Polynucleotide molecules for gene regulation in plants

Description

FIELD OF THE INVENTION

Disclosed herein are polynucleotide molecules for regulating genes in plants and methods of making and using such molecules.

BACKGROUND

The failure of herbicides to control resistant weeds is a problem especially when such weeds are growing in field of herbicide resistant crops that may have lower herbicide resistance than the weed. Herbicide-resistant weeds are identified with a variety of modes of action. Resistance resulting from selection for multiple copies of genes producing herbicide targeted 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 targeted 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. Physiol., 84(3):227-235; and Wakelin et al. (2006) Weed Res. (Oxford), 46(5):432-440. Vacuolar sequestration of glyphosate is an observed mechanism in glyphosate resistant horseweed; see Ge et al. (2010) Pest Management Sci., 66:576-576. Resistance resulting from expression of enzymes that metabolize herbicides to an inactive chemical form in hairy crabgrass is reported by Hidayat et al. (1997) Pesticide Biochem. Physiol., 57(2): 137-146. Reddy et al. (2008) J. Agric. Food Chem., 56(6):2125-2130 reported the accumulation of aminomethylphosphonic acid in plant species treated with glyphosate.

SUMMARY OF THE INVENTION

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. In an aspect of the invention, 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. In some aspects of the invention 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. In other aspects of the invention 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. In some aspects, 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.

The 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 II 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”). For example, the siRNA pathway involves the cleavage of a longer double-stranded RNA intermediate to small interfering RNAs (“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. As used herein, “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. Various embodiments of this invention include compositions including oligonucleotides or polynucleotides or a mixture of both.

Aspects of the invention include compositions and methods for: providing single-stranded RNA molecules in a plant cell for systemic regulation of genes; herbicidal treatment with compositions including surfactant and a plant lethal agent which provides single-stranded RNA for suppression of an endogenous gene in a plant cell; topical coating onto a plant surface including a surfactant (e. g., an organosilicone surfactant) and an oligonucleotide or polynucleotide molecule for suppression of an endogenous gene in a plant cell; topically applied 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. Optionally these compositions can include a non-nucleotide herbicide.

In other aspects 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.

In other aspects 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. These and other aspects of the invention are described in greater detail in the following sections.

BRIEF DESCRIPTION OF THE DRAWINGS

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 HI 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.

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 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, “21nt 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, “21nt PDS sense”) as described in Example 10.

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 bp or 198 bp 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.

FIG. 25A illustrates twelve dsRNA polynucleotides corresponding to DNA segments of approximately 250 bp 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 (Silicone Polyether Copolymer) 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 targeted 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”) targeting the endogenous EPSPS gene, or with buffer alone as a control, as described in Example 34.

FIG. 38 illustrates the effect of varying glyphosate 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. “fb 4X WM” means “followed by treatment with glyphosate (3360 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide)”.

DETAILED DESCRIPTION OF THE INVENTION

Unless otherwise stated, 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. By “non-transcribable” polynucleotides is meant that the polynucleotides do not comprise a complete polymerase II transcription unit. As used here “solution” refers to homogeneous mixtures and non-homogeneous mixtures such as suspensions, colloids, micelles, and emulsions.

Polynudeotides

As used herein, “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. 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. g., polynucleotides of 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, about 65, about 70, about 75, about 80, about 85, about 90, about 95, about 100, about 110, about 120, about 130, about 140, about 150, about 160, about 170, about 180, about 190, about 200, about 210, about 220, about 230, about 240, about 250, about 260, about 270, about 280, about 290, or about 300 nucleotides), or long polynucleotides having a length greater than about 300 nucleotides (e. g., polynucleotides of between about 300 to about 400 nucleotides, between about 400 to about 500 nucleotides, between about 500 to about 600 nucleotides, between about 600 to about 700 nucleotides, between about 700 to about 800 nucleotides, between about 800 to about 900 nucleotides, between about 900 to about 1000 nucleotides, between about 300 to about 500 nucleotides, between about 300 to about 600 nucleotides, between about 300 to about 700 nucleotides, between about 300 to about 800 nucleotides, between about 300 to about 900 nucleotides, or about 1000 nucleotides in length, or even greater than about 1000 nucleotides in length, for example up to the entire length of a target gene including coding or non-coding or both coding and non-coding portions of the target gene). Where 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. In some embodiments, the polynucleotide may be a combination of ribonucleotides and deoxyribonucleotides, e. g., synthetic polynucleotides consisting mainly of ribonucleotides but with one or more terminal deoxyribonucleotides or synthetic polynucleotides consisting mainly of deoxyribonucleotides but with one or more terminal dideoxyribonucleotides. In some embodiments, the polynucleotide includes non-canonical nucleotides such as inosine, thiouridine, or pseudouridine. In some embodiments, 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. Rev. Biochem., 67:99-134. For example, the naturally occurring phosphodiester backbone of an 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).

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. In more specific embodiments of the invention 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 combinations thereof. In some embodiments these polynucleotides include chemically modified nucleotides or non-canonical nucleotides. In embodiments of the method 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. In one embodiment 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 targeted 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 targeted for suppression. In certain other embodiments 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.

In some embodiments, 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. In some embodiments, 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. By “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. Thus, in embodiments 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. By “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. In some embodiments of this invention 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.

In one aspect of the invention 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. In one embodiment, the polynucleotides are modified Pol III genes containing sense and anti-sense DNA corresponding to RNA of the targeted 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.

Methods of making polynucleotides are well known in the art. Commercial preparation of oligonucleotides often provides 2 deoxyribonucleotides on the 3′ end of the sense strand. Long polynucleotide molecules can be synthesized from commercially available kits, e. g., 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. Alternatively, dsRNA molecules can be produced from expression cassettes in bacterial cells that have regulated or deficient RNase II enzyme activity. Long polynucleotide molecules can also be assembled from multiple RNA or DNA fragments. In some embodiments 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. In some embodiments random design or empirical selection of polynucleotide sequences is used in selecting polynucleotide sequences effective in gene silencing. In some embodiments the sequence of a polynucleotide is screened against the genomic DNA of the intended plant to minimize unintentional silencing of other genes.

The 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. In one embodiment, 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. In the examples to below to illustrate embodiments of the invention 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, 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.

Single-Stranded RNA Molecules

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.

Transferring Agents, Permeability-Enhancing Agents and Treatments

The 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. In some embodiments 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. g., to neutralize an acid, base, or oxidizing agent, or to inactivate an enzyme), a rinsing step, or combinations thereof. Embodiments of agents or treatments for conditioning of a plant to permeation by polynucleotides include emulsions, reverse emulsions, liposomes, and other micellar-like compositions. Embodiments of 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. g., inorganic ammonium ions, alkyl ammonium ions, lithium ions, polyamines such as spermine, spermidine, or putrescine, and other cations. 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. g., plant-sourced oils, crop oils (such as those listed in the 9^thCompendium of Herbicide Adjuvants, publicly available on line at www.herbicide.adjuvants.com) can be used, 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.

Examples of useful surfactants include sodium or lithium salts of fatty acids (such as tallow or tallowamines or phospholipids) and organosilicone surfactants. Other useful 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. 5905-50073-AA, currently available from Momentive Performance Materials, Albany, N.Y.). 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. g., about 0.01, 0.015, 0.02, 0.025, 0.03, 0.035, 0.04, 0.045, 0.05, 0.055, 0.06, 0.065, 0.07, 0.075, 0.08, 0.085, 0.09, 0.095, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.5 wt %) are efficacious in preparing a leaf or other plant surface for transfer of polynucleotide molecules into plant cells from a topical application on the surface.

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. 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.

Target Genes and Essential Genes

Compositions and methods of the invention are useful for modulating the expression of an endogenous or transgenic target gene in a plant cell. In various embodiments, 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. Examples of essential genes include translation initiation factor (TIF) and ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO). 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.

Compositions and Methods

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. In many embodiments 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. In aspects of the invention 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. When 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. When the conditioning and polynucleotide application are performed in separate steps, 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. In embodiments of the method, 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. g., promoters, introns, 5′ or 3′ untranslated regions, and microRNAs, trans-acting siRNAs, natural anti-sense siRNAs, and other small RNAs with regulatory function) or encoding RNAs having structural or enzymatic function (e. g., ribozymes, ribosomal RNAs, t-RNAs, aptamers, and riboswitches).

In various embodiments of the method for inducing systemic silencing of a target gene in a plant 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. In embodiments where 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. In embodiments of the method for inducing systemic silencing of a target gene in a plant, 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. In some embodiments, the conditioning includes application of a surfactant, such as organosilicone surfactants, e. g., 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). In embodiments of the method, 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.

The invention provides topical 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. Alternatively, 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. For example, in embodiments of the inventions disclosed herein 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. g., basil, parsley, coffee, or tea,), or is a fruit (e. g., apple, pear, cherry, peach, plum, apricot, banana, plantain, table grape, wine grape, citrus, avocado, mango, or berry), or is a tree grown for ornamental or commercial use (e. g., a fruit or nut tree, or is an ornamental plant (e. g., an ornamental flowering plant or shrub or turf grass). Embodiments of a plant produced by a cutting, cloning, or grafting process (i. e., a plant not grown from a seed) include fruit trees and plants including citrus, apples, avocados, tomatoes, eggplant, cucumber, melons, watermelons, and grapes as well as various ornamental plants.

Methods for Investigating Reverse Genetics

In yet another aspect, 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. In embodiments of such a method, messenger RNA encoding a protein or regulatory RNA gene is targeted 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. g., 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. In another aspect of the invention libraries of plants with a variety of transiently silenced genes are screened against libraries of compounds (e. g., herbicides, phytohormones, endogenous or exogenous defense elicitors such as salicylic acid or harpins, deficiencies of molecules providing a plant nutrient such as nitrogen, phosphorous, potassium, sulfur, calcium, magnesium, iron, and zinc) to identify interactions with such compounds. Examples of plants useful in such screens include Amaranthus palmeri and Nicotiana benthamiana.

Methods for Transgene Silencing

In still yet another aspect of the invention, 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.

Specific Applications

In a related aspect the 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. For example, 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. g., suppressing a FAD2 gene to effect a desired fatty acid profile in soybean or canola or other oilseed or suppressing a lignin biosynthetic genes such as COMT and CCOMT to provide more easily digestible forage plants. Similarly, 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. 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.

Herbicidal Compositions and Methods

An aspect of the invention provides 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. In some embodiments, 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. In one embodiment 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 When the polynucleotide molecule is designed to hybridize under physiological conditions in a plant cell to mRNA encoding an endogenous, protein or non-protein coding RNA that essential for maintaining plant growth or life and to effect gene silencing and reduction of the essential protein, 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 onto leaves of a growing plant or for application onto roots or cut stems, e. g., of hydroponically grown or pot-grown plants.

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. In one embodiment 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. g., promoters, also miRNA precursors, miRNAs, trans-acting siRNAs, and other non-coding RNAs having a regulatory function such as aptamers and riboswitches). 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 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, and (i) a double-stranded, hybridized RNA/DNA molecule; In embodiments for silencing or suppression of an endogenous gene of a volunteer plant that encodes a protein that provides herbicide resistance to the volunteer plant, the method can include applying onto the volunteer plant a quantity of the herbicide for which the protein provides resistance. 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. In some such embodiments the weed or the volunteer plant is pigweed (e. g., Palmer amaranth) and other amaranth species, mare's tail (horseweed), waterhemp, giant ragweed, common ragweed, johnsongrass, goosegrass, ryegrass, hairy crabgrass, prickly lettuce, velvetleaf, alfalfa, corn, soybean, canola, cotton, sugar beet, sugarcane, rice, or wheat. In some such embodiments the endogenous gene encodes a protein that provides herbicide tolerance; examples of such proteins are disclosed herein in the section “Herbicide-Tolerance Proteins”. In other such embodiments single-stranded RNA selectively suppresses a gene in a specific plant species but not in others, to permit selective control of that plant species. In still other such embodiments 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. In more specific embodiments the method further includes applying onto the weed or volunteer plant a quantity of non-nucleotide herbicide (e. g., glyphosate, dicamba, glufosinate or sulfonylurea) for which the protein targeted 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).

Herbicide-Tolerance Proteins

Natural (non-transgenic) and transgenic plants exhibiting herbicide tolerance (resistance) 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 targeted 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. g., a 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), a glyphosate oxidoreductase (GOX), a glyphosate decarboxylase, a glyphosate-N-acetyl transferase (GAT), a dicamba monooxygenase, a phosphinothricin acetyltransferase, a 2,2-dichloropropionic acid dehalogenase, an acetohydroxyacid synthase, an acetolactate synthase, a haloarylnitrilase, an acetyl-coenzyme A carboxylase, a dihydropteroate synthase, a phytoene desaturase, a protoporphyrin IX oxygenase, a hydroxyphenylpyruvate dioxygenase, a para-aminobenzoate synthase, a glutamine synthase, a cellulose synthase, a beta-tubulin, and a serine hydroxymethyltransferase.

Examples of 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. Patent Application Publication 2004/0177399), 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. 5,646,024); 2,2-dichloropropionic acid dehalogenase conferring tolerance to 2,2-dichloropropionic acid (Dalapon) (PCT International Application Publication WO9927116); acetohydroxyacid synthase or acetolactate synthase conferring tolerance to acetolactate synthase inhibitors such as sulfonylurea, imidazolinone, triazolopyrimidine, pyrimidyloxybenzoates and phthalide (U.S. Pat. No. 6,225,105); haloarylnitrilase (Bxn) for conferring tolerance to bromoxynil (U.S. Pat. No. 4,810,648); modified acetyl-coenzyme A carboxylase for conferring tolerance to cyclohexanedione (sethoxydim) and aryloxyphenoxypropionate (haloxyfop) (U.S. Pat. No. 6,414,222); dihydropteroate synthase (sul I) for conferring tolerance to sulfonamide herbicides (U.S. Pat. No. 5,719,046); 32 kDa photosystem II polypeptide (psbA) for conferring tolerance to triazine herbicides (Hirschberg et al., 1983, Science, 222:1346-1349); anthranilate synthase for conferring tolerance to 5-methyltryptophan (U.S. Pat. No. 4,581,847); dihydrodipicolinic acid synthase (dap A) 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. 6,268,549); modified protoporphyrinogen oxidase I (protox) for conferring tolerance to protoporphyrinogen oxidase inhibitors (U.S. Pat. No. 5,939,602); aryloxyalkanoate dioxygenase (AAD-1) for conferring tolerance to an herbicide containing an aryloxyalkanoate moiety (WO05107437); a serine hydroxymethyltransferase (US Patent Application Publication 2008/0155716), a glufosinate-tolerant glutamine synthase (US Patent Application Publication 2009/0018016). Examples of such herbicides 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). The 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.

In an embodiment the polynucleotide is admixed with the corresponding herbicide to potentiate the activity of the herbicide by providing improved herbicidal activity. In an embodiment the polynucleotide is utilized separately from the herbicide but in combination with an application of the herbicide as a pre- or post-treatment. In embodiments 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. In the field the treatment solution can be applied with a CO₂pressurized 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.

Example 1

This example illustrates the utility of the polynucleotide molecules of this invention in controlling herbicide resistant weeds. 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 targeted by the glyphosate compounds in herbicide treatments.

With reference to SEQ ID NO:1 as shown in FIG. 1, four 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.

With reference to SEQ ID NO:1 and FIG. 1, three “long” double-stranded 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 (Gaines, et al. (2010) Proceedings of the National Academy of Sciences 107(3): 1029-1034) 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. For 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. For surfactant solution pre-treatment four, fully-expanded, mature source leaves were dipped in the surfactant solution and allowed to dry. After leaf pre-treatment by carborundum solution or surfactant solution, 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-glyphosate treatment.

Results:

Six surfactant-treated, control plants (no dsRNA molecule treatment) survived glyphosate treatment. See FIG. 3A for a picture of the plants 7 days after the glyphosate treatment.

Two of four carborundum abrasive-treated, control plants (no dsRNA molecule treatment) were killed by glyphosate treatment.

Six surfactant-treated plants that were treated with glyphosate immediately after application of the mixed (short/long) dsRNA solution survived but were stunted.

Six surfactant-treated plants that were treated only with the mixed (short/long) dsRNA solution and no glyphosate survived. Five of six surfactant-treated plants that were treated with the mixed (short/long) dsRNA solutions followed by glyphosate treatment were killed.

Five of six surfactant-treated plants that were treated with glyphosate 48 hours after application of the mixed (short/long) dsRNA solution were killed.

Three of four carborundum-treated plants that were treated with glyphosate 48 hours after application of the mixed (short/long) dsRNA solution were killed.

Five of six surfactant-treated plants, that were treated with the long dsRNA solution, followed by glyphosate treatment after 72 hours, were killed; see FIG. 3B. Six of six surfactant-treated plants, that were treated with the short dsRNA solution, followed by glyphosate treatment after 72 hours, were killed; see FIG. 3C.

Example 2

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). A two-fold increase in glyphosate activity as estimated by observing plant growth (measured as plant height) was observed in the plants treated with the polynucleotide composition and herbicide as compared to control plants treated with buffer and herbicide. The plants treated with the polynucleotide composition and herbicide survived with severe stunting; the control plants treated with buffer and herbicide survived and fully recovered. Similar results were obtained with other glyphosate herbicide-sensitive weeds, i. e., glyphosate herbicide-sensitive waterhemp, redroot pigweed, giant ragweed, prickly lettuce, tobacco, and dandelion.

Example 3

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. 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.

Example 4

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). With reference to SEQ ID NO:2 and FIG. 5, 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.

Example 5

This example further illustrates the utility of polynucleotide molecules of the invention as herbicidal agents. 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 (Xanthium strumarium), blackgrass (Alopecurus myosuroides), wild oat (Avenafatua), sicklepod (Senna obtusifolia), morning glories (Ipomoea sp.), field bindweed (Convolvulus arvensis), shattercane (Sorghum bicolor), dayflower (Commelina), Spiderwort (Tradescantia sp.), ryegrass (Lolium sp.), goosegrass (Eleusine indica), horseweed (Conzya canadensis), buckhorn plantain (Plantago lanceolata), pigweed (Amaranthus palmeri), rough-fruit amaranth (Amaranthus tuberculatus), tumble pigweed (Amaranthus albus), smooth pigweed (Amaranthus hybridus), redroot pigweed (Amaranthus retroflexus), waterhemp (Amaranthus rudis/tuberculatus), slender amaranth (Amaranthus viridis), Thunberg's amaranth (Amaranthus thumbergii), spiny amaranth (Amaranthus spinosis), (Amaranthus rubra), (Amaranthus lividus), Mediterranean amaranth (Amaranthus graecizans), rough amaranth (Amaranthus chlorostachys), Powell amaranth (Amaranthus powellii), Mat amaranth (Amaranthus blitoides), Kochia (Kochia scoparia), Yellow starthistle (Centaurea solstitialis), and Velvetleaf (Abutilon theophrasti). 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 6

This example further illustrates the utility of polynucleotide molecules of the invention as herbicidal agents. 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 7

This example 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). 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.

Example 8

This example illustrates the utility of employing a synthetic Pol m gene in compositions and methods of this invention. With reference to SEQ ID NO:3 and FIG. 2, a synthetic Pol m 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. RE39,247) that imparts resistance to glyphosate herbicide when expressed in transgenic corn plants, an “AAGATTAGCACGG” element (SEQ ID NO:5, bold and underlined) embedded in the anti-sense DNA, an “ACGCATAAAAT” element (SEQ ID NO:6, bold and underlined) followed by sense DNA (lower case) and a “TTTTTT” terminator element (SEQ ID NO:7, bold and underlined). 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 thriving; control glyphosate-resistant corn plants treated only with surfactant and glyphosate herbicide are thriving.

Example 9

This example illustrates an aspect of the invention. In this example, 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).

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.

TABLE 1

Anti-sense ssDNA oligonucleotides

SEQ ID
Sequence

Name
NO:
(5′ to 3′)
Note

Anti-sense_PO1
8
ACCCTCCACGACTGCCCTTT

Anti-sense_PO2
9
GTTTCCTTCACTCTCCAGC

Anti-
10
GTAGCTTGAGCCATTATTGT

sense_PO3

Anti-
11
GTTGATGGTAGTAGCTTGAG

sense_PO4

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-
15
ACCCTCCACGACTGCCCTTT
5′-labelled with Alexa

sense_PO1_488

Fluor 488

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. A slightly time-dependent vascular uptake of the fluorescently labelled ssDNA oligonucleotides was observed (see FIG. 6). Fluorescently labelled ssDNA oligonucleotides were released from vascular tissue into cells as early as 8 h after treatment and were observed to accumulate at the leaf edge at 24 h and 48 h, suggesting a transpiration effect.

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. To assess the effects of anti-sense ssDNA oligonucleotides on EPSPS mRNA, total leaf RNA was isolated and quantitative real-time RT-PCR was performed to compare EPSPS mRNA levels. To assess the effects of anti-sense ssDNA oligonucleotides on EPSPS protein, total leaf soluble protein was isolated, separated by SDS-PAGE, and EPSPS protein levels measured by Western blot using antibodies against maize EPSPS_TIPA. Effects of anti-sense ssDNA oligonucleotides on shikimate accumulation as an indication of suppression of EPSPS were assessed in two experiments: in experiment 1, the oligonucleotide-treated leaves were incubated with 50 microgram/mL glyphosate for an additional 48 h either by petiole uptake (control leaves were permeated with the anti-sense control (SEQ ID NO:14), and additionally treated with or without 50 micrograms/mL glyphosate); in experiment 2, leaf disc assays were performed on the oligonucleotide-treated leaves, and shikimate levels measured by HPLC (controls in this case were leaves that had not been treated with oligonucleotides but incubated with 50 microgram/mL glyphosate).

TABLE 2

List of treatments using anti-sense ssDNA oligonucleotides

Final

Treatment
Anti-sense ssDNAs
concentration

#1
Anti-sense_PO1 (SEQ ID NO: 8)
5 microM

#2
Anti-sense_PO2 (SEQ ID NO: 9)
5 microM

#3
Anti-sense_PS1 (SEQ ID NO: 12)
5 microM

#4
Anti-sense_PS2 (SEQ ID NO: 13)
5 microM

#5
Anti-sense_PS1, PS2
10 microM each

(SEQ ID NOs: 12, 13)
(20 microM total)

#6
Anti-sense_PO1, PO2, PO3, PO4
5 microM each

(SEQ ID NOs: 8, 9, 10, 11)
(20 microM total)

Control
Anti-sense_ck (SEQ ID NO: 14)
5 microM or 20 microM

Results for EPSPS mRNA expression, EPSPS protein levels, and shikimate levels are shown in FIGS. 7, 8, and 9, respectively. These results demonstrate that treatment with the anti-sense ssDNA oligonucleotides systematically regulated or suppressed the target gene by decreasing levels of the target gene transcript (EPSPS mRNA) or of the protein (EPSPS) encoded by the target gene in the plant tissue. In this particular experiment, treatments #1 and #6 appeared to be more efficacious in suppressing levels of EPSPS mRNA and protein and in increasing glyphosate efficacy as evidenced by the increased accumulation of shikimate. These results also indicate that glyphosate efficacy is improved by suppressing EPSPS mRNA and protein in glyphosate-resistant Palmer amaranth.

Example 10

This example illustrates an aspect of the invention. In this example, 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. More specifically, tobacco (Nicotiana benthamiana) 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.

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. 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. Some of the polynucleotides included a T7 promoter sequence (indicated by lower-case text in Table 3) that is a promoter recognized by a bacteriophage T7 RNA polymerase.

TABLE 3

sense/

SEQ

anti-

Number of
ID

Description
sense
sequence
nucleotides
NO:

oligo 1 with
S
taatacgactcactataggGCAAGAGATGTCCTAGGTGGG
40
16

T7 promoter

oligo 2 with
S
taatacgactcactataggACAGATTTCTTCAGGAGAAACAT
44
17

T7 promoter

GG

oligo 1 w/o T7
S
GCAAGAGATGTCCTAGGTGGG
21
18

promoter

oligo 2 w/o T7
S
ACAGATTTCTTCAGGAGAAACATGG
25
19

promoter

oligo 3 mix
AS
taatacgactcactataggCATCTCCTTTAATTGTACTGCC
41 (SEQ ID
20,

with T7

(SEQ ID NO: 20) and
NO: 20), 41 (SEQ
21

promoter

taatacgactcactataggTTTAATTGTACTGCCATTATTC
ID NO: 21)

(SEQ ID NO: 21)

oligo 3 mix
AS
CATCTCCTTTAATTGTACTGCC (SEQ ID NO: 22)
22 (SEQ ID
22,

w/o T7

and TTTAATTGTACTGCCATTATTC (SEQ ID
NO: 22), 22 (SEQ
23

promoter

NO: 23)
ID NO: 23)

oligo 4 w/o T7
AS
CACTTCCATCCTCATTCAGCTCGAT
25
24

promoter

oligo 5 w/o T7
AS
ACACCTCATCTGTCACCCTATCAG
24
25

promoter

oligo 6 w/o T7
AS
CAGTCTCGTACCAATCTCCATCAT
24
26

promoter

CRW oligo
S and
taatacgactcactatagggATCCATGATATCGTGAACATC
41 (SEQ ID
27,

mixture with
AS
(SEQ ID NO: 27) and
NO: 27), 38 (SEQ
28

T7 promoter

taatacgactcactatagggGCAAAGAAAAATGCGTCG (SEQ
ID NO: 28)

ID NO: 28)

CRW oligo
S and
ATCCATGATATCGTGAACATC (SEQ ID NO: 29) and
21 (SEQ ID
29,

mixture w/o
AS
GCAAAGAAAAATGCGTCG (SEQ ID NO: 29)
NO: 29), 18 (SEQ
30

T7 promoter

ID NO: 30)

The following procedure was used for all assays described in this example. Four-week old Nicotiana benthamiana plants were used in all assays. Plants were treated with 0.1% SILWET L-77 solution freshly made with ddH2O. Two fully expanded leaves per plant (one cotyledon, one true leaf) were dipped into the SILWET L-77 solution for a few seconds, and allowed to dry for 15-30 minutes before application of the polynucleotide composition. Final concentration for each oligonucleotide or polynucleotide was 25 microM (in 0.01% SILWET L-77, 5 mM sodium phosphate buffer, pH 6.8) unless otherwise stated. 20 microliters of the solution was applied to the top surface of each of the two pre-treated leaves to provide a total of 40 microliters (1 nmol oligonucleotide or polynucleotide) for each plant. Leaf bleaching was observed 3 days post treatment.

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. 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. These results show that the combinations of oligonucleotides and polynucleotides in treatments 2, 3, 4, 8, and 11 were effective in systematically regulating (suppressing) the target gene in the treated plants; treatment 1 also effected systematic regulation (suppression) of the target gene to a lesser extent. The 200-mer dsRNA polynucleotide was also effective in systematically regulating (suppressing) the target gene in the treated plants. Oligonucleotides from a non-homologous (corn rootworm) gene (treatments 5 and 6) did not suppress the target phytoene desaturase gene. These results demonstrate that both sense and anti-sense single-stranded DNA oligonucleotides and polynucleotides were effective in systematically regulating (suppressing) the target gene in the treated plants. In this particular example, sense oligonucleotides with the T7 promoter (treatment 1) effected a weak systematic suppression of the phytoene desaturase gene, whereas sense oligonucleotides without the T7 promoter (treatment 7) did not suppress the phytoene desaturase gene. In this particular example, anti-sense oligonucleotides with the T7 promoter (treatment 2) 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 4

Bleaching
Chlorophyll
Chlorophyll

Treatment
Description
SEQ ID NO:
Comment
(day 5)
(day 7)
(day 12)

1
Oligos 1 and 2
16, 17
Sense oligos
weak
18.6
17.5

with T7

promoter

2
Oligo 3
20, 21
Anti-sense
strong
12.7
1.6

oligos with T7

promoter

3
Oligos 1, 2, and 3
16, 17, 20, 21
Sense and
strong
11.5
2.6

anti-sense

oligos with T7

promoter

4
Oligos 1, 2, 3, 4,
16, 17, 20,
Sense and
strong
15.1
2.5

5 and 6
21, 24, 25, 26
anti-sense

oligos with T7

promoter, plus

anti-sense

oligos without

T7 promoter

5
CRW oligo
27, 28
Sense and
not yet
30.8
37.3

mixture with T7

anti-sense

promoter

oligos with T7

promoter

6
CRW oligo
29, 30
Sense and
not yet
34.2
38.2

mixture without

anti-sense

T7 promoter

oligos without

T7 promoter

7
Oligos 1 and 2
18, 19
Sense oligos
not yet
32.0
41.1

without T7

without T7

promoter

promoter

8
Oligo 3 without
22, 23
Anti-sense
strong
11.3
3.2

T7 promoter

oligos without

T7 promoter

9
Oligos 1, 2, and
18, 19, 22,
Sense and
not yet
30.2
34.4

3 w/o T7
23, 24, 25, 26
anti-sense

promoter and

oligos without

oligos 4, 5, & 6

T7 promoter

10
200-mer dsRNA
RNA
Sense and
strong
11.3
4.0

polynucleotide
sequence
anti-sense

corresponding
dsRNA

to the “PDS
polynucleotide

200-mer”

segment

consisting of

nucleotides

914-1113 of

SEQ ID

NO: 2

11
1/10^thof
16, 17, 20,
Sense and
strong
11.4
4.5

Experiment 4
21, 24, 25, 26
anti-sense

oligonucleotide

oligos with T7

mixture

promoter, plus

anti-sense

oligos without

T7 promoter

12
1/100^thof
16, 17, 20,
Sense and
not yet
31.0
38.0

Experiment 4
21, 24, 25, 26
anti-sense

oligonucleotide

oligos with T7

mixture

promoter, plus

anti-sense

oligos without

T7 promoter

13
Control
(none)
Buffer only
not yet
31.2
38.4

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. 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 and PDS 33-mer anti-sense ssDNA, as well as after topical treatment with the PCR-amplified and column-purified 700-mer dsRNA polynucleotide (“PDS 700-mer dsRNA”), previously assayed PDS anti-sense 22-mer oligonucleotides with a T7 promoter (SEQ ID NOs:20 and 21) (“PDS T7 anti-sense”), or 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 (“Buffer”), or after topical treatment with heat-denatured (5 minutes at 95 degrees Celsius, then stored on ice) 700-mer dsRNA polynucleotide (“PDS 700-mer dsRNA heated”), the PDS15-mer anti-sense ssDNA, or the PDS 18-mer anti-sense ssDNA.

TABLE 5

SEQ

ID

Description
Sequence
NO:

PDS 40-mer sense ssDNA
TGTTTTATACTGAATAATG
31

GCAGTACAATTAAAGGAGA

TG

PDS 15-mer anti-sense ssDNA
CATCTCCTTTAATTG
32

PDS 18-mer anti-sense ssDNA
CATCTCCTTTAATTGTAC
33

PDS 21-mer anti-sense ssDNA
CATCTCCTTTAATTGTACT
34

GC

PDS 33-mer anti-sense ssDNA
CATCTCCTTTAATTGT
35

ACTGCCATTATTCAGTA

PDS 21-mer sense ssDNA
GCAGTACAATTAAAGGAGA
36

TG

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, “21nt 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, “21nt PDS sense”).

Example 11

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.

Palmer amaranth phytoene desaturase (PDS) has the sequence TCAATTTCATCTATGGAAGTGATTTTTGGGTCATTCTGTGAGAAATTTCAGTGTAGTAAAGTTTATG GAGCAAAGCAAAGAAATGGGCACTGCCCTTAAAGGTTGTTTGTATAGATTATCCTAGGCCAGAGCTT GAAAGTACATCCAATTTCTTGGAAGCCGCCTACTTATCTTCTACTTTCGGAATTCGCCTCGTCCTCAG AAGCCATTAGAAGTTGTAATTGCTGGAGCAGGTTTGGCTGGTCTATCCACGGCAAAGTATTTAGCTGA TGCAGGTCACAAACCCATATGTTGGAAGCACGAGATGTTTTAGGAGGAAAGGTTGCAGCGTGGAA GATGAGGATGGTGACTGGTATGAGACTGGGCTACATATATCTTTGGGGCATATCCAAATGTCCAAAA TCTATTTGGAGAACTTGGTATAAATGACCGACTGCAATGGAAGGAGCACTCTATGATTTFGCAATGC CCAGCAAGCCCGGTGAATTCAGTCGCTTTGATTTTCCCGAAATCCTGCCTGCACCATTAAATGGCATAT GGGCAATCCTAAGAAATAATGAAATGCTAACCTGGCCAGAAAAAATCAAGTTTGCCATTGGCTGTTG CCTGCTATGGCAGGCGGACAGTCATATGTTGAAGCACAAGATGGTTTGAGTGTCCAAGAGTGGATGAG AAAACAAGGAGTACCCGATCGTGTAACTGATGATGTGTTTATTGCCATGTCAAAGGCACTGAACTTCA TAAATCCCGATGAACTTTCAATGCAGTGCATCTGATTGCTCTGAACCGATTCCTGCAGGAGAAACATGG TTCTAAGATGGCCTTCCTAGACGGAAACCCTCCAGAGAGGCGTGCATGCCATTGTTAAACACATCGAGTCA CTAGGTGGTGAAGTTAAACFTAACTCTCGTATACAAAAGATTCAGTTGGACCAGAGTGGAAGCGTGAAGAGTT TTTTGCTAAATAACGGGAGGGAAATACGAGGAGATGCCTATGTTTGCCACCCCAGTTGACATCTTGAA GCTGTTACTACCTGATACTTGGAAGGAAATCTCATACTTCAAAAAACTTGAGAAATTAGTGGGCGTTC CTGTGATTAATGTTCACATATGGTJTTGACAGAAAATTAAAGAATACATATGACCATCTACTCTTCAGCA GGAGTCCTTTTGAGTGTCTATGCTGATATGTCGGAGACATGCAAGGAATATAAGGATCCAAATAGA TCCATGCTGGAATTGGTTTTGCACCCGCGGAGGAATGGATTCACGAAGCGACACTGATATATAGA GGCAACAATGAAAGAGCTGCCAAGCTTTTCCCGGATGAAATCGCTGCCGATGGAAGCAAGGCCAAG ATCCTCAAATATCATGTCGTCAAAACTCCAAGGTCGGTTATAAGACTGTACCGGATTGTGAACCTTGT CGGCCGCTGCAAAGATCACCAATAGAGGGTCTATTAGCTGGTGATACACAAAACAAAAATATTT GGCTTCTATGGAAGGTGCTGTCTTATCTGGGAAGCTTGTGCACAGGCTATCGTACAGGATTATGATCT GCTGAGTTCTCGAGCACAAAGAGAATTGGCG (SEQ ID NO:37). A 678 base pair dsRNA polynucleotide with an anti-sense strand capable of hybridizing to the RNA encoded by the nucleotides at positions 317-994 (shown as underlined text) in SEQ ID NO:37 and a 198 base pair dsRNA polynucleotide with an anti-sense strand capable of hybridizing to the RNA encoded by the nucleotides at positions 797-994 (shown as italicized and underlined text) in SEQ ID NO:37 were synthesized.

Nicotiana benthamiana phytoene desaturase has the sequence TCGAGGTCTTCGTTGGGAACTGAAAGTCAAGATGTGCTTGCAAAGGAATTTGTTATGTTTTGGTAGT AGCGACTCCATGGCATAAGTTAAGGATTCGTACTCCAAGTGCCACGACCCGAAGATTGACAAAGG ACTTTAATCCTTAAAGGTAGTCTGCATTGATATCCAAGACCAGAGCTAGACAATACAGTTAACTATT TGGAGGCGGCGTTATTATCATCATCGTTTCGTACTTCCTCACGCCCAACTAAACCATTGGAGATTGTTA TTGCTGGTGCAGGTTGGTGGTJTGTCTACAGCAAAATATCGGCAGATGCTGTCACAAACCGATA TTGCTGGAGGCAAGAGATGTCCTAGGTGGGAAGGTAGCTGCATGGAAAGATGATGATGGAGATTGGT ACGAGACTGGGTTGCACATATTCTTTGGGGCTTACCCAAATATGCAGAACCTGTTTGGAGAACTAGGG ATTGATGATCGGTTGCAGTGGAAGGAACATTCAATGATATTTGCGATGCCTAACAAGCCAGGGGAGTT CAGCCGCTTTGATTTTCCTGAAGCTCTTCCTGCGCCATTAAATGGAATTTTGGCCATACTAAAGAACAA CGAAATGCTTACGTGGCCCGAGAAAGTCAAATTTGCTATTGGACTCTTGCCAGCAATGCTTGGAGGGC AATCTTATGTTGAAGCTCAAGACGGTTTAAGTGTTAAGGACTGGATGAGAAAGCAAGGTGTGCCTGAT AGGGTGACAGATGAGGTGTTCATTGCCATGTCAAAGGCACTTAACTTCATAAACCCTGACGAGCTTTC GATGCAGTGCATTTTGATTGCTTTGAACAGATTTCTTCAGGAGAAACATGGTTCAAAAATGGCCTTTTTAGAT GGTAACCCTCCTGAGAGACTTTGCATGCCGATTGTGGAACATATTGAGTCAAAAGGTGGCCAAGTCAGACTAA ACTCACGAATAAAAAAGATCGAGCTGAATGAGGATGGAAGTGTCAAATGTTTTATACTGAATAATGGCAGTACA ATTAAAGGAGATGCTTTTGTGTTTGCCACTCCAGTGGATATCTTGAAGCTTCTTTTGCCTGAAGACTGG AAAGAGATCCCATATTTCCAAAAGTTGGAGAAGCTAGTGGGAGTTCCTGTGATAAATGTCCATATATG GTTTGACAGAAAACTGAAGAACACATCTGATAATCTGCTCTTCAGCAGAAGCCCGTTGCTCAGTGTGT ACGCTGACATGTCTGTACATGTAAGGAATATACAACCCCAATCAGTCTATGTTGGAATTGGTATTTG CACCCGCAGAAGAGTGGATAAATCGTAGTGACTCAGAAATTATTGATGCTACAATGAAGGAACTAGC GAAGC-TTTCCCTGATGAAATTTCGGCAGATCAGAGCAAAGCAAAAATATGAAGTATCATGTGTCA AAACCCCAAGGTCTGTTTATAAAACTGTGCCAGGTTGTGAACCCTGTCGGCCCTTGCAAAGATCCCCT ATAGAGGGGTTTATTTAGCTGGTGACTACACGAAACAGAAGTACTTGGCTCAATGGAAGGTGCTGT CTTATCAGGAAAGCTTTGTGCACAAGCTATTGTACAGGATTACGAGTTACTTCTTGGCCGGAGCCAGA AGATGTTGGCAGAAGCAAGCGTAGTTAGCATAGTGAACTAA (SEQ ID NO:38). A 685 base pair dsRNA polynucleotide with an anti-sense strand capable of hybridizing to the RNA encoded by the nucleotides at positions 421-1105 (shown as underlined text) in SEQ ID NO:38 and a 192 base pair dsRNA polynucleotide with an anti-sense strand capable of hybridizing to the RNA encoded by the nucleotides at positions 914-1105 (shown as italicized and underlined text) in SEQ ID NO:38 were synthesized.

An alignment of the Palmer amaranth and Nicotiana benthamiana PDS DNA sequences was performed using a global pairwise alignment (stretcher) and is illustrated in FIG. 16; with this method the two sequences showed about 71% identity (1252/1762).

Palmer amaranth plants having 16 copies of EPSPS and 5-8 inches high were treated with 0.1% SILWET L-77 solution freshly made with ddH2O. Four fully expanded leaves per plant were dipped into the SILWET L-77 solution for a few seconds, and allowed to dry for 30 minutes to 1 hour before application of the polynucleotide composition. Individual polynucleotide solutions were made for each of the 678 bp Palmer PDS dsRNA, 198 bp Palmer PDS dsRNA, the 685 bp Nicotiana benthamiana PDS dsRNA, and the 192 bp Nicotiana benthamiana PDS dsRNA (0.6 micromolar polynucleotide in 0.01% SILWET L-77, 5 mM sodium phosphate buffer, pH 6.8). 10 microliters of polynucleotide solution (or buffer as a control) was applied to the top surface of each of the four pre-treated leaves per plant to provide a total of 40 microliters for each plant. Plants were kept in a growth chamber, and leaf bleaching was observed 3 days post treatment Plants topically treated with either 678 bp Palmer PDS dsRNA or 198 bp Palmer PDS dsRNA, showed bleaching of leaves (indicating silencing of the endogenous phytoene desaturase) but Palmer amaranth plants topically treated with either 685 bp Nicotiana benthamiana PDS dsRNA or 192 bp Nicotiana benthamiana PDS dsRNA did not show bleaching of leaves. This sequence specificity demonstrates that the polynucleotide compositions and methods of the invention are useful in selective control of a given species or taxon having a specific target gene sequence, e. g., in controlling herbicide-resistant volunteer plants growing in a field of crop plants resistant to the same herbicide.

In a separate assay, Palmer amaranth plants topically treated with 678 bp Palmer PDS dsRNA (labelled “700 nt dsRNA PDS”) or 198 bp Palmer PDS dsRNA (labelled “200 nt dsRNA PDS”) showed bleaching of leaves (indicating silencing of the endogenous phytoene desaturase) but Palmer amaranth plants topically treated with a 260 base pair dsRNA of an invertebrate gene (labelled “260 nt dsRNA DV49”, from corn root worm Diabrotica virgifera) did not result in a bleaching phenotype, indicating no silencing of the endogenous phytoene desaturase (FIG. 17). This sequence specificity demonstrates that the polynucleotide compositions and methods of the invention are useful in selective control of a given species or taxon.

Example 12

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.

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. Twenty microliters of a single-stranded DNA (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).

Flowers of both control and ssDNA-treated plants were allowed to set seed. Seeds were collected from mature fruits, weighed, and allowed to germinate. Seed weights were identical (about 11 mg per 100 seeds) and seed morphology appeared similar between the ssDNA-treated and the control plants. A reduced amount of seed produced per fruit and a reduction in germination rate (4 out of 100 seeds germinated) was observed in seeds from the ssDNA-treated plants, compared to the amount of seed per fruit and germination rate (95 out of 100 seeds germinated) of seeds from control plants.

In a separate assay using a similar procedure, 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. Other plants were not conditioned with a surfactant treatment, but were treated only with 1 nanomole of the PDS ssDNA 22-mer (SEQ ID NO:39) applied either by infiltration with a needleless syringe (shown in FIG. 18B) or by hand application of drops to the leaf surface (not shown in FIG. 18B), and either as a 25 micromolar solution in 0.01% SILWET L-77 in 5 millimolar sodium phosphate buffer, pH 6.8 or as a 25 micromolar solution in 5 millimolar sodium phosphate buffer, pH 6.8 (without surfactant). Negative control plants were treated with the SILWET buffer solution without the DNA oligonucleotide. Results are depicted in FIG. 18B. All plants treated only with direct application of the PDS ssDNA (without conditioning by SILWET L-77 surfactant treatment), whether applied by infiltration or by hand application of drops, displayed bleaching of apical leaves, stems, and flowers, indicating systemic silencing of PDS.

Example 13

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.

Palmer amaranth plants having lower (fewer than 30) copy numbers of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) are susceptible to treatment with dsRNA designed to silence EPSPS followed by treatment with glyphosate (see details in Example 1). However, Palmer amaranth plants having high copy numbers of EPSPS (i. e., 30 or more copies of EPSPS) are resistant to glyphosate treatment and are a challenge for weed resistance management. For example, in one assay (results not shown) on 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. e., 8 nanomoles of short dsRNAs described in Example 1 per plant) or where a proprietary glyphosate formulation (“Roundup® WeatherMAX® brand herbicide”) combined with a tallowamine surfactant was used, glyphosate activity was improved (estimated by observing plant growth measured as plant height) but the resistant plants were not killed.

Three different glyphosate resistant high-copy Palmer amaranth lines (3 plants per replicate) were treated with dsRNA using the treatment conditions listed in Table 6, where the dsRNA delivery vehicle, permeabilization or conditioning agent, and order of steps were varied. Results are depicted in FIG. 19. Treatment with “4×” glyphosate (i. e., treatment with 3360 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide which is four-fold the standard rate of application of 840 g acid equivalent per hectare) alone did not kill 35-copy (experiment 3) or 57-copy (experiment 6) Palmer amaranth.

In one set of experiments (1-3, Table 6), including 2% ammonium sulfate in an aqueous dsRNA delivery vehicle comprising 0.1% tallowamine surfactant and 10% glycerol (experiment 2) improved the efficacy of a 10-fold dose of dsRNA followed by a 4× glyphosate application. Improved efficacy of a 10-fold dose of dsRNA followed by glyphosate application was also observed when ammonium sulfate was included in a dsRNA delivery vehicle without a tallowamine surfactant (experiment 8).

In another set of experiments (4-6, Table 6), applying the SILWET L-77 surfactant prior to applying the dsRNA in a delivery vehicle containing ammonium sulfate was effective, whereas combining the SILWET L-77 surfactant with the dsRNA in the dsRNA delivery vehicle containing ammonium sulfate was not effective. Applying glyphosate (“Roundup® WeatherMAX® brand herbicide”) at 72 hours (experiment 7) was less effective than applying glyphosate at 48 hours (experiment 2) after treatment with dsRNA.

TABLE 6

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

5
1% Silwet L-
10X
2% ammonium
4x WeatherMAX

77

sulfate
(48 h)

6
1% Silwet L-
Buffer only
2% ammonium
4x WeatherMAX

77
(control)
sulfate
(48 h)

Step 1

EPSPS

Palmer
EPSPS

dsRNA

amaranth
Copy
Experiment
relative
dsRNA delivery

line
number
number
concentration
vehicle
Step 2
Step 3*

R28
87
7
10X
2% ammonium
1% Silwet L-77
4x WeatherMAX

sulfate + 0.1%

(72 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*

R28
87
8
1% Silwet L-
10X
2% ammonium
4x WeatherMAX

77

sulfate
(72 h)

9
1% Silwet L-
Buffer only
2% ammonium
4x WeatherMAX

77
(control)
sulfate
(72 h)

*glyphosate (as the commercial formulation “Roundup ® WeatherMAX ® brand herbicide”, which contains 660 g/L glyphosate K+ salt in a carrier including the MON56151 tallowamine surfactant blend of tallowamine (16-18C) and cocoamine (12-14C) in the ratio of 55:45) is listed at the amount used (where 1X = 840 g acid equivalent per hectare of Roundup ® WeatherMAX ® brand herbicide, 4X = 3360 g acid equivalent per hectare of Roundup ® WeatherMAX ® brand herbicide) and hours after application of dsRNA

Example 14

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.

Two small 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). Two 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. 20, which also shows 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.

Application of a mixture of the four oligonucleotide-size “short” EPSPS dsRNA molecules (described in Example 1) followed by application of glyphosate replicating the treatment procedure described in Example 1 resulted in 4 out of 4 Palmer amaranth plants with 16 copies of EPSPS being killed. Using the same treatment procedure but applying short dsRNA-5 and short dsRNA-6 together resulted in 0 out of 4 Palmer amaranth plants being killed. Adding either or both short dsRNA-5 and short dsRNA-6 to the mixture of the four oligonucleotide-size “short” EPSPS dsRNA molecules (described in Example 1) resulted in 4 out of 4 Palmer amaranth plants being killed, i. e., no antagonistic effect of short dsRNA-5 and short dsRNA-6 was observed.

Example 15

Salicylic acid (SA) 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.

Example 16

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.

These assays were conducted on Palmer amaranth plants with high copy numbers (56, 63, or 100 copies) of EPSPS, using a protocol including the following steps: (1) application of dsRNA (a solution of the four oligonucleotide-size “short” EPSPS dsRNA molecules described in Example 1) in a solution containing tallowamine surfactant and glycerol; (2) application of 1% SILWET L-77 silicone surfactant; and (3) application of glyphosate (1682 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide). Spacing of the timing of the application of the polynucleotides and application of SILWET was assessed, with the SILWET spray applied at 30 minutes, 1 hour, or 2 hours after application of the dsRNA solution. In this set of assays, the three different times of the SILWET solution application all produced similar results, i. e., stunting of growth of most of the high copy plants that were treated with the dsRNA solution, as compared to control high copy plants which were treated with a control solution containing only tallowamine surfactant and glycerol.

Example 17

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.

A solution of dsRNA (a solution of the four oligonucleotide-size “short” EPSPS dsRNA molecules described in Example 1) in a solution containing 2% ammonium sulfate was applied by low-volume spray to Palmer amaranth having 16 copies of EPSPS, followed by spraying with glyphosate (1682 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide), resulting in the Palmer amaranth plants being killed.

Six Palmer amaranth plants per treatment were treated with a three-step procedure using low-volume spray: (1) spraying 1% SILWET L-77; (2) spraying 2 milliliters of a dsRNA solution containing equal amounts of the four oligonucleotide-size “short” EPSPS dsRNA molecules described in Example 1 at one of 3 doses (IX or 0.8 nanomoles per plant, 2× or 1.6 nanomoles per plant, or 4× or 3.2 nanomoles per plant); and (3) spraying glyphosate (1682 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide) at a rate of 159 liters/acre. Nine days after the glyphosate spray, all six plants sprayed with 4× (3.2 nanomoles per plant) dsRNA were killed, and the plants sprayed with 2× (1.6 nanomoles per plant) dsRNA or 1× (0.8 nanomoles per plant) dsRNA were stunted (FIG. 21A).

Several assays were carried out on glyphosate-resistant Palmer amaranth grown from field-collected seeds. Plants were treated with various protocols described below, with some plants being treated topically with a dsRNA solution and control plants being treated with the buffer (dsRNA vehicle); application was by low-volume spray. Unless otherwise noted, 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.

TABLE 7

killed plants/total plants

Assay
dsRNA-

Number
treated
control
Comments

1
2/10
0/10
dsRNA-treated survivors stunted

compared to controls (FIG. 21B)

2
7/18
4/18
dsRNA-treated survivors stunted

at 8 and 30 days after treatment,

compared to controls

3 (large
5/12
3/12
dsRNA/ammonium sulfate-treated

seedlings)

survivors more stunted after

3 (small
9/12
6/12
treatment, compared to controls

seedlings)

4
7/11
2/11
dsRNA/ammonium sulfate-treated

5
8/12
3/12
survivors more stunted after

treatment, compared to controls

6 (hand
14/18
—

drop)

6 (spray)
13/18
9/18

7
8/18
2/18

Example 18

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.

In these assays, 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. 22 as “tallowamine/AMS”), or one of the following transfection reagents: (a) a polyamine (JetPRIMEM, Polyplus-transfection SA, Illkirch, France), (b) a magnetic nanoparticle (SilenceMag, OZ Biosciences, Marseille, France), (c) a peptide (N-TER™ Nanoparticle, Sigma-Aldrich, St. Louis, Mo.), (d) a lipid (siPORT™ NeoFX™, 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. Stunting or death of the plants was observed for plants treated with dsRNA in solutions containing polyamine (JetPRIME™), peptide (N-TER™ Nanoparticle), cationic lipid/polymer (TransIT®), or tallowamine surfactant/ammonium sulfate.

Example 19

This example illustrates methods using 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) and anti-sense single-stranded RNAs (ssRNAs) 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.

Example 20

Six glyphosate-resistant Palmer amaranth plants having 16 copies of EPSPS were used per treatment in this assay. A 0.8 nanomoles (“IX”) per plant treatment of dsRNA, a ten-fold greater amount (8 nanomoles per plant treatment, “10×”) of ssDNA polynucleotides (described in Example 19) and buffer alone as a control, were applied to separate plants by hand in buffer containing 2% ammonium sulfate, followed 48 hours later by spraying with glyphosate applied at 840 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide at a rate of 159 liters/acre. FIG. 24 depicts the results. Both polynucleotide treatments gave better control of the Palmer amaranth compared to plants treated only with buffer and herbicide. Of the plants treated with the 10× ssDNA treatment, two of six were killed, and the remaining four were stunted in growth by 30%. Of the plants treated with the 1×dsRNA treatment, all six plants were killed by 8 days after WM spray or 10-day after dsRNA treatment.

Example 21

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.

Twelve dsRNAs of approximately 250 bp 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.

TABLE 8

Tiling

segment

number

SEQ

(see FIG.

ID

25A)
Sequence
NO.

1
CGCCAGGGCTGCAGACGCGTTACGTANTCGGATCCAGAATTCGTGATTAAC
41

GTCACAGCATGTCATGTAAAACACGCGAATCAGACCGGTCCACTCTTGTTT

TAATTTGAGACAATTTTGATGTTGAGTCATCCCACACCAACCCCAAAAAAT

TCAACAACAAACTCTTATAATGATTCCCTCTACTCTACTAGAGTCTACACC

AACCCACTTTCTCTTTGCCCACCAAAACTTTGGTTTGGTAAGAACT

2
CACCAACCCACTTTCTCTTTGCCCACCAAAACTTTGGTTTGGTAAGAACTA
42

AGCCCTCTTCTTTCCCTTCTCTCTCTTAAAAGCCTAAAATCCACCTAACTTT

TTCAGCCAACAAACAACGCCAAATTCAGAGGAAGAATAATGATGGCTCAA

GCTACTACCATCAACAATGGTGTCCATACTGGTCAATTGCACCATACTTTA

CCCAAAACCCAGTTACCCAAATCTTCAAAAACTCTTAATT

3
CCATACTTTACCCAAAACCCAGTTACCCAAATCTTCAAAAACTCTTAATTTT
43

GGATCAAACTTGAGAATTTCTCCAAAGTTCATGTCTTTAACCAATAAAAGA

GTTGGTGGGCAATCATCAATTGTTCCCAAGATTCAAGCTTCTGTTGCTGCT

GCAGCTGAGAAACCTTCATCTGTCCCAGAAATTGTGTTACAACCCATCAAA

GAGATCTCTGGTACTGTTCAATTGCCTGGGTCAAAGTCTTTATCC

4
TCAAAGAGATCTCTGGTACTGTTCAATTGCCTGGGTCAAAGTCTTTATCCA
44

ATCGAATCCTTCTTTTAGCTGCTTTGTCTGAGGGCACAACAGTGGTCGACA

ACTTGCTGTATAGTGATGATATTCTTTATATGTTGGACGCTCTCAGAACTCT

TGGTTTAAAAGTGGAGGATGATAGTACAGCCAAAAGGGCAGTCGTAGAGG

GTTGTGGTGGTCTGTTTCCTGTTGGTAAAGATGGAAAGGAAGAGAT

5
GAGGGTTGTGGTGGTCTGTTTCCTGTTGGTAAAGATGGAAAGGAAGAGATT
45

CAACTTTTCCTTGGTAATGCAGGAACAGCGATGCGCCCATTGACAGCTGCG

GTTGCCGTTGCTGGAGGAAATTCAAGTTATGTGCTTGATGGAGTACCAAGA

ATGAGGGAGCGCCCCATTGGGGATCTGGTAGCAGGTCTAAAGCAACTTGG

TTCAGATGTAGATTGTTTTCTTGGCACAAATTGCCCTCCTGTTCGGG

6
TGGTTCAGATGTAGATTGTTTTCTTGGCACAAATTGCCCTCCTGTTCGGGTC
46

AATGCTAAAGGAGGCCTTCCAGGGGGCAAGGTCAAGCTCTCTGGATCGGT

TAGTAGCCAATATTTAACTGCACTTCTCATGGCTACTCCTTTGGGTCTTGGA

GACGTGGAGATTGAGATAGTTGATAAATTGATTTCTGTACCGTATGTTGAA

ATGACAATAAAGTTGATGGAACGCTTTGGAGTATCCGTAGAACAT

7
TTGAAATGACAATAAAGTTGATGGAACGCTTTGGAGTATCCGTAGAACAT
47

AGTGATAGTTGGGACAGGTTCTACATTCGAGGTGGTCAGAAATACAAATCT

CCTGGAAAGGCATATGTTGAGGGTGATGCTTCAAGTGCTAGCTACTTCCTA

GCCGGAGCCGCCGTCACTGGTGGGACTGTCACTGTCAAGGGTTGTGGAAC

AAGCAGTTTACAGGGTGATGTAAAATTTGCCGAAGTTCTTGAGAAGAT

8
ACAAGCAGTTTACAGGGTGATGTAAAATTTGCCGAAGTTCTTGAGAAGAT
48

GGGTTGCAAGGTCACCTGGACAGAGAATAGTGTAACTGTTACTGGACCAC

CCAGGGATTCATCTGGAAAGAAACATCTGCGTGCTATCGACGTCAACATG

AACAAAATGCCAGATGTTGCTATGACTCTTGCAGTTGTTGCCTTGTATGCA

GATGGGCCCACCGCCATCAGAGATGTGGCTAGCTGGAGAGTGAAGGAAA

9
AGATGGGCCCACCGCCATCAGAGATGTGGCTAGCTGGAGAGTGAAGGAAA
49

CCGAACGGATGATTGCCATTTGCACAGAACTGAGAAAGCTTGGGGCAACA

GTTGAGGAAGGATCTGATTACTGTGTGATCACTCCGCCTGAAAAGCTAAAC

CCCACCGCCATTGAAACTTATGACGATCACCGAATGGCCATGGCATTCTCT

CTTGCTGCCTGTGCAGATGTTCCCGTCACTATCCTTGATCCGGGATGC

10
CTCTTGCTGCCTGTGCAGATGTTCCCGTCACTATCCTTGATCCGGGATGCAC
50

CCGTAAAACCTTCCCGGACTACTTTGATGTTTTAGAAAAGTTCGCCAAGCA

TTGATGAGTAGCTATATACGAGATCCTTAAATTGTACGCCGAAGGTTTTGA

TTTGAGTCTAATAGTAGATAAAAGGCTATAAATAAACTGGCTTTCTGCTTG

AGTAATTATGAAATTCTTTGTATTATGTTTGTGAGATTTGAAGTAGCTTATA

11
TAATTATGAAATTCTTTGTATTATGTTTGTGAGATTTGAAGTAGCTTATAAA
51

TTACAATGTACTAAAGTCTAGAAATAAGTTATGTATCTTTTAAATCAATGA

GAAATGCATACTTGAAAGGCTTGACCTTGTATTTGTGACCTAAAGAGTACT

AACTTTGGAGTTTCCAACTCATTTGTTTATCTCATTTTTTTTTAATTTTTGAT

TTAAATTGTTTATTTTTATGAGTAATCATGTATCTTTCTTATTCTAACCAAA

TGTAATACTCCTTC

12
TATGAGTAATCATGTATCTTTCTTATTCTAACCAAATGTAATACTCCTTCCA
52

ACTCTCTTTAAACGTCCACACTCTGGGCACAGAGTGTAATAGTGTGGTGGT

TGGAGTCTTTTAAGTGATTATAATAATTGTAAATGTGGTAGTTAGAATATT

TTAAGTAATGTAGGTGGGGTATTATGGTCTTGTTGAACATAGGATATTTAG

GTAAAAAATCTATGCAAAAAAAGGAAAGTAAGCAAATAAAGCGAATTGA

CCTGAAAAGAAAAGTGGACATGTATAGTGAGTTGGAGGAAGTATTTT

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. 25B and 25C. 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.

Example 22

This example illustrates methods using 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.

In one assay, glyphosate-resistant Palmer amaranth plants having 16 copies of EPSPS were sprayed with glyphosate applied at 840 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide at a rate of 159 liters/acre. Two or 24 hours after herbicide application, the plants were treated by spraying with 1% SILWET L-77. Fifteen to 20 minutes after SILWET treatment, 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. In this assay, untreated (“UT”) control plants were treated only with the 1% SILWET L-77 spray but not with herbicide or dsRNA. Results are depicted in FIG. 26. In this assay, application of 1% SILWET resulted in improved glyphosate activity by 60% when applied 2 hours after herbicide spraying and by 20% when applied 24 hours after herbicide spraying. In this assay, application of 1% SILWET followed by EPSPS dsRNA resulted in improved glyphosate activity by at least 80% when applied 2 hours after herbicide spraying and by 20% when applied 24 hours after herbicide spraying.

In another assay, Palmer amaranth plants grown from seeds in soil from a farm site in Macon, Ga. were sprayed with glyphosate applied at 840 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide at a rate of 159 liters/acre. Three days after herbicide treatment, 9 of 40 plants were killed and 3 were severely stunted. Surviving plants were sprayed with 1% SILWET L-77, followed by topical application by hand of either 8 nanomoles (“10”) per plant of the four oligonucleotide-size “short” EPSPS dsRNA molecules as described in Example 1 or buffer as a control. Three days later, 3 more plants in the dsRNA-treated group were dead and 2 more plants in the buffer-treated group were dead. At this point (6 days after the original herbicide treatment and 3 days after the SILWET/dsRNA or buffer treatment), half of the surviving plants in each group were sprayed with a second application of glyphosate (applied at the same dose as in the first application). Two weeks after this second herbicide treatment, the remaining dsRNA-treated plants showed 80% injury and the remaining buffer-treated plants showed 40% injury.

Example 23

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.

Four to six inch tall plants in a treatment area of 1 foot by 5 feet were sprayed in a single treatment with either 264 micrograms (“100×”) or 52.8 micrograms (“20×”) of the EPSPS dsRNAs in a solution that also contained 1% SILWET L-77 surfactant, 2% ammonium sulfate, and glyphosate (applied at 1682 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide at a rate of 159 liters/acre). For comparison, other plants in treatment areas of 1 foot by 5 feet were sprayed with glyphosate (in a solution that also contained 1% SILWET L-77 surfactant and 2% ammonium sulfate) applied at the same rate.

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).

Example 24

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. In this example, 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. More specifically, 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).

Lettuce PDS has the sequence ATGTCTCTGTTTGGAAATGTTTCTGCCATTAACTCAAGTGGAAAGTGTATAGTAATGAATCTTTCAAGC ACACAAATCACTTCAAGAGATTGTTTCAAGATTACCTCAGGGCAAAAAGATGTTTTGTCATTTGGATG CTGTGATGCTATGGGTAACAGATTGCAATTCCCAAGTGCTCGTTCTTTTACACCAAGATCAAAGAAGA ATGTCTCCCCTCTAAAGGTAGTTTGTGTTGATTATCCAAGACCAGATCTTGATAACACATCTAATTTCT TGGAAGCTGCTCACTTGTCTTCAACCTTCAGAACTTCCCCACGCCCATCTAAGCCATTGAAGATTGTAA TTGCTGGTGCAGGTTTAGCTGGTTTATCAACTGCTAAGTATTTAGCTGATGCAGGTCACAAGCCAATTT TACTAGAAGCAAGAGATGTTCTTGGTGGAAAGGTGGCAGCTTGGAAAGATGATGATGGAGATTGGTA TGAGACAGGTTTACACATATTCTTTGGAGCTTACCCAAATGTACAAAATTTATTTGGAGAGCTAGGAA TTAATGATAGATTACAGTGGAAGGAGCATTCTATGATATTTGCAATGCCAAATAAGCCTGGAGAATTT AGTAGGTTTGACTTCCCAGATGTTTTACCTGCACCATTGAATGGAATTTTTGCTATATTGAGGAACAAT GAAATGCTGACGTGGCCTGAGAAAGTGAAGTTTGCAATTGGGCTGTTGCCTGCAATGTTAGGTGGACA GGCTTATGTTGAGGCCCAAGATGGGCTTAGTGTTCAGGACTGGATGAGAAAGCAAGGTATACCTGATC GAGTTACTACTGAAGTGTTTATTGCAATGTCAAAAGCATTAAACTTTATAAATCCAGATGAACTTTCAA TGCAATGTATTCTCATTGCTCTAAACCGTTTTCTTCAGGAAAAGCATGGTTCCAAGATGGCATTTTTAG ATGGGAGCCCACCAGAAAGACTTTGCAAGCCAATTGTTGACCACATCGAGTCACTCGGTGGCCAAGTC AGAGTCAACTCACGAATACAAAAAATTGAGTTAAACAAAGACGGAACTGTCCGGAACTTTCTATTGAG TGATGGGAATGTTCTAGAAGCTGATGCTTATGTTTTCGCTACCCCTGTTGACATTCTCAAGCTTCTTTTA CCCGAAGAATGGAAACCAATTCCATATTTCAAAAAATTAGAGAAGTTAGTCGGTGTTCCTGTTATAAA CGTTCATATATGGTTTGACAGAAAGCTGAAAAACACATATGATCACTTACTTTTCAGTAGGTCACCTCT GCTGAGTGTGTATGCTGACATGTCAGTGACATGTAAGGAATATTATGATCCGAATAAGTCAATGTTGG AGTTGGTTCTTGCTCCAGCTGAGGAATGGATTTCAAGAAGTGACACTGATATTATTGATGCAACAATG AGTGAACTTTCAAGGCTTTTTCCTGATGAAATTGCAGCTGATCAAAGTAAAGCAAAAATCTTGAAATA TAAAGTTGTTAAAACACCAAGGTCTGTTTATAAAACTGTTCCAGATTGTGAACCATGTCGACCCCTACA AAGATCTCCAATTCAAGGATTTTATTTATCTGGTGATTATACTAAACAAAAGTATTTGGCTTCAATGGG GGGTGCTGTTTTATCTGGAAAAATTTGTGCACAAGCTATTTTACAAGATTATGAGATGCTTGCTACA (SEQ ID NO:53). 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 caaataaattttgtacamgggtaagctccaa (“HL290”, anti-sense orientation, SEQ ID NO:58). An ssDNA solution was made with an equal mixture of all five polynucleotides in 0.01% SILWET L-77 in 5 millimolar sodium phosphate buffer, pH 6.8.

Lettuce variety LS49 “Green Tower” was used in the assays. Two fully expanded leaves of each plant were dipped into a freshly made 0.1% SILWET L-77 in double-distilled water solution for a few seconds. The leaves were allowed to dry for 15-30 minutes. Each plant was then treated by applying 20 microliters ssDNA solution to the top surface of two SILWET-treated leaves (total 40 microliters per plant). Table 9 lists the assay conditions used and the observed bleaching of plants topically treated with ssDNA polynucleotides. 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.

TABLE 9

Amount of each

ssDNA applied
Earliest observation

Developmental stage
(nanomoles/plant)
of bleaching

4 weeks post-germination,
1
3 weeks post-treatment

plants have 2 fully

expanded leaves

5 weeks post-germination,
4
4 days post-treatment

plants have 4 fully

expanded leaves

The assays were repeated with 2 or 4 nanomoles ssDNA applied per plant. FIG. 29A depicts the systemic silencing evidenced by bleaching observed at 4 or 12 days after topical treatment with the polynucleotides.

The assays were repeated using each individual anti-sense ssDNAs (“HL287”, SEQ ID NO:55; “HL288”, SEQ ID NO:56; “HL289”, SEQ ID NO:57; and “HL290”, SEQ ID NO:58) with 8 nanomoles polynucleotide applied per plant; positive control plants were treated with a mixture of the four individual anti-sense ssDNAs at 2 nanomoles each (for a total of 8 nanomoles polynucleotide applied per plant) and negative control plants were treated only with buffer. FIG. 29B depicts the systemic silencing evidenced by bleaching observed at 4 after topical treatment with the anti-sense ssDNAs.

Example 25

Tomato PDS has the sequence GGGTTTATCTCGCAAGTGTGGCTATGGTGGGACGTGTCAAATTTTGGATTGTAGCCAAACATGAGATTT GATTTAAAGGGAATTGGCCAAATCACCGAAAGCAGGCATCTTCATCATAAATTAGTTTGTTTATTTATA CAGAATTATACGCTTTTACTAGTTATAGCATTCGGTATCTTTTTCTGGGTAACTGCCAAACCACCACAA ATTTCAAGTTTCCATTTAACTCTTCAACTTCAACCCAACCAAATTTATTTGCTTAATTGTGCAGAACCAC TCCCTATATCTTCTAGGTGCTTTCATTCGTTCCGAGTAAAATGCCTCAAATTGGACTTGTTTCTGCTGTT AACTTGAGAGTCCAAGGTAGTTCAGCTTATCTTTGGAGCTCGAGGTCGTCTTCTTTGGGAACTGAAAGT CGAGATGGTTGCTTGCAAAGGAATTCGTTATGTTTTGCTGGTAGCGAATCAATGGGTCATAAGTTAAA GATTCGTACTCCCCATGCCACGACCAGAAGATTGGTTAAGGACTTGGGGCCTTTAAAGGTCGTATGCA TTGATTATCCAAGACCAGAGCTGGACAATACAGTTAACTATTTGGAGGCTGCATTTTTATCATCAACGT TCCGTGCTTCTCCGCGCCCAACTAAACCATTGGAGATTGTTATTGCTGGTGCAGGTTTGGGTGGTTTGT CTACAGCAAAATATTTGGCAGATGCTGGTCACAAACCGATACTGCTGGAGGCAAGGGATGTTCTAGGT GGAAAGGTAGCTGCATGGAAAGATGATGATGGAGATTGGTACGAGACTGGTTTGCATATATTCTTTGG GGCTTACCCAAATATTCAGAACCTGTTTGGAGAATTAGGGATTAACGATCGATTGCAATGGAAGGAAC ATTCAATGATATTTGCAATGCCAAGCAAGCCAGGAGAATTCAGCCGCTTTGATTTCTCCGAAGCTTTAC CCGCTCCTTTAAATGGAATTTTAGCCATCTTAAAGAATAACGAAATGCTTACATGGCCAGAGAAAGTC AAATTTGCAATTGGACTCTTGCCAGCAATGCTTGGAGGGCAATCTTATGTTGAAGCTCAAGATGGGAT AAGTGTTAAGGACTGGATGAGAAAGCAAGGTGTGCCGGACAGGGTGACAGATGAGGTGTTCATTGCT ATGTCAAAGGCACTCAACTTTATAAACCCTGACGAACTTTCAATGCAGTGCATTTTGATCGCATTGAAC AGGTTTCTTCAGGAGAAACATGGTTCAAAAATGGCCTTTTTAGATGGTAATCCTCCTGAGAGACTTTGC ATGCCGATTGTTGAACACATTGAGTCAAAAGGTGGCCAAGTCAGACTGAACTCACGAATAAAAAAGA TTGAGCTGAATGAGGATGGAAGTGTCAAGAGTTTTATACTGAGTGACGGTAGTGCAATCGAGGGAGAT GCTTTTGTGTTTGCCGCTCCAGTGGATATTTTCAAGCTTCTATTGCCTGAAGACTGGAAAGAGATTCCA TATTTCCAAAAGTTGGAGAAGTTAGTCGGAGTACCTGTGATAAATGTACATATATGGTTTGACAGAAA ACTGAAGAACACATATGATCATTTGCTCTTCAGCAGAAGCTCACTGCTCAGTGTGTATGCTGACATGTC TGTTACATGTAAGGAATATTACAACCCCAATCAGTCTATGTTGGAATTGGTTTTTGCACCTGCAGAAGA GTGGATATCTCGCAGCGACTCAGAAATTATTGATGCAACGATGAAGGAACTAGCAACGCTTTTTCCTG ATGAAATTTCAGCAGATCAAAGCAAAGCAAAAATATTGAAGTACCATGTTGTCAAAACTCCGAGGTCT GTTTATAAAACTGTGCCAGGTTGTGAACCCTGTCGGCCTTTACAAAGATCCCCAATAGAGGGGTTTTAT TTAGCCGGTGACTACACGAAACAGAAATACTTGGCTTCAATGGAAGGCGCTGTCTTATCAGGAAAGCT TTGTGCTCAAGCTATTGTACAGGATTATGAGTTACTTGTTGGACGTAGCCAAAAGAAGTTGTCGGAAG CAAGCGTAGTTTAGCTTTGTGGTTATTATTTAGCTTCTGTACACTAAATTTATGATGCAAGAAGCGTTG TACACAACATATAGAAGAAGAGTGCGAGGTGAAGCAAGTAGGAGAAATGTTAGGAAAGCTCCTATAC AAAAGGATGGCATGTTGAAGATTAGCATCTTTTTAATCCCAAGTTTAAATATAAAGCATATTTTATGTA CCACTTTCTTTATCTGGGGTTTGTAATCCCTTTATATCTTTATGCAATCTTTACGTTAGTTAAAAAAAAA AAAAAAAAAAAAAACTCGA (SEQ ID NO:59).

A 201 nucleotide dsRNA polynucleotide with an anti-sense strand capable of hybridizing to the RNA encoded by the sequence TCGCAGCGACTCAGAAATTATTGATGCAACGATGAAGGAACTAGCAACGCTTTTTCCTGATGAAATTT CAGCAGATCAAAGCAAAGCAAAAATATTGAAGTACCATGTTGTCAAAACTCCGAGGTCTGTTTATAAA ACTGTGCCAGGTTGTGAACCCTGTCGGCCTTTACAAAGATCCCCAATAGAGGGGTTTTATTTAG (SEQ ID NO:60) which correspond to the nucleotides at positions 1724-1923 of the mRNA transcribed from the tomato PDS gene sequence (SEQ ID NO:59) was synthesized by RT PCR using oligonucleotide primers with the sequences TAATACGACTCACTATAGGGTCGCAGCGACTCAGAAATTATTG (SEQ ID NO:61, sense primer) and TAATACGACTCACTATAGGGGTAAAGGCCGACAGGGTTCACAACC (SEQ ID NO:62, anti-sense primer). 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.

Three-week old tomato seedlings were treated as follows. Two fully expanded leaves were dipped into a freshly made 0.1% SILWET L-77 solution in double-distilled water for a few seconds. The leaves were allowed to dry for 30 minutes to 1 hour. Each plant was then treated by applying 20 microliters dsRNA solution to the top surface of two SILWET-treated leaves (total 40 microliters per plant). Control plants were treated with buffer. The plants were kept in a growth chamber for observation. 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.

Example 26

This example illustrates an improvement to herbicidal compositions adapted for topical coating onto the exterior surface of a growing plant where 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. More specifically 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.

The herbicidal composition includes at least one of the following 21-base-pair double-stranded RNA polynucleotides:

(1) nDsRNA1:

(SEQ ID NO: 63)

sense strand CUACCAUCAACAAUGGUGUCC

and

(SEQ ID NO: 64)

anti-sense strand GGACACCAUUGUUGAUGGUAG

(2) nDsRNA3:

(SEQ ID NO: 65)

sense strand GUCGACAACUUGCUGUAUAGU

and

(SEQ ID NO: 66)

anti-sense strand ACUAUACAGCAAGUUGUCGAC

(3) nDsRNA4:

(SEQ ID NO: 67)

sense strand GGUCACCUGGACAGAGAAUAG

and

(SEQ ID NO: 68)

anti-sense strand CUAUUCUCUGUCCAGGUGACC

(4) nDsNA5:

(SEQ ID NO: 69)

sense strand AAUGCCAGAUGUUGCUAUGAC

and

(SEQ ID NO: 70)

anti-sense strand GUCAUAGCAACAUCUGGCAUU

A mixture of multiple polynucleotides is advantageous for preventing selection of resistance in the treated plants. In an embodiment, the herbicidal composition includes a mixture of all four of the above dsRNA polynucleotides having SEQ ID NOS: 63-70. In another embodiment, 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. In another embodiment, the herbicidal composition includes RNA/DNA hybrids with nucleotide sequences corresponding to one or more of the dsRNA sequences SEQ ID NOS: 63-70. In another embodiment, 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). Optionally, 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.

Optionally the herbicidal composition includes polynucleotides designed to regulate multiple genes in the plant. In an embodiment, 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.

In an embodiment, 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. Arabidopsis thaliana has an orthologue named AT1G17220.1 (described on the publicly available database The Arabidopsis Information Resource found online at www.arabidopsis.org/servlets/TairObject?type=locus&name=AT1G17220) and assigned GenBank accession number GI: 186478573, which has been identified as a chloroplast localized protein with similarity to bacterial translation initiation factor 2; see also Miura et al. (2007) Plant Cell, 19:1313-1328 for a description of this gene. 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.

TABLE 10

Position in

SEQ

Poly-
TIF

ID

nucleotide
sequence
Sequence
NO.

Palmer
Entire
ATGGCAACAATGGCTTCCCTAGTGAGTTTGGGAAGCTCTGGAG
71

amaranth TIF
sequence of
CAACTTGCTCAGGGCAATTGGAGGTTTCCTTTTCATTGGTTAAG

SEQ ID
AAAATTACATTGCCTAGAAGAAATTGTAGTTGCAATTTTAGGCA

NO: 71
ATTAGGAGGGGGGAGGAGATGGCGTTACGTTTCGGTGTGTAGA

CTTTCTGTCACTACTGATTATGTTTCTGAGCAAGGAAATGCTGT

TTCTCTTGAAAATGCATATAGTGAGAGTAAAGAAGAGGGTCTC

ATCTTGAAGCCTTCTCCTAAGCCGGTTTTGAAATCCGGGTCTGA

TGGAAATCGGAAATTTGGGGAGAGTTCGGTGGCGTTTTCGAGT

AATGGGAAATTGGATAATGTAGAGGAGAGGAAGAAGGTTATTG

ATTCATTGGATGAGGTATTAGAAAAGGCCGAGAGATTAGAAAC

GGCGAACTTACAAGCAGATAATAGAAAGGATAGCACAAATGTA

AATAAACCGTCTCCGAGTGTAAGTAGTTCAACCAATGGTAAAC

CTGTAAATAATTTGAACAAAGGGAAGCCTAAAGCTGCGAAGAG

CGTTTGGAGAAAGGGAAATCCAGTTTCTACTGTGCAAAAAGTA

GTGCAAGAATCTCCGAAGATTGAAAAGGTTGAGAGAGTGGAAG

CTCGAACGACCAGCCAATCGTCTGAAACGATAAGACCCCCAGT

GCCACTACAGAGGCCTGAGATTAAGTTGCAGGCAAAGCCTTCT

ACTGCTCCTCCACCCATGCCTAAGAAGCCGGTTTTGAAGGATGT

GGGGATGTCCTCCAGAGCTGATGGGAAGGACCAGTCTGTGAAA

TCTAAAGAGAGGAAGCCTATTCTAGTGGACAAATTTGCCACCA

AGAAGGCATCAGTTGATCCGTCGATTGCTCAAGCAGTAATTGC

CCCACCAAAACCTGCTAAATTTCCTTCTGGAAAGTTTAAAGATG

ATTATCGGAAGAAGGGTCTTGCAGCTGGTGGGCCGAAGAGGCG

TATGGTCAATGATGATGATATTGAAATGCATGAAGACACTTCA

GAGCTCGGTCTTTCTATTCCTGGTGCTGCTACGGCTCGGAAAGG

CAGGAAATGGAGTAAGGCAAGTCGCAAGGCTGCCAGACGCCA

AGCAGCTAGAGATGCCGCTCCTGTTAAAGTGGAAATCTTAGAG

GTTGAAGAAAAGGGCATGTCGACCGAAGAATTAGCATACAACT

TGGCTATTAGCGAAGGTGAAATTCTTGGGTACCTGTATTCTAAG

GGGATAAAACCAGATGGTGTGCAAACTCTTGACAAGGCAATGG

TAAAGATGATATGTGAAAGATATGACGTGGAGGTTTTGGACGC

ACTTTCTGAACAAATGGAAGAAATGGCTCGAAAGAAGGAAATT

TTCGACGAAGATGACCTTGACAAGCTTGAAGATAGGCCTCCTG

TGCTTACTATAATGGGTCATGTAGATCATGGCAAGACGACCCTT

CTGGATTATATACGGAAGAGCAAGGTTGCTGCTTCTGAAGCTG

GTGGGATTACACAAGGTATTGGTGCTTATAAAGTGGAAGTACC

GGTTGATGGCAAGTTGCTGCCTTGTGTCTTTCTTGACACTCCCG

GACACGAGGCGTTCGGGGCAATGAGGGCTCGTGGAGCAAGAGT

GACAGATATTGCTATTATAGTTGTAGCTGCTGACGATGGGATCC

GTCCTCAAACAAATGAAGCCATAGCACATGCAAAAGCAGCTGG

TGTACCTATTGTGGTTGCAATTAATAAGATTGACAAGGATGGG

GCTAATCCGGACCGTGTGATGCAAGAGCTTTCATCAATTGGTCT

AATGCCAGAGGATTGGGGTGGTGATACCCCAATGGTCAAGATA

AGTGCTCTAAAAGGTGAAAATGTGGACGAGTTACTCGAGACAG

CCATGCTTGTCGCCGAGTTGCAAGAGTTAAAGGCTAATCCTCAG

AGGAACGCTAAGGGCACTGTAATTGAGGCTGGTCTTCATAAAT

CAAAAGGACCCATTGCCACTTTTATTGTGCAGAATGGTACCCTC

AAACAAGGGGATACTGTAGTTTGTGGGGAAGCATTTGGGAAGG

TTCGTGCCCTATTTGATCACGGAGGGAATCGCGTTGATGAAGCT

GGTCCATCTATTCCCGTGCAGGTTATTGGATTGAATAATGTTCC

TTTTGCCGGTGATGAGTTCGAGGTAGTGAGTTCCCTTGATATAG

CTCGTGAAAAGGCAGAGGTCCGTGCAGAGTCTTTACGAAATGA

GCGTATAGCTGCTAAGGCCGGAGACGGAAAGGTTACGCTGTCA

TCCTTGGCATCGGCTGTTTCTTCAGGGAAGATGGCTGGTTTGGA

TTTGCACCAGTTAAATATCATTTTGAAGGTTGATGTTCAGGGAT

CAATCGAGGCATTGAGGCAAGCTCTAGAAGTTCTTCCTCAAGA

TAACGTCACTTTGAAGTTTCTCTTACAAGCGACCGGAGATGTTA

CTACAAGTGATGTTGATCTTGCAGTTGCTAGTAAAGCTATTATC

TTGGGGTTCAATGTGAAGGCACCAGGTTCTGTCGAAAAATTAG

CAGATAACAAAGGTGTTGAAATTCGGCTTTATAAAGTCATTTAT

GATCTAATTGACGACATGCGGAGTGCAATGGAAGGAATGCTAG

ATCCCGTTGAGGAACAAGTTGCAATTGGTTCAGCCGAAGTGCG

GGCTACATTCAGTAGTGGTAGTGGCCGTGTCGCTGGATGCATG

GTGACCGAGGGAAAGATTACCAAAGGCTGTGGGATTCGAGTGA

TACGGAAGGGAAAAACTGTCCACGTTGGAGTTCTTGATTCGTTG

CGTCGAGTAA

200 bp DNA
341-541
TTTCGAGTAATGGGAAATTGGATAATGTAGAGGAGAGGAAGAA
72

GGTTATTGATTCATTGGATGAGGTATTAGAAAAGGCCGAGAGA

TTAGAAACGGCGAACTTACAAGCAGATAATAGAAAGGATAGCA

CAAATGTAAATAAACCGTCTCCGAGTGTAAGTAGTTCAACCAA

TGGTAAACCTGTAAATAATTTGAACAAA

160 bp
342-501
Sense:
73

dsRNA

UUCGAGUAAUGGGAAAUUGGAUAAUGUAGAGGAGAGGAAGA

AGGUUAUUGAUUCAUUGGAUGAGGUAUUAGAAAAGGCCGAG

AGAUUAGAAACGGCGAACUUACAAGCAGAUAAUAGAAAGGA

UAGCACAAAUGUAAAUAAACCGUCUCCGAGUGUAAGU

Anti-sense:
74

ACUUACACUCGGAGACGGUUUAUUUACAUUUGUGCUAUCCUU

UCUAUUAUCUGCUUGUAAGUUCGCCGUUUCUAAUCUCUCGGC

CUUUUCUAAUACCUCAUCCAAUGAAUCAAUAACCUUCUUCCU

CUCCUCUACAUUAUCCAAUUUCCCAUUACUCGAA

anti-sense
555-576
ATTTCTCCAAACGCTCTTCGCA
75

DNA

TIF_AS1

anti-sense
342-363
ATCCAATTTCCCATTACTCGAA
76

DNA

TIF_AS2

anti-sense
412-433
GTTTCTAATCTCTCGGCCTTTT
77

DNA

TIF_AS3

anti-sense
488-509
TTGAACTACTTACACTCGGAG
78

DNA

TIF_AS4

anti-sense
368-389
TAACCTTCTTCCTCTCCTCTA
79

DNA

TIF_AS5

anti-sense
790-811
GTCCTTCCCATCAGCTCTGGA
80

DNA

TIF_AS6

anti-sense
1052-1073
CGTAGCAGCACCAGGAATAG
81

DNA

TIF_AS7

anti-sense
1655-1676
CAGCAGCTACAACTATAATAG
82

DNA

TIF_AS8

In an embodiment, 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. In a specific embodiment, 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 UUCGAGUAAUGGGAAAUUGGAUAAUGUAGAGGAGAGGAAGAAGGUUAUUGAUUC AUUGGAUGAGGUAUUAGAAAAGGCCGAGAGAUUAGAAACGGCGAACUUACAAGC AGAUAAUAGAAAGGAUAGCACAAAUGUAAAUAAACCGUCUCCGAGUGUAAGU (SEQ ID NO. 73) and the anti-sense sequence of ACUUACACUCGGAGACGGUUUAUUUACAUUUGUGCUAUCCUUUCUAUUAUCUGC UUGUAAGUUCGCCGUUUCUAAUCUCUCGGCCUUUUCUAAUACCUCAUCCAAUGAA UCAAUAACCUUCUUCCUCUCCUCUACAUUAUCCAAUUUCCCAUUACUCGAA (SEQ ID NO. 74).

In some embodiments, the polynucleotides are designed to regulate multiple target genes, resulting in a synergistic effect on herbicide activity. For example, 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.

The polynucleotides listed in Table 11 were produced by synthesis or by in vitro transcription.

TABLE 11

Name
Comments
Nucleotide sequences

IDT [1]
Palmer/EPSPS
Sense: CUACCAUCAACAAUGGUGUCCAUAC (SEQ ID NO. 83)

dsRNA with two 2-
Anti-sense: GUAUGGACACCAUUGUUGAUGGUAGUA (SEQ ID NO. 84)

IDT [2]
deoxyribonucleotides
Sense: AGUUGGUGGGCAAUCAUCAAUUGTT (SEQ ID NO. 85)

(in bold
Anti-sense: AACAAUUGAUGAUUGCCCACCAACUCU (SEQ ID NO. 86)

IDT [3]
underlined text) at
Sense: GGUCGACAACUUGCUGUAUAGUGAT (SEQ ID NO. 87)

3′ end of sense
Anti-sense: AUCACUAUACAGCAAGUUGUCGACCUC (SEQ ID NO. 88)

IDT [4]
strand (25-mer) and
Sense: UGCAAGGUCACCUGGACAGAGAATA (SEQ ID NO. 89)

a 2-nucleotide
Anti-sense: UAUUCUCUGUCCAGGUGACCUUGCAAC (SEQ ID NO. 90)

overhang at 3′ end

of anti-sense strand

(27-mer);

chemically

synthesized by IDT

IDT [5]
Palmer/EPSPS
Sense: AACAUGAACAAAAUGCCAGAU (SEQ ID NO. 91)

dsRNA (21-
Anti-sense: AUCUGGCAUUUUGUUCAUGUU (SEQ ID NO. 92)

mer) with blunt

ends;

chemically

synthesized by

IDT

IDT
Palmer/EPSPS
1S-Anti-sense GUAUGGACACCAUUGUUGAUGGUAGUA (SEQ ID NO. 93)

blunt[1]
dsRNA (27-
1S-Sense UACUACCAUCAACAAUGGUGUCCAUAC (SEQ ID NO. 94)

IDT blunt
mer) with blunt
2S-Anti-sense AAUAAUUGAUGAUUGCCCACCAACUCU (SEQ ID NO. 95)

[2]
ends;
2S-Sense AGAGUUGGUGGGCAAUCAUCAAUUAUU (SEQ ID NO. 96)

IDT blunt
synthesized via
3S-Anti-sense AUCACUAUACAGCAAGUUGUCGACCAC (SEQ ID NO. 97)

[3]
in vitro T7
3S-Sense GUGGUCGACAACUUGCUGUAUAGUGAU (SEQ ID NO. 98)

IDT blunt
transcription
4S-Anti-sense UAUUCUCUGUCCAGGUGACCUUGCAAC (SEQ ID NO. 99)

[4]

4S-Sense GUUGCAAGGUCACCUGGACAGAGAAUA (SEQ ID NO. 100)

3OH [1]
Palmer/EPSPS
1S-Anti-sense gGUAUGGACACCAUUGUUGAUGGUAGUAC (SEQ ID NO.

dsRNA (27-
101)

mer) with 3′-
1S-Sense GCUACCAUCAACAAUGGUGUCCAUACCAC (SEQ ID NO. 102)

3OH [2]
overhangs;
2S-Anti-sense gAAGAAUUGAUGAUUGCCCACCAACUCAC (SEQ ID NO.

synthesized via
103)

in vitro T7
2S-Sense GAGUUGGUGGGCAAUCAUCAAUUAUUCAC (SEQ ID NO. 104)

3OH [3]
transcription
3S-Anti-sense gAUCACUAUACAGCAAGUUGUCGACAC (SEQ ID NO.

105)

3S-Sense GUCGACAACUUGCUGUAUAGUGAUCAC (SEQ ID NO. 106)

3OH [4]

4S-Anti-sense gUAUUCUCUGUCCAGGUGACCUUGCACAC (SEQ ID NO.

107)

4S-Sense GUGCAAGGUCACCUGGACAGAGAAUACAC (SEQ ID NO.

108)

IDT HP [1]
Palmer/EPSPS
1S-

single strand of
GUAUGGACACCAUUGUUGAUGGUAGUAGAAAUACUACCAUCAACAA

RNA designed
UGGUGUCCAUAC (SEQ ID NO. 109)

IDT HP [2]
to self-hybridize
2S-

into a hairpin,
AAUAAUUGAUGAUUGCCCACCAACUCUGAAAAGAGUUGGUGGGCAAUC

containing anti-
AUCAAUUAUU (SEQ ID NO. 110)

IDT HP [3]
sense sequence
3S-

on the 5′ arm
AUCACUAUACAGCAAGUUGUCGACCACGAAAGUGGUCGACAACUUG

and anti-sense
CUGUAUAGUGAU (SEQ ID NO. 111)

IDT HP [4]
sequence on the
4S-

3′ arm, with an
UAUUCUCUGUCCAGGUGACCUUGCAACGAAAGUUGCAAGGUCACC

intermediate
UGGACAGAGAAUA (SEQ ID NO. 112)

GAAA

tetranucleotide

loop;

chemically

synthesized by

IDT

[TIF]
Palmer/translation
Sense:

initiation factor
UUCGAGUAAUGGGAAAUUGGAUAAUGUAGAGGAGAGGAAGAAGGUU

(TIF) dsRNA (160-
AUUGAUUCAUUGGAUGAGGUAUUAGAAAAGGCCGAGAGAUUAGAAA

mer) synthesized
CGGCGAACUUACAAGCAGAUAAUAGAAAGGAUAGCACAAAUGUAAAU

via in vitro T7
AAACCGUCUCCGAGUGUAAGU (SEQ ID NO. 73)

transcription
Anti-sense:

ACUUACACUCGGAGACGGUUUAUUUACAUUUGUGCUAUCCUUUCUAU

UAUCUGCUUGUAAGUUCGCCGUUUCUAAUCUCUCGGCCUUUUCUAAU

ACCUCAUCCAAUGAAUCAAUAACCUUCUUCCUCUCCUCUACAUUAUC

CAAUUUCCCAUUACUCGAA (SEQ ID NO. 74)

[ddATPase]
Palmer/DNA-
Sense:

dependent ATPase
GAUCACAAAUUUGCCGGUUUAUGAUCAAAUACGGAACAUAAGACAGA

(ddATPase)
UACACUUGAACACCAUGAUUCGCAUUGGGGGUGUGGUUACUCGUCGU

dsRNA (168-mer)
UCUGGAGUAUUCCCUCAGUUGAUGCAGGUGAAGUAUGACUGCAAUAA

synthesized via in
AUGUGGGGCUAUCCUGGGUCCCUUUUU (SEQ ID NO. 113)

vitro T7
Anti-sense:

transcription
AAAAAGGGACCCAGGAUAGCCCCACAUUUAUUGCAGUCAUACUUCAC

CUGCAUCAACUGAGGGAAUACUCCAGAACGACGAGUAACCACACCCC

CAAUGCGAAUCAUGGUGUUCAAGUGUAUCUGUCUUAUGUUCCGUAUU

UGAUCAUAAACCGGCAAAUUUGUGAUC (SEQ ID NO. 114)

Solutions of the polynucleotides were prepared and applied to the leaves of Palmer amaranth using the protocols described in Table 12.

TABLE 12

Protocol

number

(description)
Protocol

1
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. Spray mixture of polynucleotides in 1% Silwet L-77, 2% ammonium sulfate in 10

(1-step sprayer)
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 Milli sprayer

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)

3
1. Spray 1% Silwet as 1^ststep by regular sprayer or Milli sprayer;

(2-step hand)
2. Apply mixture of polynucleotides in 1% Silwet L-77, 2% ammonium sulfate in 10

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

3. 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)

4
1. Spray 1% Silwet as 1^ststep by regular sprayer or Milli sprayer;

(2-step sprayer)
2. Spray mixture of polynucleotides in 1% Silwet L-77, 2% ammonium sulfate in 10

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 Milli sprayer

3. 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)

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.

Combinations of polynucleotides were tested as indicated in Table 13.

TABLE 13

Amount

applied of
Total

Polynucleotides
SEQ

each
polynucleotide
EPSPS

applied in
ID

polynucleotide
applied
copy

combination
NO.
Protocol
(g/acre)
(g/acre)
number*
Results**

IDT [1]
83, 84,
1
0.29
0.87
112
75% killed

IDT [3]
87, 88

0.29

(27 DAT)

IDT [4]
89, 90

0.29

IDT [1]
83, 84,
1
0.29
1.4
112
100% killed

IDT [3]
87, 88

0.29

(27 DAT)

IDT [4]
89, 90

0.29

[TIF]
73, 74

0.50

IDT [1]
83, 84,
1
0.29
1.37
112
11.2%

IDT [3]
87, 88

0.29

stunted

IDT [4]
89, 90

0.29

(27 DAT)

[ddATPase]
113, 114

0.50

IDT [1]
83, 84,
1
0.29
1.87
112
100% killed

IDT [3]
87, 88

0.29

(27 DAT)

IDT [4]
89, 90

0.29

[TIF]
73, 74

0.50

[ddATPase]
114, 114

0.50

IDT [1]
83, 84,
1
0.29
1.2
112, 36
0% control

IDT [2]
85, 86

0.29

(11 DAT);

IDT [3]
87, 88

0.29

0% control

IDT [4]
89, 90

0.29

(31 DAT)

IDT [1]
83, 84,
1
1.4
5.8
112, 36
0% control

IDT [2]
85, 86

1.4

(11 DAT);

IDT [3]
87, 88

1.4

15% stunted

IDT [4]
89, 90

1.4

(31 DAT)

IDT [1]
83, 84,
1
2.9
12
112, 36
0% control

IDT [2]
85, 86

2.9

(11 DAT);

IDT [3]
87, 88

2.9

35% stunted

IDT [4]
89, 90

2.9

(31 DAT)

IDT [1]
83, 84,
1
5.8
23
112, 36
51% stunted

IDT [2]
85, 86

5.8

(11 DAT);

IDT [3]
87, 88

5.8

100%

IDT [4]
89, 90

5.8

stunted (31

DAT)

IDT [1]
83, 84,
2
0.29
1.2
33, 54
9% stunted

IDT [2]
85, 86

0.29

(6 DAT)

IDT [3]
87, 88

0.29

IDT [4]
89, 90

0.29

IDT [1]
83, 84,
2
5.8
23
33, 54
100% killed

IDT [2]
85, 86

5.8

(6 DAT)

IDT [3]
87, 88

5.8

IDT [4]
89, 90

5.8

IDT [1]
83, 84,
2
0.29
0.87
33, 54
20% stunted

IDT [3]
87, 88

0.29

(6 DAT)

IDT [4]
89, 90

0.29

IDT [1]
83, 84,
2
5.8
17
33, 54
100% killed

IDT [3]
87, 88

5.8

(6 DAT)

IDT [4]
89, 90

5.8

IDT [5]
91, 92
1
0.29
0.29
34, 36, 54
14.1%

stunted

(22 DAT)

IDT [5]
91, 92
1
2.9
2.9
34, 36, 54
100% kill

(22 DAT)

IDT [1]
83, 84,
1
2.9
12
34, 36, 54
100% killed

IDT [2]
85, 86

2.9

(22 DAT)

IDT [3]
87, 88

2.9

IDT [4]
89, 90

2.9

IDT [1]
83, 84,
1
2.9
14
34, 36, 54
100% killed

IDT [2]
85, 86

2.9

(22 DAT)

IDT [3]
87, 88

2.9

IDT [4]
89, 90

2.9

IDT [5]
91, 92

2.9

IDT [1]
83, 84,
1
2.9
8.7
34, 36, 54
100% killed

IDT [3]
87, 88

2.9

(22 DAT)

IDT [4]
89, 90

2.9

IDT [1]
83, 84,
1
2.9
12
34, 36, 54
100% killed

IDT [3]
87, 88

2.9

(22 DAT)

IDT [4]
89, 90

2.9

IDT [5]
91, 92

2.9

IDT [5]
91, 92
1
0.29
0.29
33, 54, 55
71%

stunted

(18 DAT)

IDT [5]
91, 92
1
2.9
2.9
33, 54, 55
100% killed

(18 DAT)

IDT [1]
83, 84,
1
0.29
1.4
33, 54, 55
100% killed

IDT [2]
85, 86

0.29

(18 DAT)

IDT [3]
87, 88

0.29

IDT [4]
89, 90

0.29

IDT [5]
91, 92

0.29

IDT [1]
83, 84,
1
0.29
1.2
33, 54, 55
100% killed

IDT [2]
85, 86

0.29

(18 DAT)

IDT [3]
87, 88

0.29

IDT [4]
89, 90

0.29

IDT HP [1]
109
3
0.29
1.2
16, 33
100% killed

IDT HP [2]
110

0.29

(18 DAT)

IDT HP [3]
111

0.29

IDT HP [4]
112

0.29

IDT [1]
83, 84,
3
0.29
1.2
16, 33
100% killed

IDT [2]
85, 86

0.29

(18 DAT)

IDT [3]
87, 88

0.29

IDT [4]
89, 90

0.29

IDT [1]
83, 84,
3
0.29
0.87
16, 36
100% killed

IDT [3]
87, 88

0.29

(18 DAT)

IDT [4]
89, 90

0.29

IDT [1]
83, 84,
3
5.8
17
16, 36
100% killed

IDT [3]
87, 88

5.8

(18 DAT)

IDT [4]
89, 90

5.8

IDT [1]
83, 84,
3
29
87
16, 36
100% killed

IDT [3]
87, 88

29

(18 DAT)

IDT [4]
89, 90

29

IDT [1]
83, 84,
3
0.29
1.1
16, 36
100% killed

IDT [2]
85, 86

0.29

(18 DAT)

IDT [3]
87, 88

0.29

IDT [4]
89, 90

0.29

3′-OH [1]
101, 102
3
Not applicable
22-26 microliters
16
100% killed

3′-OH [2]
103, 104

(by volume)

(10 DAT)

3′-OH [3]
105, 106

3′-OH [4]
107, 108

IDT Blunt [1]
93, 94
3
0.29
1.1
16
75% killed

IDT Blunt [2]
95, 96

0.29

(10 DAT)

IDT Blunt [3]
97, 98

0.29

IDT Blunt [4]
99, 100

0.29

IDT Blunt [1]
93, 94
3
5.8
23
16
100% killed

IDT Blunt [2]
95, 96

5.8

(10 DAT)

IDT Blunt [3]
97, 98

5.8

IDT Blunt [4]
99, 100

5.8

IDT [1]
83, 84,
3
29
87
16
34% stunted

IDT [2]
85, 86

29

(14 DAT)

IDT [3]
87, 88

29

IDT [2]
85, 86
3
29
87
16
48% stunted

IDT [3]
87, 88

29

(14 DAT)

IDT [4]
89, 90

29

IDT [1]
83, 84,
3
29
87
16
25% stunted

IDT [2]
85, 86

29

(14 DAT)

IDT [4]
89, 90

29

IDT [1]
83, 84,
3
29
58
16
44% stunted

IDT [4]
89, 90

29

(14 DAT)

IDT [3]
87, 88
3
29
58
16
41% stunted

IDT [4]
89, 90

29

(14 DAT)

IDT [2]
85, 86
3
29
58
16
40% stunted

IDT [4]
89, 90

29

(14 DAT)

IDT [1]
83, 84
3
29
29
16
51% stunted

(13 DAT)

IDT [2]
85, 86
3
29
29
16
0% control

(13 DAT)

IDT [3]
87, 88
3
29
29
16
51% stunted

(13 DAT)

IDT [4]
89, 90
3
29
29
16
51% stunted

(13 DAT)

IDT [1]
83, 84,
3
29
116
16
75% killed

IDT [2]
85, 86

29

(13 DAT)

IDT [3]
87, 88

29

IDT [4]
89, 90

29

*where more than one copy number is listed, the treated plants were a mixture of copy numbers

**DAT = days after treatment; “0% control” means no difference between treated and control plants was observed; stunting % is calculated as [100 − (average height of the test plants/average height of control plants) * 100]

Double-stranded 25-mer RNA polynucleotide sequences for suppression of the TIF gene in Amaranthus palmeri were designed as listed in Table 14.

TABLE 14

SEQ ID

Name
Sequence
NO:

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′

The 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.

Low-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 0.23 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.

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.

Example 27

Aspects of the invention include polynucleotide compositions and methods of use for potentiating the activity of a non-polynucleotide herbicide in a plant. For example, 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. The combination of a polynucleotide composition with a non-polynucleotide herbicide (e. g., a conventional chemical 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.

Examples of conventional chemical herbicides and their corresponding herbicide target genes are provided in Table 15.

TABLE 15

Herbicide examples
Target gene (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
Cellulose synthase

Examples of conventional chemical herbicides and their corresponding herbicide deactivation genes are provided in Table 16.

TABLE 16

Herbicide examples
Target gene (herbicide deactivation gene)

Acetochlor,
glutathione S-transferase (GST)

metolachlor

Many including SU
Mono-oxygenases including cytochromes P450

herbicides
(see, e.g., a cytochrome P450 for conferring

resistance to HPPD inhibitors, benzothia-

diazinones, sulfonylureas, and other classes

of herbicides, described in U.S. patent application

publication 2009/0011936)

Thiazopyr
esterases (e.g., esterases involved in

apoptosis or senescence)

2,4-D, metribuzin,
glucosyl transferases; malonyl transferases

Glyphosate, paraquat
Cellular compartmentation and sequestration

genes (e.g., ABC transporters)

Example 28

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 targeted 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). For each herbicide targeted gene, a solution containing a mixture of 8 anti-sense ssDNA polynucleotides in 2% ammonium sulfate in 10 millimolar sodium phosphate buffer, pH 6.8, was applied at a rate of 2.32 g/acre following application of 0.5% SILWET L-77 spray (10 gallons/acre). The tested polynucleotides and resulting phenotype observations are listed in Table 17.

TABLE 17

SEQ

Size

ID

Gene
Name
(nt)
Sequence
NO:
Phenotype

EPSPS

(See sequences provided in working
—
Topical dsRNA

Examples 1, 9, 13, 14, 21, 26)

followed by

glyphosate killed

glyphosate-

resistant Palmer

(up to 60 copies

of EPSPS) within

7-10 days

PDS
PDS sense
185
GACGGAAACCCUCCAGAGAGGCUGU
123
Topical dsRNA

GCAUGCCUAUUGUUAAACACAUCGA

caused bleaching

GUCACUAGGUGGUGAAGUUAAACUU

and stunting

AACUCUCGUAUACAAAAGAUUCAGU

phenotype, and is

UGGACCAGAGUGGAAGCGUGAAGAG

systemic.

UUUUUUGCUAAAUAACGGGAGGGAA

AUACGAGGAGAUGCCUAUGUUUUUG

CCACCCCAGU

PDS anti-sense
185
ACUGGGGUGGCAAAAACAUAGGCAU
124

CUCCUCGUAUUUCCCUCCCGUUAUUU

AGCAAAAAACUCUUCACGCUUCCAC

UCUGGUCCAACUGAAUCUUUUGUAU

ACGAGAGUUAAGUUUAACUUCACCA

CCUAGUGACUCGAUGUGUUUAACAA

UAGGCAUGCACAGCCUCUCUGGAGG

GUUUCCGUC

PPO
PPO_OLIGO1
21
GTGATATTACCTCCAACACGAT
125
Topical anti-sense

PPO_OLIGO2
21
ATAGTAAGCACAGGATCGGAG
126
DNAs caused

PPO_OLIGO3
21
CTTTCAATCCACTGTCAACCG
127
stunting of plant

PPO_OLIGO4
21
ATCAAGCGTTCGAAGACCTCAT
128
growth.

PPO_OLIGO5
21
CAGCAATGGCGGTAGGTAACA
129

PPO_OLIGO6
21
GCAATTGCCCGAATCCTTTTA
130

PPO_OLIGO7
21
TAGCTCAATATCAAGGTCCTA
131

PPO_OLIGO8
21
TCATAAGCACCCTCTATACAC
132

PAL
PAL_OLIGO1
21
TTCTTAACCTCGTCGAGATG
133
Topical anti-sense

PAL_OLIGO2
21
ATACCCGAGTATCCTTGCAAA
134
DNAs caused

PAL_OLIGO3
21
TAGGGCCCACGGCCTTGGAGT
135
stunting of plant

PAL_OLIGO4
21
AGCGGATATAACCTCAGCTAG
136
growth.

PAL_OLIGO5
21
CTTCGTGGCCCAACGAATGAC
137

PAL_OLIGO6
21
CAAGCTCGGGTCCCTGCTTGC
138

PAL_OLIGO7
21
GGAAGGTAGATGACATGAGTT
139

PAL_OLIGO8
21
GATGGCATAGTTACCACTGTC
140

HPPD
HPPD_OLIGO1
21
TCCGTAGCTTACATACCGAAG
141
Topical anti-sense

HPPD_OLIGO2
21
TCCAAGTGAATAGGAGAAACA
142
DNAs caused

HPPD_OLIGO3
21
AGCAGCTTCTGCGTCTTCTAC
143
stunting of plant

HPPD_OLIGO4
21
ACAGCACGCACGCCAAGACCG
144
growth.

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_OLIGO5
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
TATGTATGTGCCCGGTTAGCTT
164

GS
GS_OLIGO1
21
TCATATCCAAGCCAGATCCTC
165
No significant

(glutamine
GS_OLIGO2
21
TGCATCACACATCACCAAGAT
166
phenotype

synthase)
GS_OLIGO3
21
GTACTCCTGTTCAATGCCATA
167

GS_OLIGO4
21
ATTGATACCAGCATAGAGACA
168

GS_OLIGO5
21
AGCAATTCTCTCTAGAATGTA
169

GS_OLIGO6
21
CATCATTCCTCATCGACTTAG
170

GS_OLIGO7
21
CTCTCGTTGCCCTCTCCATAA
171

GS_OLIGO8
21
CAACGCCCCAGGAGAAAGTTC
172

The herbicidal activity of 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. 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 targeting HPPD, PPO, or TIF. Some plants were left untreated and were used as controls. Twenty-four hours later, untreated plants, buffer-surfactant treated plants, and buffer-surfactant-ssDNA treated plants were treated using a track-sprayer equipped with a 9501E nozzle and calibrated to deliver 93 liters of solution per hectare with a HPPD inhibitor, mesotrione (4 pounds active ingredient per gallon;), or with a PPO inhibitor, fomesafen (2 pounds active ingredient per gallon), or with a Photosystem II inhibitor, atrazine (90% active ingredient) as indicated in Table 18. Crop oil concentrate (COC) at 1% was added to all herbicide treatments. A low rate of each herbicide (mesotrione: 13 g per acre, equivalent to ⅛× 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 ⅛× of the recommended field rate,) was used to be able to detect any improvement of herbicide activity by the oligonucleotide mixture.

TABLE 18

Rate (grams

Treatment

Active
per hectare of

number
Pre-treatment
Ingredient
active ingredient)

0
Buffer-surfactant
—

1
Untreated
Mesotrione
13

2
Buffer-surfactant
Mesotrione
13

3
Buffer-surfactant-ssDNA-

HPPD

4
Buffer-surfactant-ssDNA-
Mesotrione
13

HPPD

5
Untreated
Fomesafen
16

6
Buffer-surfactant
Fomesafen
16

7
Buffer-surfactant-ssDNA-

PPO

8
Buffer-surfactant-ssDNA-
Fomesafen
16

PPO

9
Untreated
Atrazine
170

10
Buffer-surfactant-ssDNA-

TIF

11
Buffer-surfactant-ssDNA-
Atrazine
170

TIF

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). 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.

No major differences in plant height were observed between plants treated with buffer-surfactant followed by herbicide, and plants treated with herbicide only. The plants treated with HPPD anti-sense ssDNA oligonucleotides followed by mesotrione showed the greatest reduction in plant growth, measuring 100 mm, a 46% reduction compared to the buffer-surfactant treated plants. The plants treated with PPO anti-sense ssDNA oligonucleotides followed by fomesafen measured 126 mm, a 32% reduction compared to the buffer-surfactant treated plants. The plants treated with TIF anti-sense ssDNA oligonucleotides followed by atrazine measured 121 mm, a 34% reduction compared to the buffer-surfactant treated plants.

TABLE 19

Rate (grams

Treat-

per hectare
Plant
Stan-

ment
Pre-
Active
of active
height
dard

number
treatment
Ingredient
ingredient)
(mm)
Error

0
Buffer
—
—
185
15

1
Untreated
Mesotrione
13
180
18

2
Buffer
Mesotrione
13
179
18

3
ssDNA-HPPD

125
19

4
ssDNA-HPPD
Mesotrione
13
100
7

5
Untreated
Fomesafen
23
158
12

6
Buffer
Fomesafen
23
139
10

7
ssDNA-PPO

153
20

8
ssDNA-PPO
Fomesafen
23
126
6

9
Untreated
Atrazine
170
146
19

10
ssDNA-TIF

115
17

11
ssDNA-TIF
Atrazine
170
121
16

Example 29

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. For each essential gene, a solution containing the dsRNA polynucleotide in 2% ammonium sulfate in 10 millimolar sodium phosphate buffer, pH 6.8, was applied to Palmer amaranth at a rate of 240 picomole per plant following application of 0.5% SILWET L-77 spray (10 gallons/acre). The tested polynucleotides and resulting phenotype observations are listed in Table 20.

TABLE 20

SEQ

Size

ID

Gene
Name
(nt)
Sequence
NO:
Phenotype

Translation
sense
160
UUCGAGUAAUGGGAAAUUGGAUAAUGUA
73
Topical dsRNA

initiation

GAGGAGAGGAAGAAGGUUAUUGAUUCAU

caused stunting of

factor (TIF)

UGGAUGAGGUAUUAGAAAAGGCCGAGAG

plant growth.

AUUAGAAACGGCGAACUUACAAGCAGAU

AAUAGAAAGGAUAGCACAAAUGUAAAUA

AACCGUCUCCGAGUGUAAGU

anti-
160
ACUUACACUCGGAGACGGUUUAUUUACA
74

sense

UUUGUGCUAUCCUUUCUAUUAUCUGCUU

GUAAGUUCGCCGUUUCUAAUCUCUCGGCC

UUUUCUAAUACCUCAUCCAAUGAAUCAA

UAACCUUCUUCCUCUCCUCUACAUUAUCC

AAUUUCCCAUUACUCGAA

DNA-
sense
168
GAUCACAAAUUUGCCGGUUUAUGAUCAA
113
Topical dsRNA

dependent

AUACGGAACAUAAGACAGAUACACUUGA

caused stunting of

ATPase

ACACCAUGAUUCGCAUUGGGGGUGUGGU

plant growth.

(ddATPase)

UACUCGUCGUUCUGGAGUAUUCCCUCAGU

UGAUGCAGGUGAAGUAUGACUGCAAUAA

AUGUGGGGCUAUCCUGGGUCCCUUUUU

anti-
168
AAAAAGGGACCCAGGAUAGCCCCACAUUU
114

sense

AUUGCAGUCAUACUUCACCUGCAUCAACU

GAGGGAAUACUCCAGAACGACGAGUAAC

CACACCCCCAAUGCGAAUCAUGGUGUUCA

AGUGUAUCUGUCUUAUGUUCCGUAUUUG

AUCAUAAACCGGCAAAUUUGUGAUC

Hydroxy-3-
sense
200
CUGAAGCUGGUGAAGGUGAAGAUGGACG
173
No significant

Methylbut-

AAUGAAAUCUGCGAUUGGAAUUGGGACC

phenotype.

2-enyl

CUUCUUCAGGAUGGCUUGGGAGAUACGA

diphophate

UCAGGGUGUCUCUAACAGAACCACCAGAA

synthase

GAGGAGAUAGACCCUUGCAGAAGGUUGG

(HMEDS)

CAAAUCUUGGAACAAAAGCAGCUGAAAU

UCAGCAAGGAGUGGCACCAUUUGAAG

anti-
200
CUUCAAAUGGUGCCACUCCUUGCUGAAUU
174

sense

UCAGCUGCUUUUGUUCCAAGAUUUGCCA

ACCUUCUGCAAGGGUCUAUCUCCUCUUCU

GGUGGUUCUGUUAGAGACACCCUGAUCG

UAUCUCCCAAGCCAUCCUGAAGAAGGGUC

CCAAUUCCAAUCGCAGAUUUCAUUCGUCC

AUCUUCACCUUCACCAGCUUCAG

Fertilization
sense
183
UCCCAUCAAAGUUCCCUACAAAAUAUGUG
175
No significant

independent

CAGUUUCCUAUCUUCCUUGCCGCCAUUCA

phenotype.

endosperm/

UACAAACUAUGUUGAUUGUACAAGGUGG

TF (FIE)

CUUGGUGAUUUUGUUCUUUCUAAGAGUG

UUGACAAUGAGAUUGUACUGUGGGAGCC

AAUUAUGAAGGAGCAAUCUCCUGGAGAG

GGUUCAGUUGACA

anti-
183
UGUCAACUGAACCCUCUCCAGGAGAUUGC
176

sense

UCCUUCAUAAUUGGCUCCCACAGUACAAU

CUCAUUGUCAACACUCUUAGAAAGAACA

AAAUCACCAAGCCACCUUGUACAAUCAAC

AUAGUUUGUAUGAAUGGCGGCAAGGAAG

AUAGGAAACUGCACAUAUUUUGUAGGGA

ACUUUGAUGGGA

26S
sense
143
UUGUGCUUAAAACAUCGACCAGACAGAC
177
No significant

proteasome

AAUAUUUCUUCCUGUUGUUGGACUAGUU

phenotype.

ATPase

GAUCCUGAUACGCUGAAACCUGGUGAUU

subunit

UAGUUGGUGUCAACAAAGAUAGUUAUCU

RPT5B

UAUCCUGGACACUCUGCCGUCGGAAUAUG

(RPTB)

AU

anti-
143
AUCAUAUUCCGACGGCAGAGUGUCCAGG
178

sense

AUAAGAUAACUAUCUUUGUUGACACCAA

CUAAAUCACCAGGUUUCAGCGUAUCAGG

AUCAACUAGUCCAACAACAGGAAGAAAU

AUUGUCUGUCUGGUCGAUGUUUUAAGCA

CAA

ligase 1
sense
159
CGCUGCAGUUGGUGAAGUAGAUCCCGGC
179
No significant

(LIG1)

AAGGGGAUUUCACUCCGGUUUCCACGUCU

phenotype.

GGUUCGUAUCCGAGAGGAUAAAUCUCCA

GAGGACGCCACAUCAUCUGAGCAGGUGGC

GGAUAUGUACAGAUCUCAAGCAAACAAU

CCACACCGCAAAAAGAG

anti-
159
CUCUUUUUGCGGUGUGGAUUGUUUGCUU
180

sense

GAGAUCUGUACAUAUCCGCCACCUGCUCA

GAUGAUGUGGCGUCCUCUGGAGAUUUAU

CCUCUCGGAUACGAACCAGACGUGGAAAC

CGGAGUGAAAUCCCCUUGCCGGGAUCUAC

UUCACCAACUGCAGCG

tRNA
sense
159
UAAAGAUGGCGGAAAAAUCGACUAUGAU
181
No significant

synthetase

AAAUUGAUUGACAAAUUCGGCUGUCAGC

phenotype.

(tS)

GACUUGAUUUAUCGCUCAUUCAGAGAAU

UGAGCGCAUCACUGCUCGUCCUGCUCAUG

UAUUUCUUCGCCGCAACGUUUUCUUCGCU

CACCGUGAUUUGAAUGA

anti-
159
UCAUUCAAAUCACGGUGAGCGAAGAAAA
182

sense

CGUUGCGGCGAAGAAAUACAUGAGCAGG

ACGAGCAGUGAUGCGCUCAAUUCUCUGA

AUGAGCGAUAAAUCAAGUCGCUGACAGC

CGAAUUUGUCAAUCAAUUUAUCAUAGUC

GAUUUUUCCGCCAUCUUUA

Ubiquitin
sense
150
UGAAGCUGAUGCUGAAGGAAAGGAUAUU
183
No significant

specific

GAUGCUAGUGAAGUAGUUCGCCCAAGGG

phenotype.

protease 14

UGCCAUUAGAAGCUUGCCUAGCUAGCUAC

(UBP)

UCAGCUCCGGAGGAGGUGAUGGACUUCU

ACAGCACUGCAUUGAAGGCAAAGGCAAC

UGCUACAAA

anti-
150
UUUGUAGCAGUUGCCUUUGCCUUCAAUG
184

sense

CAGUGCUGUAGAAGUCCAUCACCUCCUCC

GGAGCUGAGUAGCUAGCUAGGCAAGCUU

CUAAUGGCACCCUUGGGCGAACUACUUCA

CUAGCAUCAAUAUCCUUUCCUUCAGCAUC

AGCUUCA

Serine
sense
155
ACACCUGCCCUAACAUCUCGGGGUUUUCU
185
No significant

hydroxymethiy

CGAAGAAGAUUUUGUUAAAGUGGCCGAG

phenotype.

transferase 2

UAUUUUGAUGCUGCUGUUAAGCUGGCUC

(SHMT)

UAAAAAUCAAGGCUGACACAAAAGGAAC

AAAGUUGAAGGACUUCGUUGCCACCUUG

CAGUCUGGUGUUUU

anti-
155
AAAACACCAGACUGCAAGGUGGCAACGA
186

sense

AGUCCUUCAACUUUGUUCCUUUUGUGUC

AGCCUUGAUUUUUAGAGCCAGCUUAACA

GCAGCAUCAAAAUACUCGGCCACUUUAAC

AAAAUCUUCUUCGAGAAAACCCCGAGAU

GUUAGGGCAGGUGU

Methionine-
sense
159
UGAACUACGAAGCAGGCAAAUUCUCCAA
187
No significant

tRNA

AAGUAAAGGCAUUGGAGUUUUUGGGAAU

phenotype.

ligase/synthase

GACGCCAAGAAUUCUAAUAUACCUGUAG

(MtS)

AAGUGUGGAGAUACUAUCUGCUAACAAA

CAGGCCUGAGGUAUCAGACACAUUGUUC

ACUUGGGCGGAUCUUCAAG

anti-
159
CUUGAAGAUCCGCCCAAGUGAACAAUGU
188

sense

GUCUGAUACCUCAGGCCUGUUUGUUAGC

AGAUAGUAUCUCCACACUUCUACAGGUA

UAUUAGAAUUCUUGGCGUCAUUCCCAAA

AACUCCAAUGCCUUUACUUUUGGAGAAU

UUGCCUGCUUCGUAGUUCA

Example 30

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. FIG. 34 depicts an alignment of the Nicotiana benthamiana PDS locus 1 promoter (SEQ ID NO:319) and PDS locus 2 promoter (SEQ ID NO:320); in the case of locus 1 which contains multiple transcription start sites, 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 PDS1 and PDS2 promoters are listed in Table 21.

TABLE 21

SEQ

Poly-

ID
position/

Mix
nucleotide
promoter target
Sequence
NO
dir

2
HL419
PDS promoter 1 motif
TCCCATCTCCCACATGGGTTACTG
189
590-567

target

2
HL420
PDS promoter 1 motif
CAGTAACCCATGTGGGAGATGGGA
190
567-590

target

2
HL421
PDS promoter 1 motif
GGCTGATGAAATTCAAGTGCTA
191
557-536

target

2
HL422
PDS promoter 1 motif
AAACTGAGCTTGGAAATAATC
192
517-497

target

2
HL423
PDS promoter 1 motif
GAACCCAAAATTGTCACTTTTT
193
448-427

target

3
HL424
PDS promoter 1 motif
ATGCACTTGTTTATACTCTTGTCA
194
403-438

target

3
HL425
PDS promoter 1 motif
ATTTATTAGTGTTCTAAAGAA
195
357-337

target

3
HL426
PDS promoter 1 motif
TGTAGTAGCTTATAAGATTAGCTT
196
287-264

target

3
HL427
PDS promoter 1 motif
GTTGTCCCTTTTATGGGTCTTT
197
240-183

target

3
HL428
PDS promoter 1 motif
CCCGTGCAATTTCTGGGAAGC
198
86-66

target

5
HL429
PDS promoter 2motif
ATTAGTTTTTTATACACGAAAGAT
199
1313-1336

target

5
HL430
PDS promoter 2motif
ATCTTTCGTGTATAAAAAACTAAT
200
1336-1313

target

5
HL431
PDS promoter 2motif
TTGGTGGTTTGGCCACTTCCGT
201
1291-1270

target

5
HL432
PDS promoter 2motif
TTTGTTTGCTATTTAGCTGGA
202
1256-1236

target

5
HL433
PDS promoter 2motif
CAATTTGCAGCAACTCGCACTGGA
203
1205-1182

target

6
HL434
PDS promoter 2motif
TCCCACCATTGGCTATTCCGAC
204
1156-1135

target

6
HL435
PDS promoter 2motif
CTGTCTCTCTTTTTAATTTCT
205
1105-1085

target

6
HL436
PDS promoter 2motif
CCACTTTGCACACATCTCCCACTT
206
1056-1033

target

6
HL437
PDS promoter 2motif
GAGGATCCACGTATAGTAGTAG
207
1016-995

target

6
HL438
PDS promoter 2motif
TTTAAATAAAGAAATTATTTA
208
889-869

target

1
HL439
PDS promoter1
TAATACGACTCACTATAGGGCTTGAGTTTATAACGA
209

AGCT

1
HL440
PDS promoter1
TAATACGACTCACTATAGGGCTTCTAATTTTCAAGG
210

ACG

1
HL441
PDS promoter1
AGCTTCTAATTTTCAAGGACGATA
211
Anti-

sense

1
HL442
PDS promoter1
GTCATGTGACTCCACTTTGATTTTG
212
Anti-

sense

1
HL443
PDS promoter1
CTCAATTCCGATAAATTTAAGAAAT
213
Anti-

sense

1
HL444
PDS promoter1
CGAAGCTATTGGACCGACCTAATTTC
214
Sense

1
HL445
PDS promoter1
GGAATTGAGGGCTTCCCAGAAATTGC
215
Sense

1
HL446
PDS promoter1
ATGACTTTTTGATTGGTGAAACTAA
216
Sense

4
HL447
PDS promoter2
TAATACGACTCACTATAGGTGGAACTCCAACACACA
217
Sense

AAAAATTTC

4
HL448
PDS promoter2
TAATACGACTCACTATAGGTTGAAAAATAATCATAA
218
Anti-

TTTTA

sense

4
HL449
PDS promoter2
GCATAATATATTGATCCGGTAT
219
Anti-

sense

4
HL450
PDS promoter2
CTGAAAGTTCATACATAGGTACTC
220
Anti-

sense

4
HL451
PDS promoter2
GGTACTCCAATTTTCAGTATAT
221
Anti-

sense

4
HL452
PDS promoter2
CTGAAAATTGGAGTACCTATGTAT
222
Sense

4
HL453
PDS promoter2
ATGTATGAACTTTCAGAATATTATACC
223
Sense

4
HL454
PDS promoter2
TACCGGATCAATATATTATGCT
224
Sense

Six different combinations of 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 targeting a conserved segment of the coding region of PDS1 and PDS2; negative control plants were similarly treated with a DNA oligonucleotide designed to silence green fluorescent protein (GFP). All six combinations of polynucleotides designed to target the PDS1 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 bp and targeting the PDS1 or PDS2 promoter regions also induced systemic silencing in the treated plants as evidenced by bleaching.

The following additional genomic sequences (including promoter and transcribed intron and exon sequence) listed in Table 22 were identified for Amaranthus palmeri genes for use in designing polynucleotides for topical application:

TABLE 22

SEQ

Gene

ID

Name
Sequence
NO.

ACC1
TTCAAAATGAATTTAAAATTATATAAAAATCAATATGGACACAAGACCGGAT
225

ATCAATCCGACCCGAAATAGTTGACTTGAAATCAACCTGATGACCCGAATGA

ACACCTCTAGTTATCACTAACAAGGGTCAGATTGCGTACATCAAACCCCTCA

AATCCTGCTTAGGTGGGAGCTTGTCAATGGCTTAGGGGTAACGGGAATGTGT

GTGCTATGTACATTGTGCATCTATTCTTATGCTTATTTATGTTGAGTTAGTTTT

TTTTTTGGATCAAATATAAAGAGCTTAACTTTTGTATTTTCTTGATGTGGTGT

AGTGGTGATGAAGATCAGGCTGAGAGAATCTAAATTGGCCAAAATTCTGAG

AGAACAAGAAGTGAGTTCAGCCCTTCGTGCTGCTGGTGTTGGTGTGATTAGT

TGCATCATACAGAGAGATGAAGGGCGAACTCCGATGAGGCATTCATTCTATT

GGTCAGCAGAAAAACAATATTATAGTGAGGAGCCTTTACTACGTCATTTGGA

ACCCCCTCTATCTATGTATCTCGAGCTGGTACTAGTCTCTGAACCGATTGCCT

TTCTTCTGCTTTGTTATTTTGTGTGATATTTCGACTTAAGTCTAATTTACATCG

TTTTGTACATTTGTTATC

ACC3
TTTTGCTTTTTTACTATTATTTCCTTCTTTTCAAGGATTTGAGTTGTTTATTGCT
226

GACTGCTTCCTATGTATTACCCATATGTCTCTGTATAGGCATTACGGGAGCTG

TACCTACATCTAACTCCTATACAACGTGTGAATATTGCCCGGCATCCTAATCG

CCCCACTTTTCTTGACCACGTATTCAGCATCACAGAAAAGGTTTCTGATTTAT

TATAATTTTTGTCATTTGTATTCACTCTTCAATAAAGTACATCCATTATCAAT

CTTTACGGAGGTTGTTCACACAACTTCTTGTTTCATTTTGCATAATTAGTTTGT

GGAACTACATGGAGATCGTGCTGGTTATGATGACCCTGCTATAGTTACTGGC

CTTGGTACGATAGATGGTAGGCGTTATATGTTCATTGGTCATCAAAAGGGAA

GAAATACGAAGGAAAATATTGCACGGAATTTCGGGATGCCTACTCCTCATGG

GTAAATGCTTTACTATAATGTTTTACTTTAATTTAATTACCTATGTTATTTAGG

ATGAAAATGAATACTTTTCTTATTACTATTACTTAGGTTCCTAATGCACAAAA

ACCGTAATTATTAATGTACCCTAATGGAATTAACACATGGTAATTAAGCTCT

CCGCTTTGTGTAATTAATCCAATTTTTTAGAGAGTCAAATAGTTCAGGTTAAA

CTAGAGCTTTTCATACCCAAATAATAAAACCAAGGGTAAATTTCCAAAA

ACC4
ATGTGATCAATTAAAGAAAAAGTCTAATTATATGAGCCCGTCTCACAGTGAC
227

GGAGCTATCATAGAGCCCATGGGGTCACGTGCCCTTCGGGGTTTTTAGAAAA

AATTCAAAGTATACTTTTCTATTAATAAGAGTAAAAATGTAAAATTAATATT

AAACTCTTTTGATAATAAATACTCTCTCACTTTAGTAATTTTGTCTTATTTATT

TATTTTATCTCATGTGTTTAATAAGGTCAGTTGACTTATTTTGTTCCATTTTCT

TTTATGGTATGCCGTATTTAAAATTTTAGCAAGTAAAGATAAAATAGTTGTT

AATCTTACAAATAAAACTCTATCGAAATTTCATCCATTAGTTAATGTCCCCAA

AAAGTCCGAACTACAAATCGACCACTGTCATCACATGGTGAGATAGTCTCAT

ATAAAACGAGTTCAGTTATTAAAGGAAAATAGGAAACACGAAACAGTTAAT

TTAGGCGGGGCCTATGTATTATCCAAATGTGATACTCCAGTCCACATTACTC

AGTCCTTCCAATTGAACAGTTGGCTTAATCTACCAAGCGCGTGGCCATAAAT

GCCTCTAACACTTTTCAATCTCTCAGATAACTCTCACACCACTTATCATCACA

ATTCACAATTACTCTAATTCTTTTTATTCCTTTCCATGTCGCTAATTTTCTACT

GATTCAGGTTTTATTCTCAGCTTTTATCAATTTTATTTCATGCTTTTTATGTCA

ATTTCTTGTTTCGCATTTTGTCTTCCACTTGCTGTCTGTTTTATTAATCAATTTT

GTATGATTGTTGGAATAATTGTATGTATTTTTCATGATTTTCCTCTTATGGAG

GTTCATAATGTATTGCTAGATTTGTTTACTTTCAC

ACC5
AATTTGAGCGGGAAAATTTTAATATCATTAAATAGTCTTTGCTTTAGTATATA
228

GAATAGTTAAAATTAATAGTCAAACTTATTGTAATAGCATGCACTAATCTAT

AATAATCTTATCCTGAAAGCTATAATAAAATTATAAAAAAATATATGTGAAA

AACTAATTTGAGCGGGAAAATTTTAACCAAGGGCTAACACGTATCATTAAAT

AGTCTTTACTTTAGTATATAGAATGATAATTAACGATCATAAAACAAAATTG

TCACTTTCAGTAGCAAACTTACAAAATGAGCAGAGTACCTCATATCATAAAA

TTGCTTCTTTCTCATTTGTTGTGTTGCTCTCATTTTAGGAGTTCATCGTTTATA

TCGTCGTCTTACCACTCAATCACTTTTAGATTTATTAGTAGCACTTCCTCAAT

CTACAGCAGCAATTTCTACAGTTCAACAACCTC

ACC6
GGAAAATTTACCTAGAATAATCCAATTTATTCGTGATTTTTCTACAAATTCCA
229

ACTTCAAGGGGTATTTGCCTAAAGTAATTAAACTTGGATACCCCGATGACCT

GCTATAGTAGATAATTTACCAGAAAATTAAAAATGAAAATTAATTTAAAATT

AGAGAAAAATTTTGAAATTTCATATAAAAAATTTTAAATAATAAAAAAAATA

TAAATTTTTTTGAACATTTTATTTTAATCTATCTTTTTTGAAAAAATAAAACTT

AGTTATAGCAAGTGATCTGGTCACCGGGTTTACTCTAGGAAAATATCCCTCA

AAGTTGAGATTATTCATGGTTAATAAATAGGTGAGATTATTATAGAAAAATT

ACGAATAAATTGGATTATTGTTGGTAATTTTTTTTTCAAAACTATCCCTAGGA

AGGACCTTATTAGTGATTCTCCCTCTACTTTGGAGGAGTATATTGTGGACTTC

CCATCTTCCTTAATTGTATTGTAACTTTTAACTATTGATTCTTTAAAAAAAAG

AACTTATAAAATTGTAGGGTTAATAAAATCTAAGATTTTATCTAATTTCACTT

TGATTATTCCGATTTTGTATTCACATTATTTTAAATGACATTCGTCAAATAAA

AAAAAATAGTTTCATTGCATTCCAATTTTGTTGACTAGGGGGATTAAAGAAA

GAATAGTATCAATAATCGTAATGTAGCAAGTAGTACAAAAGAAGTATATTTC

AATATGTCAAACTTTGATCTCGTTGTAACTTGTAATTTGTACGATGCGGTGTG

AATGACATACTTCACCTTTTTCATTATTTTATACTGGTAGTGACATGGGATTA

TTATTGCGATATTTGCAGTAATGAAAATTTTTTTGGTTGTTGCTTTTACAAAC

AAAAATTCTACCGAATTTTTTATTAATTTAATTCAACACGTTGGTGTTACCCA

TGATTTATAGGTCTGGGTCCGCCACTGCTAGCTAACATTAAACAATTTAACA

AACTCAATACACCAACCTAAAAATAAAATTTTTTTGGCCATAATTTTTAGAA

TTTTAGTTTTTAAACATTATATTTGGGAATTTTTTTTCCTTTTATATATATAAA

ATAAAAAAAAATCCAAAAAAGGGGACACACATTAATACACACTTGAAAGCA

TCGATGATATCGAAGAAAAACCAGATGGGGTGCCCAATTATCTTCGTCTCCT

TCGATATTATCGAATTCATTAACAACATTATATCAAAAACCAACCAAATTAC

CAACTTTCGAAACCAATATTCGCCGTATTTTTCTCTATTCAACAATCCCTACA

ATGGCGGCATTGCCAGCTTCTTCTTCTCCTGCAATTTCGGAATCACCCACTTG

CAATTTTCTTCCTATTCAAAAAATCACTACCACTCGCTTTCTAAGGTTTCATT

CGGTTTTACTCCCAAGCCTAAATTTGGCCTTTTCTCCAAGGTTTATTTTCTATC

TCTTTTTTAATTGGTTAATCAATTGGATTGTTGAATTTTTCAGGGTTTAACGG

TATAATATTTGTGGGTTTTTTCGAGTACATTCTGGGTTTGTAGTATTGGATTT

GGCATTGCTTTTAATTTTTGAGATTGGGTTTTTTGGGTTTTATTTGGTTCTTGT

GATTCAAGGTTATTGATTTGCTGCATTAAACTGTATTTATGGAATGATGTCAA

TTAACTGTTACATTACATTGCTTTATGGTTTTCATCATGCTGATTAGTGATTA

CTGTGTTTGAATCTCTTGCTTCTCTATGTACTATTTAATCTGATACAACAAGT

ACAACCTAGAAAACAGGTTAAAGGGAAATCTATAAGCTTAGTAAATTAACA

CTTGAAAGAAGCTAATGACGGAGAGAGGGGTCTTTTTGGAGAAGGCAGTTTT

CATATTATTGCTCAGTTCTCTAGTGCAGCTTTACTTCACTTAGACACTCTTAA

GTAGAGGTCATAGGTGTTCAGAATAGATCCAAAGACCCGATATTTACCGGAC

TTTGTAAACAACTTAACCCGACTTCAAAATGAATTTACAATCATATAAAAGC

AATATGGACTTAAACCGATTTTGAACCGACCTTGACCGGTTGATCCGAATGA

ATGCCTCTACTCTTAAGCATGTCAACTGTAATATGAAATAGAATTATAATAT

AAACTAAGTTCATGTTTTCTTCAACTACAAATGAAATTTTATGACCCAAATA

ATGTGTGAATACCCCCAGCAATAGGTTGAATGGCATTTAGTTCAGTTGATTTT

AGCAGACCACATCTGCCCTCATATTCCATTGTTCAGTTTAGTTGTTAGTAGCT

GTACATAATAGACTAATTAAGTTGTCATTTTGATCCATGTTATGGTTGTCTGG

GATAAACGGATTGGAATTGTATAATAAAAGTTTGGGTTAGTTTATTTTGCTCT

AGGAGGGGTTATGTCATATGTGCACTCTGTTGGCAACCCGACAATGCAAAAC

ATTTTCATACTTGGTACGTTGTTGCGTGTTTTGTGCCCTTCGTATTTTGTAACT

GTTGATGAATGTGTAAAAATATACTACATGATCATATGCTAGTAGGTCTTCTT

CACCTAGTAAAGAAATTTTTCTAACACGAGAAGTTCAAAACATATTCCCATT

ACCATTATCCAACATCAGTACCCGAGTCCAAGTAACATAGGGTGTCCCTTTA

TGATAGTATAAGAATTGGTGCATGAAAAACGCGTGATTGTAGCGAGGATAG

TAGGCGGGAGAGGTACAGGATTTGAAAATTTTGAATTGCTAAAACGCTATCA

GGATCTTGTTTTTCTTACTTTGATGTTGCTTTTTTGAAATTTGATCCAAATTGT

TAAATTATTGAGACTAATTCCTGTTGATCCTGTCGTGAACTTTGTAGAATCTT

TCAGGCCGCATTCTCACAGTGAAGGCTCAATTAAACAAGGTGAGTCTTTTTT

TGTCTTAACTCTTATGCAGTTCATTATCTCTTCTACTGATGAGAAAACCACTA

TTTGGCCTAATTCTAATTTCCTTCTAGGTTGCTTTGGATGGTTCAAATCATGC

TCCATCACCTTCGCACGAAAAATCTGGGCTACCAGCCCAAGAAAAGAAGAA

CGATGAGCCGTCTAGTGAATCTTCTCCTGCAGCATCAGTGTCTGAAGAACGA

GTCTCCGAATTCTTGAGCCAAGTTGCCGGTCTTGTCAAGTATGTAACATTCTT

TATTTTCATTCTTCCACACACTCGCAATTTGGATAACGAGATGTCTTTAGAGA

CGTCTGGGGAACAAGGGAGAAATGAGTCTAGAGGTTGCTAGAGAGAACGAG

ATAAATACTAATATATATGAATATTTCATAATCCACATTAAAAAAATACAAT

TGAATTTGCATTATGGTGAACTACCAAAGAATCGAATATTTTTTAATACTCCA

TGTTTTGTGGTCTAGACTTGTGGATTCTAGAGACATTGTAGAGTTGCAATTAA

AACAACTGGACTGTGAGATATTGATCCGCAAGCAGGAAGCTATTCCTCAACC

ACAAATTCCTAATCCTACACATGTCGTTGCAATGCAACCACCACCACCTGCT

GTAGCGTCTGCCCCAGCTCCCGTCTCTTCACCAGCCACTCCTCGTCCTGCGTT

ACCTGCCCCAGCGCCTGCTGCCACGTCAGCTAAGCCATCACTTCCACCTCTC

AAGAGCCCTATGTCAGGCACATTCTACCGTAGTCCAGCTCCTGGCGAGCCGC

CTTTCGTGAAGGTAAGTGTATACCCCTTTTTTAGTGTTGTATTTCTGTGTTATA

TCAATTTTTGCATTTTGTGAAGCTGAAAATAAATCTTTCATTTTCCATAGGTT

GGAGATAAAGTTAAGAAAGGACAAGTCATATGCATTATCGAGGCTATGAAG

TTGATGAATGAAATCGAGGTACGTATGTTATTGCTTTAAACTTCATGCCTTAG

GCCGTGAAGTT

ALS1
ACAAAAAGCACAAATTCAATAATATACTCTTTAAGTTTGTTTATCTTCTAATT
230

AGTTCGGTTAAAACGGTTCCCCACTTTCTTCTCCGACTCTCACAATTATCTTC

CCCTATTCATTTTTCTTCCACCCTCTCTAATGGCGGCTGTTTCCTTCAATATCA

ATGGTGGAAAGATTGGAACTTTATGTTCAAGACACGAATTCGTTTGTGGGTT

TGTAAGAAAATTTCATTTTAGAACTCATACTTCTATATTTGAAAAACATATGC

CAAAAACTTCAAGGTTTAAAGCAATGGAAGTTTCTGCAAATGCAACAGTAA

ATATAGTTCCTGTTTCAGCTCATTCTAGGTAATTTTATTTCTCGAAAATTTCC

GATTTACAATTAAATTAATCTTGTTTTGTAGGTAATGAATTGCAGAAGAAAT

AGATGGATTCTTATTTGTTTATTGGTATTTGTTTATAAATTTTTGTTTATATTA

GTTTCTGAATTGTGATTATTCTGATTGTATGTCAAGGTTTAGGTTGTTATTAA

TAAATGTAAATTGGATTGATTGAAGTTGCAATAAGGTGATGGCGTGATGCTG

ATTGTTGTAAATTTT

ALS2
CAACAATGAGAATTTAGAATCCATATCAATCTTGATATTCAAGGGTATTTAA
231

GTAATTAAAGAACAACCATTGTTAAGCGCCTCCACTATCTTCTTCCTTCTCAT

TCTCCATTCTCGCTTAGCTTTCCTCTCGCACTAATTACCTCCATTTGCAACCTT

TCAAGCTTTCAACAATGGCGTCCACTTCTTCAAACCCACCATTTTCCTCTTTT

ACTAAACCTAACAAAATCCCTAATCTGCAATCATCCATTTACGCTATCCCTTT

GTCCAATTCTCTTAAACCCACTTCTTCTTCTTCAATCCTCCGCCGCCCCCTTCA

AATCTCATCATCTTCTTCTCAATCACCTAAACCTAAACCTCCTTCCGCTACTA

TAACTCAATCACCTTCATCTCTCACCGATGATAAACCCTCTTCTTTTGTTTCCC

GATTTAGCCCTGAAGAACCCAGAAAAGGTTGCGATGTTCTCGTTGAAGCTCT

TGAACGTGAAGGTGTTACCGATGTTTTTGCTTACCCTGGTGGAGCATCCATG

GAAATCCATCAAGCTCTTACTCGTTCTAATATCATTAGAAATGTTCTTCCTCG

ACATGAACAAGGTGGGGTTTTCGCTGCTGAAGGCTACGCTCGTGCTACTGGA

CGCGTTGGAGTTTGTATTGCCACTTCTGGTCC

EPSPS1
ATTTGGATAACTTTTTCCTTTGATTCGAATCGGATTATTTTTAATACAGTATT
232

ATGAACTGATTTAATGAAAGTGGAGGAAGTTTCAATTTTTAAAGTTGTAGGT

GTAATGTTTTCTCATTTTGGATATGAAAGTGGAGGAAGTTTCAATTTCGAATC

ATGTTTGCCAGTTGATTCAATGAATGCTCTTGGAAATGACCAAGAGTTCAAG

GCTTCTTGTTATAAAACATTTCAATTTTGATCTAAGAATGAACTATTTAGAAC

TTAAAGTAATTAAATTATTAGTTATAACTTATAAAAAAATTCAATTTTAACCT

TAAATTTATAAATTATGACCTTAAAAAGATCAAGTATTGAACGCATATTTAG

AAAAATTATAATTCGGCTTATCAGTCTCATATTGAGACGGTCTCGTCCAAGA

CAAGTTGTATCATTTATATAATCAAATATAATTATGAGTGTATTCATGTAGGT

TTCAACTTTAAAGCCTAGGTGAAAGATATGTTGTAGCATCTTTGTGAAAGTC

AGCCTATAACTTGGTTCTAAAATTTTGAAGCATAACCATATAGTCCCTCGAA

TTCATTCAAGTTGTCCAATTTACTTTTTTATACTTGCCGAGACAACATTTAAA

CCCTTAATATTTCTAATTAATCTTAATTAAAAATTATGAAAATTTGATATTAA

TAATCTTTGTATTGAAACGAATTTAACAAGATCTCACATGACTATGTTTTAAC

TTATAGATTAAAAAAAAATACAAATTAAGAGTGATAAGTGAATAGTGCCCC

AAAACAAATGGGACAACTTAGATGAATTGGAGGTAATATTAGGTAGCAAGT

GATCACTTTAACATCAAAATTGATCACTTATAGGTTCAAATTGAAACTTTTAC

TTTAATTGATATGTTTAAATACTACTTTAAATTGAAATTGATATTTTTAAGGT

CAAAATTGAAACCTTTAAGATTATAATTGAAAATTGGCAGAAGAAAAACAA

AGAGAAAGAATATAAGACACGCAAATTGTACCGATCTACTCTTATTTCAATT

TGAGACGGTCTCGCCCAAGACTAGATGTTCGGTCATCCTACACCAACCCCAA

AAAATTCAACAACAAAGTCTTATAATGATTCCCTCTAATCTACTACAGTCTA

CACCAACCCACTTTCTCTTTGCCCACCAAAACTTTGGTTTGGTAAGAACTAAG

CCCTCTTCTTTCCCTTCTCTCTCTCTTAAAAGCCTGAAAAATCCACCTAACTTT

TTTTTAAGCCAACAAACAACGCCAAATTCAGAGAAAGAATAATGGCTCAAG

CTACTACCATCAACAATGGTGTCCAAACTGGTCAATTGCACCATACTTTACC

CAAATCCCAGTTACCCAAATCTTCAAAAACTCTTAATTTTGGATCAAACTTG

AGAATTTCTCCAAAGTTCATGTCTTTAACCAATAAAAAAGAGTTGGTGGGCA

ATCATTCAATTGTTCCCAAGATTCAAGCTTCTGTTGCTGCTGCAGCTGAGAAA

CCTTCATCTGTCCCAGAAATTGTGTTACAACCCATCAAAGAGATCTCTGGTA

CTGTTCAATTGCCTGGGTCAAAGTCTTTATCCAATCGAATCCTTCTTTTAGCT

GCTTTGTCTGAGGTATTTATTTCTCAACTGCGAAAACAATCTCTATTTGATAT

TGGAATTTATATTACATACTCCATCTTGTTGTAATTGCATTAGTAGATACTTA

TGTTTTGACCTTTGTTCATTTGTTTGTTGAATTGGTAGTGTTGAGAATTTGAAT

GTAATTATTTGTTTTTCCATGTGAATTTAATCTGATTAAATCCACTTCTTATTT

ATGTTAAGTTGCAATGATGTTTGCCAAATGGTTATCATTGAAGGATAAGTTT

GCCTACTTTTGACCCTCCCAACTTCGCGGTGGTAGAGCCATTTTATGTTATTG

GGGGAAATTAGAAAGATTTATTTGTTTTGCCTTTCGAAATAGTAGCGTTCGT

GATTCTGATTTGGGTGTCTTTATAGATATGATATATGGGTTATTCATGTAATG

TGTAGGTTTATGCATTATGTTGGATGCATGTCTGGTGTTATTGCTGTAAATGG

ATGAATGTTGTTATTTGGAGACATTTTTTCATTCATTTTTTCCCTTTTTAATTG

GAACTGGAAGAGGGAAAGTTATTGGGAGTAATTAAAAGGTTGTGAGTTCGA

TACACTGCATCAAAGACGAAGAACTTGACATAGATGTTGAAGGCTAATCCTT

ATCACTGCTTGAATTCAATATGTATCTGAAAATTTTACCCCTCTATATGCATC

TGTTTTTGCTAATAAAGTGTTTTTGGACTATCATGTTTTGTGATGCTTAAGAG

GGTGATATTACTGAGATAAATGGAAATATCAAAATAACATCTATTGTGAAGT

EPSPS2
CAAGCTTCAATTATCGTTTTCAAAATAAGTATTTCAAAGTCTATAAAGATATT
233

GTATAAGTTTTAGTTCAAATTTAATAAGTTTTTTTTTTTTTTTTTTTTTTTTTTT

TGAAAATCCAAATTGAATAAGTTAATARTTAAATTATGACATATAATTATGA

CATATAATTTGACCATGATATTTTACAATCTAACTTAATTTTGAACTTATTAT

TTCTAATATTCAATTATCGTTCTAAAAATAAGTATTTAAATTGTATAGATATA

TTGTATAACATTTAGTTCAAATTTAATTATTGATAGTTTTATTGACTATTTATT

TGGKGTTTGAAATTCATCCATAGAATGATAGAATAACACCATTTTTTATATA

ACTTCGTTCTAAAATTTTGAAGCATAACCATATACTCCCTCCAATTCATCCAA

GTTGTCCAATTTACTTTTTCATACTTGCCGAGGCAACATTTAAACCCTTAATA

TTTCTAATTAATGTTAATTAAAAATTATGAAAATTTGATATTAATAATCCTTG

TATTGAAACAAATCTAACAAGATCCCACATGACTATGTTTTAACTTATAGAT

TAAGAATAAAATACAAATTAAGAGTAATAAGTGAATAGTGTCCCAAAACAA

ATAGGACAACTTGGATGAATTGGAGGTAGTATTAGGTAGCAAGTGATCACTT

TAACATCAAAATTGATCAGTTACAGGTTCAAATTGAAACTTTTACTTTAATTG

ATATGTTTAAATACTACTTTAAATTGAAATTGATATTCTTAAGGTCAAAATTG

AAAACTTTAAGATTATAATTGAAAAATGCCCAGAAGATGAAAAAACAGAGA

GAAAGCATGTAAGACACGCAAATTGAACCAGTCTACTCTTGTTTCAATTTGA

GACGGTCTCGCCCAAGACCAGATGTTCAGTCATCCTACACCAACCCCAAAAA

ATTCAACAACAAACTCTTATAATGATTCCCTCTAATCTACTAGAGTCTACACC

AACCCACTTTCTCTTTGCCCACCAAAACTTTGGTTTGGTGAGAACTAAGCCCT

CTTCTTTCCCTTCTCTCTCTTAAAAGCCTAAAACCCACCAACTTTTTCAGCCA

AGAAACAACGCGAAATTCAGAGGAAGAATAATGGCTCAAGCTACTACCATC

AACAATGGTGTCCATACTGGTCAATTGCACCATACTTTACCCAAAACCCAGT

TACCCAAATCTTCAAAAACTCTTAATTTTGGATCAAACTTGAGAATTTCTCCA

AAGTTCATGTCTTTAACCAATAAAAGAGTTGGTGGGCAATCATCAATTGTTC

CCAAGATTCAAGCTTCTGTTGCTGCTGCAGCTGAGAAACCTTCATCTGTCCCA

GAAATTGTGTTACAACCCATCAAAGAGATCTCTGGTACTGTTCAATTGCCTG

GGTCAAAGTCTTTATCCAATCGAATCCTTCTTTTAGCTGCTTTGTCTGAGGGC

ACAACAGTGGTCGACAACTTGCTGTATAGTGATGATATTCTTTATATGTTGG

ACGCTCTCAGAACTCTTGGTTTAAAAGTGGAGGATGATAGTACAGCCAAAAG

GGCAGTCGTAGAGGGTTGTGGTGGTCTGTTTCCTGTTGGTAAAGATGGAAAG

GAAGAGATTCAACTTTTCCTTGGTAATGCAGGAACAGCGATGCGCCCATTGA

CAGCTGCGGTTGCCGTTGCTGGAGGAAATTCAAGTTATGTGCTTGATGGAGT

ACCAAGAATGAGGGAGCGCCCCATTGGGGATCTGGTAGCAGGTCTAAAGCA

ACTTGGTTCAGATGTAGATTGTTTTCTTGGCACAAATTGCCCTCCTGTTCGGG

TCAATGCTAAAGGAGGCCTTCCAGGGGGCAAGGTCAAGCTCTCTGGATCGGT

TAGTAGCCAATATTTAACTGCACTTCTCATGGCTACTCCTTTGGGTCTTGGAG

ACGTGGAGATTGAGATAGTTGATAAATTGATTTCTGTACCGTATGTTGAAAT

GACAATAAAGTTGATGGAACGCTTTGGAGTATCCGTAGAACATAGTGATAGT

TGGGACAGGTTCTACATTCGAGGTGGTCAGAAATACAAATCTCCTGGAAAGG

CATATGTTGAGGGTGATGCTTCAAGTGCTAGCTACTTCCTAGCCGGAGCCGC

CGTCACTGGTGGGACTGTCACTGTCAAGGGTTGTGGAACAAGCAGTTTACAG

GTATAATGTTAACCCTTACCCTTCACATTGTTCTGCTAAATTCTAGAGGACCC

TTTCAATTCTGGGTGGGATAAGCACGGCAATTTGACCGCAAAAAAATTGCAA

AATTATTCTGCTGATAGAACATCTCGAGATGAGATCATATTGAGTTTTGGCG

TCAACATAAACCTAATCAAATAATGAAAAATACAAACATCATATGGTTTCTT

TTGTCTTTATGACTAGACACTCTCTATTATTCCTTGATTGGGATCTTATTTGAA

ATTGCTGTGTAGCCTACACCTCATGTTCAGATTTTGTTCGTATACCAGACTTT

TCTTGATTGGGATCTTATTTGTCCCCTGGATTTTGCATAGGGTGATGTAAAAT

TTGCCGAAGTTCTTGAGAAGATGGGTTGCAAGGTCACCTGGACAGAGAATA

GTGTAACTGTTACTGGACCACCCAGGGATTCATCTGGAAAGAAACATCTGCG

TGCTATCGACGTCAACATGAACAAAATGCCAGATGTTGCTATGACTCTTGCA

GTTGTTGCCTTGTATGCAGATGGGCCCACCGCCATCAGAGATGTGGCTAGCT

GGAGAGTGAAGGAAACCGAACGGATGATTGCCATTTGCACAGAACTGAGAA

AGCTTGGGGCAACAGTTGAGGAAGGATCTGATTACTGTGTGATCACTCCGCC

TGAAAAGCTAAACCCCACCGCCATTGAAACTTATGACGATCACCGAATGGCC

ATGGCATTCTCTCTTGCTGCCTGTGCAGATGTTCCCGTCACTATCCTTGATCC

GGGATGCACCCGTAAAACCTTCCCGGACTACTTTGATGTTTTAGAAAAGTTC

GCCAAGCATTGA

GS3
TCTTAATTTGTATTTTATTATTAATCTATAAGTTAAAACATAGTCAAGTGAGA
234

TCTTGTTTGATTCGTCTCTATGCAAGGATTTTCATATCAACTTTTCATAATTTT

TGATTATACACAATTACAAATATTAACGAACGAATAAGTGCATTAAAAAGA

GTGCAAAAAGCAAATGGGACACTTGTGTTGAATAGGAGGGAGTATACATTA

AGATGAATCTAACGAGATCTCACATGGATATAATTTGTCTTCTATATATGTCT

AAAAAATCTTGATCAAATTTCTCTTTCCAAAATAGAATATTCTAAATGGGAA

GAACATTAAGAAACGGAGGGAGTACTTATAAGTTAAGATAGTTGGGGGTAT

TTAGGTAAAAAAATCTATGCCAAAAGTAGAAAGTGGACAATTAGAGTGACT

TTACTAAATAAGGAAAGTGGACATTTAAAATGAATCGGAGGGAGCATATTA

ACTTTATTTTCAAAGTGTGAAACATAATCATATTTAGGTAAAAAAATTATCA

ATTTAACGTCAAAATTGATCACAAATAGGTTAAAATTGAAATTTTTTATGTTA

ATTGATCTATTGTTCACTTTAAATTGAAATTGATATCCTTTAAGGTTAAAATT

AATACCTCTAAAATTAAAATTATTAAAGGCCCAGAAAATAAAAAAAAAAGA

AGACAGGCTATTAGTAAAATTATTAAGTATGTAAGGTTGATACACGCGCGAA

TTGAGCCGGCCCACTTTTAGTTTCAATTTGAAACAGTCTCAATCAAGACCAA

TTATTTATTATTTTATTATTTTATTGTTTTAAGCTCAATGGGTTGGACTTGATA

AATTATATTTTGAGGAGACGGGCTATTAGTAAAATTAATAGTTGGAATCTTT

TTTGATATACTATAAAAAGAGGTATCTGGTGGAGCCTTAAATCTGCGCAATT

GAAGTCCTCAATACACATCTCGCTCTTCTTATTCTCTTTCATCTATTTCCTCCT

TTGATCAAACTACGCCATGTCTCTCTTAAATGATCTCGTTAACCTTAATCTCT

CTGAAACTACCGATAAGATTATCGCTGAATACATATGGTAATACAACAATCC

TTCCTCTTTTTCATTT

GS5
AAAAAACCGTCTTATTTGTAGAAAATAAAAAACTAAAAAGTAGTATCAACTT
235

TTAGACTAGTCATAAGTGAGTGGCATCAAACTTGTTCTATAAAAAGGGAAGA

GTTCCTCAACTTGAGATTCATATTTTTTGTGATTTCTAAATAGAAGAACATAC

TCATCTTCCACTTCTCTTATTCATCAAATTTTATTTGTTCCCCAAAAAAACAT

GTCTCTTCTTACAGATCTCATCAATCTTAATCTTTCTGACTCCACTGAGAAGA

TCATTGCTGAATACATATGGTCAGTTTTCATCCCTTTTTTTTACCTTTAATCCC

ACTTTTTGTTTTTACCCACCATTTTTTTCATCTATTTTCTCTTAAAGATTTTAA

CTTTTTACTTTTTTGTGTATATAACATTCATTTTTTCAATTGGGTAGGTTAGAA

AATTTCTATAAATAAATAAATAAATNNNNNNNNNTACCTTAATCCCACTTTT

TGTTTCTACCCACCATTTTTTTCATCAATTTTTCTTAAAGATTTTAACTTTTTTT

AACTTTTTCTTGGTTTTTGTGTATATACCAATCATTTATTTTCACTAGTGTAGG

TTAAAAAATATCTAAAAATAAATAAAATAGAATAAAAATGTAATCACTAGA

TTAACCCATGAATTATTTCCCTTGTTTTTACTCAAACTTTTTACCCTTGTTAAA

AAAATAATGATATAAATAAATTTTTGAGGGTTTGTTAAACCCATATGTAATC

TATATCGAAAAAATTAGATAGCGGGTTTTGTTGTGGACAAACTAAATAACAA

ATTTAGGAATAAACTTTTGAGGGTTTATTGAAAAAATAACCCATATTTAATC

TATATCGAAAAAATGATAGCGAGCTTTGTATAGAT

HPPD
CGTCGAAGTAGAAGACGCGGAAGCTGCTTTTAACATCAGCGTTTCGCATGGG
236

GCTATTCCCTGTGTTTCTCCTATTCAATTGGAAAACGGTGTCGTTTTATCTGA

GGTTCATTTATATGGGGATGTTGTGCTTCGGTATGTAAGCTACGGAAATGAA

TGTGGGGATGTGTTTTTTCTTCCTGGGTTTGAGGAAATGCCGGAGGAATCAT

CGTTTAGAGGACTTGATTTTGGCATTCGAAGGTTGGATCATGCTGTAGGGAA

TGTCCCTGAGTTGGCTCCTGCAATTGCTTATTTGAAGAAGTTTACTGGGTTTC

ATGAGTTTGCTGAGTTTACAGCTGAAGATGTTGGGACGAGTGAAAGTGGATT

GAATTCAGCCGTATTGGCAAACAATGATGAAATGGTGTTGTTTCCGATGAAT

GAACCTGTGTATGGGACAAAAAGGAAGAGCCAAATTCAAACTTATTTGGAG

CATAATGAAGGGGCTGGTGTACAGCATTTGGCTTTGATGAGTGAAGACATAT

TTTGGACTTTAAGGGAGATGAGGAAGAGAAGTGTTCTTGGTGGGTTTGAGTT

TATGCCGTCGCCGCCTCCGACTTATTACCGGAATTTGAGGAACAGAGCTGCT

GATGTATTGAGTGAGGAGCAGATGAAGGAGTGTGAAGAGTTGGGGATTTTG

GTGGATAAAGATGATCAGGGCACTTTGCTTCAAATCTTCACCAAACCTATTG

GAGACAGGTAAATTTTAATCTTGCTTTCAATTGCTTTTGCTTGATGGATTGAC

TAGCAAATTTGATCGCATTTTGTTGCTTATATGACTTGATGATACTTCCTCTG

TTTCGAAATACTCGCTACATTCGCTACATTTTGTTTTGTGCACTATTCATCGTT

CAAGCTTATTTTACATATTGCGACTAATGTGTAACTAAAAATATAGTCAAGT

GGGATCTTGTTTGAATCGTCTAATGGCATACTTTCATCATATTAAATTTTTAT

AATTTTTAGATTAGTGTAGTTTAAGATATTAATGCTCAAAATTGTGCATTGGA

TTGCGTAAAAAAGTGAAATGTAGCAAGTATTATGAAA

PDS
AAAACCAAAGGAAATAAGTTATAGGTAGGAAAAATTGTTATTGAAGTTAAT
237

GTAGTAAACTAGTAACTTAAACTGTGATACCCCGGATTTAGCTTAAAAAGAG

ATTGATAGACTACTCATATCAACAAGGTGCATCTTCTTTTCTAGGGAGCCCAT

TTGCTAAGAACTCTACAGTTAAGCGTGCTTGGTGGGGAGCAATCTTAGGATG

GGTGACCTCCTGGGAAGTTTTCCTGGGTGCGCACGGGTGAGGCCAAAGTGCG

TTAAAAAGACTTGTGTTGGTCTGTGGGGCTTGTCTACAGTCTCCATGAGTAGT

CACCGGCGGTACGAGAGGCCGGGGTGTTACATAAACAGACTCAAAGGCGCT

AAGCCAAGTAGCCAATAGCAACATGTGTGGCCTGCGGACAGTCACAAAAAC

ACACAATTTCTTATTTTTACTCTCTTTTATCTCTTTTAGGCTTTAGCCATCAAC

AATAAAACAACATGATAAAGCAATTCATTTACTGCTAAATTCCAACAATTTG

GTCCCTTTTTCCTGTTCTTTCAGTTTCACATACCCTCTTATCAATCTATATCCA

AAACTATTTCATTTTCCAAACTCTTTTAAACCCAAAAATCAAAACTTTTGATT

GAAGAACAAACTTTGGGGGTTTTGGAAAATGAGTCATTTTGGATATGCTTGT

GCTACTCAATCCACATCAAGATATGTTCTTTTAGGAAATTCAAATAACCCCA

CTTCAATTTCATCTATTGGAAGTGATTTTTTGGGTCATTCTGTGAGAAATTTC

AGT

PPOX
TGGTACCTACCCTGTTTACATTTTCAATTTCCCCCTTTTTTCTCTACTACTCCT
238

ACTTTATTGATTCTTATCCATGTGTGTTCTATGGGAATTGACATTAATTGTTC

AGGTGTGTATGCTGGTGATCCTTCTAAGTTGAGTATGAAAGCTGCATTTGGA

AAGGTCTGGACCTTAGAGCAAAAGGGTGGTAGTATCATTGCCGGTACACTCA

AAACTATTCAGGAAAGGAAGAATAATCCTCCACCGCCTCGAGACCCGTCCGT

AATCACCATTACTCATTGCTTTCCTTCACCTTGTATCTTACCTTAATATACATG

TATTTAATTGATAATGTCACATTGCCTCATTTGCAGCCGCCTTCCTAAACCTA

AGGGCCAGACTGTTGGATCCTTTAGGAAAGGGCTCATTATGTTACCTACCGC

CATTGCTGCTAGGTATCTTTTGACTCTCAAATCTTAAATATTTCTCATCTTCTC

CTTCTGCTAATACTAGTATGTTTACCATCTTTTTATTTTTTTAGGCTTGGCAGT

AAAGTCAAACTATCGTGGACACTTTCTAATATTGATAAGTCGCTCAATGGTG

AATACAATCTCACTTATCAAACACCCGATGGACCGGTTTCTGTTAGGACCAA

AGCGGTTGTCATGACTGTCCCTTCATACATTGCAAGTAGCCTGCTTCGTCCGC

TCTCAGTGAGTATCATTCTTTCCTTCATTTCTTTTCGTTTATTGTTGTCCAATG

TCTTGTTAAACACCAGTTTGGCCTTGTGCTCGTGAATTATGGCTACAATGTTA

ACTGATTCAGGCACTGTGGGAGATGCCTAAGTTTCTAAAACCTCTGCGCATA

ATGTTTGTTTGGATGTTAGGAATTGCATTGAAAAATTGCTTTTGTGATGTTGA

TGTTAATACCAATTACAAGTGTGTTCTTCAACTTCTGCAATACCTTGTTCGAG

TGAGCTTGAGGGGGTTTAGATTAGTGTCCAATGTGAAACTAGCAAATGAACT

CCAAGCGCTGGGATAGGTCCTTGGGATGGAGCCCCTGATACCCAAGACAGT

ATTCAAACCCTCTAAGTAGAGTGAGAGATCAAGGAAAGAAACTGGGTGGTT

CCTCAAATCGTAAAAAATGAATACAGTGTCATGATTGCTAATCTTATCACAA

ATCGTAAAAAATGAATTATGGTCGATTTTGGACTATTTTTGGGTCATTTTGAG

TGAATCTCGAACTTAAAAAGCGAGTCTTCTAGCAGTTCTTGTTACAGCGGGG

CATACATAGGTAGGAATTTGGTTTTTTACTATTTGAGCCTTTTGACTGTTGTG

GCCGGTAATATGGAATAGTCTAGCACTTCTGCGTGTGTACAACTAGTATTTA

TTGTAATTATGTGATCGCACTTAACTCTCAGATAAAACCTTAAGCACTAACA

TTTTGTTTTGGTTGAAGGAATCAGGAGGAAAGAAAATTGAGGGATTTGTTGG

TATATAGATTCCTTTGTTTGGATAACAAAATTGGAGTGGAGAGATTTGGAAG

GAAGAATTTTATAGGGATTAGTTCCCATTACACTTATGTTGATTACAAAATTT

CTCCAAAAGTGGAAAGATTTTGAGTGAAAATGTTTTTTATTTCTCTTCCTCTC

CCTTTCTTTCCCTCTTAAACAAACAAGGAAAGTTAATCTTATCATTCCGTACC

TTCCCCTTCTGTTCTTTTTTTTCTCTCCAAAATTCTTATCCTAACGTAGTGTTA

TTGTCACTGTCTTATGAACGAGAATTCTTTTCTTCCTAATACTGCTTGTGTTGC

ACAGTCAATGATTTAGCTAGATCATCTTTGGTTAGCTACTCAAAATATTTACA

TAAAATACTTGTAGAAATAAATACCAATAGGTCTTGTCAAGAAGTAGTTTCA

ATGCTATAAGTTTTAACCAATCCTCAAAATTTACACCATGGAGATATCTGCG

GATAAGAACTAGTAACTGTAGCAGCTGTAACTGTTGCAATCAGTTTTATGGT

TTGCCTTGCAAATCAAACTTTGGATGTTGTTTGCCTTACAATTTGTTACTATT

ACGTGAAGTTTAGTGTTCGCCCTTCACATTGTACTTTGGTTTTTGTTTTCCTTG

CAATTTGCTCTTTGAAGTATAAAGTGCTGAGTGCTGAGTGCTGAGTGCTGAC

CTTTCCTGCTCAGGATGTTGCTGCAGATTCTCTTTCTCAATTTTACTATCCACC

AGTCGCAGCAGTGTCCCTTTCTTATCCCAAAGAAGCAATTAGACCAGAATGC

TTGATCGATGGAGAACTAAAAGGATTCGGGCAATTGCATCCTCGCAGCCAGG

GTGTGGAAACCTTGGGTATATGCTCCCATTCAACTATATCTCAATTTTTATGA

GTATTTTTCTTTCTCTGAATTATTCAATTTGGTGACGTTAAATTTTGATTGTAC

TCGACAGGAACAATTTATAGTTCATCTCTTTTCCCTGGTCGAGCACCACCTGG

TAGGACCTTGATCTTGAGCTACATTGGAGGTGCTACAAATGTTGGCATATTA

CAAAAGGCAAGTCATTTATACAATTATATCTGTTGTATCCTCAAATAAGTGG

GTATCAATCCTGACGACATGCTTGCTTGTATCGATGCAGAGTGAAGATGA

Example 31

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 23

Species/gene or

SEQ

SEQ

consensus

ID

ID

sequence
Region 1
NO:
Region 2
NO:

Euphorbia_heterophylla_1
AGTTTACAGGGAGATG
239
TCGATGTGAACATGAACAAAA
251

Contig1
TAAAGTT

TGCCAGATGTCGCTATGACATT

GGCTGTGGTTG

Euphorbia_heterophylla_2
AGTTTGCAGGGAGATG
240
TCGATGTGAATATGAACAAAAT
252

Contig1
TGAAATT

GCCAGATGTTGCTATGACATTA

GCTGTGGTTGC

Ambrosia_trifida_1Contig1
AGTTTACAGGGGGATG
241
TCGATGTTAACATGAACAAAAT
253

TAAAGTT

GCCAGATGTTGCCATGACGCTT

GCAGTCGTTGC

velvetleaf_1Contig1
AGTTTGCAGGGTGATG
242
TTGATGTCAACATGAACAAAAT
254

TAAAATT

GCCAGATGTTGCCATGACTCTC

GCTGTTGTTGC

Xanthium_strumarium_2
AGTTTGCAGGGTGATG
243
TTGATGTCAACATGAACAAAAT
255

Contig1
TGAAATT

GCCTGATGTCGCAATGACTCTT

GCTGTGGTTGC

Ipomoea_hederacea_1
AGTTTACAGGGGGATG
244
TTGATGTCAACATGAACAAAAT
256

Contig1
TTAAGTT

GCCAGATGTTGCCATGACTCTT

GCTGTAGTTGC

Chenopodium_album_1
AGTTTACAGGGTGATG
245
TTGATGTCAACATGAACAAAAT
257

Contig 1
TAAAATT

GCCAGATGTCGCAATGACTCTT

GCTGTTGTTGC

Digitaria_sanguinalis_1
AGTTTGCAGGGTGATG
246
TTGACGTCAACATGAACAAAAT
258

Contig 1
TGAAATT

GCCTGATGTCGCAATGACTCTT

GCTGTGGTTGC

Senna_obtusifolia_1Contig3
AGTTTACAGGGAGATG
247
TTGATGTCAACATGAACAAGAT
259

TAAAATT

GCCAGATGTTGCCATGACGCTT

GCTGTAGTTGC

Waterhemp_EPSPS
AGTTTACAGGGTGATG
248
TCGACGTCAACATGAATAAAAT
260

TAAAATT

GCCAGATGTTGCTATGACTCTT

GCAGTTGTTGC

Palmer_EPSPS
AGTTTACAGGGTGATG
249
TCGACGTCAACATGAACAAAA
261

TAAAATT

TGCCAGATGTTGCTATGACTCT

TGCAGTTGTTGC

palmer_1Contig1
AGTTTACAGGGTGATG
250
TCGACGTCAACATGAACAAAA
262

TAAAATT

TGCCAGATGTTGCTATGACTCT

TGCAGTTGTTGC

Table 24 lists 21-, 22-, 24-, 35-, 45-, and 55-mer dsRNA polynucleotide sequences designed based on the EPSPS consensus sequence for region 2,

(SEQ ID NO: 263)

TNGANGTcAAcATGAAcAAaATGCCaGATGTNGCNATGACNcTtGCNGT

NGTTGC.

TABLE 24

SEQ

ID

Name
Sequence
NO:

Consensus_21mer
Sense: AACAUGAACAAAAUGCCAGAU
264

dsRNA
Anti-sense: AUCUGGCAUUUUGUU
265

CAUGUU

Consensus_22mer
Sense: AACAUGAACAAAAUGCCAGAUG
266

dsRNA
Anti-sense: CAUCUGGCAUUUUGUU
267

CAUGUU

Consensus_24mer
Sense: CAACAUGAACAAAAUGCCAGAUGU
268

dsRNA
Anti-sense: ACAUCUGGCAUUUUGUUCA
269

UGUUG

Consensus_35mer
Sense: UCGACGUCAACAUGAACAAAAU
270

dsRNA
GCCAGAUGUUGCU

Anti-sense: AGCAACAUCUGGCAUUUUG
271

UUCAUGUUGACGUCGA

Consensus_45mer
Sense:
272

dsRNA
UCGACGUCAACAUGAACAAAAUGCCAGAUGU

UGCUAUGACUCUUG

Anti-sense:
273

CAAGAGUCAUAGCAACAUCUGGCAUUUUGU

UCAUGUUGACGUCGA

Consensus_55mer
Sense:
274

dsRNA
UCGACGUCAACAUGAACAAAAUGCCAG

AUGUUGCUAUGACUCUUGCAGUUGUUGC

Anti-sense:
275

GCAACAACUGCAAGAGUCAUAGCAACAUCU

GGCAUUUUGUUCAUGUUGACGUCGA

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. Following polynucleotide treatment 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 glyphosate (105 g acid equivalent per hectare of Roundup® WeatherMAX® brand herbicide). At 7 days after treatment 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. At 7 days after treatment, 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.

Example 32

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.

TABLE 25

Anti-

sense

SEQ

oligo-

ID

nucleotide
Sequence (5′-3′)
NO.
Length

HH07

TAATACGACTCACTATAGGGCTTTATTGA
276
45

ATTTAGCTATGTAATC

HH09

TAATACGACTCACTATAGGGTTTATCAAC
277
41

CAAATGTGCAGC

HH11

TAATACGACTCACTATAGGGTTGTCTGTA
278
49

CATAATTGTGAGATTTGTGG

Three-week old lettuce plants (variety SVR3603 LA) 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). To each leaf 20 microliters of a mixture of the polyphenol oxidase anti-sense polynucleotides in a solution of 0.01% (v/v) SILWET L-77 and 2% (w/v) ammonium sulfate in 5 millimolar sodium phosphate, pH 6.8, were applied as small droplets; each plant was treated with 6.7 nanomoles of each of the three polynucleotides HH07, HH09, and HH11 (for a total of 20 nanomoles per plant). 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.

Approximately 3 weeks after the topical polynucleotide treatment, “untreated” lettuce leaves (i. e., not those treated with the topical polynucleotides) were cut from the lettuce head under water and incubated in a cup with 1.33 millimolar methyl jasmonate in 5% ethanol. 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.

Example 33

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. More specifically 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. This example also illustrates the use of topically applied polynucleotides to suppress a very highly expressed gene (ribulose-1,5-bisphosphate carboxylase oxygenase) in a plant.

An anti-sense polynucleotide with the sequence CATCTCCTTTAATITGTACTGC (SEQ ID NO:34) was designed for the endogenous Nicotiana benthamiana phytoene desaturase (PDS) gene, which has the cDNA sequence fragments ATGCCCCAAATCGGACTTGTATCTGCTGTTAATTTGAGAGTCCAAGGTAATTCAGCTTATCTTTGGAGC TCGAGGTCTTCGTTGGGAACTGAAAGTCAAGATGTTTGCTTGCAAAGGAATTTGTTATGTTTTGGTAGT AGCGACTCCATGGGGCATAAGTTAAGGATTCGTACTCCAAGTGCCACGACCCGAAGATTGACAAAGG ACTTTAATCCTTTAAAGGTAGTCTGCATTGATTATCCAAGACCAGAGCTAGACAATACAGTTAACTATT TGGAGGCGGCGTTATTATCATCATCGTTTCGTACTTCCTCACGCCCAACTAAACCATTGGAGATTGTTA TTGCTGGTGCAGGTTTGGGTGGTTTGTCTACAGCAAAATATCTGGCAGATGCTGGTCACAAACCGATA TTGCTGGAGGCAAGAGATGTCCTAGGTGGGAAGGTAGCTGCATGGAAAGATGATGATGGAGATTGGT ACGAGACTGGGTTGCACATATTCTTTGGGGCTTACCCAAATATGCAGAACCTGTTTGGAGAACTAGGG ATTGATGATCGGTTGCAGTGGAAGGAACATTCAATGATATTTGCGATGCCTAACAAGCCAGGGGAGTT CAGCCGCTTTGATTTTCCTGAAGCTCTTCCTGCGCCATTAAATGGAATTTTGGCCATACTAAAGAACAA CGAAATGCTTACGTGGCCCGAGAAAGTCAAATTTGCTATTGGACTCTTGCCAGCAATGCTTGGAGGGC AATCTTATGTTGAAGCTCAAGACGGTTTAAGTGTTAAGGACTGGATGAGAAAGCAAGGTGTGCCTGAT AGGGTGACAGATGAGGTGTTCATTGCCATGTCAAAGGCACTTAACTTCATAAACCCTGACGAGCTTTC GATGCAGTGCATTTTGATTGCTTTGAACAGATTTCTTCAGGAGAAACATGGTTCAAAAATGGCCTTTTT AGATGGTAACCCTCCTGAGAGACTTTGCATGCCGATTGTGGAACATATTGAGTCAAAAGGTGGCCAAG TCAGACTAAACTCACGAATAAAAAAGATCGAGCTGAATGAGGATGGAAGTGTCAAATGTTTTATACTG AATAATGGCAGTACAATTAAAGGAGATGCTTTTGTGTTTGCCACTCCAGTGGATATCTTGAAGCTTCTT TTGCCTGAAGACTGGAAAGAGATCCCATATTTCCAAAAGTTGGAGAAGCTAGTGGGAGTTCCTGTGAT AAATGTCCATATATGGTTTGACAGAAAACTGAAGAACACATCTGATAATCTGCTCTTCAGCAGAAGCC CGTTGCTCAGTGTGTACGCTGACATGTCTGTTACATGTAAGGAATATTACAACCCCAATCAGTCTATGT TGGAATTGGTATTTGCACCCGCAGAAGAGTGGATAAATCGTAGTGACTCAGAAATTATTGATGCTACA ATGAAGGAACTAGCGAAGCTTTTCCCTGATGAAATTTCGGCAGATCAGAGCAAAGCAAAAATATTGA AGTATCATGTTGTCAAAACCCCAAGGTCTGTTTATAAAACTGTGCCAGGTTGTGAACCCTGTCGGCCCT TGCAAAGATCCCCTATAGAGGGTTTTTATTTAGCTGGTGACTACACGAAACAGAAGTACTTGGCTTCA ATGGAAGGTGCTGTCTTATCAGGAAAGCTTTGTGCACAAGCTATTGTACAGGATTACGAGTTACTTCTT GGCCGGAGCCAGAAGATGTTGGCAGAAGCAAGCGTAGTTAGCATAGTGAACTAA (SEQ ID NO:38). Anti-sense polynucleotides with the sequences CTGTGATCATCATATGTATCA (SEQ ID NO:279), CCITAACTCTCCAGCTAGCAA (SEQ ID NO:280), CAGCCCGCAAATGTCATTC (SEQ ID NO:281), GCCGTCAATGGCCGCATTGCT (SEQ ID NO:282), TCCTCCCTCAGAAAGGGCAG (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 CTTATATGTGCTTAAGCCTAACGTGCACCCGGCCCCTTAACCCCAGCAGTTTTCAATCTACCTACCGTC TCTACCATTTTCTTCTAGTTGGTGAAAATTTCTAACTTTGAGAAAACAAGCCAAAGTTTTTGTTTCTAA GAACGCAAAATGAGTGAAATTTTTTGCAGCAATGGCACAGATTAGCAGCATGAGGCAAGGGATACAG ACCCCTAATCTTAATTCCTATTTTCCTAAAACCCAAAAGGTTCCTCTTTTTTCGCATTCTATCTTCTTTG GATCAAAGAAAATAACCCAAAATTCAGCAAAATCTTTGTGGGTGTGTAAGAAAGATTCAGTTTTGAGG GTGGCAAAGTCACCTTTTAGGATTTGTGCATCAGTGGCCACTGCACAGAAGCCCAACGAGATTGTGCT GCAACCCATCAAAGATATATCAGGCACTGTTAAATTGCCTGGTTCTAAATCCCTTTCCAACCGTATTCT CCTTCTTGCTGCCCTTTCTGAGGGAAGGACTGTTGTTGACAATTTACTGAGTAGTGATGACATTCATTA CATGCTTGGTGCGTTGAAAACACTTGGACTTCATGTAGAAGATGACAATGAAAACCAACGAGCAATTG TGGAAGGTTGTGGTGGGCAGTTTCCTGTCGGCGAGAAGTCTGAGGAAGAAATCCAACTATTCCTTGGA AATGCAGGAACAGCAATGCGGCCATTGACGGCAGCAGTTACTGTAGCTGGAGGACATTCAAGATATG TACTTGATGGAGTTCCTAGGATGAGAGAGAGACCGAT (SEQ ID NO:285), CACTGACGTTGGATTAGAGGTAGGCTCCTTATATGTGCTTAAGCCTAACGTGCAGCCGGCCCCCAACC CCAGCAGTTTTCAATCTACCTACCGTCTCTACCATTTTCTTATAGTAGTTGAAAATTTCTAACTTTGAGA AAACAAGCCAAAGTTTTGTTTCTAAGAACACAAAGGGAGTGAAATTTTTTGCAGCAATGGCACAGATT AGCAGCATGAGGCAAGGGATACAGACCCCTAATCTTAATTCCTATTTTCCTAAAACCCAAAAGGTTCC TCTTTTTTCGCATTCTATCTTCATTGGATCAAAGAAAATAACCCAAAATTCAGCAAAATCTTTGTGGGT GTGTAAGAAAGATTCAGTTTTGAGGGTGGCAAAGTCACCTTTTAGGATTTGTGCATCAGTGGCCACTG CACAGAAGCCTAACGAGATTGTGCTGCAACCTATCAAAGATATATCAGGCACTGTTAAATTACCTGGT TCTAAATCCCTTTCCAATCGTATTCTCCTTCTTGCTGCCCTTTCTGAGGGAAGGACTGTTGTTGACAATT TACTGAGTAGTGATGACATTCATTACATGCTTGGTGCATTGAAAACACTTGGACTTCATGTAGAAGAT GACAATGAAAACCAACGAGCAATCGTAGAAGGTTGTGGTGGGCAGTTTCCTGTCGGCAAGAAGTCTG AGGAAGAAATCCAACTATTCCTTGGAAATGCAGGAACAGCAATGCGGCCATTGACGGCAGCAGTTAC TGTAGCTGGTGGACATTCTAGATATGTACTTGATGGAGTTCCTAGGAT (SEQ ID NO:286), and AAATTCTTGGTTCGAGGAGGTCAGAAGTACAAGTCTCCTGGAAAAGCATATGTTGAAGGAGATGCCTC AAGTGCTAGCTACTTTTTGGCGGGTGCAGCTGTCACAGGTGGAACTGTCACTGTTGAAGGTTGTGGAA CAAGCAGTTTACAGGGGGATGTTAAGTTTGCTGAGGTCCTCGAAAAGATGGGGGCAGAAGTTACATG GACAGAGAACAGTGTCACGGTTAAAGGACCTCCAAGGAACTCTTCTGGAATGAAACATTTGCGGGCTG TTGACGTTAACATGAACAAAATGCCAGATGTTGCCATGACTCTTGCTGTAGTTGCACTTTTTGCTGATA GTCCTACTGCCATAAGAGATGTTGCTAGCTGGAGAGTTAAGGAAACTGAGCGGATGATTGCCATATGC ACAGAACTTAGGAAGTTGGGTGCAACAGTTGTAGAAGGGCCAGACTACTGCATAATCACTCCACCTGA AAAGTTAAAAGTAGCGGAAATTGATACATATGATGATCACAGAATGGCCATGGCTTTCTCTCTTGCGG CTTGTGCTGATGTTCCAGTCACCATTAAGGACCCCGGTTGTACTCGCAAAACCTTCCCCAACTACTTTG ACGTTCTCCAGCAGTATTCCAAGCATTAAACCACTTTCCATTAAGAATTTTGAAAAAGAGAGACTTTG ACAACAATGGTGTCATACCGGAAGAGAAAAGCTTTGATCCAAGCTTTCAACTCCTTTTCATTTGTCATG TGATGATCATTGTATTTGTTGAAGTTGAGCTGCTTTTCTTTTGTCCAGAAGACATGTATGGATACTATTA CTATATAGTTAAGGTGAACTCAGCA (SEQ ID NO:287). 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 TGTCAAGGTTTGTCCTGG (AK202, RBCS_3-4, SEQ ID NO:295) were designed for the endogenous Nicotiana benthamiana ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO) gene, based on the Nicotiana benthamiana chloroplastic RuBisCO small chain 2A cDNA sequence fragments GCAATGGCTTCCTCAGTTCTTTCCTCAGCAGCAGTTGCCACCCGCAGCAATGTTGCTCAAGCTAACATG GTTGCACCTTTCACAGGTCTTAAGTCTGCTGCCTCATTCCCTGTTTCAAGAAAGCAAAACCTTGACATC ACTTCCATTGCCAGCAACGGCGGAAGAGTGCAATGCATGCAGGTGTGGCCACCAATTAACATGAAGA AGTATGAGACTCTCTCATACCTTCCCGATTTGAGCCAGGAGCAATTGCTCTCCGAAATTGAGTACCTTT TGAAGAATGGATGGGTTCCTTGCTTGGAATTCGAGACTGAGAAAGGATTTGTCTACCGTGAACACCAC AAGTCACCAGGATACTATGATGGCAGATACTGGACCATGTGGAAGCTACCTATGTTCGGATGCACTGA TGCCACCCAAGTGTTGGCTGAGGTGGGAGAGGCGAAGAAGGAATACCCACAGGCCTGGGTCCGTATC ATTGGATTTGACAACGTGCGTCAAGTGCAGTGCATCAGTTTCATTGCCTCCAAGCCTGACGGCTAC (SEQ ID NO:296), ACAATGGCTTCCTCAGTTCTTTCCTCAGCAGCAGTTGCCACCCGCAGCAATGTTGCTCAAGCTAACATG GTTGCACCTTTCACTGGTCTTAAGTCAGCTGCCTTTTTCCCTGTTTCAAGGAAGCAAAACCTTGACATC ACTTCCATTGCCAGCAACGGCGGAAGAGTGCAATGCATGCAGGTGTGGCCACCAATTAACAAGAAGA AGTACGAGACTCTCTCATACCTTCCTGATCTGAGCGTGGAGCAATTGCTTAGCGAAATTGAGTACCTCT TGAAAAATGGATGGGTTCCTTGCTTGGAATTCGAGACTGAGCGCGGATTTGTCTACCGTGAACACCAC AAGTCACCGGGATACTATGACGGCAGATACTGGACCATGTGGAAGTTGCCTATGTTCGGATGCACTGA TGCCACCCAAGTGTTGGCCGAGGTGGAAGAGGCGAAGAAGGCATACCCACAGGCCTGGATCCGTATT ATTGGATTCGACAACGTGCGTCAAGTGCAGTGCATCAGTTTCATTGCCTACAAGCCAGAAGGCTAC (SEQ ID NO:297), CAAGCCAACATGGTTGCACCCTTCACTGGCCTCAAGTCCGCCTCCTCCTTCCCTGTTACCAGGAAACAA AACCTTGACATTACCTCCATTGCTAGCAATGGTGGAAGAGTTCAATGCATGCAGGTGTGGCCACCAAT TAACATGAAGAAGTACGAGACACTCTCATACCTTCCTGATTTGAGCCAGGAGCAATTGCTTAGTGAAG TTGAGTACCTTTTGAAAAATGGATGGGTTCCTTGCTTGGAATTCGAGACTGAGCGTGGATTCGTCTACC GTGAACACCACAACTCACCAGGATACTACGATGGCAGATACTGGACCATGTGGAAGTTGCCCATGTTC GGGTGCACTGATGCCACTCAGGTGTTGGCTGAGGTCGAGGAGGCAAAGAAGGCTTACCCACAAGCCT GGGTTAGAATCATTGGATTCGACAACGTCCGTCAAGTGCAATGCATCAGTTTTATCGCCTCCAAGCCA GAAGGCTAC (SEQ ID NO:298), and GGCTCAGTTATGTCCTCAGCTGCCGCTGTTTCCACCGGCGCCAATGCTGTTCAAGCCAGCATGGTCGCA CCCTTCACTGGCCTCAAGGCCGCCTCCTCCTTCCCGGTTTCCAGGAAACAAAACCTTGACATTACTTCC ATTGCTAGAAATGGTGGAAGAGTCCAATGCATGCAGGTGTGGCCGCCAATTAACAAGAAGAAGTACG AGACACTCTCATACCTTCCTGATTTGAGCGTGGAGCAATTGCTTAGCGAAATTGAGTACCTTTTGAAAA ATGGATGGGTTCCTTGCTTGGAATTCGAGACTGAGCATGGATTCGTCTACCGTGAACACCACCACTCA CCAGGATACTACGATGGCAGATACTGGACGATGTGGAAGTTGCCCATGTTCGGGTGCACCGATGCCAC TCAGGTCTTGGCTGAGGTAGAGGAGGCCAAGAAGGCTTACCCACAAGCCTGGGTCAGAATCATTGGAT TCGACAACGTCCGTCAAGTGCAATGCATCAGTTTCATCGCCTACAAGCCCGAAGGCTAT (SEQ ID NO:299).

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. For PDS, 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). 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. AGO1 anti-sense polynucleotides with the sequences GGAGGCAAAATACGAGCCTCA (HL510, SEQ ID NO:300), CACTAATCTTAATACCAAACT (HL511, SEQ ID NO:301), TATGGGTCATTAGCATAGGCATTAT (HL512, SEQ ID NO:302), TCTCAAGAATATCACGCTCCC (HL513, SEQ ID NO:303), CCCTTGGGGACGCTGGCAGGTCAC (HL514, SEQ ID NO:304), TAATACGACTCACTATAGGGAGAGAGCTAGATCTTTG (HL515, SEQ ID NO:305), TAATACGACTCACTATAGGCACAGTATCTTCCTCCAACC (HL516, SEQ ID NO:306), TTGCTCATCTTAAATACATGT (HL517, SEQ ID NO:307), TCATCTTAAATACATGTTTTGTCA (HL518, SEQ ID NO:308), TTATCTTCAGGGATACATTAGC (HL519, SEQ ID NO:309), AATACTGCTTGCTCATCTTAAATA (HL520, SEQ ID NO:310), GACAATTCCAAGTTCAGTC (HL521, SEQ ID NO:311), CCGTTTTAGATCACCATAAAGAGA (HL522, SEQ ID NO:312), T1TGTCTGGTAATATCACAATC (HL523, SEQ ID NO:313) were designed for the endogenous Nicotiana benthamiana Argonaute-1 (AGO 1) gene, based on two Nicotiana benthamiana AGO1-2 partial cDNA sequences, ATGGTGAGGAAGAGGAGAACTGAGTTACCTGGTTCTGGTGAGAGCTCTGGGTCTCAAGAAACTGGCG GACAGGGTCGTGGCCAGCATCCACAGCAGCTGCACCAAGCTACCTCCCAGACTCCATATCAAACTGCA ATGACTACTCAGCCAATACCTTATGCAAGACCAACTGAAACATCCTCCGAAGCTGGTTCCTCATCTCA GCCACCTGAGCAGGCAGCTCTACAAGTGACACAACAGTTCCAGCAACTTGCTTTGCAACAAGAAGCGG CTACAACGCAAGCAGTTCCACCTGCATCAAGCAAATTACTAAGGTTTCCCCTGCGTCCAGGGAAGGGG AGCAATGGTATGAGATGCATAGTCAAAGCCAATCACTTCTTCGCAGAGCTGCCTGACAAAGACTTGCA CCAGTATGATGTCACAATTTCTCCAGAGGTGTCATCACGTGGCGTCAACCGTGCTGTCATGGCGCAACT GGTGAAGCTGTACCAAGAATCTCATCTTGGGAAGAGACTTCCAGCATATGATGGAAGGAAAAGTCTAT ACACTGCAGGGCCCCTTCCATTTGTTCAAAAAGACTTCAAAATAACTCTTATTGATGATGAGGATGGG CCTGGTGGTGCTAGAAGGGAAAGGGAATTTAAAGTTGTGATCAAATTGGCTGCCCGTGCTGATCTTCA TCACTTGGGAATGTTTTTAGAAGGGAAACAGGCTGATGCACCTCAAGAGGCGCTTCAAGTTCTGGATA TTGTTCTGCGTGAGTTGCCAACATCTAGGTTTTGTCCTGTGGGTCGTTCTTTCTATTCCCGTGATTTAGG GCGAAAGCAACCATTGGGTGAAGGTTTAGAAAGTTGGCGTGGGTTCTATCAAAGCATTCGCCCCACAC AAATGGGCTTATCACTGAACATCGATATGTCTTCCACTGCATTCATTGAGCCACTGCCAGTCATTGATT TTGTGACACAGCTTCTGAACCGAGATGTGCCATCTAGACCACTGTCTGATGCTGGCCGTGTAAAGATA AAAAAAGCTCTGAGAGGTGTGAAGGTGGAGGTTACTCATCGTGGAAATATGCGGAGGAAGTACCGCA TTTCGGGTTTAACATCTCAAGCAACAAGAGAGTTGACCTTCCCTGTTGATGAAAATGGTACAGTGAAA TCTGTAATTGAGTATTTTCGAGAAACATATGGGTTTGTAATTCAGCATACTCAGTGGCCTTGTCTACAA GTTGGAAATCAGCAGAGACCTAATTACTTGCCAATGGAAGTCTGCAAGATTGTGGAGGGACAAAGGT ACTCAAAGCGCTTGAATGAGAGACAGATTACTGCACTTCTGAAAGTGACCTGCCAGCGTCCCCAAGGG AGGGAGCGTGATATTCTTGAGACCGTACATCATAATGCCTATGCTAATGACCCATATGCCAAGGAGTT TGGTATTAAGATTAGTGACAAGTTGGCACAAGTTGAGGCTCGTATTTTGCCTCCACCTCGGCTTAAATA TCATGATAACGGTCGAGAAAAGGACTGCCTGCCACAAGTTGGCCAATGGAATATGATGAATAAGAAA ATGGTAAATGGAGGGACGGTGAACAATTGGATCTGCATAAACTTCTCTCGCAATGTGCAAGATAGTGT TGCTCATGGGTTTTGCTCTGAGCTTGCACAAATGTGCCAGATATCTGGCATGAATTTCAATCCAAATCC TGTTCTGCCACCTTCGAGTGCACGCCCTGATCAGGTCGAAAGAGTATTGAAAACTCGATTTCATGATGC TATGACTAAGTTGCAGCTGCATGGGAGAGAGCTTGATTTGCTAGTTGTCATCTTGCCAGACAATAATG GATCTCTTTATGGTGATCTGAAGCGCATTTGTGAGACTGAACTAGGAGTCGTCTCACAGTGCTGTTTGA CAAAACATGTATTTAAGATGAGCAAACAGTATCTAGCCAATGTAGCGCTGAAAATCAATGTGAAGGTG GGAGGGAGAAACACTGTGCTTGTTGATGCAATATCGAGGCGAATTCCTCTTGTCAGCGACCGGCCTAC CATCATTTTTGGTGCAGATGTCACCCACCCTCACCCTGGGGAGGACTCTAGCCCATCCATTGCCGCGGT GGTTGCTTCTCAAGATTGGCCTGAGATTACAAAGTATGCTGGTCTAGTTTCTGCTCAAGCCCATAGGCA AGAGCTTATTCAGGATCTGTACACGACTAGGCAAGATCCTGTTAAGGGGACAGTTGCTGGTGGAATGA TTAAGGACTTACTTATATCCTTCCGAAGAGCTACTGGACAAAAGCCCCAGAGAATAATTTTCTATAGG GATGGTGTTAGTGAAGGACAATTTTATCAAGTGCTTCTGTTCGAACTTGATGCGATCCGCAAAGCATGT GCGTCTTTGGAGCCAAATTATCAGCCCCCAGTCACATTTGTTGTGGTTCAGAAACGACATCACACAAG GCTTTTTGCCAATAACCACCGTGACAGAAATGCAGTTGACAGGAGCGGGAACATTATACCTGGTACTG TTGTAGATTCAAAGATATGCCACCCGACAGAGTTTGATTTCTATCTTTGTAGCCATGCCGGCATACAGG GTACGAGCCGTCCAGCTCACTACCATGTTCTATGGGACGAGAACAAATTCACAGCCGATGCGCTGCAG TCTTTGACCAACAACCTCTGCTATACATATGCAAGGTGCACGCGTTCCGTCTCCATCGTTCCCCCTGCA TATTATGCACATTTGGCAGCTTTCCGTGCTCGATTTTATATGGAGCCGGAGACATCTGACGGTGGTTCA GTAACAAGTGGGGCTGCTGGTGGCAGAGGGGGTGGTGCAGGAGCTGCTGGAAGGAACACCCGAGCCC CAAGTGCTGGTGCTGCTGTTAGACCTCTTCCTGCGCTCAAGGATAATGTGAAGAGGGTTATGTTCTACT GC (SEQ ID NO:314) and CACCTATCACTCTCTTTCTCTCTCTACAAACATATCGTGCCGTTTCTCTCTCGGCCTCTCTTCGTGTTTTA GGGCACCGTGGTGGTTGGTATCCAGGCGGCGGTTTTGAGTTATTACCATGGTGCGGAAGAAGAGGACT GATGTTCCTGGTGGTGCTGAGAGTTTTGAGTCCCATGAAACTGGAGGGGCACGAGGTGGTGCCCAACG CCCATCACAGCAGCAGCAACATCAGCATCAGCAAGGCGGAGGAAGAGGCTGGGCACCTCAGCATGGA GGACATGGTGGCCGTGGTGGTGGGGGAGCTCCACGTGGTGGAATGGCCCCTCAACAATCCTATGGTGG ACCTCCTGAATACTACCAACAGGGCAGGGGAACTCAACAGTATCAACGAGGTGGAGGACAACCCCAG CGCCGTGGTGGCATGGGGGGCCGTGGGGCACGGCCACCAGTACCCGAGCTGCACCAAGCAACCCAGA CTCCACATCAGCCTGTACCATATGGAAGACCATCAGAAACATACTCAGAGGCTGGTTCCTCGTCTCAG CCACCTGAACCAACGACACAGCAAGTGACTCAGCAATTCCAGCAACTTGTTGTGCAGCCAGAAGCAGC TGCAACCCAAGCAATACAACCAGCATCGAGCAAGTCGATGAGGTTTCCACTCCGGCCAGGAAAGGGT AGTACTGGTATTAGATGCATAGTTAAGGCCAATCACTTCTTTGCCGAGTTACCTGACAAAGATCTGCAC CAGTATGATGTTTCAATTACTCCTGAGGTCGCCTCTCGGGGTGTCAACCGGGCCGTCATGGAGCAGCT GGTGAAGCTTTATAGAGAATCCCATCTTGGGAAGAGGCTTCCAGCCTATGACGGAAGAAAAAGTCTAT ACACAGCAGGGCCCCTCCCTTTTGTTCAAAAGGATTTTAAAATCACTCTAATTGATGATGATGATGGAC CTGGTGGTGCTAGGAGGGAAAGAGAGTTTAAAGTTGTGATCAAGCTGGCGGCTCGTGCTGATCTTCAT CACTTGGGGATGTTCTTACAAGGGAGACAGGCTGATGCACCGCAAGAAGCACTTCAGGTGCTGGATAT TGTGCTACGTGAGTTGCCAACATCTAGGTATTGTCCTGTGGGCCGCTCTTTCTATTCCCCTCATTTAGGA CGAAGACAACCACTGGGTGAAGGTTTAGAGAGCTGGCGTGGCTTCTATCAAAGTATTCGTCCTACACA GATGGGATTATCCCTGAATATTGATATGTCTTCCACGGCTTTCATTGAGCCACTGCCGATTATTGACTT CGTGAGCCAGCTTCTGAATCGGGATATCTCTTCTAGACCACTGTCTGATGCTGACCGCGTTAAGATAAA GAAGGCACTGAGAGGTGTAAAGGTGGGGGTCACTCATCGTGGAAATATGCGGAGGAAGTATCGCATT TCTGGCTTGACGTCTCAAGCAACAAGAGAGTTGACTTTTCCTGTCGATGAAAGGGGTACGATGAAAGC TGTTGTGGAATATTTTCGGGAAACCTATGGTTTTGTCATTCGGCATACCCAGTGGCCTTGTCTTCAAGT TGGAAATACGCAGAGGCCAAATTACTTGCCAATGGAAGTATGTAAGATTGTAGAGGGACAGAGATAC TCAAAGCGCTTGAATGAGAGGCAGATAACAGCACTTCTAAAAGTGACCTGCCAACGTCCTCAAGAGA GAGAACGTGATATTCTTCAGACTGTTCATCACAATGCTTATGCTGATGACCCATATGCGAAGGAGTTTG GTATTAAGATCAGTGAGGAGCTTGCTCAAGTTGAGGCTCGCGTTTTGCCTGCACCTTGGCTTAAATACC ATGATACAGGTCGAGAGAAAGACTGTCTGCCACAAGTGGGCCAGTGGAATATGATGAATAAGAAAAT GGTTAATGGAGGAACAGTGAACAACTGGATCTGTGTAAACTTTTCTCGCAATGTGCAAGACACAGTTG CACGTGGATTTTGTTCCGAGCTTGCACAAATGTGCATGATATCCGGAATGAACTTCAATCCCAATCCTG TTCTACCACCAGTGAGTGCTCGCCCTGATCAAGTTGAGAGAGTCTTGAAAACTCGATTTCACGATGCTA TGACAAAGTTGCAGCCAAATGGGAGAGAGCTAGATCTTTTGATTGTGATATTACCAGACAATAACGGC TCTCTTTATGGTGATCTAAAACGGATTTGTGAAACTGAACTTGGAATTGTCTCACAATGCTGCTTGACA AAACATGTATTTAAGATGAGCAAGCAGTATTTAGCTAATGTATCCCTGAAGATAAATGTGAAGGTTGG AGGAAGAAATACTGTGCTGGTTGATGCGCTCTCTAGACGAATTCCCCTTGTCAGCGACCGCCCAACTA TCATTTTTGGTGCAGATGTCACCCATCCCCACCCTGGGGAGGATTCTAGCCCGTCAATTGCTGCGGTGG TTGCTTCTCAAGATTGGCCTGAAATTACAAAGTATGCTGGTTTGGTTTCTGCTCAAGCGCATAGGCAAG AGCTTATACAAGATCTGTACAAGACTTGGCAAGATCCAGTTAGAGGACCTGTGACTGGTGGCATGATA AAGGAATTACTTATTTCCTTCCGTCGAGCAACTGGACAGAAGCCGCAGAGAATTATATTCTACAGAGA TGGTGTTAGTGAAGGACAATTTTACCAAGTTCTTCTTTTTGAACTTGATGCAATCCGCAAGGCATGTGC ATCTTTAGAACCCAACTATCAGCCCCCGGTTACGTTTGTTGTGGTCCAGAAACGGCATCATACTAGGTT GTTTGCCAATAACCACCACGACAGAAATGCAGTTGATCGGAGTGGGAACATTTTGCCTGGTACCGTTG TAGATTCAAAGATATGCCACCCTACTGAATTTGATTTCTATCTCTGTAGCCATGCCGGCATACAGGGTA CTAGCCGCCCAGCTCATTATCATGTTCTGTGGGATGAGAACAATTTTACTGCTGACGCCCTGCAGTCTT TGACTAACAATCTTTGCTATACATATGCTAGGTGTACTCGTTCTGTCTCCATTGTTCCACCAGCATATTA TGCACATTTGGCAGCTTTCCGTGCTCGGTTTTACATGGAGCCAGAGACATCTGATAATGGATCAGTCAC AAGCGCAGCTGCTTCAAACAGAGGAGGTTTAGGAGCTATGGGAAGGAGCACGCGAGCACCAGGTGCT GGTGCTGCTGTAAGGCCCCTTCCTGCTCTCAAGGAGAATGTTAAGAGGGTTATGTTTTATTGT (SEQ ID NO:315).

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. For PDS, 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.

Example 34

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. More specifically 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.

A genomic sequence of the endogenous Zea mays 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene was identified as ACCTACTTCCCCCTCGCCCCTCTCATGGTCTCTCTCGCGCCCAGATCTGCTACTAGACGGCACCGCTGC AGCGCGTCGTGTCGCGGGGGTTGGTGGCAGGCAGCGAGAGCTTGCCGTTCCTCTCTCTCAGTTGTCAG GTCCTAGGCTCACCTCACCGGCTCCCAGCCCGCTTCTATTTCTTCCTCCCCGACCCCGTGCAGGTGGCA GTCCAGTCCACGCCACCAACCGCGAGGCGAACCAAACCAACCCACTCTCCCCAACCCCGCGCGCCCAG GCCGCCCGCCCTACCAACCATCGGCGTCGGCAATGGCGGCCATGGCGACCAAGGCCGCCGCGGGCAC CGTGTCGCTGGACCTCGCCGCGCCGCCGGCGGCGGCAGCGGCGGCGGCGGTGCAGGCGGGTGCCGAG GAGATCGTGCTGCAGCCCATCAAGGAGATCTCCGGCACCGTCAAGCTGCCGGGGTCCAAGTCGCTTTC CAACCGGATCCTCCTGCTCGCCGCCCTGTCCGAGGTGAGCGATTTTGGTGCTTGCTGCGCTGCCCTGTC TCACTGCTACCTAAATGTTTTGCCTGTCGAATACCATGGATTCTCGGTGTAATCCATCTCACGATCAGA TGCACCGCATGTCGCATGCCTAGCTCTCTCTAATTTGTCTAGTAGTTTGTATACGGATTAATATTGATA AATCGGTACCGCAAAAGCTAGGTGTAAATAAACACTAGAAAATTGGATGTTCCCCTATCGGCCTGTAC TCGGCTACTCGTTCTTGTGATGGCATGCTGTCTCTTCTTGGTGTTTGGTGAACAACCTTATGAAATTTGG GCGCAAAGAACTCGCCCTCAAGGGTTGATCTTATGCCATCGTCATGATAAACAGTGGAGCACGGACGA TCCTTTACGTTGTTTTTAACAAACTTTGTCAGAAAACTAGCATCATTAACTTCTTAATGACGATTTCACA ACAAAAAAAGGTAACCTCGCTACTAACATAACAAAATACTTGTTGCTTATTAATTATATGTTTTTTAAT CTTTGATCAGGGGACAACAGTGGTTGATAACCTGTTGAACAGTGAGGATGTCCACTACATGCTCGGGG CCTTGAGGACTCTTGGTCTCTCTGTCGAAGCGGACAAAGCTGCCAAAAGAGCTGTAGTTGTTGGCTGT GGTGGAAAGTTCCCAGTTGAGGATTCTAAAGAGGAAGTGCAGCTCTTCTTGGGGAATGCTGGAACTGC AATGCGGCCATTGACAGCAGCTGTTACTGCTGCTGGTGGAAATGCAACGTATGTTTCCTCTCTTTCTCT CTACAATACTTGCTGGAGTTAGTATGAAACCCATGGGTATGTCTAGTGGCTTATGGTGTATTGGTTTTT GAACTTCAGTTACGTGCTTGATGGAGTACCAAGAATGAGGGAGAGACCCATTGGCGACTTGGTTGTCG GATTGAAGCAGCTTGGTGCAGATGTTGATTGTTTCCTTGGCACTGACTGCCCACCTGTTCGTGTCAATG GAATCGGAGGGCTACCTGGTGGCAAGGTTAGCTACTAAGGGCCACATGTTACATTCTTCTGTAAATGG TACAACTATTGTCGAGCTTTTGCATTTGTAAGGAAAGCATTGATTGATCTGAATTTGATGCTACACCAC AAAATATCCTACAAATGGTCATCCCTAACTAGCAAACAATGAAGTAATACTTGGCATGTGTTTATCAA ATTAATTTCCATCTTCTGGGGCATTGCCTGTTTTCTAGTCTAATAGCATTTGTTTTTAGCATTAATTAGC TCTTACAATTGTTATGTTCTACAGGTCAAGCTGTCTGGCTCCATCAGCAGTCAGTACTTGAGTGCCTTG CTGATGGCTGCTCCTTTGGCTCTTGGGGATGTGGAGATTGAAATCATTGATAAATTAATCTCCATTCCC TACGTCGAAATGACATTGAGATTGATGGAGCGTTTTGGTGTGAAAGCAGAGCATTCTGATAGCTGGGA CAGATTCTACATTAAGGGAGGTCAAAAATACAAGTAAGCTCTGTAATGTATTTCACTACTTTGATGCC AATGTTTCAGTTTTCAGTTTTCCAAACAGTCGCATCAATATTTGAATAGATGCACTGTAGAAAAAAAAT CATTGCAGGGAAAAACTAGTACTGAGTATTTTGACTGTAAATTATTTTACCAGTCGGAATATAGTCAGT CTATTGGAGTCAAGAGCGTGAACCGAAATAGCCAGTTAATTATCCCATTATACAGAGGACAACCATGT ATACTATTGAAACTTGGTTTATAAGAGAATCTAGGTAGCTGGACTCGTAGCTGCTTGGCATGGATACCT TCTTATCTTTAGGAAAAGACACTTGATTTTTTTTTTCTGTGGCCCTCTATGATGTGTGAACCTGCTTCTC TATTGCTTTAGAAGGATATATCTATGTCGTTATGCAACATGCTTCCCTTAGCCATTTGTACTGAAATCA GTTTCATAAGTTCGTTAGTGGTTCCCTAAACGAAACCTTGTTTTTCTTTGCAATCAACAGGTCCCCTAA AAATGCCTATGTTGAAGGTGATGCCTCAAGCGCAAGCTATTTCTTGGCTGGTGCTGCAATTACTGGAG GGACTGTGACTGTGGAAGGTTGTGGCACCACCAGTTTGCAGGTAAAGATTTCTTGGCTGGTGCTACAA TAACTGCTTTTGTCTTTTTGGTTTCAGCATTGTTCTCAGAGTCACTAAATAACATTATCATCTGCAAATG TCAAATAGACATACTTAGGTGAATTCATGTAACCGTTTCCTTACAAATTTGCTGAAACCTCAGGGTGAT GTGAAGTTTGCTGAGGTACTGGAGATGATGGGAGCGAAGGTTACATGGACCGAGACTAGCGTAACTG TTACTGGCCCACCGCGGGAGCCATTTGGGAGGAAACACCTCAAGGCGATTGATGTCAACATGAACAA GATGCCTGATGTCGCCATGACTCTTGCTGTGGTTGCCCTCTTTGCCGATGGCCCGACAGCCATCAGAGA CGGTAAAACATTCTCAGCCCTACAACCATGCCTCTTCTACATCACTACTTGACAAGACTAAAAACTATT GGCTCGTTGGCAGTGGCTTCCTGGAGAGTAAAGGAGACCGAGAGGATGGTTGCGATCCGGACGGAGC TAACCAAGGTAAGGCTACATACTTCACATGTCTCACGTCGTCTTTCCATAGCTCGCTGCCTCTTAGCGG CTTGCCTGCGGTCGCTCCATCCTCGGTTGCTGTCTGTGTTTTCCACAGCTGGGAGCATCTGTTGAGGAA GGGCCGGACTACTGCATCATCACGCCGCCGGAGAAGCTGAACGTGACGGCGATCGACACGTACGACG ACCACAGGATGGCCATGGCCTTCTCCCTTGCCGCCTGTGCCGAGGTCCCCGTGACCATCCGGGACCCT GGGTGCACCCGGAAGACCTTCCCCGACTACTTCGATGTGCTGAGCACTTTCGTCAAGAATTAATAAAG CGTGCGATACTACCACGCAGCTTGATTGAAGTGATAGGCTTGTGCTGAGGAAATACATTTCTTTTGTTC TGTTTTTTCTCTTTCACGGGATTAAGTTTTGAGTCTGTAACGTTAGTTGTTTGTAGCAAGTTTCTATTTC GGATCTTAAGTTTGTGCACTGTAAGCCAAATTTCATTTCAAGAGTGGTTCGTTGGAATAATAAGAATA ATAAATTACGTTTCAGTGGCTGTCAAGCCTGCTGCTACGTTTTAGGAGATGGCATTAGACATTCATCAT CAACAACAATAAAACCTTTTAGCCTCAAACAATAATAGTGAAGTTATTTTTTAGTCCTAAACAAGTTGC ATTAGGATATAGTTAAAACACAAAAGAAGCTAAAGTTAGGGTTTAGACATGTGGATATTGTTTTCCAT (SEQ ID NO:316), with a 5′ untranslated region located at nucleotide positions 1-306 and a 3′ untranslated region located at nucleotide positions 3490-3907. A EPSPS cDNA sequence was identified as ACCTACTTCCCCCTCGCCCCTCTCATGGTCTCTCTCGCGCCCAGATCTGCTACTAGACGGCACCGCTGC AGCGCGTCGTGTCGCGGGGGTTGGTGGCAGGCAGCGAGAGCTTGCCGTTCCTCTCTCTCAGTTGTCAG GTCCTAGGCTCACCTCACCGGCTCCCAGCCCGCTTCTATTTCTTCCTCCCCGACCCCGTGCAGGTGGCA GTCCAGTCCACGCCACCAACCGCGAGGCGAACCAAACCAACCCACTCTCCCCAACCCCGCGCGCCCAG GCCGCCCGCCCTACCAACCATCGGCGTCGGCAATGGCGGCCATGGCGACCAAGGCCGCCGCGGGCAC CGTGTCGCTGGACCTCGCCGCGCCGCCGGCGGCGGCAGCGGCGGCGGCGGTGCAGGCGGGTGCCGAG GAGATCGTGCTGCAGCCCATCAAGGAGATCTCCGGCACCGTCAAGCTGCCGGGGTCCAAGTCGCTTTC CAACCGGATCCTCCTGCTCGCCGCCCTGTCCGAGGGGACAACAGTGGTTGATAACCTGTTGAACAGTG AGGATGTCCACTACATGCTCGGGGCCTTGAGGACTCTTGGTCTCTCTGTCGAAGCGGACAAAGCTGCC AAAAGAGCTGTAGTTGTTGGCTGTGGTGGAAAGTTCCCAGTTGAGGATTCTAAAGAGGAAGTGCAGCT CTTCTTGGGGAATGCTGGAACTGCAATGCGGCCATTGACAGCAGCTGTTACTGCTGCTGGTGGAAATG CAACTTACGTGCTTGATGGAGTACCAAGAATGAGGGAGAGACCCATTGGCGACTTGGTTGTCGGATTG AAGCAGCTTGGTGCAGATGTTGATTGTTTCCTTGGCACTGACTGCCCACCTGTTCGTGTCAATGGAATC GGAGGGCTACCTGGTGGCAAGGTCAAGCTGTCTGGCTCCATCAGCAGTCAGTACTTGAGTGCCTTGCT GATGGCTGCTCCTTTGGCTCTTGGGGATGTGGAGATTGAAATCATTGATAAATTAATCTCCATTCCCTA CGTCGAAATGACATTGAGATTGATGGAGCGTTTTGGTGTGAAAGCAGAGCATTCTGATAGCTGGGACA GATTCTACATTAAGGGAGGTCAAAAATACAAGTCCCCTAAAAATGCCTATGTTGAAGGTGATGCCTCA AGCGCAAGCTATTTCTTGGCTGGTGCTGCAATTACTGGAGGGACTGTGACTGTGGAAGGTTGTGGCAC CACCAGTTTGCAGGGTGATGTGAAGTTTGCTGAGGTACTGGAGATGATGGGAGCGAAGGTTACATGGA CCGAGACTAGCGTAACTGTTACTGGCCCACCGCGGGAGCCATTTGGGAGGAAACACCTCAAGGCGATT GATGTCAACATGAACAAGATGCCTGATGTCGCCATGACTCTTGCTGTGGTTGCCCTCTTTGCCGATGGC CCGACAGCCATCAGAGACGTGGCTTCCTGGAGAGTAAAGGAGACCGAGAGGATGGTTGCGATCCGGA CGGAGCTAACCAAGCTGGGAGCATCTGTTGAGGAAGGGCCGGACTACTGCATCATCACGCCGCCGGA GAAGCTGAACGTGACGGCGATCGACACGTACGACGACCACAGGATGGCCATGGCCTTCTCCCTTGCCG CCTGTGCCGAGGTCCCCGTGACCATCCGGGACCCTGGGTGCACCCGGAAGACCTTCCCCGACTACTTC GATGTGCTGAGCACTTTCGTCAAGAATTAATAAAGCGTGCGATACTACCACGCAGCTTGATTGAAGTG ATAGGCTTGTGCTGAGGAAATACATTTCTTTTGTTCTGTTTTTTCTCTTTCACGGGATTAAGTTTTGAGT CTGTAACGTTAGTTGTTTGTAGCAAGTTTCTATTTCGGATCTTAAGTTTGTGCACTGTAAGCCAAATTTC ATTTCAAGAGTGGTTCGTTGGAATAATAAGAATAATAAATTACGTTTCAGTGGCTGTCAAGCCTGCTG CTACGTTTTAGGAGATGGCATTAGACATTCATCATCAACAACAATAAAACCTTTTAGCCTCAAACAAT AATAGTGAAGTTATTTTTTAGTCCTAAACAAGTTGCATTAGGATATAGTTAAAACACAAAAGAAGCTA AAGTTAGGGTTTAGACATGTGGATATTGTTTTCCAT (SEQ ID NO:317). A 240 base pair double-stranded RNA polynucleotide was designed with one strand corresponding to the DNA sequence TACTTGAGTGCCTTGCTGATGGCTGCTCCTTTGGCTCTTGGGGATGTGGAGATTGAAATCATTGATAAA TTAATCTCCATTCCGTACGTCGAAATGACATTGAGATTGATGGAGCGTTTTGGTGTGAAAGCAGAGCA TTCTGATAGCTGGGACAGATTCTACATTAAGGGAGGTCAAAAATACAAGTCCCCTAAAAATGCCTATG TTGAAGGTGATGCCTCAAGCGCAAGCTATTTCTTG (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. At 8 days after treatment, two of the three polynucleotide-treated plants were stunted with damaged or dead apical leaves (similar to the phenotype observed in similarly EPSPS polynucleotide-treated Nicotiana benthamiana plants), whereas all three of the control plants had normal growth and morphology (FIG. 37).

Example 35

The efficacy of different substances (including salts, a chelating agent, a humectant, and polyamines) as polynucleotide transferring agents or as enhancers of a known polynucleotide transferring agent was investigated. Ammonium sulfate had previously been shown to enhance permeability of plants to polynucleotides (see, e. g., Example 13). Table 26 lists the effect on herbicidal activity (presented as percent of weed control/kill, and as plant height) of ammonium sulfate and EDTA as additives to 1% SILWET L-77 spray solutions of topically applied polynucleotides (RNA) on glyphosate-resistant Palmer amaranth plants. In this particular experiment, ethylenediaminetetraacetic acid (EDTA) 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 26

Treatment
Palmer control (%)
Palmer height (cm)

No addition
0
7.5

+2% ammonium sulfate
43
1.8

+0.004% EDTA
45
1.0

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. In this particular experiment, 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 27

Treatment
Palmer control (%)
Palmer height (cm)

No addition
0
16.0

+2% sodium chloride
15
15.0

+2% sodium sulfate
7
17.0

+2% ammonium sulfate
54
9.3

+2% ammonium chloride
52
10.3

+2% tetramethylammonium
19
15.0

chloride

+2% tetraethylammonium
27
12.0

chloride

+2% tetrapropylammonium
34
11.0

bromide

+2% tetrabutylphosphonium
19
13.3

bromide

+2% tetrabutylphosphonium
55
5.3

bromide

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.

TABLE 28

Treatment
Palmer control (%)
Palmer height (cm)

No addition
0
16.0

Silwet L-77/AMS
54
9.3

(no glycerin)

Silwet L-77/AMS + 0.5%
57
6.3

glycerin

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. A mixture of 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 glyphosate 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.

TABLE 29

Treatment
Palmer control (%)
Palmer height (cm)

No addition
0
16

K + glyphosate
23
12.3

K + glyphosate + EPSPS
32
10.8

polynucleotides

IPA + glyphosate
9
14.5

IPA + glyphosate + EPSPS
66
5.5

polynucleotides

MEA + glyphosate
9
14.5

MEA + glyphosate + EPSPS
66
5.5

polynucleotides

The effect of the polyamine cations spermine (N,N′-bis(3-aminopropyl)butane-1,4-diamine) and spermidine (N-(3-aminopropyl)butane-1,4-diamine) on herbicidal activity of topically applied polynucleotides (RNA) on glyphosate-resistant Palmer amaranth plants was investigated. 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. 1; 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 glyphosate 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. Treatment with dsRNA and 10 millimolar spermine followed by glyphosate treatment killed glyphosate-resistant Palmer amaranth with 33-copy EPSPS and severely injured and stunted glyphosate-resistant Palmer amaranth with 36-copy EPSPS. Treatment with 10 mM spermidine alone stunted 33-copy glyphosate-resistant Palmer amaranth. In this particular experiment, neither spermine nor spermidine at 1 or 10 millimolar performed as well as 2% ammonium sulfate.

Example 36

The efficacy of different surfactants as polynucleotide transferring agents was tested in polynucleotide spray solutions applied to glyphosate-resistant Palmer amaranth. Break-Thru surfactants were obtained from Evonik Industries; SILWET surfactants were obtained from Momentive. Spray solutions were prepared the same day as spraying. A mixture of EPSPS polynucleotides (IDT [1] (SEQ ID NO:83-84), IDT [3] (SEQ ID NO:87-88), and IDT [4] (SEQ ID NO:89-90)) was added to spray solutions 15 to 50 minutes before spraying and 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. Between 10 and 225 micrograms total polynucleotides were applied to each plant, depending on the experiment; typically 23 micrograms total polynucleotides were applied per plant. 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. An overall plant injury score between 0 and 3 was given each treatment based on the combined analysis of Control, Height, Fresh Weight and Visual Plant Phenotype, where “3” is strong herbicidal activity, “2” is moderate activity, “1” is mild activity and “0” is no activity observed after correction for any observed injury caused by treatment with glyphosate alone; results are shown in Table 30.

Physical properties of the different surfactants were also investigated and listed in Table 30. Seventy milliliters of surfactant solution (0.5% surfactant in aqueous solution containing 2% ammonium sulfate, buffer (20 millimolar potassium phosphate, pH 6.8), with or without an EPSPS polynucleotide (IDT [2] (SEQ ID NO:85-86), 0.09 milligrams/milliliter) added, were prepared on the same day as measurement. Dynamic surface tension was measured at ambient room temperature (22 to 23 degrees Celsius) on a Kruss BP100 tensiometer using the maximum bubble pressure method plotting surface tension versus surface age. 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.

TABLE 30

Palmer
Surface tension

CAS

Surfactant
Surfactant
injury

delta

Surfactant name
number
Chemistry
Type
Class
score
literature
1250 ms
20-500 ms
HLB

Break-Thru S 321
na
polyether-
organosilicone
nonionic
3
na
22.7
27.1
40.0

modified

polysiloxane

Break-Thru S 200
67674-67-3
polyether-
organosilicone
nonionic
3
22
26.9
23.0

modified

polysiloxane

Break-Thru OE 441
68937-55-3
polyether-
organosilicone
nonionic
1
na
43.8
2.9
40.0

modified

polysiloxane

Break-Thru S 278
27306-78-1
polyether-
organosilicone
nonionic
2
21
24.2
23.4

modified

polysiloxane

Break-Thru S 243
na
polyether-
organosilicone
nonionic
2
47
50.3
7.7
16.7

modified

polysiloxane

Silwet L-77
27306-78-1
trisiloxane;
organosilicone
nonionic
3
20.5
26.4
23.4
13.5

polyalkylene

oxide-modified

polymethylsiloxane

Silwet HS 429
na
hydrolytically
organosilicone
nonionic
3
32-40
40.1
12.1

stable silicone

Silwet HS 312
na
silicone
organosilicone
nonionic
3
26.7
29.5
11.3

Break-Thru S 233
134180-76-0
trisiloxane
organosilicone
nonionic
3
23
26.1
10.0

Claims

1. A method of delivering a double-stranded RNA (dsRNA) polynucleotide to the interior of a cell of a plant comprising: applying the dsRNA polynucleotide and a transferring agent selected from an organosilicone surfactant and a cationic lipid to an exterior surface of the plant, wherein the transferring agent facilitates permeation of the dsRNA polynucleotide from the exterior surface of the plant to the interior of the plant cell without the aid of a physical abrasive, andwherein the dsRNA polynucleotide is 21 to 700 base pairs in length and comprises a nucleotide sequence that is identical or complementary to at least 21 contiguous nucleotides of an endogenous gene or a transcribed RNA of the plant.
2. The method of claim 1, wherein the plant is growing in a field.
3. The method of claim 1, wherein the plant is a pigweed, velvetleaf, waterhemp, prickly lettuce, dandelion, alfalfa, corn, soybean, canola, cotton, sugar beet, sugarcane, wheat, or rice plant.
4. The method of claim 1, wherein the plant is a weed or volunteer plant.
5. The method of claim 1, wherein the plant is resistant to one or more of glyphosate, dicamba and sulfonylurea.
6. The method of claim 1, wherein the cell is a leaf cell.
7. The method of claim 1, wherein the dsRNA polynucleotide and the transferring agent are applied separately.
8. The method of claim 1, wherein the dsRNA polynucleotide and the transferring agent are applied concurrently.
9. The method of claim 1, wherein the organosilicone surfactant is a silicone polyether copolymer.
10. The method of claim 9, wherein the silicone polyether copolymer is a copolymer of polyalkylene oxide modified heptamethyl trisiloxane and allyloxypolypropylene glycol methylether.
11. The method of claim 1, further comprising applying an organic or an inorganic salt.
12. The method of claim 11, wherein the salt is an ammonium salt.
13. The method of claim 12, wherein the ammonium salt is ammonium sulfate.
14. The method of claim 1, wherein the dsRNA polynucleotide and the transferring agent are applied onto the exterior surface of the plant by a spray apparatus.
15. The method of claim 1, wherein the endogenous gene: (i) is an essential gene, (ii) encodes a protein that provides herbicide resistance, or (iii) transcribes to an RNA regulatory agent.
16. The method of claim 1, wherein the endogenous gene encodes a protein selected from the group consisting of a 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), an acetohydroxyacid synthase, an acetolactate synthase (ALS), an acetyl-coenzyme A carboxylase (ACCase), a dihydropteroate synthase, a phytoene desaturase (PDS), a protoporphyrin IX oxygenase (PPO), a hydroxyphenylpyruvate dioxygenase (HPPD), a para-aminobenzoate synthase, a glutamine synthase (GS), a glufosinate-tolerant glutamine synthase, a 1-deoxy-D-xylulose 5-phosphate (DOXP) synthase, a dihydropteroate (DHP) synthase, a phenylalanine ammonia lyase (PAL), a glutathione S-transferase (GST), a D1 protein of photosystem II, a mono-oxygenase, a cytochrome P450, a cellulose synthase, a beta-tubulin, and a serine hydroxymethyltransferase.
17. The method of claim 1, wherein the endogenous gene is a native gene or a recombinant transgene.
18. The method of claim 1, further comprising applying a non-polynucleotide herbicide.
19. The method of claim 18, wherein the non-polynucleotide herbicide is selected from the group consisting of glyphosate, dicamba, phosphinothricin, bromoxynil, ioxynil and chlorsulfuron.

CROSS-REFERENCE TO RELATED APPLICATIONS AND INCORPORATION OF SEQUENCE LISTING

This application is a Divisional of U.S. patent application Ser. No. 13/042,856 filed 8 Mar. 2011, issued as U.S. Pat. No. 9,121,022, which claims the benefit of priority of U.S. Provisional Patent Applications 61/311,762 filed 8 Mar. 2010, 61/349,807 filed 28 May 2010, and 61/381,556 filed 10 Sep. 2010, which are incorporated by reference in their entirety herein. The sequence listing that is contained in the file named “38-21_56855_D.txt”, which is 133 kilobytes (measured in operating system MS-Windows) and was created on 7 Mar. 2011 and was filed in U.S. patent application Ser. No. 13/042,856 on 8 Mar. 2011 is incorporated herein by reference.

US Referenced Citations (381)

Number	Name	Date	Kind
3687808	Merigan et al.	Aug 1972	A
3791932	Schuurs et al.	Feb 1974	A
3839153	Schuurs et al.	Oct 1974	A
3850578	McConnell	Nov 1974	A
3850752	Schuurs et al.	Nov 1974	A
3853987	Dreyer	Dec 1974	A
3867517	Ling	Feb 1975	A
3879262	Schuurs et al.	Apr 1975	A
3901654	Gross	Aug 1975	A
3935074	Rubenstein et al.	Jan 1976	A
3984533	Uzgiris	Oct 1976	A
3996345	Ullman et al.	Dec 1976	A
4034074	Miles	Jul 1977	A
4098876	Piasio et al.	Jul 1978	A
4469863	Ts'o et al.	Sep 1984	A
4476301	Imbach et al.	Oct 1984	A
4535060	Comai	Aug 1985	A
4581847	Hibberd et al.	Apr 1986	A
4666828	Gusella	May 1987	A
4683202	Mullis	Jul 1987	A
4761373	Anderson et al.	Aug 1988	A
4769061	Comai	Sep 1988	A
4801531	Frossard	Jan 1989	A
4810648	Stalker	Mar 1989	A
4879219	Wands et al.	Nov 1989	A
4940835	Shah et al.	Jul 1990	A
4971908	Kishore et al.	Nov 1990	A
5004863	Umbeck	Apr 1991	A
5011771	Bellet et al.	Apr 1991	A
5013659	Bedbrook et al.	May 1991	A
5015580	Christou et al.	May 1991	A
5023243	Tullis	Jun 1991	A
5034506	Summerton et al.	Jul 1991	A
5094945	Comai	Mar 1992	A
5141870	Bedbrook et al.	Aug 1992	A
5145783	Kishore et al.	Sep 1992	A
5159135	Umbeck	Oct 1992	A
5166315	Summerton et al.	Nov 1992	A
5177196	Meyer, Jr. et al.	Jan 1993	A
5185444	Summerton et al.	Feb 1993	A
5188642	Shah et al.	Feb 1993	A
5188897	Suhadolnik et al.	Feb 1993	A
5192659	Simons	Mar 1993	A
5214134	Weis et al.	May 1993	A
5216141	Benner	Jun 1993	A
5235033	Summerton et al.	Aug 1993	A
5264423	Cohen et al.	Nov 1993	A
5264562	Matteucci	Nov 1993	A
5264564	Matteucci	Nov 1993	A
5272057	Smulson et al.	Dec 1993	A
5276019	Cohen et al.	Jan 1994	A
5281521	Trojanowski et al.	Jan 1994	A
5286634	Stadler et al.	Feb 1994	A
5286717	Cohen et al.	Feb 1994	A
5304732	Anderson et al.	Apr 1994	A
5310667	Eichholtz et al.	May 1994	A
5312910	Kishore et al.	May 1994	A
5321131	Agrawal et al.	Jun 1994	A
5331107	Anderson et al.	Jul 1994	A
5339107	Henry et al.	Aug 1994	A
5346107	Bouix et al.	Sep 1994	A
5378824	Bedbrook et al.	Jan 1995	A
5390667	Kumakura et al.	Feb 1995	A
5392910	Bell et al.	Feb 1995	A
5393175	Courville	Feb 1995	A
5399676	Froehler	Mar 1995	A
5405938	Summerton et al.	Apr 1995	A
5405939	Suhadolnik et al.	Apr 1995	A
5416011	Hinchee et al.	May 1995	A
5453496	Caruthers et al.	Sep 1995	A
5455233	Spielvogel et al.	Oct 1995	A
5459127	Feigner et al.	Oct 1995	A
5460667	Moriyuki et al.	Oct 1995	A
5462910	Ito et al.	Oct 1995	A
5463174	Moloney et al.	Oct 1995	A
5463175	Barry et al.	Oct 1995	A
5466677	Baxter et al.	Nov 1995	A
5470967	Huie et al.	Nov 1995	A
5476925	Letsinger et al.	Dec 1995	A
5489520	Adams et al.	Feb 1996	A
5489677	Sanghvi et al.	Feb 1996	A
5491288	Chaubet et al.	Feb 1996	A
5510471	Lebrun et al.	Apr 1996	A
5518908	Corbin et al.	May 1996	A
5519126	Hecht	May 1996	A
5536821	Agrawal et al.	Jul 1996	A
5538880	Lundquist et al.	Jul 1996	A
5541306	Agrawal et al.	Jul 1996	A
5541307	Cook et al.	Jul 1996	A
5550111	Suhadolnik et al.	Aug 1996	A
5550318	Adams et al.	Aug 1996	A
5550398	Kocian et al.	Aug 1996	A
5550468	Häberlein et al.	Aug 1996	A
5558071	Ward et al.	Sep 1996	A
5561225	Maddry et al.	Oct 1996	A
5561236	Leemans et al.	Oct 1996	A
5563253	Agrawal et al.	Oct 1996	A
5569834	Hinchee et al.	Oct 1996	A
5571799	Tkachuk et al.	Nov 1996	A
5587361	Cook et al.	Dec 1996	A
5591616	Hiei et al.	Jan 1997	A
5593874	Brown et al.	Jan 1997	A
5596086	Matteucci et al.	Jan 1997	A
5597717	Guerineau et al.	Jan 1997	A
5602240	De Mesmaeker et al.	Feb 1997	A
5605011	Bedbrook et al.	Feb 1997	A
5608046	Cook et al.	Mar 1997	A
5610289	Cook et al.	Mar 1997	A
5618704	Sanghvi et al.	Apr 1997	A
5623070	Cook et al.	Apr 1997	A
5625050	Beaton et al.	Apr 1997	A
5627061	Barry et al.	May 1997	A
5633360	Bischofberger et al.	May 1997	A
5633435	Barry et al.	May 1997	A
5633448	Lebrun et al.	May 1997	A
5639024	Mueller et al.	Jun 1997	A
5646024	Leemans et al.	Jul 1997	A
5648477	Leemans et al.	Jul 1997	A
5663312	Chaturvedula	Sep 1997	A
5677437	Teng et al.	Oct 1997	A
5677439	Weis et al.	Oct 1997	A
5719046	Guerineau et al.	Feb 1998	A
5721138	Lawn	Feb 1998	A
5731180	Dietrich	Mar 1998	A
5739180	Taylor-Smith	Apr 1998	A
5746180	Jefferson et al.	May 1998	A
5767361	Dietrich	Jun 1998	A
5767373	Ward et al.	Jun 1998	A
5780708	Lundquist et al.	Jul 1998	A
5804425	Barry et al.	Sep 1998	A
5824877	Hinchee et al.	Oct 1998	A
5837848	Ely et al.	Nov 1998	A
5859347	Brown et al.	Jan 1999	A
5866775	Eichholtz et al.	Feb 1999	A
5874265	Adams et al.	Feb 1999	A
5879903	Strauch et al.	Mar 1999	A
5914451	Martinell et al.	Jun 1999	A
5919675	Adams et al.	Jul 1999	A
5928937	Kakefuda et al.	Jul 1999	A
5939602	Volrath et al.	Aug 1999	A
5969213	Adams et al.	Oct 1999	A
5981840	Zhao et al.	Nov 1999	A
5985793	Sandbrink et al.	Nov 1999	A
RE36449	Lebrun et al.	Dec 1999	E
6040497	Spencer et al.	Mar 2000	A
6056938	Unger et al.	May 2000	A
6069115	Pallett et al.	May 2000	A
6084089	Mine et al.	Jul 2000	A
6084155	Volrath et al.	Jul 2000	A
6118047	Anderson et al.	Sep 2000	A
6121513	Zhang et al.	Sep 2000	A
6130366	Herrera-Estrella et al.	Oct 2000	A
6140078	Sanders et al.	Oct 2000	A
6153812	Fry et al.	Nov 2000	A
6160208	Lundquist et al.	Dec 2000	A
6177616	Bartsch et al.	Jan 2001	B1
6194636	McElroy et al.	Feb 2001	B1
6225105	Sathasivan et al.	May 2001	B1
6225114	Eichholtz et al.	May 2001	B1
6232526	McElroy et al.	May 2001	B1
6245968	Boudec et al.	Jun 2001	B1
6248876	Barry et al.	Jun 2001	B1
6252138	Karimi et al.	Jun 2001	B1
RE37287	Lebrun et al.	Jul 2001	E
6268549	Sailland et al.	Jul 2001	B1
6271359	Norris et al.	Aug 2001	B1
6282837	Ward et al.	Sep 2001	B1
6288306	Ward et al.	Sep 2001	B1
6288312	Christou et al.	Sep 2001	B1
6294714	Matsunaga et al.	Sep 2001	B1
6326193	Liu et al.	Dec 2001	B1
6329571	Hiei	Dec 2001	B1
6348185	Piwnica-Worms	Feb 2002	B1
6365807	Christou et al.	Apr 2002	B1
6384301	Martinell et al.	May 2002	B1
6385902	Schipper et al.	May 2002	B1
6399861	Anderson et al.	Jun 2002	B1
6403865	Koziel et al.	Jun 2002	B1
6414222	Gengenbach et al.	Jul 2002	B1
6421956	Boukens et al.	Jul 2002	B1
6426446	McElroy et al.	Jul 2002	B1
6433252	Kriz et al.	Aug 2002	B1
6437217	McElroy et al.	Aug 2002	B1
6453609	Soll et al.	Sep 2002	B1
6479291	Kumagai et al.	Nov 2002	B2
6506559	Fire et al.	Jan 2003	B1
6642435	Antoni et al.	Nov 2003	B1
6644341	Chemo et al.	Nov 2003	B1
6645914	Woznica	Nov 2003	B1
6768044	Boudec et al.	Jul 2004	B1
6992237	Habben et al.	Jan 2006	B1
7022896	Weeks et al.	Apr 2006	B1
7026528	Cheng et al.	Apr 2006	B2
RE39247	Barry et al.	Aug 2006	E
7105724	Weeks et al.	Sep 2006	B2
7297541	Moshiri et al.	Nov 2007	B2
7304209	Zink et al.	Dec 2007	B2
7312379	Andrews et al.	Dec 2007	B2
7323310	Peters et al.	Jan 2008	B2
7371927	Yao et al.	May 2008	B2
7392379	Le Pennec et al.	Jun 2008	B2
7405347	Hammer et al.	Jul 2008	B2
7406981	Hemo et al.	Aug 2008	B2
7462379	Fukuda et al.	Dec 2008	B2
7485777	Nakajima et al.	Feb 2009	B2
7525013	Hildebrand et al.	Apr 2009	B2
7550578	Budworth et al.	Jun 2009	B2
7622301	Ren et al.	Nov 2009	B2
7657299	Huizenga et al.	Feb 2010	B2
7671254	Tranel et al.	Mar 2010	B2
7714188	Castle et al.	May 2010	B2
7738626	Weese et al.	Jun 2010	B2
7807791	Sekar et al.	Oct 2010	B2
7838263	Dam et al.	Nov 2010	B2
7838733	Wright et al.	Nov 2010	B2
7842856	Tranel et al.	Nov 2010	B2
7884262	Clemente et al.	Feb 2011	B2
7910805	Duck et al.	Mar 2011	B2
7935869	Pallett et al.	May 2011	B2
7943819	Baum et al.	May 2011	B2
7973218	McCutchen et al.	Jul 2011	B2
8090164	Bullitt et al.	Jan 2012	B2
8143480	Axtell et al.	Mar 2012	B2
8548778	Hart et al.	Oct 2013	B1
8554490	Tang et al.	Oct 2013	B2
9121022	Sammons et al.	Sep 2015	B2
9445603	Baum et al.	Sep 2016	B2
20010006797	Kumagai et al.	Jul 2001	A1
20010042257	Connor-Ward et al.	Nov 2001	A1
20020069430	Kiaska et al.	Jun 2002	A1
20020114784	Li et al.	Aug 2002	A1
20030150017	Mesa et al.	Aug 2003	A1
20030154508	Stevens et al.	Aug 2003	A1
20030167537	Jiang	Sep 2003	A1
20040029275	Brown et al.	Feb 2004	A1
20040053289	Allen et al.	Mar 2004	A1
20040055041	Labate et al.	Mar 2004	A1
20040072692	Hoffman et al.	Apr 2004	A1
20040082475	Hoffman et al.	Apr 2004	A1
20040123347	Hinchey et al.	Jun 2004	A1
20040126845	Eenennaam et al.	Jul 2004	A1
20040133944	Hake et al.	Jul 2004	A1
20040147475	Li et al.	Jul 2004	A1
20040177399	Hammer et al.	Sep 2004	A1
20040216189	Houmard et al.	Oct 2004	A1
20040244075	Cal et al.	Dec 2004	A1
20040250310	Shukla et al.	Dec 2004	A1
20050005319	della-Cioppa et al.	Jan 2005	A1
20050044591	Yao et al.	Feb 2005	A1
20050215435	Menges et al.	Sep 2005	A1
20050250647	Hills et al.	Nov 2005	A1
20060009358	Kibler et al.	Jan 2006	A1
20060021087	Baum et al.	Jan 2006	A1
20060040826	Eaton et al.	Feb 2006	A1
20060111241	Gerwick, III et al.	May 2006	A1
20060130172	Whaley et al.	Jun 2006	A1
20060135758	Wu	Jun 2006	A1
20060200878	Lutfiyya et al.	Sep 2006	A1
20060223708	Hoffman et al.	Oct 2006	A1
20060223709	Helmke et al.	Oct 2006	A1
20060247197	Van De Craen et al.	Nov 2006	A1
20060272049	Waterhouse et al.	Nov 2006	A1
20060276339	Windsor et al.	Dec 2006	A1
20070011775	Allen et al.	Jan 2007	A1
20070021360	Nyce et al.	Jan 2007	A1
20070050863	Tranel et al.	Mar 2007	A1
20070124836	Baum et al.	May 2007	A1
20070199095	Allen et al.	Aug 2007	A1
20070250947	Boukharov et al.	Oct 2007	A1
20070259785	Heck et al.	Nov 2007	A1
20070269815	Rivory et al.	Nov 2007	A1
20070281900	Cui et al.	Dec 2007	A1
20070300329	Allen et al.	Dec 2007	A1
20080022423	Roberts et al.	Jan 2008	A1
20080050342	Fire et al.	Feb 2008	A1
20080092256	Kohn	Apr 2008	A1
20080113351	Naito et al.	May 2008	A1
20080155716	Sonnewald et al.	Jun 2008	A1
20080214443	Baum et al.	Sep 2008	A1
20090011934	Zawierucha et al.	Jan 2009	A1
20090018016	Duck et al.	Jan 2009	A1
20090036311	Witschel et al.	Feb 2009	A1
20090054240	Witschel et al.	Feb 2009	A1
20090075921	Ikegawa et al.	Mar 2009	A1
20090098614	Zamore et al.	Apr 2009	A1
20090118214	Paldi et al.	May 2009	A1
20090137395	Chicoine et al.	May 2009	A1
20090165153	Wang et al.	Jun 2009	A1
20090165166	Feng et al.	Jun 2009	A1
20090172838	Axtell et al.	Jul 2009	A1
20090188005	Boukharov et al.	Jul 2009	A1
20090205079	Kumar et al.	Aug 2009	A1
20090215628	Witschel et al.	Aug 2009	A1
20090285784	Raemaekers et al.	Nov 2009	A1
20090293148	Ren et al.	Nov 2009	A1
20090298787	Raemaekers et al.	Dec 2009	A1
20090306189	Raemaekers et al.	Dec 2009	A1
20090307803	Baum et al.	Dec 2009	A1
20100005551	Roberts et al.	Jan 2010	A1
20100048670	Biard et al.	Feb 2010	A1
20100068172	Van De Craen	Mar 2010	A1
20100071088	Sela et al.	Mar 2010	A1
20100099561	Selby et al.	Apr 2010	A1
20100100988	Tranel et al.	Apr 2010	A1
20100152443	Hirai et al.	Jun 2010	A1
20100154083	Ross et al.	Jun 2010	A1
20100192237	Ren et al.	Jul 2010	A1
20100247578	Salama	Sep 2010	A1
20110015084	Christian et al.	Jan 2011	A1
20110015284	Dees et al.	Jan 2011	A1
20110028412	Cappello et al.	Feb 2011	A1
20110035836	Eudes et al.	Feb 2011	A1
20110041400	Trias Vila et al.	Feb 2011	A1
20110053226	Rohayem	Mar 2011	A1
20110098180	Michel et al.	Apr 2011	A1
20110105327	Nelson	May 2011	A1
20110105329	Song et al.	May 2011	A1
20110112570	Mannava et al.	May 2011	A1
20110126310	Feng et al.	May 2011	A1
20110126311	Velcheva et al.	May 2011	A1
20110152339	Brown et al.	Jun 2011	A1
20110152346	Karleson et al.	Jun 2011	A1
20110152353	Koizumi	Jun 2011	A1
20110160082	Woo et al.	Jun 2011	A1
20110166022	Israels et al.	Jul 2011	A1
20110166023	Nettleton-Hammond et al.	Jul 2011	A1
20110171176	Baas et al.	Jul 2011	A1
20110171287	Saarma et al.	Jul 2011	A1
20110177949	Krapp et al.	Jul 2011	A1
20110185444	Li et al.	Jul 2011	A1
20110185445	Bogner et al.	Jul 2011	A1
20110191897	Poree et al.	Aug 2011	A1
20110201501	Song et al.	Aug 2011	A1
20110296555	Ivashuta et al.	Dec 2011	A1
20110296556	Sammons et al.	Dec 2011	A1
20120036594	Cardoza et al.	Feb 2012	A1
20120107355	Harris et al.	May 2012	A1
20120108497	Paldi et al.	May 2012	A1
20120137387	Baum et al.	May 2012	A1
20120150048	Kang et al.	Jun 2012	A1
20120156784	Adams, Jr. et al.	Jun 2012	A1
20120164205	Baum et al.	Jun 2012	A1
20120185967	Sela et al.	Jul 2012	A1
20120198586	Narva et al.	Aug 2012	A1
20120230565	Steinberg et al.	Sep 2012	A1
20120258646	Sela et al.	Oct 2012	A1
20130003213	Kabelac et al.	Jan 2013	A1
20130041004	Drager et al.	Feb 2013	A1
20130047297	Sammons et al.	Feb 2013	A1
20130047298	Tang	Feb 2013	A1
20130060133	Kassab et al.	Mar 2013	A1
20130067618	Ader et al.	Mar 2013	A1
20130084243	Goetsch et al.	Apr 2013	A1
20130096073	Sidelman	Apr 2013	A1
20130097726	Ader et al.	Apr 2013	A1
20130212739	Giritch et al.	Aug 2013	A1
20130226003	Edic et al.	Aug 2013	A1
20130247247	Ader et al.	Sep 2013	A1
20130254940	Ader et al.	Sep 2013	A1
20130254941	Ader et al.	Sep 2013	A1
20130288895	Ader et al.	Oct 2013	A1
20130318657	Avniel et al.	Nov 2013	A1
20130318658	Ader et al.	Nov 2013	A1
20130324842	Mittal et al.	Dec 2013	A1
20130326731	Ader et al.	Dec 2013	A1
20140018241	Sammons et al.	Jan 2014	A1
20140057789	Sammons et al.	Feb 2014	A1
20140109258	Van De Craen et al.	Apr 2014	A1
20140230090	Avniel et al.	Aug 2014	A1
20140274712	Finnessy et al.	Sep 2014	A1
20140275208	Hu et al.	Sep 2014	A1
20140296503	Avniel et al.	Oct 2014	A1
20150096079	Avniel et al.	Apr 2015	A1
20150143580	Beattie et al.	May 2015	A1
20150159156	Inberg et al.	Jun 2015	A1
20150203867	Beattie et al.	Jul 2015	A1
20150240258	Beattie et al.	Aug 2015	A1
20160015035	Tao	Jan 2016	A1
20160029644	Tao	Feb 2016	A1
20170159064	Carbonell	Jun 2017	A1
20170211085	Kotchoni	Jul 2017	A1

Foreign Referenced Citations (244)

Number	Date	Country
2008258254	Jul 2014	AU
101279950	Oct 2008	CN
101279951	Oct 2008	CN
101914540	Dec 2010	CN
102822350	Dec 2012	CN
288618	Apr 1991	DE
10000600	Jul 2001	DE
10116399	Oct 2002	DE
10256353	Jun 2003	DE
10256354	Jun 2003	DE
10256367	Jun 2003	DE
10204951	Aug 2003	DE
10234875	Feb 2004	DE
10234876	Feb 2004	DE
102004054666	May 2006	DE
102005014638	Oct 2006	DE
102005014906	Oct 2006	DE
102007012168	Sep 2008	DE
102010042866	May 2011	DE
0 804 600	Nov 1997	EP
1 157 991	Nov 2001	EP
1 238 586	Sep 2002	EP
1 416 049	May 2004	EP
2 147 919	Jan 2010	EP
2 160 098	Nov 2010	EP
2 530 159	Mar 2011	EP
2 305 813	Apr 2011	EP
2 545 182	Jan 2013	EP
2001253874	Sep 2001	JP
2002080454	Mar 2002	JP
2002138075	May 2002	JP
2002145707	May 2002	JP
2002220389	Aug 2002	JP
2003064059	Mar 2003	JP
2003096059	Apr 2003	JP
2004051628	Feb 2004	JP
2004107228	Apr 2004	JP
2005008583	Jan 2005	JP
2005239675	Sep 2005	JP
2005314407	Nov 2005	JP
2006232824	Sep 2006	JP
2006282552	Oct 2006	JP
2007153847	Jun 2007	JP
2007161701	Jun 2007	JP
2007182404	Jul 2007	JP
2008074840	Apr 2008	JP
2008074841	Apr 2008	JP
2008133207	Jun 2008	JP
2008133218	Jun 2008	JP
2008169121	Jul 2008	JP
2009067739	Apr 2009	JP
2009114128	May 2009	JP
2009126792	Jun 2009	JP
2009137851	Jun 2009	JP
WO 8911789	Dec 1989	WO
WO 9534659	Dec 1995	WO
WO 9534668	Dec 1995	WO
WO 96005721	Feb 1996	WO
WO 96033270	Oct 1996	WO
WO 96038567	Dec 1996	WO
WO 96040964	Dec 1996	WO
WO 9749816	Dec 1997	WO
WO 99024585	May 1999	WO
WO 9926467	Jun 1999	WO
WO 9927116	Jun 1999	WO
WO 9932619	Jul 1999	WO
WO 9961631	Dec 1999	WO
WO 9967367	Dec 1999	WO
WO 0032757	Jun 2000	WO
WO 00044914	Aug 2000	WO
WO 0107601	Feb 2001	WO
WO 0214472	Feb 2002	WO
WO 02066660	Aug 2002	WO
WO 03000679	Jan 2003	WO
WO 03006422	Jan 2003	WO
WO 03012052	Feb 2003	WO
WO 03013247	Feb 2003	WO
WO 03016308	Feb 2003	WO
WO 03020704	Mar 2003	WO
WO 03022051	Mar 2003	WO
WO 03022831	Mar 2003	WO
WO 03022843	Mar 2003	WO
WO 03029243	Apr 2003	WO
WO 03037085	May 2003	WO
WO 03037878	May 2003	WO
WO 03045878	Jun 2003	WO
WO 03050087	Jun 2003	WO
WO 03051823	Jun 2003	WO
WO 03051824	Jun 2003	WO
WO 03051846	Jun 2003	WO
WO 03064625	Aug 2003	WO
WO 03076409	Sep 2003	WO
WO 03077648	Sep 2003	WO
WO 03087067	Oct 2003	WO
WO 03090539	Nov 2003	WO
WO 03091217	Nov 2003	WO
WO 03093269	Nov 2003	WO
WO 03104206	Dec 2003	WO
WO 2004002947	Jan 2004	WO
WO 2004002981	Jan 2004	WO
WO 2004005485	Jan 2004	WO
WO 2004009761	Jan 2004	WO
WO 2004011429	Feb 2004	WO
WO 2004022771	Mar 2004	WO
WO 2004029060	Apr 2004	WO
WO 2004035545	Apr 2004	WO
WO 2004035563	Apr 2004	WO
WO 2004035564	Apr 2004	WO
WO 2004037787	May 2004	WO
WO 2004049806	Jun 2004	WO
WO 2004062351	Jul 2004	WO
WO 2004067518	Aug 2004	WO
WO 2004067527	Aug 2004	WO
WO 2004074443	Sep 2004	WO
WO 2004077950	Sep 2004	WO
WO 2005000824	Jan 2005	WO
WO 2005003362	Jan 2005	WO
WO 2005007627	Jan 2005	WO
WO 2005007860	Jan 2005	WO
WO 2005040152	May 2005	WO
WO 2005047233	May 2005	WO
WO 2005047281	May 2005	WO
WO 2005061443	Jul 2005	WO
WO 2005061464	Jul 2005	WO
WO 2005068434	Jul 2005	WO
WO 2005070889	Aug 2005	WO
WO 2005089551	Sep 2005	WO
WO 2005095335	Oct 2005	WO
WO 2005107437	Nov 2005	WO
WO 2005110068	Nov 2005	WO
WO 2006006569	Jan 2006	WO
WO 2006024820	Mar 2006	WO
WO 2006029828	Mar 2006	WO
WO 2006029829	Mar 2006	WO
WO 2006037945	Apr 2006	WO
WO 2006050803	May 2006	WO
WO 2006074400	Jul 2006	WO
WO 2006090792	Aug 2006	WO
WO 2006123088	Nov 2006	WO
WO 2006125687	Nov 2006	WO
WO 2006125688	Nov 2006	WO
WO 2006138638	Dec 2006	WO
WO 2007003294	Jan 2007	WO
WO2007007316	Jan 2007	WO
WO 2007024783	Mar 2007	WO
WO 2007026834	Mar 2007	WO
WO 2007035650	Mar 2007	WO
WO 2007039454	Apr 2007	WO
WO 2007050715	May 2007	WO
WO 2007051462	May 2007	WO
WO 2007070389	Jun 2007	WO
WO 2007071900	Jun 2007	WO
WO 2007070389	Jun 2007	WO
WO 2007074405	Jul 2007	WO
WO 2007077201	Jul 2007	WO
WO 2007077247	Jul 2007	WO
WO 2007080126	Jul 2007	WO
WO 2007080127	Jul 2007	WO
WO 2007083193	Jul 2007	WO
WO 2007096576	Aug 2007	WO
WO 2007051462	Oct 2007	WO
WO 2007051462	Oct 2007	WO
WO 2007119434	Oct 2007	WO
WO 2007134984	Nov 2007	WO
WO 2008007100	Jan 2008	WO
WO 2008009908	Jan 2008	WO
WO 2008029084	Mar 2008	WO
WO 2008042231	Apr 2008	WO
WO 2008059948	May 2008	WO
WO 2008063203	May 2008	WO
WO 2008071918	Jun 2008	WO
WO 2008074991	Jun 2008	WO
WO 2008084073	Jul 2008	WO
WO 2008100426	Aug 2008	WO
WO 2008102908	Aug 2008	WO
WO 2008148223	Dec 2008	WO
WO 2008152072	Dec 2008	WO
WO 2008152073	Dec 2008	WO
WO 2009000757	Dec 2008	WO
WO 2009005297	Jan 2009	WO
WO 2009035150	Mar 2009	WO
WO 2009046384	Apr 2009	WO
WO 2009063180	May 2009	WO
WO 2009068170	Jun 2009	WO
WO 2009068171	Jun 2009	WO
WO 2009086041	Jul 2009	WO
WO 2009090401	Jul 2009	WO
WO 2009090402	Jul 2009	WO
WO 2009115788	Sep 2009	WO
WO 2009116558	Sep 2009	WO
WO 2009125401	Oct 2009	WO
WO 2009152995	Dec 2009	WO
WO 2009158258	Dec 2009	WO
WO 2010012649	Feb 2010	WO
WO 2010026989	Mar 2010	WO
WO 2010034153	Apr 2010	WO
WO 2010049270	May 2010	WO
WO 2010049369	May 2010	WO
WO 2010049405	May 2010	WO
WO 2010049414	May 2010	WO
WO 2010056519	May 2010	WO
WO 2010063422	Jun 2010	WO
WO 2010069802	Jun 2010	WO
WO 2010078906	Jul 2010	WO
WO 2010078912	Jul 2010	WO
WO 2010104217	Sep 2010	WO
WO 2010108611	Sep 2010	WO
WO 2010112826	Oct 2010	WO
WO 2010116122	Oct 2010	WO
WO 2010119906	Oct 2010	WO
WO 2010130970	Nov 2010	WO
WO 2011001434	Jan 2011	WO
WO 2011003776	Jan 2011	WO
WO 2011035874	Mar 2011	WO
WO 2011045796	Apr 2011	WO
WO 2011065451	Jun 2011	WO
WO 2011067745	Jun 2011	WO
WO 2011080674	Jul 2011	WO
WO 2011112570	Sep 2011	WO
WO 2011132127	Oct 2011	WO
WO 2012001626	Jan 2012	WO
WO 2012056401	May 2012	WO
WO 2012092580	Jul 2012	WO
WO 2013010691	Jan 2013	WO
WO 2013025670	Feb 2013	WO
WO 2013025670	Mar 2013	WO
WO 2013039990	Mar 2013	WO
WO 2013040005	Mar 2013	WO
WO 2013040021	Mar 2013	WO
WO 2013040033	Mar 2013	WO
WO 2013040049	Mar 2013	WO
WO 2013040057	Mar 2013	WO
WO 2013040116	Mar 2013	WO
WO 2013040117	Mar 2013	WO
WO 2013153553	Oct 2013	WO
WO 2013175480	Nov 2013	WO
WO 2014022739	Feb 2014	WO
WO 2014106837	Jul 2014	WO
WO 2014106838	Jul 2014	WO
WO 2014151255	Sep 2014	WO
WO 2014164761	Oct 2014	WO
WO 2014164797	Oct 2014	WO
WO 2014164797	Oct 2014	WO
WO 2015010026	Jan 2015	WO

Non-Patent Literature Citations (584)

Entry
Wiesman et al (J. Biotechnology, 2007, 130: 85-94).
Sun et al (Plant J, 2005, 44: 128-138).
Orbovic et al (J. Amer. Soc. Hort. Sci., 2001, 126(4): 486-490).
Widholm et al (Phyisologia Plantarum, 2001, 112: 540-545).
Pasloske (2001, Ribonuclease Inhibitors. In: Schein C.H. (eds) Nuclease Methods and Protocols. Methods in Molecular Biology, vol. 160. Humana Press) (Year: 2001).
Tenllado et al (BMC Biotechnology, 2003, 3:3).
Tenllado et al (Virus Research, 2004, 102: 85-96).
Communication pursuant to Article 94(3) EPC dated Mar. 24, 2016, in European Patent Application No. 12 831 684.1.
Communication pursuant to Article 94(3) EPC dated Mar. 24, 2016, in European Patent Application No. 12 830 932.5.
Communication pursuant to Article 94(3)EPC dated Mar. 9, 2016, in European Patent Application No. 12 831 166.9.
Communication pursuant to Article 94(3) EPC dated Mar. 18, 2016, in European Patent Application No. 12 832 160.1.
Communication pursuant to Article 94(3) EPC dated Jan. 14, 2016, in European Patent Application No. 12 832 415.9.
Database Accession No. HD315444, “Sequence 192160 from Patent EP2213738,” (2010).
Extended European Search Report dated Jan. 20, 2016, in European Patent Application No. 13 794 339.5.
First Office Action dated Feb. 2, 2016, in Chinese Patent Application No. 201380039346.6.
GenBank Accession No. GU120406, “Chrysomela tremulae ribosomal protein L7 (RpL7) mRNA, complete cds,” (2009) Retrieved from the internet, U RL: <http://www.ncbi.nlm.nih.gov/nuccore/GU120406>.
GenBank Accession No. Q4GXM3_BIPLU, “Ribosomal protein L7e” (2006) [Retrieved on Feb. 5, 2016] Retrieved from the internet, URL: <http://www.ncbi.nlm.nih.gov/protein/Q4GXM3>.
Gudkov, “Minireview: The L7/L12 ribosomal domain of the ribosome: structural and functional studies,” FEBS Letters, 407:253-256 (1997).
Heffer et al., “Rapid isolation of gene homologs across taxa: Efficient identification and isolation of gene orthologs from non-model organism genomes, a technical report,” EvoDevo Journal, 2(7):1-5 (2011).
Knudsen, “Promoter2.0: for the recognition of Poll promoter sequences,” Bioniformatics, 15(5):356-361 (1999).
Migge et al., “Greenhouse-grown conditionally lethal tobacco plants obtained by expression of plastidic glutamine synthetase antisense RNA may contribute to biological safety,” Plant Science 153:107-112 (2000).
Office Action dated Apr. 13, 2016, in Chinese Patent Application No. 201280053985.3.
Patent Examination Report No. 1 dated Feb. 8, 2016, in Australian Patent Application No. 2014262189.
Promoter Prediction for SEQ ID No. 1702 from 13/612929/MK/, Promoter 2.0 Prediction Results, pp. 1-4 (2016).
Salanenka et al.,“Seedcoat Permeability: Uptake and Post-germination Transport of Applied Model Tracer Compounds,” HortScience, 46(4):622-626 (2011).
Scott et al., Botanical Insecticides for Controlling Agricultural Pests: Piperamides and the Colorado Potato Beetle Leptinotarsa decemlineata Say (Coleoptera: Chrysomelidae), Archives of Insect Biochemistry and Physiology, 54:212-225 (2003).
Second Office Action dated Mar. 4, 2016, in Chinese Patent Application No. 201280054820.8.
Second Office Action dated Feb. 25, 2016, in Chinese Patent Application No. 201280054179.8.
Shintani et al., “Antisense Expression and Overexpression of Biotin Carboxylase in Tobacco Leaves,” Plant Physiol., 114:881-886 (1997).
Written Opinion dated Apr. 7, 2016, in Singapore Patent Application No. 201206152-9.
Zhang et al., “Development and Validation of Endogenous Reference Genes for Expression Profiling of Medaka (Oryzias latipes) Exposed to Endocrine Disrupting Chemicals by Quantitative Real-Time RT-PCR,” Toxicological Sciences, 95(2):356-368 (2007).
Alarcón-Reverte et al., “Resistance to ACCase-inhibiting herbicides in the weed Lolium multiflorum,” Comm. Appl. Biol. Sci., 73(4):899-902 (2008).
Amarzguioui et al., “An algorithm for selection of functional siRNA sequences,” Biochemical and Biophysical Research Communications, 316:1050-1058 (2004).
Ambrus et al., “The Diverse Roles of RNA Helicases in RNAi,” Cell Cycle, 8(21):3500-3505 (2009).
Anonymous, “A handbook for high-level expression and purification of 6xHis-tagged proteins,” The QUIexpressionist, (2003).
An et al., “Transient RNAi Induction against Endogenous Genes in Arabidopsis Protoplasts Using in Vitro-Prepared Double-Stranded RNA,” Biosci Biotechnol Biochem, 69(2):415-418 (2005).
Aoki et al., “In Vivo Transfer Efficiency of Antisense Oligonucleotides into the Myocardium Using HVJ—Liposome Method,” Biochem Biophys Res Commun, 231:540-545 (1997).
Arpaia et al., “Production of transgenic eggplant (Solanum melongena L.) resistant to Colorado Potato Beetle (Leptinotarsa decemlineata Say),” (1997) Theor. Appl. Genet., 95:329-334 (1997).
Artmymovich, “Using RNA interference to increase crop yield and decrease pest damage,” MMG 445 Basic Biotech., 5(1):7-12 (2009).
Australian Patent Examination report No. 1 dated Nov. 11, 2013, in Australian Application No. 2011224570.
Axtell et al., “A Two-Hit Trigger for siRNA Biogenesis in Plants,” Cell, 127:565-577 (2006).
Baerson et al., “Glyphosate-Resistant Goosegrass. Identification of a Mutation in the Target Enzyme 5-Enolpyruvylshikimate-3-Phosphate Synthase,” Plant Physiol., 129(3):1265-1275 (2002).
Baulcombe, “RNA silencing and heritable epigenetic effects in tomato and Arabidopsis,” Abstract 13th Annual Fall Symposium, Plant Genomes to Phenomes, Donald Danforth Plant Science Center, 28-30 (2011).
Bannerjee et al., “Efficient production of transgenic potato (S. tuberosum L. ssp. andigena) plants via Agrobacterium tumefaciens-mediated transformation,” Plant Sci., 170:732 738 (2006).
Bayer et al., “Programmable ligand-controlled riboregulators of eukaryotic gene expression,” Nature Biotechnol., 23(3):337-343 (2005).
Beal, et al., “Second Structural Motif for Recognition of DNA by Oligonucleotide-Directed Triple-Helix Formation,” Science, 251:1360-1363 (1992).
Becker et al., “Fertile transgenic wheat from microprojectile bombardment of scutellar tissue,” The Plant Journal, 5(2):299-307 (1994).
Bhargava et al., “Long double-stranded RNA-mediated RNA interference as a tool to achieve site-specific silencing of hypothalamic neuropeptides,” Brain Research Protocols, 13:115-125 (2004).
Boletta et al., “High Efficient Non-Viral Gene Delivery to the Rat Kidney by Novel Polycationic Vectors,” J. Am Soc. Nephrol., 7:1728 (1996).
Bolognesi et al., “Characterizing the Mechanism of Action of Double-Stranded RNA Activity against Western Corn Rootworm(Diabrotica virgifera virgifera LeConte),” PLoS ONE 7(10):e47534 (2012).
Bolter et al., “A chloroplastic inner envelope membrane protease is essential for plant development,” FEBS Letters, 580:789-794 (2006).
Breaker et al., “A DNA enzyme with Mg2+-dependent RNA phosphoesterase activity,” Chemistry and Biology, 2:655-660 (1995).
Butler et al., “Priming and re-drying improve the survival of mature seeds of Digitalis purpurea during storage,” Annals of Botany, 103:1261-1270 (2009).
Bytebier et al., “T-DNA organization in tumor cultures and transgenic plants of the monocotyledon Asparagus officinalis,” Proc. Natl. Acad. Sci. U.S.A., 84:5345-5349 (1987).
Chabbouh et al., “Cucumber mosaic virus in artichoke,” FAO Plant Protection Bulletin, 38:52-53 (1990).
Chakravarty et al., “Genetic Transformation in Potato: Approaches and Strategies,” Amer J Potato Res, 84:301 311 (2007).
Chee et al., “Transformation of Soybean (Glycine max) by Infecting Germinating Seeds with Agrobacterium tumefaciens,” Plant Physiol., 91:1212-1218 (1989).
Chen et al., “In Vivo Analysis of the Role of atTic20 in Protein Import into Chloroplasts,” The Plant Cell, 14:641-654 (2002).
Cheng et al., “Production of fertile transgenic peanut (Arachis hypogaea L.) plants using Agrobacterium tumefaciens,” Plant Cell Reports, 15:653-657 (1996).
Chi et al., “The Function of RH22, a DEAD RNA Helicase, in the Biogenesis of the 50S Ribosomal Subunits of Arabidopsis Chloroplasts,” Plant Physiology, 158:693-707 (2012).
Chinese Office Action dated Aug. 28, 2013 in Chinese Application No. 201180012795.2.
Clough et al., “Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana,” The Plant Journal, 16(6):735-743 (1998).
CN101914540 Patent Diclosure, “Introduction of RNA into plant by interference,” (2010).
Colombian Office Action dated Aug. 2, 2013 in Application No. 12 152898.
Colombian Office Action dated Feb. 21, 2014 in Application No. 12 152898.
Cooney et al., “Site-Specific Oligonucleotide Binding Represses Transcription of the Human c-myc Gene in Vitro,” Science ,241:456-459 (1988).
Colbourne et al., “The Ecoresponsive Genome of Daphnia pulex,” Science, 331(6017):555-561 (2011).
COST Action FA0806 progress report “Plant virus control employing RNA-based vaccines: A novel non-transgenic strategy” (2010).
Dalmay et al., “An RNA-Depenedent RNA Polymerase Gene in Arabidopsis is Required for Posttranscriptional Gene Silencing Mediated by a Transgene but Not by a Virus,” Cell, 101:543-553 (2000).
Datebase EMBL CBIB Daphnia—XP-002732239 (2011).
Davidson et al., “Engineering regulatory RNAs,” TRENDS in Biotechnology, 23(3):109-112 (2005).
De Block, et al. “Engineering herbicide resistance in plants by expression of a detoxifying enzyme,” EMBO J. 6(9):2513-2519 (1987).
De Framond, “MINI-Ti: A New Vector Strategy for Plant Genetic Engineering,” Nature Biotechnology, 1:262-269 (1983).
Della-Cioppa et al., “Import of a precursor protein into chloroplasts is inhibited by the herbicide glyphosate,” The EMBO Journal, 7(5):1299-1305 (1988).
“Devgen, The mini-Monsanto,” KBC Securities (2006).
Diallo et al., “Long Endogenous dsRNAs Can Induce Complete Gene Silencing in Mammalian Cells and Primary Cultures,” Oligonucleotides, 13:381-392 (2003).
Du et al., “A systematic analysis of the silencing effects of an active siRNA at all single-nucleotide mismatched target sites,” Nucleic Acids Research, 33(5):1671-1677 (2005).
Dunoyer et al., “Small RNA Duplexes Function as Mobile Silencing Signals Between Plant Cells,” Science, 328:912-916 (2010).
Ellington et al., “In vitro selection of RNA molecules that bind specific ligands,” Nature, 346:818-822 (1990).
Eurasian Office Action dated Feb. 24, 2014, in Application No. 201201264.
European Cooperation in the field of Scientific and Technical Research—Memorandum of Understanding for COST Action FA0806 (2008).
European Supplemental Search Report dated Oct. 8, 2013 in Application No. 11753916.3.
Farooq et al., “Rice seed priming,” IPRN, 30(2):45-48 (2005).
Fire et al., “Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans,” Nature, 391:806-811 (1998).
Fukuhara et al., “Enigmatic Double-Stranded RNA in Japonica Rice,” Plant Molecular Biology, 21:1121-1130 (1993).
Fukuhara et al., “The Unusual Structure of a Novel RNA Replicon in Rice,” The Journal of Biological Chemistry, 270(30):18147-18149 (1995).
Fukuhara et al., “The wide distribution of endornaviruses, large double-stranded RNA replicons with plasmid-like properties,” Archives of Virology, 151:995-1002 (2006).
Further Examination Report issued in New Zealand Patent Application No. 601784 dated May 16, 2014.
Gaines et al., “Gene amplification confers glyphosate resistance in Amaranthus palmeri,” Proc. Natl. Acad. Sci. USA, 107(3):1029-1034 (2010).
Gallie et al., “Identification of the motifs within the tobacco mosaic virus 5′-leader responsible for enhancing translation,” Nucleic Acids Res., 20(17):4631-4638 (1992).
Gan et al., “Bacterially expressed dsRNA protects maize against SCMV infection,” Plant Cell Rep, 11:1261-1268 (2010).
Ge et al., “Rapid vacuolar sequestration: the horseweed glyphosate resistance mechanism,” Pest Management Sci., 66:345-348 (2010).
GenBank accession No. AY545657.1, published 2004.
GenBank Accession No. DY640489, PU2_plate27_F03 PU2 Prunus persica cDNA similar to expressed mRNA inferred from Prunus persica hypothetical domain/motif containing IPR011005:Dihydropteroate synthase-like, MRNA sequence (2006) [Retrieved on Feb. 4, 2013]. Retrieved from the internet <URL: http://www.ncbi.nlm.nih.gov/nucest/DY640489>.
GenBank Accession No. EU24568—“Amaranthus hypochondriacus acetolactate synthase (ALS) gene,” (2007).
GenBank Accession No. FJ972198, Solanum lycopersicum cultivar Ailsa Craig dihydropterin pyrophosphokinase-dihydropteroate synthase (HPPK-DHPS) gene, complete cds (2010) [Retrieved on Nov. 26, 2012]. Retrieved from the internet ,URL: http://www.ncbi.nlm.nih.gov/nuccore/FJ972198>.
GenBank accession No. GI:186478573, published Jan. 22, 2014.
GenEmbl FJ861243, published Feb. 3, 2010.
Gutensohn et al., “Functional analysis of the two Arabidopsis homologues of Toc34, a component of the chloroplast protein import apparatus,” The Plant Journal, 23(6):771-783 (2000).
Haigh, “The Priming of Seeds: Investigation into a method of priming large quantities of seeds using salt solution,” Thesis submitted to Macquarie University (1983).
Hamilton et al. “Guidelines for the Identification and Characterization of Plant Viruses,” J. gen. Virol., 54:223-241 (1981).
Hamilton et al., “Two classes of short interfering RNA in RNA silencing,” EMBO J., 21(17):4671-4679 (2002).
Han et al., “Molecular Basis for the Recognition of Primary microRNAs by the Drosha-DGCR8 Complex,” Cell, 125(5):887-901 (2006).
Hannon, “RNA interference,” Nature,481:244-251 (2002).
Hardegree, “Drying and storage effects on germination of primed grass seeds,” Journal of Range Management, 47(3):196-199 (1994).
Herman et al., “A three-component dicamba O-demethylase from Pseudomonas maltophilia, strain DI-6: gene isolation, characterization, and heterologous expression,” J. Biol. Chem., 280: 24759-24767 (2005).
Hidayat et al., “Enhanced Metabolism of Fluazifop Acid in a Biotype of Digitaria sanguinalis Resistant to the Herbicide Fluazifop-P-Butyl,” Pesticide Biochem. Physiol., 57:137-146 (1997).
Himber et al., “Transitivity-dependant and—independent cell-to-cell movement of RNA silencing,” The EMBO Journal, 22(17):4523-4533 (2003).
Hirschberg et al., “Molecular Basis of Herbicide Resistance in Amaranthus hybridus,” Science, 222:1346-1349 (1983).
Hoekema et al., “A binary plant vector strategy based on separation of vir- and T-region of the Agrobacterium tumefaciens Ti-plasmid,” Nature, 303:179-180 (1983).
Hofgen et al., “Repression of Acetolactate Synthase Activity through Antisense Inhibition: Molecular and Biochemical Analysis of Transgenic Potato (Solanum tuberosum L. cv Desiree) Plants,” Plant Physiol., 107(2):469-477 (1995).
Hsieh et al., “A library of siRNA duplexes targeting the phosphoinositide 3-kinase pathway: determinants of gene silencing for use in cell-based screens,” Nucleic Acids Res., 32(3):893-901 (2004).
Huesken et al., “Design of a genome-wide siRNA library using an artificial neural network,” Nature Biotechnology, 23(8): 995-1001 (2005).
Hunter et al., “RNA Interference Strategy to suppress Psyllids & Leafhoppers,” International Plant and Animal Genome XIX, 15-19 (2011).
Ichihara et al., “Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities,” Nucleic Acids Res., 35(18):e123 (2007).
International Preliminary Report on Patentability dated Sep. 11, 2014, in International Application No. PCT/IL13/50447.
International Search Report dated Mar. 12, 2013 in International Application No. PCT/US 12/54789.
International Search Report and the Written Opinion dated May 10, 2011, in International Application No. PCT/US 11/27528.
International Search Report and the Written Opinion dated Feb. 25, 2013, in International Application No. PCT/US 12/54883.
International Search Report and the Written Opinion dated Feb. 27, 2013, in International Application No. PCT/US 12/54814.
International Search Report and the Written Opinion dated Feb. 27, 2013, in International Application No. PCT/US 12/54842.
International Search Report and the Written Opinion dated Feb. 27, 2013, in International Application No. PCT/US 12/54862.
International Search Report and the Written Opinion dated Feb. 27, 2013, in International Application No. PCT/US 12/54894.
International Search Report and the Written Opinion dated Feb. 27, 2013, in International Application No. PCT/US 12/54974.
International Search Report and the Written Opinion dated Feb. 27, 2013, in International Application No. PCT/US 12/54980.
International Search Report and the Written Opinion dated Jul. 15, 2014, International Application No. PCT/US2014/025305.
Invitation to Pay Additional Fees dated May 6, 2014, in International Application No. PCT/IL2013/051083.
Invitation to Pay Additional Fees dated May 6, 2014, in International Application No. PCT/IL2013/051085.
Invitation to Pay Additional Fees dated Nov. 25, 2014, in International Application No. PCT/US2014/047204.
Isaacs et al., “Engineered riboregulators enable post-transcriptional control of gene expression,” Nature Biotechnology, 22(7):841-847 (2004).
Ji et al., “Regulation of small RNA stability: methylation and beyond,” Cell Research, 22:624-636 (2012).
Jones-Rhoades et al., “MicroRNAs and Their Regulatory Roles in Plants,” Annu. Rev. Plant Biol., 57:19-53 (2006).
Josse et al., “A DELLA in Disguise: SPATULA Restrains the Growth of the Developing Arabidopsis Seedling,” Plant Cell, 23:1337-1351 (2011).
Kam et al., “Nanotube Molecular Transporters: Internalization of Carbon Nanotube—Protein Conjugates into Mammalian Cells,” J Am. Chem. Soc., 126(22):6850-6851 (2004).
Katoh et al., “Specific residues at every third position of siRNA shape its efficient RNAi activity,” Nucleic Acids Res., 35(4): e27 (2007).
Kertbundit et al. “In vivo random β-glucuronidase gene fusions in Arabidopsis thaliana,” Proc. Natl. Acad. Sci. U S A., 88:5212-5216 (1991).
Khachigian, “DNAzymes: Cutting a path to a new class of therapeutics,” Curr Opin Mol Ther 4(2):119-121 (2002).
Khodakovskaya et al., “Carbon Nanotubes are Able to Penetrate Plant Seed Coat and Dramatically Affect Seed Germination and Plant Growth,” ACS Nano, 3(10):3221-3227 (2009).
Kirkwood, “Use and Mode of Action of Adjuvants for Herbicides: A Review of some Current Work,” Pestic Sci., 38:93-102 (1993).
Klahre et al., “High molecular weight RNAs and small interfering RNAs induce systemic posttranscriptional gene silencing in plants,” Proc. Natl. Acad. Sci. USA, PNAS, 99(18):11981-11986 (2002).
Kronenwett et al., “Oligodeoxyribonucleotide Uptake in Primary Human Hematopoietic Cells is Enhanced by Cationic Lipids and Depends on the Hematopoietic Cell Subset,” Blood, 91(3):852-862 (1998).
Kumar et al., “Sequencing, De Novo Assembly and Annotation of the Colorado Potato Beetle, Leptinotarsa decemlineata,Transcriptome,” PLoS One, 9(1):e86012 (2014).
Kusaba et al., “Low glutelin content1: A Dominant Mutation That Suppresses the Glutelin Multigene Family via RNA Silencing ni Rice,” The Plant Cell, 15(6):1455-1467 (2003).
Kusaba, “RNA interference in crop plants,” Curr Opin Biotechnol, 15(2):139-143 (2004).
Lavigne et al., “Enhanced antisense inhibition of human immunodeficiency virus type 1 in cell cultures by DLS delivery system,” Biochem Biophys Res Commun, 237:566-571 (1997).
Lesnik et al., “Prediction of rho-independent transcriptional terminators in Escherichia coli,” Nucleic Acids Research, 29(17):3583-3594 (2001).
Li et al., “Establishment of a highly efficient transformation system for pepper (Capsicum annuum L.),” Plant Cell Reports, 21: 785-788 (2003).
Li et al., “The FAST technique: a simplified Agrobacterium-based transformation method for transient gene expression analysis in seedlings of Arabidopsis and other plant species,” Plant Methods, 5(6):1-15 (2009).
Liu et al., “Comparative study on the interaction of DNA with three different kinds of surfactants and the formation of multilayer films,” Bioelectrochemistry, 70:301-307 (2007).
Liu et al., “Carbon Nanotubes as Molecular Transporters for Walled Plant Cells,” Nano Letters, 9(3):1007-1010 (2009).
Llave et al., “Endogenous and Silencing-Associated Small RNAs in Plants,” The Plant Cell, 14:1605-1619 (2002).
Lu et al., “RNA silencing in plants by the expression of siRNA duplexes,” Nucleic Acids Res., 32(21):e171 (2004).
Lu et al., “OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics,” Nucleic Acids Research, 36:W104-W108 (2008).
Luft, “Making sense out of antisense oligodeoxynucleotide delivery: getting there is half the fun,” J Mol Med, 76:75-76 (1998).
Maas et al., “Mechanism and optimized conditions for PEG mediated DNA transfection into plant protoplasts,” Plant Cell Reports, 8:148-149 (1989).
Maher III et al., “Inhibition of DNA binding proteins by oligonucleotide-directed triple helix formation,” Science, 245(4919):725-730 (1989).
Makkouk et al., “Virus Diseases of Peas, Beans, and Faba Bean in the Mediterranean region,” Adv Virus Res, 84:367-402 (2012).
Mandal et al., “Adenine riboswitches and gene activation by disruption of a transcription terminator,” Nature Struct. Mol. Biol., 11(1):29-35 (2004).
Mandal et al., “Gene Regulation by Riboswitches,” Nature Reviews \| Molecular Cell Biology, 5:451-463 (2004).
Masoud et al., “Constitutive expression of an inducible β-1,3-glucanase in alfalfa reduces disease severity caused by the oomycete pathogen Phytophthora megasperma f. sp medicaginis, but does not reduce disease severity of chitincontaining fungi,” Transgenic Research, 5:313-323 (1996).
Matveeva et al., “Prediction of antisense oligonucleotide efficacy by in vitro methods,” Nature Biotechnology, 16:1374-1375 (1998).
Meinke, et al., “Identifying essential genes in Arabidopsis thaliana,” Trends Plant Sci., 13(9):483-491 (2008).
Meins et al., “RNA Silencing Systems and Their Relevance to Plant Development,” Annu. Rev. Cell Dev. Biol., 21:297-318 (2005).
Melnyk et al., “Intercellular and systemic movement of RNA silencing signals,” The EMBO Journal, 30:3553-3563 (2011).
Misawa et al., “Functional expression of the Erwinia uredovora carotenoid biosynthesis gene crtl in transgenic plants showing an increase of β-carotene biosynthesis activity and resistance to the bleaching herbicide norflurazon,” The Plant Journal, 4(5):833-840 (1993).
Molnar et al., “Plant Virus-Derived Small Interfering RNAs Originate redominantly from Highly Structured Single-Stranded Viral RNAs,” Journal of Virology, 79(12):7812-7818 (2005).
Molnar et al., “Small Silencing RNAs in Plants are Mobile and Direct Epigenetic Modification in Recipient Cells,” Science, 328:872-875 (2010).
Moriyama et al., “Double-stranded RNA in rice: a novel RNA replicon in plants,” Molecular & General Genetics, 248(3):364-369 (1995).
Moriyama et al., “Stringently and developmentally regulated levels of a cytoplasmic double-stranded RNA and its high-efficiency transmission via egg and pollen in rice,” Plant Molecular Biology, 31:713-719 (1996).
Morrissey et al., “Potent and persistent in vivo anti-HBV activity of chemically modified siRNAs,” Nat Biotechnol. 23(8):1002-1007 (2005).
Moser et al., “Sequence-Specific Cleavage of Double Helical DNA by Triple Helix Formation,” Science, 238:645-646 (1987).
Nowak et al., “A new and efficient method for inhibition of RNA viruses by DNA interference,” The FEBS Journal, 276:4372-4380 (2009).
Office Action dated Feb. 17, 2014, in Mexican Patent Application No. MX/a/2012/010479.
Office Action dated Nov. 19, 2014, in Eurasian Patent Application No. 201201264/28.
Office Action dated Jan. 6, 2015, in Japanese Patent Application No. 2012-557165.
Ongvarrasopone et al., “A Simple and Cost Effective Method to Generate dsRNA for RNAi Studies in Invertebrates,” Science Asia, 33:35-39 (2007).
Paddison et al., “Stable suppression of gene expression by RNAi in mammalian cells,” Proc. Natl Acad. Sci. USA, 99(3):1443-1448 (2002).
Palauqui et al., “Activation of systemic acquired silencing by localised introduction of DNA,” Current Biology, 9:59-66 (1999).
Paungfoo-Lonhienne et al., “DNA uptake by Arabidopsis induces changes in the expression of CLE peptides which control root morphology,” Plant Signaling & Behavior, 5(9):1112-1114 (2010).
Paungfoo-Lonhienne et al., “DNA is Taken up by Root Hairs and Pollen, and Stimulates Root and Pollen Tube Growth,” Plant Physiology, 153:799-805 (2010).
Pei et al., “On the art of identifying effective and specific siRNAs,” Nature Methods, 3(9):670-676 (2006).
Peretz et al., “A Universal Expression/Silencing Vector in Plants,” Plant Physiology, 145:1251-1263 (2007).
Pormprom et al., “Glutamine synthetase mutation conferring target-site-based resistance to glufosinate in soybean cell selections,” Pest Manag Sci, 2009; 65(2):216-222 (2009).
Qiwei,“Progress in DNA interference,” Progress in Veterinary Medicine, 30(1):71-75 (2009).
Rajur et al., “Covalent Protein—Oligonucleotide Conjugates for Efficient Delivery of Antisense Molecules,” Bioconjug Chem., 8:935-940 (1997).
Reddy et al “Organosilicone Adjuvants Increased the Efficacy of Glyphosate for Control of Weeds in Citrus (Citrus spp.)” HortScience (1992) 27(9):1003-1005.
Reddy et al., “Aminomethylphosphonic Acid Accumulation in Plant Species Treated with Glyphosate,” J Agric. Food Chem., 56(6):2125-2130 (2008).
Rey et al., “Diversity of Dicotyledenous-Infecting Geminiviruses and Their Associated DNA Molecules in Southern Africa, Including the South-West Indian Ocean Islands,” Viruses, 4:1753-1791 (2012).
Reynolds et al., “Rational siRNA design for RNA interference,” Nat Biotechnol, 22(3):326-330 (2004).
Reynolds et al., “Rational siRNA design for RNA interference,” Nature Biotechnology, 22:326-330 (2004).
Ryabov et al., “Cell-to-Cell, but Not Long-Distance, Spread of RNA Silencing That is Induced in Individual Epidermal Cells,” Journal of Virology, 78(6):3149-3154 (2004).
Santoro et al., “A general purpose RNA-cleaving DNA enzyme,” Proc. Natl. Acad. Sci. USA, 94:4262-4266 (1997).
Sathasivan et al., “Nucleotide sequence of a mutant acetolactate synthase gene from an imidazolinone-resistant Arabidopsis thaliana var. Columbia,” Nucleic Acids Research, 18(8):2188-2193 (1990).
Schwab et al., “RNA silencing amplification in plants: Size matters,” PNAS, 107(34):14945-14946 (2010).
Schwember et al., “Drying Rates following Priming Affect Temperature Sensitivity of Germination and Longevity of Lettuce Seeds,” HortScience, 40(3):778-781 (2005).
Second Chinese Office Action issued in Chinese Patent Application No. 201180012795.2, dated Jun. 10, 2014.
Seidman et al., “The potential for gene repair via triple helix formation,” J Clin Invest., 112(4):487-494 (2003).
Selvarani et al., “Evaluation of seed priming methods to improve seed vigour of onion (Allium cepa cv. Aggregatum) and carrot (Daucus carota),” Journal of Agricultural Technology, 7(3):857-867 (2011).
Sharma et al., “A simple and efficient Agrobacterium-mediate procedure for transformation of tomato,” J. Biosci., 34(3):423 433 (2009).
Sijen et al., “On the Role of RNA Amplification in dsRNA-Triggered Gene Silencing,” Cell, 107:465-476 (2001).
Silwet L-77 Spray Adjuvant for agricultural applications, product description from Momentive Performance Materials, Inc. (2003).
Singh et al., “Absorption and translocation of glyphosate with conventional and organosilicone adjuvants,” Weed Biology and Management, 8:104-111 (2008).
Steeves et al., “Transgenic soybeans expressing siRNAs specific to a major sperm protein gene suppress Heterodera glycines reproduction,” Funct. Plant Biol., 33:991-999 (2006).
Stock et al., “Possible Mechanisms for Surfactant-Induced Foliar Uptake of Agrochemicals,” Pestic. Sci., 38:165-177 (1993).
Strat et al., “Specific and nontoxic silencing in mammalian cells with expressed long dsRNAs,” Nucleic Acids Research, 34(13):3803-3810 (2006).
Sudarsan et al., “Metabolite-binding RNA domains are present in the genes of eukaryotes,” RNA, 9:644-647 (2003).
Sun et al., “Antisense oligodeoxynucleotide inhibition as a potent strategy in plant biology: identification of SUSIBA2 as a transcriptional activator in plant sugar signalling,” The Plant Journal, 44:128-138 (2005).
Sun et al., “A Highly efficient Transformation Protocol for Micro-Tom, a Model Cultivar for Tomato Functional Genomics,” Plant Cell Physiol., 47(3):426-431 (2006).
Sun et al., “Sweet delivery—sugar translocators as ports of entry for antisense oligodeoxynucleotides in plant cells,” The Plant Journal, 52:1192-1198 (2007).
Takasaki et al., “An Effective Method for Selecting siRNA Target Sequences in Mammalian Cells,” Cell Cycle, 3:790-795 (2004).
Templeton et al., “Improved DNA: liposome complexes for increased systemic delivery and gene expression,” Nature Biotechnology, 15:647-652 (1997).
Tenllado et al., “Crude extracts of bacterially expressed dsRNA can be used to protect plants against virus infection,” BMC Biotechnology, 3(3):1-11 (2003).
Tenllado et al., “RNA interference as a new biotechnological tool for the control of virus diseases in plants,” Virus Research, 102:85-96 (2004).
Tepfer, “Risk assessment of virus resistant transgenic plants,” Annual Review of Phytopathology, 40:467-491 (2002).
The Seed Biology Place, Website Gerhard Leubner Lab Royal Holloway, University of London, <http://www.seedbiology.de/seedtechnology.asp.
Third Party Submission filed on Nov. 29, 2012 in U.S. Appl. No. 13/042,856.
Thompson, et al., “Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice,” Nucl. Acids Res., 22(22):4673-4680 (1994).
Timmons et al., “Specific interference by ingested dsRNA,” Nature, 395:854 (1998).
Tomari et al., “Perspective: machines for RNAi,” Genes & Dev., 19:517-529 (2005).
Töpfer et al., “Uptake and Transient Expression of Chimeric Genes in Seed-Derived Embryos,” Plant Cell, 1:133-139 (1989).
Toriyama et al., “Transgenic Rice Plants After Direct Gene Transfer Into Protoplasts,” Bio/Technology, 6:1072-1074 (1988).
Tran et al., “Control of specific gene expression in mammalian cells by co-expression of long complementary RNAs,” FEBS Lett.;573(1-3):127-134 (2004).
Tuschl, “RNA Interference and Small Interfering RNAs,” ChemBiochem. 2(4):239-245 (2001).
Tuschl, “Expanding small RNA interference,” Nature Biotechnol., 20: 446-448 (2002).
Ui-Tei et al., “Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference,” Nucleic Acids Res., 32(3): 936-948 (2004).
Unnamalai et al., “Cationic oligopeptide-mediated delivery of dsRNA for post-transcriptional gene silencing in plant cells,” FEBS Letters, 566:307-310 (2004).
Urayama et al., “Knock-down of OsDCL2 in Rice Negatively Affects Maintenance of the Endogenous dsRNA Virus, Oryza sativa Endornavirus,” Plant and Cell Physiology, 51(1):58-67 (2010).
Van de Wetering et al., “Specific inhibition of gene expression using a stably integrated, inducible small-interfering-RNA vector,” EMBO Rep., 4(6):609-615 (2003).
Vasil et al., “Herbicide Resistant Fertile Transgenic Wheat Plants Obtained by Microprojectile Bombardment of Regenerable Embryogenic Callus,” Bio/Technology,10:667-674 (1992).
Vaucheret, “Post-transcriptional small RNA pathways in plants: mechanisms and regulations,” Genes Dev., 20:759-771 (2006).
Vencill et al., “Resistance of Weeds to Herbicides,” Herbicides and Environment, 29:585-594 (2011).
Verma et al., “Modified oligonucleotides: synthesis and strategy for users,” Annu. Rev. Biochem., 67:99-134 (1998).
Vert et al., “An accurate and interpretable model for siRNA efficacy prediction,” BMC Bioinformatics, 7:520 (2006).
Vionnet et al., “Systemic Spread of Sequence-Specific Transgene RNA Degradation in Plants is Initiated by Localized Introduction of Ectopic Promoterless DNA,” Cell, 95:177-187 (1998).
Wakelin et al., “A target-site mutation is present in a glyphosate-resistant Lolium rigidum population,” Weed Res. (Oxford), 46(5):432-440 (2006).
Walton et al., “Prediction of antisense oligonucleotide binding affinity to a structured RNA target,” Biotechnol Bioeng 65(1):1-9 (1999).
Wan et al., “Generation of Large Numbers of Independently Transformed Fertile Barley Plants,” Plant Physiol., 104:37-48 (1994).
Wardell,“Floral Activity in Solutions of Deoxyribonucleic Acid Extracted from Tobacco Stems,” Plant Physiol, 57:855-861 (1976).
Wardell, “Floral Induction of Vegetative Plants Supplied a Purified Fraction of Deoxyribonucleic Acid from Stems of Flowering Plants,” Plant Physiol, 60:885-891 (1977).
Waterhouse et al., “Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA,” Proc Natl Acad Sci USA, 95 13959-13964 (1998).
Welch et al., “Expression of ribozymes in gene transfer systems to modulate target RNA levels,” Curr Opin Biotechnol. 9(5):486-496 (1998).
Wilson, et al., “Transcription termination at intrinsic terminators: The role of the RNA hairpin,” Proc. Natl. Acad. Sci. USA, 92:8793-8797 (1995).
Winkler et al., “Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression,” Nature, 419:952-956 (2002).
Written Opinion dated May 8, 2014, in International Application No. PCT/IL2013/050447.
Written Opinion dated Sep. 1, 2014, in Singapore Patent Application No. 201206152-9.
Yin et al., “Production of double-stranded RNA for interference with TMV infection utilizing a bacterial prokaryotic expression system,” Appl. Microbiol. Biotechnol., 84(2):323-333 (2009).
YouTube video by General Electric Company “Silwet Surfactants,” screen shot taken on Jan. 11, 2012 of video of www.youtube.com/watch?v=WBw7nXMqHk8 (uploaded Jul. 13, 2009).
Zagnitko, “Lolium regidum clone LS1 acetyl-CoA carboxylase mRNA, partial cds; nuclear gene for plastid product,” GenBank: AF359516.1, 2 pages (2001).
Zagnitko, et al., “An isoleucine/leucine residue in the carboxyltransferase domain of acetyl-CoA carboxylase is critical for interaction with aryloxyphenoxypropionate and cyclohexanedione inhibitors,” PNAS, 98(12):6617-6622 (2001).
Zhang et al., “Agrobacterium-mediated transformation of Arabidopsis thaliana using the floral dip method,” Nature Protocols, 1(2):1-6 (2006).
Zhang et al., “Cationic lipids and polymers mediated vectors for delivery of siRNA,” Journal of Controlled Release, 123:1-10 (2007).
Zhang et al., “A novel rice gene, NRR responds to macronutrient deficiency and regulates root growth,” Mol Plant, 5(1):63-72 (2012).
Zhao et al., “Phyllotreta striolata (Coleoptera: Chrysomelidae):Arginine kinase cloning and RNAi-based pest control,” European Journal of Entomology, 105(5):815-822 (2008).
Zhu et al., “Ingested RNA interference for managing the populations of the Colorado potato beetle, Leptinotarsa decemlineata,” Pest Manag Sci, 67:175-182 (2010).
Andersen et al., “Delivery of siRNA from lyophilized polymeric surfaces,” Bomaterials, 29:506-512 (2008).
Anonymous, “A handbook for high-level expression and purification of 6xHis-tagged proteins,” The QiaEpressionist, (2003).
Anonymous, “Devgen, The mini-Monsanto,” KBC Securities (2006).
Artymovich, “Using RNA interference to increase crop yield and decrease pest damage,” MMG 445 Basic Biotech., 5(1):712 (2009).
Brodersen et al., “The diversity of RNA silencing pathways in plants,” Trends in Genetics, 22(5):268-280 (2006).
Chabannes et al., “In situ analysis of lignins in transgenic tobacco reveals a differential impact of individual transformations on the spatial patterns of lignin deposition at the cellular and subcellular levels,” The Plant Journal, 28(3):271-282 (2001).
Communication pursuant to Article 94(3) EPC dated Jun. 26, 2015, in European Patent Application No. 11 753 916.3.
Communication pursuant to Article 94(3) EPC dated Oct. 23, 2015, in European Patent Application No. 12 831 945.6.
Dalakouras et al., “Induction of Silencing in Plants by High-Pressure Spraying of In vitro-Synthesized Small RNAs,” Frontiers in Plant Science, 7(1327):1-5 (2016).
Extended European Search Report dated Oct. 8, 2013, in European Patent Application No. 11753916.3.
Extended European Search Report dated Sep. 29, 2016, in European Patent Application No. 14778840.0.
First Examination Report dated Apr. 23, 2013, in New Zealand Patent Application No. 601784.
First Examination Report dated Jul. 28, 2014, in New Zealand Patent Application No. 627060.
Fukunaga el al., “dsRNA with 5′ overhangs v contributes to endogenous and antiviral RNA silencing pathways in plants,” The EMBO Journal, 28(5):545-555 (2009).
Further Examination Report dated May 16, 2014, in New Zealand Patent Application No. 601784.
GenBank Accession No. AY545657.1 (2004).
GenBank Accession No. DY640489, “PU2_plate27_F03_PU2 Prunus persica cDNA similar to expressed mRNA inferred from Prunus persica hypothetical domain/motif cont aining IPR011005:Dihydropteroate synthase-like, MRNA sequence” (2006).
GenBank Accession No. EU024568, “Amaranthus hypochondriacus acetolactate synthase (ALS) gene” (2007).
GenBank Accession No. FJ972198, “Solanum lycopersicum cultivar Ailsa Craig dihydropterin pyrophosphokinase-dihydropteroate synthase (HPPK-DHPS) gene, complete cds” (2010).
GenBank Accession No. GI:186478573 (2014).
GenBank Accession No. GU120406, “Chrysomela tremulae ribosomal protein L7 (RpL7) mRNA, complete cds” (2009).
GenBank Accession No. HD 5444, “Sequence 192160 from Patent EP2213738” (2010).
GenBank Accession No. Q4GXM3_BIPLU, “Ribosomal protein L7e” (2006).
GenEmbl Accession No. FJ861243 (2010).
Gong et al., “Silencing of Rieske iron-sulfur protein using chemically synthesised siRNA as a potential biopesticide against Plutella xylostella,” Pest Manag Sci, 67:514-520 (2011).
Hewezi et al., “Local infiltration of high- and low-molecular-weight RNA from silenced sunflower (Helianthus annuus L.) plants triggers post-transcriptional gene silencing in non-silenced plants,” Plant Biotechnology Journal, 3:81-89 (2005).
Ichihara et al., “Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities,” Nucleic Acids Res., 35(18):e 123 (2007).
International Preliminary Report on Patentability dated Sep. 11, 2014, in International Application No. PCT/IL2013/050447.
International Search Report and the Written Opinion dated Feb. 25, 2013, in International Application No. PCT/US2012/054883.
International Search Report and the Written Opinion dated Feb. 27, 2013, in International Application No. PCT/US2012/054814.
International Search Report and the Written Opinion dated Feb. 27, 2013, in International Application No. PCT/US2012/054842.
International Search Report and the Written Opinion dated Feb. 27, 2013, in International Application No. PCT/US2012/054862.
International Search Report and the Written Opinion dated Feb. 27, 2013, in International Application No. PCT/US2012/054894.
International Search Report and the Written Opinion dated Feb. 27, 2013, in International Application No. PCT/US2012/054974.
International Search Report and the Written Opinion dated Feb. 27, 2013, in International Application No. PCT/US2012/054980.
International Search Report and the Written Opinion dated Jul. 15, 2014, in International Application No. PCT/US2014/025305.
International Search Report and the Written Opinion dated Jul. 22, 2014, in International Application No. PCT/IL2013/051083.
International Search Report and the Written Opinion dated Jul. 22, 2014, in International Application No. PCT/IL2013/051085.
International Search Report and the Written Opinion dated Jul. 24, 2014, in International Application No. PCT/US2014/026036.
International Search Report and the Written Opinion dated May 10, 2011, in International Application No. PCT/US2011/027528.
International Search Report and the Written Opinion dated Oct. 1, 2013, in International Application No. PCT/IL2013/050447.
International Search Report and Written Opinion dated Aug. 25, 2014, in International Application No. PCT/US2014/023503.
International Search Report and Written Opinion dated Aug. 27, 2014, in International Application No. PCT/US2014/023409.
International Search Report dated Mar. 12, 2013, in International Application No. PCT/US2012/054789.
Lee et al., “Aptamer Database,” Nucleic Acids Research, 32:D95-D100 (2004).
Leopold et al., “Chapter 4: Moisture as a Regulator of Physiological Reaction in Seeds,” Seed Moisture, 14:51-69 (1989).
Liu et al., “DNAzyme-mediated recovery of small recombinant RNAs from a 5S rRNA-derived chimera expressed in Escherichia coli,” BMC Biotechnology, 10:85 (2010).
Liu, “Influence of Sugars on the Foliar Uptake of Bentazone and Glyphosate,” New Zealand Plant Protection, 55:159-162 (2002).
Luque et al., “Water Permeability of Isolated Cuticular Membranes: A Structural Analysis,” Archives of Biochemistry and Biophysics, 317(2):417-422 (1995).
Manoharan, “Oligonucleotide Conjugates as Potential Antisense Drugs with Improved Uptake, Biodistribution, Targeted Delivery, and Mechanism of Action,” Antisense & Nucleic Acid Drug Development, 12:103-128 (2002).
Misawa et al., “Expression of an Erwinia phytoene desaturase gene not only confers multiple resistance to herbicides interfering with carotenoid biosynthesis but also alters xanthophyll metabolism in transgenic plants,” The Plant Journal, 6(4):481-489 (1994).
Miura et al., “The Balance between Protein Synthesis and Degradation in Chloroplasts Determines Leaf Variegation in Arabidopsis yellow variegated Mutants,” The Plant Cell, 19:1313-1328 (2007).
Non-Final Office Action dated Nov. 9, 2016, in U.S. Appl. No. 14/901,003.
Office Action dated Sep. 5, 2016, in Ukrainian Patent Application No. a 2014 03846.
Office Action dated Nov. 15, 2016, in Mexican Patent Application. No. MX/a/2014/003068.
Office Action dated Nov. 3, 2014, in Chinese Patent Application No. 201180012795.2.
Parera et al., “Dehydration Rate after Solid Matrix Priming Alters Seed Performance of Shrunken-2 Corn,” J. Amer. Soc. Hort. Sci., 119(3):629-635 (1994).
Pornprom et al., “Glutamine synthetase mutation conferring target-site-based resistance to glufosinate in soybean cell selections,” Pest Manag Sci, 2009; 65(2):216-222 (2009).
Preston et al., “Multiple effects of a naturally occurring proline to threonine substitution within acetolactate synthase in two herbicide-resistant populations of Lactuca serriola,” Pesticide Biochem. Physiol., 84(3):227-235 (2006).
Qiwei, “Advance in DNA interference,” Progress in Veterinary Medicine, 30(1):71-75 (2009).
Reddy et al “Organosilicone Adjuvants Increased the Efficacy of Glyphosate for Control of Weeds in Citrus (Citrus spp.)” HortScience 27(9):1003-1005 (1992).
Schönherr, “Water Permeability of Isolated Cuticular Membranes: The Effect of pH and Cations on Diffusion, Hydrodynamic Permeability and Size of Polar Pores in the Cutin Matrix,” Planta, 128:113-126 (1976).
Shaoquan, “The action target of herbicide and the innovation of a new variety,” Chemical Industry Press, 23-24 (2001).
Second Chinese Office Action dated Jun. 10, 2014, in Chinese Patent Application No. 201180012795.2.
Unniraman et al., “Alternate Paradigm for Intrinsic Transcription Termination in Eubacteria,” The Journal of Biological Chemistry, 276(45)(9):41850-41855 (2001).
Voinnet et al., “Systemic Spread of Sequence-Specific Transgene RNA Degradation in Plants is Initiated by Localized Introduction of Ectopic Promoterless DNA,” Cell, 95:177-187 (1998).
Waterhouse et al., “Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA,” Proc. Natl Acad Sci USA, 95 13959-13964 (1998).
Wiesman et al., “Novel cationic vesicle platform derived from vernonia oil for efficient delivery of DNA through plant cuticle membranes,” Journal of Biotechnology, 130:85-94 (2007).
Agricultural Chemical Usage 2006 Vegetables Summary, Agricultural Statistics Board, NASS, USDA, pp. 1-372 (2007).
Al-Kaff et al., “Plants rendered herbicide-susceptible by cauliflower mosaic virus-elicited suppression of a 35S promoter-regulated transgene,” Nature Biotechnology, 18:995-999 (2000).
Balibrea et al., “Extracellular Invertase is an Essential Component of Cytokinin-Mediated Delay of Senescence,” The Plant Cell, 16(5):1276-1287 (2004).
Bart et al., “A novel system for gene silencing using siRNAs in rice leaf and stem-derived protoplasts,” Plant Methods, 2(13):1-9 (2006).
Basu et al., “Weed genomics: new tools to understand weed biology,” TRENDS in Plant Science, 9(8):391-398 (2004).
Busch et al., “RNAi for discovery of novel crop protection products,” Pflanzenschutz-Nachrichten Bayer, 58(1):34-50 (2005).
Chen et al., “Transfection and Expression of Plasmid DNA in Plant Cells by an Arginine-Rich Intracellular Delivery Peptide without Protoplast Preparation,” FEBS Letters 581, pp. 1891-1897 (2007).
Colliver et al., “Differential modification of flavonoid and isoflavonoid biosynthesis with an antisense chalcone synthase construct in transgenic Lotus corniculatus,” Plant Molecular Biology, 35:509-522 (1997).
Concise Descriptions of Relevance filed by a third party on Nov. 29, 2012, in U.S. Appl. No. 13/042,856.
Dawson et al., “cDNA cloning of the complete genome of tobacco mosaic virus and production of infectious transcripts,” Proc. Natl. Acad. Sci. USA, 83:1832-1836 (1986).
Feuillet et al., “Crop genome sequencing: lessons and rationales,” Trends Plant Sci., 16:77-88 (2011).
Final Office Action dated Apr. 7, 2016, in U.S. Appl. No. 13/619,980.
Final Office Action dated Dec. 17, 2015, in U.S. Appl. No. 14/335,135.
Final Office Action dated Feb. 17, 2016, in U.S. Appl. No. 13/612,929.
Final Office Action dated Feb. 4, 2016, in U.S. Appl. No. 13/612,936.
Final Office Action dated Jun. 30, 2016, in U.S. Appl. No. 13/901,326.
Final Office Action dated Mar. 2, 2016, in U.S. Appl. No. 13/612,995.
Final Office Action dated Mar. 21, 2016, in U.S. Appl. No. 13/612,925.
Final Office Action dated May 26, 2016, in U.S. Appl. No. 14/532,596.
Final Office Action dated Sep. 9, 2016, in U.S. Appl. No. 13/612,954.
Final Office Action dated Nov. 19, 2015, in U.S. Appl. No. 13/612,941.
Final Office Action dated Sep. 9, 2016, in U.S. Appl. No. 14/608,951.
Final Office Action dated Sep. 9, 2016, in U.S. Appl. No. 14/603,347.
Final Office Action dated Oct. 20, 2016, in U.S. Appl. No. 14/480,199.
Final Office Action dated Oct. 22, 2015, in U.S. Appl. No. 14/608,951.
Fraley et al., “Liposome-mediated delivery of tobacco mosaic virus RNA into tobacco protoplasts: A sensitive assay for monitoring liposome-protoplast interactions,” Proc Natl Acad Sci U S A., 79(6):1859-1863 (1982).
Gan et al., “Inhibition of Leaf Senescence by Autoregulated Production of Cytokinin,” Science, 270:1986-1988 (1995).
Gao et al., “Nonviral Methods for siRNA Delivery,” Molecular Pharmaceutics, 6(3):651-658 (2008).
GenBank Accession No. CB377464, “CmaE1_37_J02_T3 Cowpea weevil larvae Lambda Zap Express Library Callosobruchus maculatus cDNA, mRNA sequence,” (2007).
GenBank Accession No. EW765249, “ST020010B10C12 Normalized and subtracted western corn rootwonn female head cDNA library Diabrotica virgifera virgifera cDNA clone STO20010B10C12 5-, mRNA sequence,” (2007).
GenBank Accession No. EW771198, “ST020010B10C12 Normalized and subtracted western corn rootworm female head cDNA library Diabrotica virgifera virgifera cDNA clone STO20010B10C12 5-, mRNA sequence,” (2007).
GenBank Accession No. FE348695, “CBIB7954.fwd CBIB_Daphnia_pulex_Chosen_One_Library_2 Daphnia pulex cDNA clone CBIB7954 5′, mRNA sequence” (2011).
GenBank Accession No. U87257.1, “Daucus carota 4-hydroxyphenylpyruvate dioxygenase mRNA, complete cds” (1997).
GenBank Accession No. XM_014456745.1, Predicted: Myotis lucifugus ribonucleoprotein, PTB-binding 2 (RAVER2), transcript variant X3, mRNA,: (2015).
GenBank Accession No. Y08611.1, “P.sativum mRNA for dihydropterin pyrophosphokinase/dihydropteroate synthase.” (2006).
Gossamer Threads, Compendium of Herbicide Adjuvants: Organo-Silicone Surfactant, p. 1-4 (1998).
Hajirezaei et al., “Impact of elevated cytosolic and apoplastic invertase activity on carbon metabolism during potato tuber development,” Journal of Experimental Botany, 51:439-445 (2000).
Holtra et al., “Assessment of the Physiological Condition of Salvinia natans L. Exposed to Copper(II) Ions,” Environ. Protect. Eng., 41:147-158 (2015).
International Preliminary Report on Patentability dated Sep. 11, 2012, in International Application No. PCT/US2011/027528.
International Rice Genome Sequencing Project, The map-based sequence of the rice genome, Nature, 436(11):793-800 (2005).
International Search Report and Written Opinion dated May 26, 2016, in International Application No. PCT/US2016/014344.
Jin et al., “Posttranslational Elevation of Cell Wall Invertase Activity by Silencing its Inhibitor in Tomato Delays Leaf Senescence and Increases Seed Weight and Fruit Hexose Level,” The Plant Cell, 21:2072-2089 (2009).
Kaloumenos et al., “Identification of a Johnsongrass (Sorghum halepense) Biotype Resistant to ACCase-Inhibiting Herbicides in Northern Greece,” Weed Technol, 23:470-476 (2009).
Kambiranda et al., “Relationship Between Acid Invertase Activity and Sugar Content in Grape Species,” Journal of Food Biochemistry, 35:1646-1652 (2011).
Kim et al., “Optimization of Conditions for Transient Agrobacterium-Mediated Gene Expression Assays in Arabidopsis,” Plant Cell Reports, 28:1159-1167 (2009).
Kirkwood, “Herbicides and Plants,” Botanical Journal of Scotland,46(3):447-462 (1993).
Liu et al., “Identification and Application of a Rice Senescence-Associated Promoter,” Plant Physiology, 153:1239-1249 (2010).
Mora et al., “How Many Species Are There on Earth and in the Ocean?,” PLOS Biol., 9(8):e100127, p. 1-8 (2011).
Mount et al., “Gene and Metabolite Regulatory Network Analysis of Early Developing Fruit Tissues Highlights New Candidate Genes for the Control of Tomato Fruit Composition and Development,” Plant Physiology, 149:1505-1528 (2009).
Non-Final Office Action dated Aug. 19, 2016, in U.S. Appl. No. 13/612,925.
Non-Final Office Action dated Aug. 19, 2016, in U.S. Appl. No. 13/612,929.
Non-Final Office Action dated Apr. 29, 2016, in U.S. Appl. No. 13/583,302.
Non-Final Office Action dated Aug. 10, 2016, in U.S. Appl. No. 13/612,995.
Non-Final Office Action dated Aug. 3, 2016, in U.S. Appl. No. 14/015,715.
Non-Final Office Action dated Aug. 8, 2016, in U.S. Appl. No. 13/612,936.
Non-Final Office Action dated Dec. 17, 2015, in U.S. Appl. No. 14/532,596.
Non-Final Office Action dated Feb. 10, 2016, in U.S. Appl. No. 13/901,326.
Non-Final Office Action dated Feb. 23, 2016, in U.S. Appl. No. 14/603,347.
Non-Final Office Action dated Feb. 23, 2016, in U.S. Appl. No. 14/608,951.
Non-Final Office Action dated Sep. 6, 2016, in U.S. Appl. No. 14/335,135.
Non-Final Office Action dated Mar. 1, 2016, in U.S. Appl. No. 13/612,954.
Non-Final Office Action dated Oct. 3, 2016, in U.S. Appl. No. 14/403,491.
Non-Final Office Action dated Sep. 1, 2015, in U.S. Appl. No. 13/612,954.
Non-Final Office Action dated Sep. 11, 2015, in U.S. Appl. No. 13/612,925.
Non-Final Office Action dated Sep. 4, 2015, in U.S. Appl. No. 13/612,995.
Nookaraju et al., “Molecular approaches for enhancing sweetness in fruits and vegetables,” Scientia Horticulture, 127:1-15 (2010).
Notice of Allowance dated Apr. 11, 2016, in U.S. Appl. No. 13/612,985.
Notice of Allowance dated Apr. 19, 2016, in U.S. Appl. No. 13/612,941.
Notice of Allowance dated Apr. 20, 2016, in U.S. Appl. No. 13/612,948.
Notice of Allowance dated Feb. 23, 2015, in U.S. Appl. No. 13/042,856.
Notice of Allowance dated Jun. 2, 2015, in U.S. Appl. No. 13/042,856.
Office Action dated Aug. 28, 2013, in Chinese Patent Application No. 201180012795.2.
Office Action dated Jul. 18, 2016, in Indonesian Patent Application No. W00201203610.
Office Action dated Aug. 25, 2016, in Eurasian Patent Application No. 201201264.
Office Action dated Feb. 24, 2014, in Eurasian Patent Application No. 201201264.
Office Action dated Jun. 20, 2016, in Chinese Patent Application No. 201280054819.5.
Office Action dated Jun. 24, 2016, in Chinese Patent Application No. 201280053984.9.
Patent Examination Report No. 1 dated Jun. 17, 2016, in Australian Patent Application No. 2012308659.
Patent Examination Report No. 1 dated Jun. 17, 2016, in Australian Patent Application No. 2012308660.
Patent Examination Report No. 1 dated Nov. 11, 2013, in Australian Patent Application No. 2011224570.
Promoter Prediction for SEQ ID No. 4 from U.S. Appl. No. 13/612,995/MK/, Promoter 2.0 Prediction Results, pp. 1-3 (2016).
Promoter Prediction for SEQ ID No. 7 from U.S. Appl. No. 13/612,936/MK/, Promoter 2.0 Prediction Results, pp. 1-2 (2016).
Promoter Prediction for SEQ ID No. 8 from U.S. Appl. No. 13/612,925/MK/, Promoter 2.0 Prediction Results, pp. 1-6 (2016).
Restriction Requirement dated Jul. 15, 2016, in U.S. Appl. No. 14/143,748.
Restriction Requirement dated Jul. 18, 2016, in U.S. Appl. No. 14/143,836.
Restriction Requirement dated Oct. 13, 2016, in U.S. Appl. No. 14/206,707.
Restriction Requirement dated Oct. 28, 2015, in U.S. Appl. No. 14/603,347.
Restriction Requirement dated Sep. 2, 2015, in U.S. Appl. No. 14/532,596.
Roberts, “Fast-track applications: The potential for direct delivery of proteins and nucleic acids to plant cells for the discovery of gene function,” Plant Methods, 1(12):1-3 (2005).
Robson et al., “Leaf senescence is delayed in maize expressing the Agrobacterium IPT gene under the control of a novel maize senescence-enhanced promoter,” Plant Biotechnology Journal, 2:101-112 (2004).
Roitsch et al., “Extracellular invertase: key metabolic enzyme and PR protein,” Journal of Experimental Botany, 54(382):513-524 (2003).
Roitsch et al., “Function and regulation of plant invertases: sweet sensations,” Trades in Plant Science, 9(12):606-613 (2004).
Ruan et al., “Suppression of Sucrose Synthase Gene Expression Represses Cotton Fiber Cell Initiation, Elongation, and Seed Development,” The Plant Cell, 15:952-964 (2003).
Showalter, “Structure and Function of Plant Cell Wall Proteins,” The Plant Cell, 5:9-23 (1993).
Song et al., “Herbicide,” New Heterocyclic Pesticide, Chemical Industry Press, 354-356 (2011).
Stevens, “Organosilicone Surfactants as Adjuvants for Agrochemicals,” Journal of Pesticide Science, 38:103-122 (1993).
Tang et al., “Efficient delivery of small interfering RNA to plant cells by a nanosecond pulsed laser-induced stress wave for posttranscriptional gene silencing,” Plant Science, 171:375-381 (2006).
Tenllado et al., “Double-Stranded RNA-Mediated Interference with Plant Virus Infection,” Journal of Virology, 75(24):12288-12297 (2001).
Thomas et al., “Size constraints for targeting post-transcriptional gene silencing and for RNA-directed methylation in Nicotiana benthamiana using a potato virus X vector,” The Plant Journal, 25(4):417-425 (2001).
Tomlinson et al., “Evidence that the hexose-to-sucrose ratio does not control the switch to storage product accumulation in oilseeds: analysis of tobacco seed development and effects of overexpressing apoplastic invertase,” Journal of Experimental Botany, 55(406):2291-2303 (2004).
Widholm et al., “Glyphosate selection of gene amplification in suspension cultures of 3 plant species,” Phyisologia plantarum, 112:540-545 (2001).
Wild Carrot, Noxious Weed Control Board (NWCB) of Washington State (2010) <www.nwcb.wa.gov/detail.asp?weed=46>.
Zhang et al., “Chapter 10: New Characteristics of Pesticide Research & Development,” New Progress of the world agriculture chemicals, p. 209 (2010).
Agrios, Plant Pathology (Second Edition), 2:466-470 (1978).
Andersson et al., “A novel selection system for potato transformation using a mutated AHAS gene,” Plant Cell Reports, 22(4):261-267 (2003).
Anonymous, “Agronomy Facts 37: Adjuvants for enhancing herbicide performance,” n.p., 1-8, (Jan. 26, 2000), Web, (Jan. 21, 2014).
Anonymous, “Do Monsanto have the next big thing?,” Austalian Herbicide Resistance Initiative (AHRI), (Apr. 23, 2013) Web. (Jan. 19, 2015).
Bai et al., “Naturally Occurring Broad-Spectrum Powdery Mildew Resistance in a Central American Tomato Accession is Caused by Loss of Mlo Function,” MPMI, 21(1):30-39 (2008).
Bourgeois et al., “Field and producer survey of ACCase resistant wild oat in Manitoba,” Canadian Journal of Plant Science, 709-715 (1997).
Brugière et al., “Glutamine Synthetase in the Phloem Plays a Major Role in Controlling Proline Production,” The Plant Cell, 11:1995-2011 (1999).
Busi et al., “Gene flow increases the initial frequency of herbicide resistance alleles in unselectedpopulations,” Agriculture, Ecosystems and Environments, Elsevier, Amsterdam, NL, 142(3):403-409 (2011).
Campbell et al., “Gene-knockdown in the honey bee mite Varroa destructor by a non-invasive approach: studies on a glutathione S-transferase,” Parasites & Vectors, 3(1):73, pp. 1-10 (2010).
Chang et al., “Cellular Internalization of Fluorescent Proteins via Arginine-rich Intracellular Delivery Peptide in Plant Cells,” Plant Cell Physiol., 46(3):482-488 (2005).
Chupp et al., “Chapter 8: White Rust,” Vegetable Diseases and Their Control, The Ronald Press Company, New York, pp. 267-269 (1960).
Communication pursuant to Article 94(3) EPC dated Jun. 26, 2015, as received in European Patent Application No. 11 753 916.3.
Communication pursuant to Article 94(3) EPC dated Oct. 23, 2015, as received in European Patent Application No. 12 831 945.6.
Coticchia et al., “Calmodulin modulates Akt activity in human breast cancer cell lines,” Breast Cancer Res. Treat, 115:545-560 (2009).
Desai et al., “Reduction in deformed wing virus infection in larval and adult honey bees (Apis mellifera L.) by double-stranded RNA ingestion,” Insect Molecular Biology, 21(4):446-455 (2012).
Dietemann et al., “Varroa destructor: research avenues towards sustainable control,” Journal of Apicultural Research, 51(1):125-132 (2012).
Emery et al., “Radial Patterning of Arabidopsis Shoots by Class III HD-ZIP and KANADI Genes,” Current Biology, 13:1768-1774 (2003).
Extended European Search Report dated Feb. 2, 2015, in European Patent Application No. 12 830 932.5.
Extended European Search Report dated Feb. 27, 2015, in European Patent Application No. 12 832 160.1.
Extended European Search Report dated Feb. 3, 2015, in European Patent Application No. 12 831 945.6.
Extended European Search Report dated Jan. 21, 2015, in European Patent Application No. 12 832 415.9.
Extended European Search Report dated Jan. 29, 2015, in European Patent Application No. 12 831 567.8.
Extended European Search Report dated Jun. 29, 2015, in European Patent Application No. 12 831 494.5.
Extended European Search Report dated Mar. 17, 2015, in European Patent Application No. 12 831 684.1.
Extended European Search Report dated Mar. 3, 2015, in European Patent Application No. 12 831 166.9.
Final Office Action dated Nov. 10, 2015, in U.S. Appl. No. 13/612,985.
Final Office Action dated Nov. 7, 2013, in U.S. Appl. No. 13/042,856.
Final Office Action dated Nov. 30, 2015, in U.S. Appl. No. 13/612,948.
First Office Action dated Sep. 9, 2015, in Chinese Patent Application No. 201280055409.2.
First Office Action dated Mar. 12, 2015, in Chinese Patent Application No. 201280053984.9.
First Office Action dated Mar. 2, 2015, in Chinese Patent Application No. 201280054819.5.
First Office Action dated May 27, 2015, in Chinese Patent Application No. 201280054179.8.
First Office Action dated Jul. 7, 2015, in Chinese Patent Application No. 201280054820.8.
First Office Action dated Aug. 31, 2015, in Chinese Patent Application No. 201280053985.3.
Fukunaga et al., “dsRNA with 5′ overhangs contributes to endogenous and antiviral RNA silencing pathways in plants,” The EMBO Journal, 28(5):545-555 (2009).
Gao et al., “Down-regulation of acetolactate synthase compromises 01-1-mediated resistance to powdery mildew in tomato,” BMC Plant Biology, 14 (2014).
Garbian et al., “Bidirectional Transfer of RNAi between Honey Bee and Varroa destructor: Varroa Gene Silencing Reduces Varroa Population,” 8(12):1-9:e1003035 (2012).
Gressel et al., “A strategy to provide long-term control of weedy rice while mitigating herbicide resistance transgene flow, and its potential use for other crops with related weeds,” Pest Manag Sci, 65(7):723-731 (2009).
Harrison et al., “Does Lowering Glutamine Synthetase Activity in Nodules Modigy Nitrogen Metabolism and Growth of Lotus japonicus?,” Plant Physiology, 133:253-262 (2003).
International Preliminary Report on Patentability (Chapter II) dated Jul. 24, 2015, in International Application No. PCT/US2014/047204.
International Search Report and Written Opinion dated Feb. 23, 2015, in International Application No. PCT/US2014/063832.
International Search Report and Written Opinion dated Jul. 8, 2015, in International Application No. PCT/US2015/011408.
International Search Report and Written Opinion dated Mar. 26, 2015, in International Application No. PCT/U82014/069353.
International Search Report and Written Opinion dated Nov. 24, 2015, in International Application No. PCT/US2015/037522.
International Search Report and Written Opinion dated Nov. 27, 2015, in International Application No. PCT/US2015/037015.
Invitation to Pay Additional Fees dated Sep. 8, 2015, in International Application No. PCT/US2015/037015.
Invitation to Pay Additional Fees dated Sep. 9, 2015, in International Application No. PCT/US2015/037522.
Jofre-Garfias et al., “Agrobacterium-mediated transformation of Amaranthus hypochondriacus: light- and tissue-specific expression of a pea chlorophyll a/b-binding protein promoter,” Plant Cell Reports, 16:847-852 (1997).
Khan et al., “Matriconditioning of Vegetable Seeds to Improve Stand Establishment in Early Field Plantings,” J. Amer. Soc. Hort. Sci., 117(1):41-47 (1992).
Kim et al., “Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy,” Nature Biotechnology, 23(2):222-226 (2005).
Lein et al., “Target-based discovery of novel herbicides,” Current Opinion in Plant Biology, 7:219-225 (2004).
Leopold et al., “Chapter 4: Moisture as a Regulator of Physiological Reaction in Seeds,” Seed Moisture, CSSA Special Publication No. 14, pp. 51-69 (1989).
Lermontova et al., “Reduced activity of plastid protoporphyrinogen oxidase causes attenuated photodynamic damage during high-light compared to low-light exposure,” The Plant Journal, 48(4):499-510 (2006).
MacKenzie et al., “Transgenic Nicotiana debneyii expressing viral coat protein are resistant to potato virus S infection,” Journal of General Virology, 71:2167-2170 (1990).
Maori et al., “IAPV, a bee-affecting virus associated with Colony Collapse Disorder can be silenced by dsRNA ingestion,” Insect Molecular Biology, 18(1):55-60 (2009).
Molina et al., “Inhibition of protoporphyrinogen oxidase expression in Arabidopsis causes a lesion-mimic phenotype that induces systemic acquired resistance,” The Plant Journal, 17(6):667-678 (1999).
Non-Final Office Action dated Apr. 11, 2013, in U.S. Appl. No. 13/042,856.
Non-Final Office Action dated Aug. 12, 2015, in U.S. Appl. No. 13/612,936.
Non-Final Office Action dated Aug. 13, 2015, in U.S. Appl. No. 13/612,929.
Non-Final Office Action dated Jul. 23, 2015, in U.S. Appl. No. 14/335,135.
Non-Final Office Action dated Jul. 30, 2014, in U.S. Appl. No. 13/042,856.
Non-Final Office Action dated Jun. 5, 2015, in U.S. Appl. No. 13/612,948.
Non-Final Office Action dated Jun. 8, 2015, in U.S. Appl. No. 13/612,941.
Non-Final Office Action dated Mar. 30, 2015, in U.S. Appl. No. 13/583,302.
Non-Final Office Action dated May 15, 2015, in U.S. Appl. No. 14/608,951.
Non-Final Office Action dated May 22, 2015, in U.S. Appl. No. 13/612,985.
Nord-Larsen et al., “Cloning, characterization and expression analysis of tonoplast intrinsic proteins and glutamine synthetase in ryegrass (Lolium perenne L.),” Plant Cell Reports, 28(10):1549-1562 (2009).
Notice of Allowance dated Oct. 5, 2015, in U.S. Appl. No. 13/583,302.
Office Action dated Jul. 23, 2015, in Ukrainian Patent Application No. 201211548.
Office Action dated Oct. 5, 2015, in Eurasian Patent Application No. 201201264/28.
Orbović et al., “Foliar-Applied Surfactants and Urea Temporarily Reduce Carbon Assimilation of Grapefruit Leaves,” J. Amer. Soc. Hort. Sci., 126(4):486-490 (2001).
Ouellet et al., “Members of the Acetohydroxyacid Synthase Muligene Family of Brassica Napus Have Divergent Patterns of Expression,” The Plant Journal, Blackwell Scientific Publications, Oxford, GB, 2(3):321-330 (1992).
Partial Supplementary European Search Report dated Mar. 2, 2015, in European Patent Application No. 12 831 494.5.
Pratt et al., “Amaranthus rudis and A. tuberculatus, One Species or Two?,” Journal of the Torrey Botanical Society, 128(3):282-296 (2001).
Restriction Requirement dated Apr. 21, 2015, in U.S. Appl. No. 13/612,954.
Restriction Requirement dated Feb. 12, 2015, in U.S. Appl. No. 13/612,985.
Restriction Requirement dated Mar. 12, 2015, in U.S. Appl. No. 13/612,948.
Restriction Requirement dated Mar. 4, 2015, in U.S. Appl. No. 13/612,941.
Restriction Requirement dated May 4, 2015, in U.S. Appl. No. 13/612,929.
Restriction Requirement dated May 5, 2015, in U.S. Appl. No. 13/612,936.
Restriction Requirement dated May 7, 2015, in U.S. Appl. No. 13/612,925.
Restriction Requirement dated May 7, 2015, in U.S. Appl. No. 13/612,995.
Restriction Requirement dated Oct. 2, 2012, in U.S. Appl. No. 13/042,856.
Restriction Requirement dated Oct. 21, 2014, in U.S. Appl. No. 13/583,302.
Riggin et al., “Characterization of de novo transcriptome for waterhemp (Amaranthus tuberculatus) using GS-FLX 454 pyrosequencing and its application for studies of herbicide target-site genes,” Pest Manag. Sci., 66:1042-1052 (2010).
Rose et al., “Functional polarity is introduced by Dicer processing of short substrate RNAs,” Nucleic Acids Research, 33(13):4140-4156 (2005).
Rothnie et al., Pararetroviruses and Retroviruses: A Comparative Review of Viral Structure and Gene Expression Strategies, Advances in Virus Research, 44:1-67 (1994).
Schweizer et al., “Double-stranded RNA interferes with gene function at the single-cell level in cereals,” The Plant Journal, 24(6):895-903 (2000).
Senthil-Kumar et al., “A systematic study to determine the extent of gene silencing in Nicotiana benthamiana and other Solanaceae species when heterologous gene sequences are used for virus-induced gene silencing,” New Phytologist, 176:782-791 (2007).
Snead et al., “Molecular basis for improved gene silencing by Dicer substrate interfering RNA compared with other siRNA variants,” Nucleic Acids Research, 41(12):6209-6221 (2013).
Stevens et al., “New Formulation Technology—SILWET® Organosilicone Surfactants Have Physical and Physiological Properties Which Enhance the Performance of Sprays,” Proceedings of the 9th Australian Weeds Conference, pp. 327-331 (1990).
Street, “Why is DNA (and not RNA) a stable storage form for genetic information?,” Biochemistry Revisited, pp. 1-4 (2008).
Sutton et al., “Activity of mesotrione on resistant weeds in maize,” Pest Manag. Sci., 58:981-984 (2002).
Tank Mixing Chemicals Applied to Peanut Crops: Are the Chemicals Compatible?, College of Agriculture & Life Sciences, NC State University, AGW-653, pp. 1-11 (2004).
Taylor, “Seed Storage, Germination and Quality,” The Physiology of Vegetable Crops, pp. 1-36 (1997).
Temple et al., “Can glutamine synthetase activity levels be modulated in transgenic plants by the use of recombinant DNA technology?” Transgenic Plants and Plant Biochemistry, 22(4):915-920 (1994).
Temple et al., “Down-regulation of specific members of the glutamine synthetase gene family in Alfalfa by antisense RNA technology,” Plant Molecular Biology, 37:535-547 (1998).
Tranel et al., “Resistance of weeds to ALS-inhibiting herbicides: what have we learned?,” Weed Science, 50:700-712 (2002).
Tsugawa et al., “Efficient transformation of rice protoplasts mediated by a synthetic polycationic amino polymer,” Theor Appl Genet, 97:1019-1026 (1998).
Vermeulen et al., “The contributions of dsRNA structure to Dicer specificity and efficiency,” RNA, 11(5):674-682 (2005).
Wang et al., “Foliar uptake of pesticides—Present status and future challenge,” ScienceDirect, 87:1-8 (2007).
Xu et al., Characterization and Functional Analysis of the Calmodulin-Binding Domain of Racl GTPase, Plos One, 7(8)1-12:e42975 (2012).
Ascencio-Ibanez et al., “DNA abrasion onto plants is an effective method for geminivirus infection and virus-induced gene silencing,” 6Journal of Virological Methods, 142:198-203 (2007).
Bachman et al., “Characterization of the spectrum of insecticidal activity of a double-stranded RNA with targeted activity against Western Corn Rootworm (Diabrotica virgifera virgifera LeConte),” Transgenic Res., pp. 1-16 (2013).
Bedell et al., “Sorghum Genome Sequencing by Methylation Filtration,” PLOS Biology, 3(1):E13/104-115 (2005).
Burgos et al., “Review: Confirmation of Resistance to Herbicides and Evaluation of Resistance Levels,” Weed Science, 61 (1):4-20 (2013).
Eamens et al., “RNA Silencing in Plants: Yesterday, Today, and Tomorrow,” Plant Physiology, 147(2):456-468 (2008).
Fernandez et al., “Uptake of Hydrophilic Solutes Through Plant Leaves: Current State of Knowledge and Perspectives of Foliar Fertilization,” Critical Reviews in Plant Sciences, 28:36-38 (2009).
Final Office Action dated Nov. 10, 2016, in U.S. Appl. No. 13/583,302.
Friedberg, “Automated protein function prediction—the genomic challenge,” Briefings in Bioinformatics, 7(3):225-242 (2006).
Funke et al., “Molecular basis for herbicide resistance in Roundup Ready crops,” PNAS, 103:13010-13015 (2006).
Gaskin et al., “Novel organosilicone adjuvants to reduce agrochemical spray volumes on row crops,” New Zealand Plant Protection, 53:350-354 (2000).
GenBank Accession No. EF143582 (2007).
Hagio, “Chapter 25: Direct Gene Transfer into Plant Mature Seeds via Electroporation After Vacuum Treatment,” Electroporation and Sonoporation in Developmental Biology, p. 285-293 (2009).
Hess, “Surfactants and Additives,” 1999 Proceedings of the California Weed Science Society, 51:156-172 (1999).
Huang et al., “In Vivo Analyses of the Roles of Essential Omp85-Related Proteins in the Chloroplast Outer Envelope Membrane,” Plant Physiol., 157:147-159 (2011).
Jacque et al., “Modulation of HIV-1 replication by RNA interference,” Nature, 418, 435-438 (2002).
Jang et al., “Resistance to herbicides caused by single amino acid mutations in acetyl-CoA carboxylase in resistant populations of grassy weeds,” New Phytologist, 197(4):1110-1116 (2013).
Kikkert et al., “Stable Transformation of Plant Cells by Particle Bombardment/Biolistics,” Methods in Molecular Biology, 286:61-78 (2005).
Li et al., “A Simplified Seed Transformation Method for Obtaining Transgenic Brassica napus Plants,” Agricultural Sciences in China, 8(6):658-663 (2009).
Liu et al, “The Helicase and RNaseIIIa Domains of Arabidopsis Dicer-Like 1 Modulate Catalytic Parameters during MicroRNA Biogenesis,” Plant Physiology, 159:748-758 (2012).
McGinnis, “RNAi for functional genomics in plants,” Brief Funct Genomics, 9(2):111-7 (2010).
Office Action dated Aug. 1, 2017, in European Patent Application No. 12 830 932.5.
Office Action dated Aug. 14, 2017, in Israeli Patent Application No. 235878.
Office Action dated Aug. 22, 2017, in Korean Patent Application No. 10-2012-7023415.
Office Action dated Aug. 3, 2017, in Chinese Patent Application No. 201480014392.5 (with English translation).
Office Action dated Aug. 3, 2017, in European Patent Application No. 12 831 684.1.
Office Action dated Aug. 8, 2017, in Chilean Patent Application No. 201501874.
Office Action dated Dec. 13, 2016, in Ukrainian Patent Application No. a 2014 03843.
Office Action dated Dec. 14, 2016, in Ukrainian Patent Application No. a 2014 03850.
Office Action dated Dec. 15, 2016, in Ukrainian Patent Application No. a 2014 03845.
Office Action dated Dec. 15, 2016, in Ukrainian Patent Application No. a 2014 03852.
Office Action dated Dec. 15, 2016, in Ukrainian Patent Application No. a 2014 03849.
Office Action dated Dec. 27, 2016, in Ukrainian Patent Application No. a 2012 11548.
Office Action dated Jul. 11, 2017, in Mexican Patent Application No. MX/a/2015/013118 (with English translation).
Office Action dated Jul. 3, 2017, in Mexican Patent Application No. MX/a/2015/012632 (with English translation).
Office Action dated Jul. 6, 2017, in Mexican Patent Application No. MX/a/2015/013103 (with English translation).
Office Action dated Mar. 16, 2017, in Chinese Patent Application No. 201280054819.5.
Office Action dated May 3, 2016, in Chilean Patent Application No. 201601057.
Patent Examination Report No. 1 dated Jun. 8, 2017, in Australian Patent Application No. 2012308686.
Powles et al., “Evolution in Action: Plants Resistant to Herbicides,” Annual Review of Plant Biology, 61(1):317-347 (2010).
Protoplasts, Bio/Technology, 6:1072-1074 (1988).
Rakoczy-Trojanowska, “Alternative Methods of Plant Transformation—a short review,” Cellular & Molecular Biology Letters, 7:849-858 (2002).
Regalado, “The Next Great GMO Debate,” MIT Technology Review,pp. 1-19 (2015).
Reither et al., “Specificity of DNA triple helix formation analyzed by a FRET assay,” BMC Biochemistry, 3:27 (2002).
Ryan, “Human endogenous retroviruses in health and disease: a symbiotic perspective,” Journal of the Royal Society of Medicine, 97:560-565 (2004).
Small, “RNAi for revealing and engineering plant gene functions,” Current Opinion in Biotechnology, 18:148-153 (2007).
Statement of Grounds and Particulars dated Sep. 1, 2017, in Australian U.S. Patent No. 2014262189.
Stevens, “Formulation of Sprays to Improve the Efficacy of Foliar Fertilisers,” New Zealand Journal of Forestry Science, 24(1):27-34 (1994).
Stevens, “Organosilicone Surfactants as Adjuvants for Agrochemicals,” New Zealand Journal of Forestry Science, 24:27-34 (1994).
Trucco et al., “Amaranthus hybridus can be pollinated frequently by A. tuberculatus under filed conditions,” Heredity, 94:64-70 (2005).
Turina et al., “Tospoviruses in the Mediterranean Area,” Advances in Virus Research, 84:403-437 (2012).
Unniraman et al., “Conserved Economics of Transcription Termination in Eubacteria,” Nucleic Acids Research, 30(3):675-684 (2002).
Voinnet, “Origin, Biogenesis, and Activity of Plant MicroRNAs,” Cell, 136:669-687 (2009).
Wild Carrot, Noxious Weed Control Board (NWCB) of Washington State (2010).
Written Opinion dated Mar. 6, 2017, in Singaporean Patent Application No. 2012061529.
Zhang et al., “DEG: a database of essential genes,” Nucleic Acids Res., 32:D271-D272 (2004).
Zhang et al., “Transgenic rice plants produced by electroporation-mediated plasmid uptake into protoplasts,” The Plant Cell Rep., 7:379-384 (1988).
Zhong et al., “A forward genetic screen to explore chloroplast protein import in vivo identifies Moco sulfurase, pivotal for ABA and IAA biosynthesis and purine turnover,” The Plant Journal, 63:44-59 (2010).

Related Publications (1)

	Number	Date	Country
	20140057789 A1	Feb 2014	US

Provisional Applications (3)

Number	Date	Country
61311762	Mar 2010	US
61349087	May 2010	US
61381556	Sep 2010	US

Divisions (1)

	Number	Date	Country
Parent	13042856	Mar 2011	US
Child	14015785		US

Polynucleotide molecules for gene regulation in plants

Information

Patent Number

Date Filed

Date Issued

Inventors

Original Assignees

Examiners

Agents

CPC

Field of Search

US

International Classifications

Disclaimer

Term Extension

Abstract