# Patent

## Title
Modulation of abscisic acid

## Abstract

Compositions and methods for modulating abscisic acid (ABA) perception and signal transduction in developing seed are provided. The methods and compositions find use in increasing yield in plants. Compositions comprise genetic constructs known to affect ABA sensitivity, particularly ABA biosynthetic mutants and fragments and variants thereof. Such compositions can be expressed with seed-preferred promoters.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a continuation of U.S. application Ser. No. 09/715,774, filed Nov. 17, 2000, which claims the benefit of U.S. Provisional Application No. 60/166,080, filed Nov. 17, 1999, the contents of which are hereby incorporated by reference in their entirety.


FIELD OF THE INVENTION
The present invention is drawn to methods for the genetic modification of plants, particularly for modulating plant response to abscisic acid.
BACKGROUND OF THE INVENTION
Abscisic acid (ABA) is a phytohormone that plays an essential regulatory role for a variety of physiological processes. The phytohormone is involved in embryo development, seed dormancy, transpiration, and adaptation to environmental stresses. ABA regulates many agronomically important aspects of plant development including synthesis of seed storage proteins and lipids as well as regulating stomatal closure. The analysis of ABA-responsive promoters has revealed a diversity of potential cis-acting regulatory elements.
Mutations in ABA biosynthesis are known in a variety of plant species. See, for example, Leung and Giraudat (1998) Annu. Rev. Plant Physiol. Plant Mol. Biol. 49:199-222, and the references cited therein. In Arabidopsis, a number of genetically distinct Arabidopsis acid-insensitive loci have been identified. These mutants were selected based on the ability of seeds to germinate in the presence of inhibitory concentrations of ABA. The mutations have also been shown to affect several additional aspects of seed development, including accumulation of storage proteins and lipids, chlorophyll breakdown, and desiccation tolerance.
To date, numerous mutants and genes have been characterized in plants. Five mutationally identified ABA response loci have been cloned. These represent three classes of proteins. The classes include two orthologous transcriptional regulators (Viviparousl-Vp1) of maize and ABA-insensitive 3 of Arabidopsis (ABI3), two highly homologous members of the protein phosphotase 2C family, and a farnesyl transferase of Arabidopsis. See, for example, McCarty et al. (1991) Cell 66:895-905; Giraudat et al. (1992) Plant Cell 4:1251-1261; Leung et al. (1994) Science 264:1448-1452; Leung et al. (1997) Plant Cell 9:759-771; and Cuither et al. (1996) Science 273:1239-1241.
During the maturation phase of seed development, the embryo becomes quiescent in tissues that are destined to remain viable and the dry seed acquire tolerance to desiccation. In maize and other grasses, this includes cells in the aleurone layer of the seed endosperm. The viviparous mutants of maize are blocked in the maturation program. Thus, the mutant embryo proceeds precociously into seedling development while attached to the mother plant. The nine characterized vivipary loci affect early steps in the biosynthesis of carotenoids and abscisic acid. vp1 embryos exhibit reduced sensitivity to ABA in culture. It has been suggested that the initial Vp1 may encode a factor involved in ABA perception.
At the molecular level, embryonic maturation is associated with a broad range of gene activation. Many of the genes expressed are regulated by the hormone ABA. However, the molecular mechanisms of ABA action are largely unknown.
ABA mediated growth control is a fundamental response of plants to adverse environmental conditions. Because little is known about the molecular mechanism of ABA-mediated growth control, methods are needed to modulate the response of plants to ABA, particularly to increase yield.
SUMMARY OF THE INVENTION
Compositions and methods for increasing yield in plants, particularly seed plants, are provided. The methods involve modulating abscisic acid (ABA) perception and signal transduction in developing seed. Methods are useful for protecting plants against the harmful/detrimental effects of stress and adverse environmental conditions. Compositions comprise genetic constructs known to affect ABA sensitivity in a plant or plant cell. Of particular interest are ABA-associated sequences. Such sequences include mutants, fragments and variants thereof, as well as antisense nucleotide sequences, for genes and mutants involved in the perception and signal transduction of ABA. The DNA sequences may be provided in constructs for temporal, developmental, and tissue specificity.
Compositions are useful in methods for increasing yield in plants under stress, particularly abiotic stress. In this manner, detrimental effects of ABA on ear and kernel growth are ablated.
Transformed plants, plant cells, tissues, and seeds are additionally provided.


DETAILED DESCRIPTION OF THE INVENTION
Methods for modulating early plant response to abscisic acid (ABA) are provided, particularly to insulate crop yield by ablating the detrimental effects of ABA on seed development. In particular, the invention provides compositions and methods for disrupting ABA signaling or function. The compositions and methods are useful for disrupting ABA function in a tissue and developmental-preferred manner to insulate female reproductive tissue growth from stress and adverse environmental conditions.
For purposes of the invention “early plant response” is intended the development of reproductive tissue, seed development, endosperm development, and seed maturation. ABA is involved in many other physiological and developmental processes throughout the life cycle of plants, including seed dormancy, adaptation to abiotic environmental stresses, such as cold, drought, salinity, etc., accumulation of nutritive reserves, acquisition of desiccation tolerance, stomatal closure, and the like. In the early phases, the phytohormone ABA regulates seed maturation and the maintenance of embryo dormancy. Later, at the onset of ontogenesis, ABA mediates several adaptational responses towards environmental cues such as desiccation, cold, salt stress, and other stresses, and acts as a negative growth regulator. Generally, ABA imposes a bimodal growth control by regulating the potential of the cell to enlarge, possibly by turgor control, and by inducing mitotic growth arrest in plants in accordance with its role as a negative growth regulator.
The invention involves controlling or modulating the early response of the plant to the signaling of ABA. By “modulating” is intended the up-regulation or down-regulation of the plant response to ABA. For purposes of the invention, modulation is generally down-regulation by the disruption of ABA synthesis or the disruption of the perception and signal transduction of ABA. It is recognized that total disruption of ABA function in plants is not practical as ABA performs many useful roles in plant development. For purposes of the invention, it is generally preferable to disrupt the effects of ABA at the site of the eventual effect, i.e. ears and kernels for cereal crops. In this manner, disruption of ABA perception or its signal transduction provides an effective strategy in insulating cereal female reproductive tissue growth from stress.
Environmental stresses following fertilization inhibit early events in establishment of sink capacity and can decrease yield. In cereals, for example, the endosperm is the major source of stored reserves within the mature seed. Storage capacity is established during an early stage of seed development. Recognizing ABA involvement in early plant responses to stress, the present invention is drawn to ablating the detrimental effects of ABA on the developing seed and improve the nature and quantity of seed and seed products, particularly cereals and grains. See, Mambelli and Setter (1998) Physiologia Plantarum 104:266-72 and Tuberosa et al. (1998) Theor. Appl. Genet 744-55.
As indicated, the invention comprises introducing sequences that modulate ABA perception and signal transduction into a target plant. By “sequences that modulate ABA perception and signal transduction” and “sequences involved in the perception and signal transduction of ABA” are intended mutants and genes that disrupt ABA synthesis or its perception and signal transduction. These mutants, genes, and sequences that disrupt ABA synthesis or its perception or signal transduction, are also called “ABA-associated sequences” herein. Such sequences include, but are not limited to, ABA-insensitive and hypersensitive mutants or antisense sequences corresponding to the mutant or wild-type genes. ABA mutants are known in the art and include abi1-5, era 1-3 (Cutler et al. (1996) Science 273:1239-41), gca1/8 (Benning et al. (1996) Proc. Workshop Abscisic Acid Signal Transduction in Arabidopsis, Madrid, p. 34), axr2 (Wilson et al. (1990) Mol. Gen. Genet. 222:377-83), jarl (Staswick et al. (1992) Proc. Natl. Acad. Sci. USA 89:6837-40), jin4 (Berger et al. (1996) Plant Physiol. 111:525-31), bri1 (Clouse et al. (1996) Plant Physiol. 111:671-78), sax (Arabidopsis thaliana); vp1 (McCarty et al. (1991) Cell 66:895-905 and Robichaud et al. (1986) J. Plant Physiol. 126:235-42), and real (Sturaro et al. (1996) J. Exp. Bot. 47:755-62) (Zea mays); cool (Raskin et al. (1988) Planta 173:73-78) (Hordeum vulgare); aba1 (Bitoun et al. (1990) Mol. Gen. Genet. 220:234-39 and Leydecker et al. (1995) Plant Physiol. 107:1427-31) (Nicotiana plumbaginifolia); and the like. These and other ABA-associated mutants can be used in the practice of the invention.
By “corresponding” to a gene or sequence is intended that the sequence is capable of hybridizing to the gene or sequence to the extent necessary to disrupt transcription. It is recognized that depending on the ABA-associated sequence utilized in the invention, the coding sequence or the antisense sequence may be preferred. However, the coding sequence may also be used to co-suppress expression of the target gene. For example, one strategy includes expression of mutant genes, such as abi1 or abi2 with an early kernel/embryo promoter to dominantly disrupt ABA action in tissues at early stages. Such an approach would not disrupt the later required ABA function in seed maturation. Alternatively, wild-type alleles of genes such as Vp1 may be down-regulated by co-suppression or antisense strategies to disrupt ABA action. In this latter example, an early kernel/embryo promoter may be used to drive expression of a coding sequence for Vp1(to co-suppress) or to drive expression of an antisense sequence for Vp1. A third example includes the transformation of a plant with a promoter for late period kernel development driving a wild-type Vp1 sequence. This transformed plant can then be crossed to a vp1 mutant plant. In this example, the inability of the vp1 mutant to be induced by ABA works to insulate early kernels from deleterious effects. At the same time, the DNA construct supplies kernels with the ability to mature normally. Thus, as described more fully below, several candidate gene targets are available to be coupled with promoters with limited expression patterns to provide increased yield stability in the face of abiotic stress.
The viviparous-1 (Vp1) gene of maize is required for expression of the maturation program in seed development. VP1 is a novel transcription factor possibly involved in potentiation of a seed-specific hormone response. The nucleic acid and amino acid sequence of Vp1 is in SEQ ID NOS: 1 and 2. The viviparous mutants of maize are blocked in the maturation program. As a result, the mutant embryo proceeds precociously into seedling development while attached to the mother plant. Several vivipary mutants have been identified. Further characteristics of a loss of function vp1 mutant include, for example, an ABA insensitive phenotype (i.e., a reduced sensitivity to germination inhibition by exogenous ABA in culture) and/or a decrease in Em promoter activation. It is well within skill in the art to identify loss of function mutations in Vp1 that are useful in the methods of the present invention. For example, Hill et al. ((1996) Journal Biological Chemistry 7:3366) have identified a role for the NH2-terminal acidic region and the highly conserved BR1 domain of VP 1 as being essential for VP1 function. Other vp1 mutants are known. See, for example, Neill et al. (1986) Planta 169:87-96; McCarthy et al. (1991) Cell 66:895-905; Robichaud et al. (1980) Dev. Genet. 1:325-330; Robichaud and Sussex (1987) Plant Physiol. 130:181-188; Robichaud et al. (1986) J. Plant Physiol. 126:235-42; McCarthy et al. (1990) Physiol. Plant 81:267-72; and, Eyster et al. (1931) Genetics 16:457-590; all of which are herein incorporated by reference.
Arabidopsis ABA-insensitive, ABI, mutants are also available. Such mutants have pleiotropic defects in seed development, including decreased sensitivity to ABA inhibition of germination in altered seed-specific gene expression. See, Finkelstein et al. (1998) The Plant Cell 10:1043-1045; Leung et al. (1994) Science 264:1448-1452; Leung (1997) Plant Cell 9:759-771; Giraudat et al. (1992) Plant Cell 4:1251-1261; Myer et al. (1994) Science 264:1452-1455; Koornneef et al. (1989) Plant Physiol. 90:463-469; Nambara et al. (1992) Plant J. 2:435-441; Finkelstein and Somerville (1990) Plant Physiol. 94:1172-1179; Leung and Giraudat (1998) Annu. Rev. Plant Physiol. Plant Mol. Biol. 49:199-222; Robinson and Hill (1999) Plant, Cell and Environment 22:117-123; and Rodriguez et al. (1998) FEBS Letters 421:185-190, and the references cited therein, all of which are herein incorporated by reference. In addition, the nucleic acid and amino acid sequences of wild type ABI1, ABI2, ABI3, and ABI4 are set forth in SEQ ID NOS:3-10. Other ABA-associated mutants include bri1 from Arabidopsis thaliana the sequence of which can be found in Genbank Accession No. AF017056 and Li et al. (1997) Cell 90:929-938, both of which are herein incorporated by reference.
An abi mutant of interest includes, for example, abi1. abi1 is a dominant mutation in the structural part of the ABI1 gene. The mutation has been characterized and comprises a nucleotide base transition from guanine to adenine and changes the DNA sequence GGC to GAC, thus causing the wild type glycine residue at amino acid position 180 of SEQ ID NO:3 to be replaced with aspartic acid (Meyer et al. (1994) Science 264:1452-1455). abi2 is another dominant mutation of interest in the methods of the invention. abi2 is characterized by a GGC to GAC transition leading to the replacement the Gly residue at amino acid position 168 of SEQ ID NO:6 to Asp (Rodriquez et al. (1998) FEBS Letters 421:18-190). It is well within skill in the art to identify other mutations (both dominant and recessive) in other ABA-associated sequences that will be useful in the methods of the present invention.
Such mutants listed above are designated “ABA-associated mutants.” By “ABA-associated mutants” is intended genes and sequences which disrupt ABA signaling and/or perception in a plant. Utilizing the sequences above, related sequences from other plants, including cereals, can be isolated. In some instances, it may be beneficial to use the ABA-associated sequence that corresponds with a sequence from the target plant of interest. For example, for use in maize, the maize homolog of the ABA-associated sequence, or a sequence corresponding to the maize homolog, may be preferred.
The invention utilizes the ABA-associated sequences to control the plant response to ABA. Generally, it will be beneficial to block ABA signaling or perception to prevent a loss of yield. Utilizing the ABA-associated sequences, coding sequences, and antisense sequences, the expression and perception of ABA in a plant can be controlled. As described in more detail below, such sequences can be introduced into plants of interest by recombinant methods as well as by traditional breeding methods.
The nucleotide sequences of the invention can be used to isolate corresponding sequences from other organisms, particularly other plants more particularly cereals. In this manner, methods such as PCR, hybridization, and the like can be used to identify such sequences based on their sequence homology to the ABA-associated sequences known in the art. Sequences may be isolated based on their sequence identity to the entire ABA-associated sequence or to fragments thereof.
In a PCR approach, oligonucleotide primers can be designed for use in PCR reactions to amplify corresponding DNA sequences from cDNA or genomic DNA extracted from any plant of interest. Methods for designing PCR primers and PCR cloning are generally known in the art and are disclosed in Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.). See also Innis et al., eds. (1990) PCR Protocols: A Guide to Methods and Applications (Academic Press, New York); Innis and Gelfand, eds. (1995) PCR Strategies (Academic Press, New York); and Innis and Gelfand, eds. (1999) PCR Methods Manual (Academic Press, New York). Known methods of PCR include, but are not limited to, methods using paired primers, nested primers, single specific primers, degenerate primers, gene-specific primers, vector-specific primers, partially-mismatched primers, and the like.
In hybridization techniques, all or part of a known nucleotide sequence is used as a probe that selectively hybridizes to other corresponding nucleotide sequences present in a population of cloned genomic DNA fragments or cDNA fragments (i.e., genomic or cDNA libraries) from a chosen plant. The hybridization probes may be genomic DNA fragments, cDNA fragments, RNA fragments, or other oligonucleotides, and may be labeled with a detectable group such as 32P, or any other detectable marker. Thus, for example, probes for hybridization can be made by labeling synthetic oligonucleotides based on the ABA-associated sequences of the invention. Methods for preparation of probes for hybridization and for construction of cDNA and genomic libraries are generally known in the art and are disclosed in Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.).
For example, an entire ABA-associated sequence, or one or more portions thereof, may be used as a probe capable of specifically hybridizing to corresponding sequences and messenger RNAs. To achieve specific hybridization under a variety of conditions, such probes include sequences that are unique among the sequences of interest and are preferably at least about 10 nucleotides in length, and most preferably at least about 20 nucleotides in length. Such probes may be used to amplify corresponding sequences from a chosen plant by PCR. This technique may be used to isolate additional coding sequences from a desired plant or as a diagnostic assay to determine the presence of coding sequences in a plant. Hybridization techniques include hybridization screening of plated DNA libraries (either plaques or colonies; see, for example, Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.).
Hybridization of such sequences may be carried out under stringent conditions. By “stringent conditions” or “stringent hybridization conditions” is intended conditions under which a probe will hybridize to its target sequence to a detectably greater degree than to other sequences (e.g., at least 2-fold over background). Stringent conditions are sequence-dependent and will be different in different circumstances. By controlling the stringency of the hybridization and/or washing conditions, target sequences that are 100% complementary to the probe can be identified (homologous probing). Alternatively, stringency conditions can be adjusted to allow some mismatching in sequences so that lower degrees of similarity are detected (heterologous probing). Generally, a probe is less than about 1000 nucleotides in length, preferably less than 500 nucleotides in length.
Typically, stringent conditions will be those in which the salt concentration is less than about 1.5 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C. for long probes (e.g., greater than 50 nucleotides). Duration of hybridization is generally less than about 24 hours, usually about 4 to 12. Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. Exemplary low stringency conditions include hybridization with a buffer solution of 30 to 35% formamide, 1 M NaCl, 1% SDS (sodium dodecyl sulphate) at 37° C., and a wash in 1× to 2×SSC (20×SSC=3.0 M NaCl/0.3 M trisodium citrate) at 50 to 55° C. Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37° C., and a wash in 0.5× to 1×SSC at 55 to 60° C. Exemplary high stringency conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 0.1×SSC at 60 to 65° C.
Specificity is typically the function of post-hybridization washes, the critical factors being the ionic strength and temperature of the final wash solution. For DNA-DNA hybrids, the Tm can be approximated from the equation of Meinkoth and Wahl (1984) Anal. Biochem. 138:267-284: Tm=81.5° C.+16.6 (log M)+0.41 (% GC)−0.61 (% form)−500/L; where M is the molarity of monovalent cations, % GC is the percentage of guanosine and cytosine nucleotides in the DNA, % form is the percentage of formamide in the hybridization solution, and L is the length of the hybrid in base pairs. The Tm is the temperature (under defined ionic strength and pH) at which 50% of a complementary target sequence hybridizes to a perfectly matched probe. Tm is reduced by about 1° C. for each 1% of mismatching; thus, Tm, hybridization, and/or wash conditions can be adjusted to hybridize to sequences of the desired identity. For example, if sequences with ≧90% identity are sought, the Tm can be decreased 10° C. Generally, stringent conditions are selected to be about 5° C. lower than the thermal melting point (Tm) for the specific sequence and its complement at a defined ionic strength and pH. However, severely stringent conditions can utilize a hybridization and/or wash at 1, 2, 3, or 4° C. lower than the thermal melting point (Tm); moderately stringent conditions can utilize a hybridization and/or wash at 6, 7, 8, 9, or 10° C. lower than the thermal melting point (Tm); low stringency conditions can utilize a hybridization and/or wash at 11, 12, 13, 14, 15, or 20° C. lower than the thermal melting point (Tm). Using the equation, hybridization and wash compositions, and desired Tm, those of ordinary skill will understand that variations in the stringency of hybridization and/or wash solutions are inherently described. If the desired degree of mismatching results in a Tm of less than 45° C. (aqueous solution) or 32° C. (formamide solution), it is preferred to increase the SSC concentration so that a higher temperature can be used. An extensive guide to the hybridization of nucleic acids is found in Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Acid Probes, Part I, Chapter 2 (Elsevier, N.Y.); and Ausubel et al., eds. (1995) Current Protocols in Molecular Biology, Chapter 2 (Greene Publishing and Wiley-Interscience, New York). See Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.).
Thus, isolated “corresponding ABA-associated sequences” that modulate the plant response to ABA and which hybridize under stringent conditions to the ABA-associated sequences disclosed herein, or to fragments thereof, are encompassed by the present invention. Such sequences will be at least about 40% to 50% homologous, about 60%, 65%, or 70% homologous, and even at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more homologous with the disclosed sequences. That is, the sequence identity of sequences may range, sharing at least about 40% to 50%, about 60%, 65%, or 70%, and even at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity.
The ABA-associated sequences of the invention can be utilized with tissue or developmental-specific promoters to disrupt ABA function in a tissue or a developmentally specific manner. Promoters of particular interest include seed-preferred promoters, particularly early kernel/embryo promoters and late kernel/embryo promoters.
Kernel development post-pollination is divided into approximately three primary phases. The lag phase of kernel growth occurs from about 0 to 10-12 days after pollination. During this phase the kernel is not growing significantly in mass, but rather important events are being carried out that will determine kernel vitality (i.e., number of cells). The linear grain fill stage occurs from about 10-12 to about 40 DAP. During this stage of kernel development, the kernel attains almost all of its final mass and various storage products (i.e., starch, protein, oil) are produced. Finally, the maturation phase occurs from about 40 DAP to harvest. During this phase of kernel development the kernel becomes quiescent and begins to dry down in preparation for a long period of dormancy prior to germination. As defined herein “Early kernel/embryo promoters” are promoters that are on during the first phase of development (i.e., from about 0 to about 12 DAP). “Late kernel/embryo promoters”, as defined herein, are on from about 12 DAP through maturation. The choice of the promoter will depend on the ABA associated sequence utilized.
Early kernel/embryo promoters include, for example, cim1, a pollen and whole kernel specific promoter that is active 5 DAP. See, for example, WO 00/11177, which is herein incorporated by reference. Other early kernel/embryo promoters include the seed-preferred promoters end1, which is active 7-10 DAP, and end2, which is active 9-14 DAP in the whole kernel and active 10 DAP in the endosperm and pericarp. See, for example, WO 00/12733, herein incorporated by reference. Additional early kernel/embryo promoters that find use in the methods of the present invention include the seed-preferred promoter lpt2 (SEQ ID NO:13) which is active 6 to 24 DAP (U.S. Pat. No. 5,525,716, herein incorporated by reference).
Such early kernel/embryo promoters can be used with genes or mutants in the perception/signal transduction pathway for ABA. In this manner, mutant genes such as abi1 or abi2 operably linked to an early kernel/embryo promoter would dominantly disrupt ABA action in tissues prior to the later required ABA function in seed maturation. Alternatively, an early kernel/embryo promoter can be operably linked to a wild type (co suppression) or antisence nucleotide sequence of an ABA associated sequence. The early kernel/embryo promoter would be utilized to disrupt ABA action in tissues prior to seed maturation.
Late kernel/embryo promoters include, for example, promoters from oleosin genes. See, for example, Plant et al. (1994) Plant Mol. Biol. 25:193-205; Keddie et al. (1994) Plant Mol. Biol. 24:327-40; Keddie et al. (1992) Plant Mol. Biol. 19:443-53; and Hong et al. (1997) 34:549-55; herein incorporated by reference. See also, Genbank Accession Nos. U71381 (SEQ ID NO:11), AF134411 (SEQ ID NO:12), and U.S. Pat. No. 5,977,436, which contain oleosin promoter sequences from Glycine max, Brassica juncea, and Arabidopsis thaliana, respectively. All of these references are herein incorporated by reference. Additional late kernel/embryo promoters include, smilps, an embryo specific promoter that is active 13-14 DAP and cz19B1a whole kernel specific promoter that is active 13-40 DAP. See, for example, WO 00/11177, which is herein incorporated by reference. The seed-preferred promoter a13 is active 24-40 days after flowering and may also be used in the methods of the invention. See, for example, WO 00/40710, which is herein incorporated by reference.
Late kernel/promoters, such as those from oleosin genes, can be used to drive expression of a wild-type Vp1 allele. Such plants can then be crossed to a plant having a vp1 mutant. In this example, the inability of the vp1 mutant allele to be complemented by ABA would insulate early kernels from deleterious effects. The Vp1 gene product is on very early in kernel development. In the presence of ABA, the VP1 becomes effective. The engineered gene supplied by the transgenic parent would supply the kernels with the ability to mature normally. As used herein, an “endogenous ABA associated sequence” is defined as any ABA associated sequence not introduced into the plant via a transformation event.
Such ABA-associated genes can be utilized to control the effects of stress on the plant. Since the accumulation of nutritive reserves in the acquisition of desiccation tolerance are associated with the expression of specific sets of mRNAs. Transcripts encoding either storage proteins or late-embryogenesis-abundant (LEA) proteins thought to participate in desiccation tolerance can be precociously induced by exogenous ABA in cultured embryos. Thus, late expression of ABA genes can be coupled with transgenic seed storage proteins to increase nutritive reserves in seeds.
By “introducing” sequences that modulate ABA perception and signal transduction into a target plant encompasses any means for incorporating the sequence of interest into the target plant. Such means includes conventional breeding methods, genetic transformation methods, or other such means as may be available. The methods of the invention do not depend on a particular method for introducing a nucleotide construct to a plant, only that the nucleotide construct gains access to the interior of at least one cell of the plant. By “stable transformation” is intended that the nucleotide construct introduced into a plant integrates into the genome of the plant and is capable of being inherited by progeny thereof.
Wild-type alleles of genes such as Vp1 may be down-regulated with early promoters via either cosuppression or antisense strategies. It is recognized that with these nucleotide sequences, antisense constructions complementary to at least a portion of the messenger RNA (mRNA) for the ABA-associated sequences can be constructed. Antisense nucleotides are constructed to hybridize with the corresponding mRNA. Modifications of the antisense sequences may be made as long as the sequences hybridize to and interfere with expression of the corresponding mRNA. In this manner, antisense constructions having 70%, preferably 80%, more preferably 85% sequence similarity to the corresponding antisensed sequences may be used. Furthermore, portions of the antisense nucleotides may be used to disrupt the expression of the target gene. Generally, sequences of at least 50 nucleotides, 100 nucleotides, 200 nucleotides, or greater may be used.
Methods for suppressing gene expression in plants using nucleotide sequences in the sense orientation are known in the art. The methods generally involve transforming plants with a DNA construct comprising a promoter that drives expression in a plant operably linked to at least a portion of a nucleotide sequence that corresponds to the transcript of the endogenous gene (i.e, an ABA-associated sequence). Typically, such a nucleotide sequence has substantial sequence identity to the sequence of the transcript of the endogenous gene, preferably greater than about 65% sequence identity, more preferably greater than about 85% sequence identity, most preferably greater than about 95% sequence identity. See, U.S. Pat. Nos. 5,283,184 and 5,034,323; herein incorporated by reference.
It is recognized that fragments and/or variants of the ABA-associated genes can be utilized in the invention. Fragments and variants of the ABA-associated nucleotide sequences and proteins encoded thereby are thus encompassed by the present invention. By “fragment” is intended a portion of the nucleotide sequence or a portion of the amino acid sequence and hence protein encoded thereby. Fragments of a nucleotide sequence may encode protein fragments that retain the biological activity of the native protein and hence act to modulate responses to ABA. Alternatively, fragments of a nucleotide sequence that are useful as hybridization probes generally do not encode fragment proteins retaining biological activity. Thus, fragments of a nucleotide sequence may range from at least about 20 nucleotides, about 50 nucleotides, about 100 nucleotides, and up to the full-length nucleotide sequence of the invention.
By “variants” is intended substantially similar sequences. For nucleotide sequences naturally occurring variants such as these can be identified with the use of well-known molecular biology techniques, as, for example, with polymerase chain reaction (PCR) and hybridization techniques as outlined below. Variant nucleotide sequences also include synthetically derived nucleotide sequences, such as those generated, for example, by using site-directed mutagenesis. Generally, variants of a particular nucleotide sequence of the invention will have at least about 40%, 50%, 60%, 65%, 70%, generally at least about 75%, 80%, 85%, preferably at least about 90%, 92%, 94%, 95%, 96%, 97%, and more preferably at least about 98%, 99% or more sequence identity to that particular nucleotide sequence as determined by sequence alignment programs described elsewhere herein using default parameters.
Methods of alignment of sequences for comparison are well known in the art. Thus, the determination of percent identity between any two sequences can be accomplished using a mathematical algorithm. Non-limiting examples of such mathematical algorithms are the algorithm of Myers and Miller (1988) CABIOS 4:11-17; the local homology algorithm of Smith et al. (1981) Adv. Appl. Math. 2:482; the homology alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443-453; the search-for-similarity-method of Pearson and Lipman (1988) Proc. Natl. Acad. Sci. 85:2444-2448; the algorithm of Karlin and Altschul (1990) Proc. Natl. Acad. Sci. USA 872264, modified as in Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-5877.
Computer implementations of these mathematical algorithms can be utilized for comparison of sequences to determine sequence identity. Such implementations include, but are not limited to: CLUSTAL in the PC/Gene program (available from Intelligenetics, Mountain View, Calif.); the ALIGN program (Version 2.0) and GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Version 8 (available from Genetics Computer Group (GCG), 575 Science Drive, Madison, Wis., USA). Alignments using these programs can be performed using the default parameters. The CLUSTAL program is well described by Higgins et al. (1988) Gene 73:237-244 (1988); Higgins et al. (1989) CABIOS 5:151-153; Corpet et al. (1988) Nucleic Acids Res. 16:10881-90; Huang et al. (1992) CABIOS 8:155-65; and Pearson et al. (1994) Meth. Mol. Biol. 24:307-331. The ALIGN program is based on the algorithm of Myers and Miller (1988) supra. A PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used with the ALIGN program when comparing amino acid sequences. The BLAST programs of Altschul et al (1990) J Mol. Biol. 215:403 are based on the algorithm of Karlin and Altschul (1990) supra. BLAST nucleotide searches can be performed with the BLASTN program, score=100, wordlength=12, to obtain nucleotide sequences homologous to a nucleotide sequence encoding a protein of the invention. BLAST protein searches can be performed with the BLASTX program, score=50, wordlength=3, to obtain amino acid sequences homologous to a protein or polypeptide of the invention. To obtain gapped alignments for comparison purposes, Gapped BLAST (in BLAST 2.0) can be utilized as described in Altschul et al. (1997) Nucleic Acids Res. 25:3389. Alternatively, PSI-BLAST (in BLAST 2.0) can be used to perform an iterated search that detects distant relationships between molecules. See Altschul et al. (1997) supra. When utilizing BLAST, Gapped BLAST, PSI-BLAST, the default parameters of the respective programs (e.g., BLASTN for nucleotide sequences, BLASTX for proteins) can be used. See the website at ncbi.nlm.nih.gov. Alignment may also be performed manually by inspection.
Unless otherwise stated, sequence identity/similarity values provided herein refer to the value obtained using GAP Version 10 using the following parameters: % identity using GAP Weight of 50 and Length Weight of 3; % similarity using Gap Weight of 12 and Length Weight of 4, or any equivalent program. 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 the preferred program.
GAP uses the algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48: 443-453, to find the alignment of two complete sequences that maximizes the number of matches and minimizes the number of gaps. GAP considers all possible alignments and gap positions and creates the alignment with the largest number of matched bases and the fewest gaps. It allows for the provision of a gap creation penalty and a gap extension penalty in units of matched bases. GAP must make a profit of gap creation penalty number of matches for each gap it inserts. If a gap extension penalty greater than zero is chosen, GAP must, in addition, make a profit for each gap inserted of the length of the gap times the gap extension penalty. Default gap creation penalty values and gap extension penalty values in Version 10 of the Wisconsin Genetics Software Package for protein sequences are 8 and 2, respectively. For nucleotide sequences the default gap creation penalty is 50 while the default gap extension penalty is 3. The gap creation and gap extension penalties can be expressed as an integer selected from the group of integers consisting of from 0 to 200. Thus, for example, the gap creation and gap extension penalties can be 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65 or greater.
GAP presents one member of the family of best alignments. There may be many members of this family, but no other member has a better quality. GAP displays four figures of merit for alignments: Quality, Ratio, Identity, and Similarity. The Quality is the metric maximized in order to align the sequences. Ratio is the quality divided by the number of bases in the shorter segment. Percent Identity is the percent of the symbols that actually match. Percent Similarity is the percent of the symbols that are similar. Symbols that are across from gaps are ignored. A similarity is scored when the scoring matrix value for a pair of symbols is greater than or equal to 0.50, the similarity threshold. The scoring matrix used in Version 10 of the Wisconsin Genetics Software Package is BLOSUM62 (see Henikoff and Henikoff (1989) Proc. Natl. Acad. Sci. USA 89:10915).
By “variant” protein is intended a protein derived from the native protein by deletion (so-called truncation) or addition of one or more amino acids to the N-terminal and/or C-terminal end of the native protein; deletion or addition of one or more amino acids at one or more sites in the native protein; or substitution of one or more amino acids at one or more sites in the native protein. Such variants may result from, for example, genetic polymorphism or from human manipulation.
The proteins of the invention may be altered in various ways including amino acid substitutions, deletions, truncations, and insertions. Methods for such manipulations are generally known in the art. Methods for mutagenesis and nucleotide sequence alterations are well known in the art. See, for example, Kunkel (1985) Proc. Natl. Acad. Sci. USA 82:488-492; Kunkel et al. (1987) Methods in Enzymol. 154:367-382; U.S. Pat. No. 4,873,192; Walker and Gaastra, eds. (1983) Techniques in Molecular Biology (MacMillan Publishing Company, New York) and the references cited therein. Guidance as to appropriate amino acid substitutions that do not affect biological activity of the protein of interest may be found in the model of Dayhoff et al. (1978) Atlas of Protein Sequence and Structure (Natl. Biomed. Res. Found., Washington, D.C.), herein incorporated by reference. Conservative substitutions, such as exchanging one amino acid with another having similar properties, may be preferred.
Thus, the genes and nucleotide sequences of the invention include both the naturally occurring sequences as well as mutant forms. Likewise, the proteins of the invention encompass both naturally occurring proteins as well as variations and modified forms thereof. Such variants will continue to possess the desired activity. Obviously, the mutations that will be made in the DNA encoding the variant must not place the sequence out of reading frame and preferably will not create complementary regions that could produce secondary mRNA structure. See, EP Patent Application Publication No. 75,444.
The deletions, insertions, and substitutions of the protein sequences encompassed herein are not expected to produce radical changes in the characteristics of the protein. However, when it is difficult to predict the exact effect of the substitution, deletion, or insertion in advance of doing so, one skilled in the art will appreciate that the effect will be evaluated by routine screening assays.
Variant nucleotide sequences and proteins also encompass sequences and proteins derived from a mutagenic and recombinogenic procedure such as DNA shuffling. With such a procedure, one or more different ABA-associated coding sequences can be manipulated to create a new ABA-associated protein possessing the desired properties. In this manner, libraries of recombinant polynucleotides are generated from a population of related sequence polynucleotides comprising sequence regions that have substantial sequence identity and can be homologously recombined in vitro or in vivo. Strategies for such DNA shuffling are known in the art. See, for example, Stemmer (1994) Proc. Natl. Acad. Sci. USA 91:10747-10751; Stemmer (1994) Nature 370:389-391; Crameri et al. (1997) Nature Biotech. 15:436-438; Moore et al. (1997) J. Mol. Biol. 272:336-347; Zhang et al. (1997) Proc. Natl. Acad. Sci. USA 94:4504-4509; Crameri et al. (1998) Nature 391:288-291; and U.S. Pat. Nos. 5,605,793 and 5,837,458.
The ABA-associated sequences of the invention are provided in expression cassettes for expression in the plant of interest. The cassette will include 5′ and 3′ regulatory sequences operably linked to an ABA-associated sequence of the invention. By “operably linked” is intended a functional linkage between a promoter and a second sequence, wherein the promoter sequence initiates and mediates transcription of the DNA sequence corresponding to the second sequence. Generally, operably linked means that the nucleic acid sequences being linked are contiguous and, where necessary to join two protein coding regions, contiguous and in the same reading frame. The cassette may additionally contain at least one additional gene to be cotransformed into the organism. Alternatively, the additional gene(s) can be provided on multiple expression cassettes.
Such an expression cassette is provided with a plurality of restriction sites for insertion of the sequence of interest to be under the transcriptional regulation of the regulatory regions. The expression cassette may additionally contain selectable marker genes.
The expression cassette will include in the 5′-3′ direction of transcription, a transcriptional and translational initiation region, a DNA sequence of the invention, and a transcriptional and translational termination region functional in plants. The transcriptional initiation region, the promoter, may be native or analogous or foreign or heterologous to the plant host. Additionally, the promoter may be the natural sequence or alternatively a synthetic sequence. By “foreign” is intended that the transcriptional initiation region is not found in the native plant into which the transcriptional initiation region is introduced. As used herein, a chimeric gene comprises a coding sequence operably linked to a transcription initiation region that is heterologous to the coding sequence. While it may be preferable to express the sequences using heterologous promoters, the native promoter sequences may be used. Thus, the phenotype of the plant or plant cell is altered.
The termination region may be native with the transcriptional initiation region, may be native with the operably linked DNA sequence of interest, or may be derived from another source. 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) Cell 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 Acid Res. 15:9627-9639.
Where appropriate, the gene(s) may be optimized for increased expression in the transformed plant. That is, the genes can be synthesized using plant-preferred codons for improved expression. Methods are available in the art for synthesizing plant-preferred genes. See, for example, U.S. Pat. Nos. 5,380,831, and 5,436,391, and Murray et al. (1989) Nucleic Acids Res. 17:477-498, herein incorporated by reference.
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.
The expression cassettes may additionally contain 5′ leader sequences in the expression cassette construct. Such leader sequences can act to enhance translation. Translation leaders are known in the art and include: picomavirus leaders, for example, EMCV leader (Encephalomyocarditis 5′ noncoding region) (Elroy-Stein et al. (1989) PNAS USA 86:6126-6130); potyvirus leaders, for example, TEV leader (Tobacco Etch Virus) (Allison et al. (1986); MDMV leader (Maize Dwarf Mosaic Virus); Virology 154:9-20), and human immunoglobulin heavy-chain binding protein (BiP), (Macejak et al. (1991) Nature 353:90-94); untranslated leader from the coat protein mRNA of alfalfa mosaic virus (AMV RNA 4) (Jobling et al. (1987) Nature 325:622-625); tobacco mosaic virus leader (TMV) (Gallie et al. (1989) in Molecular Biology of RNA, ed. Cech (Liss, New York), pp. 237-256); and maize chlorotic mottle virus leader (MCMV) (Lommel et al. (1991) Virology 81:382-385). See also, Della-Cioppa et al. (1987) Plant Physiol. 84:965-968. Other methods known to enhance translation can also be utilized, for example, introns, and the like.
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.
Transformation protocols as well as protocols for introducing nucleotide 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 nucleotide sequences into plant cells and subsequent insertion into the plant genome include microinjection (Crossway et al. (1986) Biotechniques 4:320-334), electroporation (Riggs et al. (1986) Proc. Natl. Acad. Sci. USA 83:5602-5606, Agrobacterium-mediated transformation (Townsend et al., U.S. Pat. No. 5,563,055; U.S. Pat. No. 5,981,840), direct gene transfer (Paszkowski et al. (1984) EMBO J. 3:2717-2722), and ballistic particle acceleration (see, for example, Sanford et al., U.S. Pat. No. 4,945,050; Tomes et al. (1995) “Direct DNA Transfer into Intact Plant Cells via Microprojectile Bombardment,” in Plant Cell, Tissue, and Organ Culture: Fundamental Methods, ed. Gamborg and Phillips (Springer-Verlag, Berlin); and McCabe et al. (1988) Biotechnology 6:923-926). 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); Tomes, U.S. Pat. No. 5,240,855; Buising et al., U.S. Pat. Nos. 5,322,783 and 5,324,646; Tomes et al. (1995) “Direct DNA Transfer into Intact Plant Cells via Microprojectile Bombardment,” in Plant Cell, Tissue, and Organ Culture: Fundamental Methods, ed. Gamborg (Springer-Verlag, Berlin) (maize); 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; Bowen et al., U.S. Pat. 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, N.Y.), 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.
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 hybrid having constitutive expression of the desired phenotypic characteristic identified. Two or more generations may be grown to ensure that constitutive expression of the desired phenotypic characteristic is stably maintained and inherited and then seeds harvested to ensure constitutive expression of the desired phenotypic characteristic has been achieved.
The present invention may be used for transformation of any plant species, including, but not limited to, monocots and dicots. Examples of plants 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 batatus), cassava (Manihot esculenta), coffee (Coffea spp.), coconut (Cocos nucifera), pineapple (Ananas comosus), citrus 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 (Euphorbiapulcherrima), 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). Preferably, plants of the present invention are crop plants (for example, corn, alfalfa, sunflower, Brassica, soybean, cotton, safflower, peanut, sorghum, wheat, millet, tobacco, etc.), more preferably corn and soybean plants, yet more preferably corn plants.
Plants of particular 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 following examples are offered by way of illustration and not by way of limitation.
EXPERIMENTAL
Transformation and Regeneration of Transgenic Plants
Example 1
Transformation and Regeneration of Transgenic Maize Plants
Immature maize embryos from greenhouse donor plants are bombarded with a plasmid containing the ABI3 sequence operably linked to an early kernel/embryo promoter plus a plasmid containing the selectable marker gene PAT (Wohlleben et al. (1988) Gene 70:25-37) that confers resistance to the herbicide Bialaphos. Transformation is performed as follows. All media recipes are below.
Preparation of Target Tissue
The ears are surface sterilized in 30% Chlorox 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 2.5-cm target zone in preparation for bombardment.
Preparation of DNA
A plasmid vector comprising the ABI3 sequence operably linked to an early kernel/embryo promoter is made. This plasmid DNA plus plasmid DNA containing a PAT selectable marker is precipitated onto 1.1 μm (average diameter) tungsten pellets using a CaCl2 precipitation procedure as follows:
100 μl prepared tungsten particles in water
10 μl (1 μg) DNA in TrisEDTA buffer (1 μg total)
100 μl 2.5 M CaCl2 
10 μl 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 μl 100% ethanol is added to the final tungsten particle pellet. For particle gun bombardment, the tungsten/DNA particles are briefly sonicated and 10 μl spotted onto the center of each macrocarrier and allowed to dry about 2 minutes before bombardment.
Particle Gun Treatment
The sample plates are bombarded at level #4 in particle gun #HE34-1 or #HE34-2. All samples receive a single shot at 650 PSI, with a total of ten aliquots taken from each tube of prepared particles/DNA.
Subsequent Treatment
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.
Bombardment and Culture Media
Bombardment medium (560Y) comprises 4.0 g/l N6 basal salts (SIGMA C-1416), 1.0 ml/l Eriksson's Vitamin Mix (1000× SIGMA-1511), 0.5 mg/l thiamine HCl, 120.0 g/l sucrose, 1.0 mg/l 2,4-D, and 2.88 g/l L-proline (brought to volume with D-I H2O following adjustment to pH 5.8 with KOH); 2.0 g/l Gelrite (added after bringing to volume with D-I H2O); and 8.5 mg/l silver nitrate (added after sterilizing the medium and cooling to room temperature). Selection medium (560R) comprises 4.0 g/l N6 basal salts (SIGMA C-1416), 1.0 ml/l Eriksson's Vitamin Mix (1000× SIGMA-1511), 0.5 mg/l thiamine HCl, 30.0 g/l sucrose, and 2.0 mg/l 2,4-D (brought to volume with D-I H2O following adjustment to pH 5.8 with KOH); 3.0 g/l Gelrite (added after bringing to volume with D-I H2O); and 0.85 mg/l silver nitrate and 3.0 mg/l bialaphos(both added after sterilizing the medium and cooling to room temperature).
Plant regeneration medium (288J) comprises 4.3 g/l MS salts (GIBCO 11117-074), 5.0 ml/l MS vitamins stock solution (0.100 g nicotinic acid, 0.02 g/l thiamine HCL, 0.10 g/l pyridoxine HCL, and 0.40 g/l glycine brought to volume with polished D-I H2O) (Murashige and Skoog (1962) Physiol. Plant. 15:473), 100 mg/l myo-inositol, 0.5 mg/l zeatin, 60 g/l sucrose, and 1.0 ml/l of 0.1 mM abscisic acid (brought to volume with polished D-I H2O after adjusting to pH 5.6); 3.0 g/l Gelrite (added after bringing to volume with D-I H2O); and 1.0 mg/l indoleacetic acid and 3.0 mg/l bialaphos (added after sterilizing the medium and cooling to 60° C.). Hormone-free medium (272V) comprises 4.3 g/l MS salts (GIBCO 11117-074), 5.0 ml/l MS vitamins stock solution (0.100 g/l nicotinic acid, 0.02 g/l thiamine HCL, 0.10 g/l pyridoxine HCL, and 0.40 g/l glycine brought to volume with polished D-I H2O), 0.1 g/l myo-inositol, and 40.0 g/l sucrose (brought to volume with polished D-I H2O after adjusting pH to 5.6); and 6 g/l bacto-agar (added after bringing to volume with polished D-I H2O), sterilized and cooled to 60° C.
Example 2
Agrobacterium-Mediated Transformation
For Agrobacterium-mediated transformation of maize with an ABI3 sequence operably linked to an early kernel/embryo promoter, preferably the method of Zhao is employed (U.S. Pat. No. 5,981,840, and PCT patent publication WO98/32326; the contents of which are hereby incorporated by reference). Briefly, immature embryos are isolated from maize and the embryos contacted with a suspension of Agrobacterium, where the bacteria are capable of transferring the ABI3 sequence operably linked to an early kernel/embryo promoter 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 preferably 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). Preferably 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 of Agrobacterium without the addition of a selective agent for plant transformants (step 3: resting step). Preferably 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). Preferably, 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 preferably calli grown on selective medium are cultured on solid medium to regenerate the plants.
Example 3
Soybean Embryo Transformation
Soybean embryos are bombarded with a plasmid containing the ABI3 nucleotide sequence operably linked to an early embryo/kernel promoter as follows. To induce somatic embryos, cotyledons, 3-5 mm in length dissected from surface-sterilized, immature seeds of the soybean cultivar A2872, are cultured in the light or dark at 26° C. on an appropriate agar medium for six to ten weeks. Somatic embryos producing secondary embryos are then excised and placed into a suitable liquid medium. After repeated selection for clusters of somatic embryos that multiplied as early, globular-staged embryos, the suspensions are maintained as described below.
Soybean embryogenic suspension cultures can maintained in 35 ml liquid media on a rotary shaker, 150 rpm, at 26° C. with florescent lights on a 16:8 hour day/night schedule. Cultures are subcultured every two weeks by inoculating approximately 35 mg of tissue into 35 ml of liquid medium.
Soybean embryogenic suspension cultures may then be transformed by the method of particle gun bombardment (Klein et al. (1987) Nature (London) 327:70-73, U.S. Pat. No. 4,945,050). A Du Pont Biolistic PDS1000/HE instrument (helium retrofit) can be used for these transformations.
A selectable marker gene that can be used to facilitate soybean transformation is a transgene composed of the 35S promoter from Cauliflower Mosaic Virus (Odell et al. (1985) Nature 313:810-812), the hygromycin phosphotransferase gene from plasmid pJR225 (from E. coli; Gritz et al. (1983) Gene 25:179-188), and the 3′ region of the nopaline synthase gene from the T-DNA of the Ti plasmid of Agrobacterium tumefaciens. The expression cassette comprising the ABI3 nucleotide sequence operably linked to an early kernel/embryo promoter can be isolated as a restriction fragment. This fragment can then be inserted into a unique restriction site of the vector carrying the marker gene.
To 50 μl of a 60 mg/ml 1 μm gold particle suspension is added (in order): 5 μl DNA (1 μg/μl), 20 μl spermidine (0.1 M), and 50 μl CaCl2 (2.5 M). The particle preparation is then agitated for three minutes, spun in a microfuge for 10 seconds and the supernatant removed. The DNA-coated particles are then washed once in 400 μl 70% ethanol and resuspended in 40 μl of anhydrous ethanol. The DNA/particle suspension can be sonicated three times for one second each. Five microliters of the DNA-coated gold particles are then loaded on each macro carrier disk.
Approximately 300-400 mg of a two-week-old suspension culture is placed in an empty 60×15 mm petri dish and the residual liquid removed from the tissue with a pipette. For each transformation experiment, approximately 5-10 plates of tissue are normally bombarded. Membrane rupture pressure is set at 1100 psi, and the chamber is evacuated to a vacuum of 28 inches mercury. The tissue is placed approximately 3.5 inches away from the retaining screen and bombarded three times. Following bombardment, the tissue can be divided in half and placed back into liquid and cultured as described above.
Five to seven days post bombardment, the liquid media may be exchanged with fresh media, and eleven to twelve days post-bombardment with fresh media containing 50 mg/ml hygromycin. This selective media can be refreshed weekly. Seven to eight weeks post-bombardment, green, transformed tissue may be observed growing from untransformed, necrotic embryogenic clusters. Isolated green tissue is removed and inoculated into individual flasks to generate new, clonally propagated, transformed embryogenic suspension cultures. Each new line may be treated as an independent transformation event. These suspensions can then be subcultured and maintained as clusters of immature embryos or regenerated into whole plants by maturation and germination of individual somatic embryos.
Example 4
Sunflower Meristem Tissue Transformation
Sunflower meristem tissues are transformed with an expression cassette containing the ABI3 sequence operably linked to an early kernel embryo promoter as follows (see also European Patent Number EP 0 486233, herein incorporated by reference, and Malone-Schoneberg et al. (1994) Plant Science 103:199-207). Mature sunflower seed (Helianthus annuus L.) are dehulled using a single wheat-head thresher. Seeds are surface sterilized for 30 minutes in a 20% Clorox bleach solution with the addition of two drops of Tween 20 per 50 ml of solution. The seeds are rinsed twice with sterile distilled water.
Split embryonic axis explants are prepared by a modification of procedures described by Schrammeijer et al. (Schrammeijer et al. (1990) Plant Cell Rep. 9: 55-60). Seeds are imbibed in distilled water for 60 minutes following the surface sterilization procedure. The cotyledons of each seed are then broken off, producing a clean fracture at the plane of the embryonic axis. Following excision of the root tip, the explants are bisected longitudinally between the primordial leaves. The two halves are placed, cut surface up, on GBA medium consisting of Murashige and Skoog mineral elements (Murashige et al. (1962) Physiol. Plant., 15: 473-497), Shepard's vitamin additions (Shepard (1980) in Emergent Techniques for the Genetic Improvement of Crops (University of Minnesota Press, St. Paul, Minn.), 40 mg/l adenine sulfate, 30 g/l sucrose, 0.5 mg/l 6-benzyl-aminopurine (BAP), 0.25 mg/l indole-3-acetic acid (IAA), 0.1 mg/l gibberellic acid (GA3), pH 5.6, and 8 g/l Phytagar.
The explants are subjected to microprojectile bombardment prior to Agrobacterium treatment (Bidney et al. (1992) Plant Mol. Biol. 18: 301-313). Thirty to forty explants are placed in a circle at the center of a 60×20 mm plate for this treatment. Approximately 4.7 mg of 1.8 mm tungsten microprojectiles are resuspended in 25 ml of sterile TE buffer (10 mM Tris HCl, 1 mM EDTA, pH 8.0) and 1.5 ml aliquots are used per bombardment. Each plate is bombarded twice through a 150 mm nytex screen placed 2 cm above the samples in a PDS 1000® particle acceleration device.
Disarmed Agrobacterium tumefaciens strain EHA105 is used in all transformation experiments. A binary plasmid vector comprising the expression cassette that contains the AB13 gene operably linked to an early kernel/embryo promoter is introduced into Agrobacterium strain EHA105 via freeze-thawing as described by Holsters et al. (1978) Mol. Gen. Genet. 163:181-187. This plasmid further comprises a kanamycin selectable marker gene (i.e, nptII). Bacteria for plant transformation experiments are grown overnight (28° C. and 100 RPM continuous agitation) in liquid YEP medium (10 gm/l yeast extract, 10 gm/l Bactopeptone, and 5 gm/l NaCl, pH 7.0) with the appropriate antibiotics required for bacterial strain and binary plasmid maintenance. The suspension is used when it reaches an OD600 of about 0.4 to 0.8. The Agrobacterium cells are pelleted and resuspended at a final OD600 of 0.5 in an inoculation medium comprised of 12.5 mM MES pH 5.7, 1 gm/l NH4Cl, and 0.3 gm/l MgSO4.
Freshly bombarded explants are placed in an Agrobacterium suspension, mixed, and left undisturbed for 30 minutes. The explants are then transferred to GBA medium and co-cultivated, cut surface down, at 26° C. and 18-hour days. After three days of co-cultivation, the explants are transferred to 374B (GBA medium lacking growth regulators and a reduced sucrose level of 1%) supplemented with 250 mg/l cefotaxime and 50 mg/l kanamycin sulfate. The explants are cultured for two to five weeks on selection and then transferred to fresh 374B medium lacking kanamycin for one to two weeks of continued development. Explants with differentiating, antibiotic-resistant areas of growth that have not produced shoots suitable for excision are transferred to GBA medium containing 250 mg/l cefotaxime for a second 3-day phytohormone treatment. Leaf samples from green, kanamycin-resistant shoots are assayed for the presence of NPTII by ELISA and for the presence of transgene expression by assaying for a modulation in the plant response to ABA.
NPTII-positive shoots are grafted to Pioneer® hybrid 6440 in vitro-grown sunflower seedling rootstock. Surface sterilized seeds are germinated in 48-0 medium (half-strength Murashige and Skoog salts, 0.5% sucrose, 0.3% gelrite, pH 5.6) and grown under conditions described for explant culture. The upper portion of the seedling is removed, a 1 cm vertical slice is made in the hypocotyl, and the transformed shoot inserted into the cut. The entire area is wrapped with parafilm to secure the shoot. Grafted plants can be transferred to soil following one week of in vitro culture. Grafts in soil are maintained under high humidity conditions followed by a slow acclimatization to the greenhouse environment. Transformed sectors of T0 plants (parental generation) maturing in the greenhouse are identified by, for example, NPTII ELISA of leaf extracts while transgenic seeds harvested from NPTII-positive T0 plants are identified by assaying for a modulation in the plant response to ABA.
Example 5
Transgenic maize plants are generated by the methods of example 1 using a DNA construction comprising a wild type Vp1 sequence (SEQ ID NO:1) operably linked to the oleosin promoter. The plasmid further contains the selectable marker PAT (Wohlleben et al. (1998) Gene 70:25-37). As described in Example 1, plants having stably incorporated the oleosin:Vp1 DNA construct are isolated.
Maize plants having a loss of function mutation in vp1 are isolated as described in Eyster et al. (1931) Genetics 16:574-590, herein incorporated by reference. Such plants are characterized as having a reduced sensitivity to ABA. Transgenic maize plants having stably incorporated the oleosin:Vp1 DNA construct are crossed to the maize plant having the vp1 loss of function mutation. The resulting progeny are backcrossed to produce a plant having the following genotype: vp1/vp1; oleosin:Vp1/oleosin:Vp1. This plant will be insulated from the deleterious effects of ABA in the early embryo and will be supplied with VP1 in late kernel/embryo development, allowing kernels to mature normally.
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

1. A method for increasing yield in a maize plant under an abiotic environmental stress said method comprising the steps of:
(a) transforming stably maize plant cells with a DNA construct which comprises a nucleotide sequence encoding a polypeptide having at least 95% amino acid sequence identity to the amino acid sequence as set forth in SEQ ID NO:4, wherein the nucleotide sequence is operably linked to an early kernel/embryo promoter that is active during the first phase of seed development, wherein the first phase of seed development is from 0 to about 12 days after pollination (DAP), wherein said early kernel/embryo promoter is heterologous to said nucleotide sequence, and wherein said early kernel/embryo promoter is inactive in the embryo during the maturation phase of seed development;
(b) regenerating transgenic maize plants from the transformed maize plant cells of step (a);
(c) growing the transformed maize plants of step (b) under an abiotic environmental stress, and expressing said polypeptide during the early phase of maize kernel/embryo development to reduce sensitivity to abscisic acid (ABA) during said early phase of maize kernel/embryo development, wherein said kernel/embryo is being produced on said transformed maize plant, thereby reducing the detrimental effects of said stress on the developing maize plant seed; and
(d) harvesting mature seeds from the transformed maize plants of step (c) to determine yield, whereby said method results in an increased yield as compared to a maize plant lacking said DNA construct.

2. The method of claim 1, wherein said polypeptide has the amino acid sequence as set forth in SEQ ID NO: 4.

3. The method of claim 1, wherein said nucleotide sequence has at least 95% sequence identity to the nucleotide sequence as set forth in SEQ ID NO: 3.

4. The method of claim 1, wherein said nucleotide sequence is set forth in SEQ ID NO: 3.