lettuce leaves i. e., not those treated with the topical polynucleotides
  • Leaves were inspected for central rib browning and photographed every 24 hours. Samples were taken from the remaining plants and frozen for small RNA and mRNA analysis
  • Plants treated with the polyphenol oxidase anti-sense polynucleotides HH07, HH09, and HH11 showed significant reduction in central rib browning after treatment with methyl jasmonate. Plants treated with HH02-05 (anti-sense to phytoene desaturase) as a control showed a small reduction in central rib browning compared to the buffer-treated control.
  • This example illustrates an herbicidal composition adapted for topical coating onto the exterior surface of a growing plant comprising surfactant and at least one plant lethal agent, the improvement wherein the plant lethal agent includes polynucleotides having a sequence essentially identical or complementary to sequence of a plant gene or sequence of the plant gene's transcribed RNA, the polynucleotides effecting systemic suppression of the plant gene.
  • this example illustrates an herbicidal composition adapted for topical coating onto the exterior surface of a growing plant comprising surfactant and at least one plant lethal agent, the improvement wherein the plant lethal agent includes polynucleotides effecting suppression of the endogenous phytoene desaturase (PDS), 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), or ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO) genes from Nicotiana benthamiana.
  • PDS phytoene desaturase
  • EPSPS 5-enolpyruvylshikimate-3-phosphate synthase
  • RuBisCO ribulose-1,5-bisphosphate carboxylase oxygenase
  • An anti-sense polynucleotide with the sequence CATCTCCTTTAATTGTACTGC was designed for the endogenous Nicotiana benthamiana phytoene desaturase (PDS) gene, which has the cDNA sequence fragments ATGCCCCAAATCGGACTTGTATCTGCTGTTAATTTGAGAGTCCAAGGTAATTCAGCTTATCTTTGGA GCTCGAGGTCTTCGTTGGGAACTGAAAGTCAAGATGTTTGCTTGCAAAGGAATTTGTTATGTTTTG GTAGTAGCGACTCCATGGGGCATAAGTTAAGGATTCGTACTCCAAGTGCCACGACCCGAAGATTG ACAAAGGACTTTAATCCTTTAAAGGTAGTCTGCATTGATTATCCAAGACCAGCTAGACAATACA GTTAACTATTTGGAGGCGGCGTTATTATCATCATCGTTTCGTACTTCCTCACGCCCAACTAAACCAT TGGAGATTGTTATTGCTGGTGCAGGTTTGGGTGGTTTGTCTACAGCAAAATATCTG
  • Anti-sense polynucleotides with the sequences CTGTGATCATCATATGTATCA (SEQ ID NO:279), CCTTAACTCTCCAGCTAGCAA (SEQ ID NO:280), CAGCCCGCAAATGTTTCATTC (SEQ ID NO:281), GCCGTCAATGGCCGCATTGCT (SEQ ID NO:282), TCCTTCCCTCAGAAAGGGCAG (SEQ ID NO:283), and TTGCCTCATGCTGCTAATCTG (SEQ ID NO:284) were designed for the endogenous Nicotiana benthamiana 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene, based on the Nicotiana benthamiana EPSPS cDNA sequence CTTATATGTGCTTAAGCCTAACGTGCACCCGGCCCCTTAACCCCAGCAGTTTTCAATCTACCTACCG TCTCTACCATTTTCTTCTAGTTGGTGAAAATTTCTAACTTTGAGAAAACAAGCCAAAGTTTTTGTTT CT
  • Anti-sense polynucleotides with the sequences CCACATGGTCCAGTATCTGCC (AK195, RBCS — 1-2-3-4, SEQ ID NO:288), CAAGCAAGGAACCCATCCATT (AK196, RBCS — 1-2-3-4, SEQ ID NO:289), GGCCACACCTGCATGCATTGC (AK197, RBCS — 1-2-3-4, SEQ ID NO:290), GTGTTCACGGTAGACAAATCC (AK198, RBCS — 1-2, SEQ ID NO:291), TGCACTGCACTTGACGCACGT (AK199, RBCS — 1-2, SEQ ID NO:292), AACTGATGCATTGCACTTGAC (AK200, RBCS — 3-4, SEQ ID NO:293), CAAATCAGGAAGGTATGAGAG (AK201, RBCS — 3-4, SEQ ID NO:294), and TGTCAAGGTTTTGTTTCCTGG (AK202, RBCS — 3
  • Nicotiana benthamiana plants were treated using a procedure similar to that described in Example 12.
  • Polynucleotide solution (or mixed polynucleotides in the case of EPSPS and RuBisCO) were prepared in 0.01% (v/v) Silwet L-77 and 2% (w/v) ammonium sulfate in 5 millimolar sodium phosphate, pH 6.8.
  • Two fully expanded leaves per plant were dipped into 0.1% Silwet L-77 solution freshly made with ddH2O for a few seconds, and allowed to dry. About 30 minutes later, 20 microliters of polynucleotide solution, was applied to each of the two pre-treated leaves.
  • each of 5 plants received 25 nanomoles of the PDS anti-sense polynucleotide (SEQ ID NO:34); for EPSPS, each of 5 plants received 50 nanomoles of each EPSPS anti-sense polynucleotide (SEQ ID NOS:279-284); and for RuBisCO, each of 5 plants received 50 nanomoles of each RuBisCO anti-sense polynucleotide (SEQ ID NOS:288-295). Paired control plants were treated with buffer (0.01% (v/v) Silwet L-77 and 2% (w/v) ammonium sulfate in 5 millimolar sodium phosphate, pH 6.8).
  • FIGS. 36A-36B The results measured as plant height at 12 days (PDS and EPSPS) or 10 days (RuBisCO) after treatment, are shown in FIGS. 36A-36B .
  • Plants treated with the PDS anti-sense polynucleotide displayed severe stunting ( FIG. 36A ) and bleaching.
  • Plants treated with the EPSPS anti-sense polynucleotides displayed severe stunting ( FIG. 36B ) and severe damage to the meristem and stem tissues.
  • Plants treated with the RuBisCO anti-sense polynucleotides displayed severe stunting ( FIG. 36C ) and malformed apical tissues.
  • a second set of experiments was designed to investigate the effects of silencing a component of the endogenous RNAi silencing pathway in a plant.
  • Argonaute (AGO) proteins are components of the RNA-induced silencing complex (RISC) which binds small RNAs in the RNAi silencing process. Suppression of Argonaute would be expected to reduce the observed phenotypic effect caused by an RNAi silencing process.
  • Nicotiana benthamiana plants were treated using a procedure similar to that described in Example 12.
  • Polynucleotide solution (or mixed polynucleotides in the case of AGO1) were prepared in 0.01% (v/v) Silwet L-77 and 2% (w/v) ammonium sulfate in 5 millimolar sodium phosphate, pH 6.8.
  • Two fully expanded leaves per plant were dipped into 0.1% Silwet L-77 solution freshly made with ddH2O for a few seconds, and allowed to dry. About 30 minutes later, 20 microliters of polynucleotide solution was applied to each of the two pre-treated leaves.
  • each of 5 plants received 25 nanomoles of the PDS anti-sense polynucleotide (SEQ ID NO:34); for AGO1, each of 5 plants received 50 nanomoles of each of the 14 AGO1 anti-sense polynucleotides (SEQ ID NOS:300-313); for PDS and AGO combined treatments, each of 5 plants received 25 nanomoles of the PDS anti-sense polynucleotide (SEQ ID NO:34) and 50 nanomoles of each of the 14 AGO1 anti-sense polynucleotides (SEQ ID NOS:300-313) applied on separate leaves.
  • Paired control plants were treated with buffer (0.01% (v/v) Silwet L-77 and 2% (w/v) ammonium sulfate in 5 millimolar sodium phosphate, pH 6.8). No difference was observed between plants treated with the AGO1 anti-sense polynucleotides and the plants treated with buffer alone. Plants treated with the PDS anti-sense polynucleotide displayed systemic bleaching. Plants treated with both the PDS anti-sense polynucleotide and the separately applied AGO1 anti-sense polynucleotides did not display systemic bleaching, indicating that suppression of AGO1 blocked the systemic spread of the silencing signal.
  • This example illustrates a method for inducing systemic regulation of a target endogenous gene in a growing plant comprising topically coating onto leaves of said growing plant polynucleotides having sequence essentially identical to, or essentially complementary to, a sequence of 18 or more contiguous nucleotides in either said target endogenous gene or messenger RNA transcribed from said target endogenous gene, whereby said polynucleotides permeate the interior of said growing plant and induce systemic regulation of said target endogenous gene.
  • this example illustrates use of a composition comprising surfactant and polynucleotides to at least transiently induce systemic regulation of the endogenous Zea mays 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene.
  • EPSPS 5-enolpyruvylshikimate-3-phosphate synthase
  • EPSPS 5-enolpyruvylshikimate-3-phosphate synthase
  • a EPSPS cDNA sequence was identified as ACCTACTTCCCCCTCGCCCCTCTCATGGTCTCTCTCGCGCCCAGATCTGCTACTAGACGGCACCGCT GCAGCGCGTCGTGTCGCGGGGGTTGGTGGCAGGCAGCGAGAGCTTGCCGTTCCTCTCTCTCTCAGTTG TCAGGTCCTAGGCTCACCTCACCGGCTCCCAGCCCGCTTCTATTTCTTCCTCCCCGACCCCGTGCAG GTGGCAGTCCAGTCCACGCCACCAACCGCGAGGCGAACCAAACCAACCCACTCTCCCCAACCCCG CGCGCCCAGGCCGCCCGCCCTACCAACCATCGGCGTCGGCAATGGCGGCCATGGCGACCAAGGCC GCCGCGGGCACCGTGTCGCTGGACCAACCATCGGCGTCGGCAATGGCGGCCATGGCGACCAAGGCC GCCGCGGGCACCGTGTCGCTGGACCTCGCCGCGCCGCGGCGGCAGCGGCGGCGGCGGCGGCGGTGCA GGCGGGTGCCGAGGAGATCGTGCTGC
  • a 240 base pair double-stranded RNA polynucleotide was designed with one strand corresponding to the DNA sequence TACTTGAGTGCCTTGCTGATGGCTGCTCCTTTGGCTCTTGGGGATGTGGAGATTGAAATCATTGATA AATTAATCTCCATTCCGTACGTCGAAATGACATTGAGATTGATGGAGCGTTTTGGTGTGAAAGCAG AGCATTCTGATAGCTGGGACAGATTCTACATTAAGGGAGGTCAAAAATACAAGTCCCCTAAAAAT GCCTATGTTGAAGGTGATGCCTCAAGCGCAAGCTATTTCTTG (SEQ ID NO:318) which corresponds to a 240 nucleotide segment located at nucleotide positions 937-1176 of the EPSPS cDNA sequence.
  • Zea mays (Gaspe) seeds were germinated on germination paper. Seedlings were transferred to 4 inch pots and plants were grown in a growth chamber. Three 17-day-old plants were topically treated with polynucleotides and three plants were used as controls. Two lower leaves of each plant were marked and then pre-treated by dipping in a solution of 0.1% Silwet L-77. About 30 minutes after the surfactant pre-treatment, 20 microliters of treatment solution was applied to the upper side of each of the two pre-treated leaves.
  • Treatment solution consisted of a mixture of 100 microliters of 2 ⁇ buffer solution, 90 microliters water, 10 microliters of a 4.6 micrograms/microliter solution of the EPSPS dsRNA (with one strand corresponding to SEQ ID NO:318); the 2 ⁇ buffer solution was a mixture of 200 microliters of 0.1% Silwet L-77, 200 microliters 50 millimolar sodium phosphate, 146 microliters 34% ammonium phosphate, and 454 microliters water.
  • ethylenediaminetetraacetic acid at 0.004% was found to act similarly to 2% ammonium sulfate in the spray solution, enhancing the efficacy of the polynucleotides and potentiating the herbicidal activity of glyphosate.
  • Table 27 lists the effect on herbicidal activity (presented as percent of weed control/kill, and as plant height) of various salts including inorganic salts (sodium chloride, sodium sulfate, ammonium sulfate, ammonium chloride) and organic salts (tetramethylammonium chloride, tetraethylammonium chloride, tetrapropylammonium bromide, and tetrabutylphosphonium bromide) as additives to 1% Silwet L-77 spray solutions of topically applied polynucleotides (RNA) on glyphosate-resistant Palmer amaranth plants.
  • inorganic salts sodium chloride, sodium sulfate, ammonium sulfate, ammonium chloride
  • organic salts tetramethylammonium chloride, tetraethylammonium chloride, tetrapropylammonium bromide, and tetrabutylphospho
  • ammonium chloride and tetrabutylphosphonium bromide were found to act similarly to ammonium sulfate in the spray solution, enhancing the efficacy of the polynucleotides and potentiating the herbicidal activity of glyphosate.
  • Table 28 lists the effect of the humectant glycerin on herbicidal activity (presented as percent of weed control/kill, and as plant height) of topically applied polynucleotides (RNA) on glyphosate-resistant Palmer amaranth plants. Glycerin was found to enhance the efficacy of the polynucleotides, potentiating the herbicidal activity of glyphosate.
  • FIG. 38 depicts the effect of varying glyphosate counter-ions on herbicidal activity (presented as percent of weed control/kill, and as plant height) of topically applied polynucleotides (RNA) on glyphosate-resistant Palmer amaranth plants.
  • EPSPS polynucleotides (IDT [1] (SEQ ID NO:83-84), IDT [2] (SEQ ID NO:85-86), IDT [3] (SEQ ID NO:87-88), and IDT [4] (SEQ ID NO:89-90)) in 0.5% Silwet L-77, 2% ammonium sulfate in 10 millimolar sodium phosphate buffer, pH 6.8 with 0.2% Roundup® WeatherMax® carrier (MON56151 tallowamine surfactant blend of tallowamine (16-18C) and cocoamine (12-14C) in the ratio of 55:45) and 1682 g acid equivalent per hectare of one of the glyphosate salts; K+ glyphosate, isopropylammonium+ glyphosate or monoethanolammonium+ glyphosate at 215 liters/acre by Milli spray on 3 replicates of 4-6 inch glyphosate-resistant Palmer amaranth containing 16 copies of EPSPS.
  • Plant height was scored at 21 days after glyphos ate treatment. Results (presented as percent of weed control/kill, and as plant height) are given in Table 29.
  • the isopropylammonium and monoethanolammonium salts of glyphosate provided better herbicidal activity compared to the potassium salt.
  • spermine N,N′-bis(3-aminopropyl)butane-1,4-diamine
  • spermidine N-(3-aminopropyl)butane-1,4-diamine
  • Polynucleotide solutions were prepared using a mixture of equal amounts of the four oligonucleotide-size “short” dsRNA molecules described in Example 1, which have an anti-sense strand designed to hybridize to the mRNA transcribed from the Palmer amaranth EPSPS gene (SEQ ID NO:1) at positions 14-38 (short dsRNA-1), positions 153-177 (short dsRNA-2), 345-369 (short dsRNA-3), and 1105-1129 (short dsRNA-4), as indicated by underlined nucleotides in FIG.
  • the dsRNAs had a two nucleotide overhang at the 3′ end of the anti-sense strand, and had two deoxynucleotides as the terminal nucleotides at the 3′ end of the sense strand.
  • the dsRNA polynucleotide solutions were prepared with either 1 or 10 millimolar spermine or spermidine or 2% ammonium sulfate, in a 10 millimolar sodium phosphate (pH 6.8) buffer.
  • Control solutions (without polynucleotides) were prepared with either 1 or 10 millimolar spermine or spermidine or 2% ammonium sulfate, in a 10 millimolar sodium phosphate (pH 6.8) buffer.
  • Glyphosate-resistant Palmer amaranth plants (33, 36, or 57 copies EPSPS) were pre-sprayed with 1% Silwet L-77.
  • the dsRNA polynucleotide solutions (11.6 grams/acre) or buffer solutions were applied as drops on four lower fully expanded leaves of glyphos ate resistant Palmer amaranth by pipetting.
  • Two days following polynucleotide treatment the plants were sprayed with glyphosate (3360 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide). Plants were photographed at 14 days after glyphosate treatment; results are shown in FIG. 39 .
  • EPSPS polynucleotides IDT [1] (SEQ ID NO:83-84), IDT [3] (SEQ ID NO:87-88), and IDT [4] (SEQ ID NO:89-90)
  • EPSPS polynucleotides IDT [1] (SEQ ID NO:83-84), IDT [3] (SEQ ID NO:87-88), and IDT [4] (SEQ ID NO:89-90)
  • spray solutions 15 to 50 minutes before spraying 1- to 2-milliliters applied using a custom low-dead-volume (“milli”) sprayer to one-to-four inch glyphosate-resistant (R-22) Palmer amaranth plants grown from cuttings.
  • milli custom low-dead-volume
  • R-22 glyphosate-resistant
  • Treated plants were placed in a greenhouse set for either a 26.7/21.1 degrees Celsius or 29.4/21.1 degrees Celsius 14/10 hour temperature and supplemental light schedule. After 2 to 3 days, the plants were sprayed with glyphosate (“2 ⁇ Wmax” or 1682 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide) by regular sprayer (10 gallons/acre) and returned to the greenhouse. The amount of control (visual injury) relative to unsprayed treatments, plant height and pictures of Palmer amaranth were collected at different time intervals up to 21 days after glyphosate treatment. Fresh weight of above-soil plant material was collected at the last time point.
  • the instrument was set to automatically detect the surface and immerse the capillary to a depth of 10 mm
  • Surface tension measurements for three surface ages (approximately 20, 500 and 1250 ms) were recorded.
  • Surface tension in dynes per cm was reported at the 1250 ms interval as an approximation of static surface tension and the change between 20 and 500 ms was reported as an estimate of the dynamic surface tension.
  • Hydrophile-lipophile balance (HLP) values for the surfactants were obtained from surfactant references and product information.

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