WO2000060089A1 - Procede de reproduction d'un trait genetique - Google Patents

Procede de reproduction d'un trait genetique Download PDF

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Publication number
WO2000060089A1
WO2000060089A1 PCT/US2000/009448 US0009448W WO0060089A1 WO 2000060089 A1 WO2000060089 A1 WO 2000060089A1 US 0009448 W US0009448 W US 0009448W WO 0060089 A1 WO0060089 A1 WO 0060089A1
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plant
gene
vector
transformed
promoter
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PCT/US2000/009448
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English (en)
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Michael Fromm
James Zhang
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Mendel Biotechnology, Inc.
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Priority to JP2000609580A priority Critical patent/JP2003525589A/ja
Priority to EP00925906A priority patent/EP1192255A1/fr
Priority to CA002367408A priority patent/CA2367408A1/fr
Priority to AU44528/00A priority patent/AU4452800A/en
Priority to US09/958,131 priority patent/US6946586B1/en
Publication of WO2000060089A1 publication Critical patent/WO2000060089A1/fr
Priority to US10/412,699 priority patent/US7345217B2/en
Priority to US11/986,992 priority patent/US8809630B2/en
Priority to US14/177,551 priority patent/US20140201864A1/en
Priority to US14/463,524 priority patent/US20150166614A1/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)
    • C12N15/8216—Methods for controlling, regulating or enhancing expression of transgenes in plant cells
    • 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
    • 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
    • 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

  • This invention is in the field of plant molecular biology.
  • this invention relates to a method for breeding plants for improved agricultural traits.
  • the invention provides a method for systematically screening for traits associated with the altered expression of a gene of interest in plants.
  • the method comprises providing a first pool of donor vectors, wherein each donor vector comprises a transactivator and a second pool of receptor vectors, wherein each receptor vector comprises a transactivator binding site operably linked to a different gene of interest.
  • a first plant is transformed with a member of the donor vector pool and a second plant transformed with a member of the receptor vector pool to generate first transformed plants comprising the donor vector and a second transformed plant comprising the receptor vector.
  • First and second transformed plants are crossed to generate a hybrid plant.
  • Both first and second transformed plants have a wild type phenotype because the expression levels of the gene of interest is not altered from that in a nontransformed plant.
  • the phenotype of the hybrid plant comprising both transactivator and the gene of interest may be different from wild type because the expression levels of the gene of interest is altered compared with that of a nontransformed plant. The phenotype of these plants is investigated to identify a hybrid plant with an improved trait.
  • the transactivator may be operably linked to (1 ) a constitutive promoter, (2) an inducible promoter, (3) a tissue active or specific promoter or (4) a developmental-stage active or specific promoter.
  • a constitutive promoter When the transactivator is linked to a constitutive promoter, changes in expression of a gene will be observed in all tissues and at all times and a broad overview of the effects of the expression of the gene on a plant will be observed.
  • the expression of the gene may be turned on or off in a particular tissue such as seed, roots, flowers, leaves, shoots, fruits or stems, during a particular period in development, such as early, middle or late stages in development, or under particular conditions, such as specific environmental or disease stresses.
  • a plant may be transformed with more than one receptor vector or with more than one donor vector.
  • the gene of interest may be any gene, but is preferably a regulatory gene such as a transcription factor, a phosphatase or a protein kinase.
  • the genes of interest are all the transcription factors identified in a plant, such as those identified in Arabidopsis thaliana. These genes collectively control all gene expression in plants and thus control all plant traits.
  • the gene may be in a sense orientation for overexpression analysis or in an antisense orientation for underexpression analysis. Additionally, the gene may be a full length coding sequence for a gene or a fragment of a gene, in particular a fragment with biological activity.
  • the donor and receptor vectors may also include first and second selectable markers, respectively, to assist in selecting transformed hybrid plants.
  • the invention provides a method for breeding plants for a desired or improved trait.
  • the method involves crossing a member of a first pool of plants, each plant in this pool having been transformed with an donor vector comprising a transactivator, with a member of a second pool of plants, each plant in this pool having been transformed with a receptor vector comprising a transactivator binding site operably linked to a different gene of interest to generate a collection of hybrid plants.
  • Traditional plant breeding techniques are used to obtain transgenic plants having both donor and receptor vectors and exhibiting a desired or improved trait.
  • the invention provides a transgenic plant generated by the method described above.
  • the invention is a plant breeding kit.
  • the plant breeding kit comprises (a) a pool of activator vectors, wherein each donor vector comprises a transactivator; and (b) a pool of receptor vectors, wherein each receptor vector comprises a transactivator binding site operably linked to a different gene of interest.
  • the vectors may also include first and second selectable markers to assist in selecting transformed hybrid plants.
  • the transactivator may be operably linked to (1 ) a constitutive promoter, (2) an inducible promoter, (3) a tissue active or specific promoter or (4) a developmental- stage active or specific promoter.
  • the invention is a method for modifying the patterns of gene expression in a plant.
  • the method first entails providing a first pool of donor vectors, wherein each activator vector member comprises a transactivator, and a second pool of receptor vectors, wherein each receptor vector member comprises a transactivator binding site operably linked to a regulatory gene.
  • Activator and receptor vector members are transformed into first and second plants. Transformed first and second plants are crossed to generate a hybrid plant with modified patterns of gene expression.
  • a “transgenic or transformed plant” refers to a plant which contains a recombinant polynucleotide introduced by transformation. Transformation means introducing a nucleotide sequence in a plant in any manner to cause stable or transient expression of the sequence. This may be achieved by transfection with viral vectors, transformation with piasmids, such as Agrobacterium-base ⁇ vectors, or introduction of naked DNA by eiectroporation, lipofection, or particle gun acceleration.
  • a transformed plant may refer to a whole plant as well as to seed, plant tissue, plant cells or any other plant material, and to the plant's progeny.
  • a “vector” is a nucleic acid construct, generated recombinantly or synthetically, comprising nucleic acid elements that can cause expression of a gene.
  • a “donor vector” is a construct for expression of a polynucleotide sequence for a transactivator gene. The transactivator gene is operably linked to a promoter.
  • the promoter region may include tissue active-or-specific promoters, developmental stage active-or-specific promoters, inducible promoters or constitutive promoters.
  • a "receptor vector” is a construct for expression of a gene of interest such as regulatory gene.
  • the receptor vector includes the sequence for a transactivator binding site.
  • the construct sequence may also include promoters, operators, enhancer regions, silencer regions, polyadenylation sites, translation initiation sites and the like.
  • a “gene of interest” is a polynucleotide sequence for a regulatory gene such as a transcription factor, a protein kinase or a phosphatase. These sequences may be in a sense or antisense orientation, or partial or complete gene sequences.
  • a nucleotide sequence is "operably linked" when it is placed into a functional relationship with another nucleotide sequence. For example, a promoter or enhancer is operably linked to a gene coding sequence if the presence of the promoter or enhancer increases the level of expression of the gene coding sequence
  • a “pool” entails a group of at least two members, preferably at least 10 members, more preferably at least 100 members.
  • a pool can be all the identified genes of a certain type in a plant such as all identified transcription factors derived from a plant, as exemplified by up to 1 ,700 transcription factors identified in Arabidopsis thaliana
  • altered or modified expression in reference to polynucleotide or polypeptide expression refers to an expression pattern in a transgenic plant that is different from the expression pattern in the wild type plant or a reference plant; for example, by expression in a cell type other than a cell type in which the sequence is expressed in the wild type plant, or by expression at a time other than at the time the sequence is expressed in the wild type plant, or by a response to different inducible agents, such as hormones or environmental signals, or at different expression levels (either higher or lower) compared with those found in a wild type plant.
  • the term also refers to lowering the levels of expression to below the detection level or completely abolishing expression.
  • the resulting expression pattern may be transient or stable, constitutive or inducible.
  • Trait refers to the physiological, morphological or physical characteristics of a plant or particular plant material These characteristics may be visible to the human eye, such as germination rates or seed size, or be measurable by laboratory techniques, such as the protein, starch or oil content of seed by biochemical assays or changes in the expression level of genes by employing Northerns, RT PCR or microarray gene expression assays
  • Trait modifications or improvements of particular interest include those to seed, fruit, root, flower, leaf, stem, shoot, seedling or the like, including- enhanced tolerance to environmental conditions including freezing, chilling, heat, drought, water saturation, radiation and ozone; enhanced resistance to microbial, fungal or viral diseases; resistance to nematodes, decreased herbicide sensitivity, enhanced tolerance of heavy metals (or enhanced ability to take up heavy metals), enhanced growth under poor photoconditions (e.g., low light and/or short day length), or changes in expression levels of genes of interest
  • Other traits that may modified relate to the production of plant metabolites, such as variations in the production of taxol, tocopherol, tocotnenol, sterols, phytosterols, vitamins, wax monomers, anti-oxidants, ammo acids, lignins, cellulose, tannins, prenyllipids (such as chlorophylls and carotenoids), glucosinolates, and terpenoids, enhanced or compositionally altered protein or oil production
  • Physical plant characteristics that may be modified include cell development, fruit and seed size and number, yields of plant parts such as stems, leaves and roots, the stability of the seeds during storage, characteristics of the seed pod (e.g., susceptibility to shattering), root hair length and quantity, internode distances, or the quality of seed coat.
  • Plant growth characteristics that may be modified include growth rate, germination rate of seeds, vigor of plants and seedlings, leaf and flower senescence, male sterility, apomixis, flowering time, flower abscission, rate of nitrogen uptake, biomass or transpiration characteristics, as well as plant architecture characteristics such as apical dominance, branching patterns, number of organs, organ identity, organ shape or size.
  • Hybrid plant refers to a plant generated by crossing two plants of interest, propagating by seed or tissue and then growing the plants. When plants are crossed sexually, the step of pollination may include cross pollination or self pollination or back crossing with an untransformed plant or another transformed plant. Hybrid plants include first generation and later generation plants.
  • the present invention provides a method to manipulate and improve a plant trait.
  • the method combines the power of genomics with plant breeding techniques.
  • the expression levels of known genes of interest in a plant can be altered constitutively, or altered selectively to monitor tissue specific expression, inducible expression, developmental-stage specific expression or the like in a high-throughput manner.
  • Phenotypic changes resulting from expressing specific plant genes at different levels, at different times, under different types of stress, in different plant tissues or the like is then screened. Finally, plants with improved traits are selected.
  • the method entails transforming a first plant with a member of a first pool of donor vectors.
  • Each donor vector includes a transactivator that is placed under the control of a different promoter so that the expression of the transactivator can be controlled under different conditions.
  • the method entails transforming a second plant with a member of a second pool of receptor vectors.
  • the receptor construct comprises a transactivator binding site for binding a transactivator.
  • the transactivator binding site is operably linked to a gene of interest which permits overexpression (for example, by using sense constructs) or underexpression (for example, by using antisense constructs) of the gene when transactivator expression is turned on.
  • genes that affect polygenic traits such as regulatory genes.
  • This method is an improvement of the method described in Liu et al. US Patent No. 5,968,793 and Guyer et al. (1998) Genetics 149: 633-639, that describe methods wherein both donor and receptor vectors are transformed into the same plant to regulate gene expression and to observe trait improvements in a plant.
  • Our method provides a greater degree of flexibility and speed for observing the effects of selective gene expression on the traits of a plant. Trait improvements for any plant may be investigated by this method.
  • the plant may be a crop plant such as soybean, wheat, corn, potato, cotton, rice, oilseed rape (including canola), sunflower, alfalfa, sugarcane and turf; or a fruit or vegetable plant, such as apple, banana, blackberry, blueberry, strawberry, and raspberry, cantaloupe, carrot, cauliflower, coffee, cucumber, eggplant, grape, honeydew, lettuce, mango, melon, onion, papaya, peas, peppers, pineapple, spinach, squash, sweet corn, tobacco, tomato, watermelon, rosaceous fruits (such as peach, cherry and plum) and vegetable brassicas (such as broccoli, cabbage, cauliflower, brussel sprouts and kohlrabi).
  • a crop plant such as soybean, wheat, corn, potato, cotton, rice, oilseed rape (including canola), sunflower, alfalfa, sugarcane and turf
  • a fruit or vegetable plant such as apple, banana, blackberry, blueberry, strawberry, and raspberry, cantaloupe, carrot, cauliflower, coffee, cucumber,
  • Other crops, fruits and vegetables whose trait may be improved include barley, sorghum, currant, avocado, citrus fruits such as oranges, lemons, grapefruit and tangerines, artichoke, currant, cherries, nuts such as the walnut and peanut, pear, endive, leek, roots, such as arrowroot, beet, cassava, turnip, radish, yam, sweet potato and beans.
  • FIG. 1 An activator plant is grown from seed derived from plants that have been transformed with a construct containing one of ten different promoters linked to a transactivator gene (in this Figure a fusion of the Lac I binding domain and the Gal4 transactivation domain)
  • a target plant is transformed with a construct containing the Laci binding sites linked to one of over 1 ,700 transcription factor genes that have been identified from Arabidopsis thaliana The target plant does not express the plant transcription factor unless the transactivator is present
  • the donor construct compnses a recombinant polypeptide sequence which encodes a DNA binding domain fused to a transcription activation domain.
  • This recombinant polynucleotide is the transactivator.
  • a DNA binding domain is a sequence that binds to DNA with some degree of specificity.
  • a common feature of some activation domains is that they are designed to form amphiphilic alpha helices with excess positive or negative charge (Giniger and Ptashne (1987) Nature 330:670-672, Gill and Ptashne (1987) Cell 51 :121-126, Estruch et al (1994) Nucl. Acids Res. 22:3983-3989).
  • Examples include the transcription activation region of VP16 or GAL4 (Moore et al. (1998) Proc. Natl. Acad. Sci. USA 95: 376-381 ; and Aoyama et al. (1995) Plant Cell 7:1773-1785), peptides derived from bacterial sequences (Ma and Ptashne (1987) Ce// 51 ; 113-119) and synthetic peptides (Giniger and Ptashne, supra).
  • Exemplary transactivators are those described in Brent and Ptashne, US Patent No. 4,833,080, herein incorporated by reference or in Hasselhoff and Hodge, WO97/30164.
  • Va ⁇ ous promoter sequences are available which may be used to control expression of the transactivator. Such promoters may be utilized to initiate transcription of a nucleic acid sequence of interest operably linked to the promoter region.
  • viral promoters may be utilized in plant expression vectors These include the 35S RNA and 19S RNA promoters of CaMV (B ⁇ sson, et al., Nature, 310:511 , 1984; Odell, et al., Nature, 313:810, 1985); the promoter from Figwort Mosaic Virus (FMV) (Gowda, et al., J. Cell Biochem , 13D: 301 , 1989) and the coat protein promoter of TMV (Takamatsu, et al., EMBO J. 6.307, 1987) Additional promoters include the nopa ne synthase promoter (An et al., (1988) Plant Physiol. 88:547); and the octopine synthase promoter (Fromm et al., (1989) Plant Cell ! : 977)
  • the donor construct may include one or more inducible promoters.
  • inducible promoters useful in plants include those induced by chemical means, such as the yeast metallothionein promoter which is activated by copper ions (Mett, et al., (1993) Proc. Natl. Acad. Sci., U.S.A., 90:4567), In2-1 and ln2-2 regulator sequences which are activated by substituted benzenesulfonamides, e.g., herbicide safeners (Hershey, et al., (1991 ) Plant Mol. Biol., 17.679); and the GRE regulatory sequences which are induced by glucocorticoids (Schena, et al. (1991 ), Proc. Natl. Acad. Sci., U.S.A., 88:10421 ).
  • Plant promoters also include the light-inducible promoter from the smail subunit of nbulose bis-phosphate carboxylase (ssRUBISCO) (Coruzzi, et al., (1984) EMBO J., 3:1671 ; Broglie, et al., (1984) Science, 224:838), promoters regulated by heat (Callis et al., (1988) Plant Physiol. 88:965; Ainley, et al. (1993) Plant Mol. Biol. 22. 13-23; hormones, such as abscisic acid (Marcotte et al., (1989) Plant Cell !
  • ssRUBISCO nbulose bis-phosphate carboxylase
  • wounding e.g., wunl, Siebertz et al., (1989) Plant Cell 1 : 961 ; and chemicals such as methyl jasminate or salicylic acid (Gatz et al., (1997) Ann. Rev. Plant Physiol. Plant Mol. Biol. 48: 89-108).
  • Tissue specific promoters may also be utilized for expression of genes in plants.
  • Tissue specific promoters useful in transgenic plants include the cdc2a promoter and cyc07 promoter (Ito, et al.,(1994) Plant Mol. Biol., 24:863; Martinez, et al. (1992) Proc. Natl. Acad. Sci. USA, 89:7360; Medford, et al., (1991) Plant Cell, 3:359; Terada, et al. (1993) Plant Journal, 3:241 ; Horbach, et al., (1993) Plant Journal, 4.411).
  • Additional tissue specific promoters that are utilized in plants include the histone promoter (Atanassova, et al., (1992) Plant Journal,
  • CAD ⁇ nnamyl alcohol dehydrogenase
  • timing of the expression can be controlled by using promoters such as those acting at senescence (Gan and Amasino (1995) Science 270: 1986-1988); or late seed development (Odell et al. (1994) Plant Physiol. 106:447-458).
  • promoters include root-specific promoters such as root-specific promoters disclosed in US Patent Nos. 5,618,988, 5,837,848 and 5,905,186 or the prxEa promoter in Wanapu and Shinmyo (1996) Ann. N Y Acad. Sci. 782:107-113 or Miao et al. (1991 ) Plant Cell 3:1 1-22 or Hirel et al. (1992) Plant Mol. Biol. 20:207-218), seed-specific promoters such as the napin, phaseolin or DC3 promoter described in US Pat. No. 5,773,697, the oleate 12-hydroxylase: desaturase promoter from Lesquerella (Broun et al (1998) Plant J. 13:201-210), the oleosin promoter or Arabidopsis (Plant et al (1994 ) Plant Mol. Biol. 25:193-
  • zein promoter of maize (Russel et al (1997) Transgenic Res. 6:157-168), the glutelin promoters of rice (Washida et al. Plant Mol Biol. (1999) 40:1-12) and maize (Thomas et al (1990) Plant Cell 2:1171-1 180), fruit-specific promoters such as those active during fruit ripening (such as the dru 1 promoter (US Pat. No. 5,783,393), or the 2A11 promoter (US Pat. No. 4,943,674) and the tomato polygalacturonase promoter (Bird et al. (1988) Plant Mol. Biol.
  • pollen- active promoters such as PTA29, PTA26 and PTA13 (US Pat. No. 5,792,929), promoters active in vascular tissue (Ringii and Keller (1998) Plant Mol. Biol. 37:977-988), flower-specific (Kaiser et al, (1995) Plant Mol. Biol. 28:231-243), pollen (Baerson et al. (1994) Plant Mol. Biol. 26:1947-1959), carpeis (Ohl et al.
  • Preferred inducible or tissue-specific promoters include Rd 29a (Yamaguchi-Shinozaki and Shinozaki (1993) Plant Physiol. Mar;101 :1119-20), , LTP1 (Thoma et al. (1994) Plant Physiol. 105(1 ):35-45), STM (Long et al. (1996)
  • the donor construct may also include additional sequences such as selectable markers linked to a constitutive promoter for selecting plants containing the donor construct in field trials or tissue culture. These may include the acetoacetate synthase gene for chlorosulfuron resistance or the gene that confers resistance to cyanamide.
  • Plant transformation constructs may also include RNA processing signals, for example, introns, which may be positioned upstream or downstream of the open reading frame sequence (ORF).
  • expression constructs may also include additional regulatory sequences from the 3'-untranslated region of plant genes, e.g., a 3' terminator region to increase mRNA stability of the mRNA, such as the Pl-ll terminator region of potato or the octopine or nopaline synthase 3' terminator regions.
  • the receptor construct comprises one or more DNA binding sites for one of the transactivators described above, such as those disclosed in US Patent No. 4833,080, operably linked to a gene of interest, such as a transcription factor, phosphatase or kinase.
  • a gene of interest such as a transcription factor, phosphatase or kinase.
  • the transcription factors contained in the construct may be derived from one or more of the transcription factor families described below.
  • the plant transcription factors may belong to one of the following transcription factor families: the AP2 (APETALA2) domain transcription factor family (Riechmann and Meyerowitz (1998) J. Biol. Chem. 379:633-646); the MYB transcription factor family (Martin and Paz-Ares, (1997) Trends Genet. 13:67-73); the MADS domain transcription factor family (Riechmann and Meyerowitz (1997)
  • DNA-binding protein (DBP) family (Tucker et al. (1994) EMBO J. 13:2994-3002); the bZIP family of transcription factors (Foster et al. (1994) FASEB J. 8:192-200); the Box P-binding protein (the BPF-1 ) family (da Costa e Silva et al. (1993) Plant J. 4:125-135); the high mobility group (HMG) family (Bustin and Reeves (1996J Prog. Nucl. Acids Res. Mol. Biol. 54:35-100); the scarecrow (SCR) family (Di
  • transcription factors may be identified by screening polynucleotide or polypeptide sequence databases, such as GenBank, using using sequence alignment methods and homology calculations, such as those desc ⁇ bed in Altschul et al. (1994) Nature Genetics 6: 119-129.
  • NCBI Basic Local Alignment Search Tool BLAST
  • BLAST Altschul et al. (1990) Basic local alignment search tool. J. Mol. Biol. 215 403-410
  • NCBI National Center for Biotechnology Information
  • NCBI National Center for Biotechnology Information
  • a program that identifies particular sequence motifs may be employed along with specific characteristic consensus sequences, such as FIND PATTERN (GCG, Madison, Wl).
  • FIND PATTERN GCG, Madison, Wl
  • Exemplary transcription factors which can be employed in the invention include those disclosed in Zhang et al. US Serial Application No 09/394,519, filed September 13, 1999, entitled “Plant Gene Sequences I", Keddie et al. US
  • the transcription factors encompass the naturally occu ⁇ ng sequences as well as non-naturally occurring sequences which are derivatives of the transcription factors described above
  • the ammo acid sequence encoding the binding protein may be a naturally occurring sequence such as the ones shown above or a non-naturally occunng sequence using domains of transcription factors described above fused in frame, but not necessarily adjacent, with functional domains derived from other sequences or sources
  • the invention includes polypeptides derived from shuffling regions of transcription factors described above by methods described in M shuil and Stemmer, US
  • Patent No. 5,837,458 entitled “Methods and Compositions for Cellular and Metabolic Engineering” and Stemmer and Crame ⁇
  • the particular arrangement of the transcription factor sequence in the transformation vector will be selected according to the type of expression of the sequence that is desired.
  • a transcription factor coding sequence may be operably linked to a constitutive high-level promoter such as the CaMV 35S promoter. Generally, this will require the full length sequence encoding the transcription factor.
  • a reduction of transcription factor activity in the transgenic plant may be obtained by introducing into plants antisense constructs based on the transc ⁇ ption factor cDNA.
  • the transc ⁇ ption factor cDNA is arranged in reverse orientation relative to the promoter sequence in the transformation vector.
  • the introduced sequence need not be the full length transcnption factor cDNA or gene, and need not be exactly homologous to the transc ⁇ ption factor cDNA or gene found in the plant type to be transformed. Generally, however, where the introduced sequence is of shorter length, a higher degree of homology to the native transc ⁇ ption factor sequence will be needed for effective antisense suppression.
  • RNA encoded by the transcription factor cDNA (or variants thereof) is overexpressed may also be used to obtain co-suppression of the endogenous transcription factor gene in the manner described in U S. Patent No. 5,231 ,020 to Jorgensen.
  • Such co-suppression does not require that the entire transcription factor cDNA be introduced into the plant cells, nor does it require that the introduced sequence be exactly identical to the endogenous transcription factor gene
  • the suppressive efficiency will be enhanced as (1 ) the introduced sequence is lengthened and (2) the sequence similarity between the introduced sequence and the endogenous transcription factor gene is increased
  • supression on a transcription gene activity may be obtained by double stranded RNA-mediated interference (Voinnet, et al (1998) Cell 95, 177-187, Waterhouse, et al (1998) Proc Natl. Acad.
  • the receptor vector may also include additional sequences such as selectable markers linked to a constitutive promoter for selecting plants containing the activatorconstruct in field trials or tissue culture. These may include the acetoacetate synthase gene for chlorosulfuron resistance or the gene that confers resistance to cyanamide.
  • Any of the identified sequences may be incorporated into a cassette or vector for expression in plants.
  • a number of expression vectors suitable for stable transformation of plant cells or for the establishment of transgenic plants have been described including those described in Weissbach and Weissbach, (1989) Methods for Plant Molecular Biology, Academic Press, and Gelvin et al., (1990) Plant Molecular Biology Manual, Kluwer Academic Publishers. Specific examples include those derived from a Ti plasmid of Agrobacte ⁇ um tumefaciens, as well as those disclosed by Herrera-Estrella, L, et al., (1983) Nature 303: 209, Bevan, M.,
  • non-Ti vectors can be used to transfer the DNA into plants and cells by using free DNA delivery techniques.
  • free DNA delivery techniques may involve, for example, the use of iiposomes, electroporation, microprojectile bombardment, silicon carbide wiskers, and viruses.
  • transgenic plants such as wheat, rice (Christou, P., (1991) Bio/Technology 9: 957-962) and corn (Gordon-Kamm, W., (1990) Plant Cell 2: 603-618) can be produced.
  • An immature embryo can also be a good target tissue for direct DNA delivery techniques by using the particle gun (Weeks, T. et al., (1993) Plant Physiol. 102:
  • plant transformation vectors include one or more cloned plant coding sequences (genomic or cDNA) under the transcriptional control of 5' and
  • Such plant transformation vectors typically also contain a promoter (e.g., a regulatory region controlling inducible or constitutive, environmentally-or developmentally-regulated, or cell- or tissue-specific expression), a transcription initiation start site, an RNA processing signal (such as intron spiice sites), a transcription termination site, and/or a poiyadenylation signal.
  • a promoter e.g., a regulatory region controlling inducible or constitutive, environmentally-or developmentally-regulated, or cell- or tissue-specific expression
  • RNA processing signal such as intron spiice sites
  • transcription termination site such as intron spiice sites
  • poiyadenylation signal such as intron spiice sites
  • Standard techniques may be used to transform plants with the above described vectors to overexpress or underexpress the genes of interest in plants in order to understand a gene's effect on a plant's phenotype. Additionally, combinations of transactivator or donor rvectors may be used to transform plants to understand the contribution of multiple genes of interest to a trait.
  • Exemplary plants to be transformed may be any higher plant, including monocotyledonous and dicotyledenous plants.
  • Suitable protocols are available for Leguminosae (alfalfa, soybean, clover, etc.), Umbelliferae (Carrot, celery, parsnip), Cruciferae (cabbage, radish, rapeseed, broccoli, etc.), Curcurbitaceae (melons and cucumber), Gramineae (wheat, corn, rice, barley, millet, etc.), Solanaceae (potato, tomato, tobacco, peppers, etc.), and various other crops See protocols described in Ammirato et al. (1984) Handbook of Plant Cell Culture -Crop Species. Macmillan Publ. Co. Shimamoto et al. (1989) Nature 338:274-
  • Transformation and regeneration of both monocotyledonous and dicotyledonous plant cells is now routine, and the selection of the most appropriate transformation technique will be determined by the practitioner.
  • the choice of method will vary with the type of plant to be transformed; those skilled in the art will recognize the suitability of particular methods for given plant types. Suitable methods may include, but are not limited to: electroporation of plant protoplasts; liposome-mediated transformation; polyethylene glycol (PEG) mediated transformation; transformation using viruses; micro-injection of plant cells; micro-projectile bombardment of plant cells; vacuum infiltration; and Agrobacterium tumeficiens (AT) mediated transformation.
  • transformed plants may be selected using a dominant selectable marker incorporated into the transformation vector.
  • a dominant selectable marker will confer antibiotic or herbicide resistance on the seedlings of transformed plants, and selection of transformants can be accomplished by exposing the seedlings to appropriate concentrations of the antibiotic or herbicide.
  • Plants transformed with any of the donor vector may be crossed with plants transformed with any of the receptor vectors as described in Figure 1.
  • Plants transformed with a receptor vector for a specific transcription factor in a sense or antisense configuration
  • Plants transformed with a receptor vector for a specific transcription factor can be crossed with a variety of plants transformed with donor vectors comprising a variety of different promoters, including constitutive, inducible or tissue-specific vectors to investigate the effects of trancription factor expression throughout the plant, under specific conditions such as environmental stresses, disease, or the like, in specific tissues, such as seeds, roots, flowers, stems, leaves, fruits or the like. Seeds are collected and hybrid plants are grown to maturity. These plants can then be screened to identify plants with valuable traits.
  • plants may be grown in the presence of first and second herbicide resistant selectable markers. Seed obtained from herbicide resistant regenerated plants may be crossed further to generate later generation hybrid plants. Additional details in crop breeding techniques, in particular those for tomatoes are described in US Patent No. 5,817,913, herein incorporated by reference.
  • the present invention is a plant breeding kit.
  • seed or plants are provided, wherein a first pool of seed or plants is provided that are transformed with the donor vector and a second pool of seed or plants is provided that are transformed with the receptor vector. Then plant breeders can cross plants from first and second pools as described above to breed plants with improved traits.
  • EXAMPLES The invention is illustrated by Examples wherein six different donor vectors having a constitutive, an inducible promoter or a tissue specific promoter operably linked to either of two different transactivators are prepared. Additionally the invention is illustrated by the preparation of eight different receptor vectors comprising a transactivator binding site operably linked to a transcription factor. Donor and receptor vectors are then transformed into different tomato plants.
  • Transformed tomato plants having different donor vectors are then crossed with transformed tomato plants having different receptor vector. Improved traits can be screened for in the progeny.
  • the piasmid vector pMEN020 was the vector used for donor and receptor vector construction.
  • the pMEN020 piasmid construct is a binary cloning vector that contains both E. coli and Agrobacterium tumefaciens origins of DNA replication but no vir genes encoding proteins essential for the transfer and integration of the target gene inserted in the T-DNA region.
  • PMEN020 requires the trfA gene product to replicate in Agrobacterium.
  • the strain of Agrobacterium containing this trfA gene is called the ABI strain and is described in U.S. Patent Nos. 5,773,701 and 5,773,696.
  • This cloning vector serves as an £ coli- Agrobacterium tumefaciens shuttle vector. All of the cloning steps are carried out in E. coli before the vector is introduced into ABI strain of Agrobacterium tumefaciens.
  • Two different sets of constructs which are based on bacterial DNA binding proteins LexA and Lacl, respectively, were prepared.
  • LexA the construct was prepared in two steps. First, an intermediate construct was generated containing the LexA protein and the gal4 activation domain. In the intermediate construct, four fragments were generated separately and fused by overlap extension PCR. The first fragment was the 35S minimal promoter and omega translation enhancer; The fragment was amplified from construct SLJ4D4 (Jones et al 1992 Transgenic Research 1 :285) using primers 011731 (SEQ ID No. 1 ): GCCCAAGCTTTGAGCTCCGCGGCCGCAAGACCCTTCCTCTATATAAGGAAGTTCA and 011733 (SEQ ID No.
  • ACGCTTCCATGGTAATTGTAAATGTAATTGTAATGTTGT The second fragment was the lexA gene of E coli; it was amplified from piasmid pLexA (Clontech, Palo Alto, CA) using primers 011732 (SEQ ID No. 3): TTACAATTACCATGGAAGCGTTAACGGCCAGGCAACAAGA and 01 17717 (SEQ ID No. 4): TATTCCCACTTTGATTAAAATTGGGGAATTCCAGCCAGTCGCCGT.
  • the third fragment was the gal4 transcription activation domain; it was amplified from pGAD424 (aa 768-881 , Clontech) by primers 011715 (SEQ ID No. 5): GGCTGGAATTCCCCAATTTTAATCAAAGTGGGAA and 011718 (SEQ ID No. 6): AAGCTCTAGCTACTC I I I I I I I I GGGTTTGGTGGGGT.
  • the fourth fragment was the E9 transcription terminator (Fluhr et al 1986 EMBO J. 5:2063); it was amplified from pMON10098 using primers 011716 (SEQ ID No. 7): AAGAGTAGCTAGAGCTTTCGTTCGTATCA and 011719 (SEQ ID No.
  • the lacl system was constructed in a similar fashion as the lexA system, in two steps.
  • the translation initiation of the lacl gene was changed to ATG from GTG and a mutation at position 17 (Y to H, Lehming et al 1987 EMBO J 6:3145) was introduced.
  • the lacl gene was cloned from E coli genomic DNA by PCR amplification using primers 016400 (SEQ ID No. 9): CATGCCATGGAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTC
  • a multiple cloning site was added upstream of the Lacl (LexA)/gal4 fusion protein by 011731 to facilitate the cloning of promoter fragments.
  • full 35S promoters may be cloned upstream of the Lacl (LexA)/gal4 fusion protein by using restriction enzymes Hind III and Notl.
  • Inducible promoters from plant genomic DNAs can be isolated by PCR amplification using primers flanking the promoter region and containing suitable restriction sites for cloning into the activation vector.
  • the rd29a gene was characterized by Shmozaki's group in Japan (Yamaguchi-Shinozaki and Shinozaki (1993) Plant Physiol. 101 11 19-1 120) The rd29a gene expression is induced by desiccation, salt stress and exogenous ABA treatment (Yamaguchi-
  • a genomic clone carrying the rd29a promoter was identified by using rd29a as a search word at the www site of NCBI.
  • the sequence for the rd29a promoter is located in the region between nucleotide positions 3892 to 5390
  • rc.29a-pr ⁇ mer1 (SEQ ID No. 11)- GCCCA ⁇ GCTTGGTTGCTATGGTAGGGACTAT; and r /29a-pr ⁇ mer2 (SEQ ID No. 12): ATAAGAATGCGGCCGCGAGAGATAAAGGGACACGTATGAAGC
  • rd29a-p ⁇ mer1 includes a Hind III (AAGCTT) restriction site near the 5'-end of the primer and ⁇ d29a-pr ⁇ mer2 has a Notl (GCGGCCGC) restriction site near 5'-end of the primer.
  • DNA was used as a template in a PCR reaction under conditions suggested by the manufacturer (Boeh ⁇ nger Mannheim).
  • the reaction conditions that were used in this PCR experiment are as follows: Segment 1 : 94°C, 2 minutes, Segment 2. 94°C, 30 seconds; 60°C, 1 minute; 72°C, 3 minutes, for a total of 35 cycles; Segment 3. 72°C for 10 minutes.
  • a PCR product of 1525 base pair is expected.
  • the PCR products were subject to electrophoresis in a 0.8% agarose gel and visualized by ethidium bromide staining.
  • the DNA fragments containing the inducible promoter were excised and purified using a Qiaquick gel extraction kit (Qiagen, CA). The purified PCR product can then be digested with Hindlll and Notl, and cloned into the Hindlll and Notl sites of LexA and Lacl based donor vectors.
  • tissue specific promoters from plant genomic DNAs can also be isolated by PCR amplification.
  • the non-specific iipid transfer protein (or LTP1 ) promoter is specific for the epidermis layer of plants (Thoma et al, Plant Physiol.
  • LTP promoter The sequence for the LTP promoter is located in the region between nucleotide positions 1 to 1130 (Accession No M80567)
  • the following two primers were designed to amplify this promoter region from Arabidopsis genomic DNA LTP -pr ⁇ mer1 (SEQ ID No 13) GCCC4 .GC7TGATTAACTTGCATTACAGTTGGGAAGT, and L7Pf-p ⁇ mer2 (SEQ ID No 14) ATAAGAATGCGGCCGCGGTACGTATATGTTATGTGGTGTGAATG
  • LTP -pr ⁇ mer1 SEQ ID No 13
  • GCCC4 .GC7TGATTAACTTGCATTACAGTTGGGAAGT
  • L7Pf-p ⁇ mer2 SEQ ID No 14
  • LTP7-p ⁇ mer1 includes a Hind III (AAGCTT) restriction site near the 5'-end of the primer, and LTP7-p ⁇ mer2 has a Notl (GCGGCCGC) restriction site near 5'-end of the primer
  • AAGCTT Hind III
  • GCGGCCGC Notl
  • the receptor vector includes a corresponding binding region for the transactivator factor prepared above, in this case a LexA or Lacl binding site, and a gene of interest, such as a transcription factor Two versions of the cloning vector will be built, one each for Lexa and
  • GGCCCAAGCTTAATTGTGAGCGCTCACAATTCATGAATTGTGAGCGCTCACA ATT PCR product by primers 016415 and 016416, using pMEN20 as template, will include two copies of the lacl binding sites, the 35S minimal promoter, and the multiple cloning site of pMEN20
  • the CBF1 coding region can be amplified by PCR using primers 011700 (SEQ ID No 18).
  • ACGCGTCGACGACTGAGAACTCTAGTAACTACGTA and 011702 SEQ ID No. 19
  • PCR product approximately 780 bp, can be digested with
  • a seed specific transcription factor ATML1 (Lu et al. (1996) during embryonic pattern formation and defines a new class of homeobox genes Plant Cell 8(12):2155-68, GenBank Accession No. U37589) can be amplified by PCR using primers 05184 (SEQ ID No. 20):
  • CGGGGTACCCTTCTCCACAAGTAAGGGAACCAGA and 05185 (SEQ ID No. 21 ): ATAAGAATGCGGCCGCCCTCCCCTTTCACTCTTACCTTCCGAA.
  • the resulting PCR product approximately 2,400 bp, can be digested with Kpnl and Notl and cloned into the Kpnl and Notl sites of the receptor vector.
  • a root specific transcription factor PRL2 (Newman, et al. (1994)
  • Plant Physiol. 106, 1241-1255) was obtained from a full length expressed sequence tag (GenBank Accession No. R86816)
  • the cDNA can be isolated from the library vector by using the Sail and Notl enzymes, and then it can be cloned into the Sail and Notl sites of the receptor sites.
  • a ATHB-12 Lee et al. (1998) Plant Mol Biol. 37:377-84) was subcloned into the receptor vector by using Sail and Notl as previously described.
  • Tomato transformations are performed using the following procedure. Tomato seeds are sterilized in 50 % bleach solution for 20-30 minutes and rinsed at least 3 times with sterile water. The seed are placed in magenta jars that contain the following media: 1X MS Salts, 1X Gamborg's Vitamins, 2% sucrose, and 0.8% phytagar. The seeds are germinated for 7-10 days at 25°C with 16 hours of light. Agrobacterium from glycerol stock is inoculated into 5 ml of LB or YEP with the appropriate antibiotics, and the culture grown at 28°C overnight with shaking at 250 rpm.
  • the bacteria are spun down and resuspended in liquid germination media to a concentration of 0.2 OD600.
  • the cotyledons from 7-10 days old seedlings are cut into 0.5cm pieces, and transferred to a co-cultivation plate with (D1-) media containing the following: 1X MS salts, 1X Gamborg's Vitamins, 3% glucose. 1 mg/L zeatin, 0.8% (w/v) phytagar, pH to 5.8, and 375 uM Acetosy ⁇ ngone.
  • a first pool of tomatoes can be transformed with vectors comprising a constitutive promoter (35S promoter) or an inducible promoter (rd29a or Itp1 ) in combination with either lexA/Gal4 or Iacl/Gal4 transactivators
  • a second pool of tomatoes can be transformed with vectors comprising lexA or lacl binding sites in combination with either CBF, PRL2,
  • First and second pools of tomato plants are components of the plant breeding kit.
  • TO the initial transgenic plant produced from tissue culture, S1-S4 or F1-F4.
  • the S numbers are for self pollinations, while the F number is a cross between two lines.
  • a TO plant can be both self pollinated (S1 seeds produced) and outcrossed to an donor line initially (F1 seeds produced)
  • F1 S2 would be the selfed progenies of a F1 parent
  • the transformed TO plants will be grown to maturity in greenhouses (the plants can be scored with cyanamide herbicides if escapes are a problem). Some of the flowers will be crossed to TO plants containing the donor vector (The F1 progeny of this cross will be segregating for both genes). Several flowers will be crossed to obtain at least 100 seeds. The self pollinated seeds (S1 ) will be saved for later crosses to different activator promoters.
  • the F1 progeny will be screened by spraying chlorsuifuron and cyanamide to find the progeny containing both the donor (chlorsuifuron resistant) and receptor (cyanamide resistant) vectors (heterozygous for both). Both chlorsuifuron resistance and cyanamide resistance are dominant in their effects, so phenotypes resistant to both herbicides and thus containing both genes should be observable in the F1 progeny. The presence of two distinguishable herbicidal markers greatly facilitates determining the genotype.
  • the F1 progeny may be screened by RT-PCR . F1 S2 plants are segregating for both the activator and receptor genes.
  • F1 S2S3 plants (100% resistant to both chlorsuifuron and cyanamide).
  • Single plant analysis of these F1 S2S3 plants can be performed. These are homozygous for both the donor and receptor vectors and can be more extensively studied in this generation. Alternatively, the seeds from the F1 S2S2 plants can be bulked up for detailed studies.
  • Plants are screened for desired plant phenotypes for each gene. Initially studies may be preformed using two component systems where transcription factor expression is activated with the CaMV 35S activator gene. Transcription factors which appear to play a role in interesting phenotypes can then be further investigated by crossing specific receptor vectors with tissue-specific or inducible activator lines, such as fruit specific activator lines, or environmental or disease- inducible lines or deveiopmental-stage specific lines.
  • tissue-specific or inducible activator lines such as fruit specific activator lines, or environmental or disease- inducible lines or deveiopmental-stage specific lines.
  • Particular traits of interest in tomato include increased levels of carotenoids (particularly lycopene), increased levels of soluble solids, and enhanced disease resistance.

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Abstract

Cette invention concerne un procédé de criblage appliqué à un trait associé à l'expression altérée d'un gène d'intérêt dans des végétaux. Ce procédé repose sur une méthode combinatoire qui fait intervenir des méthodes classiques de reproduction de végétaux pour modifier des modes d'expression d'un gène d'intérêt. L'invention concerne également des kits à utiliser avec ces procédés et des plantes transgéniques obtenus par lesdits procédés.
PCT/US2000/009448 1998-09-22 2000-04-06 Procede de reproduction d'un trait genetique WO2000060089A1 (fr)

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CA002367408A CA2367408A1 (fr) 1999-04-07 2000-04-06 Procede de reproduction d'un trait genetique
AU44528/00A AU4452800A (en) 1999-04-07 2000-04-06 Genetic trait breeding method
US09/958,131 US6946586B1 (en) 1999-04-07 2000-04-06 Genetic trait breeding method
US10/412,699 US7345217B2 (en) 1998-09-22 2003-04-10 Polynucleotides and polypeptides in plants
US11/986,992 US8809630B2 (en) 1998-09-22 2007-11-26 Polynucleotides and polypeptides in plants
US14/177,551 US20140201864A1 (en) 1998-09-22 2014-02-11 Polynucleotides and Polypeptides in Plants
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