WO2011153418A2 - Compositions and methods for insecticidal control of stinkbugs - Google Patents

Compositions and methods for insecticidal control of stinkbugs Download PDF

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Publication number
WO2011153418A2
WO2011153418A2 PCT/US2011/039042 US2011039042W WO2011153418A2 WO 2011153418 A2 WO2011153418 A2 WO 2011153418A2 US 2011039042 W US2011039042 W US 2011039042W WO 2011153418 A2 WO2011153418 A2 WO 2011153418A2
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Prior art keywords
plant
silencing element
sequence
polynucleotide
pest
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PCT/US2011/039042
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French (fr)
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WO2011153418A3 (en
Inventor
Karen E. Broglie
David C. Cerf
Rafael Herrmann
Albert L. Lu
Brian Mcgonigle
James K. Presnail
Original Assignee
Broglie Karen E
Cerf David C
Rafael Herrmann
Lu Albert L
Brian Mcgonigle
Presnail James K
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Application filed by Broglie Karen E, Cerf David C, Rafael Herrmann, Lu Albert L, Brian Mcgonigle, Presnail James K filed Critical Broglie Karen E
Priority to CA 2799453 priority Critical patent/CA2799453A1/en
Priority to BR112012030913A priority patent/BR112012030913A2/en
Publication of WO2011153418A2 publication Critical patent/WO2011153418A2/en
Publication of WO2011153418A3 publication Critical patent/WO2011153418A3/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
    • C12N15/8271—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance
    • C12N15/8279—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for biotic stress resistance, pathogen resistance, disease resistance
    • C12N15/8286—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for biotic stress resistance, pathogen resistance, disease resistance for insect resistance
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01N—PRESERVATION OF BODIES OF HUMANS OR ANIMALS OR PLANTS OR PARTS THEREOF; BIOCIDES, e.g. AS DISINFECTANTS, AS PESTICIDES OR AS HERBICIDES; PEST REPELLANTS OR ATTRACTANTS; PLANT GROWTH REGULATORS
    • A01N57/00—Biocides, pest repellants or attractants, or plant growth regulators containing organic phosphorus compounds
    • A01N57/10—Biocides, pest repellants or attractants, or plant growth regulators containing organic phosphorus compounds having phosphorus-to-oxygen bonds or phosphorus-to-sulfur bonds
    • A01N57/16—Biocides, pest repellants or attractants, or plant growth regulators containing organic phosphorus compounds having phosphorus-to-oxygen bonds or phosphorus-to-sulfur bonds containing heterocyclic radicals
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01N—PRESERVATION OF BODIES OF HUMANS OR ANIMALS OR PLANTS OR PARTS THEREOF; BIOCIDES, e.g. AS DISINFECTANTS, AS PESTICIDES OR AS HERBICIDES; PEST REPELLANTS OR ATTRACTANTS; PLANT GROWTH REGULATORS
    • A01N65/00—Biocides, pest repellants or attractants, or plant growth regulators containing material from algae, lichens, bryophyta, multi-cellular fungi or plants, or extracts thereof
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01N—PRESERVATION OF BODIES OF HUMANS OR ANIMALS OR PLANTS OR PARTS THEREOF; BIOCIDES, e.g. AS DISINFECTANTS, AS PESTICIDES OR AS HERBICIDES; PEST REPELLANTS OR ATTRACTANTS; PLANT GROWTH REGULATORS
    • A01N65/00—Biocides, pest repellants or attractants, or plant growth regulators containing material from algae, lichens, bryophyta, multi-cellular fungi or plants, or extracts thereof
    • A01N65/40—Liliopsida [monocotyledons]
    • A01N65/44—Poaceae or Gramineae [Grass family], e.g. bamboo, lemon grass or citronella grass
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8216—Methods for controlling, regulating or enhancing expression of transgenes in plant cells
    • C12N15/8218—Antisense, co-suppression, viral induced gene silencing [VIGS], post-transcriptional induced gene silencing [PTGS]
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/14—Type of nucleic acid interfering N.A.
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/50—Physical structure
    • C12N2310/53—Physical structure partially self-complementary or closed
    • C12N2310/531—Stem-loop; Hairpin
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A40/00—Adaptation technologies in agriculture, forestry, livestock or agroalimentary production
    • Y02A40/10—Adaptation technologies in agriculture, forestry, livestock or agroalimentary production in agriculture
    • Y02A40/146—Genetically Modified [GMO] plants, e.g. transgenic plants

Definitions

  • the present invention relates generally to methods of molecular biology and gene silencing to control pests.
  • Insect pests are a serious problem in agriculture. They destroy millions of acres of staple crops such as corn, soybeans, peas, and cotton. Yearly, these pests cause over $100 billion dollars in crop damage in the U.S. alone. In an ongoing seasonal battle, farmers must apply billions of gallons of synthetic pesticides to combat these pests.
  • microbial pesticides particularly those obtained from Bacillus strains, have played an important role in agriculture as alternatives to chemical pest control.
  • Agricultural scientists have developed crop plants with enhanced insect resistance by genetically engineering crop plants to produce insecticidal proteins from Bacillus.
  • corn and cotton plants genetically engineered to produce Cry toxins see, e.g., Aronson (2002) Cell Mol. Life Sci. 59(3):417-425; Schnepf et al. (1998) Microbiol. Mol. Biol. Rev. 62(3):775-806
  • Cry toxins see, e.g., Aronson (2002) Cell Mol. Life Sci. 59(3):417-425; Schnepf et al. (1998) Microbiol. Mol. Biol. Rev. 62(3):775-806
  • these Bt insecticidal proteins only protect plants from a relatively narrow range of pests.
  • a silencing element that, when ingested by a pest, such as a Pentatomidae plant pest including for example, a N. viridula (southern green stink bug), Acrosternum hilare (green stinkbug), Piezodorus guildini (redbanded stinkbug), and/or Halymorpha halys (Brown marmorated stinkbug).
  • plant pest is capable of decreasing the expression of a target sequence in the pest.
  • the decrease in expression of the target sequence controls the pest and thereby the methods and compositions are capable of limiting damage to a plant.
  • the present invention provides various target polynucleotides as set forth in SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 11 1,
  • silencing elements which when ingested by the pest, decrease the level of expression of one or more of the target polynucleotides. Plants, plant parts, plant cells, bacteria and other host cells comprising the silencing elements or an active variant or fragment thereof are also provided.
  • a method for controlling a pest such as a Pentatomidae plant pest, such as, for example, a N. viridula, Acrosternum hilare, Piezodorus guildini, and/or Halvmorpha halys plant pest.
  • the method comprises feeding to a pest a composition comprising a silencing element, wherein the silencing element, when ingested by the pest, reduces the level of a target sequence in the pest and thereby controls the pest.
  • methods to protect a plant from a pest Such methods comprise introducing into the plant or plant part a silencing element of the invention. When the plant expressing the silencing element is ingested by the pest, the level of the target sequence is decreased and the pest is controlled.
  • Figure 1 shows the Southern Green Stinkbug feeding assay results with soybean embryo tissue transformed with hairpin RNA silencing contracts.
  • Figure 2 shows the Southern Green Stinkbug feeding assay results with soybean embryo tissue transformed with amiRNA silencing constructs.
  • RNAi discovery methods rely on evaluation of known classes of sensitive genes (transcription factors, housekeeping genes etc.).
  • the target polynucleotide set forth herein were identified based solely on high throughput screens of a library of over 1000 expressed sequence tags from N. viridula. This screen allowed for the discovery of many novel sequences, many of which have extremely low or no homology to known sequences. This method provided the advantage of having no built in bias to genes that are frequently highly conserved across taxa.
  • many novel targets for RNAi as well as known genes not previously shown to be sensitive to RNAi have been identified.
  • a silencing element that, when ingested by a pest, such as a Pentatomidae plant pest or, for example, a N. viridula, Acrosternum hilare, Piezodorus guildini, and/or Halymorpha halys plant pest, is capable of decreasing the expression of a target sequence in the pest.
  • the decrease in expression of the target sequence controls the pest and thereby the methods and compositions are capable of limiting damage to a plant or plant part.
  • the present invention provides target polynucleotides as set forth in SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,
  • Silencing elements designed in view of these target polynucleotides are provided which, when ingested by the pest, decrease the expression of one or more of the target sequences and thereby controls the pest (i.e., has insecticidal activity).
  • controlling a pest or “controls a pest” is intended any affect on a pest that results in limiting the damage that the pest causes.
  • Controlling a pest includes, but is not limited to, killing the pest, inhibiting development of the pest, altering fertility or growth of the pest in such a manner that the pest provides less damage to the plant, decreasing the number of offspring produced, producing less fit pests, producing pests more susceptible to predator attack, or deterring the pests from eating the plant.
  • Reducing the level of expression of the target polynucleotide or the polypeptide encoded thereby, in the pest results in the suppression, control, and/or killing the invading pathogenic organism.
  • Reducing the level of expression of the target sequence of the pest will reduce the disease symptoms resulting from pathogen challenge by at least about 2% to at least about 6%, at least about 5% to about 50%, at least about 10% to about 60%, at least about 30% to about 70%, at least about 40% to about 80%, or at least about 50% to about 90% or greater.
  • the methods of the invention can be utilized to control pests, particularly, Pentatomidae plant pest or a N viridula, Acrosternum hilare, Piezodorus guildini, and/or Halymorpha halys plant pest.
  • Assays that measure the control of a pest are commonly known in the art, as are methods to quantitate disease resistance in plants following pathogen infection. See, for example, U.S. Patent No. 5,614,395, herein incorporated by reference. Such techniques include, measuring over time, the average lesion diameter, the pathogen biomass, and the overall percentage of decayed plant tissues. See, for example, Thomma et al. (1998) Plant Biology 95: 15107-1511 1, herein incorporated by reference. See, also Baum et al. (2007) Nature Biotech 11 : 1322-1326 and WO 2007/035650 which proved both whole plant feeding assays and corn root feeding assays. Both of these references are herein incorporated by reference in their entirety. See, also the examples below. The invention is drawn to compositions and methods for protecting plants from a plant pest, such as Pentatomidae plant pests or N. viridula, Acrosternum hilare,
  • Piezodorus guildini, and or Halymorpha halys plant pests or inducing resistance in a plant to a plant pest such as Pentatomidae plant pests or N. viridula, Acrosternum hilare, Piezodorus guildini, and or Halymorpha halys plant pests.
  • Pentatomidae plant pest is used to refer to any member of the Pentatomidae family. Accordingly, the compositions and methods are also useful in protecting plants against any Pentatomidae plant pest including representative genera and species such as, but not limited to, Acrocorisellus (A. serraticollis), Acrosternum (A. adelpha, A. hilare, A.
  • herbidum A. scutellatum
  • Agonoscelis A. nubila
  • Alcaeorrhynchus A. grandis, A. phymatophorus
  • Amaurochrous A. brevitylus
  • Apateticus A. anatarius, A. bracteatus, A. cynicus, A. lineolatus, A. marginiventris
  • Apoecilus Arma (A. custos)
  • Arvelius Bagrada
  • Banasa B. calva, B. dimiata, B. grisea, B. induta, B. sordida
  • Brochymena B. affinis, B. cariosa, B. haedula, B.
  • Chlorochroa C. belfragii, C, kanei, C. norlandi, C. senilis, C. viridicata
  • Chlorocoris C. distinctus, C flaviviridis, C. hebetatus, C. subrugosus, C. tau
  • Codophila C. remota, C. sulcata, C. varius
  • Coenus C. delius, C. inermis, C. tarsalis
  • Cosmopepla C.
  • Nezara N. smaragdulus, N. viridula (southern green stink bug)J, Oebalus (0. grisescens, 0. insularis, 0. mexicanus, 0. pugnax, 0. typhoeus), Oechalia (0. schellenbergii (spined predatory shield bug)J, Okeanos (0. quelpartensis), Oplomus (0. catena, 0. dichrous, 0. tripustulatus), Palomena (P. prasina (green shield bug)), Parabrochymena, Pentatoma (P. angulata, P. illuminata, P.
  • a "target sequence” or “target polynucleotide” comprises any sequence in the pest that one desires to reduce the level of expression. In specific embodiments, decreasing the level of the target sequence in the pest controls the pest.
  • the target sequence can be essential for growth and development. While the target sequence can be expressed in any tissue of the pest, in specific embodiments, the sequences targeted for suppression in the pest are expressed in cells of the gut tissue of the pest, cells in the midgut of the pest, and cells lining the gut lumen or the midgut. Such target sequences can be involved in, for example, gut cell metabolism, growth or differentiation.
  • Non- limiting examples of target sequences of the invention include a polynucleotide set forth in SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108
  • decreasing the level of expression of one or more of these target sequences in a Pentatomidae plant pest or a N. viridula, Acrosternum hilare, Piezodorus guildini, and/or Halymorpha halys plant pest controls the pest.
  • silencing element is intended a polynucleotide which when ingested by a pest, is capable of reducing or eliminating the level or expression of a target
  • the silencing element employed can reduce or eliminate the expression level of the target sequence by influencing the level of the target RNA transcript or, alternatively, by influencing translation and thereby affecting the level of the encoded polypeptide. Methods to assay for functional silencing elements that are capable of reducing or eliminating the level of a sequence of interest are disclosed elsewhere herein.
  • a single polynucleotide employed in the methods of the invention can comprise one or more silencing elements to the same or different target polynucleotides.
  • the silencing element can be produced in vivo (i.e., in a host cell such as a plant or microorganism) or in vitro.
  • the target sequence is not endogenous to the plant.
  • the silencing element controls pests, preferably the silencing element has no effect on the normal plant or plant part.
  • silencing elements can include, but are not limited to, a sense suppression element, an antisense suppression element, a double stranded RNA, a siRNA, an amiRNA, a miRNA, or a hairpin suppression element.
  • a sense suppression element an antisense suppression element
  • a double stranded RNA a siRNA
  • an amiRNA an miRNA
  • a hairpin suppression element a silencing element that can be employed to decrease expression of these target Pentatomidae plant pest sequences or N.
  • viridula, Acrosternum hilare, Piezodorus guildini, and/ 'or Halymorpha halys plant pest sequences comprise fragments and variants of the sense or antisense sequence or consists of the sense or antisense sequence of the sequence set forth in SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91,
  • silencing elements include, for example, SEQ ID NOS: 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 305, 306, 307, 308, 309, 310, 311, 312, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, or 336 or active variants or fragments thereof.
  • the silencing element can further comprise additional sequences that advantageously effect transcription and/or the stability of a resulting transcript.
  • the silencing elements can comprise at least one thymine residue at the 3' end.
  • the silencing elements can have at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more thymine residues at the 3' end.
  • enhancer suppressor elements can also be employed in conjunction with the silencing elements disclosed herein.
  • the polynucleotide or polypeptide level of the target sequence is statistically lower than the polynucleotide level or polypeptide level of the same target sequence in an appropriate control pest which is not exposed to (i.e., has not ingested) the silencing element.
  • reducing the polynucleotide level and/or the polypeptide level of the target sequence in a pest according to the invention results in less than 95%, less than 90%>, less than 80%>, less than 70%, less than 60%, less than 50%, less than 40%, less than 30%, less than 20%, less than 10%), or less than 5%> of the polynucleotide level, or the level of the polypeptide encoded thereby, of the same target sequence in an appropriate control pest.
  • Methods to assay for the level of the RNA transcript, the level of the encoded polypeptide, or the activity of the polynucleotide or polypeptide are discussed elsewhere herein. i. Sense Suppression Elements
  • a “sense suppression element” comprises a polynucleotide designed to express an RNA molecule corresponding to at least a part of a target messenger RNA in the "sense" orientation. Expression of the RNA molecule comprising the sense suppression element reduces or eliminates the level of the target polynucleotide or the polypeptide encoded thereby.
  • the polynucleotide comprising the sense suppression element may correspond to all or part of the sequence of the target polynucleotide, all or part of the 5' and/or 3' untranslated region of the target polynucleotide, all or part of the coding sequence of the target polynucleotide, or all or part of both the coding sequence and the untranslated regions of the target polynucleotide.
  • a sense suppression element has substantial sequence identity to the target polynucleotide, typically greater than about 65% sequence identity, greater than about 85% sequence identity, about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity. See, U.S. Patent Nos. 5,283, 184 and 5,034,323; herein incorporated by reference.
  • the sense suppression element can be any length so long as it allows for the suppression of the targeted sequence.
  • the sense suppression element can be, for example, 15, 16, 17, 18 19, 20, 22, 25, 30, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 900, 1000, 1100, 1200, 1300 nucleotides or longer of the target polynucleotides set forth in any of SEQ ID NO: 1-292 or 302-304.
  • the sense suppression element can be, for example, about 15-25, 25-100, 100-150, 150- 200, 200-250, 250-300, 300-350, 350-400, 450-500, 500-550, 550-600, 600-650, 650-700, 700-750, 750-800, 800-850, 850-900, 900-950, 950-1000, 1000-1050, 1050-1 100, 1 100- 1200, 1200-1300, 1300-1400, 1400-1500, 1500-1600, 1600-1700, 1700-1800 nucleotides or longer of the target polynucleotides set forth in any of SEQ ID NO: 1-292 or 302-304.
  • Antisense Suppression Elements can be, for example, about 15-25, 25-100, 100-150, 150- 200, 200-250, 250-300, 300-350, 350-400, 450-500, 500-550, 550-600, 600-650, 650-700, 700-750, 750-800, 800-850, 850
  • an “antisense suppression element” comprises a polynucleotide which is designed to express an RNA molecule complementary to all or part of a target messenger RNA. Expression of the antisense RNA suppression element reduces or eliminates the level of the target polynucleotide.
  • the polynucleotide for use in antisense suppression may correspond to all or part of the complement of the sequence encoding the target polynucleotide, all or part of the complement of the 5' and/or 3' untranslated region of the target polynucleotide, all or part of the complement of the coding sequence of the target polynucleotide, or all or part of the complement of both the coding sequence and the untranslated regions of the target polynucleotide.
  • the antisense suppression element may be fully complementary (i.e., 100% identical to the complement of the target sequence) or partially complementary (i.e., less than 100% identical to the complement of the target sequence) to the target polynucleotide.
  • the antisense suppression element comprises at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%o, 98%), or 99% sequence complementarity to the target polynucleotide.
  • Antisense suppression may be used to inhibit the expression of multiple proteins in the same plant. See, for example, U.S. Patent No. 5,942,657.
  • the antisense suppression element can be complementary to a portion of the target polynucleotide. Generally, sequences of at least 15, 20, 22, 25, 50, 100, 200, 300, 400, 450 nucleotides or greater of the sequence set forth in any of SEQ ID NO: 1-292 or 302-304 may be used.
  • a “double stranded RNA silencing element” or “dsRNA” comprises at least one transcript that is capable of forming a dsRNA either before or after ingestion by a pest.
  • a “dsRNA silencing element” includes a dsRNA, a transcript or polyribonucleotide capable of forming a dsRNA or more than one transcript or polyribonucleotide capable of forming a dsRNA.
  • “Double stranded RNA” or “dsRNA” refers to a polyribonucleotide structure formed either by a single self-complementary RNA molecule or a
  • dsRNA molecule(s) employed in the methods and compositions of the invention mediate the reduction of expression of a target sequence, for example, by mediating RNA interference "RNAi" or gene silencing in a sequence-specific manner.
  • RNAi RNA interference
  • the dsRNA is capable of reducing or eliminating the level or expression of a target polynucleotide or the polypeptide encoded thereby in a pest.
  • the dsRNA can reduce or eliminate the expression level of the target sequence by influencing the level of the target RNA transcript, by influencing translation and thereby affecting the level of the encoded polypeptide, or by influencing expression at the pre- transcriptional level (i.e., via the modulation of chromatin structure, methylation pattern, etc., to alter gene expression).
  • Verdel et al (2004) Science 303 :672- 676; Pal-Bhadra et al (2004) Science 303:669-672; Allshire (2002) Science 297: 1818- 1819; Volpe et al. (2002) Science 297: 1833-1837; Jenuwein (2002) Science 297:2215- 2218; and Hall et al.
  • dsRNA is meant to encompass other terms used to describe nucleic acid molecules that are capable of mediating RNA interference or gene silencing, including, for example, short-interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), hairpin RNA, short hairpin RNA (shRNA), post-transcriptional gene silencing RNA (ptgsRNA), and others.
  • siRNA short-interfering RNA
  • dsRNA double-stranded RNA
  • miRNA micro-RNA
  • shRNA short hairpin RNA
  • ptgsRNA post-transcriptional gene silencing RNA
  • At least one strand of the duplex or double-stranded region of the dsRNA shares sufficient sequence identity or sequence complementarity to the target polynucleotide to allow for the dsRNA to reduce the level of expression of the target sequence.
  • the strand that is complementary to the target polynucleotide is the "antisense strand” and the strand homologous to the target polynucleotide is the "sense strand.”
  • the dsRNA comprises a hairpin RNA.
  • a hairpin RNA comprises an RNA molecule that is capable of folding back onto itself to form a double stranded structure. Multiple structures can be employed as hairpin elements.
  • the dsRNA suppression element comprises a hairpin element which comprises in the following order, a first segment, a second segment, and a third segment, where the first and the third segment share sufficient complementarity to allow the transcribed RNA to form a double-stranded stem-loop structure.
  • the "second segment" of the hairpin comprises a "loop” or a "loop region.”
  • loop region may be substantially single stranded and act as a spacer between the self-complementary regions of the hairpin stem-loop.
  • the loop region can comprise a random or nonsense nucleotide sequence and thus not share sequence identity to a target polynucleotide.
  • the loop region comprises a sense or an antisense RNA sequence or fragment thereof that shares identity to a target polynucleotide. See, for example, International Patent Publication No. WO 02/00904, herein incorporated by reference.
  • the loop region can be optimized to be as short as possible while still providing enough intramolecular flexibility to allow the formation of the base-paired stem region. Accordingly, the loop sequence is generally less than 1000, 900, 800, 700, 600, 500, 400, 300, 200, 100, 50, 25, 20, 15, 10 nucleotides or less.
  • the "first" and the “third” segment of the hairpin RNA molecule comprise the base-paired stem of the hairpin structure.
  • the first and the third segments are inverted repeats of one another and share sufficient complementarity to allow the formation of the base-paired stem region.
  • the first and the third segments are fully complementary to one another.
  • the first and the third segment may be partially complementary to each other so long as they are capable of hybridizing to one another to form a base-paired stem region.
  • the amount of complementarity between the first and the third segment can be calculated as a percentage of the entire segment.
  • the first and the third segment of the hairpin RNA generally share at least 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, up to and including 100% complementarity.
  • the first and the third segment are at least about 1000, 500, 400, 300, 200, 100, 50, 40, 30, 25, 22, 20, 19, 18, 17, 16, 15 or 10 nucleotides in length.
  • the length of the first and/or the third segment is about 10-100 nucleotides, about 10 to about 75 nucleotides, about 10 to about 50 nucleotides, about 10 to about 40 nucleotides, about 10 to about 35 nucleotides, about 10 to about 30 nucleotides, about 10 to about 25 nucleotides, about 10 to about 19 nucleotides, about 50 nucleotides to about 100 nucleotides, about 100 nucleotides to about 150 nucleotides, about 150 nucleotides to about 200 nucleotides, about 200 nucleotides to about 250 nucleotides, about 250 nucleotides to about 300 nucleotides, about 300 nucleotides to about 350 nucleotides, about 350 nucleotides to about 400 nu
  • the length of the first and/or the third segment comprises at least 10-19 nucleotides; 19-35 nucleotides; 30-45 nucleotides; 40-50 nucleotides; 50-100 nucleotides; 100-300 nucleotides; about 500 -700 nucleotides; about 700-900 nucleotides; about 900-1100 nucleotides; about 1300 -1500 nucleotides; about 1500 - 1700 nucleotides; about 1700 - 1900 nucleotides; about 1900 - 2100 nucleotides; about 2100 - 2300 nucleotides; or about 2300 - 2500 nucleotides. See, for example, International Publication No.
  • the first and the third segment comprise at least 19 nucleotides having at least 85% complementary to the first segment.
  • the first and the third segments which form the stem-loop structure of the hairpin comprises 3' or 5' overhang regions having unpaired nucleotide residues.
  • the sequences used in the first, the second, and/or the third segments comprise domains that are designed to have sufficient sequence identity to a target polynucleotide of interest and thereby have the ability to decrease the level of expression of the target polynucleotide.
  • the specificity of the inhibitory RNA transcripts is therefore generally conferred by these domains of the silencing element.
  • the first, second and/or third segment of the silencing element comprise a domain having at least 10, at least 15, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 40, at least 50, at least 100, at least 200, at least 300, at least 500, at least 1000, or more than 1000 nucleotides that share sufficient sequence identity to the target polynucleotide to allow for a decrease in expression levels of the target polynucleotide when expressed in an appropriate cell.
  • the domain is between about 15 to 50 nucleotides, about 19-35 nucleotides, about 25-50 nucleotides, about 19 to 75 nucleotides, about 40-90 nucleotides about 15-100 nucleotides 10- 100 nucleotides, about 10 to about 75 nucleotides, about 10 to about 50 nucleotides, about 10 to about 40 nucleotides, about 10 to about 35 nucleotides, about 10 to about 30 nucleotides, about 10 to about 25 nucleotides, about 10 to about 19 nucleotides, about 50 nucleotides to about 100 nucleotides, about 100 nucleotides to about 150 nucleotides, about 150 nucleotides to about 200 nucleotides, about 200 nucleotides to about 250 nucleotides, about 250 nucleotides to about 300 nucleotides, about 300 nucleotides to about 350 nucleotides, about 350 nucleotides to
  • the length of the first and/or the third segment comprises at least 10-19 nucleotides, 19-35 nucleotides, 30-45 nucleotides, 40-50 nucleotides, 50-100 nucleotides, or about 100-300 nucleotides.
  • the domain of the first, the second, and/or the third segment has 100% sequence identity to the target polynucleotide.
  • the domain of the first, the second and/or the third segment having homology to the target polypeptide have at least 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%), 99%o, or greater sequence identity to a region of the target
  • sequence identity of the domains of the first, the second and/or the third segments to the target polynucleotide need only be sufficient to decrease expression of the target polynucleotide of interest. See, for example, Chuang and Meyerowitz (2000) Proc. Natl. Acad. Sci. USA 97:4985-4990; Stoutjesdijk et al. (2002) Plant Physiol.
  • the amount of complementarity shared between the first, second, and/or third segment and the target polynucleotide or the amount of complementarity shared between the first segment and the third segment may vary depending on the organism in which gene expression is to be controlled. Some organisms or cell types may require exact pairing or 100% identity, while other organisms or cell types may tolerate some mismatching. In some cells, for example, a single nucleotide mismatch in the targeting sequence abrogates the ability to suppress gene expression.
  • the suppression cassettes of the invention can be used to target the suppression of mutant genes, for example, oncogenes whose transcripts comprise point mutations and therefore they can be specifically targeted using the methods and compositions of the invention without altering the expression of the remaining wild-type allele.
  • any region of the target polynucleotide can be used to design the domain of the silencing element that shares sufficient sequence identity to allow expression of the hairpin transcript to decrease the level of the target polynucleotide.
  • the domain can be designed to share sequence identity to the 5' untranslated region of the target polynucleotide(s), the 3' untranslated region of the target polynucleotide(s), exonic regions of the target polynucleotide(s), intronic regions of the target polynucleotide(s), and any combination thereof.
  • a domain of the silencing element shares sufficient homology to at least about 15, 16, 17, 18, 19, 20, 22, 25 or 30 consecutive nucleotides from about nucleotides 1-50, 25-75, 75-125, 50-100, 125-175,
  • the synthetic oligodeoxyribonucleotide/RNAse H method can be used to determine sites on the target mRNA that are in a conformation that is susceptible to RNA silencing. See, for example, Vickers et al. (2003) J. Biol. Chem 278:7108-7118 and Yang et al. (2002) Proc. Natl. Acad. Sci. USA 99:9442-9447, herein incorporated by reference. These studies indicate that there is a significant correlation between the RNase- H-sensitive sites and sites that promote efficient siR A-directed mRNA degradation.
  • the hairpin silencing element may also be designed such that the sense sequence or the antisense sequence do not correspond to a target polynucleotide.
  • the sense and antisense sequence flank a loop sequence that comprises a nucleotide sequence corresponding to all or part of the target polynucleotide.
  • it is the loop region that determines the specificity of the RNA interference. See, for example, WO 02/00904, herein incorporated by reference.
  • transcriptional gene silencing may be accomplished through use of a hairpin suppression element where the inverted repeat of the hairpin shares sequence identity with the promoter region of a target polynucleotide to be silenced.
  • a hairpin suppression element where the inverted repeat of the hairpin shares sequence identity with the promoter region of a target polynucleotide to be silenced.
  • any silencing element that encodes a hairpin suppression construct non-limiting examples of such hairpin constructs are set forth in SEQ ID NO: 293 which targets SEQ ID NO: 278; SEQ ID NOS: 294, 295 and 296 which target SEQ ID NO: 279; SEQ ID NOS: 297 and 298 which target SEQ ID NO:280; SEQ ID NO:299 which targets SEQ ID NO:281 ; SEQ ID NO: 300 which targets SEQ ID NO: 282; and SEQ ID NO: 301 which targets SEQ ID NO: 283; or active variants or fragments thereof.
  • the dsRNA can comprise a small RNA (sRNA).
  • sRNAs can comprise both micro RNA (miRNA) and short-interfering RNA (siRNA) (Meister and Tuschl (2004) Nature 431 :343-349 and Bonetta et al. (2004) Nature Methods 1 :79-86).
  • miRNA micro RNA
  • siRNA short-interfering RNA
  • "MicroRNAs” or “miRNAs” are regulatory agents comprising about 19 to about 24 nucleotides (nt) in length, which are highly efficient at inhibiting the expression of target polynucleotides. See, for example Javier et al. (2003) Nature 425: 257-263, herein incorporated by reference.
  • the silencing element can be designed to express a dsRNA molecule that forms a hairpin structure containing a 21 nucleotide sequence that is complementary to the target polynucleotide of interest.
  • the miRNA can be an "artificial miRNA” or “amiRNA” which comprises a miRNA sequence that is synthetically designed to silence a target sequence.
  • the final (mature) miRNA When expressing an miRNA, the final (mature) miRNA is present in a duplex in a precursor backbone structure, the two strands being referred to as the miRNA (the strand that will eventually basepair with the target) and miRNA* (star sequence).
  • This final miRNA is a substrate for a form of dicer that removes the miRNA/miRNA* duplex from the precursor, after which, similarly to siRNAs, the duplex can be taken into the RISC complex. It has been demonstrated that miRNAs can be transgenically expressed and be effective through expression of a precursor form, rather than the entire primary form (Panzotto et al. (2004) Genes & Development 18 :2237-2242 and Guo et al. (2005) Plant Cell 17: 1376-1386).
  • the silencing element for miRNA interference comprises a miRNA precursor backbone.
  • the miRNA precursor backbone comprises a DNA sequence having the miRNA and star sequences. When expressed as an RNA, the structure of the miRNA precursor backbone is such as to allow for the formation of a hairpin RNA structure that can be processed into a miRNA.
  • the miRNA precursor backbone comprises a genomic miRNA precursor sequence, wherein said sequence comprises a native precursor in which an heterologous (artificial) miRNA and star sequence are inserted.
  • a "star sequence” is the sequence within a miRNA precursor backbone that is complementary to the miRNA and forms a duplex with the miRNA to form the stem structure of a hairpin RNA.
  • the star sequence can comprise less than 100% complementarity to the miRNA sequence.
  • the star sequence can comprise at least 99%, 98%, 97%, 96%, 95%, 90%, 85%, 80% or lower sequence complementarity to the miRNA sequence as long as the star sequence has sufficient complementarity to the miRNA sequence to form a double stranded structure.
  • the star sequence comprises a sequence having 1, 2, 3, 4, 5 or more mismatches with the miRNA sequence and still has sufficient complementarity to form a double stranded structure with the miRNA sequence resulting in production of miRNA and suppression of the target sequence.
  • the miRNA precursor backbones can be from any plant. In some embodiments, the miRNA precursor backbone is from a monocot. In other embodiments, the miRNA precursor backbone is from a dicot. In further embodiments, the backbone is from maize or soybean. MicroRNA precursor backbones have been described previously.
  • US20090155910A1 discloses the following soybean miRNA precursor backbones: 156c, 159, 166b, 168c, 396b and 398b
  • US20090155909Al discloses the following maize miRNA precursor backbones: 159c, 164h, 168a, 169r, and 396h. Each of these references is incorporated by reference in their entirety.
  • the miRNA precursor backbone can be altered to allow for efficient insertion of heterologous miRNA and star sequences within the miRNA precursor backbone.
  • the miRNA segment and the star segment of the miRNA precursor backbone are replaced with the heterologous miRNA and the heterologous star sequences, designed to target any sequence of interest, using a PCR technique and cloned into an expression construct. It is recognized that there could be alterations to the position at which the artificial miRNA and star sequences are inserted into the backbone.
  • the miRNA sequences disclosed herein can have a "U” at the 5'-end, a "C” or “G” at the 19 th nucleotide position, and an "A” or “U” at the 10th nucleotide position.
  • the miRNA design is such that the miRNA have a high free delta-G as calculated using the ZipFold algorithm (Markham, N. R. & Zuker, M. (2005) Nucleic Acids Res. 33: W577-W581.)
  • a one base pair change can be added within the 5' portion of the miRNA so that the sequence differs from the target sequence by one nucleotide.
  • compositions of the invention employ silencing elements that when transcribed "form" a dsRNA molecule. Accordingly, the heterologous
  • a chimeric polynucleotide that can selectively silence the target polynucleotide can be generated by expressing a chimeric construct comprising the target sequence for a miRNA or siRNA to a sequence corresponding to all or part of the gene or genes to be silenced.
  • the dsRNA is "formed" when the target for the miRNA or siRNA interacts with the miRNA present in the cell. The resulting dsRNA can then reduce the level of expression of the gene or genes to be silenced.
  • the construct can be designed to have a target for an endogenous miRNA or alternatively, a target for a heterologous and/or synthetic miRNA can be employed in the construct. If a heterologous and/or synthetic miRNA is employed, it can be introduced into the cell on the same nucleotide construct as the chimeric polynucleotide or on a separate construct. As discussed elsewhere herein, any method can be used to introduce the construct comprising the heterologous miRNA.
  • target sequences disclosed herein can be used to design any silencing element that encodes a miRNA
  • non-limiting examples of such miRNA constructs include SEQ ID NOS: 311, 312, 327, 328, 335 or 336 which target SEQ ID NO: 304; SEQ ID NOS: 307, 308, 323, 324, 331 or 332 which target SEQ ID NO: 278; SEQ ID NOS: 309, 310, 325, 326, 333 or 334 which target SEQ ID NO: 303; and SEQ ID NOS: 305, 306, 321, 322, 329 or 330 which target SEQ ID NO: 302; or active variants or fragments thereof.
  • fragment is intended a portion of the polynucleotide or a portion of the amino acid sequence and hence protein encoded thereby. Fragments of a polynucleotide may encode protein fragments that retain the biological activity of the native protein.
  • fragments of a polynucleotide that are useful as a silencing element do not need to encode fragment proteins that retain biological activity.
  • fragments of a nucleotide sequence may range from at least about 10, about 15, about 16, about 17, about 18, about 19, about 20 nucleotides, about 22 nucleotides, about 50 nucleotides, about 75 nucleotides, about 100 nucleotides, 200 nucleotides, 300 nucleotides, 400 nucleotides, 500 nucleotides, 600 nucleotides, 700 nucleotides and up to the full-length polynucleotide employed in the invention.
  • fragments of a nucleotide sequence may range from 1-50, 25-75, 75-125, 50-100, 125-175, 175-225, 100-150, 150-200, 200-250, 225- 275, 275-325, 250-300, 325-375, 375-425, 300-350, 350-400, 425-475, 400-450, 475-525, 450-500, 525-575, 575-625, 550-600, 625-675, 675-725, 600-650, 625-675, 675-725, 650- 700, 725-825, 825-875, 750-800, 875-925, 925-975, 850-900, 925-975, 975-1025, 950- 1000, 1000-1050, 1025-1075, 1075-1 125, 1050-1100, 1125-1 175, 1 100-1200, 1175-1225, 1225-1275, 1200-1300, 1325-1375, 1375-1425, 1300-1400, 1425-14
  • fragments of the various target sequences i.e. SEQ ID NOS: 1-292 and 302-304
  • SEQ ID NOS:293-301 or 321-336 fragments of the various silencing elements provided herein.
  • fragments of a nucleotide sequence that are useful as silencing elements may range from at least about 10, about 15, about 16, about 17, about 18, about 19, about 20 nucleotides, about 22 nucleotides, about 50 nucleotides, about 75 nucleotides, about 100 nucleotides, 200 nucleotides, 300 nucleotides, 400 nucleotides, 500 nucleotides, 600 nucleotides, 700 nucleotides and up to the full-length polynucleotide sequences of SEQ ID NOS: 1-304 or 321-336.
  • fragments of a nucleotide sequence that are useful as silencing elements may range from 1-50, 25-75, 75-125, 50-100, 125-175, 175-225, 100-150, 150- 200, 200-250, 225-275, 275-325, 250-300, 325-375, 375-425, 300-350, 350-400, 425-475, 400-450, 475-525, 450-500, 525-575, 575-625, 550-600, 625-675, 675-725, 600-650, 625- 675, 675-725, 650-700, 725-825, 825-875, 750-800, 875-925, 925-975, 850-900, 925-975, 975-1025, 950-1000, 1000-1050, 1025-1075, 1075-1 125, 1050-1100, 1125-1175, 1 100- 1200, 1175-1225, 1225-1275, 1200-1300, 1325-1375, 1375-1425
  • SEQ ID NOS: 1-292 or 302-304 include, for example, SEQ ID NOS: 284-292 or 305-312.
  • variants is intended to mean substantially similar sequences.
  • a variant comprises a deletion and/or addition of one or more nucleotides at one or more internal sites within the native polynucleotide and/or a substitution of one or more nucleotides at one or more sites in the native polynucleotide.
  • a variant of a polynucleotide that is useful as a silencing element will retain the ability to reduce expression of the target polynucleotide and, in some embodiments, thereby control a pest of interest.
  • a "native" polynucleotide or polypeptide comprises a naturally occurring nucleotide sequence or amino acid sequence, respectively.
  • conservative variants include those sequences that, because of the degeneracy of the genetic code, encode the amino acid sequence of one of the polypeptides employed in the invention.
  • Variant polynucleotides also include synthetically derived polynucleotide, such as those generated, for example, by using site-directed mutagenesis, but continue to retain the desired activity.
  • variants of a particular polynucleotide of the invention will have at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to that particular polynucleotide as determined by sequence alignment programs and parameters described elsewhere herein.
  • Variants of a particular polynucleotide of the invention can also be evaluated by comparison of the percent sequence identity between the polypeptide encoded by a variant polynucleotide and the polypeptide encoded by the reference polynucleotide. Percent sequence identity between any two polypeptides can be calculated using sequence alignment programs and parameters described elsewhere herein.
  • the percent sequence identity between the two encoded polypeptides is at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity.
  • sequence relationships between two or more polynucleotides or polypeptides are used to describe the sequence relationships between two or more polynucleotides or polypeptides: (a) “reference sequence”, (b) “comparison window”, (c) “sequence identity”, and, (d) “percentage of sequence identity.”
  • reference sequence is a defined sequence used as a basis for sequence comparison.
  • a reference sequence may be a subset or the entirety of a specified sequence; for example, as a segment of a full-length cDNA or gene sequence, or the complete cDNA or gene sequence.
  • comparison window makes reference to a contiguous and specified segment of a polynucleotide sequence, wherein the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two polynucleotides.
  • the comparison window is at least 20 contiguous nucleotides in length, and optionally can be 30, 40, 50, 100, or longer.
  • sequence identity/similarity values provided herein refer to the value obtained using GAP Version 10 using the following parameters: % identity and % similarity for a nucleotide sequence using GAP Weight of 50 and Length Weight of 3, and the nwsgapdna.cmp scoring matrix; % identity and % similarity for an amino acid sequence using GAP Weight of 8 and Length Weight of 2, and the BLOSUM62 scoring matrix; or any equivalent program thereof.
  • equivalent program is intended any sequence comparison program that, for any two sequences in question, generates an alignment having identical nucleotide or amino acid residue matches and an identical percent sequence identity when compared to the corresponding alignment generated by GAP Version 10.
  • sequence identity or “identity” in the context of two polynucleotides or polypeptide sequences makes reference to the residues in the two sequences that are the same when aligned for maximum correspondence over a specified comparison window.
  • sequence identity or “identity” in the context of two polynucleotides or polypeptide sequences makes reference to the residues in the two sequences that are the same when aligned for maximum correspondence over a specified comparison window.
  • percentage of sequence identity is used in reference to proteins it is recognized that residue positions which are not identical often differ by conservative amino acid substitutions, where amino acid residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or hydrophobicity) and therefore do not change the functional properties of the molecule.
  • sequences differ in conservative substitutions the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution.
  • Sequences that differ by such conservative substitutions are said to have "sequence similarity" or "similarity”. Means for making this adjustment are well known to those of skill in the art. Typically this involves scoring a conservative substitution as a partial rather than a full mismatch, thereby increasing the percentage sequence identity. Thus, for example, where an identical amino acid is given a score of 1 and a non-conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1. The scoring of conservative substitutions is calculated, e.g., as implemented in the program PC/GENE (Intelligenetics, Mountain View, California).
  • percentage of sequence identity means the value determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison, and multiplying the result by 100 to yield the percentage of sequence identity.
  • a method for identifying a silencing element from the target polynucleotides set froth in SEQ ID NO: 1-292 or 302-304 comprises obtaining a candidate fragment of any one of SEQ ID NO: 1-292 or 302-304 which is of sufficient length to act as a silencing element and thereby reduce the expression of the target polynucleotide and/or control a desired pest; expressing said candidate
  • polynucleotide and/or controls a desired pest.
  • Methods of identifying such candidate fragments based on the desired pathway for suppression are known.
  • various bioinformatics programs can be employed to identify the region of the target
  • polynucleotide is not intended to limit the present invention to polynucleotides comprising DNA.
  • polynucleotides can comprise ribonucleotides and combinations of ribonucleotides and deoxyribonucleotides. Such deoxyribonucleotides and ribonucleotides include both naturally occurring molecules and synthetic analogues.
  • the polynucleotides of the invention also encompass all forms of sequences including, but not limited to, single- stranded forms, double-stranded forms, hairpins, stem-and-loop structures, and the like.
  • the polynucleotide encoding the silencing element or in specific embodiments employed in the methods and compositions of the invention can be provided in expression cassettes for expression in a plant or organism of interest. It is recognized that multiple silencing elements including multiple identical silencing elements, multiple silencing elements targeting different regions of the target sequence, or multiple silencing elements from different target sequences can be used. In this embodiment, it is recognized that each silencing element can be contained in a single or separate cassette, DNA construct, or vector. As discussed, any means of providing the silencing element is contemplated.
  • a plant or plant cell can be transformed with a single cassette comprising DNA encoding one or more silencing elements or separate cassettes comprising each silencing element can be used to transform a plant or plant cell or host cell.
  • a plant transformed with one component can be subsequently transformed with the second component.
  • One or more silencing elements can also be brought together by sexual crossing. That is, a first plant comprising one component is crossed with a second plant comprising the second component. Progeny plants from the cross will comprise both components.
  • the expression cassette can include 5' and 3' regulatory sequences operably linked to the polynucleotide of the invention.
  • "Operably linked” is intended to mean a functional linkage between two or more elements.
  • an operable linkage between a polynucleotide of the invention and a regulatory sequence i.e., a promoter
  • Operably linked elements may be contiguous or non-contiguous. When used to refer to the joining of two protein coding regions, by operably linked is intended that the coding regions are in the same reading frame.
  • the cassette may additionally contain at least one additional polynucleotide to be cotransformed into the organism.
  • the additional polypeptide(s) can be provided on multiple expression cassettes.
  • Expression cassettes can be provided with a plurality of restriction sites and/or recombination sites for insertion of the polynucleotide to be under the transcriptional regulation of the regulatory regions.
  • the expression cassette may additionally contain selectable marker genes.
  • the expression cassette can include in the 5'-3' direction of transcription, a transcriptional and translational initiation region (i.e., a promoter), a polynucleotide comprising the silencing element employed in the methods and compositions of the invention, and a transcriptional and translational termination region (i.e., termination region) functional in plants.
  • the double stranded RNA is expressed from a suppression cassette.
  • Such a cassette can comprise two convergent promoters that drive transcription of an operably linked silencing element.
  • Convergent promoters refers to promoters that are oriented on either terminus of the operably linked silencing element such that each promoter drives transcription of the silencing element in opposite directions, yielding two transcripts.
  • the convergent promoters allow for the transcription of the sense and anti-sense strand and thus allow for the formation of a dsRNA.
  • the regulatory regions (i.e., promoters, transcriptional regulatory regions, and translational termination regions) and/or the polynucleotides employed in the invention may be native/analogous to the host cell or to each other.
  • the regulatory regions and/or the polynucleotide employed in the invention may be heterologous to the host cell or to each other.
  • heterologous in reference to a sequence is a sequence that originates from a foreign species, or, if from the same species, is substantially modified from its native form in composition and/or genomic locus by deliberate human intervention.
  • a promoter operably linked to a heterologous polynucleotide is from a species different from the species from which the polynucleotide was derived, or, if from the same/analogous species, one or both are substantially modified from their original form and/or genomic locus, or the promoter is not the native promoter for the operably linked polynucleotide.
  • a chimeric gene comprises a coding sequence operably linked to a transcription initiation region that is heterologous to the coding sequence.
  • the termination region may be native with the transcriptional initiation region, may be native with the operably linked polynucleotide encoding the silencing element, may be native with the plant host, or may be derived from another source (i.e., foreign or heterologous) to the promoter, the polynucleotide comprising silencing element, the plant host, or any combination thereof.
  • Convenient termination regions are available from the Ti-plasmid of A. tumefaciens, such as the octopine synthase and nopaline synthase termination regions. See also Guerineau et al. (1991) Mol. Gen. Genet.
  • sequence modifications are known to enhance gene expression in a cellular host. These include elimination of sequences encoding spurious polyadenylation signals, exon-intron splice site signals, transposon-like repeats, and other such well- characterized sequences that may be deleterious to gene expression.
  • the G-C content of the sequence may be adjusted to levels average for a given cellular host, as calculated by reference to known genes expressed in the host cell. When possible, the sequence is modified to avoid predicted hairpin secondary mRNA structures.
  • the various DNA fragments may be manipulated, so as to provide for the DNA sequences in the proper orientation and, as appropriate, in the proper reading frame.
  • adapters or linkers may be employed to join the DNA fragments or other manipulations may be involved to provide for convenient restriction sites, removal of superfluous DNA, removal of restriction sites, or the like.
  • in vitro mutagenesis, primer repair, restriction, annealing, resubstitutions, e.g., transitions and transversions may be involved.
  • a number of promoters can be used in the practice of the invention.
  • the polynucleotide encoding the silencing element can be combined with constitutive, tissue- preferred, or other promoters for expression in plants.
  • Such constitutive promoters include, for example, the core promoter of the Rsyn7 promoter and other constitutive promoters disclosed in WO 99/43838 and U.S. Patent No. 6,072,050; the core CaMV 35S promoter (Odell et al. (1985) Nature 313:810-812); rice actin (McElroy et al. (1990) Plant Cell 2: 163-171); ubiquitin (Christensen et al. (1989) Plant Mol. Biol. 12:619-632 and Christensen et al. (1992) Plant Mol. Biol. 18:675-689); pEMU (Last et al. (1991) Theor. Appl. Genet.
  • an inducible promoter for instance, a pathogen-inducible promoter could also be employed.
  • Such promoters include those from pathogenesis-related proteins (PR proteins), which are induced following infection by a pathogen; e.g., PR proteins, SAR proteins, beta-l,3-glucanase, chitinase, etc. See, for example, Redolfi et al. (1983) Neth. J. Plant Pathol. 89:245-254; Uknes et al. (1992) Plant Cell 4:645-656; and Van Loon (l%5) Plant Mol Virol. 4: 111-1 16. See also WO 99/43819, herein incorporated by reference.
  • a wound-inducible promoter may be used in the constructions of the invention.
  • wound-inducible promoters include potato proteinase inhibitor (pin II) gene (Ryan (1990) Ann. Rev. Phytopath. 28:425-449; Duan et al. (1996) Nature Biotechnology 14:494-498); wunl and wun2, U.S. Patent No. 5,428, 148; winl and win2 (Stanford et al. (1989) Mol.
  • Chemical-regulated promoters can be used to modulate the expression of a gene in a plant through the application of an exogenous chemical regulator.
  • the promoter may be a chemical-inducible promoter, where application of the chemical induces gene expression, or a chemical-repressible promoter, where application of the chemical represses gene expression.
  • Chemical-inducible promoters are known in the art and include, but are not limited to, the maize In2-2 promoter, which is activated by benzenesulfonamide herbicide safeners, the maize GST promoter, which is activated by hydrophobic electrophilic compounds that are used as pre-emergent herbicides, and the tobacco PR- la promoter, which is activated by salicylic acid.
  • promoters of interest include steroid-responsive promoters (see, for example, the glucocorticoid-inducible promoter in Schena et al. (1991) Proc. Natl. Acad. Sci. USA 88: 10421-10425 and McNellis et al. (1998) Plant J. 14(2):247-257) and tetracycline- inducible and tetracycline-repressible promoters (see, for example, Gatz et al. (1991) Mol. Gen. Genet. 227:229-237, and U.S. Patent Nos. 5,814,618 and 5,789,156), herein incorporated by reference.
  • steroid-responsive promoters see, for example, the glucocorticoid-inducible promoter in Schena et al. (1991) Proc. Natl. Acad. Sci. USA 88: 10421-10425 and McNellis et al. (1998) Plant J. 14
  • Tissue-preferred promoters can be utilized to target enhanced expression within a particular plant tissue.
  • Tissue-preferred promoters include Yamamoto et al. (1997) Plant J. 12(2):255-265; Kawamata et al. (1997) Plant Cell Physiol. 38(7):792-803; Hansen et al. (1997) Mol. Gen Genet. 254(3):337-343; Russell et al. (1997) Transgenic Res. 6(2): 157- 168; Rinehart et al. (1996) Plant Physiol. 1 12(3): 1331-1341 ; Van Camp et al. (1996) Plant Physiol. 112(2):525-535; Canevascini et al. (1996) Plant Physiol.
  • the various silencing elements disclosed herein are expressed using a seed-preferred promoter.
  • “Seed-preferred" promoters include both “seed-specific” promoters (those promoters active during seed development such as promoters of seed storage proteins) as well as “seed-germinating” promoters (those promoters active during seed germination). See Thompson et al. (1989) BioEssays 10: 108, herein incorporated by reference.
  • Such seed-preferred promoters include, but are not limited to, Ciml (cytokinin- induced message); Kunitz trypsin inhibitor 3 (kti3) (Genbank accession AF233296); glycinin-1 genes (Genbank accession AB353075.1); cZ19B l (maize 19 kDa zein); milps (myo-inositol-1 -phosphate synthase) (see WO 00/11 177 and U.S. Patent No. 6,225,529; herein incorporated by reference).
  • Gamma-zein is an endosperm-specific promoter.
  • Globulin 1 (Glb-1) is a representative embryo-specific promoter.
  • seed- preferred promoters include, but are not limited to, bean ⁇ -phaseolin, napin, ⁇ -conglycinin alpha (Genbank accession GU723691), soybean lectin, cruciferin, and the like.
  • seed-preferred promoters include, but are not limited to, maize 1 kDa zein, 22 kDa zein, 27 kDa zein, gamma-zein, waxy, shrunken 1, shrunken 2, Globulin 1, etc. See also WO 00/12733, where seed-preferred promoters from endl and end2 genes are disclosed; herein incorporated by reference.
  • Leaf-preferred promoters are known in the art. See, for example, Yamamoto et al. (1997) Plant J. 12(2):255-265; Kwon ei «/. (1994) Plant Physiol. 105:357-67; Yamamoto et al. (1994) Plant Cell Physiol. 35(5):773-778; Gotor et al. (1993) Plant J. 3 :509-18; Orozco et al. (1993) Plant Mol. Biol. 23(6): 1 129-1138; and Matsuoka et al. (1993) Proc. Natl. Acad. Sci. USA 90(20):9586-9590.
  • Root-preferred promoters are known and can be selected from the many available from the literature or isolated de novo from various compatible species. See, for example, Hire et al. (1992) Plant Mol. Biol. 20(2):207-218 (soybean root-specific glutamine synthetase gene); Keller and Baumgartner (1991) Plant Cell 3(10): 1051-1061 (root- specific control element in the GRP 1.8 gene of French bean); Sanger et al. (1990) Plant Mol. Biol. 14(3):433-443 (root-specific promoter of the mannopine synthase (MAS) gene of Agrobacterium tumefaciens); and Miao et al.
  • MAS mannopine synthase
  • the promoters of these genes were linked to a ⁇ - glucuronidase reporter gene and introduced into both the nonlegume Nicotiana tabacum and the legume Lotus corniculatus , and in both instances root-specific promoter activity was preserved.
  • Leach and Aoyagi (1991) describe their analysis of the promoters of the highly expressed rolC and rolD root-inducing genes of Agrobacterium rhizogenes (see Plant Science (Limerick) 79(l):69-76). They concluded that enhancer and tissue-preferred DNA determinants are dissociated in those promoters. Teeri et at.
  • the plant-expressed promoter is a vascular- specific promoter such as a phloem-specific promoter.
  • a "vascular-specific" promoter as used herein, is a promoter which is at least expressed in vascular cells, or a promoter which is preferentially expressed in vascular cells. Expression of a vascular-specific promoter need not be exclusively in vascular cells, expression in other cell types or tissues is possible.
  • a "phloem-specific promoter” as used herein, is a plant-expressible promoter which is at least expressed in phloem cells, or a promoter which is preferentially expressed in phloem cells.
  • a phloem-specific promoter need not be exclusively in phloem cells, expression in other cell types or tissues, e.g., xylem tissue, is possible.
  • a phloem-specific promoter is a plant-expressible promoter at least expressed in phloem cells, wherein the expression in non-phloem cells is more limited (or absent) compared to the expression in phloem cells.
  • vascular- specific or phloem-specific promoters include but are not limited to the promoters selected from the group consisting of: the SCSV3, SCSV4, SCSV5, and SCSV7 promoters (Schunmann et al. (2003) Plant Functional Biology 30:453-60; the rolC gene promoter of Agrobacterium rhizogenes(Kiyokawa et al. (1994) Plant Physiology 104:801-02; Pandolfmi et al. (2003) BioMedCentral (BMC)
  • Possible promoters also include the Black Cherry promoter for Prunasin Hydrolase (PH DL1.4 PRO) (US Patent No. 6,797, 859), Thioredoxin H promoter from cucumber and rice (Fukuda A et al. (2005). Plant Cell Physiol. 46(11): 1779-86), Rice (RSs 1) (Shi, T. Wang et al. (1994). J. Exp. Bot. 45(274): 623-631) and maize sucrose synthese -1 promoters (Yang., N-S. et al. (1990) PNAS 87:4144-4148), PP2 promoter from pumpkin Guo, H. et al.
  • the expression cassette can also comprise a selectable marker gene for the selection of transformed cells.
  • Selectable marker genes are utilized for the selection of transformed cells or tissues.
  • Marker genes include genes encoding antibiotic resistance, such as those encoding neomycin phosphotransferase II (NEO) and hygromycin phosphotransferase (HPT), as well as genes conferring resistance to herbicidal compounds, such as glufosinate ammonium, bromoxynil, imidazolinones, and 2,4-dichlorophenoxyacetate (2,4-D).
  • Additional selectable markers include phenotypic markers such as ⁇ -galactosidase and fluorescent proteins such as green fluorescent protein (GFP) (Su et al (2004) Biotechnol Bioeng 55:610-9 and Fetter et al (2004) Plant Cell 7(5:215-28), cyan fl orescent protein (CYP) (Bolte et al. (2004) J. Cell Science 777:943-54 and Kato et al. (2002) Plant Physiol 729:913-42), and yellow florescent protein (PhiYFPTM from Evrogen, see, Bolte et al. (2004) J. Cell Science 777:943-54).
  • GFP green fluorescent protein
  • CYP cyan fl orescent protein
  • PhiYFPTM yellow florescent protein
  • One or more of the polynucleotides comprising the silencing element can be provided as an external composition such as a spray or powder to the plant, plant part, seed, a pest, or an area of cultivation.
  • a plant is transformed with a DNA construct or expression cassette for expression of at least one silencing element.
  • the silencing element when ingested by an insect, can reduce the level of a target pest sequence and thereby control the pest (i.e., a Pentatomidae plant pest including a N. viridula, Acrosternum Mare, Piezodorus guildini, and/or Halymorpha halys.
  • composition can comprise a cell (such as plant cell or a bacterial cell), in which a polynucleotide encoding the silencing element is stably incorporated into the genome and operably linked to promoters active in the cell.
  • a cell such as plant cell or a bacterial cell
  • a polynucleotide encoding the silencing element is stably incorporated into the genome and operably linked to promoters active in the cell.
  • compositions comprising a mixture of cells, some cells expressing at least one silencing element are also encompassed. In other embodiments, compositions comprising the silencing elements are not contained in a cell. In such embodiments, the composition can be applied to an area inhabited by a pest. In one embodiment, the composition is applied externally to a plant (i.e., by spraying a field or area of cultivation) to protect the plant from the pest.
  • composition of the invention can further be formulated as bait.
  • the compositions comprise a food substance or an attractant which enhances the attractiveness of the composition to the pest.
  • composition comprising the silencing element can be formulated in an agriculturally suitable and/or environmentally acceptable carrier.
  • Such carriers can be any material that the animal, plant or environment to be treated can tolerate.
  • the carrier must be such that the composition remains effective at controlling a pest.
  • compositions may include compounds that increase the half-life of a composition.
  • polynucleotides comprising sequences encoding the silencing element can be used to transform organisms to provide for host organism production of these components, and subsequent application of the host organism to the environment of the target pest(s).
  • host organisms include baculoviruses, bacteria, and the like.
  • the combination of polynucleotides encoding the silencing element may be introduced via a suitable vector into a microbial host, and said host applied to the environment, or to plants or animals.
  • the term "introduced” in the context of inserting a nucleic acid into a cell means “transfection” or “transformation” or “transduction” and includes reference to the incorporation of a nucleic acid into a eukaryotic or prokaryotic cell where the nucleic acid may be stably incorporated into the genome of the cell (e.g., chromosome, plasmid, plastid, or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (e.g., transfected mRNA).
  • Microbial hosts that are known to occupy the "phytosphere" (phylloplane, phyllosphere, rhizosphere, and/or rhizoplana) of one or more crops of interest may be selected.
  • These microorganisms are selected so as to be capable of successfully competing in the particular environment with the wild-type microorganisms, provide for stable maintenance and expression of the sequences encoding the silencing element, and desirably, provide for improved protection of the components from environmental degradation and inactivation.
  • microorganisms include bacteria, algae, and fungi.
  • microorganisms such as bacteria, e.g., Pseudomonas, Erwinia, Serratia, Klebsiella, Xanthomonas, Streptomyces, Rhizobium, Rhodopseudomonas, Methylius, Agrobacterium, Acetobacter, Lactobacillus, Arthrobacter, Azotobacter, Leuconostoc, and Alcaligenes
  • fungi particularly yeast, e.g., Saccharomyces, Cryptococcus, Kluyveromyces,
  • Rhodotorula Sporobolomyces, Rhodotorula, and Aureobasidium.
  • phytosphere bacterial species as Pseudomonas syringae, Pseudomonas fluorescens, Serratia marcescens, Acetobacter xylinum, Agrobacteria, Rhodopseudomonas spheroides, Xanthomonas campestris, Rhizobium melioti, Alcaligenes entrophus, Clavibacter xyli and Azotobacter vinlandir, and phytosphere yeast species such as Rhodotorula rubra, R. glutinis, R. marina, R.
  • expression cassettes can be constructed which include the nucleotide constructs of interest operably linked with the transcriptional and translational regulatory signals for expression of the nucleotide constructs, and a nucleotide sequence homologous with a sequence in the host organism, whereby integration will occur, and/or a replication system that is functional in the host, whereby integration or stable maintenance will occur.
  • Transcriptional and translational regulatory signals include, but are not limited to, promoters, transcriptional initiation start sites, operators, activators, enhancers, other regulatory elements, ribosomal binding sites, an initiation codon, termination signals, and the like. See, for example, U.S. Patent Nos. 5,039,523 and 4,853,331 ; EPO 0480762A2;
  • Suitable host cells include the prokaryotes and the lower eukaryotes, such as fungi.
  • Illustrative prokaryotes, both Gram-negative and Gram-positive, include
  • Enterobacteriaceae such as Escherichia, Erwinia, Shigella, Salmonella, and Proteus
  • Bacillaceae Rhizobiceae, such as Rhizobium
  • Spirillaceae such as photobacterium, Zymomonas , Serratia, Aeromonas, Vibrio, Desulfovibrio, Spirillum
  • Lactobacillaceae Pseudomonadaceae, such as Pseudomonas and Acetobacter
  • Azotobacteraceae and Nitrobacteraceae are Among eukaryotes are fungi, such as Phycomycetes and Ascomycetes, which includes yeast, such as Saccharomyces and Schizosaccharomyces; and
  • Basidiomycetes yeast such as Rhodotorula, Aureobasidium, Sporobolomyces, and the like.
  • Characteristics of particular interest in selecting a host cell for purposes of the invention include ease of introducing the coding sequence into the host, availability of expression systems, efficiency of expression, stability in the host, and the presence of auxiliary genetic capabilities. Characteristics of interest for use as a pesticide
  • microcapsule include protective qualities, such as thick cell walls, pigmentation, and intracellular packaging or formation of inclusion bodies; leaf affinity; lack of mammalian toxicity; attractiveness to pests for ingestion; and the like. Other considerations include ease of formulation and handling, economics, storage stability, and the like.
  • Host organisms of particular interest include yeast, such as Rhodotorula spp.,
  • Saccharomyces cerevisiae Bacillus thuringiensis, Escherichia coli, Bacillus subtilis, and the like.
  • sequences encoding the silencing elements encompassed by the invention can be introduced into microorganisms that multiply on plants (epiphytes) to deliver these components to potential target pests.
  • Epiphytes for example, can be gram-positive or gram-negative bacteria.
  • the silencing element can be fermented in a bacterial host and the resulting bacteria processed and used as a microbial spray in the same manner that Bacillus thuringiensis strains have been used as insecticidal sprays. Any suitable microorganism can be used for this purpose. Pseudomonas has been used to express Bacillus
  • the components of the invention are produced by introducing heterologous genes into a cellular host. Expression of the heterologous sequences results, directly or indirectly, in the intracellular production of the silencing element.
  • These compositions may then be formulated in accordance with conventional techniques for application to the environment hosting a target pest, e.g., soil, water, and foliage of plants. See, for example, EPA 0192319, and the references cited therein.
  • a transformed microorganism can be formulated with an acceptable carrier into separate or combined compositions that are, for example, a suspension, a solution, an emulsion, a dusting powder, a dispersible granule, a wettable powder, and an emulsifiable concentrate, an aerosol, an impregnated granule, an adjuvant, a coatable paste, and also encapsulations in, for example, polymer substances.
  • compositions disclosed above may be obtained by the addition of a surface- active agent, an inert carrier, a preservative, a humectant, a feeding stimulant, an attractant, an encapsulating agent, a binder, an emulsifier, a dye, a UV protectant, a buffer, a flow agent or fertilizers, micronutrient donors, or other preparations that influence plant growth.
  • One or more agrochemicals including, but not limited to, herbicides, insecticides, fungicides, bactericides, nematicides, molluscicides, acaracides, plant growth regulators, harvest aids, and fertilizers, can be combined with carriers, surfactants or adjuvants customarily employed in the art of formulation or other components to facilitate product handling and application for particular target pests.
  • Suitable carriers and adjuvants can be solid or liquid and correspond to the substances ordinarily employed in formulation technology, e.g., natural or regenerated mineral substances, solvents, dispersants, wetting agents, tackifiers, binders, or fertilizers.
  • the active ingredients of the present invention are normally applied in the form of compositions and can be applied to the crop area, plant, or seed to be treated.
  • the compositions may be applied to grain in preparation for or during storage in a grain bin or silo, etc.
  • the compositions may be applied simultaneously or in succession with other compounds.
  • Methods of applying an active ingredient or a composition that contains at least one silencing element include, but are not limited to, foliar application, seed coating, and soil application. The number of applications and the rate of application depend on the intensity of infestation by the corresponding pest.
  • Suitable surface-active agents include, but are not limited to, anionic compounds such as a carboxylate of, for example, a metal; carboxylate of a long chain fatty acid; an N-acylsarcosinate; mono- or di-esters of phosphoric acid with fatty alcohol ethoxylates or salts of such esters; fatty alcohol sulfates such as sodium dodecyl sulfate, sodium octadecyl sulfate, or sodium cetyl sulfate; ethoxylated fatty alcohol sulfates; ethoxylated alkylphenol sulfates; lignin sulfonates; petroleum sulfonates; alkyl aryl sulfonates such as alkyl-benzene sulfonates or lower alkylnaphtalene sulfonates, e.g., butyl-naphthalene sulfonate; salt
  • Non-ionic agents include condensation products of fatty acid esters, fatty alcohols, fatty acid amides or fatty-alkyl- or alkenyl-substituted phenols with ethylene oxide, fatty esters of polyhydric alcohol ethers, e.g., sorbitan fatty acid esters, condensation products of such esters with ethylene oxide, e.g., polyoxyethylene sorbitan fatty acid esters, block copolymers of ethylene oxide and propylene oxide, acetylenic glycols such as 2,4,7,9-tetraethyl-5-decyn-4,7-diol, or ethoxylated acetylenic glycols.
  • Examples of a cationic surface-active agent include, for instance, an aliphatic mono-, di-, or polyamine such as an acetate, naphthenate or oleate; or oxygen-containing amine such as an amine oxide of polyoxyethylene alkylamine; an amide-linked amine prepared by the condensation of a carboxylic acid with a di- or polyamine; or a quaternary ammonium salt.
  • examples of inert materials include, but are not limited to, inorganic minerals such as kaolin, phyllosilicates, carbonates, sulfates, phosphates, or botanical materials such as cork, powdered corncobs, peanut hulls, rice hulls, and walnut shells.
  • compositions comprising the silencing element can be in a suitable form for direct application or as a concentrate of primary composition that requires dilution with a suitable quantity of water or other dilutant before application.
  • compositions can be applied to the environment of an insect pest (such as a Pentatomidae plant pest or a N. viridula, Acrosternum hilare, Piezodorus guildini, and/or Halymorpha halys plant pest) by, for example, spraying, atomizing, dusting, scattering, coating or pouring, introducing into or on the soil, introducing into irrigation water, by seed treatment or general application or dusting at the time when the pest has begun to appear or before the appearance of pests as a protective measure.
  • insect pest such as a Pentatomidae plant pest or a N. viridula, Acrosternum hilare, Piezodorus guildini, and/or Halymorpha halys plant pest
  • microorganism(s) may be mixed with grain to protect the grain during storage. It is generally important to obtain good control of pests in the early stages of plant growth, as this is the time when the plant can be most severely damaged.
  • the compositions can conveniently contain another insecticide if this is thought necessary.
  • the composition(s) is applied directly to the soil, at a time of planting, in granular form of a composition of a carrier and dead cells of a Bacillus strain or transformed microorganism of the invention.
  • Another embodiment is a granular form of a composition
  • a composition comprising an agrochemical such as, for example, a herbicide, an insecticide, a fertilizer, in an inert carrier, and dead cells of a Bacillus strain or transformed microorganism of the invention.
  • the methods of the invention involve introducing a polynucleotide into a plant.
  • a plant cell having stably incorporated into its genome a heterologous polynucleotide comprising any of the various silencing elements provided herein. It is recognized that the silencing element, when ingested by a Pentatomidae plant pest, can reduce the level of expression of any of the target sequences descrbed herein (i.e. SEQ ID NOS: 1-292 or 302-304).
  • "Introducing" is intended to mean presenting to the plant the polynucleotide in such a manner that the sequence gains access to the interior of a cell of the plant.
  • the methods of the invention do not depend on a particular method for introducing a sequence into a plant, only that the polynucleotide or polypeptides gains access to the interior of at least one cell of the plant. Methods for introducing
  • polynucleotides into plants are known in the art including, but not limited to, stable transformation methods, transient transformation methods, and virus-mediated methods.
  • “Stable transformation” is intended to mean that the nucleotide construct introduced into a plant integrates into the genome of the plant and is capable of being inherited by the progeny thereof.
  • “Transient transformation” is intended to mean that a polynucleotide is introduced into the plant and does not integrate into the genome of the plant or a polypeptide is introduced into a plant.
  • Transformation protocols as well as protocols for introducing polypeptides or polynucleotide sequences into plants may vary depending on the type of plant or plant cell, i.e., monocot or dicot, targeted for transformation. Suitable methods of introducing polypeptides and polynucleotides into plant cells include microinjection (Crossway et al. (1986) Biotechniques 4:320-334), electroporation (iggs et al. (1986) Proc. Natl. Acad. Sci. USA 83:5602-5606, Agrobacterium- edmted transformation (U.S. Patent No.
  • the silencing element sequences of the invention can be provided to a plant using a variety of transient transformation methods.
  • transient transformation methods include, but are not limited to, the introduction of the protein or variants and fragments thereof directly into the plant or the introduction of the transcript into the plant.
  • Such methods include, for example, microinjection or particle bombardment. See, for example, Crossway et al. (1986) Mol Gen. Genet. 202: 179-185; Nomura et al, (1986) Plant Sci. 44:53-58; Hepler et al. (1994) Proc. Natl. Acad. Sci. 91: 2176-2180 and Hush et al.
  • polynucleotides can be transiently transformed into the plant using techniques known in the art. Such techniques include viral vector system and the precipitation of the polynucleotide in a manner that precludes subsequent release of the DNA. Thus, the transcription from the particle-bound DNA can occur, but the frequency with which it is released to become integrated into the genome is greatly reduced. Such methods include the use of particles coated with polyethylimine (PEI; Sigma #P3143).
  • the polynucleotide of the invention may be introduced into plants by contacting plants with a virus or viral nucleic acids.
  • such methods involve incorporating a nucleotide construct of the invention within a viral DNA or RNA molecule.
  • promoters of the invention also encompass promoters utilized for transcription by viral RNA polymerases. Methods for introducing polynucleotides into plants and expressing a protein encoded therein, involving viral DNA or RNA molecules, are known in the art. See, for example, U.S. Patent Nos. 5,889,191, 5,889,190, 5,866,785, 5,589,367, 5,316,931, and Porta et al. (1996) Molecular
  • the insertion of the polynucleotide at a desired genomic location is achieved using a site-specific recombination system. See, for example, W099/25821, W099/25854, WO99/25840, W099/25855, and W099/25853, all of which are herein incorporated by reference.
  • the polynucleotide of the invention can be contained in transfer cassette flanked by two non-recombinogenic recombination sites.
  • the transfer cassette is introduced into a plant having stably incorporated into its genome a target site which is flanked by two non- recombinogenic recombination sites that correspond to the sites of the transfer cassette.
  • An appropriate recombinase is provided and the transfer cassette is integrated at the target site.
  • the polynucleotide of interest is thereby integrated at a specific chromosomal position in the plant genome.
  • the cells that have been transformed may be grown into plants in accordance with conventional ways. See, for example, McCormick et al. (1986) Plant Cell Reports 5:81- 84. These plants may then be grown, and either pollinated with the same transformed strain or different strains, and the resulting progeny having constitutive expression of the desired phenotypic characteristic identified. Two or more generations may be grown to ensure that expression of the desired phenotypic characteristic is stably maintained and inherited and then seeds harvested to ensure expression of the desired phenotypic characteristic has been achieved. In this manner, the present invention provides transformed seed (also referred to as "transgenic seed") having a polynucleotide of the invention, for example, an expression cassette of the invention, stably incorporated into their genome.
  • the term plant also includes plant cells, plant protoplasts, plant cell tissue cultures from which plants can be regenerated, plant calli, plant clumps, and plant cells that are intact in plants or parts of plants such as embryos, pollen, ovules, seeds, leaves, flowers, branches, fruit, kernels, ears, cobs, husks, stalks, roots, root tips, anthers, and the like. Grain is intended to mean the mature seed produced by commercial growers for purposes other than growing or reproducing the species. Progeny, variants, and mutants of the regenerated plants are also included within the scope of the invention, provided that these parts comprise the introduced polynucleotides.
  • the present invention may be used for transformation of any plant species, including, but not limited to, monocots and dicots.
  • plant species of interest include, but are not limited to, corn (Zea mays), Brassica sp. (e.g., B. napus, B.
  • rapa, B.juncea particularly those Brassica species useful as sources of seed oil, alfalfa (Medicago sativa), rice (Oryza sativa), rye (Secale cereale), sorghum (Sorghum bicolor, Sorghum vulgare), millet (e.g., pearl millet (Pennisetum glaucum), proso millet (Panicum miliaceum), foxtail millet (Setaria italica), finger millet (Eleusine coracana)), sunflower (Helianthus annuus), safflower (Carthamus tinctorius), wheat (Triticum aestivum), soybean (Glycine max), tobacco (Nicotiana tabacum), potato (Solanum tuberosum), peanuts (Arachis hypogaea), cotton (Gossypium barbadense, Gossypium hirsutum), sweet potato (Ipomoea batatas), cassava (
  • Vegetables include tomatoes (Lycopersicon esculentum), lettuce (e.g., Lactuca sativa), green beans (Phaseolus vulgaris), lima beans (Phaseolus limensis), peas (Lathyrus spp.), and members of the genus Cucumis such as cucumber (C. sativus), cantaloupe (C. cantalupensis), and musk melon (C melo).
  • tomatoes Locopersicon esculentum
  • lettuce e.g., Lactuca sativa
  • green beans Phaseolus vulgaris
  • lima beans Phaseolus limensis
  • peas Lathyrus spp.
  • members of the genus Cucumis such as cucumber (C. sativus), cantaloupe (C. cantalupensis), and musk melon (C melo).
  • Ornamentals include azalea (Rhododendron spp.), hydrangea (Macrophylla hydrangea), hibiscus (Hibiscus rosasanensis), roses (Rosa spp.), tulips (Tulipa spp.), daffodils (Narcissus spp.), petunias (Petunia hybrida), carnation (Dianthus caryophyllus), poinsettia (Euphorbia pulcherrima), and chrysanthemum.
  • Conifers that may be employed in practicing the present invention include, for example, pines such as loblolly pine (Pinus taeda), slash pine (Pinus elliotii), ponderosa pine (Pinus ponderosa), lodgepole pine (Pinus contorta), and Monterey pine (Pinus radiata); Douglas-fir (Pseudotsuga menziesii); Western hemlock (Tsuga canadensis); Sitka spruce (Picea glauca); redwood (Sequoia sempervirens); true firs such as silver fir (Abies amabilis) and balsam fir (Abies balsamea); and cedars such as Western red cedar (Thuja plicata) and Alaska yellow-cedar (Chamaecyparis nootkatensis).
  • pines such as loblolly pine (Pinus taeda), slash pine (P
  • plants of the present invention are crop plants (for example, corn, alfalfa, sunflower, Brassica, soybean, cotton, safflower, peanut, sorghum, wheat, millet, tobacco, etc.).
  • corn and soybean plants and sugarcane plants are optimal, and in yet other embodiments corn plants are optimal.
  • plants of interest include grain plants that provide seeds of interest, oil-seed plants, and leguminous plants.
  • Seeds of interest include grain seeds, such as corn, wheat, barley, rice, sorghum, rye, etc.
  • Oil-seed plants include cotton, soybean, safflower, sunflower, Brassica, maize, alfalfa, palm, coconut, etc.
  • Leguminous plants include beans and peas. Beans include guar, locust bean, fenugreek, soybean, garden beans, cowpea, mungbean, lima bean, fava bean, lentils, chickpea, etc.
  • the plants/plant cells and/or seeds comprising an expression construct comprise a silencing element directed to a target sequence provided herein (i.e. SEQ ID NOS: 1-292 or 302-304) operably linked to a seed-preferred promoter.
  • the methods of the invention comprise methods for controlling a pest (i.e., a Pentatomidae plant pest, such as, N. viridula, Acrosternum hilare, Piezodorus guildini, and/or Halymorpha halys plant pest).
  • a pest i.e., a Pentatomidae plant pest, such as, N. viridula, Acrosternum hilare, Piezodorus guildini, and/or Halymorpha halys plant pest.
  • the method comprises feeding to a pest a composition comprising a silencing element of the invention, wherein said silencing element, when ingested by a pest (i.e., a Pentatomidae plant pest including N. viridula,
  • Acrosternum hilare, Piezodorus guildini, and 'or Halymorpha halys reduces the level of a target polynucleotide of the pest and thereby controls the pest.
  • the pest can be fed the silencing element in a variety of ways. For example, in one embodiment, the
  • polynucleotide comprising the silencing element is introduced into a plant.
  • Pentatomidae plant pest or N. viridula, Acrosternum hilare, Piezodorus guildini, and/or
  • the silencing element is delivered to the pest.
  • the silencing element can be expressed constitutively or alternatively, it may be produced in a stage-specific manner by employing the various inducible or tissue -preferred or developmentally regulated promoters that are discussed elsewhere herein.
  • the silencing element is operably linked to a seed-preferred promoter.
  • the silencing element expressed in the roots, stalk or stem, leaf including pedicel, xylem and phloem, fruit or reproductive tissue, silk, flowers and all parts therein or any combination thereof.
  • a composition comprising at least one silencing element of the invention is applied to a plant.
  • the silencing element can be formulated in an agronomically suitable and/or environmentally acceptable carrier, which is preferably, suitable for dispersal in fields.
  • the carrier can also include compounds that increase the half life of the composition.
  • the composition comprising the silencing element is formulated in such a manner such that it persists in the environment for a length of time sufficient to allow it to be delivered to a pest.
  • the composition can be applied to an area inhabited by a pest.
  • the composition is applied externally to a plant (i.e., by spraying a field) to protect the plant from pests.
  • the constructs of the present invention can be stacked with any combination of polynucleotide sequences of interest in order to create plants with a desired trait.
  • a trait refers to the phenotype derived from a particular sequence or groups of sequences.
  • the polynucleotides of the present invention may be stacked with any other polynucleotides encoding polypeptides having pesticidal and/or insecticidal activity, such as other Bacillus thuringiensis toxic proteins (described in U.S. Patent Nos. 5,366,892; 5,747,450; 5,737,514; 5,723,756; 5,593,881 ; and Geiser et al.
  • the combinations generated can also include multiple copies of any one of the polynucleotides of interest.
  • the polynucleotides of the present invention can also be stacked with any other gene or combination of genes to produce plants with a variety of desired trait combinations including, but not limited to, traits desirable for animal feed such as high oil genes (e.g., U.S. Patent No. 6,232,529); balanced amino acids (e.g., hordothionins (U.S. Patent Nos.
  • polynucleotides of the present invention can also be stacked with traits desirable for disease or herbicide resistance (e.g., fumonisin detoxification genes (U.S. Patent No. 5,792,931); avirulence and disease resistance genes (Jones et al. (1994) Science 266:789; Martin et al. (1993) Science 262: 1432; Mindrinos et al.
  • diseases or herbicide resistance e.g., fumonisin detoxification genes (U.S. Patent No. 5,792,931)
  • avirulence and disease resistance genes Jones et al. (1994) Science 266:789; Martin et al. (1993) Science 262: 1432; Mindrinos et al.
  • acetolactate synthase (ALS) mutants that lead to herbicide resistance such as the S4 and/or Hra mutations
  • inhibitors of glutamine synthase such as phosphinothricin or basta (e.g., bar gene); and glyphosate resistance (EPSPS gene)
  • traits desirable for processing or process products such as high oil (e.g., U.S. Patent No. 6,232,529 ); modified oils (e.g., fatty acid desaturase genes (U.S. Patent No.
  • modified starches e.g., ADPG pyrophosphorylases (AGPase), starch synthases (SS), starch branching enzymes (SBE), and starch debranching enzymes (SDBE)
  • polymers or bioplastics e.g., U.S. Patent No. 5.602,321 ; beta-ketothiolase, polyhydroxybutyrate synthase, and acetoacetyl-CoA reductase (Schubert et al. (1988) J Bacteriol. 170:5837-5847) facilitate expression of polyhydroxyalkanoates (PHAs)); the disclosures of which are herein incorporated by reference.
  • polynucleotides of the present invention could also combine with polynucleotides providing agronomic traits such as male sterility (e.g., see U.S. Patent No. 5.583,210), stalk strength, flowering time, or transformation technology traits such as cell cycle regulation or gene targeting (e.g., WO 99/61619, WO 00/17364, and WO 99/25821); the disclosures of which are herein incorporated by reference.
  • agronomic traits such as male sterility (e.g., see U.S. Patent No. 5.583,210), stalk strength, flowering time, or transformation technology traits such as cell cycle regulation or gene targeting (e.g., WO 99/61619, WO 00/17364, and WO 99/25821); the disclosures of which are herein incorporated by reference.
  • stacked combinations can be created by any method including, but not limited to, cross-breeding plants by any conventional or TopCross methodology, or genetic transformation. If the sequences are stacked by genetically transforming the plants, the polynucleotide sequences of interest can be combined at any time and in any order. For example, a transgenic plant comprising one or more desired traits can be used as the target to introduce further traits by subsequent transformation. The traits can be introduced simultaneously in a co-transformation protocol with the polynucleotides of interest provided by any combination of transformation cassettes. For example, if two sequences will be introduced, the two sequences can be contained in separate
  • transformation cassettes trans or contained on the same transformation cassette (cis). Expression of the sequences can be driven by the same promoter or by different promoters. In certain cases, it may be desirable to introduce a transformation cassette that will suppress the expression of the polynucleotide of interest. This may be combined with any combination of other suppression cassettes or overexpression cassettes to generate the desired combination of traits in the plant. It is further recognized that polynucleotide sequences can be stacked at a desired genomic location using a site-specific recombination system. See, for example, W099/25821, W099/25854, WO99/25840, W099/25855, and W099/25853, all of which are herein incorporated by reference.
  • the methods and compositions employ a first polynucleotide comprising a silencing element for a target pest sequence operably linked to a promoter active in the plant cell; and, a second polynucleotide comprising a suppressor enhancer element comprising the target pest sequence or an active variant or fragment thereof operably linked to a promoter active in the plant cell.
  • the combined expression of the silencing element with suppressor enhancer element leads to an increased amplification of the inhibitory RNA produced from the silencing element over that achievable with only the expression of the silencing element alone.
  • the methods and compositions further allow for the production of a diverse population of RNAi species that can enhance the effectiveness of disrupting target gene expression.
  • the suppressor enhancer element when expressed in a plant cell in combination with the silencing element, the methods and composition can allow for the systemic production of RNAi throughout the plant; the production of greater amounts of RNAi than would be observed with just the silencing element construct alone; and, the improved loading of RNAi into the phloem of the plant, thus providing better control of phloem feeding insects by an RNAi approach.
  • compositions provide improved methods for the delivery of inhibitory RNA to the target organism. See, for example, U.S. Application No. 12/351,093, entitled “Compositions and Methods for the Suppression of Target Polynucleotides", filed January 9, 2009 and herein incorporated by reference in its entirety.
  • a "suppressor enhancer element” comprises a polynucleotide comprising the target sequence to be suppressed or an active fragment or variant thereof. It is recognize that the suppressor enhancer element need not be identical to the target sequence, but rather, the suppressor enhancer element can comprise a variant of the target sequence, so long as the suppressor enhancer element has sufficient sequence identity to the target sequence to allow for an increased level of the RNAi produced by the silencing element over that achievable with only the expression of the silencing element. Similarly, the suppressor enhancer element can comprise a fragment of the target sequence, wherein the fragment is of sufficient length to allow for an increased level of the RNAi produced by the silencing element over that achievable with only the expression of the silencing element. Thus, in specific embodiments, the suppressor enhancer element comprises a polynucleotide set forth in SEQ ID NO: 1-292, or 302-304 or an active variant or fragment thereof.
  • the suppressor enhancer elements employed can comprise fragments of the target sequence derived from different region of the target sequence (i.e., from the 3'UTR, coding sequence, intron, and/or 5'UTR).
  • the suppressor enhancer element can be contained in an expression cassette, as described elsewhere herein, and in specific embodiments, the suppressor enhancer element is on the same or on a different DNA vector or construct as the silencing element.
  • the suppressor enhancer element can be operably linked to a promoter as disclosed herein. It is recognized that the suppressor enhancer element can be expressed constitutively or alternatively, it may be produced in a stage-specific manner employing the various inducible or tissue-preferred or developmentally regulated promoters that are discussed elsewhere herein.
  • RNAi RNAi-derived RNAi
  • the plant or plant parts of the invention have an improved loading of RNAi into the phloem of the plant than would be observed with the expression of the silencing element construct alone and, thus provide better control of phloem feeding insects by an RNAi approach.
  • the plants, plant parts, and plant cells of the invention can further be characterized as allowing for the production of a diversity of RNAi species that can enhance the effectiveness of disrupting target gene expression.
  • the combined expression of the silencing element and the suppressor enhancer element increases the concentration of the inhibitory RNA in the plant cell, plant, plant part, plant tissue or phloem over the level that is achieved when the silencing element is expressed alone.
  • an "increased level of inhibitory RNA” comprises any statistically significant increase in the level of RNAi produced in a plant having the combined expression when compared to an appropriate control plant.
  • an increase in the level of RNAi in the plant, plant part or the plant cell can comprise at least about a 1%, about a l%-5%, about a 5% -10%, about a 10%-20%, about a 20%-30%, about a 30%- 40%, about a 40%-50%, about a 50%-60%, about 60-70%, about 70%-80%, about a 80%- 90%, about a 90%- 100% or greater increase in the level of RNAi in the plant, plant part, plant cell, or phloem when compared to an appropriate control.
  • the increase in the level of RNAi in the plant, plant part, plant cell, or phloem can comprise at least about a 1 fold, about a 1 fold-5 fold, about a 5 fold -10 fold, about a 10 fold-20 fold, about a 20 fold -30 fold, about a 30 fold -40 fold, about a 40 fold-50 fold, about a 50 fold- 60 fold, about 60 fold -70 fold, about 70 fold-80 fold, about a 80 fold-90 fold, about a 90 fold- 100 fold or greater increase in the level of RNAi in the plant, plant part, plant cell or phloem when compared to an appropriate control.
  • Methods to assay for an increase in the level of RNAi are discussed elsewhere herein. on- limiting examples of methods and compositions disclosed herein are as follows:
  • nucleotide sequence selected from the group consisting of:
  • nucleotide sequence comprising at least 90% sequence identity to any one of SEQ ID NOS: 279, 302, 281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 14, 18, 263, 17, 30, 34, 337, 338, 339, 340, 341, 342, 343, 344, 305, 306, 307, 308, 309, 310, 311, 312, 293, 294, 295, 296, 297, 298, 299, 300, 301, 321, 322, 323, 324, 325, 326, 327 or 328 or a complement thereof, wherein said polynucleotide encodes a silencing element having insecticidal activity against a Pentatomidae plant pest;
  • nucleotide sequence comprising at least 19 consecutive nucleotides of any one of SEQ ID NOS: 279, 302, 281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 17, 30, 34, 14, 18 or 263 or a complement thereof, wherein said polynucleotide encodes a silencing element having insecticidal activity against a
  • An expression cassette comprising a heterologous polynucleotide of embodiment 1 or 2 operably linked to a seed-preferred promoter.
  • said first segment comprises at least about 19 nucleotides having at least 90% sequence complementarity to a target sequence set forth in SEQ ID NOS: 279, 302,
  • said second segment comprises a loop of sufficient length to allow the silencing element to be transcribed as a hairpin RNA
  • said third segment comprises at least about 19 nucleotides having at least
  • target sequence comprises the sequences set forth any one of SEQ ID NOS: 284, 285, 286, 287, 288, 289, 290, 291, 292, 337, 338, 339, 340, 341, 342, 343 or 344 or a sequence having at least 90% sequence identity to SEQ ID NOS: 284, 285, 286, 287, 288, 289, 290, 291, 292, 337, 338, 339, 340, 341, 342, 343 or 344.
  • polynucleotide wherein the first and the second convergent promoters are capable of driving expression of the polynucleotide.
  • a host cell comprising a heterologous expression cassette of any one of embodiments 3-9.
  • a plant cell having stably incorporated into its genome a heterologous
  • polynucleotide comprising a silencing element operably linked to a seed-preferred promoter, wherein said silencing element, when ingested by a Pentatomidae plant pest, reduces the level of expression of any one of the target sequences set forth in SEQ ID NOS: 279, 302, 281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 14, 18, 263, 17, 30, 34, 337, 338, 339, 340, 341, 342, 343, 344, 305, 306, 307, 308, 309, 310, 311, 312, 293, 294, 295, 296, 297, 298, 299, 300, 301, 321, 322, 323, 324, 325, 326, 327 or 328 in said Pentatomidae plant pest and thereby controls the Pentatomidae plant pest.
  • nucleotide sequence comprising at least 90% sequence identity to any one of SEQ ID NOS: 279, 302, 281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 14, 18, 263, 17, 30, 34, 337, 338, 339, 340, 341, 342, 343, 344, 305, 306, 307, 308, 309, 310, 311, 312, 293, 294, 295, 296, 297, 298, 299, 300, 301, 321, 322, 323, 324, 325, 326, 327 or 328 or a complement thereof,
  • said silencing element when ingested by a Pentatomidae plant pest, reduces the level of a target sequence in said Pentatomidae plant pest and thereby controls the Pentatomidae plant pest.
  • silencing element comprises the sequences set forth in any one of SEQ ID NOS: 284, 285, 286, 287, 288, 289, 290, 291, 292, 305, 306, 307, 308, 309, 310, 311, 312, 17, 30, 34, 337, 338, 339, 340, 341, 342, 343 or 344 or a complement thereof.
  • polynucleotide comprising the silencing element comprises, in the following order, a first segment, a second segment, and a third segment, wherein
  • said first segment comprises at least about 19 nucleotides having at least 90% sequence complementarity to a target sequence set forth in SEQ ID NOS: 279, 302, 281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 14, 18, 263, 17, 30, 34, 337, 338, 339, 340, 341, 342, 343, 344, 305, 306, 307, 308, 309, 310, 31 1, 312, 293, 294, 295, 296, 297, 298, 299, 300, 301, 321, 322, 323, 324, 325, 326, 327 or 328;
  • said second segment comprises a loop of sufficient length to allow the silencing element to be transcribed as a hairpin RNA
  • said third segment comprises at least about 19 nucleotides having at least 85% complementarity to the first segment.
  • a plant or plant part comprising a plant cell of any one of embodiments 11-22.
  • a method of controlling a Pentatomidae plant pest comprising feeding to a Pentatomidae plant pest a composition comprising a silencing element, wherein said silencing element, when ingested by said Pentatomidae plant pest, reduces the level of expression of any one of the target Pentatomidae plant pest sequences set forth in SEQ ID NOS: 279, 302, 281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 17, 30, 34, 14, 18 or 263 and thereby controls the Pentatomidae plant pest.
  • nucleotide sequence comprising at least 90% sequence identity to any one of SEQ ID NOS: 279, 302, 281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 14, 18, 263, 17, 30, 34, 337, 338, 339, 340, 341, 342, 343, 344, 305, 306, 307, 308, 309, 310, 311, 312, 293, 294, 295, 296, 297, 298, 299, 300, 301, 321, 322, 323, 324, 325, 326, 327 or 328 or a complement thereof, wherein said silencing element, when ingested by a Pentatomidae plant pest, reduces the level of a target sequence in said Pentatomidae plant pest and thereby controls the Pentatomidae plant pest.
  • silencing element comprises the sequence set forth in any one of SEQ ID NOS: 284, 285, 286, 287, 288, 289, 290, 291, 292, 305, 306, 307, 308, 309, 310, 31 1, 312, 17, 30, 34, 337, 338, 339, 340, 341, 342, 343 or 344 or a complement thereof.
  • composition comprises a plant or plant part having stably incorporated into its genome a polynucleotide comprising said silencing element, wherein said silencing element is operably linked to a seed-preferred promoter.
  • a polynucleotide comprising the sense or antisense sequence of the sequence set forth in SEQ ID NOS: 284, 285, 286, 287, 288, 289, 290, 291, 292, 17, 30, 34, 14, 18, 263, 337, 338, 339, 340, 341, 342, 343, 344, 305, 306, 307, 308, 309, 310, 31 1 or 312 or a complement thereof; or,
  • a polynucleotide comprising the sense or antisense sequence of a sequence having at least 95% sequence identity to the sequence set forth in SEQ ID NOS: 284, 285, 286, 287, 288, 289, 290, 291, 292, 17, 30, 34, 14, 18, 263, 337, 338, 339, 340, 341, 342, 343, 344, 305, 306, 307, 308, 309, 310, 31 1 or 312 or a complement thereof;
  • polynucleotide comprising the silencing element comprises, in the following order, a first segment, a second segment, and a third segment, wherein
  • said first segment comprises at least about 20 nucleotides having at least 90%) sequence complementarity to the target polynucleotide
  • said second segment comprises a loop of sufficient length to allow the silencing element to be transcribed as a hairpin RNA; and, c) said third segment comprises at least about 20 nucleotides having at least 85% complementarity to the first segment.
  • silencing element is flanked by a first operably linked convergent promoter at one terminus of the silencing element and a second operably linked convergent promoter at the opposing terminus of the polynucleotide, wherein the first and the second convergent promoters are capable of driving expression of the silencing element.
  • Example 1 In vitro transcription dsRNA screening method
  • RNAi insecticidal activity of RNAi.
  • a library of over 1000 expressed sequence tags was subjected to in vitro transcription and individual samples tested against 2nd instar nymphs of N. viriduia.
  • Table 1 provides the blast homology (Gene ID) of the various silencing elements (clone name) disclosed herein and also provides bioassay data demonstrating the insecticidal activity of the various sequences when fed to N. viriduia. Table 1.
  • Samples for dose response assays is produced in the same manner with the following modification; samples is further purified using column purification prior to enzymatic treatment. Samples is also normalized to 0.5ug/ul and all samples are evaluated by gel electrophoresis. Dose response assays is performed with the following rates; 50, 25, 12, 6, 3, and 1.5 ppm
  • DNA sequences which encode double stranded RNAs which were shown to have insecticidal activity against N. viridula using the assay described in Example 1 are set forth in SEQ ID NOS: 1-139.
  • Immature maize embryos from greenhouse donor plants are bombarded with a plasmid containing the silencing element of the invention operably linked to either a tissue specific, tissue selective, or constitutive promoter and the selectable marker gene PAT (Wohlleben et al. (1988) Gene 70:25-37), which confers resistance to the herbicide Bialaphos.
  • the promoter employed is a seed-preferred promoter.
  • the constructs will express a long double stranded RNA or a miRNA of the target sequence set forth in SEQ ID NOS: 1-292 or 302-304 or a fragment thereof.
  • the target sequence comprises the sequences set forth in SEQ ID NOS: 278, 279, 280, 281, 282, 283, 302, 303 or 304.
  • Such a construct can be linked to a promoter active in maize.
  • the selectable marker gene is provided on a separate plasmid. Transformation is performed as follows. Media recipes follow below. Preparation of Target Tissue
  • the ears are husked and surface sterilized in 30% Clorox bleach plus 0.5% Micro detergent for 20 minutes, and rinsed two times with sterile water.
  • the immature embryos are excised and placed embryo axis side down (scutellum side up), 25 embryos per plate, on 560Y medium for 4 hours and then aligned within the 2.5cm target zone in preparation for bombardment.
  • a plasmid vector comprising the silencing element of interest operably linked to either the tissue specific, tissue selective, or constitutive promoter is made.
  • This plasmid DNA plus plasmid DNA containing a PAT selectable marker is precipitated onto 1.1 ⁇ (average diameter) tungsten pellets using a CaCl 2 precipitation procedure as follows: 100 ⁇ prepared tungsten particles in water; 10 ⁇ (1 ⁇ g) DNA in Tris EDTA buffer (1 ⁇ g total DNA); 100 ⁇ 2.5 M CaCl 2 ; and, 10 ⁇ 0.1 M spermidine.
  • Each reagent is added sequentially to the tungsten particle suspension, while maintained on the multitube vortexer.
  • the final mixture is sonicated briefly and allowed to incubate under constant vortexing for 10 minutes.
  • the tubes are centrifuged briefly, liquid removed, washed with 500 ml 100% ethanol, and centrifuged for 30 seconds. Again the liquid is removed, and 105 ⁇ 100% ethanol is added to the final tungsten particle pellet.
  • tungsten/DNA particles are briefly sonicated and 10 ⁇ spotted onto the center of each macrocarrier and allowed to dry about 2 minutes before bombardment.
  • sample plates are bombarded at level #4 in a particle gun. All samples receive a single shot at 650 PSI, with a total often aliquots taken from each tube of prepared particles/DNA.
  • the embryos are kept on 560Y medium for 2 days, then transferred to 560R selection medium containing 3 mg/liter Bialaphos, and subcultured every 2 weeks. After approximately 10 weeks of selection, selection-resistant callus clones are transferred to 288J medium to initiate plant regeneration. Following somatic embryo maturation (2-4 weeks), well-developed somatic embryos are transferred to medium for germination and transferred to the lighted culture room. Approximately 7-10 days later, developing plantlets are transferred to 272V hormone-free medium in tubes for 7-10 days until plantlets are well established.
  • Plants are then transferred to inserts in flats (equivalent to 2.5" pot) containing potting soil and grown for 1 week in a growth chamber, subsequently grown an additional 1-2 weeks in the greenhouse, then transferred to classic 600 pots (1.6 gallon) and grown to maturity.
  • Plants are monitored and scored for the appropriate marker, such as the control of a Pentatomidae plant pest, such as a N. viridula plant pest.
  • a Pentatomidae plant pest such as a N. viridula plant pest.
  • Ro maize plants are fed to N. viridula 2nd instar nymphs. Contamination and larval quality are monitored. Larval mass and survivorship are recorded for analysis. A one-way ANOVA analysis and a Dunnett's test is performed on the larval mass data to look for statistical significance compared to an untransformed negative control maize plant diet.
  • N. viriduia 2 nd instar nymph stunting is measured after feeding on two events and compared to growth of larvae fed on negative control plants.
  • transgenic corn plants (Ro) generated are planted into 10-inch pots containing Metromix soil after reaching an appropriate size. After allowing the N. viriduia 2 nd instar nymphs to feed on the plant, plants are removed from the soil and washed so that the relevant plant parts can be evaluated for larval feeding. Plant damage is rated using routine methods to score the level of damage.
  • Bombardment medium comprises 4.0 g/1 N6 basal salts (SIGMA C-1416), 1.0 ml/1 Eriksson's Vitamin Mix (1000X SIGMA- 1511), 0.5 mg/1 thiamine HC1, 120.0 g/1 sucrose, 1.0 mg/1 2,4-D, and 2.88 g/1 L-proline (brought to volume with D-I H 2 0 following adjustment to pH 5.8 with KOH); 2.0 g/1 Gelrite (added after bringing to volume with D-I 3 ⁇ 40); and 8.5 mg/1 silver nitrate (added after sterilizing the medium and cooling to room temperature).
  • Selection medium comprises 4.0 g/1 N6 basal salts (SIGMA C-1416), 1.0 ml/1 Eriksson's Vitamin Mix (1000X SIGMA- 1511), 0.5 mg/1 thiamine HC1, 30.0 g/1 sucrose, and 2.0 mg/1 2,4-D (brought to volume with D-I H 2 0 following adjustment to pH 5.8 with KOH); 3.0 g/1 Gelrite (added after bringing to volume with D-I H 2 0); and 0.85 mg/1 silver nitrate and 3.0 mg/1 bialaphos (both added after sterilizing the medium and cooling to room temperature).
  • Plant regeneration medium (288J) comprises 4.3 g/1 MS salts (GIBCO 11 117-074), 5.0 ml/1 MS vitamins stock solution (0.100 g nicotinic acid, 0.02 g/1 thiamine HC1, 0.10 g/1 pyridoxine HC1, and 0.40 g/1 glycine brought to volume with polished D-I H 2 0)
  • Hormone-free medium comprises 4.3 gfl MS salts (GIBCO 11 117-074), 5.0 ml/1 MS vitamins stock solution (0.100 g/1 nicotinic acid, 0.02 g/1 thiamine HC1, 0.10 g/1 pyridoxine HC1, and 0.40 g/1 glycine brought to volume with polished D-I H 2 0), 0.1 g/1 myo-inositol, and 40.0 g/1 sucrose (brought to volume with polished D-I H 2 0 after adjusting pH to 5.6); and 6 g/1 bacto-agar (added after bringing to volume with polished D-I H 2 0), sterilized and cooled to 60°C.
  • Example 4 Agrobacterium-mQdiatQd Transformation of Maize
  • Such a construct can, for example, express a long double stranded RNA or a miRNA of the target sequence set forth in SEQ ID NOS: 1-292 or 302-304.
  • the promoter employed is a seed-preferred promoter.
  • the target sequence comprises the sequence set forth in SEQ ID NOS: 278, 279, 280, 281, 282, 283, 302, 303 or 304.
  • Such a construct can be linked to the dMMB promoter.
  • immature embryos are isolated from maize and the embryos contacted with a suspension of Agrobacterium, where the bacteria are capable of transferring the polynucleotide comprising the silencing element to at least one cell of at least one of the immature embryos (step 1 : the infection step).
  • the immature embryos are immersed in an Agrobacterium suspension for the initiation of inoculation.
  • the embryos are co-cultured for a time with the Agrobacterium (step 2: the co-cultivation step).
  • the immature embryos are cultured on solid medium following the infection step. Following this co- cultivation period an optional "resting" step is contemplated.
  • step 3 resting step.
  • the immature embryos are cultured on solid medium with antibiotic, but without a selecting agent, for elimination of Agrobacterium and for a resting phase for the infected cells.
  • step 4 the selection step.
  • the immature embryos are cultured on solid medium with a selective agent resulting in the selective growth of transformed cells.
  • step 5 the regeneration step
  • calli grown on selective medium are cultured on solid medium to regenerate the plants.
  • Assays for insecticidal activity can be performed as described above in Example 3.
  • Example 5 Soybean Embryo Transformation
  • Soybean embryogenic suspension cultures (cv. Jack) are maintained in 35 ml liquid medium SB 196 (see recipes below) on rotary shaker, 150 rpm, 26°C with cool white fluorescent lights on 16:8 hr day/night photoperiod at light intensity of
  • Cultures are subcultured every 7 days to two weeks by inoculating approximately 35 mg of tissue into 35 ml of fresh liquid SB196 (the preferred subculture interval is every 7 days).
  • Soybean embryogenic suspension cultures are transformed with a plasmid containing the silencing element of the invention operably linked to either a tissue specific, tissue selective, or constitutive promoter by the method of particle gun bombardment (Klein et al. (1987) Nature, 327:70).
  • the promoter employed is a seed-preferred promoter.
  • the constructs will express a long double stranded RNA or a miRNA of the target sequence set forth in SEQ ID NOS: 1-292 or 302-304 or a fragment thereof.
  • the target sequence comprises the sequences set forth in SEQ ID NOS: 278, 279, 280, 281, 282, 283, 302, 303 or 304. Soybean Embryogenic Suspension Culture Initiation
  • Soybean cultures are initiated twice each month with 5-7 days between each initiation.
  • soybeans with immature seeds from available soybean plants 45-55 days after planting are picked, removed from their shells and placed into a sterilized magenta box.
  • the soybean seeds are sterilized by shaking them for 15 minutes in a 5% Clorox solution with 1 drop of ivory soap (95 ml of autoclaved distilled water plus 5 ml Clorox and 1 drop of soap). Mix well.
  • Seeds are rinsed using 2 1 -liter bottles of sterile distilled water and those less than 4 mm are placed on individual microscope slides. The small end of the seed are cut and the cotyledons pressed out of the seed coat. Cotyledons are transferred to plates containing SB1 medium (25-30 cotyledons per plate). Plates are wrapped with fiber tape and stored for 8 weeks. After this time secondary embryos are cut and placed into SB 196 liquid media for 7 days.
  • Plasmid DNA for plasmid Either an intact plasmid or a DNA plasmid fragment containing the genes of interest and the selectable marker gene are used for bombardment. Plasmid DNA for
  • fragments of the plasmids carrying the silencing element of interest are obtained by gel isolation of double digested plasmids. In each case, 100 ug of plasmid DNA is digested in 0.5 ml of the specific enzyme mix that is appropriate for the plasmid of interest. The resulting DNA fragments are separated by gel electrophoresis on 1% SeaPlaque GTG agarose
  • DNA fragments containing silencing element of interest are cut from the agarose gel.
  • DNA is purified from the agarose using the GELase digesting enzyme following the manufacturer's protocol.
  • a 50 ⁇ aliquot of sterile distilled water containing 3 mg of gold particles (3 mg gold) is added to 5 ⁇ of a 1 DNA solution (either intact plasmid or DNA fragment prepared as described above), 50 ⁇ 2.5M CaCl2 and 20 ⁇ of 0.1 M spermidine.
  • the mixture is shaken 3 min on level 3 of a vortex shaker and spun for 10 sec in a bench microfuge. After a wash with 400 ⁇ 100% ethanol the pellet is suspended by sonication in 40 ⁇ of 100% ethanol.
  • Five ⁇ of DNA suspension is dispensed to each flying disk of the Biolistic PDS1000/HE instrument disk. Each 5 ⁇ aliquot contains approximately 0.375 mg gold per bombardment (i.e. per disk).
  • Tissue is bombarded 1 or 2 shots per plate with membrane rupture pressure set at 1100 PSI and the chamber evacuated to a vacuum of 27-28 inches of mercury. Tissue is placed approximately 3.5 inches from the retaining / stopping screen.
  • Transformed embryos were selected either using hygromycin (when the hygromycin phosphotransferase, HPT, gene was used as the selectable marker) or chlorsulfuron (when the acetolactate synthase, ALS, gene was used as the selectable marker).
  • HPT Hygromycin
  • the tissue is placed into fresh SB 196 media and cultured as described above.
  • the SB 196 is exchanged with fresh SB 196 containing a selection agent of 30 mg/L hygromycin.
  • the selection media is refreshed weekly.
  • green, transformed tissue may be observed growing from untransformed, necrotic embryogenic clusters. Isolated, green tissue is removed and inoculated into multiwell plates to generate new, clonally propagated, transformed embryogenic suspension cultures.
  • the tissue is divided between 2 flasks with fresh SB 196 media and cultured as described above.
  • the SB 196 is exchanged with fresh SB196 containing selection agent of 100 ng/ml Chlorsulfuron.
  • the selection media is refreshed weekly.
  • green, transformed tissue may be observed growing from untransformed, necrotic embryogenic clusters. Isolated, green tissue is removed and inoculated into multiwell plates containing SB 196 to generate new, clonally propagated, transformed embryogenic suspension cultures.
  • the tissue In order to obtain whole plants from embryogenic suspension cultures, the tissue must be regenerated.
  • Embryos are cultured for 4-6 weeks at 26°C in SB 196 under cool white fluorescent (Phillips cool white Econowatt F40/CW/RS/EW) and Agro (Phillips F40 Agro) bulbs (40 watt) on a 16:8 hr photoperiod with light intensity of 90-120 uE/m2s. After this time embryo clusters are removed to a solid agar media, SB 166, for 1-2 weeks. Clusters are then subcultured to medium SB 103 for 3 weeks. During this period, individual embryos can be removed from the clusters and screened for the appropriate marker or the ability of the plant, when injected with the silencing elements, to control the Pentatomidae plant pest or the N. viridufa plant pest. Embryo Desiccation and Germination
  • Matured individual embryos are desiccated by placing them into an empty, small petri dish (35 x 10 mm) for approximately 4-7 days. The plates are sealed with fiber tape (creating a small humidity chamber). Desiccated embryos are planted into SB71-4 medium where they were left to germinate under the same culture conditions described above. Germinated plantlets are removed from germination medium and rinsed thoroughly with water and then planted in Redi-Earth in 24-cell pack tray, covered with clear plastic dome. After 2 weeks the dome is removed and plants hardened off for a further week. If plantlets looked hardy they are transplanted to 10" pot of Redi-Earth with up to 3 plantlets per pot.
  • SB 1 solid medium (per liter) comprises: 1 pkg. MS salts (Gibco/ BRL - Cat# 111 17-066); 1 ml B5 vitamins 1000X stock; 31.5 g sucrose; 2 ml 2,4-D (20mg/L final concentration); pH 5.7; and, 8 g TC agar.
  • SB 166 solid medium (per liter) comprises: 1 pkg. MS salts (Gibco/ BRL - Cat# 111 17-066); 1 ml B5 vitamins 1000X stock; 60 g maltose; 750 mg MgC12 hexahydrate; 5 g activated charcoal; pH 5.7; and, 2 g gelrite.
  • SB 103 solid medium (per liter) comprises: 1 pkg.
  • MS salts (Gibco/BRL - Cat#
  • SB 71-4 solid medium (per liter) comprises: 1 bottle Gamborg's B5 salts w/ sucrose (Gibco/BRL - Cat# 21153-036); pH 5.7; and, 5 g TC agar.
  • 2,4-D stock is obtained premade from Phytotech cat# D 295 - concentration is 1 mg/ml.
  • B5 Vitamins Stock (per 100 ml) which is stored in aliquots at -20C comprises: 10 g myo-inositol; 100 mg nicotinic acid; 100 mg pyridoxine HC1; and, 1 g thiamine. If the solution does not dissolve quickly enough, apply a low level of heat via the hot stir plate.
  • Chlorsulfuron Stock comprises lmg / ml in 0.01 N Ammonium Hydroxide Example 6.
  • SiR As were generated to target the cDNA sequence set forth in SEQ ID NOS: 140, 143, 146, 149, 152, 155, 158, 161, 164, 167, 170, 173, 176, 179, 182, 185, 188, 191, 194, 197, 200, 203, 206, 209, 212, 215, 218, 221, 224, 227, 230, 233, 236, 239, 242, 245, 248, 251, 254, 257, 260, 263, 266, 269, 273, and 276.
  • Table 2 provides the clone name of the silencing element and the closest homology for the target sequence (gene name).
  • Table 3 provides the clone name, the target cDNA, the sense and antisense siRNA sequence, and the respective SEQ ID NOS.
  • Table 4 provides the bioassays for each of the siRNAs shown in Table 3.
  • the construct can comprise, for example, the maize ubiquitin promoter/5 'UTR/ 1 st intron operably linked to a sequence comprising SEQ ID NO: 141 which is operably linked to the ADHl intron followed by the sequence comprising SEQ ID NO: 142. It is recognized that any of the siRNA described in Example 6 can be generated employing a simlar construct design.
  • Hairpin constructs for in vivo expression and testing of dsRNAs were assembled via Gateway technology using procedures and practices well known to those skilled in the art of molecular biology.
  • Target gene fragments were generated by PCR using gene specific sense and antisense primers containing Gateway attB4
  • the former destination vector contains the 193 bp intron2 fragment of the potato LSI gene flanked by attR4-R3 sites at the 5' end and attR3-R4 sites at the 3' end.
  • LR recombination yields a hairpin segment comprised of sense and antisense target gene fragments separated by an intron loop.
  • promoter sequences upstream and termination sequences downstream, of the hairpin segment are provided by a 1946 bp soybean ubiquitin promoter-5' UTR-Intronl fragment and termination sequences are provided by an 888bp 3 ' fragment of the Arabidopsis ubiquitinlO gene.
  • Other promoter sequences providing constitutive or appropriate tissue specific expression may additionally be used.
  • the final plant expression construct is produced by a second LR reaction in which the entire hairpin cassette is moved into a vector (PHP25224) which provides a plant selectable marker (herbicide resistant acetolactate synthase gene) for stable
  • siRNAs artificial microRNAs
  • amiRNA have a high free delta-G as calculated using the ZipFold algorithm (Markham, N. R. & Zuker, M. (2005) Nucleic Acids Res. 33: W577-W581.)
  • a one base pair change was added to the 5' portion of the amiRNA so that the sequence differed from the target sequence by one nucleotide.
  • the amiRNAs that were used to silence SGSB genes are given in Table 6. Table 6: amiRNA Sequences
  • Target amiRNA amiRNA precursor GENE ID SEQ amiRNA Sequence SEQ ID NO: 1
  • Star sequences are those that base pair with the amiRNA sequences in the precursor RNA, to form imperfect stem structures. To form a perfect stem structure the star sequence would be the exact reverse complement of the amiRNA.
  • the soybean genomic miRNA precursor gene, miR159 was converted to amiRNA precursors by DNA synthesis (Genscript; Piscataway, NJ). DNA fragments were synthesized with flanking Avrll and Hpal sites and were cloned by restriction enzyme digestion followed by DNA ligation downstream of the GmUbiquitin promoter-5'UTR- Intronl fragment in the UBQ-Kozack OXOXalt7 vector. LR recombination reaction between this intermediate and the vector QC479i produced the eight final plant expression constructs given in Table 8.
  • Soybean embryogenic suspension cultures (cv. Jack) were maintained in 35 mL liquid medium SB 196 (infra) on a rotary shaker, 150 rpm, 26 °C with cool white fluorescent lights on 16:8 hr day/night photoperiod at light intensity of 60-85 uE/m2/s. Cultures were sub-cultured every 7 days to two weeks by inoculating approximately 35 mg of tissue into 35 mL of fresh liquid SB 196 (the preferred subculture interval is every 7 days).
  • Soybean embryogenic suspension cultures were transformed with the soybean expression plasmids described in Example 8 by the method of particle gun bombardment (Klein et al., Nature, 327:70 (1987)) using a DuPont Biolistic PDS1000/HE instrument (helium retrofit) for all transformations.
  • Soybean cultures were initiated twice each month with 5-7 days between each initiation. Pods with immature seeds from available soybean plants 45-55 days after planting were picked, removed from their shells and placed into a sterilized magenta box. The soybean seeds were sterilized by shaking them for 15 min in a 5% Clorox solution with 1 drop of ivory soap (i.e., 95 mL of autoc laved distilled water plus 5 mL Clorox and 1 drop of soap, mixed well). Seeds were rinsed using 2 1 -liter bottles of sterile distilled water and those less than 4 mm were placed on individual microscope slides. The small end of the seed was cut and the cotyledons pressed out of the seed coat.
  • Cotyledons were transferred to plates containing SB 199 medium (25-30 cotyledons per plate) for 2 weeks, then transferred to SB1 for 2-4 weeks. Plates were wrapped with fiber tape. After this time secondary embryos were cut and placed into SB 196 liquid media for 7 days.
  • Either an intact plasmid or a DNA plasmid fragment containing the genes of interest and the selectable marker gene may be used for bombardment.
  • pDNAs were isolated from bacterial transformants using a Qiagen mini-prep kit. DNA concentrations were determined by UV absorbance. Each silencing construct and hygromycin selectable marker plasmid (PHP 18956) were combined in a 9: 1 weight ratio to give a 1 ug/ul DNA solution.
  • Transformed embryos were selected using hygromycin as the selectable marker. Specifically, following bombardment, the tissue was placed into fresh SB 196 media and cultured as described above. Six to eight days post-bombardment, the SB 196 is exchanged with fresh SB 196 containing 30 mg/L hygromycin. The selection media was refreshed bi-weekly. Four to six weeks post-selection, green, transformed tissue was observed growing from untransformed, necrotic embryogenic clusters. Isolated, green tissue was removed and inoculated into multi-well plates to generate new, clonally propagated, transformed embryogenic suspension cultures.
  • Transformed embryogenic clusters were cultured for 1-3 weeks at 26 °C in SB 196 under cool white fluorescent (Phillips cool white Econowatt F40/CW/RS/EW) and Agro (Phillips F40 Agro) bulbs (40 watt) on a 16:8 hr photoperiod with light intensity of 90-120 ⁇ /m s. Embryo clusters were then removed to SB228 (SHaM) liquid media, 35 ml in 250ml Erlenmeyer flask, for 2-3 weeks.
  • SB228 SB228
  • Tissue cultured in SB228 was maintained on a rotary shaker, 130 rpm, 26°C with cool white fluorescent lights on 16:8 hr day/night photoperiod at light intensity of 60-85 uE/m2/s. After this time, embryos were harvested and used in stinkbug feeding assays.
  • Bottle(s) should be wrapped in foil to omit light.
  • experiments set forth in example 9 can be employed with silencing elements operably linked to a seed-preferred promoter, such as, for example, those provided by the b-conglycinin-alpha (Genbank accession GU723691), Kunitz trypsin inhibitor 3 (AF233296), or the glycinin-1 (AB353075.1) genes.
  • a seed-preferred promoter such as, for example, those provided by the b-conglycinin-alpha (Genbank accession GU723691), Kunitz trypsin inhibitor 3 (AF233296), or the glycinin-1 (AB353075.1) genes.
  • Figures 1 and 2 show the results of insect feeding assays performed using embryo tissue transformed with the silencing construct DNAs listed in Tables 5 and 8. Each symbol corresponds to insect mortality scores averaged over the 4 replicate assays for each event. Controls correspond to feeding assays conducted using non-trans genie soybean embryo tissue. For all of the constructs, several transgenic events could be found which gave insect mortality scores greater than the controls. For some constructs, more than 50% of the events produced insect mortality at a rate significantly greater than controls. Variation in apparent efficacy from event to event is to be expected due to variation in construct expression with random integration of the construct DNA in the soybean genome.
  • Example 11 Assay of Transgenic Soybean Plants for Efficacy against
  • Silencing constructs can be stably expressed in insect feeding tissue for efficacy testing of transgenic plants against southern green stinkbug.
  • the DNA constructs described in Example 8 can be used for this purpose. These consist of trait gene hairpin or miRNA gene cassettes both of which are constitutively regulated by a soybean ubiquitin promoter-5'UTR-Intronl fragment. Similar constructs can be built using other constitutive promoters as provided for example by soybean elongation factor 1 alpha (ACUPO 1009998) or arabidopsis ubiquitin (L05399.1) genes.
  • tissue specific expression and in some embodiments seed-preferred promoters can be produced by the use of seed storage protein promoters including those provided by the beta- conglycinin-alpha (Genbank accession GU723691), Kunitz trypsin inhibitor 3
  • entry clones generated as described in Example 8 above, are combined in an LR clonase reaction with a variant of the destination vector, pKB499, modified to contain a seed storage protein promoter in place of the Gm-Ubiquitin promoter. This first LR reaction generates the promoter- hairpin-terminator cassette.
  • the final plant expression construct is produced by a second LR reaction in which the entire hairpin cassette is moved into a vector (PHP25224) which provides a plant selectable marker gene (herbicide resistant acetolactate synthase) for stable transformation experiments.
  • a vector PGP25224
  • plant selectable marker gene herbicide resistant acetolactate synthase
  • a single DNA fragment containing both the trait gene and the plant selectable marker gene is prepared by restriction enzyme digestion followed by gel purification of restricted pDNA.
  • 10 ⁇ g of plasmid DNA is used in 0.15 mL of the specific enzyme mix described below. Plasmids are digested with Ascl (100 units) in NEBuffer 4 (20 mM Tris-acetate, 10 mM magnesium acetate, 50 mM potassium acetate, 1 mM dithiothreitol, pH 7.9), 100 ⁇ . BSA, and 5 mM beta-mercaptoethanol at 37 °C for 3 hrs.
  • DNA fragments are separated by gel electrophoresis on 1% agarose gel and the DNA fragment containing the trait gene- selectable marker gene cassettes are cut from the agarose gel.
  • DNA is purified from the agarose using Qiagen's Quick Spin extraction method following the manufacturer's suggested protocol. Gold particles are coated with purified DNA fragments and used for biolistic introduction of DNA into soybean embryo cultures using the procedure outlined in Example 5.
  • First generation transgenic plants can be assayed for insecticidal activity in individual plant cages.
  • plants When the plant has started to produce green pods approximately 1- 2 inches in length, plants are removed to individual bug tent cages (BioQuip, CA). The cage is infested with 50 newly emerged second instar southern green stinkbugs (Nezara viridula). The nymphs are allowed to feed for 1 week at which time a count of surviving insects is performed.
  • Counts are facilitated by using an aspirating device with removable vials and caps to collect insects and a hand held counting device to count each insect as it is aspirated. Counts can later be verified by freezing the sample and counting again under magnification where a measure of growth can also be performed on collected insects.

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Abstract

Methods and compositions are provided which employ a silencing element that, when ingested by a pest, such as a Pentatomidae plant pest or a N. viridula, Acrosternum hilare, Piezodorus guildini, and/or Halymorpha halys plant pest, decrease the expression of a target sequence in the pest. In specific embodiments, the decrease in expression of the target sequence controls the pest and thereby the methods and compositions are capable of limiting damage to a plant. The present invention provides various target polynucleotides set forth in any one of SEQ ID NOS: 1-292 or 302-304 or active variants and fragments thereof, wherein a decrease in expression of one or more the sequences in the target pest controls the pest (i.e., has insecticidal activity). Further provided are silencing elements which when ingested by the pest decrease the level of the target polypeptide and thereby control the pest. In specific embodiment, the pest is Pentatomidae. Plants, plant part, bacteria and other host cells comprising the silencing elements or an active variant or fragment thereof of the invention are also provided.

Description

COMPOSITIONS AND METHODS
FOR INSECTICIDAL CONTROL OF STINKBUGS
REFERENCE TO A SEQUENCE LISTING SUBMITTED AS A TEXT FILE VIA EFS-WEB
The official copy of the sequence listing is submitted concurrently with the specification as a text file via EFS-Web, in compliance with the American Standard Code for Information Interchange (ASCII), with a file name of 403168SEQLIST.txt, a creation date of June 2, 2011 and a size of 195 KB. The sequence listing filed via EFS-Web is part of the specification and is hereby incorporated in its entirety by reference herein. FIELD OF THE INVENTION
The present invention relates generally to methods of molecular biology and gene silencing to control pests.
BACKGROUND OF THE INVENTION
Insect pests are a serious problem in agriculture. They destroy millions of acres of staple crops such as corn, soybeans, peas, and cotton. Yearly, these pests cause over $100 billion dollars in crop damage in the U.S. alone. In an ongoing seasonal battle, farmers must apply billions of gallons of synthetic pesticides to combat these pests. Other methods employed in the past delivered insecticidal activity by microorganisms or genes derived from microorganisms expressed in transgenic plants. For example, certain species of microorganisms of the genus Bacillus are known to possess pesticidal activity against a broad range of insect pests including Lepidoptera, Diptera, Coleoptera, Hemiptera, and others. In fact, microbial pesticides, particularly those obtained from Bacillus strains, have played an important role in agriculture as alternatives to chemical pest control. Agricultural scientists have developed crop plants with enhanced insect resistance by genetically engineering crop plants to produce insecticidal proteins from Bacillus. For example, corn and cotton plants genetically engineered to produce Cry toxins (see, e.g., Aronson (2002) Cell Mol. Life Sci. 59(3):417-425; Schnepf et al. (1998) Microbiol. Mol. Biol. Rev. 62(3):775-806) are now widely used in American agriculture and have provided the farmer with an alternative to traditional insect-control methods. However, these Bt insecticidal proteins only protect plants from a relatively narrow range of pests.
Moreover, these modes of insecticidal activity provided varying levels of specificity and, in some cases, caused significant environmental consequences.
Previous control of stinkbugs relied on broad spectrum insecticides. With the adoption of transgenic controls for major lepidopteran pests in several crops, these insecticides are no longer used and stinkbugs have become a major secondary pest. No successful use of transgenic control of stinkbugs has been described or adopted. This may be due in part to the extra oral digestion employed by stinkbugs where digestive enzymes are injected into the host plant prior to feeding. This makes it difficult to find proteins that survive long enough to manifest activity against these insects. RNAi may overcome that feeding behavior by relying on double stranded RNAs rather than proteins. Thus, there is an immediate need for alternative methods to control pests.
BRIEF SUMMARY OF THE INVENTION
Methods and compositions are provided which employ a silencing element that, when ingested by a pest, such as a Pentatomidae plant pest including for example, a N. viridula (southern green stink bug), Acrosternum hilare (green stinkbug), Piezodorus guildini (redbanded stinkbug), and/or Halymorpha halys (Brown marmorated stinkbug). plant pest, is capable of decreasing the expression of a target sequence in the pest. In specific embodiments, the decrease in expression of the target sequence controls the pest and thereby the methods and compositions are capable of limiting damage to a plant. The present invention provides various target polynucleotides as set forth in SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 11 1, 1 12, 113, 1 14, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172,
173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 302, 303 or 304 or active variants or fragments thereof, wherein a decrease in expression of one or more the sequences in the target pest controls the pest (i.e., has insecticidal activity). Further provided are silencing elements, which when ingested by the pest, decrease the level of expression of one or more of the target polynucleotides. Plants, plant parts, plant cells, bacteria and other host cells comprising the silencing elements or an active variant or fragment thereof are also provided.
In another embodiment, a method for controlling a pest, such as a Pentatomidae plant pest, such as, for example, a N. viridula, Acrosternum hilare, Piezodorus guildini, and/or Halvmorpha halys plant pest, is provided. The method comprises feeding to a pest a composition comprising a silencing element, wherein the silencing element, when ingested by the pest, reduces the level of a target sequence in the pest and thereby controls the pest. Further provided are methods to protect a plant from a pest. Such methods comprise introducing into the plant or plant part a silencing element of the invention. When the plant expressing the silencing element is ingested by the pest, the level of the target sequence is decreased and the pest is controlled.
BRIEF DESCRIPTION OF THE DRAWINGS
Figure 1 shows the Southern Green Stinkbug feeding assay results with soybean embryo tissue transformed with hairpin RNA silencing contracts.
Figure 2 shows the Southern Green Stinkbug feeding assay results with soybean embryo tissue transformed with amiRNA silencing constructs.
DETAILED DESCRIPTION OF THE INVENTION
The present inventions now will be described more fully hereinafter with reference to the accompanying drawings, in which some, but not all embodiments of the inventions are shown. Indeed, these inventions may be embodied in many different forms and should not be construed as limited to the embodiments set forth herein; rather, these embodiments are provided so that this disclosure will satisfy applicable legal requirements. Like numbers refer to like elements throughout.
Many modifications and other embodiments of the inventions set forth herein will come to mind to one skilled in the art to which these inventions pertain having the benefit of the teachings presented in the foregoing descriptions and the associated drawings. Therefore, it is to be understood that the inventions are not to be limited to the specific embodiments disclosed and that modifications and other embodiments are intended to be included within the scope of the appended claims. Although specific terms are employed herein, they are used in a generic and descriptive sense only and not for purposes of limitation.
I. Overview
Frequently, RNAi discovery methods rely on evaluation of known classes of sensitive genes (transcription factors, housekeeping genes etc.). In contrast, the target polynucleotide set forth herein were identified based solely on high throughput screens of a library of over 1000 expressed sequence tags from N. viridula. This screen allowed for the discovery of many novel sequences, many of which have extremely low or no homology to known sequences. This method provided the advantage of having no built in bias to genes that are frequently highly conserved across taxa. As a result, many novel targets for RNAi as well as known genes not previously shown to be sensitive to RNAi have been identified.
As such, methods and compositions are provided which employ a silencing element that, when ingested by a pest, such as a Pentatomidae plant pest or, for example, a N. viridula, Acrosternum hilare, Piezodorus guildini, and/or Halymorpha halys plant pest, is capable of decreasing the expression of a target sequence in the pest. In specific embodiments, the decrease in expression of the target sequence controls the pest and thereby the methods and compositions are capable of limiting damage to a plant or plant part. The present invention provides target polynucleotides as set forth in SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 1 11, 112, 1 13, 114, 115, 116, 117, 118, 1 19, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135,
136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 21 1, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 302, 303, or 304. or active variants and fragments thereof. Silencing elements designed in view of these target polynucleotides are provided which, when ingested by the pest, decrease the expression of one or more of the target sequences and thereby controls the pest (i.e., has insecticidal activity).
As used herein, by "controlling a pest" or "controls a pest" is intended any affect on a pest that results in limiting the damage that the pest causes. Controlling a pest includes, but is not limited to, killing the pest, inhibiting development of the pest, altering fertility or growth of the pest in such a manner that the pest provides less damage to the plant, decreasing the number of offspring produced, producing less fit pests, producing pests more susceptible to predator attack, or deterring the pests from eating the plant.
Reducing the level of expression of the target polynucleotide or the polypeptide encoded thereby, in the pest results in the suppression, control, and/or killing the invading pathogenic organism. Reducing the level of expression of the target sequence of the pest will reduce the disease symptoms resulting from pathogen challenge by at least about 2% to at least about 6%, at least about 5% to about 50%, at least about 10% to about 60%, at least about 30% to about 70%, at least about 40% to about 80%, or at least about 50% to about 90% or greater. Hence, the methods of the invention can be utilized to control pests, particularly, Pentatomidae plant pest or a N viridula, Acrosternum hilare, Piezodorus guildini, and/or Halymorpha halys plant pest.
Assays that measure the control of a pest are commonly known in the art, as are methods to quantitate disease resistance in plants following pathogen infection. See, for example, U.S. Patent No. 5,614,395, herein incorporated by reference. Such techniques include, measuring over time, the average lesion diameter, the pathogen biomass, and the overall percentage of decayed plant tissues. See, for example, Thomma et al. (1998) Plant Biology 95: 15107-1511 1, herein incorporated by reference. See, also Baum et al. (2007) Nature Biotech 11 : 1322-1326 and WO 2007/035650 which proved both whole plant feeding assays and corn root feeding assays. Both of these references are herein incorporated by reference in their entirety. See, also the examples below. The invention is drawn to compositions and methods for protecting plants from a plant pest, such as Pentatomidae plant pests or N. viridula, Acrosternum hilare,
Piezodorus guildini, and or Halymorpha halys plant pests or inducing resistance in a plant to a plant pest, such as Pentatomidae plant pests or N. viridula, Acrosternum hilare, Piezodorus guildini, and or Halymorpha halys plant pests. As used herein "Pentatomidae plant pest" is used to refer to any member of the Pentatomidae family. Accordingly, the compositions and methods are also useful in protecting plants against any Pentatomidae plant pest including representative genera and species such as, but not limited to, Acrocorisellus (A. serraticollis), Acrosternum (A. adelpha, A. hilare, A. herbidum, A. scutellatum), Agonoscelis (A. nubila), Alcaeorrhynchus (A. grandis, A. phymatophorus), Amaurochrous (A. brevitylus), Apateticus (A. anatarius, A. bracteatus, A. cynicus, A. lineolatus, A. marginiventris), Apoecilus, Arma (A. custos), Arvelius, Bagrada, Banasa (B. calva, B. dimiata, B. grisea, B. induta, B. sordida), Brochymena (B. affinis, B. cariosa, B. haedula, B. hoppingi, B. sulcata), Carbula (C. obtusangula, C. sinica), Chinavia, Chlorochroa (C. belfragii, C, kanei, C. norlandi, C. senilis, C. viridicata), Chlorocoris (C. distinctus, C flaviviridis, C. hebetatus, C. subrugosus, C. tau), Codophila (C. remota, C. sulcata, C. varius), Coenus (C. delius, C. inermis, C. tarsalis), Cosmopepla (C.
bimaculata, C. binotata, C. carnifex, C. decorata, C. intergressus), Dalpada (D. oculata), Dendrocoris (D. arizonesis, D. fruticicola, D. humeralis, D. parapini, D. reticulatus), Dolycoris (D. baccarum (sloe bug)), Dybowskyia (D. reticulata), Edessa, Erthesina (E. fullo), Eurydema (E. dominulus, E. gebleri (shield bug), E. pulchra, E. rugosa), Euschistus (E. biformis, E. integer, E. quadrator, E. servus, E. tristigma), Euthyrhynchus (E.
floridanus, E. macronemis), Gonopsis (G. coccinea), Graphosoma (G. lineatum (stink bug), G. rubrolineatum), Halyomorpha (H halys (brown marmorated stink bug)J, Halys (H sindillus, H. sulcatus), Holcostethus (H abbreviatus, H. fulvipes, H. limbolarius, H piceus, H. sphacelatus), Homalogonia (H. obtusa), Hymenarcys (H aequalis, H crassa, H. nervosa, H. perpuncata, H. reticulata), Lelia (L. decempunctata), Lineostethus, Loxa (L. flavicollis, L. viridis), Mecidea (M. indicia, M. major, M. minor), Megarrhamphus (M. hastatus), Menecles (M. insertus, M. portacrus), Mormidea (M. cubrosa, M. lugens, M. pama, M. pictiventris, M. ypsilon), Moromorpha (M. tetra), Murgantia (M. angularis, M. tessellata, M. varicolor, M. violascens), Neottiglossa (N. californica, N. cavifrons, N. coronaciliata, N. sulcifrons, N. undata), Nezara (N. smaragdulus, N. viridula (southern green stink bug)J, Oebalus (0. grisescens, 0. insularis, 0. mexicanus, 0. pugnax, 0. typhoeus), Oechalia (0. schellenbergii (spined predatory shield bug)J, Okeanos (0. quelpartensis), Oplomus (0. catena, 0. dichrous, 0. tripustulatus), Palomena (P. prasina (green shield bug)), Parabrochymena, Pentatoma (P. angulata, P. illuminata, P.
japonica, P. kunmingensis, P. metalUfera, P. parataibaiensis, P. rufipes, P. semiannulata, P. viridicornuta), Perillus (P. bioculatus, P. confluens, P. strigipes), Picromerus (P. griseus), Piezodorus (P. degeeri, P. guildinii, P. lituratus (gorse shield bug)), Pinthaeus (P. humeralis), Plautia (P. crossota, P. stali (brown-winged green bug)), Podisus (P. maculiventris), Priassus (P. testaceus), Prionosoma, Proxys (P. albopunctulatus, P.
punctulatus, P. victor), Rhaphigaster (R. nebulosa), Scotinophara (S. horvathi), Stiretrus (S. anchorago, S. fimbriatus), Thyanta (T. accerra, T. calceata, T. casta, T. perditor, T. pseudocasta), Trichopepla (T. aurora, T. dubia, T. pilipes, T. semivittata, T. vandykei), Tylospilus, and Zicrona.
II. Target Sequences
As used herein, a "target sequence" or "target polynucleotide" comprises any sequence in the pest that one desires to reduce the level of expression. In specific embodiments, decreasing the level of the target sequence in the pest controls the pest. For instance, the target sequence can be essential for growth and development. While the target sequence can be expressed in any tissue of the pest, in specific embodiments, the sequences targeted for suppression in the pest are expressed in cells of the gut tissue of the pest, cells in the midgut of the pest, and cells lining the gut lumen or the midgut. Such target sequences can be involved in, for example, gut cell metabolism, growth or differentiation. Non- limiting examples of target sequences of the invention include a polynucleotide set forth in SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 1 11, 112, 113, 114, 115, 1 16, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163,
164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 302, 303, or 304. As exemplified elsewhere herein, decreasing the level of expression of one or more of these target sequences in a Pentatomidae plant pest or a N. viridula, Acrosternum hilare, Piezodorus guildini, and/or Halymorpha halys plant pest controls the pest.
III. Silencing Elements
By "silencing element" is intended a polynucleotide which when ingested by a pest, is capable of reducing or eliminating the level or expression of a target
polynucleotide or the polypeptide encoded thereby. The silencing element employed can reduce or eliminate the expression level of the target sequence by influencing the level of the target RNA transcript or, alternatively, by influencing translation and thereby affecting the level of the encoded polypeptide. Methods to assay for functional silencing elements that are capable of reducing or eliminating the level of a sequence of interest are disclosed elsewhere herein. A single polynucleotide employed in the methods of the invention can comprise one or more silencing elements to the same or different target polynucleotides. The silencing element can be produced in vivo (i.e., in a host cell such as a plant or microorganism) or in vitro.
In specific embodiments, the target sequence is not endogenous to the plant. In other embodiments, while the silencing element controls pests, preferably the silencing element has no effect on the normal plant or plant part.
As discussed in further detail below, silencing elements can include, but are not limited to, a sense suppression element, an antisense suppression element, a double stranded RNA, a siRNA, an amiRNA, a miRNA, or a hairpin suppression element. Non- limiting examples of silencing elements that can be employed to decrease expression of these target Pentatomidae plant pest sequences or N. viridula, Acrosternum hilare, Piezodorus guildini, and/ 'or Halymorpha halys plant pest sequences comprise fragments and variants of the sense or antisense sequence or consists of the sense or antisense sequence of the sequence set forth in SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 1 13, 114, 115, 116, 117, 1 18, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178,
179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 21 1, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 302, 303, or 304 or a biologically active variant or fragment thereof. Additional sequences that can be employed as silencing elements include, for example, SEQ ID NOS: 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 305, 306, 307, 308, 309, 310, 311, 312, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, or 336 or active variants or fragments thereof. The silencing element can further comprise additional sequences that advantageously effect transcription and/or the stability of a resulting transcript. For example, the silencing elements can comprise at least one thymine residue at the 3' end. This can aid in stabilization. Thus, the silencing elements can have at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more thymine residues at the 3' end. As discussed in further detail below, enhancer suppressor elements can also be employed in conjunction with the silencing elements disclosed herein.
By "reduces" or "reducing" the expression level of a polynucleotide or a polypeptide encoded thereby is intended to mean, the polynucleotide or polypeptide level of the target sequence is statistically lower than the polynucleotide level or polypeptide level of the same target sequence in an appropriate control pest which is not exposed to (i.e., has not ingested) the silencing element. In particular embodiments of the invention, reducing the polynucleotide level and/or the polypeptide level of the target sequence in a pest according to the invention results in less than 95%, less than 90%>, less than 80%>, less than 70%, less than 60%, less than 50%, less than 40%, less than 30%, less than 20%, less than 10%), or less than 5%> of the polynucleotide level, or the level of the polypeptide encoded thereby, of the same target sequence in an appropriate control pest. Methods to assay for the level of the RNA transcript, the level of the encoded polypeptide, or the activity of the polynucleotide or polypeptide are discussed elsewhere herein. i. Sense Suppression Elements
As used herein, a "sense suppression element" comprises a polynucleotide designed to express an RNA molecule corresponding to at least a part of a target messenger RNA in the "sense" orientation. Expression of the RNA molecule comprising the sense suppression element reduces or eliminates the level of the target polynucleotide or the polypeptide encoded thereby. The polynucleotide comprising the sense suppression element may correspond to all or part of the sequence of the target polynucleotide, all or part of the 5' and/or 3' untranslated region of the target polynucleotide, all or part of the coding sequence of the target polynucleotide, or all or part of both the coding sequence and the untranslated regions of the target polynucleotide.
Typically, a sense suppression element has substantial sequence identity to the target polynucleotide, typically greater than about 65% sequence identity, greater than about 85% sequence identity, about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity. See, U.S. Patent Nos. 5,283, 184 and 5,034,323; herein incorporated by reference. The sense suppression element can be any length so long as it allows for the suppression of the targeted sequence. The sense suppression element can be, for example, 15, 16, 17, 18 19, 20, 22, 25, 30, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 900, 1000, 1100, 1200, 1300 nucleotides or longer of the target polynucleotides set forth in any of SEQ ID NO: 1-292 or 302-304. In other embodiments, the sense suppression element can be, for example, about 15-25, 25-100, 100-150, 150- 200, 200-250, 250-300, 300-350, 350-400, 450-500, 500-550, 550-600, 600-650, 650-700, 700-750, 750-800, 800-850, 850-900, 900-950, 950-1000, 1000-1050, 1050-1 100, 1 100- 1200, 1200-1300, 1300-1400, 1400-1500, 1500-1600, 1600-1700, 1700-1800 nucleotides or longer of the target polynucleotides set forth in any of SEQ ID NO: 1-292 or 302-304. ii. Antisense Suppression Elements
As used herein, an "antisense suppression element" comprises a polynucleotide which is designed to express an RNA molecule complementary to all or part of a target messenger RNA. Expression of the antisense RNA suppression element reduces or eliminates the level of the target polynucleotide. The polynucleotide for use in antisense suppression may correspond to all or part of the complement of the sequence encoding the target polynucleotide, all or part of the complement of the 5' and/or 3' untranslated region of the target polynucleotide, all or part of the complement of the coding sequence of the target polynucleotide, or all or part of the complement of both the coding sequence and the untranslated regions of the target polynucleotide. In addition, the antisense suppression element may be fully complementary (i.e., 100% identical to the complement of the target sequence) or partially complementary (i.e., less than 100% identical to the complement of the target sequence) to the target polynucleotide. In specific embodiments, the antisense suppression element comprises at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%o, 98%), or 99% sequence complementarity to the target polynucleotide. Antisense suppression may be used to inhibit the expression of multiple proteins in the same plant. See, for example, U.S. Patent No. 5,942,657. Furthermore, the antisense suppression element can be complementary to a portion of the target polynucleotide. Generally, sequences of at least 15, 20, 22, 25, 50, 100, 200, 300, 400, 450 nucleotides or greater of the sequence set forth in any of SEQ ID NO: 1-292 or 302-304 may be used. Methods for using antisense suppression to inhibit the expression of endogenous genes in plants are described, for example, in Liu et al (2002) Plant Physiol. 129: 1732-1743 and U.S. Patent Nos. 5,759,829 and 5,942,657, each of which is herein incorporated by reference.
Hi. Double Stranded RNA Suppression Element
A "double stranded RNA silencing element" or "dsRNA" comprises at least one transcript that is capable of forming a dsRNA either before or after ingestion by a pest. Thus, a "dsRNA silencing element" includes a dsRNA, a transcript or polyribonucleotide capable of forming a dsRNA or more than one transcript or polyribonucleotide capable of forming a dsRNA. "Double stranded RNA" or "dsRNA" refers to a polyribonucleotide structure formed either by a single self-complementary RNA molecule or a
polyribonucleotide structure formed by the expression of least two distinct RNA strands. The dsRNA molecule(s) employed in the methods and compositions of the invention mediate the reduction of expression of a target sequence, for example, by mediating RNA interference "RNAi" or gene silencing in a sequence-specific manner. In the context of the present invention, the dsRNA is capable of reducing or eliminating the level or expression of a target polynucleotide or the polypeptide encoded thereby in a pest.
The dsRNA can reduce or eliminate the expression level of the target sequence by influencing the level of the target RNA transcript, by influencing translation and thereby affecting the level of the encoded polypeptide, or by influencing expression at the pre- transcriptional level (i.e., via the modulation of chromatin structure, methylation pattern, etc., to alter gene expression). See, for example, Verdel et al (2004) Science 303 :672- 676; Pal-Bhadra et al (2004) Science 303:669-672; Allshire (2002) Science 297: 1818- 1819; Volpe et al. (2002) Science 297: 1833-1837; Jenuwein (2002) Science 297:2215- 2218; and Hall et al. (2002) Science 297:2232-223 '. Methods to assay for functional dsRNA that are capable of reducing or eliminating the level of a sequence of interest are disclosed elsewhere herein. Accordingly, as used herein, the term "dsRNA" is meant to encompass other terms used to describe nucleic acid molecules that are capable of mediating RNA interference or gene silencing, including, for example, short-interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), hairpin RNA, short hairpin RNA (shRNA), post-transcriptional gene silencing RNA (ptgsRNA), and others.
In specific embodiments, at least one strand of the duplex or double-stranded region of the dsRNA shares sufficient sequence identity or sequence complementarity to the target polynucleotide to allow for the dsRNA to reduce the level of expression of the target sequence. As used herein, the strand that is complementary to the target polynucleotide is the "antisense strand" and the strand homologous to the target polynucleotide is the "sense strand."
In another embodiment, the dsRNA comprises a hairpin RNA. A hairpin RNA comprises an RNA molecule that is capable of folding back onto itself to form a double stranded structure. Multiple structures can be employed as hairpin elements. In specific embodiments, the dsRNA suppression element comprises a hairpin element which comprises in the following order, a first segment, a second segment, and a third segment, where the first and the third segment share sufficient complementarity to allow the transcribed RNA to form a double-stranded stem-loop structure.
The "second segment" of the hairpin comprises a "loop" or a "loop region." These terms are used synonymously herein and are to be construed broadly to comprise any nucleotide sequence that confers enough flexibility to allow self-pairing to occur between complementary regions of a polynucleotide (i.e., segments 1 and 3 which form the stem of the hairpin). For example, in some embodiments, the loop region may be substantially single stranded and act as a spacer between the self-complementary regions of the hairpin stem-loop. In some embodiments, the loop region can comprise a random or nonsense nucleotide sequence and thus not share sequence identity to a target polynucleotide. In other embodiments, the loop region comprises a sense or an antisense RNA sequence or fragment thereof that shares identity to a target polynucleotide. See, for example, International Patent Publication No. WO 02/00904, herein incorporated by reference. In specific embodiments, the loop region can be optimized to be as short as possible while still providing enough intramolecular flexibility to allow the formation of the base-paired stem region. Accordingly, the loop sequence is generally less than 1000, 900, 800, 700, 600, 500, 400, 300, 200, 100, 50, 25, 20, 15, 10 nucleotides or less.
The "first" and the "third" segment of the hairpin RNA molecule comprise the base-paired stem of the hairpin structure. The first and the third segments are inverted repeats of one another and share sufficient complementarity to allow the formation of the base-paired stem region. In specific embodiments, the first and the third segments are fully complementary to one another. Alternatively, the first and the third segment may be partially complementary to each other so long as they are capable of hybridizing to one another to form a base-paired stem region. The amount of complementarity between the first and the third segment can be calculated as a percentage of the entire segment. Thus, the first and the third segment of the hairpin RNA generally share at least 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, up to and including 100% complementarity.
The first and the third segment are at least about 1000, 500, 400, 300, 200, 100, 50, 40, 30, 25, 22, 20, 19, 18, 17, 16, 15 or 10 nucleotides in length. In specific embodiments, the length of the first and/or the third segment is about 10-100 nucleotides, about 10 to about 75 nucleotides, about 10 to about 50 nucleotides, about 10 to about 40 nucleotides, about 10 to about 35 nucleotides, about 10 to about 30 nucleotides, about 10 to about 25 nucleotides, about 10 to about 19 nucleotides, about 50 nucleotides to about 100 nucleotides, about 100 nucleotides to about 150 nucleotides, about 150 nucleotides to about 200 nucleotides, about 200 nucleotides to about 250 nucleotides, about 250 nucleotides to about 300 nucleotides, about 300 nucleotides to about 350 nucleotides, about 350 nucleotides to about 400 nucleotides, about 400 nucleotide to about 500 nucleotides, about 600 nt, about 700 nt, about 800 nt, about 900 nt, about 1000 nt, about 1100 nt, about 1200 nt, 1300 nt, 1400 nt, 1500 nt, 1600 nt, 1700 nt, 1800 nt, 1900 nt, 2000 nt or longer. In other embodiments, the length of the first and/or the third segment comprises at least 10-19 nucleotides; 19-35 nucleotides; 30-45 nucleotides; 40-50 nucleotides; 50-100 nucleotides; 100-300 nucleotides; about 500 -700 nucleotides; about 700-900 nucleotides; about 900-1100 nucleotides; about 1300 -1500 nucleotides; about 1500 - 1700 nucleotides; about 1700 - 1900 nucleotides; about 1900 - 2100 nucleotides; about 2100 - 2300 nucleotides; or about 2300 - 2500 nucleotides. See, for example, International Publication No. WO 0200904. In specific embodiments, the first and the third segment comprise at least 19 nucleotides having at least 85% complementary to the first segment. In still other embodiments, the first and the third segments which form the stem-loop structure of the hairpin comprises 3' or 5' overhang regions having unpaired nucleotide residues.
In specific embodiments, the sequences used in the first, the second, and/or the third segments comprise domains that are designed to have sufficient sequence identity to a target polynucleotide of interest and thereby have the ability to decrease the level of expression of the target polynucleotide. The specificity of the inhibitory RNA transcripts is therefore generally conferred by these domains of the silencing element. Thus, in some embodiments of the invention, the first, second and/or third segment of the silencing element comprise a domain having at least 10, at least 15, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 40, at least 50, at least 100, at least 200, at least 300, at least 500, at least 1000, or more than 1000 nucleotides that share sufficient sequence identity to the target polynucleotide to allow for a decrease in expression levels of the target polynucleotide when expressed in an appropriate cell. In other embodiments, the domain is between about 15 to 50 nucleotides, about 19-35 nucleotides, about 25-50 nucleotides, about 19 to 75 nucleotides, about 40-90 nucleotides about 15-100 nucleotides 10- 100 nucleotides, about 10 to about 75 nucleotides, about 10 to about 50 nucleotides, about 10 to about 40 nucleotides, about 10 to about 35 nucleotides, about 10 to about 30 nucleotides, about 10 to about 25 nucleotides, about 10 to about 19 nucleotides, about 50 nucleotides to about 100 nucleotides, about 100 nucleotides to about 150 nucleotides, about 150 nucleotides to about 200 nucleotides, about 200 nucleotides to about 250 nucleotides, about 250 nucleotides to about 300 nucleotides, about 300 nucleotides to about 350 nucleotides, about 350 nucleotides to about 400 nucleotides, about 400 nucleotide to about 500 nucleotides or longer. In other embodiments, the length of the first and/or the third segment comprises at least 10-19 nucleotides, 19-35 nucleotides, 30-45 nucleotides, 40-50 nucleotides, 50-100 nucleotides, or about 100-300 nucleotides.
In specific embodiments, the domain of the first, the second, and/or the third segment has 100% sequence identity to the target polynucleotide. In other embodiments, the domain of the first, the second and/or the third segment having homology to the target polypeptide have at least 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%), 99%o, or greater sequence identity to a region of the target
polynucleotide. The sequence identity of the domains of the first, the second and/or the third segments to the target polynucleotide need only be sufficient to decrease expression of the target polynucleotide of interest. See, for example, Chuang and Meyerowitz (2000) Proc. Natl. Acad. Sci. USA 97:4985-4990; Stoutjesdijk et al. (2002) Plant Physiol.
129: 1723-1731; Waterhouse and Helliwell (2003) Nat. Rev. Genet. 4:29-38; Pandolfini et al. BMC Biotechnology 3:7, and U.S. Patent Publication No. 20030175965; each of which is herein incorporated by reference. A transient assay for the efficiency of hpRNA constructs to silence gene expression in vivo has been described by Panstruga et al. (2003) Mol. Biol. Rep. 30: 135-140, herein incorporated by reference.
The amount of complementarity shared between the first, second, and/or third segment and the target polynucleotide or the amount of complementarity shared between the first segment and the third segment (i.e., the stem of the hairpin structure) may vary depending on the organism in which gene expression is to be controlled. Some organisms or cell types may require exact pairing or 100% identity, while other organisms or cell types may tolerate some mismatching. In some cells, for example, a single nucleotide mismatch in the targeting sequence abrogates the ability to suppress gene expression. In these cells, the suppression cassettes of the invention can be used to target the suppression of mutant genes, for example, oncogenes whose transcripts comprise point mutations and therefore they can be specifically targeted using the methods and compositions of the invention without altering the expression of the remaining wild-type allele.
Any region of the target polynucleotide can be used to design the domain of the silencing element that shares sufficient sequence identity to allow expression of the hairpin transcript to decrease the level of the target polynucleotide. For instance, the domain can be designed to share sequence identity to the 5' untranslated region of the target polynucleotide(s), the 3' untranslated region of the target polynucleotide(s), exonic regions of the target polynucleotide(s), intronic regions of the target polynucleotide(s), and any combination thereof. In specific embodiments, a domain of the silencing element shares sufficient homology to at least about 15, 16, 17, 18, 19, 20, 22, 25 or 30 consecutive nucleotides from about nucleotides 1-50, 25-75, 75-125, 50-100, 125-175,
175-225, 100-150, 150-200, 200-250, 225-275, 275-325, 250-300, 325-375, 375-425, 300- 350, 350-400, 425-475, 400-450, 475-525, 450-500, 525-575, 575-625, 550-600, 625-675, 675-725, 600-650, 625-675, 675-725, 650-700, 725-825, 825-875, 750-800, 875-925, 925- 975, 850-900, 925-975, 975-1025, 950-1000, 1000-1050, 1025-1075, 1075-1125, 1050- 1100, 1125-1175, 1 100-1200, 1 175-1225, 1225-1275, 1200-1300, 1325-1375, 1375-1425, 1300-1400, 1425-1475, 1475-1525, 1400-1500, 1525-1575, 1575-1625, 1625-1675, 1675- 1725, 1725-1775, 1775-1825, 1825-1875, 1875-1925, 1925-1975, 1975-2025, 2025-2075, 2075-2125, 2125-2175, 2175-2225, 1500-1600, 1600-1700, 1700-1800, 1800-1900, 1900- 2000 of the target sequence. In some instances to optimize the siRNA sequences employed in the hairpin, the synthetic oligodeoxyribonucleotide/RNAse H method can be used to determine sites on the target mRNA that are in a conformation that is susceptible to RNA silencing. See, for example, Vickers et al. (2003) J. Biol. Chem 278:7108-7118 and Yang et al. (2002) Proc. Natl. Acad. Sci. USA 99:9442-9447, herein incorporated by reference. These studies indicate that there is a significant correlation between the RNase- H-sensitive sites and sites that promote efficient siR A-directed mRNA degradation.
The hairpin silencing element may also be designed such that the sense sequence or the antisense sequence do not correspond to a target polynucleotide. In this embodiment, the sense and antisense sequence flank a loop sequence that comprises a nucleotide sequence corresponding to all or part of the target polynucleotide. Thus, it is the loop region that determines the specificity of the RNA interference. See, for example, WO 02/00904, herein incorporated by reference.
In addition, transcriptional gene silencing (TGS) may be accomplished through use of a hairpin suppression element where the inverted repeat of the hairpin shares sequence identity with the promoter region of a target polynucleotide to be silenced. See, for example, Aufsatz et al. (2002) PNAS 99 (Suppl. 4): 16499- 16506 and Mette et al. (2000) £ 5O J 19(19):5194-5201.
While the various target sequences disclosed herein can be used to design any silencing element that encodes a hairpin suppression construct, non-limiting examples of such hairpin constructs are set forth in SEQ ID NO: 293 which targets SEQ ID NO: 278; SEQ ID NOS: 294, 295 and 296 which target SEQ ID NO: 279; SEQ ID NOS: 297 and 298 which target SEQ ID NO:280; SEQ ID NO:299 which targets SEQ ID NO:281 ; SEQ ID NO: 300 which targets SEQ ID NO: 282; and SEQ ID NO: 301 which targets SEQ ID NO: 283; or active variants or fragments thereof.
In other embodiments, the dsRNA can comprise a small RNA (sRNA). sRNAs can comprise both micro RNA (miRNA) and short-interfering RNA (siRNA) (Meister and Tuschl (2004) Nature 431 :343-349 and Bonetta et al. (2004) Nature Methods 1 :79-86). "MicroRNAs" or "miRNAs" are regulatory agents comprising about 19 to about 24 nucleotides (nt) in length, which are highly efficient at inhibiting the expression of target polynucleotides. See, for example Javier et al. (2003) Nature 425: 257-263, herein incorporated by reference. For miRNA interference, the silencing element can be designed to express a dsRNA molecule that forms a hairpin structure containing a 21 nucleotide sequence that is complementary to the target polynucleotide of interest. The miRNA can be an "artificial miRNA" or "amiRNA" which comprises a miRNA sequence that is synthetically designed to silence a target sequence.
When expressing an miRNA, the final (mature) miRNA is present in a duplex in a precursor backbone structure, the two strands being referred to as the miRNA (the strand that will eventually basepair with the target) and miRNA* (star sequence). This final miRNA is a substrate for a form of dicer that removes the miRNA/miRNA* duplex from the precursor, after which, similarly to siRNAs, the duplex can be taken into the RISC complex. It has been demonstrated that miRNAs can be transgenically expressed and be effective through expression of a precursor form, rather than the entire primary form (Panzotto et al. (2004) Genes & Development 18 :2237-2242 and Guo et al. (2005) Plant Cell 17: 1376-1386).
The silencing element for miRNA interference comprises a miRNA precursor backbone. The miRNA precursor backbone comprises a DNA sequence having the miRNA and star sequences. When expressed as an RNA, the structure of the miRNA precursor backbone is such as to allow for the formation of a hairpin RNA structure that can be processed into a miRNA. In some embodiments, the miRNA precursor backbone comprises a genomic miRNA precursor sequence, wherein said sequence comprises a native precursor in which an heterologous (artificial) miRNA and star sequence are inserted.
As used herein, a "star sequence" is the sequence within a miRNA precursor backbone that is complementary to the miRNA and forms a duplex with the miRNA to form the stem structure of a hairpin RNA. In some embodiments, the star sequence can comprise less than 100% complementarity to the miRNA sequence. Alternatively, the star sequence can comprise at least 99%, 98%, 97%, 96%, 95%, 90%, 85%, 80% or lower sequence complementarity to the miRNA sequence as long as the star sequence has sufficient complementarity to the miRNA sequence to form a double stranded structure. In still further embodiments, the star sequence comprises a sequence having 1, 2, 3, 4, 5 or more mismatches with the miRNA sequence and still has sufficient complementarity to form a double stranded structure with the miRNA sequence resulting in production of miRNA and suppression of the target sequence. The miRNA precursor backbones can be from any plant. In some embodiments, the miRNA precursor backbone is from a monocot. In other embodiments, the miRNA precursor backbone is from a dicot. In further embodiments, the backbone is from maize or soybean. MicroRNA precursor backbones have been described previously. For example, US20090155910A1 (WO 2009/079532) discloses the following soybean miRNA precursor backbones: 156c, 159, 166b, 168c, 396b and 398b, and US20090155909Al (WO 2009/079548) discloses the following maize miRNA precursor backbones: 159c, 164h, 168a, 169r, and 396h. Each of these references is incorporated by reference in their entirety.
Thus, the miRNA precursor backbone can be altered to allow for efficient insertion of heterologous miRNA and star sequences within the miRNA precursor backbone. In such instances, the miRNA segment and the star segment of the miRNA precursor backbone are replaced with the heterologous miRNA and the heterologous star sequences, designed to target any sequence of interest, using a PCR technique and cloned into an expression construct. It is recognized that there could be alterations to the position at which the artificial miRNA and star sequences are inserted into the backbone. Detailed methods for inserting the miRNA and star sequence into the miRNA precursor backbone are described elsewhere herein (see, Example 8) and are also described in, for example, US Patent Applications 20090155909A1 and US20090155910A1, herein incorporated by reference in their entirety.
When designing a miRNA sequence and star sequence, various design choices can be made. See, for example, Schwab R, et al. (2005) Dev Cell 8: 17-27. In non- limiting embodiments, the miRNA sequences disclosed herein can have a "U" at the 5'-end, a "C" or "G" at the 19th nucleotide position, and an "A" or "U" at the 10th nucleotide position. In other embodiments, the miRNA design is such that the miRNA have a high free delta-G as calculated using the ZipFold algorithm (Markham, N. R. & Zuker, M. (2005) Nucleic Acids Res. 33: W577-W581.) Optionally, a one base pair change can be added within the 5' portion of the miRNA so that the sequence differs from the target sequence by one nucleotide.
The methods and compositions of the invention employ silencing elements that when transcribed "form" a dsRNA molecule. Accordingly, the heterologous
polynucleotide being expressed need not form the dsRNA by itself, but can interact with other sequences in the plant cell or in the pest gut after ingestion to allow the formation of the dsRNA. For example, a chimeric polynucleotide that can selectively silence the target polynucleotide can be generated by expressing a chimeric construct comprising the target sequence for a miRNA or siRNA to a sequence corresponding to all or part of the gene or genes to be silenced. In this embodiment, the dsRNA is "formed" when the target for the miRNA or siRNA interacts with the miRNA present in the cell. The resulting dsRNA can then reduce the level of expression of the gene or genes to be silenced. See, for example, US Application Publication 2007-0130653, entitled "Methods and Compositions for Gene Silencing", herein incorporated by reference. The construct can be designed to have a target for an endogenous miRNA or alternatively, a target for a heterologous and/or synthetic miRNA can be employed in the construct. If a heterologous and/or synthetic miRNA is employed, it can be introduced into the cell on the same nucleotide construct as the chimeric polynucleotide or on a separate construct. As discussed elsewhere herein, any method can be used to introduce the construct comprising the heterologous miRNA.
While the various target sequences disclosed herein can be used to design any silencing element that encodes a miRNA, non-limiting examples of such miRNA constructs include SEQ ID NOS: 311, 312, 327, 328, 335 or 336 which target SEQ ID NO: 304; SEQ ID NOS: 307, 308, 323, 324, 331 or 332 which target SEQ ID NO: 278; SEQ ID NOS: 309, 310, 325, 326, 333 or 334 which target SEQ ID NO: 303; and SEQ ID NOS: 305, 306, 321, 322, 329 or 330 which target SEQ ID NO: 302; or active variants or fragments thereof.
IV. Variants and Fragments
By "fragment" is intended a portion of the polynucleotide or a portion of the amino acid sequence and hence protein encoded thereby. Fragments of a polynucleotide may encode protein fragments that retain the biological activity of the native protein.
Alternatively, fragments of a polynucleotide that are useful as a silencing element do not need to encode fragment proteins that retain biological activity. Thus, fragments of a nucleotide sequence may range from at least about 10, about 15, about 16, about 17, about 18, about 19, about 20 nucleotides, about 22 nucleotides, about 50 nucleotides, about 75 nucleotides, about 100 nucleotides, 200 nucleotides, 300 nucleotides, 400 nucleotides, 500 nucleotides, 600 nucleotides, 700 nucleotides and up to the full-length polynucleotide employed in the invention. Alternatively, fragments of a nucleotide sequence may range from 1-50, 25-75, 75-125, 50-100, 125-175, 175-225, 100-150, 150-200, 200-250, 225- 275, 275-325, 250-300, 325-375, 375-425, 300-350, 350-400, 425-475, 400-450, 475-525, 450-500, 525-575, 575-625, 550-600, 625-675, 675-725, 600-650, 625-675, 675-725, 650- 700, 725-825, 825-875, 750-800, 875-925, 925-975, 850-900, 925-975, 975-1025, 950- 1000, 1000-1050, 1025-1075, 1075-1 125, 1050-1100, 1125-1 175, 1 100-1200, 1175-1225, 1225-1275, 1200-1300, 1325-1375, 1375-1425, 1300-1400, 1425-1475, 1475-1525, 1400- 1500, 1525-1575, 1575-1625, 1625-1675, 1675-1725, 1725-1775, 1775-1825, 1825-1875, 1875-1925, 1925-1975, 1975-2025, 2025-2075, 2075-2125, 2125-2175, 2175-2225, 1500-
1600, 1600-1700, 1700-1800, 1800-1900, 1900-2000 of any one of SEQ ID NO S: 1-304 or 321-336. Methods to assay for the activity of a desired silencing element are described elsewhere herein.
Encompassed herein are fragments of the various target sequences (i.e. SEQ ID NOS: 1-292 and 302-304) which are useful as silencing elements and fragments of the various silencing elements provided herein (i.e. SEQ ID NOS:293-301 or 321-336). Thus, fragments of a nucleotide sequence that are useful as silencing elements may range from at least about 10, about 15, about 16, about 17, about 18, about 19, about 20 nucleotides, about 22 nucleotides, about 50 nucleotides, about 75 nucleotides, about 100 nucleotides, 200 nucleotides, 300 nucleotides, 400 nucleotides, 500 nucleotides, 600 nucleotides, 700 nucleotides and up to the full-length polynucleotide sequences of SEQ ID NOS: 1-304 or 321-336. Alternatively, fragments of a nucleotide sequence that are useful as silencing elements may range from 1-50, 25-75, 75-125, 50-100, 125-175, 175-225, 100-150, 150- 200, 200-250, 225-275, 275-325, 250-300, 325-375, 375-425, 300-350, 350-400, 425-475, 400-450, 475-525, 450-500, 525-575, 575-625, 550-600, 625-675, 675-725, 600-650, 625- 675, 675-725, 650-700, 725-825, 825-875, 750-800, 875-925, 925-975, 850-900, 925-975, 975-1025, 950-1000, 1000-1050, 1025-1075, 1075-1 125, 1050-1100, 1125-1175, 1 100- 1200, 1175-1225, 1225-1275, 1200-1300, 1325-1375, 1375-1425, 1300-1400, 1425-1475, 1475-1525, 1400-1500, 1525-1575, 1575-1625, 1625-1675, 1675-1725, 1725-1775, 1775- 1825, 1825-1875, 1875-1925, 1925-1975, 1975-2025, 2025-2075, 2075-2125, 2125-2175,
2175-2225, 1500-1600, 1600-1700, 1700-1800, 1800-1900, 1900-2000 of any one of SEQ ID NOS: 1-304 or 321-336. Methods to assay for the activity of a desired silencing element are described elsewhere herein. Various, non-limiting examples of fragments of SEQ ID NOS: 1-292 or 302-304 are provided herein and include, for example, SEQ ID NOS: 284-292 or 305-312.
"Variants" is intended to mean substantially similar sequences. Thus, further provided are variants of the various sequences set forth in SEQ ID NOS: 1-336. For polynucleotides, a variant comprises a deletion and/or addition of one or more nucleotides at one or more internal sites within the native polynucleotide and/or a substitution of one or more nucleotides at one or more sites in the native polynucleotide. A variant of a polynucleotide that is useful as a silencing element will retain the ability to reduce expression of the target polynucleotide and, in some embodiments, thereby control a pest of interest. As used herein, a "native" polynucleotide or polypeptide comprises a naturally occurring nucleotide sequence or amino acid sequence, respectively. For polynucleotides, conservative variants include those sequences that, because of the degeneracy of the genetic code, encode the amino acid sequence of one of the polypeptides employed in the invention. Variant polynucleotides also include synthetically derived polynucleotide, such as those generated, for example, by using site-directed mutagenesis, but continue to retain the desired activity. Generally, variants of a particular polynucleotide of the invention (i.e., a silencing element) will have at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to that particular polynucleotide as determined by sequence alignment programs and parameters described elsewhere herein.
Variants of a particular polynucleotide of the invention (i.e., the reference polynucleotide) can also be evaluated by comparison of the percent sequence identity between the polypeptide encoded by a variant polynucleotide and the polypeptide encoded by the reference polynucleotide. Percent sequence identity between any two polypeptides can be calculated using sequence alignment programs and parameters described elsewhere herein. Where any given pair of polynucleotides employed in the invention is evaluated by comparison of the percent sequence identity shared by the two polypeptides they encode, the percent sequence identity between the two encoded polypeptides is at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity.
The following terms are used to describe the sequence relationships between two or more polynucleotides or polypeptides: (a) "reference sequence", (b) "comparison window", (c) "sequence identity", and, (d) "percentage of sequence identity."
(a) As used herein, "reference sequence" is a defined sequence used as a basis for sequence comparison. A reference sequence may be a subset or the entirety of a specified sequence; for example, as a segment of a full-length cDNA or gene sequence, or the complete cDNA or gene sequence.
(b) As used herein, "comparison window" makes reference to a contiguous and specified segment of a polynucleotide sequence, wherein the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two polynucleotides. Generally, the comparison window is at least 20 contiguous nucleotides in length, and optionally can be 30, 40, 50, 100, or longer. Those of skill in the art understand that to avoid a high similarity to a reference sequence due to inclusion of gaps in the polynucleotide sequence a gap penalty is typically introduced and is subtracted from the number of matches.
Unless otherwise stated, sequence identity/similarity values provided herein refer to the value obtained using GAP Version 10 using the following parameters: % identity and % similarity for a nucleotide sequence using GAP Weight of 50 and Length Weight of 3, and the nwsgapdna.cmp scoring matrix; % identity and % similarity for an amino acid sequence using GAP Weight of 8 and Length Weight of 2, and the BLOSUM62 scoring matrix; or any equivalent program thereof. By "equivalent program" is intended any sequence comparison program that, for any two sequences in question, generates an alignment having identical nucleotide or amino acid residue matches and an identical percent sequence identity when compared to the corresponding alignment generated by GAP Version 10.
(c) As used herein, "sequence identity" or "identity" in the context of two polynucleotides or polypeptide sequences makes reference to the residues in the two sequences that are the same when aligned for maximum correspondence over a specified comparison window. When percentage of sequence identity is used in reference to proteins it is recognized that residue positions which are not identical often differ by conservative amino acid substitutions, where amino acid residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or hydrophobicity) and therefore do not change the functional properties of the molecule. When sequences differ in conservative substitutions, the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution. Sequences that differ by such conservative substitutions are said to have "sequence similarity" or "similarity". Means for making this adjustment are well known to those of skill in the art. Typically this involves scoring a conservative substitution as a partial rather than a full mismatch, thereby increasing the percentage sequence identity. Thus, for example, where an identical amino acid is given a score of 1 and a non-conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1. The scoring of conservative substitutions is calculated, e.g., as implemented in the program PC/GENE (Intelligenetics, Mountain View, California). (d) As used herein, "percentage of sequence identity" means the value determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison, and multiplying the result by 100 to yield the percentage of sequence identity.
A method is further provided for identifying a silencing element from the target polynucleotides set froth in SEQ ID NO: 1-292 or 302-304. Such methods comprise obtaining a candidate fragment of any one of SEQ ID NO: 1-292 or 302-304 which is of sufficient length to act as a silencing element and thereby reduce the expression of the target polynucleotide and/or control a desired pest; expressing said candidate
polynucleotide fragment in an appropriate expression cassette to produce a candidate silencing element and determining is said candidate polynucleotide fragment has the activity of a silencing element and thereby reduce the expression of the target
polynucleotide and/or controls a desired pest. Methods of identifying such candidate fragments based on the desired pathway for suppression are known. For example, various bioinformatics programs can be employed to identify the region of the target
polynucleotides that could be exploited to generate a silencing element. See, for example, Elbahir et al. (2001) Genes and Development 15: 188-200, Schwartz et al. (2003) Cell 115: 199-208, Khvorova et al. (2003) Cell 115:209-216. See also, siRNA at Whitehead (jura.wi.mit.edu/bioc/siRNAext/) which calculates the binding energies for both sense and antisense siRNAs. See, also genscript.com/ssl-bin app/rnai?op=known; Block-iT™ RNAi designer from Invitrogen and GenScript siRNA Construct Builder.
V. DNA constructs
The use of the term "polynucleotide" is not intended to limit the present invention to polynucleotides comprising DNA. Those of ordinary skill in the art will recognize that polynucleotides can comprise ribonucleotides and combinations of ribonucleotides and deoxyribonucleotides. Such deoxyribonucleotides and ribonucleotides include both naturally occurring molecules and synthetic analogues. The polynucleotides of the invention also encompass all forms of sequences including, but not limited to, single- stranded forms, double-stranded forms, hairpins, stem-and-loop structures, and the like.
The polynucleotide encoding the silencing element or in specific embodiments employed in the methods and compositions of the invention can be provided in expression cassettes for expression in a plant or organism of interest. It is recognized that multiple silencing elements including multiple identical silencing elements, multiple silencing elements targeting different regions of the target sequence, or multiple silencing elements from different target sequences can be used. In this embodiment, it is recognized that each silencing element can be contained in a single or separate cassette, DNA construct, or vector. As discussed, any means of providing the silencing element is contemplated. A plant or plant cell can be transformed with a single cassette comprising DNA encoding one or more silencing elements or separate cassettes comprising each silencing element can be used to transform a plant or plant cell or host cell. Likewise, a plant transformed with one component can be subsequently transformed with the second component. One or more silencing elements can also be brought together by sexual crossing. That is, a first plant comprising one component is crossed with a second plant comprising the second component. Progeny plants from the cross will comprise both components.
The expression cassette can include 5' and 3' regulatory sequences operably linked to the polynucleotide of the invention. "Operably linked" is intended to mean a functional linkage between two or more elements. For example, an operable linkage between a polynucleotide of the invention and a regulatory sequence (i.e., a promoter) is a functional link that allows for expression of the polynucleotide of the invention. Operably linked elements may be contiguous or non-contiguous. When used to refer to the joining of two protein coding regions, by operably linked is intended that the coding regions are in the same reading frame. The cassette may additionally contain at least one additional polynucleotide to be cotransformed into the organism. Alternatively, the additional polypeptide(s) can be provided on multiple expression cassettes. Expression cassettes can be provided with a plurality of restriction sites and/or recombination sites for insertion of the polynucleotide to be under the transcriptional regulation of the regulatory regions. The expression cassette may additionally contain selectable marker genes.
The expression cassette can include in the 5'-3' direction of transcription, a transcriptional and translational initiation region (i.e., a promoter), a polynucleotide comprising the silencing element employed in the methods and compositions of the invention, and a transcriptional and translational termination region (i.e., termination region) functional in plants. In other embodiment, the double stranded RNA is expressed from a suppression cassette. Such a cassette can comprise two convergent promoters that drive transcription of an operably linked silencing element. "Convergent promoters" refers to promoters that are oriented on either terminus of the operably linked silencing element such that each promoter drives transcription of the silencing element in opposite directions, yielding two transcripts. In such embodiments, the convergent promoters allow for the transcription of the sense and anti-sense strand and thus allow for the formation of a dsRNA.
The regulatory regions (i.e., promoters, transcriptional regulatory regions, and translational termination regions) and/or the polynucleotides employed in the invention may be native/analogous to the host cell or to each other. Alternatively, the regulatory regions and/or the polynucleotide employed in the invention may be heterologous to the host cell or to each other. As used herein, "heterologous" in reference to a sequence is a sequence that originates from a foreign species, or, if from the same species, is substantially modified from its native form in composition and/or genomic locus by deliberate human intervention. For example, a promoter operably linked to a heterologous polynucleotide is from a species different from the species from which the polynucleotide was derived, or, if from the same/analogous species, one or both are substantially modified from their original form and/or genomic locus, or the promoter is not the native promoter for the operably linked polynucleotide. As used herein, a chimeric gene comprises a coding sequence operably linked to a transcription initiation region that is heterologous to the coding sequence.
The termination region may be native with the transcriptional initiation region, may be native with the operably linked polynucleotide encoding the silencing element, may be native with the plant host, or may be derived from another source (i.e., foreign or heterologous) to the promoter, the polynucleotide comprising silencing element, the plant host, or any combination thereof. Convenient termination regions are available from the Ti-plasmid of A. tumefaciens, such as the octopine synthase and nopaline synthase termination regions. See also Guerineau et al. (1991) Mol. Gen. Genet. 262: 141-144; Proudfoot (1991) O?// 64:671-674; Sanfacon et al. (1991) Genes Dev. 5: 141-149; Mogen et al. (1990) Plant Cell 2: 1261-1272; Munroe et al. (1990) Gene 91 : 151-158; Ballas et al. (1989) Nucleic Acids Res. 17:7891-7903; and Joshi et al. (1987) Nucleic Acids Res.
15:9627-9639. Additional sequence modifications are known to enhance gene expression in a cellular host. These include elimination of sequences encoding spurious polyadenylation signals, exon-intron splice site signals, transposon-like repeats, and other such well- characterized sequences that may be deleterious to gene expression. The G-C content of the sequence may be adjusted to levels average for a given cellular host, as calculated by reference to known genes expressed in the host cell. When possible, the sequence is modified to avoid predicted hairpin secondary mRNA structures.
In preparing the expression cassette, the various DNA fragments may be manipulated, so as to provide for the DNA sequences in the proper orientation and, as appropriate, in the proper reading frame. Toward this end, adapters or linkers may be employed to join the DNA fragments or other manipulations may be involved to provide for convenient restriction sites, removal of superfluous DNA, removal of restriction sites, or the like. For this purpose, in vitro mutagenesis, primer repair, restriction, annealing, resubstitutions, e.g., transitions and transversions, may be involved.
A number of promoters can be used in the practice of the invention. The polynucleotide encoding the silencing element can be combined with constitutive, tissue- preferred, or other promoters for expression in plants.
Such constitutive promoters include, for example, the core promoter of the Rsyn7 promoter and other constitutive promoters disclosed in WO 99/43838 and U.S. Patent No. 6,072,050; the core CaMV 35S promoter (Odell et al. (1985) Nature 313:810-812); rice actin (McElroy et al. (1990) Plant Cell 2: 163-171); ubiquitin (Christensen et al. (1989) Plant Mol. Biol. 12:619-632 and Christensen et al. (1992) Plant Mol. Biol. 18:675-689); pEMU (Last et al. (1991) Theor. Appl. Genet. 81 :581-588); MAS (Velten et al. (1984) EMBO J. 3:2723-2730); ALS promoter (U.S. Patent No. 5,659,026); soybean elongation factor 1A (ACUP01009998), and the like. Other constitutive promoters include, for example, U.S. Patent Nos. 5,608, 149; 5,608, 144; 5,604, 121; 5,569,597; 5,466,785;
5,399,680; 5,268,463; 5,608, 142; and 6,177,61 1.
An inducible promoter, for instance, a pathogen-inducible promoter could also be employed. Such promoters include those from pathogenesis-related proteins (PR proteins), which are induced following infection by a pathogen; e.g., PR proteins, SAR proteins, beta-l,3-glucanase, chitinase, etc. See, for example, Redolfi et al. (1983) Neth. J. Plant Pathol. 89:245-254; Uknes et al. (1992) Plant Cell 4:645-656; and Van Loon (l%5) Plant Mol Virol. 4: 111-1 16. See also WO 99/43819, herein incorporated by reference. Additionally, as pathogens find entry into plants through wounds or insect damage, a wound-inducible promoter may be used in the constructions of the invention. Such wound-inducible promoters include potato proteinase inhibitor (pin II) gene (Ryan (1990) Ann. Rev. Phytopath. 28:425-449; Duan et al. (1996) Nature Biotechnology 14:494-498); wunl and wun2, U.S. Patent No. 5,428, 148; winl and win2 (Stanford et al. (1989) Mol.
Gen. Genet. 215:200-208); systemin (McGurl et al. (1992) Science 225: 1570-1573); WIPl (Rohmeier et al. (1993) Plant Mol. Biol. 22:783-792; Eckelkamp et al. (1993) FEBS Letters 323:73-76); MPI gene (Corderok et al. (1994) Plant J. 6(2): 141-150); and the like, herein incorporated by reference.
Chemical-regulated promoters can be used to modulate the expression of a gene in a plant through the application of an exogenous chemical regulator. Depending upon the objective, the promoter may be a chemical-inducible promoter, where application of the chemical induces gene expression, or a chemical-repressible promoter, where application of the chemical represses gene expression. Chemical-inducible promoters are known in the art and include, but are not limited to, the maize In2-2 promoter, which is activated by benzenesulfonamide herbicide safeners, the maize GST promoter, which is activated by hydrophobic electrophilic compounds that are used as pre-emergent herbicides, and the tobacco PR- la promoter, which is activated by salicylic acid. Other chemical-regulated promoters of interest include steroid-responsive promoters (see, for example, the glucocorticoid-inducible promoter in Schena et al. (1991) Proc. Natl. Acad. Sci. USA 88: 10421-10425 and McNellis et al. (1998) Plant J. 14(2):247-257) and tetracycline- inducible and tetracycline-repressible promoters (see, for example, Gatz et al. (1991) Mol. Gen. Genet. 227:229-237, and U.S. Patent Nos. 5,814,618 and 5,789,156), herein incorporated by reference.
Tissue-preferred promoters can be utilized to target enhanced expression within a particular plant tissue. Tissue-preferred promoters include Yamamoto et al. (1997) Plant J. 12(2):255-265; Kawamata et al. (1997) Plant Cell Physiol. 38(7):792-803; Hansen et al. (1997) Mol. Gen Genet. 254(3):337-343; Russell et al. (1997) Transgenic Res. 6(2): 157- 168; Rinehart et al. (1996) Plant Physiol. 1 12(3): 1331-1341 ; Van Camp et al. (1996) Plant Physiol. 112(2):525-535; Canevascini et al. (1996) Plant Physiol. 112(2):513-524; Yamamoto et al. (1994) Plant Cell Physiol. 35(5):773-778; Lam (1994) Results Probl. Cell Differ. 20: 181-196; Orozco et al. (1993) Plant Mol Biol. 23(6): 1129-1138; Matsuoka et al. (1993) Proc Natl. Acad. Sci. USA 90(20):9586-9590; and Guevara-Garcia et al. (1993) Plant J. 4(3):495-505. Such promoters can be modified, if necessary, for weak expression.
In one embodiment, the various silencing elements disclosed herein are expressed using a seed-preferred promoter. "Seed-preferred" promoters include both "seed-specific" promoters (those promoters active during seed development such as promoters of seed storage proteins) as well as "seed-germinating" promoters (those promoters active during seed germination). See Thompson et al. (1989) BioEssays 10: 108, herein incorporated by reference. Such seed-preferred promoters include, but are not limited to, Ciml (cytokinin- induced message); Kunitz trypsin inhibitor 3 (kti3) (Genbank accession AF233296); glycinin-1 genes (Genbank accession AB353075.1); cZ19B l (maize 19 kDa zein); milps (myo-inositol-1 -phosphate synthase) (see WO 00/11 177 and U.S. Patent No. 6,225,529; herein incorporated by reference). Gamma-zein is an endosperm-specific promoter. Globulin 1 (Glb-1) is a representative embryo-specific promoter. For dicots, seed- preferred promoters include, but are not limited to, bean β-phaseolin, napin, β-conglycinin alpha (Genbank accession GU723691), soybean lectin, cruciferin, and the like. For monocots, seed-preferred promoters include, but are not limited to, maize 1 kDa zein, 22 kDa zein, 27 kDa zein, gamma-zein, waxy, shrunken 1, shrunken 2, Globulin 1, etc. See also WO 00/12733, where seed-preferred promoters from endl and end2 genes are disclosed; herein incorporated by reference.
Leaf-preferred promoters are known in the art. See, for example, Yamamoto et al. (1997) Plant J. 12(2):255-265; Kwon ei «/. (1994) Plant Physiol. 105:357-67; Yamamoto et al. (1994) Plant Cell Physiol. 35(5):773-778; Gotor et al. (1993) Plant J. 3 :509-18; Orozco et al. (1993) Plant Mol. Biol. 23(6): 1 129-1138; and Matsuoka et al. (1993) Proc. Natl. Acad. Sci. USA 90(20):9586-9590.
Root-preferred promoters are known and can be selected from the many available from the literature or isolated de novo from various compatible species. See, for example, Hire et al. (1992) Plant Mol. Biol. 20(2):207-218 (soybean root-specific glutamine synthetase gene); Keller and Baumgartner (1991) Plant Cell 3(10): 1051-1061 (root- specific control element in the GRP 1.8 gene of French bean); Sanger et al. (1990) Plant Mol. Biol. 14(3):433-443 (root-specific promoter of the mannopine synthase (MAS) gene of Agrobacterium tumefaciens); and Miao et al. (1991) Plant Cell 3(1): 1 1-22 (full-length cDNA clone encoding cytosolic glutamine synthetase (GS), which is expressed in roots and root nodules of soybean). See also Bogusz et al. (1990) Plant Cell 2(7):633-641, where two root-specific promoters isolated from hemoglobin genes from the nitrogen- fixing nonlegume Parasponia andersonii and the related non-nitrogen-fixing nonlegume Trema tomentosa are described. The promoters of these genes were linked to a β- glucuronidase reporter gene and introduced into both the nonlegume Nicotiana tabacum and the legume Lotus corniculatus , and in both instances root-specific promoter activity was preserved. Leach and Aoyagi (1991) describe their analysis of the promoters of the highly expressed rolC and rolD root-inducing genes of Agrobacterium rhizogenes (see Plant Science (Limerick) 79(l):69-76). They concluded that enhancer and tissue-preferred DNA determinants are dissociated in those promoters. Teeri et at. (1989) used gene fusion to lacZ to show that the Agrobacterium T-DNA gene encoding octopine synthase is especially active in the epidermis of the root tip and that the TR2' gene is root specific in the intact plant and stimulated by wounding in leaf tissue, an especially desirable combination of characteristics for use with an insecticidal or larvicidal gene (see EMBO J. 8(2):343-350). The T 1' gene, fused to nptll (neomycin phosphotransferase II) showed similar characteristics. Additional root-preferred promoters include the VfENOD-GRP3 gene promoter (Kuster et al. (1995) Plant Mol. Biol. 29(4):759-772); and rolB promoter (Capana et al. (1994) Plant Mol. Biol. 25(4):681-691. See also U.S. Patent Nos.
5,837,876; 5,750,386; 5,633,363; 5,459,252; 5,401,836; 5, 1 10,732; and 5,023, 179.
In one embodiment of this invention the plant-expressed promoter is a vascular- specific promoter such as a phloem-specific promoter. A "vascular-specific" promoter, as used herein, is a promoter which is at least expressed in vascular cells, or a promoter which is preferentially expressed in vascular cells. Expression of a vascular-specific promoter need not be exclusively in vascular cells, expression in other cell types or tissues is possible. A "phloem-specific promoter" as used herein, is a plant-expressible promoter which is at least expressed in phloem cells, or a promoter which is preferentially expressed in phloem cells.
Expression of a phloem-specific promoter need not be exclusively in phloem cells, expression in other cell types or tissues, e.g., xylem tissue, is possible. In one embodiment of this invention, a phloem-specific promoter is a plant-expressible promoter at least expressed in phloem cells, wherein the expression in non-phloem cells is more limited (or absent) compared to the expression in phloem cells. Examples of suitable vascular- specific or phloem-specific promoters in accordance with this invention include but are not limited to the promoters selected from the group consisting of: the SCSV3, SCSV4, SCSV5, and SCSV7 promoters (Schunmann et al. (2003) Plant Functional Biology 30:453-60; the rolC gene promoter of Agrobacterium rhizogenes(Kiyokawa et al. (1994) Plant Physiology 104:801-02; Pandolfmi et al. (2003) BioMedCentral (BMC)
Biotechnology 3:7, (www.biomedcentral.com/1472-6750/3/7); Graham et al. (1997) Plant Mol. Biol. 33:729-35; Guivarc'h et al. (1996); Almon et al. (1997) Plant Physiol.
115: 1599-607; the rolA gene promoter of Agrobacterium rhizogenes (Dehio et al. (1993)
Plant Mol. Biol. 23: 1 199-210); the promoter of the Agrobacterium tumefaciens T-DNA gene 5 (Korber et al. (1991) EMBO J. 10:3983-91); the rice sucrose synthase RSsl gene promoter (Shi et al. (1994) J. Exp. Bot. 45:623-31); the CoYMV or Commelina yellow mottle badnavirus promoter (Medberry et al. (1992) Plant Cell 4: 185-92; Zhou et al. (1998) Chin. J. Biotechnol. 14:9-16); the CFDV or coconut foliar decay virus promoter (Rohde et al. (1994) Plant Mol. Biol. 27:623-28; Hehn and Rhode (1998) J. Gen. Virol. 79: 1495-99); the RTBV or rice tungro bacilliform virus promoter (Yin and Beachy (1995) Plant J. 7:969-80; Yin et al. (1997) Plant J. 12: 1 179-80); the pea glutamin synthase GS3A gene (Edwards et al. (1990) Proc. Natl. Acad. Sci. USA 87:3459-63; Brears et al. (1991) Plant J. 1 :235-44); the inv CD1 11 and inv CD141 promoters of the potato invertase genes (Hedley et al. (2000) J. Exp. Botany 51:817-21); the promoter isolated from Arabidopsis shown to have phloem-specific expression in tobacco by Kertbundit et al. (1991) Proc. Natl. Acad. Sci. USA 88:5212-16); the VAHOX1 promoter region (Tornero et al. (1996) Plant J. 9:639-48); the pea cell wall invertase gene promoter (Zhang et al. (1996) Plant Physiol. 1 12 : 1 111 - 17); the promoter of the endogenous cotton protein related to chitinase of US published patent application 20030106097, an acid invertase gene promoter from carrot (Ramloch-Lorenz et al. (1993) The Plant J. 4:545-54); the promoter of the sulfate transporter geneSultrl; 3 (Yoshimoto et al. (2003) Plant Physiol. 131 : 151 1-17); a promoter of a sucrose synthase gene (Nolte and Koch (1993) Plant Physiol. 101 :899-905); and the promoter of a tobacco sucrose transporter gene (Kuhn et al. (1997) Science 275- 1298-1300).
Possible promoters also include the Black Cherry promoter for Prunasin Hydrolase (PH DL1.4 PRO) (US Patent No. 6,797, 859), Thioredoxin H promoter from cucumber and rice (Fukuda A et al. (2005). Plant Cell Physiol. 46(11): 1779-86), Rice (RSs 1) (Shi, T. Wang et al. (1994). J. Exp. Bot. 45(274): 623-631) and maize sucrose synthese -1 promoters (Yang., N-S. et al. (1990) PNAS 87:4144-4148), PP2 promoter from pumpkin Guo, H. et al. (2004) Transgenic Research 13:559-566), At SUC2 promoter (Truernit, E. et al. (1995) Planta 196(3):564-70., At SAM-1 (S-adenosylmethionine synthetase) (Mijnsbrugge KV. et al. (1996) Planr. Cell. Physiol. 37(8): 1 108-1 115), and the Rice tungro bacilliform virus (RTBV) promoter (Bhattacharyya-Pakrasi et al. (1993) Plant J. 4(l):71-79).
The expression cassette can also comprise a selectable marker gene for the selection of transformed cells. Selectable marker genes are utilized for the selection of transformed cells or tissues. Marker genes include genes encoding antibiotic resistance, such as those encoding neomycin phosphotransferase II (NEO) and hygromycin phosphotransferase (HPT), as well as genes conferring resistance to herbicidal compounds, such as glufosinate ammonium, bromoxynil, imidazolinones, and 2,4-dichlorophenoxyacetate (2,4-D).
Additional selectable markers include phenotypic markers such as β-galactosidase and fluorescent proteins such as green fluorescent protein (GFP) (Su et al (2004) Biotechnol Bioeng 55:610-9 and Fetter et al (2004) Plant Cell 7(5:215-28), cyan fl orescent protein (CYP) (Bolte et al. (2004) J. Cell Science 777:943-54 and Kato et al. (2002) Plant Physiol 729:913-42), and yellow florescent protein (PhiYFP™ from Evrogen, see, Bolte et al. (2004) J. Cell Science 777:943-54). For additional selectable markers, see generally, Yarranton (1992) Curr. Opin. Biotech. 3:506-51 1; Christopherson et al. (1992) Proc. Natl. Acad. Set USA 89:6314-6318; Yao et al. (1992) Cell 71:63-72; Reznikoff (1992) Mol.
Microbiol. 6:2419-2422; Barkley et al. (1980) in The Operon, pp. 177-220; Hu et al. (1987) Cell 48:555-566; Brown e^/. (1987) Cell 49:603-612; Figge et al. (1988) Cell 52:713-722; Deuschle et al. (1989) Proc. Natl. Acad. Sci. USA 86:5400-5404; Fuerst et al. (1989) Proc. Natl. Acad. Sci. USA 86:2549-2553; Deuschle et al. (1990) Science 248:480-483; Gossen (1993) Ph.D. Thesis, University of Heidelberg; Reines et al. (1993) Proc. Natl. Acad. Sci. USA 90: 1917-1921; Labow et al. (1990) Mol. Cell. Biol. 10:3343-3356; Zambretti et al (1992) Proc. Natl. Acad. Sci. USA 89:3952-3956; Bairn et al. (1991) Proc. Natl Acad. Sci. USA 88:5072-5076; Wyborski et al. (1991) Nucleic Acids Res. 19:4647-4653; Hillenand- Wissman (1989) Topics Mol. Struc. Biol. 10: 143-162; Degenkolb et al. (1991) Antimicrob. Agents Chemother. 35: 1591-1595; Kleinschnidt et al. (1988) Biochemistry 27: 1094-1104; Bonin (1993) Ph.D. Thesis, University of Heidelberg; Gossen et al. (1992) Proc. Natl. Acad. Sci. USA 89:5547-5551; C iva l/. (1992) Antimicrob. Agents Chemother. 36:913-919; Hlavka et al. (1985) Handbook of Experimental Pharmacology, Vol. 78 ( Springer- Verlag, Berlin); Gill et al. (1988) Nature 334:721-724. Such disclosures are herein incorporated by reference. The above list of selectable marker genes is not meant to be limiting. Any selectable marker gene can be used in the present invention. VI. Compositions Comprising Silencing Elements
One or more of the polynucleotides comprising the silencing element can be provided as an external composition such as a spray or powder to the plant, plant part, seed, a pest, or an area of cultivation. In another example, a plant is transformed with a DNA construct or expression cassette for expression of at least one silencing element. In either composition, the silencing element, when ingested by an insect, can reduce the level of a target pest sequence and thereby control the pest (i.e., a Pentatomidae plant pest including a N. viridula, Acrosternum Mare, Piezodorus guildini, and/or Halymorpha halys. It is recognized that the composition can comprise a cell (such as plant cell or a bacterial cell), in which a polynucleotide encoding the silencing element is stably incorporated into the genome and operably linked to promoters active in the cell.
Compositions comprising a mixture of cells, some cells expressing at least one silencing element are also encompassed. In other embodiments, compositions comprising the silencing elements are not contained in a cell. In such embodiments, the composition can be applied to an area inhabited by a pest. In one embodiment, the composition is applied externally to a plant (i.e., by spraying a field or area of cultivation) to protect the plant from the pest.
The composition of the invention can further be formulated as bait. In this embodiment, the compositions comprise a food substance or an attractant which enhances the attractiveness of the composition to the pest.
The composition comprising the silencing element can be formulated in an agriculturally suitable and/or environmentally acceptable carrier. Such carriers can be any material that the animal, plant or environment to be treated can tolerate. Furthermore, the carrier must be such that the composition remains effective at controlling a pest.
Examples of such carriers include water, saline, Ringer's solution, dextrose or other sugar solutions, Hank's solution, and other aqueous physiologically balanced salt solutions, phosphate buffer, bicarbonate buffer and Tris buffer. In addition, the composition may include compounds that increase the half-life of a composition.
It is recognized that the polynucleotides comprising sequences encoding the silencing element can be used to transform organisms to provide for host organism production of these components, and subsequent application of the host organism to the environment of the target pest(s). Such host organisms include baculoviruses, bacteria, and the like. In this manner, the combination of polynucleotides encoding the silencing element may be introduced via a suitable vector into a microbial host, and said host applied to the environment, or to plants or animals.
The term "introduced" in the context of inserting a nucleic acid into a cell, means "transfection" or "transformation" or "transduction" and includes reference to the incorporation of a nucleic acid into a eukaryotic or prokaryotic cell where the nucleic acid may be stably incorporated into the genome of the cell (e.g., chromosome, plasmid, plastid, or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (e.g., transfected mRNA).
Microbial hosts that are known to occupy the "phytosphere" (phylloplane, phyllosphere, rhizosphere, and/or rhizoplana) of one or more crops of interest may be selected. These microorganisms are selected so as to be capable of successfully competing in the particular environment with the wild-type microorganisms, provide for stable maintenance and expression of the sequences encoding the silencing element, and desirably, provide for improved protection of the components from environmental degradation and inactivation.
Such microorganisms include bacteria, algae, and fungi. Of particular interest are microorganisms such as bacteria, e.g., Pseudomonas, Erwinia, Serratia, Klebsiella, Xanthomonas, Streptomyces, Rhizobium, Rhodopseudomonas, Methylius, Agrobacterium, Acetobacter, Lactobacillus, Arthrobacter, Azotobacter, Leuconostoc, and Alcaligenes, fungi, particularly yeast, e.g., Saccharomyces, Cryptococcus, Kluyveromyces,
Sporobolomyces, Rhodotorula, and Aureobasidium. Of particular interest are such phytosphere bacterial species as Pseudomonas syringae, Pseudomonas fluorescens, Serratia marcescens, Acetobacter xylinum, Agrobacteria, Rhodopseudomonas spheroides, Xanthomonas campestris, Rhizobium melioti, Alcaligenes entrophus, Clavibacter xyli and Azotobacter vinlandir, and phytosphere yeast species such as Rhodotorula rubra, R. glutinis, R. marina, R. aurantiaca, Cryptococcus albidus, C. diffluens, C. laurentii, Saccharomyces rosei, S. pretoriensis, S. cerevisiae, Sporobolomyces rosues, S. odorus, Kluyveromyces veronae, and Aureobasidium pollulans. Of particular interest are the pigmented microorganisms.
A number of ways are available for introducing the polynucleotide comprising the silencing element into the microbial host under conditions that allow for stable maintenance and expression of such nucleotide encoding sequences. For example, expression cassettes can be constructed which include the nucleotide constructs of interest operably linked with the transcriptional and translational regulatory signals for expression of the nucleotide constructs, and a nucleotide sequence homologous with a sequence in the host organism, whereby integration will occur, and/or a replication system that is functional in the host, whereby integration or stable maintenance will occur.
Transcriptional and translational regulatory signals include, but are not limited to, promoters, transcriptional initiation start sites, operators, activators, enhancers, other regulatory elements, ribosomal binding sites, an initiation codon, termination signals, and the like. See, for example, U.S. Patent Nos. 5,039,523 and 4,853,331 ; EPO 0480762A2;
Sambrook et at. (2000); Molecular Cloning: A Laboratory Manual (3r^ ed.; Cold Spring Harbor Laboratory Press, Plainview, NY); Davis et al. (1980) Advanced Bacterial
Genetics (Cold Spring Harbor Laboratory, Cold Spring Harbor, NY); and the references cited therein.
Suitable host cells include the prokaryotes and the lower eukaryotes, such as fungi. Illustrative prokaryotes, both Gram-negative and Gram-positive, include
Enterobacteriaceae, such as Escherichia, Erwinia, Shigella, Salmonella, and Proteus; Bacillaceae; Rhizobiceae, such as Rhizobium; Spirillaceae, such as photobacterium, Zymomonas , Serratia, Aeromonas, Vibrio, Desulfovibrio, Spirillum; Lactobacillaceae; Pseudomonadaceae, such as Pseudomonas and Acetobacter; Azotobacteraceae and Nitrobacteraceae. Among eukaryotes are fungi, such as Phycomycetes and Ascomycetes, which includes yeast, such as Saccharomyces and Schizosaccharomyces; and
Basidiomycetes yeast, such as Rhodotorula, Aureobasidium, Sporobolomyces, and the like.
Characteristics of particular interest in selecting a host cell for purposes of the invention include ease of introducing the coding sequence into the host, availability of expression systems, efficiency of expression, stability in the host, and the presence of auxiliary genetic capabilities. Characteristics of interest for use as a pesticide
microcapsule include protective qualities, such as thick cell walls, pigmentation, and intracellular packaging or formation of inclusion bodies; leaf affinity; lack of mammalian toxicity; attractiveness to pests for ingestion; and the like. Other considerations include ease of formulation and handling, economics, storage stability, and the like.
Host organisms of particular interest include yeast, such as Rhodotorula spp.,
Aureobasidium spp., Saccharomyces spp., and Sporobolomyces spp. , phylloplane organisms such as Pseudomonas spp. , Erwinia spp., and Flavobacterium spp. , and other such organisms, including Pseudomonas aeruginosa, Pseudomonas fluorescens,
Saccharomyces cerevisiae, Bacillus thuringiensis, Escherichia coli, Bacillus subtilis, and the like.
The sequences encoding the silencing elements encompassed by the invention can be introduced into microorganisms that multiply on plants (epiphytes) to deliver these components to potential target pests. Epiphytes, for example, can be gram-positive or gram-negative bacteria.
The silencing element can be fermented in a bacterial host and the resulting bacteria processed and used as a microbial spray in the same manner that Bacillus thuringiensis strains have been used as insecticidal sprays. Any suitable microorganism can be used for this purpose. Pseudomonas has been used to express Bacillus
thuringiensis endotoxins as encapsulated proteins and the resulting cells processed and sprayed as an insecticide Gaertner et al. (1993), in Advanced Engineered Pesticides, ed. L. Kim (Marcel Decker, Inc.).
Alternatively, the components of the invention are produced by introducing heterologous genes into a cellular host. Expression of the heterologous sequences results, directly or indirectly, in the intracellular production of the silencing element. These compositions may then be formulated in accordance with conventional techniques for application to the environment hosting a target pest, e.g., soil, water, and foliage of plants. See, for example, EPA 0192319, and the references cited therein.
In the present invention, a transformed microorganism can be formulated with an acceptable carrier into separate or combined compositions that are, for example, a suspension, a solution, an emulsion, a dusting powder, a dispersible granule, a wettable powder, and an emulsifiable concentrate, an aerosol, an impregnated granule, an adjuvant, a coatable paste, and also encapsulations in, for example, polymer substances.
Such compositions disclosed above may be obtained by the addition of a surface- active agent, an inert carrier, a preservative, a humectant, a feeding stimulant, an attractant, an encapsulating agent, a binder, an emulsifier, a dye, a UV protectant, a buffer, a flow agent or fertilizers, micronutrient donors, or other preparations that influence plant growth. One or more agrochemicals including, but not limited to, herbicides, insecticides, fungicides, bactericides, nematicides, molluscicides, acaracides, plant growth regulators, harvest aids, and fertilizers, can be combined with carriers, surfactants or adjuvants customarily employed in the art of formulation or other components to facilitate product handling and application for particular target pests. Suitable carriers and adjuvants can be solid or liquid and correspond to the substances ordinarily employed in formulation technology, e.g., natural or regenerated mineral substances, solvents, dispersants, wetting agents, tackifiers, binders, or fertilizers. The active ingredients of the present invention (i.e., at least one silencing element) are normally applied in the form of compositions and can be applied to the crop area, plant, or seed to be treated. For example, the compositions may be applied to grain in preparation for or during storage in a grain bin or silo, etc. The compositions may be applied simultaneously or in succession with other compounds. Methods of applying an active ingredient or a composition that contains at least one silencing element include, but are not limited to, foliar application, seed coating, and soil application. The number of applications and the rate of application depend on the intensity of infestation by the corresponding pest.
Suitable surface-active agents include, but are not limited to, anionic compounds such as a carboxylate of, for example, a metal; carboxylate of a long chain fatty acid; an N-acylsarcosinate; mono- or di-esters of phosphoric acid with fatty alcohol ethoxylates or salts of such esters; fatty alcohol sulfates such as sodium dodecyl sulfate, sodium octadecyl sulfate, or sodium cetyl sulfate; ethoxylated fatty alcohol sulfates; ethoxylated alkylphenol sulfates; lignin sulfonates; petroleum sulfonates; alkyl aryl sulfonates such as alkyl-benzene sulfonates or lower alkylnaphtalene sulfonates, e.g., butyl-naphthalene sulfonate; salts of sulfonated naphthalene-formaldehyde condensates; salts of sulfonated phenol-formaldehyde condensates; more complex sulfonates such as the amide sulfonates, e.g., the sulfonated condensation product of oleic acid and N-methyl taurine; or the dialkyl sulfosuccinates, e.g., the sodium sulfonate or dioctyl succinate. Non-ionic agents include condensation products of fatty acid esters, fatty alcohols, fatty acid amides or fatty-alkyl- or alkenyl-substituted phenols with ethylene oxide, fatty esters of polyhydric alcohol ethers, e.g., sorbitan fatty acid esters, condensation products of such esters with ethylene oxide, e.g., polyoxyethylene sorbitan fatty acid esters, block copolymers of ethylene oxide and propylene oxide, acetylenic glycols such as 2,4,7,9-tetraethyl-5-decyn-4,7-diol, or ethoxylated acetylenic glycols. Examples of a cationic surface-active agent include, for instance, an aliphatic mono-, di-, or polyamine such as an acetate, naphthenate or oleate; or oxygen-containing amine such as an amine oxide of polyoxyethylene alkylamine; an amide-linked amine prepared by the condensation of a carboxylic acid with a di- or polyamine; or a quaternary ammonium salt. Examples of inert materials include, but are not limited to, inorganic minerals such as kaolin, phyllosilicates, carbonates, sulfates, phosphates, or botanical materials such as cork, powdered corncobs, peanut hulls, rice hulls, and walnut shells.
The compositions comprising the silencing element can be in a suitable form for direct application or as a concentrate of primary composition that requires dilution with a suitable quantity of water or other dilutant before application.
The compositions (including the transformed microorganisms) can be applied to the environment of an insect pest (such as a Pentatomidae plant pest or a N. viridula, Acrosternum hilare, Piezodorus guildini, and/or Halymorpha halys plant pest) by, for example, spraying, atomizing, dusting, scattering, coating or pouring, introducing into or on the soil, introducing into irrigation water, by seed treatment or general application or dusting at the time when the pest has begun to appear or before the appearance of pests as a protective measure. For example, the composition(s) and/or transformed
microorganism(s) may be mixed with grain to protect the grain during storage. It is generally important to obtain good control of pests in the early stages of plant growth, as this is the time when the plant can be most severely damaged. The compositions can conveniently contain another insecticide if this is thought necessary. In an embodiment of the invention, the composition(s) is applied directly to the soil, at a time of planting, in granular form of a composition of a carrier and dead cells of a Bacillus strain or transformed microorganism of the invention. Another embodiment is a granular form of a composition comprising an agrochemical such as, for example, a herbicide, an insecticide, a fertilizer, in an inert carrier, and dead cells of a Bacillus strain or transformed microorganism of the invention. VII Plants, Plant Parts, and Methods of Introducing Sequences into Plants
The methods of the invention involve introducing a polynucleotide into a plant. In one embodiment, a plant cell is provided having stably incorporated into its genome a heterologous polynucleotide comprising any of the various silencing elements provided herein. It is recognized that the silencing element, when ingested by a Pentatomidae plant pest, can reduce the level of expression of any of the target sequences descrbed herein (i.e. SEQ ID NOS: 1-292 or 302-304). "Introducing" is intended to mean presenting to the plant the polynucleotide in such a manner that the sequence gains access to the interior of a cell of the plant. The methods of the invention do not depend on a particular method for introducing a sequence into a plant, only that the polynucleotide or polypeptides gains access to the interior of at least one cell of the plant. Methods for introducing
polynucleotides into plants are known in the art including, but not limited to, stable transformation methods, transient transformation methods, and virus-mediated methods.
"Stable transformation" is intended to mean that the nucleotide construct introduced into a plant integrates into the genome of the plant and is capable of being inherited by the progeny thereof. "Transient transformation" is intended to mean that a polynucleotide is introduced into the plant and does not integrate into the genome of the plant or a polypeptide is introduced into a plant.
Transformation protocols as well as protocols for introducing polypeptides or polynucleotide sequences into plants may vary depending on the type of plant or plant cell, i.e., monocot or dicot, targeted for transformation. Suitable methods of introducing polypeptides and polynucleotides into plant cells include microinjection (Crossway et al. (1986) Biotechniques 4:320-334), electroporation ( iggs et al. (1986) Proc. Natl. Acad. Sci. USA 83:5602-5606, Agrobacterium- edmted transformation (U.S. Patent No.
5,563,055 and U.S. Patent No. 5,981,840), direct gene transfer (Paszkowski et al. (1984) EMBO J. 3:2717-2722), and ballistic particle acceleration (see, for example, U.S. Patent Nos. 4,945,050; U.S. Patent No. 5,879,918; U.S. Patent No. 5,886,244; and, 5,932,782; Tomes et al. (1995) in Plant Cell, Tissue, and Organ Culture: Fundamental Methods, ed. Gamborg and Phillips (Springer-Verlag, Berlin); McCabe et al. (1988) Biotechnology 6:923-926); and Led transformation (WO 00/28058). Also see Weissinger et al. (1988) Ann. Rev. Genet. 22:421-477; Sanford et al. (1987) Particulate Science and Technology 5:27-37 (onion); Christou et al. (1988) Plant Physiol. 87:671-674 (soybean); McCabe et al. (1988) Bio/Technology 6:923-926 (soybean); Finer and McMullen (1991) In Vitro Cell Dev. Biol. 27P: 175-182 (soybean); Singh et al. (1998) Theor. Appl. Genet. 96:319-324 (soybean); Datta et al. (1990) Biotechnology 8:736-740 (rice); Klein et al. (1988) Proc.
Natl. Acad. Sci. USA 85:4305-4309 (maize); Klein et al. (1988) Biotechnology 6:559-563 (maize); U.S. Patent Nos. 5,240,855; 5,322,783; and, 5,324,646; Klein et al. (1988) Plant Physiol 91:440-444 (maize); Fromm et al. (1990) Biotechnology 8:833-839 (maize); Hooykaas-Van Slogteren et al. (1984) Nature (London) 311 :763-764; U.S. Patent No. 5,736,369 (cereals); Bytebier et al. (1987) Proc. Natl. Acad. Sci. USA 84:5345-5349
(Liliaceae); De Wet et al. (1985) in The Experimental Manipulation of Ovule Tissues, ed. Chapman et al. (Longman, New York), pp. 197-209 (pollen); Kaeppler et al. (1990) Plant Cell Reports 9:415-418 and Kaeppler et al. (1992) Theor. Appl. Genet. 84:560-566 (whisker-mediated transformation); D'Halluin et al. (1992) Plant Cell 4: 1495-1505 (electroporation); Li et al. (1993) Plant Cell Reports 12:250-255 and Christou and Ford (1995) Annals of Botany 75:407-413 (rice); Osjoda et al. (1996) Nature Biotechnology 14:745-750 (maize via Agrobacterium tumefaciens); all of which are herein incorporated by reference.
In specific embodiments, the silencing element sequences of the invention can be provided to a plant using a variety of transient transformation methods. Such transient transformation methods include, but are not limited to, the introduction of the protein or variants and fragments thereof directly into the plant or the introduction of the transcript into the plant. Such methods include, for example, microinjection or particle bombardment. See, for example, Crossway et al. (1986) Mol Gen. Genet. 202: 179-185; Nomura et al, (1986) Plant Sci. 44:53-58; Hepler et al. (1994) Proc. Natl. Acad. Sci. 91: 2176-2180 and Hush et al. (1994) The Journal of Cell Science 707:775-784, all of which are herein incorporated by reference. Alternatively, polynucleotides can be transiently transformed into the plant using techniques known in the art. Such techniques include viral vector system and the precipitation of the polynucleotide in a manner that precludes subsequent release of the DNA. Thus, the transcription from the particle-bound DNA can occur, but the frequency with which it is released to become integrated into the genome is greatly reduced. Such methods include the use of particles coated with polyethylimine (PEI; Sigma #P3143).
In other embodiments, the polynucleotide of the invention may be introduced into plants by contacting plants with a virus or viral nucleic acids. Generally, such methods involve incorporating a nucleotide construct of the invention within a viral DNA or RNA molecule. Further, it is recognized that promoters of the invention also encompass promoters utilized for transcription by viral RNA polymerases. Methods for introducing polynucleotides into plants and expressing a protein encoded therein, involving viral DNA or RNA molecules, are known in the art. See, for example, U.S. Patent Nos. 5,889,191, 5,889,190, 5,866,785, 5,589,367, 5,316,931, and Porta et al. (1996) Molecular
Biotechnology 5:209-221 ; herein incorporated by reference.
Methods are known in the art for the targeted insertion of a polynucleotide at a specific location in the plant genome. In one embodiment, the insertion of the polynucleotide at a desired genomic location is achieved using a site-specific recombination system. See, for example, W099/25821, W099/25854, WO99/25840, W099/25855, and W099/25853, all of which are herein incorporated by reference. Briefly, the polynucleotide of the invention can be contained in transfer cassette flanked by two non-recombinogenic recombination sites. The transfer cassette is introduced into a plant having stably incorporated into its genome a target site which is flanked by two non- recombinogenic recombination sites that correspond to the sites of the transfer cassette. An appropriate recombinase is provided and the transfer cassette is integrated at the target site. The polynucleotide of interest is thereby integrated at a specific chromosomal position in the plant genome.
The cells that have been transformed may be grown into plants in accordance with conventional ways. See, for example, McCormick et al. (1986) Plant Cell Reports 5:81- 84. These plants may then be grown, and either pollinated with the same transformed strain or different strains, and the resulting progeny having constitutive expression of the desired phenotypic characteristic identified. Two or more generations may be grown to ensure that expression of the desired phenotypic characteristic is stably maintained and inherited and then seeds harvested to ensure expression of the desired phenotypic characteristic has been achieved. In this manner, the present invention provides transformed seed (also referred to as "transgenic seed") having a polynucleotide of the invention, for example, an expression cassette of the invention, stably incorporated into their genome.
As used herein, the term plant also includes plant cells, plant protoplasts, plant cell tissue cultures from which plants can be regenerated, plant calli, plant clumps, and plant cells that are intact in plants or parts of plants such as embryos, pollen, ovules, seeds, leaves, flowers, branches, fruit, kernels, ears, cobs, husks, stalks, roots, root tips, anthers, and the like. Grain is intended to mean the mature seed produced by commercial growers for purposes other than growing or reproducing the species. Progeny, variants, and mutants of the regenerated plants are also included within the scope of the invention, provided that these parts comprise the introduced polynucleotides.
The present invention may be used for transformation of any plant species, including, but not limited to, monocots and dicots. Examples of plant species of interest include, but are not limited to, corn (Zea mays), Brassica sp. (e.g., B. napus, B. rapa, B.juncea), particularly those Brassica species useful as sources of seed oil, alfalfa (Medicago sativa), rice (Oryza sativa), rye (Secale cereale), sorghum (Sorghum bicolor, Sorghum vulgare), millet (e.g., pearl millet (Pennisetum glaucum), proso millet (Panicum miliaceum), foxtail millet (Setaria italica), finger millet (Eleusine coracana)), sunflower (Helianthus annuus), safflower (Carthamus tinctorius), wheat (Triticum aestivum), soybean (Glycine max), tobacco (Nicotiana tabacum), potato (Solanum tuberosum), peanuts (Arachis hypogaea), cotton (Gossypium barbadense, Gossypium hirsutum), sweet potato (Ipomoea batatas), cassava (Manihot esculenta), coffee (Coffea spp.), coconut (Cocos nucifera), pineapple (Ananas comosus), cirrus trees (Citrus spp.), cocoa (Theobroma cacao), tea (Camellia sinensis), banana (Musa spp.), avocado (Persea americana), fig (Ficus casica), guava (Psidium guajava), mango (Mangifera indica), olive (Olea europaea), papaya (Carica papaya), cashew (Anacardium occidentale), macadamia (Macadamia integrifolia), almond (Prunus amygdalus), sugar beets (Beta vulgaris), sugarcane (Saccharum spp.), oats, barley, vegetables, ornamentals, and conifers.
Vegetables include tomatoes (Lycopersicon esculentum), lettuce (e.g., Lactuca sativa), green beans (Phaseolus vulgaris), lima beans (Phaseolus limensis), peas (Lathyrus spp.), and members of the genus Cucumis such as cucumber (C. sativus), cantaloupe (C. cantalupensis), and musk melon (C melo). Ornamentals include azalea (Rhododendron spp.), hydrangea (Macrophylla hydrangea), hibiscus (Hibiscus rosasanensis), roses (Rosa spp.), tulips (Tulipa spp.), daffodils (Narcissus spp.), petunias (Petunia hybrida), carnation (Dianthus caryophyllus), poinsettia (Euphorbia pulcherrima), and chrysanthemum.
Conifers that may be employed in practicing the present invention include, for example, pines such as loblolly pine (Pinus taeda), slash pine (Pinus elliotii), ponderosa pine (Pinus ponderosa), lodgepole pine (Pinus contorta), and Monterey pine (Pinus radiata); Douglas-fir (Pseudotsuga menziesii); Western hemlock (Tsuga canadensis); Sitka spruce (Picea glauca); redwood (Sequoia sempervirens); true firs such as silver fir (Abies amabilis) and balsam fir (Abies balsamea); and cedars such as Western red cedar (Thuja plicata) and Alaska yellow-cedar (Chamaecyparis nootkatensis). In specific embodiments, plants of the present invention are crop plants (for example, corn, alfalfa, sunflower, Brassica, soybean, cotton, safflower, peanut, sorghum, wheat, millet, tobacco, etc.). In other embodiments, corn and soybean plants and sugarcane plants are optimal, and in yet other embodiments corn plants are optimal.
Other plants of interest include grain plants that provide seeds of interest, oil-seed plants, and leguminous plants. Seeds of interest include grain seeds, such as corn, wheat, barley, rice, sorghum, rye, etc. Oil-seed plants include cotton, soybean, safflower, sunflower, Brassica, maize, alfalfa, palm, coconut, etc. Leguminous plants include beans and peas. Beans include guar, locust bean, fenugreek, soybean, garden beans, cowpea, mungbean, lima bean, fava bean, lentils, chickpea, etc. In specific embodiments, the plants/plant cells and/or seeds comprising an expression construct comprise a silencing element directed to a target sequence provided herein (i.e. SEQ ID NOS: 1-292 or 302-304) operably linked to a seed-preferred promoter. VIII. Methods of Use
The methods of the invention comprise methods for controlling a pest (i.e., a Pentatomidae plant pest, such as, N. viridula, Acrosternum hilare, Piezodorus guildini, and/or Halymorpha halys plant pest). The method comprises feeding to a pest a composition comprising a silencing element of the invention, wherein said silencing element, when ingested by a pest (i.e., a Pentatomidae plant pest including N. viridula,
Acrosternum hilare, Piezodorus guildini, and 'or Halymorpha halys), reduces the level of a target polynucleotide of the pest and thereby controls the pest. The pest can be fed the silencing element in a variety of ways. For example, in one embodiment, the
polynucleotide comprising the silencing element is introduced into a plant. As the Pentatomidae plant pest or N. viridula, Acrosternum hilare, Piezodorus guildini, and/or
Halymorpha halys plant pest feeds on the plant or part thereof expressing these sequences, the silencing element is delivered to the pest. When the silencing element is delivered to the plant in this manner, it is recognized that the silencing element can be expressed constitutively or alternatively, it may be produced in a stage-specific manner by employing the various inducible or tissue -preferred or developmentally regulated promoters that are discussed elsewhere herein. In one embodiment, the silencing element is operably linked to a seed-preferred promoter. In specific embodiments, the silencing element expressed in the roots, stalk or stem, leaf including pedicel, xylem and phloem, fruit or reproductive tissue, silk, flowers and all parts therein or any combination thereof.
In another method, a composition comprising at least one silencing element of the invention is applied to a plant. In such embodiments, the silencing element can be formulated in an agronomically suitable and/or environmentally acceptable carrier, which is preferably, suitable for dispersal in fields. In addition, the carrier can also include compounds that increase the half life of the composition. In specific embodiments, the composition comprising the silencing element is formulated in such a manner such that it persists in the environment for a length of time sufficient to allow it to be delivered to a pest. In such embodiments, the composition can be applied to an area inhabited by a pest. In one embodiment, the composition is applied externally to a plant (i.e., by spraying a field) to protect the plant from pests. In certain embodiments, the constructs of the present invention can be stacked with any combination of polynucleotide sequences of interest in order to create plants with a desired trait. A trait, as used herein, refers to the phenotype derived from a particular sequence or groups of sequences. For example, the polynucleotides of the present invention may be stacked with any other polynucleotides encoding polypeptides having pesticidal and/or insecticidal activity, such as other Bacillus thuringiensis toxic proteins (described in U.S. Patent Nos. 5,366,892; 5,747,450; 5,737,514; 5,723,756; 5,593,881 ; and Geiser et al. (1986) Gene 48: 109), lectins (Van Damme et al. (1994) Plant Mol. Biol. 24:825, pentin (described in U.S. Patent No. 5,981,722), and the like. The combinations generated can also include multiple copies of any one of the polynucleotides of interest. The polynucleotides of the present invention can also be stacked with any other gene or combination of genes to produce plants with a variety of desired trait combinations including, but not limited to, traits desirable for animal feed such as high oil genes (e.g., U.S. Patent No. 6,232,529); balanced amino acids (e.g., hordothionins (U.S. Patent Nos. 5,990,389; 5,885,801 ; 5,885,802; and 5,703,409); barley high lysine (Williamson et al. (1987) Eur. J. Biochem. 165:99-106; and WO 98/20122) and high methionine proteins (Pedersen et al. (1986) J. Biol. Chem. 261 :6279; Kirihara et al. (1988) Gene 71 :359; and Musumura et al. (1989) Plant Mol. Biol. 12: 123)); increased digestibility (e.g., modified storage proteins (U.S. Application Serial No. 10/053,410, filed November 7, 2001); and thioredoxins (U.S. Application Serial No. 10/005,429, filed December 3, 2001)); the disclosures of which are herein incorporated by reference.
The polynucleotides of the present invention can also be stacked with traits desirable for disease or herbicide resistance (e.g., fumonisin detoxification genes (U.S. Patent No. 5,792,931); avirulence and disease resistance genes (Jones et al. (1994) Science 266:789; Martin et al. (1993) Science 262: 1432; Mindrinos et al. (1994) Cell 78: 1089); acetolactate synthase (ALS) mutants that lead to herbicide resistance such as the S4 and/or Hra mutations; inhibitors of glutamine synthase such as phosphinothricin or basta (e.g., bar gene); and glyphosate resistance (EPSPS gene)); and traits desirable for processing or process products such as high oil (e.g., U.S. Patent No. 6,232,529 ); modified oils (e.g., fatty acid desaturase genes (U.S. Patent No. 5,952,544; WO 94/11516)); modified starches (e.g., ADPG pyrophosphorylases (AGPase), starch synthases (SS), starch branching enzymes (SBE), and starch debranching enzymes (SDBE)); and polymers or bioplastics (e.g., U.S. Patent No. 5.602,321 ; beta-ketothiolase, polyhydroxybutyrate synthase, and acetoacetyl-CoA reductase (Schubert et al. (1988) J Bacteriol. 170:5837-5847) facilitate expression of polyhydroxyalkanoates (PHAs)); the disclosures of which are herein incorporated by reference. One could also combine the polynucleotides of the present invention with polynucleotides providing agronomic traits such as male sterility (e.g., see U.S. Patent No. 5.583,210), stalk strength, flowering time, or transformation technology traits such as cell cycle regulation or gene targeting (e.g., WO 99/61619, WO 00/17364, and WO 99/25821); the disclosures of which are herein incorporated by reference.
These stacked combinations can be created by any method including, but not limited to, cross-breeding plants by any conventional or TopCross methodology, or genetic transformation. If the sequences are stacked by genetically transforming the plants, the polynucleotide sequences of interest can be combined at any time and in any order. For example, a transgenic plant comprising one or more desired traits can be used as the target to introduce further traits by subsequent transformation. The traits can be introduced simultaneously in a co-transformation protocol with the polynucleotides of interest provided by any combination of transformation cassettes. For example, if two sequences will be introduced, the two sequences can be contained in separate
transformation cassettes (trans) or contained on the same transformation cassette (cis). Expression of the sequences can be driven by the same promoter or by different promoters. In certain cases, it may be desirable to introduce a transformation cassette that will suppress the expression of the polynucleotide of interest. This may be combined with any combination of other suppression cassettes or overexpression cassettes to generate the desired combination of traits in the plant. It is further recognized that polynucleotide sequences can be stacked at a desired genomic location using a site-specific recombination system. See, for example, W099/25821, W099/25854, WO99/25840, W099/25855, and W099/25853, all of which are herein incorporated by reference.
Methods and compositions are further provided which allow for an increase in
RNAi produced from the silencing element. In such embodiments, the methods and compositions employ a first polynucleotide comprising a silencing element for a target pest sequence operably linked to a promoter active in the plant cell; and, a second polynucleotide comprising a suppressor enhancer element comprising the target pest sequence or an active variant or fragment thereof operably linked to a promoter active in the plant cell. The combined expression of the silencing element with suppressor enhancer element leads to an increased amplification of the inhibitory RNA produced from the silencing element over that achievable with only the expression of the silencing element alone. In addition to the increased amplification of the specific RNAi species itself, the methods and compositions further allow for the production of a diverse population of RNAi species that can enhance the effectiveness of disrupting target gene expression. As such, when the suppressor enhancer element is expressed in a plant cell in combination with the silencing element, the methods and composition can allow for the systemic production of RNAi throughout the plant; the production of greater amounts of RNAi than would be observed with just the silencing element construct alone; and, the improved loading of RNAi into the phloem of the plant, thus providing better control of phloem feeding insects by an RNAi approach. Thus, the various methods and
compositions provide improved methods for the delivery of inhibitory RNA to the target organism. See, for example, U.S. Application No. 12/351,093, entitled "Compositions and Methods for the Suppression of Target Polynucleotides", filed January 9, 2009 and herein incorporated by reference in its entirety.
As used herein, a "suppressor enhancer element" comprises a polynucleotide comprising the target sequence to be suppressed or an active fragment or variant thereof. It is recognize that the suppressor enhancer element need not be identical to the target sequence, but rather, the suppressor enhancer element can comprise a variant of the target sequence, so long as the suppressor enhancer element has sufficient sequence identity to the target sequence to allow for an increased level of the RNAi produced by the silencing element over that achievable with only the expression of the silencing element. Similarly, the suppressor enhancer element can comprise a fragment of the target sequence, wherein the fragment is of sufficient length to allow for an increased level of the RNAi produced by the silencing element over that achievable with only the expression of the silencing element. Thus, in specific embodiments, the suppressor enhancer element comprises a polynucleotide set forth in SEQ ID NO: 1-292, or 302-304 or an active variant or fragment thereof.
It is recognized that multiple suppressor enhancer elements from the same target sequence or from different target sequences, or from different regions of the same target sequence can be employed. For example, the suppressor enhancer elements employed can comprise fragments of the target sequence derived from different region of the target sequence (i.e., from the 3'UTR, coding sequence, intron, and/or 5'UTR). Further, the suppressor enhancer element can be contained in an expression cassette, as described elsewhere herein, and in specific embodiments, the suppressor enhancer element is on the same or on a different DNA vector or construct as the silencing element. The suppressor enhancer element can be operably linked to a promoter as disclosed herein. It is recognized that the suppressor enhancer element can be expressed constitutively or alternatively, it may be produced in a stage-specific manner employing the various inducible or tissue-preferred or developmentally regulated promoters that are discussed elsewhere herein.
In specific embodiments, employing both a silencing element and the suppressor enhancer element the systemic production of RNAi occurs throughout the entire plant. In further embodiments, the plant or plant parts of the invention have an improved loading of RNAi into the phloem of the plant than would be observed with the expression of the silencing element construct alone and, thus provide better control of phloem feeding insects by an RNAi approach. In specific embodiments, the plants, plant parts, and plant cells of the invention can further be characterized as allowing for the production of a diversity of RNAi species that can enhance the effectiveness of disrupting target gene expression.
In specific embodiments, the combined expression of the silencing element and the suppressor enhancer element increases the concentration of the inhibitory RNA in the plant cell, plant, plant part, plant tissue or phloem over the level that is achieved when the silencing element is expressed alone.
As used herein, an "increased level of inhibitory RNA" comprises any statistically significant increase in the level of RNAi produced in a plant having the combined expression when compared to an appropriate control plant. For example, an increase in the level of RNAi in the plant, plant part or the plant cell can comprise at least about a 1%, about a l%-5%, about a 5% -10%, about a 10%-20%, about a 20%-30%, about a 30%- 40%, about a 40%-50%, about a 50%-60%, about 60-70%, about 70%-80%, about a 80%- 90%, about a 90%- 100% or greater increase in the level of RNAi in the plant, plant part, plant cell, or phloem when compared to an appropriate control. In other embodiments, the increase in the level of RNAi in the plant, plant part, plant cell, or phloem can comprise at least about a 1 fold, about a 1 fold-5 fold, about a 5 fold -10 fold, about a 10 fold-20 fold, about a 20 fold -30 fold, about a 30 fold -40 fold, about a 40 fold-50 fold, about a 50 fold- 60 fold, about 60 fold -70 fold, about 70 fold-80 fold, about a 80 fold-90 fold, about a 90 fold- 100 fold or greater increase in the level of RNAi in the plant, plant part, plant cell or phloem when compared to an appropriate control. Methods to assay for an increase in the level of RNAi are discussed elsewhere herein. on- limiting examples of methods and compositions disclosed herein are as follows:
1. An isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of:
(a) the nucleotide sequence comprising any one of SEQ ID NOS: 279, 302,
281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 14, 18, 263, 17, 30, 34, 337, 338, 339, 340, 341, 342, 343, 344, 305, 306, 307, 308, 309, 310, 31 1, 312, 293, 294, 295, 296, 297, 298, 299, 300, 301, 321, 322, 323, 324, 325, 326, 327 or 328 or a complement thereof;
(b) the nucleotide sequence comprising at least 90% sequence identity to any one of SEQ ID NOS: 279, 302, 281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 14, 18, 263, 17, 30, 34, 337, 338, 339, 340, 341, 342, 343, 344, 305, 306, 307, 308, 309, 310, 311, 312, 293, 294, 295, 296, 297, 298, 299, 300, 301, 321, 322, 323, 324, 325, 326, 327 or 328 or a complement thereof, wherein said polynucleotide encodes a silencing element having insecticidal activity against a Pentatomidae plant pest;
(c) the nucleotide sequence comprising at least 19 consecutive nucleotides of any one of SEQ ID NOS: 279, 302, 281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 17, 30, 34, 14, 18 or 263 or a complement thereof, wherein said polynucleotide encodes a silencing element having insecticidal activity against a
Pentatomidae plant pest; and,
(d) the nucleotide sequence that hybridizes under stringent conditions to the full length complement of the nucleotide sequence of a), wherein said stringent conditions comprise hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37°C, and a wash in 0.1X SSC at 60°C to 65°C, wherein said polynucleotide encodes a silencing element having insecticidal activity against a Pentatomidae plant pest.
2. The isolated polynucleotide of embodiment 1, wherein said Pentatomidae plant pest is a N. viridula plant pest.
3. An expression cassette comprising a heterologous polynucleotide of embodiment 1 or 2 operably linked to a seed-preferred promoter.
4. The expression cassette of embodiment 3, wherein said polynucleotide is expressed as a double stranded RNA.
5. The expression cassette of embodiment 3, wherein said polynucleotide comprise a silencing element which is expressed as a hairpin RNA. 6. The expression cassette of embodiment 5, wherein the silencing element comprises, in the following order, a first segment, a second segment, and a third segment, wherein
a) said first segment comprises at least about 19 nucleotides having at least 90% sequence complementarity to a target sequence set forth in SEQ ID NOS: 279, 302,
281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 17, 30, 34, 14, 18 or 263;
b) said second segment comprises a loop of sufficient length to allow the silencing element to be transcribed as a hairpin RNA; and,
c) said third segment comprises at least about 19 nucleotides having at least
85% complementarity to the first segment.
7. The expression cassette of embodiment 6, wherein said target sequence comprises the sequences set forth any one of SEQ ID NOS: 284, 285, 286, 287, 288, 289, 290, 291, 292, 337, 338, 339, 340, 341, 342, 343 or 344 or a sequence having at least 90% sequence identity to SEQ ID NOS: 284, 285, 286, 287, 288, 289, 290, 291, 292, 337, 338, 339, 340, 341, 342, 343 or 344.
8. The expression cassette of embodiment 6, wherein said expression cassette comprises any one of SEQ ID NOS: 293, 294, 295, 296, 297, 298, 299, 300, 301, 321, 322, 323, 324, 325, 326, 327 or 328.
9. The expression cassette of embodiment 3, wherein said polynucleotide is flanked by a first operably linked convergent promoter at one terminus of the polynucleotide and a second operably linked convergent promoter at the opposing terminus of the
polynucleotide, wherein the first and the second convergent promoters are capable of driving expression of the polynucleotide.
10. A host cell comprising a heterologous expression cassette of any one of embodiments 3-9.
11. A plant cell having stably incorporated into its genome a heterologous
polynucleotide comprising a silencing element operably linked to a seed-preferred promoter, wherein said silencing element, when ingested by a Pentatomidae plant pest, reduces the level of expression of any one of the target sequences set forth in SEQ ID NOS: 279, 302, 281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 14, 18, 263, 17, 30, 34, 337, 338, 339, 340, 341, 342, 343, 344, 305, 306, 307, 308, 309, 310, 311, 312, 293, 294, 295, 296, 297, 298, 299, 300, 301, 321, 322, 323, 324, 325, 326, 327 or 328 in said Pentatomidae plant pest and thereby controls the Pentatomidae plant pest.
12. The plant cell of embodiment 11, wherein said silencing element comprises
a) a fragment of at least 19 consecutive nucleotides of SEQ ID NOS: 279, 302,
281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 17, 30, 34, 14, 18 or 263 or a complement thereof; or,
b) the nucleotide sequence comprising at least 90% sequence identity to any one of SEQ ID NOS: 279, 302, 281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 14, 18, 263, 17, 30, 34, 337, 338, 339, 340, 341, 342, 343, 344, 305, 306, 307, 308, 309, 310, 311, 312, 293, 294, 295, 296, 297, 298, 299, 300, 301, 321, 322, 323, 324, 325, 326, 327 or 328 or a complement thereof,
wherein said silencing element, when ingested by a Pentatomidae plant pest, reduces the level of a target sequence in said Pentatomidae plant pest and thereby controls the Pentatomidae plant pest.
13. The plant cell of embodiment 12, wherein the Pentatomidae plant pest is a N. viridula plant pest.
14. The plant cell of any one of embodiment 1 1, 12 or 13, wherein said silencing element comprises the sequences set forth in any one of SEQ ID NOS: 284, 285, 286, 287, 288, 289, 290, 291, 292, 305, 306, 307, 308, 309, 310, 311, 312, 17, 30, 34, 337, 338, 339, 340, 341, 342, 343 or 344 or a complement thereof.
15. The plant cell of embodiment 11-14, wherein said plant cell comprises the expression cassette of embodiment 9.
16. The plant cell of any one of embodiments 11-14, wherein said silencing element expresses a double stranded RNA.
17. The plant cell of any one of embodiments 11-15, wherein said silencing element expresses a hairpin RNA.
18. The plant cell of embodiment 17, wherein said polynucleotide comprising the silencing element comprises, in the following order, a first segment, a second segment, and a third segment, wherein
a) said first segment comprises at least about 19 nucleotides having at least 90% sequence complementarity to a target sequence set forth in SEQ ID NOS: 279, 302, 281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 14, 18, 263, 17, 30, 34, 337, 338, 339, 340, 341, 342, 343, 344, 305, 306, 307, 308, 309, 310, 31 1, 312, 293, 294, 295, 296, 297, 298, 299, 300, 301, 321, 322, 323, 324, 325, 326, 327 or 328;
b) said second segment comprises a loop of sufficient length to allow the silencing element to be transcribed as a hairpin RNA; and,
c) said third segment comprises at least about 19 nucleotides having at least 85% complementarity to the first segment.
19. The plant cell of any one of embodiments 11-18, wherein said plant cell is from a monocot.
20. The plant cell of embodiment 19, wherein said monocot is maize, barley, millet, wheat or rice.
21. The plant cell of any one of embodiments 11-18, wherein said plant cell is from a dicot.
22. The plant cell of embodiment 21, wherein said plant is soybean, canola, alfalfa, sunflower, safflower, tobacco, Arabidopsis, or cotton.
23. A plant or plant part comprising a plant cell of any one of embodiments 11-22.
24. A transgenic seed from the plant of embodiment 23, wherein said transgenic seed comprises said heterologous polynucleotide comprising said silencing element.
25. A method of controlling a Pentatomidae plant pest comprising feeding to a Pentatomidae plant pest a composition comprising a silencing element, wherein said silencing element, when ingested by said Pentatomidae plant pest, reduces the level of expression of any one of the target Pentatomidae plant pest sequences set forth in SEQ ID NOS: 279, 302, 281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 17, 30, 34, 14, 18 or 263 and thereby controls the Pentatomidae plant pest.
26. The method of embodiment 25, wherein said silencing element comprises
a) a fragment of at least 19 consecutive nucleotides of SEQ ID NOS: 279, 302, 281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 17, 30, 34, 14, 18 or 263 or a complement thereof; or,
b) the nucleotide sequence comprising at least 90% sequence identity to any one of SEQ ID NOS: 279, 302, 281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 14, 18, 263, 17, 30, 34, 337, 338, 339, 340, 341, 342, 343, 344, 305, 306, 307, 308, 309, 310, 311, 312, 293, 294, 295, 296, 297, 298, 299, 300, 301, 321, 322, 323, 324, 325, 326, 327 or 328 or a complement thereof, wherein said silencing element, when ingested by a Pentatomidae plant pest, reduces the level of a target sequence in said Pentatomidae plant pest and thereby controls the Pentatomidae plant pest.
27. The method of embodiment 26, wherein said Pentatomidae plant pest comprises a N. viridula plant pest.
28. The method of any one of embodiments 26 or 27, wherein said silencing element comprises the sequence set forth in any one of SEQ ID NOS: 284, 285, 286, 287, 288, 289, 290, 291, 292, 305, 306, 307, 308, 309, 310, 31 1, 312, 17, 30, 34, 337, 338, 339, 340, 341, 342, 343 or 344 or a complement thereof.
29. The method of any one of embodiments 25-28, wherein said composition comprises a plant or plant part having stably incorporated into its genome a polynucleotide comprising said silencing element, wherein said silencing element is operably linked to a seed-preferred promoter.
30. The method of any one of embodiments 25-29, wherein said silencing element comprises
a) a polynucleotide comprising the sense or antisense sequence of the sequence set forth in SEQ ID NOS: 284, 285, 286, 287, 288, 289, 290, 291, 292, 17, 30, 34, 14, 18, 263, 337, 338, 339, 340, 341, 342, 343, 344, 305, 306, 307, 308, 309, 310, 31 1 or 312 or a complement thereof; or,
b) a polynucleotide comprising the sense or antisense sequence of a sequence having at least 95% sequence identity to the sequence set forth in SEQ ID NOS: 284, 285, 286, 287, 288, 289, 290, 291, 292, 17, 30, 34, 14, 18, 263, 337, 338, 339, 340, 341, 342, 343, 344, 305, 306, 307, 308, 309, 310, 31 1 or 312 or a complement thereof;
31. The method of any one of embodiments 25-30, wherein said silencing element expresses a double stranded RNA.
32. The method of any one of embodiments 25-30, wherein said silencing element comprises a hairpin RNA.
33. The method of embodiment 32, wherein said polynucleotide comprising the silencing element comprises, in the following order, a first segment, a second segment, and a third segment, wherein
a) said first segment comprises at least about 20 nucleotides having at least 90%) sequence complementarity to the target polynucleotide;
b) said second segment comprises a loop of sufficient length to allow the silencing element to be transcribed as a hairpin RNA; and, c) said third segment comprises at least about 20 nucleotides having at least 85% complementarity to the first segment.
34. The method of any one of embodiments 29-30, wherein said silencing element is flanked by a first operably linked convergent promoter at one terminus of the silencing element and a second operably linked convergent promoter at the opposing terminus of the polynucleotide, wherein the first and the second convergent promoters are capable of driving expression of the silencing element.
35. The method of embodiment 29, wherein said plant is a monocot.
36. The method of embodiment 35, wherein said monocot is maize, barley, millet, wheat or rice.
37. The method of embodiment 29, wherein said plant is a dicot.
38. The method of embodiment 37, wherein said plant is soybean, canola, alfalfa, sunflower, safflower, tobacco, Arabidopsis, or cotton. The following examples are offered by way of illustration and not by way of limitation.
EXPERIMENTAL
Example 1 : In vitro transcription dsRNA screening method
A high throughput survey of candidate genes from the stinkbug Nezara viriduia was performed for their potential utility as a target for RNAi leading to mortality
(insecticidal activity of RNAi). A library of over 1000 expressed sequence tags was subjected to in vitro transcription and individual samples tested against 2nd instar nymphs of N. viriduia.
The insects were fed the sample in an insect assay format. After 6 days, the number of dead nymphs was recorded. Table 1 provides the blast homology (Gene ID) of the various silencing elements (clone name) disclosed herein and also provides bioassay data demonstrating the insecticidal activity of the various sequences when fed to N. viriduia. Table 1.
clone name Gene ID 6 day score #dead / 10 inv' c.pk008.f8.f no hits 10 inv' c.pk003.n13.f conserved hypothetical protein 10 inv' c.pk003.o24.f conserved hypothetical protein 7 inv' c.pk004.a3.f cathepsin L1 precursor 9 inv' c.pk004.a23.f no hits 9 inv' c.pk004.b4.f forked protein 8 inv' c.pk004.b6.f ribosomal protein L24e 9 inv' c.pk004.b17.f no hits 8
nonspecific lipid transfer protein/sterol
inv' c.pk004.b23.f carrier protein 9 inv' c.pk004.c1 1 .f soldier specific protein 7 inv' c.pk004.c12.f no hits 10 inv' c.pk004.d4.f no hits 8
oligomycin sensitivity conferral
inv' c.pk004.d16.f
protein//ATP synthase 10 inv' c.pk004.d17.f no hits 10 inv' c.pk004.d19.f no hits 7 inv' c.pk004.d20.f no hits 9 inv' c.pk004.e6.f mitochondrial protein PTCD3 10 inv' c.pk004.e11 .f adapter molecule Crk 10 inv' c.pk004.e24.f cytochrome P450 10 inv' c.pk004.f2.f no hits 8 inv' c.pk004.f10.f no hits 7 inv' c.pk004.f12.f no hits 8 inv' C.pk004.f17.f similar to dipteran sequences 7 inv' C.pk004.f24.f no hits 8 inv' C.pk004.g13.f no hits 8 inv' c.pk004.g20.f vertebrate homology 9 inv' c.pk004.g22.f no hits 10 inv' c.pk004.g23.f no hits 8 inv' c.pk004.h18.f salivary protein 10 inv' c.pk004.h20.f lin-52 homolog 8 inv' c.pk004.h21 .f cyclin t 10
similar to complement component 1 q
inv' c.pk004.h23.f subcomponent binding protein-like
protein 9 inv' c.pk004.h24.f similar to prefoldin subunit 10 inv' c.pk004.i1 .f hsp70 10 inv' c.pk004.i4.f serine/threonine kinase 9 inv' c.pk004.i7.f no hits 9 inv' c.pk004.i14.f cytochrome P450 10 inv' c.pk005.f6.f U6 snRNA-associated Sm-like protein 7 inv' c.pk005.f8.f NADH dehydrogenase subunit 2 10 inv' c.pk005.f20.f apolipprotein D 7 inv' c.pk005.h1.f similar to Gag protein 10 inv' C.pk005.i21 .f no hits 8 inv' C.pk005.j1 1 .f no hits 8 inv' C.pk005.j17.f Homo sapiens 3 BAC RP1 1 -666A9 9 inv' c.pk005.k12.f no hits 7 inv' c.pk005.l13.f no hits 10 inv' c.pk005.m5.f no hits 10 similar to translation initiation factor 3,
inv' c.pk005.m16.f subunit S8 8 inv' c.pk006.j24.f no hits 9 inv' C.pk006.k4.f no hits 7 inv' c.pk006.k18.f acyl-CoA binding protein 7 inv' c.pk006.k20.f E3 ubiquitin ligase/zinc finger protein 9 inv' c.pk006.k21 .f no hits 8 nervana 3/similar to
sodium/potassium-dependent atpase
inv' c.pk006.l7.f beta-2 subunit 7 inv' c.pk006.m2.f no hits 10 inv' c.pk006.m13.f no hits 10 inv' c.pk006.o14.f no hits 10 ubiquinol-cytochrome c reductase
inv' c.pk006.p4.f complex 1 1 kDa protein 10 inv' c.pk006.p8.f similar to ATPase inhibitor-like protein 10 inv' c.pk006.p11 .f 40S ribosomal protein S7 9 similar to Drosophila and pea aphid
inv' c.pk006.p14.f sequences 10 homology to insect sequences
inv' c.pk007.a5.f (Nasonia, Tribolium, Drosophila 8 inv' c.pk007.b6.f no hits 9 inv' c.pk007.c6.f no hits 10 inv' c.pk007.c9.f conserved hypothetical protein 10 inv' c.pk007.d17.f putative ferritin 10 inv' c.pk007.e5.f fatty acyl-CoA elongase 10 inv' c.pk007.e21 .f aldehyde dehydrogenase 9 inv' c.pk007.f1 .f no hits 10 inv' c.pk007.f9.f beta-tubulin 10 inv' c.pk007. l 2.f no hits 10 mitochondrial import receptor subunit
inv' c.pk007.f19.f tom40 [Aedes aegypti] 10 inv' c.pk007.f24.f no hits 9 inv' c.pk007.g6.f no hits 10 putative odorant-binding protein
inv' c.pk007.g17.f precursor 10 inv' c.pk007.h7.f no hits 7 inv' c.pk007.h11 .f no hits 8 inv' c.pk007.h19.f no hits 7 inv' C.pk007.i7.f transposase 10 venom prophenoloxidase-activating
inv' c.pk007.i16.f protease 10 inv' c.pk007.j14.f no hits 10 inv' C.pk007.j19.f no hits 10 inv' C.pk007.j21 .f conserved hypothetical protein 9 succinate dehydrogenase, inv' c.pk007.j23.f cytochrome B small subunit 7 inv' c.pk007.j24.f no hits 8 inv' c.pk007.k17.f conserved hypothetical protein 9 inv' C.pk007.l5.f no hits 9 inv' c.pk007.l8.f transmembrane protein, putative 9 inv' c.pk007.H 1 .f no hits 10 inv' c.pk007.m6.f conserved hypothetical protein 10 inv' c.pk007.m21 .f no hits 9 inv' c.pk007.o14.f proteasome beta subunit 7 inv' C.pk007.p17.f no hits 7 inv' c.pk008.c8.f ribosomal protein L35Ae 7 inv' c.pk008.c15.f similar to prohibitin 8 inv' c.pk008.c17.f no hits 7 inv' c.pk008.d1.f conserved hypothetical protein 9 inv' c.pk008.d3.f conserved hypothetical protein 7 inv' c.pk008.e11 .f no hits 10 inv' c.pk008.e15.f no hits 10 inv' c.pk008.f3.f conserved hypothetical protein 9 inv' c.pk008.f5.f no hits 8 inv' c.pk008.f8.f no hits 10 inv' c.pk008.f23.f no hits 10 inv' c.pk008.g7.f no hits 7 inv' c.pk008.g22.f no hits 7 inv' c.pk008.h23.f putative ribosomal protein S26 10 inv' c.pk008.h24.f similar to mevalonate kinase 10 inv' c.pk008.i10.f no hits 9 inv' c.pk008.i21 .f putative accessory gland protein 9 similar to eukaryotic translation
inv' c.pk008.j20.f initiation factor 3 subunit 2 beta 8 inv' c.pk008.k24.f no hits 7 similar to phosphatase and actin
inv' c.pk008.l1 1 .f regulator 9 inv' c.pk008.p18.f no hits 9 inv' c.pk009.b14.f no hits 8 inv' c.pk009.b21 .f ribosomal protein S20 7 inv' c.pk009.e9.f no hits 9 similar to sarco(endo)plasmic
inv' c.pk009.e10.f reticulum-type calcium ATPase 7 similar to serine/threonine protein
kinase death domain protein, pelle- inv' c.pk009.e17.f like 9 inv' c.pk009.f12.f no hits 10 inv' c.pk009.f17.f no hits 7 inv' C.pk009.f19.f no hits 9 inv' c.pk009.g2.f no hits 8 inv' c.pk009.g21 .f no hits 8 inv' c.pk009.h21 .f no hits 10 inv' c.pk009.i13.f no hits 10 inv' c.pk009.i24.f no hits 7 inv' c.pk009.k4.f no hits 8 inv' C.pk009.k8.f conserved hypothetical protein 10 inv' c.pk010.a13.f no hits 7 inv' c.pk010.a16.f arginyl-tRNA synthetase 7 inv' c.pk010.b7.f similar to tar RNA binding protein 10 inv' c.pk010.e5.f no hits 7 inv' c.pk010.n9.f no hits 7 inv' c.pk010.n24.f no hits 10 inv' C.pk010.p16.f cytochrome c oxidase subunit II 7 inv' c.pk010.p20.f no hits 8 inv' c.pk01 1 .a20.f no hits 7 inv' c.pk01 1 .b11 .f no hits 7 Sequences displaying insecticidal activity are advanced to confirmation and further evaluation of activity against other stinkbug pests. The assay is scored for activity 6 days post infestation. The possible scores are dead, severely stunted (little or now growth but alive), stunted (growth to second instar but not equivalent to controls), or no activity. Samples demonstrating mortality or severe stunting are advanced to confirmation.
Following confirmation, a simple dose response assay is performed with N.
viridula.. Samples for dose response assays is produced in the same manner with the following modification; samples is further purified using column purification prior to enzymatic treatment. Samples is also normalized to 0.5ug/ul and all samples are evaluated by gel electrophoresis. Dose response assays is performed with the following rates; 50, 25, 12, 6, 3, and 1.5 ppm
Example 2. Sequences Having Insecticidal Activity
DNA sequences which encode double stranded RNAs which were shown to have insecticidal activity against N. viridula using the assay described in Example 1 are set forth in SEQ ID NOS: 1-139.
Example 3. Transformation of Maize
Immature maize embryos from greenhouse donor plants are bombarded with a plasmid containing the silencing element of the invention operably linked to either a tissue specific, tissue selective, or constitutive promoter and the selectable marker gene PAT (Wohlleben et al. (1988) Gene 70:25-37), which confers resistance to the herbicide Bialaphos. In one embodiment, the promoter employed is a seed-preferred promoter. In one embodiment, the constructs will express a long double stranded RNA or a miRNA of the target sequence set forth in SEQ ID NOS: 1-292 or 302-304 or a fragment thereof. In specific embodiments, the target sequence comprises the sequences set forth in SEQ ID NOS: 278, 279, 280, 281, 282, 283, 302, 303 or 304. Such a construct can be linked to a promoter active in maize. Alternatively, the selectable marker gene is provided on a separate plasmid. Transformation is performed as follows. Media recipes follow below. Preparation of Target Tissue
The ears are husked and surface sterilized in 30% Clorox bleach plus 0.5% Micro detergent for 20 minutes, and rinsed two times with sterile water. The immature embryos are excised and placed embryo axis side down (scutellum side up), 25 embryos per plate, on 560Y medium for 4 hours and then aligned within the 2.5cm target zone in preparation for bombardment.
A plasmid vector comprising the silencing element of interest operably linked to either the tissue specific, tissue selective, or constitutive promoter is made. This plasmid DNA plus plasmid DNA containing a PAT selectable marker is precipitated onto 1.1 μιη (average diameter) tungsten pellets using a CaCl2 precipitation procedure as follows: 100 μΐ prepared tungsten particles in water; 10 μΐ (1 μg) DNA in Tris EDTA buffer (1 μg total DNA); 100 μΐ 2.5 M CaCl2; and, 10 μΐ 0.1 M spermidine.
Each reagent is added sequentially to the tungsten particle suspension, while maintained on the multitube vortexer. The final mixture is sonicated briefly and allowed to incubate under constant vortexing for 10 minutes. After the precipitation period, the tubes are centrifuged briefly, liquid removed, washed with 500 ml 100% ethanol, and centrifuged for 30 seconds. Again the liquid is removed, and 105 μΐ 100% ethanol is added to the final tungsten particle pellet. For particle gun bombardment, the
tungsten/DNA particles are briefly sonicated and 10 μΐ spotted onto the center of each macrocarrier and allowed to dry about 2 minutes before bombardment.
The sample plates are bombarded at level #4 in a particle gun. All samples receive a single shot at 650 PSI, with a total often aliquots taken from each tube of prepared particles/DNA.
Following bombardment, the embryos are kept on 560Y medium for 2 days, then transferred to 560R selection medium containing 3 mg/liter Bialaphos, and subcultured every 2 weeks. After approximately 10 weeks of selection, selection-resistant callus clones are transferred to 288J medium to initiate plant regeneration. Following somatic embryo maturation (2-4 weeks), well-developed somatic embryos are transferred to medium for germination and transferred to the lighted culture room. Approximately 7-10 days later, developing plantlets are transferred to 272V hormone-free medium in tubes for 7-10 days until plantlets are well established. Plants are then transferred to inserts in flats (equivalent to 2.5" pot) containing potting soil and grown for 1 week in a growth chamber, subsequently grown an additional 1-2 weeks in the greenhouse, then transferred to classic 600 pots (1.6 gallon) and grown to maturity.
Plants are monitored and scored for the appropriate marker, such as the control of a Pentatomidae plant pest, such as a N. viridula plant pest. For example, Ro maize plants are fed to N. viridula 2nd instar nymphs. Contamination and larval quality are monitored. Larval mass and survivorship are recorded for analysis. A one-way ANOVA analysis and a Dunnett's test is performed on the larval mass data to look for statistical significance compared to an untransformed negative control maize plant diet. N. viriduia 2nd instar nymph stunting is measured after feeding on two events and compared to growth of larvae fed on negative control plants.
In other assays, transgenic corn plants (Ro) generated are planted into 10-inch pots containing Metromix soil after reaching an appropriate size. After allowing the N. viriduia 2nd instar nymphs to feed on the plant, plants are removed from the soil and washed so that the relevant plant parts can be evaluated for larval feeding. Plant damage is rated using routine methods to score the level of damage.
Bombardment medium (560Y) comprises 4.0 g/1 N6 basal salts (SIGMA C-1416), 1.0 ml/1 Eriksson's Vitamin Mix (1000X SIGMA- 1511), 0.5 mg/1 thiamine HC1, 120.0 g/1 sucrose, 1.0 mg/1 2,4-D, and 2.88 g/1 L-proline (brought to volume with D-I H20 following adjustment to pH 5.8 with KOH); 2.0 g/1 Gelrite (added after bringing to volume with D-I ¾0); and 8.5 mg/1 silver nitrate (added after sterilizing the medium and cooling to room temperature). Selection medium (560R) comprises 4.0 g/1 N6 basal salts (SIGMA C-1416), 1.0 ml/1 Eriksson's Vitamin Mix (1000X SIGMA- 1511), 0.5 mg/1 thiamine HC1, 30.0 g/1 sucrose, and 2.0 mg/1 2,4-D (brought to volume with D-I H20 following adjustment to pH 5.8 with KOH); 3.0 g/1 Gelrite (added after bringing to volume with D-I H20); and 0.85 mg/1 silver nitrate and 3.0 mg/1 bialaphos (both added after sterilizing the medium and cooling to room temperature).
Plant regeneration medium (288J) comprises 4.3 g/1 MS salts (GIBCO 11 117-074), 5.0 ml/1 MS vitamins stock solution (0.100 g nicotinic acid, 0.02 g/1 thiamine HC1, 0.10 g/1 pyridoxine HC1, and 0.40 g/1 glycine brought to volume with polished D-I H20)
(Murashige and Skoog (1962) Physiol. Plant. 15:473), 100 mg/1 myo-inositol, 0.5 mg/1 zeatin, 60 g/1 sucrose, and 1.0 ml/1 of 0.1 mM abscisic acid (brought to volume with polished D-I H20 after adjusting to pH 5.6); 3.0 g/1 Gelrite (added after bringing to volume with D-I H20); and 1.0 mg/1 indoleacetic acid and 3.0 mg/1 bialaphos (added after sterilizing the medium and cooling to 60°C). Hormone-free medium (272V) comprises 4.3 gfl MS salts (GIBCO 11 117-074), 5.0 ml/1 MS vitamins stock solution (0.100 g/1 nicotinic acid, 0.02 g/1 thiamine HC1, 0.10 g/1 pyridoxine HC1, and 0.40 g/1 glycine brought to volume with polished D-I H20), 0.1 g/1 myo-inositol, and 40.0 g/1 sucrose (brought to volume with polished D-I H20 after adjusting pH to 5.6); and 6 g/1 bacto-agar (added after bringing to volume with polished D-I H20), sterilized and cooled to 60°C. Example 4. Agrobacterium-mQdiatQd Transformation of Maize
For Agrobacterium -mediated transformation of maize with a silencing element of the invention, the method of Zhao is employed (U.S. Patent No. 5,981,840, and PCT patent publication W098/32326; the contents of which are hereby incorporated by reference). Such a construct can, for example, express a long double stranded RNA or a miRNA of the target sequence set forth in SEQ ID NOS: 1-292 or 302-304. In one embodiment, the promoter employed is a seed-preferred promoter. In specific embodiments, the target sequence comprises the sequence set forth in SEQ ID NOS: 278, 279, 280, 281, 282, 283, 302, 303 or 304. Such a construct can be linked to the dMMB promoter. Briefly, immature embryos are isolated from maize and the embryos contacted with a suspension of Agrobacterium, where the bacteria are capable of transferring the polynucleotide comprising the silencing element to at least one cell of at least one of the immature embryos (step 1 : the infection step). In this step the immature embryos are immersed in an Agrobacterium suspension for the initiation of inoculation. The embryos are co-cultured for a time with the Agrobacterium (step 2: the co-cultivation step). The immature embryos are cultured on solid medium following the infection step. Following this co- cultivation period an optional "resting" step is contemplated. In this resting step, the embryos are incubated in the presence of at least one antibiotic known to inhibit the growth oi Agrobacterium without the addition of a selective agent for plant transformants (step 3 : resting step). The immature embryos are cultured on solid medium with antibiotic, but without a selecting agent, for elimination of Agrobacterium and for a resting phase for the infected cells. Next, inoculated embryos are cultured on medium containing a selective agent and growing transformed callus is recovered (step 4: the selection step). The immature embryos are cultured on solid medium with a selective agent resulting in the selective growth of transformed cells. The callus is then regenerated into plants (step 5: the regeneration step), and calli grown on selective medium are cultured on solid medium to regenerate the plants. Assays for insecticidal activity can be performed as described above in Example 3. Example 5: Soybean Embryo Transformation
Culture Conditions
Soybean embryogenic suspension cultures (cv. Jack) are maintained in 35 ml liquid medium SB 196 (see recipes below) on rotary shaker, 150 rpm, 26°C with cool white fluorescent lights on 16:8 hr day/night photoperiod at light intensity of
60-85 uE/m2/s. Cultures are subcultured every 7 days to two weeks by inoculating approximately 35 mg of tissue into 35 ml of fresh liquid SB196 (the preferred subculture interval is every 7 days).
Soybean embryogenic suspension cultures are transformed with a plasmid containing the silencing element of the invention operably linked to either a tissue specific, tissue selective, or constitutive promoter by the method of particle gun bombardment (Klein et al. (1987) Nature, 327:70). In one embodiment, the promoter employed is a seed-preferred promoter. In one embodiment, the constructs will express a long double stranded RNA or a miRNA of the target sequence set forth in SEQ ID NOS: 1-292 or 302-304 or a fragment thereof. In specific embodiments, the target sequence comprises the sequences set forth in SEQ ID NOS: 278, 279, 280, 281, 282, 283, 302, 303 or 304. Soybean Embryogenic Suspension Culture Initiation
Soybean cultures are initiated twice each month with 5-7 days between each initiation.
Pods with immature seeds from available soybean plants 45-55 days after planting are picked, removed from their shells and placed into a sterilized magenta box. The soybean seeds are sterilized by shaking them for 15 minutes in a 5% Clorox solution with 1 drop of ivory soap (95 ml of autoclaved distilled water plus 5 ml Clorox and 1 drop of soap). Mix well. Seeds are rinsed using 2 1 -liter bottles of sterile distilled water and those less than 4 mm are placed on individual microscope slides. The small end of the seed are cut and the cotyledons pressed out of the seed coat. Cotyledons are transferred to plates containing SB1 medium (25-30 cotyledons per plate). Plates are wrapped with fiber tape and stored for 8 weeks. After this time secondary embryos are cut and placed into SB 196 liquid media for 7 days. Preparation of DNA for Bombardment
Either an intact plasmid or a DNA plasmid fragment containing the genes of interest and the selectable marker gene are used for bombardment. Plasmid DNA for
bombardment are routinely prepared and purified using the method described in the Promega™ Protocols and Applications Guide, Second Edition (page 106). Fragments of the plasmids carrying the silencing element of interest are obtained by gel isolation of double digested plasmids. In each case, 100 ug of plasmid DNA is digested in 0.5 ml of the specific enzyme mix that is appropriate for the plasmid of interest. The resulting DNA fragments are separated by gel electrophoresis on 1% SeaPlaque GTG agarose
(BioWhitaker Molecular Applications) and the DNA fragments containing silencing element of interest are cut from the agarose gel. DNA is purified from the agarose using the GELase digesting enzyme following the manufacturer's protocol.
A 50 μΐ aliquot of sterile distilled water containing 3 mg of gold particles (3 mg gold) is added to 5 μΐ of a 1
Figure imgf000062_0001
DNA solution (either intact plasmid or DNA fragment prepared as described above), 50 μΐ 2.5M CaCl2 and 20 μΐ of 0.1 M spermidine. The mixture is shaken 3 min on level 3 of a vortex shaker and spun for 10 sec in a bench microfuge. After a wash with 400 μΐ 100% ethanol the pellet is suspended by sonication in 40 μΐ of 100% ethanol. Five μΐ of DNA suspension is dispensed to each flying disk of the Biolistic PDS1000/HE instrument disk. Each 5 μΐ aliquot contains approximately 0.375 mg gold per bombardment (i.e. per disk).
Tissue Preparation and Bombardment with DNA
Approximately 150-200 mg of 7 day old embryonic suspension cultures are placed in an empty, sterile 60 x 15 mm petri dish and the dish covered with plastic mesh. Tissue is bombarded 1 or 2 shots per plate with membrane rupture pressure set at 1100 PSI and the chamber evacuated to a vacuum of 27-28 inches of mercury. Tissue is placed approximately 3.5 inches from the retaining / stopping screen.
Selection of Transformed Embryos
Transformed embryos were selected either using hygromycin (when the hygromycin phosphotransferase, HPT, gene was used as the selectable marker) or chlorsulfuron (when the acetolactate synthase, ALS, gene was used as the selectable marker). Hygromycin (HPT) Selection
Following bombardment, the tissue is placed into fresh SB 196 media and cultured as described above. Six days post-bombardment, the SB 196 is exchanged with fresh SB 196 containing a selection agent of 30 mg/L hygromycin. The selection media is refreshed weekly. Four to six weeks post selection, green, transformed tissue may be observed growing from untransformed, necrotic embryogenic clusters. Isolated, green tissue is removed and inoculated into multiwell plates to generate new, clonally propagated, transformed embryogenic suspension cultures.
Chlorsulfuron (ALS) Selection
Following bombardment, the tissue is divided between 2 flasks with fresh SB 196 media and cultured as described above. Six to seven days post-bombardment, the SB 196 is exchanged with fresh SB196 containing selection agent of 100 ng/ml Chlorsulfuron. The selection media is refreshed weekly. Four to six weeks post selection, green, transformed tissue may be observed growing from untransformed, necrotic embryogenic clusters. Isolated, green tissue is removed and inoculated into multiwell plates containing SB 196 to generate new, clonally propagated, transformed embryogenic suspension cultures.
Regeneration of Soybean Somatic Embryos into Plants
In order to obtain whole plants from embryogenic suspension cultures, the tissue must be regenerated.
Embryo Maturation
Embryos are cultured for 4-6 weeks at 26°C in SB 196 under cool white fluorescent (Phillips cool white Econowatt F40/CW/RS/EW) and Agro (Phillips F40 Agro) bulbs (40 watt) on a 16:8 hr photoperiod with light intensity of 90-120 uE/m2s. After this time embryo clusters are removed to a solid agar media, SB 166, for 1-2 weeks. Clusters are then subcultured to medium SB 103 for 3 weeks. During this period, individual embryos can be removed from the clusters and screened for the appropriate marker or the ability of the plant, when injected with the silencing elements, to control the Pentatomidae plant pest or the N. viridufa plant pest. Embryo Desiccation and Germination
Matured individual embryos are desiccated by placing them into an empty, small petri dish (35 x 10 mm) for approximately 4-7 days. The plates are sealed with fiber tape (creating a small humidity chamber). Desiccated embryos are planted into SB71-4 medium where they were left to germinate under the same culture conditions described above. Germinated plantlets are removed from germination medium and rinsed thoroughly with water and then planted in Redi-Earth in 24-cell pack tray, covered with clear plastic dome. After 2 weeks the dome is removed and plants hardened off for a further week. If plantlets looked hardy they are transplanted to 10" pot of Redi-Earth with up to 3 plantlets per pot.
Media Recipes
SB 196 - FN Lite liquid proliferation medium (per liter) -
MS FeEDTA - lOOx Stock 1 10 ml
MS Sulfate - lOOx Stock 2 10 ml
FN Lite Halides - lOOx Stock 3 10 ml
FN Lite Ρ,Β,Μο - lOOx Stock 4 10 ml
B5 vitamins (lml/L) 1.0 ml
2,4-D (lOmg/L final concentration) 1.0 ml
KN03 2.83 gm
(NH4 )2 SO 4 0.463 gm
Asparagine 1.0 gm
Sucrose (1%) 10 gm
pH 5.8
FN Lite Stock Solutions
Stock # 1000ml 500ml
1 MS Fe EDTA lOOx Stock
Na2 EDTA* 3.724 g 1.862 g
FeS04 - 7H20 2.784 g 1.392 g
Add first, dissolve in dark bottle while stirring 2 MS Sulfate ΙΟΟχ stock
MgS04 - 7H20 37.0 g 18.5 g
MnS04 - H20 1.69 g 0.845 g
ZnS04 - 7H20 0.86 g 0.43 g
Q1SO4 - 5H20 0.0025 g 0.00125 g
3 FN Lite Halides lOOx Stock
CaCl - 2H20 30.0 g 15.0 g
KI 0.083 g 0.0715 g
CoCl2 - 6H20 0.0025 g 0.00125 g
4 FN Lite Ρ,Β,Μο lOOx Stock
H2P04 18.5 g 9.25 g
H3BO3 0.62 g 0.31 g
Na2Mo04 - 2H20 0.025 g 0.0125 g
SB 1 solid medium (per liter) comprises: 1 pkg. MS salts (Gibco/ BRL - Cat# 111 17-066); 1 ml B5 vitamins 1000X stock; 31.5 g sucrose; 2 ml 2,4-D (20mg/L final concentration); pH 5.7; and, 8 g TC agar.
SB 166 solid medium (per liter) comprises: 1 pkg. MS salts (Gibco/ BRL - Cat# 111 17-066); 1 ml B5 vitamins 1000X stock; 60 g maltose; 750 mg MgC12 hexahydrate; 5 g activated charcoal; pH 5.7; and, 2 g gelrite.
SB 103 solid medium (per liter) comprises: 1 pkg. MS salts (Gibco/BRL - Cat#
111 17-066); 1 ml B5 vitamins 1000X stock; 60 g maltose; 750 mg MgC12 hexahydrate; pH 5.7; and, 2 g gelrite.
SB 71-4 solid medium (per liter) comprises: 1 bottle Gamborg's B5 salts w/ sucrose (Gibco/BRL - Cat# 21153-036); pH 5.7; and, 5 g TC agar.
2,4-D stock is obtained premade from Phytotech cat# D 295 - concentration is 1 mg/ml.
B5 Vitamins Stock (per 100 ml) which is stored in aliquots at -20C comprises: 10 g myo-inositol; 100 mg nicotinic acid; 100 mg pyridoxine HC1; and, 1 g thiamine. If the solution does not dissolve quickly enough, apply a low level of heat via the hot stir plate. Chlorsulfuron Stock comprises lmg / ml in 0.01 N Ammonium Hydroxide Example 6. Expression of Silencing Elements Comprising siRNAs
SiR As were generated to target the cDNA sequence set forth in SEQ ID NOS: 140, 143, 146, 149, 152, 155, 158, 161, 164, 167, 170, 173, 176, 179, 182, 185, 188, 191, 194, 197, 200, 203, 206, 209, 212, 215, 218, 221, 224, 227, 230, 233, 236, 239, 242, 245, 248, 251, 254, 257, 260, 263, 266, 269, 273, and 276. Table 2 provides the clone name of the silencing element and the closest homology for the target sequence (gene name). Table 3 provides the clone name, the target cDNA, the sense and antisense siRNA sequence, and the respective SEQ ID NOS. Table 4 provides the bioassays for each of the siRNAs shown in Table 3.
Table 2
Figure imgf000067_0001
fable 3 (Note: the sense RNA primer sequence and the antisense RNA primer sequences shown in table 3 were generated having 2 thymine residues at lie 3' end.)
Figure imgf000068_0001
Figure imgf000069_0001
Figure imgf000070_0001
fable 4
Figure imgf000071_0003
Figure imgf000071_0001
Figure imgf000071_0002
Figure imgf000072_0002
Figure imgf000072_0003
Figure imgf000072_0001
invlc.pk005.k24.f Example 7. Constructs expressing siRNAs
siRNAs designed to target the cDNA sequence set forth in SEQ ID NOS: 140, 143, 146, 149, 152, 155, 158, 161, 164, 167, 170, 173, 176, 179, 182, 185, 188, 191, 194, 197, 200, 203, 206, 209, 212, 215, 218, 221, 224, 227, 230, 233, 236, 239, 242, 245, 248, 251, 254, 257, 260, 263, 266, 269, 272, and 275 can be engineered to be expressed in planta. The construct can comprise, for example, the maize ubiquitin promoter/5 'UTR/ 1st intron operably linked to a sequence comprising SEQ ID NO: 141 which is operably linked to the ADHl intron followed by the sequence comprising SEQ ID NO: 142. It is recognized that any of the siRNA described in Example 6 can be generated employing a simlar construct design.
Example 8. Generation of silencing constructs for in vivo testing experiments
The activity of 9 dsRNAs listed in Table 1, was confirmed on repeated testing and the target genes advanced for further evaluation in in planta assays. For this purpose, 2 different types of constructs were assembled. In one, 2 SGSB target gene fragments, separated by a spiceosomal intron, were assembled in opposite orientations with respect to each other to produce a hairpin RNA. In planta produced hairpin RNAs are expected to be processed to yield siRNAs which upon uptake into insects, mediate RNAi inhibition of SGSB target gene expression. In the second, small 21-mer SGSB gene sequences are incorporated into a micro RNA backbone to produce an artificial pre-miRNA. Processing of the pre-miRNA in vivo releases the 21-nt miRNA that targets the SGSB gene for silencing.
Hairpin constructs for in vivo expression and testing of dsRNAs were assembled via Gateway technology using procedures and practices well known to those skilled in the art of molecular biology. Target gene fragments were generated by PCR using gene specific sense and antisense primers containing Gateway attB4
(CAACTTTGTATAGAAAAGTTG (SEQ ID NO: 345)) and attB3
(CAACTTTGTATAATAAAGTTG (SEQ ID NO: 346)) sequences, respectively. The amplified DNA fragments were recombined into the pDONR vector, PHP36164 containing attP4-attP3 sites in a reaction catalyzed by BP Clonase. The resultant entry clones containing target gene fragments flanked by attL 4 and attL3 sites were then used to generate an expression construct by performing 2 sequential LR recombination reactions, first with the vector pKB499 and then with the vector PHP25224. The former destination vector contains the 193 bp intron2 fragment of the potato LSI gene flanked by attR4-R3 sites at the 5' end and attR3-R4 sites at the 3' end. LR recombination yields a hairpin segment comprised of sense and antisense target gene fragments separated by an intron loop. In planta expression is regulated by placement of the appropriate regulatory
elements, promoter sequences upstream and termination sequences downstream, of the hairpin segment. In this particular example, promoter sequences are provided by a 1946 bp soybean ubiquitin promoter-5' UTR-Intronl fragment and termination sequences are provided by an 888bp 3 ' fragment of the Arabidopsis ubiquitinlO gene. Other promoter sequences providing constitutive or appropriate tissue specific expression may additionally be used. The final plant expression construct is produced by a second LR reaction in which the entire hairpin cassette is moved into a vector (PHP25224) which provides a plant selectable marker (herbicide resistant acetolactate synthase gene) for stable
transformation experiments. In Table 5, the 9 entries correspond to hairpin constructs that were assembled and tested in soybean embryos for efficacy against Southern Green
Stinkbug (SGSB).
Table 5: Hairpin constructs for SGSB target gene silencing
Construct
SEQ ID NO
SEQ ID Fragment Fragment (without
Gene ID SEQ length (bp) NO Location SEQ ID NO Construct promoter) invlc.pk004.e6.f:fis 1054 278 2-537 284 PHP49713 293 invlc.pk004.h20.f:fis 861 279 72-677 285 PHP48181 294 invlc.pk004.h20.f:fis 861 279 72-834 286 pKB505 295 invlc.pk004.h20.f:fis 861 279 72-439 287 pKB506 296 invlc.pk004.il.f:fis 992 280 27-511 288 PHP48183 297 invlc.pk004.il.f:fis 992 280 488-938 289 pKB508 298 invlc.pk008.m9.f:fis 858 281 2-800 290 PHP49450 299 invlc.pk011.f6.f:fis 792 282 19-594 291 PHP49451 300 invlc.pk010.gl3.f:fis 643 283 4-785 292 PHP49480 301
Silencing constructs encoding artificial microRNAs (amiRNAs) that would have the ability to silence Southern Green Stinkbug genes were designed largely according to rules described in Schwab R, et al. (2005) Dev Cell 8: 17-27. To summarize, microRNA sequences are 21 nucleotides in length, start at their 5'-end with a "U", display 5'
instability relative to their star sequence which is achieved by including a C or G at
position 19, and their 10th nucleotide is either an "A" or an "U". An additional
requirement for artificial microRNA design was that the amiRNA have a high free delta-G as calculated using the ZipFold algorithm (Markham, N. R. & Zuker, M. (2005) Nucleic Acids Res. 33: W577-W581.) Optionally, a one base pair change was added to the 5' portion of the amiRNA so that the sequence differed from the target sequence by one nucleotide. The amiRNAs that were used to silence SGSB genes are given in Table 6. Table 6: amiRNA Sequences
Target amiRNA amiRNA precursor GENE ID SEQ amiRNA Sequence SEQ ID
ID NO NO
Nv-MCS Frgl invlc.pk005.h23.f 302 taagtaccatgtccaacgcca 305
Nv-MCS Frg2 invlc.pk005.h23.f 302 tattacaataactgaccaccc 306
Nv-MMitpro2 invlc.pk004.e6.f:fis 278 tccta ctacatatttcca ccc 307
Nv-MitprotCD3 invlc.pk004.e6.f:fis 278 tattccttctatcttctccca 308
Nv-Madapmol2 invlc.pk004.ell.f:fis 303 taaagtatattaataattctt 309
Nv-MadadapC Kl invlc.pk004.ell.f:fis 303 ttactatcttcccttacacaa 310
Nv-MNHIA invlc.pk004.dl7.f:fis 304 tacgaagagataacacaagat 311
Nv-MNHIB invlc.pk004.dl7.f:fis 304 taacaaaacaaaaaaaaactg 312
"Star sequences" are those that base pair with the amiRNA sequences in the precursor RNA, to form imperfect stem structures. To form a perfect stem structure the star sequence would be the exact reverse complement of the amiRNA. The soybean precursor sequence miR159 as described in Zhang, B. at al. (2008) Planta 229: 161-182 was folded with MFold (M. Zuker (2003) Nucleic Acids Res. 31 : 3406-15; and D.H.
Mathews, J. et al. (1999) J. Mol. Biol. 288: 911-940). The miRNA sequence was then replaced with the amiRNA sequence and the endogenous star sequence was replaced with the exact reverse complement of the amiRNA. Changes in the artificial star sequence were introduced so that the structure of the stem would remain the same as the endogenous structure. The altered sequence was then folded with mfold and the original and altered structures were compared by eye. If necessary, further alternations to the artificial star sequence were introduced to maintain the original structure. The DNA sequences corresponding to the artificial star sequences that were used to silence the desired target genes are shown in Table 7. Table 7: amiRNA Star Sequences amiRNA precursor GENE ID amiRNA Sequence SEQ ID
NO
Nv-MCS Frgl-Star invlc.pk005.h23.f tggcgttggactaggtacttt 313 Nv-MCS Frg2-Star invlc.pk005.h23.f gggtggtcagtatttgtaatt 314 Nv-MMitpro2 -Star invlc.pk004.e6.f:fis gggtggaaataattagtaggt 315 Nv-MitprotCD3 -Star invlc.pk004.e6.f:fis tgggagaagatcaaaggaatt 316 Nv-Madapmol2-Star invlc.pk004.ell.f:fis aagaattattataatactttt 317 Nv-MadadapCRKl-Star invlc.pk004.ell.f:fis ttgtgtaagggttgatagtat 318 Nv-MN H1A-Star invlc.pk004.dl7.f:fis atcttgtgttaaatcttcgtt 319 Nv-MN H1B-Star invlc.pk004.dl7.f:fis cagttttttttgcttttgttt 320
The soybean genomic miRNA precursor gene, miR159, was converted to amiRNA precursors by DNA synthesis (Genscript; Piscataway, NJ). DNA fragments were synthesized with flanking Avrll and Hpal sites and were cloned by restriction enzyme digestion followed by DNA ligation downstream of the GmUbiquitin promoter-5'UTR- Intronl fragment in the UBQ-Kozack OXOXalt7 vector. LR recombination reaction between this intermediate and the vector QC479i produced the eight final plant expression constructs given in Table 8.
Figure imgf000076_0001
The SEQ ID NOS for the various target genes advanced for further evaluation in in planta assays are summarized in Table 9. Table?.
Figure imgf000077_0001
promoter) 289 (hairpin RNA)
298 (hairpin RNA construct without
promoter) invlc.pk005.h23i 302 263, 337, 329 (amiRNA precursor sequence with 264 (sense siRNA, RNA sequence)
338 promoter) 265 (anti-sense siRNA, RNA sequence)
330 (amiRNA precursor sequence with 305 (miRNA)
promoter) 306 (miRNA)
321 (miRNA precursor sequence)
322 (miRNA precursor sequence) invlc.pk008.m9.f:fls 281 290 299 (hairpin RNA construct without 290 (hairpin RNA)
promoter) invlc.pk010.gl3.f:fis 283 292 301 (hairpin RNA construct without 292 (hairpin RNA)
promoter) invlc.pkOl l.f6.f:fis 282 291 300 (hairpin RNA construct without 291 (hairpin RNA)
promoter)
Example 9. Transformation of Somatic Soybean Embryo Cultures
Culture Conditions:
Soybean embryogenic suspension cultures (cv. Jack) were maintained in 35 mL liquid medium SB 196 (infra) on a rotary shaker, 150 rpm, 26 °C with cool white fluorescent lights on 16:8 hr day/night photoperiod at light intensity of 60-85 uE/m2/s. Cultures were sub-cultured every 7 days to two weeks by inoculating approximately 35 mg of tissue into 35 mL of fresh liquid SB 196 (the preferred subculture interval is every 7 days).
Soybean embryogenic suspension cultures were transformed with the soybean expression plasmids described in Example 8 by the method of particle gun bombardment (Klein et al., Nature, 327:70 (1987)) using a DuPont Biolistic PDS1000/HE instrument (helium retrofit) for all transformations.
Soybean Embryogenic Suspension Culture Initiation:
Soybean cultures were initiated twice each month with 5-7 days between each initiation. Pods with immature seeds from available soybean plants 45-55 days after planting were picked, removed from their shells and placed into a sterilized magenta box. The soybean seeds were sterilized by shaking them for 15 min in a 5% Clorox solution with 1 drop of ivory soap (i.e., 95 mL of autoc laved distilled water plus 5 mL Clorox and 1 drop of soap, mixed well). Seeds were rinsed using 2 1 -liter bottles of sterile distilled water and those less than 4 mm were placed on individual microscope slides. The small end of the seed was cut and the cotyledons pressed out of the seed coat. Cotyledons were transferred to plates containing SB 199 medium (25-30 cotyledons per plate) for 2 weeks, then transferred to SB1 for 2-4 weeks. Plates were wrapped with fiber tape. After this time secondary embryos were cut and placed into SB 196 liquid media for 7 days.
Preparation of DNA for Bombardment:
Either an intact plasmid or a DNA plasmid fragment containing the genes of interest and the selectable marker gene may be used for bombardment. In the present example, pDNAs were isolated from bacterial transformants using a Qiagen mini-prep kit. DNA concentrations were determined by UV absorbance. Each silencing construct and hygromycin selectable marker plasmid (PHP 18956) were combined in a 9: 1 weight ratio to give a 1 ug/ul DNA solution. A 50 μΐ aliquot of sterile distilled water containing 1 mg of gold particles was added to 5 of a 1 μg/μL DNA solution (intact silencing and selectable marker plasmids as described above), 50 μΐ, 2.5M CaCl2 and 20 μΐ, of 0.1 M spermidine. The mixture was pulsed 5 times on level 4 of a vortex shaker and spun for 5 sec in a bench microfuge. After a wash with 150 μΐ, of 100% ethanol, the pellet was suspended by sonication in 85ul of 100% ethanol. Five μΐ, of DNA suspension was dispensed to each flying disk of the Biolistic PDS1000/HE instrument disk. Each 5 μΐ^ aliquot contained approximately 0.058 mg gold particles per bombardment (i.e., per disk). Tissue Preparation and Bombardment with DNA:
Approximately 100-150 mg of 7 day old embryonic suspension cultures were placed in an empty, sterile 60 x 15 mm petri dish and the dish was placed inside of an empty 150 x 25mm Petri dish. Tissue was bombarded 1 shot per plate with membrane rupture pressure set at 650 PSI and the chamber was evacuated to a vacuum of 27-28 inches of mercury. Tissue was placed approximately 2.5 inches from the retaining /stopping screen.
Selection of Transformed Embryos:
Transformed embryos were selected using hygromycin as the selectable marker. Specifically, following bombardment, the tissue was placed into fresh SB 196 media and cultured as described above. Six to eight days post-bombardment, the SB 196 is exchanged with fresh SB 196 containing 30 mg/L hygromycin. The selection media was refreshed bi-weekly. Four to six weeks post-selection, green, transformed tissue was observed growing from untransformed, necrotic embryogenic clusters. Isolated, green tissue was removed and inoculated into multi-well plates to generate new, clonally propagated, transformed embryogenic suspension cultures.
Embryo Maturation:
Transformed embryogenic clusters were cultured for 1-3 weeks at 26 °C in SB 196 under cool white fluorescent (Phillips cool white Econowatt F40/CW/RS/EW) and Agro (Phillips F40 Agro) bulbs (40 watt) on a 16:8 hr photoperiod with light intensity of 90-120 μΕ/m s. Embryo clusters were then removed to SB228 (SHaM) liquid media, 35 ml in 250ml Erlenmeyer flask, for 2-3 weeks. Tissue cultured in SB228 was maintained on a rotary shaker, 130 rpm, 26°C with cool white fluorescent lights on 16:8 hr day/night photoperiod at light intensity of 60-85 uE/m2/s. After this time, embryos were harvested and used in stinkbug feeding assays.
Media Recipes:
SB 196 - FN Lite Liquid Proliferation Medium, pH 5.8 (p.
MS FeEDTA - lOOx Stock 1 10 mL
MS Sulfate - lOOx Stock 2 10 mL
FN Lite Halides - lOOx Stock 3 10 mL
FN Lite P, B, Mo - lOOx Stock 4 10 mL
B5 vitamins (1 mL/L) 1.0 mL
2,4-D (lOmg'L final concentration) 1.0 mL
KN03 2.83 gm
(NH4)2S04 0.463 gm
asparagine 1.0 gm
sucrose (1%) 10 gm
FN Lite Stock Solutions
Stock Number 1000 mL 500 mL
1 MS Fe EDTA lOOx Stock
Na2 EDTA* 3.724 g 1.862 g
FeS04 - 7H20 2.784 g 1.392 g
Add first, dissolve in dark bottle while stirring
MS Sulfate lOOx stock
MgS04 - 7H20 37.0 g 18.5 g
MnS04 - H20 1.69 g 0.845 g
ZnS04 - 7H20 0.86 g 0.43 g
CuS04 - 5H20 0.0025 g 0.00125 g
FN Lite Halides lOOx Stock
CaCl2 - 2H20 30.0 g 15.0 g
I 0.083 g 0.0715 g
CoCl2 - 6H20 0.0025 g 0.00125 g
FN Lite P, B, Mo lOOx Stock
H2P04 18.5 g 9.25 g H3BO3 0.62 g 0.31 g
Na2Mo04 - 2H20 0.025 g 0.0125 g
SB1 Solid Medium, pH5.7 (per liter)
1 package MS salts (Gibco/ BRL - Cat. No. 111 17-066)
1 mL B5 vitamins 1000X stock 31.5 g glucose
2 mL 2,4-D (20 mg/L final concentration)
8 g TC agar
SB 199 Solid Medium (per liter)
1 package MS salts (Gibco/ BRL - Cat. No. 111 17-066)
1 mL B5 vitamins 1000X stock
30g Sucrose
4 ml 2,4-D (40 mg/L final concentration)
pH 7.0
2 gm Gelrite
SB 71-4 Solid Medium (per liter)
1 bottle Gamborg's B5 salts w/ sucrose (Gibco/ BRL - Cat. No. 21153-036) pH 5.7
5 g TC agar
2,4-D Stock
Obtain premade from Phytotech Cat. No. D 295 - concentration 1 mg/mL B5 Vitamins Stock (per 100 mL)
Store aliquots at -20 °C
10 g myo-inositol
100 mg nicotinic acid
100 mg pyridoxine HC1
1 g thiamine
If the solution does not dissolve quickly enough, apply a low level of heat via the hot stir plate.
SB 228- Soybean Histodifferentiation & Maturation (SHaM) (per liter)
DDI H20 600ml
FN-Lite Macro Salts for SHaM 10X 100ml
MS Micro Salts lOOOx 1ml
MS FeEDTA lOOx 10ml
CaCl lOOx 6.82ml
B5 Vitamins lOOOx 1ml
L-Methionine 0.149g
Sucrose 30g Sorbitol 30g
Adjust volume to 900ml
pH 5.8
Autoclave
Add to cooled media (<30C):
*Glutamine (Final cone. 30mM) 4% 1 10ml
*Note: Final volume will be 1010ml after glutamine addition..
FN-lite Macro for SHAM 10X- Stock #1 (per liter)
(NH4)2S04 (Ammonium Sulfate) 4.63g
K 03 (Potassium Nitrate) 28.3g
MgSO4*7H20 (Magnesium Sulfate Heptahydrate) 3.7g
KH2P04 (Potassium Phosphate, Monobasic) 1.85g
Bring to volume
Autoclave
MS Micro 1000X- Stock #2 (per 1 liter)
H3BO3 (Boric Acid) 6.2g
MnS04*H20 (Manganese Sulfate Monohydrate) 16.9g
ZnSO4*7H20 (Zinc Sulfate Heptahydrate) 8.6g
Na2MoO4*2H20 (Sodium Molybdate Dihydrate) 0.25g
CuSO4*5H20 (Copper Sulfate Pentahydrate) 0.025g
CoCl2*6H20 (Cobalt Chloride Hexahydrate) 0.025g
KI (Potassium Iodide) 0.8300g
Bring to volume
Autoclave FeEDTA 100X- Stock #3 (per liter)
Na2EDTA* (Sodium EDTA) 3.73g
FeSO4*7H20 (Iron Sulfate Heptahydrate) 2.78g
*EDTA must be completely dissolved before adding iron
Bring to Volume
Solution is photosensitive. Bottle(s) should be wrapped in foil to omit light.
Autoclave
Ca 100X- Stock #4 (per liter)
CaCl2*2H20 (Calcium Chloride Dihydrate) 44g
Bring to Volume
Autoclave
B5 Vitamin 1000X- Stock #5 (per liter)
Thiamine*HCl lOg
Nicotinic Acid lg Pyridoxine*HCl
Myo-Inositol
Bring to Volume
Store frozen
4% Glutamine- Stock #6 (per liter)
DDI water heated to 30°C 900ml
L-Glutamine 40g
Gradually add while stirring and applying low heat.
Do not exceed 35°C.
Bring to Volume
Filter Sterilize
Store frozen *
*Note: Warm thawed stock in 31°C bath to fully dissolve crystals
It is recognized that the experiments set forth in example 9 can be employed with silencing elements operably linked to a seed-preferred promoter, such as, for example, those provided by the b-conglycinin-alpha (Genbank accession GU723691), Kunitz trypsin inhibitor 3 (AF233296), or the glycinin-1 (AB353075.1) genes.
Example 10. Assay of Transgenic Soybean Embryos for Efficacy Against Southern Green Stinkbug
Cultures of SHaM maturated embryos, as described in Example 9, were harvested by filtration and used in feeding bioassays with 2nd instar southern green stinkbugs. A typical soy embryo transformation experiment yielded 20 to 30 independent events that were each evaluated in 4 replicate assays. Each assay was set up in a 35 mm petri dish that contained a moistened Whatman filter disc and a H20 soaked cotton pellet along with 450-500 mg of soy embryo tissue. Embryo samples were infested with 5-2nd instar SGSBs, and the petri plate was covered and incubated at 27C, 65% RH for 4 days. At this time, the sample was replenished with fresh tissue and the incubation was continued for 4 additional days at which time, the assays were scored for insect stunting and mortality.
Figures 1 and 2 show the results of insect feeding assays performed using embryo tissue transformed with the silencing construct DNAs listed in Tables 5 and 8. Each symbol corresponds to insect mortality scores averaged over the 4 replicate assays for each event. Controls correspond to feeding assays conducted using non-trans genie soybean embryo tissue. For all of the constructs, several transgenic events could be found which gave insect mortality scores greater than the controls. For some constructs, more than 50% of the events produced insect mortality at a rate significantly greater than controls. Variation in apparent efficacy from event to event is to be expected due to variation in construct expression with random integration of the construct DNA in the soybean genome. Example 11. Assay of Transgenic Soybean Plants for Efficacy Against
Southern Green Stinkbug
Silencing constructs can be stably expressed in insect feeding tissue for efficacy testing of transgenic plants against southern green stinkbug. The DNA constructs described in Example 8 can be used for this purpose. These consist of trait gene hairpin or miRNA gene cassettes both of which are constitutively regulated by a soybean ubiquitin promoter-5'UTR-Intronl fragment. Similar constructs can be built using other constitutive promoters as provided for example by soybean elongation factor 1 alpha (ACUPO 1009998) or arabidopsis ubiquitin (L05399.1) genes. Alternatively, tissue specific expression and in some embodiments seed-preferred promoters can be produced by the use of seed storage protein promoters including those provided by the beta- conglycinin-alpha (Genbank accession GU723691), Kunitz trypsin inhibitor 3
(AF233296), or the glycinin-1 (AB353075.1) genes. To produce seed specific hairpin constructs (i.e. long dsRNA constructs and miRNA constructs), entry clones, generated as described in Example 8 above, are combined in an LR clonase reaction with a variant of the destination vector, pKB499, modified to contain a seed storage protein promoter in place of the Gm-Ubiquitin promoter. This first LR reaction generates the promoter- hairpin-terminator cassette. The final plant expression construct is produced by a second LR reaction in which the entire hairpin cassette is moved into a vector (PHP25224) which provides a plant selectable marker gene (herbicide resistant acetolactate synthase) for stable transformation experiments. For assembly of tissue specific miRNA constructs, the procedure outlined in Example 8 would be followed with final cloning of the artificial miR159 segment into a suitable plant expression vector that provides regulatory sequences of any one of the above seed storage protein promoters.
For biolistic transformation of soybean embryos as described in Example 5, a single DNA fragment containing both the trait gene and the plant selectable marker gene is prepared by restriction enzyme digestion followed by gel purification of restricted pDNA. In the case of both constitutive and tissue specific silencing constructs, 10 μg of plasmid DNA is used in 0.15 mL of the specific enzyme mix described below. Plasmids are digested with Ascl (100 units) in NEBuffer 4 (20 mM Tris-acetate, 10 mM magnesium acetate, 50 mM potassium acetate, 1 mM dithiothreitol, pH 7.9), 100 μ^ιηΐ. BSA, and 5 mM beta-mercaptoethanol at 37 °C for 3 hrs. The resulting DNA fragments are separated by gel electrophoresis on 1% agarose gel and the DNA fragment containing the trait gene- selectable marker gene cassettes are cut from the agarose gel. DNA is purified from the agarose using Qiagen's Quick Spin extraction method following the manufacturer's suggested protocol. Gold particles are coated with purified DNA fragments and used for biolistic introduction of DNA into soybean embryo cultures using the procedure outlined in Example 5.
First generation transgenic plants can be assayed for insecticidal activity in individual plant cages. When the plant has started to produce green pods approximately 1- 2 inches in length, plants are removed to individual bug tent cages (BioQuip, CA). The cage is infested with 50 newly emerged second instar southern green stinkbugs (Nezara viridula). The nymphs are allowed to feed for 1 week at which time a count of surviving insects is performed. Counts are facilitated by using an aspirating device with removable vials and caps to collect insects and a hand held counting device to count each insect as it is aspirated. Counts can later be verified by freezing the sample and counting again under magnification where a measure of growth can also be performed on collected insects. Fully grown insects equivalent to controls are given a score of 0. Insects demonstrating 20-60% stunting are given a score of 1. Insects demonstrating 60-100% stunting (size equivalent to original infested insects) are given a score of 2 and dead insects are scored 3. Selected plants demonstrating high insecticidal activity are recovered from the tents, treated with Marathon insecticide, and returned to growth chambers or greenhouses to complete the reproductive phase and seed production.
The article "a" and "an" are used herein to refer to one or more than one (i.e., to at least one) of the grammatical object of the article. By way of example, "an element" means one or more element.
All publications and patent applications mentioned in the specification are indicative of the level of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference. Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be obvious that certain changes and modifications may be practiced within the scope of the appended claims.

Claims

THAT WHICH IS CLAIMED:
1. An isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of:
(a) the nucleotide sequence comprising any one of SEQ ID NOS: 279,
302, 281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 14, 18, 263, 17, 30, 34, 337, 338, 339, 340, 341, 342, 343, 344, 305, 306, 307, 308, 309, 310, 311, 312, 293, 294, 295, 296, 297, 298, 299, 300, 301, 321, 322, 323, 324, 325, 326, 327 or 328 or a complement thereof;
(b) the nucleotide sequence comprising at least 90% sequence identity to any one of SEQ ID NOS: 279, 302, 281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 14, 18, 263, 17, 30, 34, 337, 338, 339, 340, 341, 342, 343, 344, 305, 306, 307, 308, 309, 310, 31 1, 312, 293, 294, 295, 296, 297, 298, 299, 300, 301, 321, 322, 323, 324, 325, 326, 327 or 328 or a complement thereof, wherein said polynucleotide encodes a silencing element having insecticidal activity against a
Pentatomidae plant pest;
(c) the nucleotide sequence comprising at least 19 consecutive nucleotides of any one of SEQ ID NOS: 279, 302, 281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 17, 30, 34, 14, 18 or 263 or a complement thereof, wherein said polynucleotide encodes a silencing element having insecticidal activity against a Pentatomidae plant pest; and,
(d) the nucleotide sequence that hybridizes under stringent conditions to the full length complement of the nucleotide sequence of a), wherein said stringent conditions comprise hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37°C, and a wash in 0. IX SSC at 60°C to 65°C, wherein said polynucleotide encodes a silencing element having insecticidal activity against a Pentatomidae plant pest.
2. The isolated polynucleotide of claim 1, wherein said Pentatomidae plant pest is a N. viridula plant pest.
3. An expression cassette comprising a heterologous polynucleotide of claim 1 or 2 operably linked to a seed-preferred promoter.
4. The expression cassette of claim 3, wherein said polynucleotide is expressed as a double stranded RNA.
5. The expression cassette of claim 3, wherein said polynucleotide comprise a silencing element which is expressed as a hairpin RNA.
6. The expression cassette of claim 5, wherein the silencing element comprises, in the following order, a first segment, a second segment, and a third segment, wherein
a) said first segment comprises at least about 19 nucleotides having at least 90% sequence complementarity to a target sequence set forth in SEQ ID NOS: 279, 302, 281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 17, 30, 34, 14, 18 or 263;
b) said second segment comprises a loop of sufficient length to allow the silencing element to be transcribed as a hairpin RNA; and,
c) said third segment comprises at least about 19 nucleotides having at least 85%) complementarity to the first segment.
7. The expression cassette of claim 6, wherein said target sequence comprises the sequences set forth any one of SEQ ID NOS: 284, 285, 286, 287, 288, 289, 290, 291,
292, 337, 338, 339, 340, 341, 342, 343 or 344 or a sequence having at least 90% sequence identity to SEQ ID NOS: 284, 285, 286, 287, 288, 289, 290, 291, 292, 337, 338, 339, 340, 341, 342, 343 or 344.
8. The expression cassette of claim 6, wherein said expression cassette comprises any one of SEQ ID NOS: 293, 294, 295, 296, 297, 298, 299, 300, 301, 321, 322, 323, 324, 325, 326, 327 or 328.
9. The expression cassette of claim 3, wherein said polynucleotide is flanked by a first operably linked convergent promoter at one terminus of the polynucleotide and a second operably linked convergent promoter at the opposing terminus of the
polynucleotide, wherein the first and the second convergent promoters are capable of driving expression of the polynucleotide.
10. A host cell comprising a heterologous expression cassette of any one of claims 3-9.
1 1. A plant cell having stably incorporated into its genome a heterologous polynucleotide comprising a silencing element operably linked to a seed-preferred promoter, wherein said silencing element, when ingested by a Pentatomidae plant pest, reduces the level of expression of any one of the target sequences set forth in SEQ ID NOS: 279, 302, 281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 14, 18, 263, 17, 30, 34, 337, 338, 339, 340, 341, 342, 343, 344, 305, 306, 307, 308, 309, 310, 311, 312, 293, 294, 295, 296, 297, 298, 299, 300, 301, 321, 322, 323, 324, 325, 326, 327 or 328 in said Pentatomidae plant pest and thereby controls the Pentatomidae plant pest.
12. The plant cell of claim 11, wherein said silencing element comprises
a) a fragment of at least 19 consecutive nucleotides of SEQ ID NOS: 279,
302, 281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 17,
30, 34, 14, 18 or 263 or a complement thereof; or,
b) the nucleotide sequence comprising at least 90% sequence identity to any one of SEQ ID NOS: 279, 302, 281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 14, 18, 263, 17, 30, 34, 337, 338, 339, 340, 341, 342, 343, 344,
305, 306, 307, 308, 309, 310, 311, 312, 293, 294, 295, 296, 297, 298, 299, 300, 301, 321,
322, 323, 324, 325, 326, 327 or 328 or a complement thereof,
wherein said silencing element, when ingested by a Pentatomidae plant pest, reduces the level of a target sequence in said Pentatomidae plant pest and thereby controls the Pentatomidae plant pest.
13. The plant cell of claim 12, wherein the Pentatomidae plant pest is a ΛΓ. viridula plant pest.
14. The plant cell of any one of claim 11, 12 or 13, wherein said silencing element comprises the sequences set forth in any one of SEQ ID NOS: 284, 285, 286, 287, 288, 289, 290, 291, 292, 305, 306, 307, 308, 309, 310, 311, 312, 17, 30, 34, 337, 338, 339, 340, 341, 342, 343 or 344 or a complement thereof.
15. The plant cell of claim 11-14, wherein said plant cell comprises the expression cassette of claim 9.
16. The plant cell of any one of claims 11-14, wherein said silencing element expresses a double stranded RNA.
17. The plant cell of any one of claims 11-15, wherein said silencing element expresses a hairpin RNA. 18. The plant cell of claim 17, wherein said polynucleotide comprising the silencing element comprises, in the following order, a first segment, a second segment, and a third segment, wherein
a) said first segment comprises at least about 19 nucleotides having at least 90% sequence complementarity to a target sequence set forth in SEQ ID NOS: 279, 302, 281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 14,
18, 263, 17, 30, 34, 337, 338, 339, 340, 341, 342, 343, 344, 305, 306, 307, 308, 309, 310, 311, 312, 293, 294, 295, 296, 297, 298, 299, 300, 301, 321, 322, 323, 324, 325, 326, 327 or 328;
b) said second segment comprises a loop of sufficient length to allow the silencing element to be transcribed as a hairpin RNA; and,
c) said third segment comprises at least about 19 nucleotides having at least 85% complementarity to the first segment.
19. The plant cell of any one of claims 11-18, wherein said plant cell is from a monocot.
20. The plant cell of claim 19, wherein said monocot is maize, barley, millet, wheat or rice.
21. The plant cell of any one of claims 11-18, wherein said plant cell is from a dicot.
22. The plant cell of claim 21, wherein said plant is soybean, canola, alfalfa, sunflower, safflower, tobacco, Arabidopsis, or cotton.
23. A plant or plant part comprising a plant cell of any one of claims 11-22.
24. A transgenic seed from the plant of claim 23, wherein said transgenic seed comprises said heterologous polynucleotide comprising said silencing element.
25. A method of controlling a Pentatomidae plant pest comprising feeding to a Pentatomidae plant pest a composition comprising a silencing element, wherein said silencing element, when ingested by said Pentatomidae plant pest, reduces the level of expression of any one of the target Pentatomidae plant pest sequences set forth in SEQ ID NOS: 279, 302, 281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 17, 30, 34, 14, 18 or 263 and thereby controls the Pentatomidae plant pest.
26. The method of claim 25, wherein said silencing element comprises
a) a fragment of at least 19 consecutive nucleotides of SEQ ID NOS: 279,
302, 281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 17,
30, 34, 14, 18 or 263 or a complement thereof; or,
b) the nucleotide sequence comprising at least 90% sequence identity to any one of SEQ ID NOS: 279, 302, 281, 304, 280, 283, 282, 303, 278, 284, 285, 286, 287, 288, 289, 290, 291, 292, 14, 18, 263, 17, 30, 34, 337, 338, 339, 340, 341, 342, 343, 344,
305, 306, 307, 308, 309, 310, 311, 312, 293, 294, 295, 296, 297, 298, 299, 300, 301, 321,
322, 323, 324, 325, 326, 327 or 328 or a complement thereof,
wherein said silencing element, when ingested by a Pentatomidae plant pest, reduces the level of a target sequence in said Pentatomidae plant pest and thereby controls the Pentatomidae plant pest.
27. The method of claim 26, wherein said Pentatomidae plant pest comprises a N. viridula plant pest.
28. The method of any one of claims 26 or 27, wherein said silencing element comprises the sequence set forth in any one of SEQ ID NOS: 284, 285, 286, 287, 288, 289, 290, 291, 292, 305, 306, 307, 308, 309, 310, 31 1, 312, 17, 30, 34, 337, 338, 339, 340, 341, 342, 343 or 344 or a complement thereof.
29. The method of any one of claims 25-28, wherein said composition comprises a plant or plant part having stably incorporated into its genome a polynucleotide comprising said silencing element, wherein said silencing element is operably linked to a seed-preferred promoter.
30. The method of any one of claims 25-29, wherein said silencing element comprises
a) a polynucleotide comprising the sense or antisense sequence of the sequence set forth in SEQ ID NOS: 284, 285, 286, 287, 288, 289, 290, 291, 292, 17, 30, 34, 14, 18, 263, 337, 338, 339, 340, 341, 342, 343, 344, 305, 306, 307, 308, 309, 310, 31 1 or 312 or a complement thereof; or,
b) a polynucleotide comprising the sense or antisense sequence of a sequence having at least 95% sequence identity to the sequence set forth in SEQ ID NOS: 284, 285, 286, 287, 288, 289, 290, 291, 292, 17, 30, 34, 14, 18, 263, 337, 338, 339, 340, 341, 342, 343, 344, 305, 306, 307, 308, 309, 310, 31 1 or 312 or a complement thereof.
31. The method of any one of claims 25-30, wherein said silencing element expresses a double stranded RNA.
32. The method of any one of claims 25-30, wherein said silencing element comprises a hairpin RNA.
33. The method of claim 32, wherein said polynucleotide comprising the silencing element comprises, in the following order, a first segment, a second segment, and a third segment, wherein
a) said first segment comprises at least about 20 nucleotides having at least 90% sequence complementarity to the target polynucleotide;
b) said second segment comprises a loop of sufficient length to allow the silencing element to be transcribed as a hairpin RNA; and,
c) said third segment comprises at least about 20 nucleotides having at least 85%o complementarity to the first segment.
34. The method of any one of claims 29-30, wherein said silencing element is flanked by a first operably linked convergent promoter at one terminus of the silencing element and a second operably linked convergent promoter at the opposing terminus of the polynucleotide, wherein the first and the second convergent promoters are capable of driving expression of the silencing element.
35. The method of claim 29, wherein said plant is a monocot.
36. The method of claim 35, wherein said monocot is maize, barley, millet, wheat or rice,
37. The method of claim 29, wherein said plant is a dicot.
38. The method of claim 37, wherein said plant is soybean, canola, alfalfa, sunflower, safflower, tobacco, Arabidopsis, or cotton.
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