Methods and compositions for short stature plants through manipulation of gibberellin metabolism to increase harvestable yield

Abstract

The present disclosure provides compositions and methods for altering gibberellin (GA) content in corn or other cereal plants. Methods and compositions are also provided for altering the expression of genes related to gibberellin biosynthesis through suppression, mutagenesis and / or editing of specific subtypes of endogenous GA3 oxidase genes. Modified plant cells and plants having a mutation or genomic edit that reduces the expression and / or activity of the endogenous GA3 oxidase gene are further provided comprising reduced gibberellin levels and improved phenotypes or traits, such as reduced plant height and increased lodging resistance, but without off-types particularly in the female organ or ear.

Description

METHODS AND COMPOSITIONS FOR SHORT STATURE PLANTS THROUGH MANIPULATION OF GIBBERELLIN METABOLISM TO INCREASE HARVESTABLE YIELDCROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims the priority benefit of United States Provisional Application Serial Nos. 63 / 520,915 and 63 / 520,898, each filed on August 21, 2023, which are incorporated herein by reference in their entirety.INCORPORATION OF SEQUENCE LISTING

[0002] The sequence listing file named “BCS236343_SeqListing”, which is 492 kilobytes in size (measured in MS-WINDOWS) and was created on August 15, 2024, is submitted herewith and incorporated herein by reference in its entirety.BACKGROUNDField

[0003] The present disclosure relates to compositions and methods for improving traits, such as lodging resistance and increased yield, in monocot or cereal plants including corn.Related Art

[0004] Gibberellins (gibberellic acids or GAs) are plant hormones that regulate a number of major plant growth and developmental processes. Manipulation of GA levels in semi-dwarf wheat, rice and sorghum plant varieties led to increased yield and reduced lodging in these cereal crops during the 20thcentury, which was largely responsible for the Green Revolution. However, successful yield gains in other cereal crops, such as corn, have not been realized through manipulation of the GA pathway. Indeed, some mutations in the GA pathway genes have been associated with various off-types or plant heights that are too severely reduced in corn that are incompatible with yield, which has led researchers away from finding semi-dwarf, high-yielding corn varieties via manipulation of the GA pathway.

[0005] There is a need in the art for the development of monocot or cereal crop plants, such as corn, having mutations in genes affecting plant height and increased yield and / or resistance to lodging without off-types or a severe reduction in plant height.BRIEF DESCRIPTION OF THE DRAWINGS

[0006] FIG. 1 shows reduced plant heights of corn inbred plants expressing a GA20 oxidase suppression construct across eight transformation events in comparison to inbred control plants;

[0007] FIG. 2A shows a reduced plant height on average of hybrid com plants expressing a GA20 oxidase suppression construct in comparison to hybrid control plants;

[0008] FIG. 2B shows an image of a wild type hybrid control plant (left) next to a hybrid corn plant expressing a GA20 oxidase suppression construct (right) having a reduced plant height;

[0009] FIG. 3 A shows an increased stem diameter on average of hybrid corn plants expressing a GA20 oxidase suppression construct in comparison to hybrid control plants;

[0010] FIG. 3B shows an image of a cross-section of the stalk of a wild type hybrid control plant (left) next to a cross-section of the stalk of a hybrid com plant expressing a GA20 oxidase suppression construct (right) having an increased stem diameter;

[0011] FIG. 4 shows an increased fresh ear weight on average of hybrid corn plants expressing a GA20 oxidase suppression construct in comparison to hybrid control plants;

[0012] FIG. 5 shows the increased fresh ear weight on average of hybrid com plants expressing a GA20 oxidase suppression construct in two field trials in comparison to wild type hybrid control plants in response to a wind event that caused greater lodging in the hybrid control plants;

[0013] FIG. 6 shows an increased harvest index of hybrid corn plants expressing a GA20 oxidase suppression construct in comparison to hybrid control plants;

[0014] FIG. 7 shows an increase in the average grain yield estimate of hybrid corn plants expressing a GA20 oxidase suppression construct in comparison to hybrid control plants;

[0015] FIG. 8 shows an increased prolificacy score on average of hybrid corn plants expressing a GA20 oxidase suppression construct in comparison to hybrid control plants;

[0016] FIG. 9 shows the change in plant height over time during developmental stages VI 1 to beyond R1 between transgenic com plants and control;

[0017] FIG. 10 shows a graph comparing measurements of stable oxygen isotope ratios (518O) as an indication of stomatai conductance and water levels in leaf tissue at R5 stage between transgenic corn plants and control;

[0018] FIG. 11 shows a graph comparing root front velocity during developmental stages VI 0 to beyond R2 between transgenic and control plants at both SAP and HD conditions using sensors at different soil depths that detect changes in water levels indicating the presence of roots at that depth;

[0019] FIG. 12A shows differences in stomatai conductance during the morning and afternoon between transgenic corn plants and control under normal and drought conditions in the greenhouse;

[0020] FIG. 12B shows differences in photosynthesis during the morning and afternoon between transgenic corn plants and control under normal and drought conditions in the greenhouse;

[0021] FIG. 13 A shows differences in miRNA expression levels in bulk stem tissue, or separated vascular and non-vascular stem tissues, of transgenic corn plants versus control; and

[0022] FIG. 13B shows differences in GA20 oxidase_3 and GA20 oxidase_5 mRNA transcript expression levels in bulk stem tissue, or separated vascular and non-vascular stem tissues, of transgenic corn plants versus control.

[0023] FIG. 14 illustrates the different zygosities for an inversion edit in the 3’ UTR of the Zm.GA3ox_l gene with hybridization between the complementary UTR sequences of the wild-type and inversion edit alleles resulting in RNA suppression or silencing of the Zm.GA3ox_l gene only in heterozygous plants (FIG. 1 C), whereas a plant homozygous for the wild-type allele (FIG. 14 A) or the inversion edit allele (FIG. 14B) would not have hybridization of complementary sequences and RNA suppression or silencing of the Zm.GA3ox_l gene. Edited alleles of the Zm.GA3ox_l gene containing an inversion in the 5’ UTR of the Zm.GA3ox_l gene could be made to produce a similar effect on expression of the Zm.GA3ox_l gene.

[0024] FIG. 15 provides an illustration comparing the wild type (WT) and an edited allele of the Zm.GA3ox_l gene, with the edited allele having a deletion and inversion in the 3’ UTR region.

[0025] FIG. 16 provides an illustration of the approximate positions of the gRNA target sites within the 2,000 bp promoter region upstream of the transcription start site (TSS) of the Zm.GA3ox_l gene used to generate mutations in the promoter region of the Zm.GA3ox_l gene.DETAILED DESCRIPTIONDefinitions

[0026] To facilitate understanding of the disclosure, several terms and abbreviations as used herein are defined below as follows:

[0027] The term “and / or” when used in a list of two or more items, means that any one of the listed items can be employed by itself or in combination with any one or more of the listed items. For example, the expression “A and / or B” is intended to mean either or both of A and B - z.e., A alone, B alone, or A and B in combination. The expression “A, B and / or C” is intended to mean A alone, B alone, C alone, A and B in combination, A and C in combination, B and C in combination, or A, B, and C in combination.

[0028] The term “about” as used herein, is intended to qualify the numerical values that it modifies, denoting such a value as variable within a margin of error. When no particular margin of error, such as a standard deviation to a mean value, is recited, the term “about” should be understood to mean that range which would encompass the recited value and the range which would be included by rounding up or down to that figure, taking into account significant figures.

[0029] The term “cereal plant” as used herein refers a monocotyledonous (monocot) crop plant that is in the Poaceae or Gramineae family of grasses and is typically harvested for its seed, including, for example, wheat, com, rice, millet, barley, sorghum, oat and rye. As commonly understood, a “corn plant” or “maize plant” refers to any plant of species Zea mays and includes all plant varieties that can be bred with corn, including wild maize species.

[0030] The terms “percent identity” or “percent identical” as used herein in reference to two or more nucleotide or protein sequences is calculated by (i) comparing two optimally aligned sequences (nucleotide or protein) over a window of comparison, (ii) determining the number of positions at which the identical nucleic acid base (for nucleotide sequences) or amino acid residue (for proteins) occurs in both sequences to yield the number of matched positions, (iii) dividing the number of matched positions by the total number of positions in the window of comparison, and then (iv) multiplying this quotient by 100% to yield the percent identity. For purposes of calculating “percent identity” between DNA and RNA sequences, a uracil (U) of a RNA sequence is considered identical to a thymine (T) of a DNA sequence. If the window of comparison is defined as a region of alignment between two or more sequences (i.e., excluding nucleotides at the 5’ and 3’ ends of aligned polynucleotide sequences, or amino acids at the N-terminus andC-terminus of aligned protein sequences, that are not identical between the compared sequences), then the “percent identity” may also be referred to as a “percent alignment identity”. If the “percent identity” is being calculated in relation to a reference sequence without a particular comparison window being specified, then the percent identity is determined by dividing the number of matched positions over the region of alignment by the total length of the reference sequence. Accordingly, for purposes of the present disclosure, when two sequences (query and subject) are optimally aligned (with allowance for gaps in their alignment), the “percent identity” for the query sequence is equal to the number of identical positions between the two sequences divided by the total number of positions in the query sequence over its length (or a comparison window), which is then multiplied by 100%.

[0031] It is recognized that residue positions of proteins that are not identical often differ by conservative amino acid substitutions, where amino acid residues are substituted for other amino acid residues with similar size and chemical properties (e.g., charge, hydrophobicity, polarity, etc.), and therefore may not change the functional properties of the molecule. When sequences differ in conservative substitutions, the percent sequence similarity may be adjusted upwards to correct for the conservative nature of the non-identical substitution(s). Sequences that differ by such conservative substitutions are said to have “sequence similarity” or “similarity.” Thus, “percent similarity” or “percent similar” as used herein in reference to two or more protein sequences is calculated by (i) comparing two optimally aligned protein sequences over a window of comparison, (ii) determining the number of positions at which the same or similar amino acid residue occurs in both sequences to yield the number of matched positions, (iii) dividing the number of matched positions by the total number of positions in the window of comparison (or the total length of the reference or query protein if a window of comparison is not specified), and then (iv) multiplying this quotient by 100% to yield the percent similarity. Conservative amino acid substitutions for proteins are known in the art.

[0032] For optimal alignment of sequences to calculate their percent identity or similarity, various pairwise or multiple sequence alignment algorithms and programs are known in the art, such as ClustalW, or Basic Local Alignment Search Tool® (BLAST®), etc., that may be used to compare the sequence identity or similarity between two or more nucleotide or protein sequences. Although other alignment and comparison methods are known in the art, the alignment between two sequences (including the percent identity ranges described above) may be as determined by the ClustalW or BLAST® algorithm, see, e.g., Chenna R. et al., “Multiple sequence alignment withthe Clustal series of programs,” Nucleic Acids Research 31 : 3497-3500 (2003); Thompson JD et al., “Clustal W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice,” Nucleic Acids Research 22: 4673-4680 (1994); and Larkin MA et al., “Clustal W and Clustal X version 2.0,” Bioinformatics 23: 2947-48 (2007); and Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) "Basic local alignment search tool." J. Mol. Biol. 215:403-410 (1990), the entire contents and disclosures of which are incorporated herein by reference.

[0033] The terms “percent complementarity” or “percent complementary”, as used herein in reference to two nucleotide sequences, is similar to the concept of percent identity but refers to the percentage of nucleotides of a query sequence that optimally base-pair or hybridize to nucleotides of a subject sequence when the query and subject sequences are linearly arranged and optimally base paired without secondary folding structures, such as loops, stems or hairpins. Such a percent complementarity may be between two DNA strands, two RNA strands, or a DNA strand and a RNA strand. The “percent complementarity” is calculated by (i) optimally base-pairing or hybridizing the two nucleotide sequences in a linear and fully extended arrangement (i.e., without folding or secondary structures) over a window of comparison, (ii) determining the number of positions that base-pair between the two sequences over the window of comparison to yield the number of complementary positions, (iii) dividing the number of complementary positions by the total number of positions in the window of comparison, and (iv) multiplying this quotient by 100% to yield the percent complementarity of the two sequences. Optimal base pairing of two sequences may be determined based on the known pairings of nucleotide bases, such as G-C, A-T, and A-U, through hydrogen bonding. If the “percent complementarity” is being calculated in relation to a reference sequence without specifying a particular comparison window, then the percent identity is determined by dividing the number of complementary positions between the two linear sequences by the total length of the reference sequence. Thus, for purposes of the present disclosure, when two sequences (query and subject) are optimally base-paired (with allowance for mismatches or non-base-paired nucleotides but without folding or secondary structures), the “percent complementarity” for the query sequence is equal to the number of base-paired positions between the two sequences divided by the total number of positions in the query sequence over its length (or by the number of positions in the query sequence over a comparison window), which is then multiplied by 100%.

[0034] The term “operably linked” refers to a functional linkage between a promoter or other regulatory element and an associated transcribable DNA sequence or coding sequence of a gene (or transgene), such that the promoter, etc., operates or functions to initiate, assist, affect, cause, and / or promote the transcription and expression of the associated transcribable DNA sequence or coding sequence, at least in certain cell(s), tissue(s), developmental stage(s), and / or condition(s).

[0035] The term “plant-expressible promoter” refers to a promoter that can initiate, assist, affect, cause, and / or promote the transcription and expression of its associated transcribable DNA sequence, coding sequence or gene in a plant cell or tissue.

[0036] The term “heterologous” in reference to a promoter or other regulatory sequence in relation to an associated polynucleotide sequence (e.g., a transcribable DNA sequence or coding sequence or gene) is a promoter or regulatory sequence that is not operably linked to such associated polynucleotide sequence in nature - e.g., the promoter or regulatory sequence has a different origin relative to the associated polynucleotide sequence and / or the promoter or regulatory sequence is not naturally occurring in a plant species to be transformed with the promoter or regulatory sequence.

[0037] The term “recombinant” in reference to a polynucleotide (DNA or RNA) molecule, protein, construct, vector, etc., refers to a polynucleotide or protein molecule or sequence that is man-made and not normally found in nature, and / or is present in a context in which it is not normally found in nature, including a polynucleotide (DNA or RNA) molecule, protein, construct, etc., comprising a combination of two or more polynucleotide or protein sequences that would not naturally occur together in the same manner without human intervention, such as a polynucleotide molecule, protein, construct, etc., comprising at least two polynucleotide or protein sequences that are operably linked but heterologous with respect to each other. For example, the term “recombinant” can refer to any combination of two or more DNA or protein sequences in the same molecule (e.g., a plasmid, construct, vector, chromosome, protein, etc.) where such a combination is man-made and not normally found in nature. As used in this definition, the phrase “not normally found in nature” means not found in nature without human introduction. A recombinant polynucleotide or protein molecule, construct, etc., may comprise polynucleotide or protein sequence(s) that is / are (i) separated from other polynucleotide or protein sequence(s) that exist in proximity to each other in nature, and / or (ii) adjacent to (or contiguous with) other polynucleotide or protein sequence(s) that are not naturally in proximity with each other. Such a recombinant polynucleotide molecule, protein, construct, etc., may also refer to a polynucleotide or proteinmolecule or sequence that has been genetically engineered and / or constructed outside of a cell. For example, a recombinant DNA molecule may comprise any engineered or man-made plasmid, vector, etc., and may include a linear or circular DNA molecule. Such plasmids, vectors, etc., may contain various maintenance elements including a prokaryotic origin of replication and selectable marker, as well as one or more transgenes or expression cassettes perhaps in addition to a plant selectable marker gene, etc.

[0038] As used herein, the term “isolated” refers to at least partially separating a molecule from other molecules typically associated with it in its natural state. In one embodiment, the term “isolated” refers to a DNA molecule that is separated from the nucleic acids that normally flank the DNA molecule in its natural state. For example, a DNA molecule encoding a protein that is naturally present in a bacterium would be an isolated DNA molecule if it was not within the DNA of the bacterium from which the DNA molecule encoding the protein is naturally found. Thus, a DNA molecule fused to or operably linked to one or more other DNA molecule(s) with which it would not be associated in nature, for example as the result of recombinant DNA or plant transformation techniques, is considered isolated herein. Such molecules are considered isolated even when integrated into the chromosome of a host cell or present in a nucleic acid solution with other DNA molecules.

[0039] As used herein, an “encoding region” or “coding region” refers to a portion of a polynucleotide that encodes a functional unit or molecule (e.g., without being limiting, a mRNA, protein, or non-coding RNA sequence or molecule).

[0040] As used herein, “modified” in the context of a plant, plant seed, plant part, plant cell, and / or plant genome, refers to a plant, plant seed, plant part, plant cell, and / or plant genome comprising an engineered change in the expression level and / or coding sequence of one or more GA oxidase gene(s) relative to a wild-type or control plant, plant seed, plant part, plant cell, and / or plant genome, such as via (A) a transgenic event comprising a suppression construct or transcribable DNA sequence encoding a non-coding RNA that targets one or more GA3 and / or GA20 oxidase genes for suppression, or (B) a genome editing event or mutation affecting (e.g., reducing or eliminating) the expression level and / or activity of one or more endogenous GA3 and / or GA20 oxidase genes. Indeed, the term “modified” may further refer to a plant, plant seed, plant part, plant cell, and / or plant genome having one or more mutations affecting expression of one or more endogenous GA oxidase genes, such as one or more endogenous GA3 and / or GA20 oxidase genes, introduced through chemical mutagenesis, transposon insertion or excision, or anyother known mutagenesis technique, or introduced through genome editing (z.e., a targeted genome editing technique). For clarity, therefore, a modified plant, plant seed, plant part, plant cell, and / or plant genome includes a mutated, edited and / or transgenic plant, plant seed, plant part, plant cell, and / or plant genome having a modified expression level, expression pattern, and / or coding sequence of one or more GA oxidase gene(s) relative to a wild-type or control plant, plant seed, plant part, plant cell, and / or plant genome. Modified plants or seeds may contain various molecular changes that affect expression of GA oxidase gene(s), such as GA3 and / or GA20 oxidase gene(s), including genetic and / or epigenetic modifications. Modified plants, plant parts, seeds, etc., may have been subjected to mutagenesis, genome editing or site-directed integration (e.g., without being limiting, via methods using site-specific nucleases), genetic transformation (e.g., without being limiting, via methods of Agrobacterium transformation or microprojectile bombardment), or a combination thereof. Such “modified” plants, plant seeds, plant parts, and plant cells include plants, plant seeds, plant parts, and plant cells that are offspring, progeny or derived from “modified” plants, plant seeds, plant parts, and plant cells that retain the molecular change (e.g., change in expression level and / or activity) to the one or more GA oxidase genes. A modified seed provided herein may give rise to a modified plant provided herein. A modified plant, plant seed, plant part, plant cell, or plant genome provided herein may comprise a recombinant DNA construct or vector or genome edit as provided herein. A “modified plant product” may be any product made from a modified plant, plant part, plant cell, or plant chromosome provided herein, or any portion or component thereof.

[0041] As used herein, the term “control plant” (or likewise a “control” plant seed, plant part, plant cell and / or plant genome) refers to a plant (or plant seed, plant part, plant cell and / or plant genome) that is used for comparison to a modified plant (or modified plant seed, plant part, plant cell and / or plant genome) and has the same or similar genetic background (e.g., same parental lines, hybrid cross, inbred line, testers, etc.) as the modified plant (or plant seed, plant part, plant cell and / or plant genome), except for a transgenic and / or genome editing event(s) affecting one or more GA oxidase genes. For example, a control plant may be an inbred line that is the same as the inbred line used to make the modified plant, or a control plant may be the product of the same hybrid cross of inbred parental lines as the modified plant, except for the absence in the control plant of any transgenic or genome editing event(s) affecting one or more GA oxidase genes. For purposes of comparison to a modified plant, plant seed, plant part, plant cell and / or plant genome, a “wild-type plant” (or likewise a “wild-type” plant seed, plant part, plant cell and / or plant genome) refers to a non-transgenic and non-genome edited control plant, plant seed, plant part,plant cell and / or plant genome. As used herein, a “control” plant, plant seed, plant part, plant cell and / or plant genome may also be a plant, plant seed, plant part, plant cell and / or plant genome having a similar (but not the same or identical) genetic background to a modified plant, plant seed, plant part, plant cell and / or plant genome, if deemed sufficiently similar for comparison of the characteristics or traits to be analyzed.

[0042] As used herein, “locus” is a chromosomal or genomic locus or region where a polymorphic nucleic acid, trait determinant, gene, or marker is located. A “locus” can be shared by two homologous chromosomes to refer to their corresponding locus or region. As used herein, “allele” refers to an alternative nucleic acid sequence of a gene, or at a particular locus (e.g., a nucleic acid sequence of a gene or locus that is different than other alleles for the same gene or locus). Such an allele can be considered (i) wild-type, or (ii) mutant if one or more mutations or edits are present in the nucleic acid sequence of the mutant allele relative to the wild-type allele. As used herein, a “mutant gene” or “mutant allele” refers to a gene or allele having one or more mutations or edits in the nucleic acid sequence of the gene or allele relative to a wild-type gene or wild-type allele, wherein the mutant gene or mutant allele has a reduced and / or altered expression and / or a reduced and / or altered activity relative to a wild-type gene or wild-type allele. As used herein, a “wild-type gene” or “wild-type allele” refers to a gene or allele having a sequence or genotype that is most common in a particular plant species, or another sequence or genotype with natural variations, polymorphisms, or other silent mutations relative to the most common sequence or genotype that do not significantly impact the expression and activity of the gene or allele. Indeed, a “wild-type” gene or allele contains no variation, polymorphism, or any other type of mutation that substantially affects the normal function, activity, expression, or phenotypic consequence of the gene or allele. A mutant allele for a gene may be a loss-of-function allele and / or have a reduced or eliminated activity or expression level for the gene relative to the wild-type allele. A mutant allele may be a hypomorphic allele with a reduced activity and / or expression relative to the wild-type allele. A mutant allele may be a null allele with no activity and / or expression relative to the wild-type allele. A mutant allele of a gene or locus may have one or more mutations introduced into the gene or locus via any mutagenesis and / or targeted genome editing technique. For diploid organisms such as corn, a first allele can occur on one chromosome, and a second allele can occur at the same locus on a second homologous chromosome. If one allele at a locus on one chromosome of a plant is a mutant allele and the other corresponding allele on the homologous chromosome of the plant is wild-type, then the plant is described as being heterozygous for the mutant allele. However, if both alleles at a locus are mutant alleles, then theplant is described as being homozygous for the mutant alleles. A plant homozygous for mutant alleles at a locus may comprise the same mutant allele or different mutant alleles if heteroallelic or biallelic.

[0043] As used herein, a “target site” for genome editing refers to the location of a polynucleotide sequence within a plant genome that is bound and cleaved by a site-specific nuclease introducing a double stranded break (or single-stranded nick) into the nucleic acid backbone of the polynucleotide sequence and / or its complementary DNA strand. A target site may comprise at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 29, or at least 30 consecutive nucleotides. A “target site” for a RNA-guided nuclease may comprise the sequence of either complementary strand of a double-stranded nucleic acid (DNA) molecule or chromosome at the target site. A site-specific nuclease may bind to a target site, such as via a non-coding guide RNA (e.g., without being limiting, a CRISPR RNA (crRNA) or a single-guide RNA (sgRNA) as described further below). A non-coding guide RNA provided herein may be complementary to a target site (e.g., complementary to either strand of a double-stranded nucleic acid molecule or chromosome at the target site). It will be appreciated that perfect identity or complementarity may not be required for a non-coding guide RNA to bind or hybridize to a target site. For example, at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, or at least 8 mismatches (or more) between a target site and a non-coding RNA may be tolerated. A “target site” also refers to the location of a polynucleotide sequence within a plant genome that is bound and cleaved by another site-specific nuclease that may not be guided by a non-coding RNA molecule, such as a meganuclease, zinc finger nuclease (ZFN), or a transcription activator-like effector nuclease (TALEN), to introduce a double stranded break (or single-stranded nick) into the polynucleotide sequence and / or its complementary DNA strand. As used herein, a “target region” or a “targeted region” refers to a polynucleotide sequence or region that is flanked by two or more target sites. Without being limiting, in some embodiments a target region may be subjected to a mutation, deletion, insertion or inversion. As used herein, “flanked” when used to describe a target region of a polynucleotide sequence or molecule, refers to two or more target sites of the polynucleotide sequence or molecule surrounding the target region, with one target site on each side of the target region. Apart from genome editing, the term “target site” may also be used in the context of gene suppression to refer to a portion of a mRNA molecule (e.g., a “recognition site”) that is complementary to at least a portion of a non-coding RNA molecule (e.g., a miRNA, siRNA, etc.) encoded by a suppression construct.

[0044] As used herein, a “donor molecule”, “donor template”, or “donor template molecule” (collectively a “donor template”), which may be a recombinant DNA donor template, is defined as a nucleic acid molecule having a nucleic acid template or insertion sequence for site-directed, targeted insertion or recombination into the genome of a plant cell via repair of a nick or double-stranded DNA break in the genome of a plant cell. For example, a “donor template” may be used for site-directed integration of a transgene or suppression construct, or as a template to introduce a mutation, such as an insertion, deletion, etc., into a target site within the genome of a plant. A targeted genome editing technique provided herein may comprise the use of one or more, two or more, three or more, four or more, or five or more donor molecules or templates. A “donor template” may be a single-stranded or double-stranded DNA or RNA molecule or plasmid. An “insertion sequence” of a donor template is a sequence designed for targeted insertion into the genome of a plant cell, which may be of any suitable length. For example, the insertion sequence of a donor template may be between 2 and 50,000, between 2 and 10,000, between 2 and 5000, between 2 and 1000, between 2 and 500, between 2 and 250, between 2 and 100, between 2 and 50, between 2 and 30, between 15 and 50, between 15 and 100, between 15 and 500, between 15 and 1000, between 15 and 5000, between 18 and 30, between 18 and 26, between 20 and 26, between 20 and 50, between 20 and 100, between 20 and 250, between 20 and 500, between 20 and 1000, between 20 and 5000, between 20 and 10,000, between 50 and 250, between 50 and 500, between 50 and 1000, between 50 and 5000, between 50 and 10,000, between 100 and 250, between 100 and 500, between 100 and 1000, between 100 and 5000, between 100 and 10,000, between 250 and 500, between 250 and 1000, between 250 and 5000, or between 250 and 10,000 nucleotides or base pairs in length. A donor template may also have at least one homology sequence or homology arm, such as two homology arms, to direct the integration of a mutation or insertion sequence into a target site within the genome of a plant via homologous recombination, wherein the homology sequence or homology arm(s) are identical or complementary, or have a percent identity or percent complementarity, to a sequence at or near the target site within the genome of the plant. When a donor template comprises homology arm(s) and an insertion sequence, the homology arm(s) will flank or surround the insertion sequence of the donor template.

[0045] An insertion sequence of a donor template may comprise one or more genes or sequences that each encode a transcribed non-coding RNA or mRNA sequence and / or a translated protein sequence. A transcribed sequence or gene of a donor template may encode a protein or a non-coding RNA molecule. An insertion sequence of a donor template may comprise a polynucleotide sequence that does not comprise a functional gene or an entire gene sequence (e.g.,the donor template may simply comprise regulatory sequences, such as a promoter sequence, or only a portion of a gene or coding sequence), or may not contain any identifiable gene expression elements or any actively transcribed gene sequence. Further, the donor template may be linear or circular, and may be single-stranded or double-stranded. A donor template may be delivered to the cell as a naked nucleic acid (e.g., via particle bombardment), as a complex with one or more delivery agents (e.g., liposomes, proteins, pol oxamers, T-strand encapsulated with proteins, etc.), or contained in a bacterial or viral delivery vehicle, such as, for example, Agrobacterium tumefaciens or a geminivirus, respectively. An insertion sequence of a donor template provided herein may comprise a transcribable DNA sequence that may be transcribed into an RNA molecule, which may be non-coding and may or may not be operably linked to a promoter and / or other regulatory sequence.

[0046] According to some embodiments, a donor template may not comprise an insertion sequence, and instead comprise one or more homology sequences that include(s) one or more mutations, such as an insertion, deletion, substitution, etc., relative to the genomic sequence at a target site within the genome of a plant, such as at or near a GA3 oxidase or GA20 oxidase gene within the genome of a plant. Alternatively, a donor template may comprise an insertion sequence that does not comprise a coding or transcribable DNA sequence, wherein the insertion sequence is used to introduce one or more mutations into a target site within the genome of a plant, such as at or near a GA3 oxidase or GA20 oxidase gene within the genome of a plant.

[0047] A donor template provided herein may comprise at least one, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, or at least ten genes or transcribable DNA sequences. Alternatively, a donor template may comprise no genes. Without being limiting, a gene or transcribable DNA sequence of a donor template may include, for example, an insecticidal resistance gene, an herbicide tolerance gene, a nitrogen use efficiency gene, a water use efficiency gene, a nutritional quality gene, a DNA binding gene, a selectable marker gene, an RNAi or suppression construct, a site-specific genome modification enzyme gene, a single guide RNA of a CRISPR / Cas9 system, a geminivirus-based expression cassette, or a plant viral expression vector system. According to other embodiments, an insertion sequence of a donor template may comprise a transcribable DNA sequence that encodes a non-coding RNA molecule, which may target a GA oxidase gene, such as a GA3 oxidase or GA20 oxidase gene, for suppression. A donor template may comprise a promoter, such as a tissue-specific or tissue-preferred promoter, a constitutive promoter, or an inducible promoter. A donor templatemay comprise a leader, enhancer, promoter, transcriptional start site, 5’-UTR, one or more exon(s), one or more intron(s), transcriptional termination site, region or sequence, 3’-UTR, and / or polyadenylation signal. The leader, enhancer, and / or promoter may be operably linked to a gene or transcribable DNA sequence encoding a non-coding RNA, a guide RNA, an mRNA and / or protein.

[0048] As used herein, a “vascular promoter” refers to a plant-expressible promoter that drives, causes or initiates expression of a transcribable DNA sequence or transgene operably linked to such promoter in one or more vascular tissue(s) of the plant, even if the promoter is also expressed in other non-vascular plant cell(s) or tissue(s). Such vascular tissue(s) may comprise one or more of the phloem, vascular parenchymal, and / or bundle sheath cell(s) or tissue(s) of the plant. A “vascular promoter” is distinguished from a constitutive promoter in that it has a regulated and relatively more limited pattern of expression that includes one or more vascular tissue(s) of the plant. A vascular promoter includes both vascular-specific promoters and vascular-preferred promoters.

[0049] As used herein, a “leaf promoter” refers to a plant-expressible promoter that drives, causes or initiates expression of a transcribable DNA sequence or transgene operably linked to such promoter in one or more leaf tissue(s) of the plant, even if the promoter is also expressed in other non-leaf plant cell(s) or tissue(s). A leaf promoter includes both leaf-specific promoters and leaf-preferred promoters. A “leaf promoter” is distinguished from a vascular promoter in that it is expressed more predominantly or exclusively in leaf tissue(s) of the plant relative to other plant tissues, whereas a vascular promoter is expressed in vascular tissue(s) more generally including vascular tissue(s) outside of the leaf, such as the vascular tissue(s) of the stem, or stem and leaves, of the plant.

[0050] As used herein, the term “homozygous” refers to a genotype comprising two identical alleles at a given locus in a diploid genome, or a genotype comprising two non-identical mutant alleles at a given locus in a diploid genome. The latter genotype comprising two non-identical mutant alleles is also referred to as being heteroallelic or transheterozygous, or as a heteroallelic combination. As used herein, “heterozygous” describes a genotype comprising a mutant allele and a wild-type allele at a given locus in a diploid genome.

[0051] As used herein, an “upstream region” of a plant gene, such as a GA20 oxidase or a GA3 oxidase gene, refers to the promoter and intergenic regions of the plant genome, including the genomic sequence of such regions, that are immediately upstream (in the 5’ direction) of thetranscription start site of the gene (z.e., immediately upstream of the transcribable DNA region or sequence and 5’ untranslated region of the gene). For clarity, an “upstream region” of a gene includes the “promoter region” of the gene.

[0052] As used herein, a “downstream region” of a plant gene, such as a GA20 oxidase or a GA3 oxidase gene, refers to the intergenic region of the plant genome, including the genomic sequence of such region, that is immediately downstream (in the 3’ direction) of the transcription termination site of the gene (z.e., immediately downstream of the transcribable DNA region or sequence of the gene).

[0053] As used herein, an “intergenic region” of a plant gene refers to the region of the plant genome, including the genomic sequence of such region, that is immediately upstream (in the 5’ direction) of the promoter region of the gene or immediately downstream (in the 3’ direction) of the transcription termination site of the gene (z.e., immediately downstream of the transcribable DNA region or sequence of the gene) and spans to a neighboring gene in the plant genome that is upstream or downstream, respectively, of the plant gene but does not include any promoter or transcribable DNA regions of the neighboring gene.

[0054] As used herein, a “promoter region” of a plant gene, such as a GA20 oxidase or a GA3 oxidase gene, refers to the region of the plant genome, including the genomic sequence of such region, that is immediately upstream (in the 5’ direction) of the transcription start site of the gene (z.e., immediately upstream of the transcribable DNA region or sequence and 5’ untranslated region of the gene) and includes or is likely to include one or more promoter, enhancer or other regulatory expression elements for the gene.

[0055] As used herein, a “transcribable DNA region” of a plant gene, such as a GA20 oxidase or a GA3 oxidase gene, refers to the region in the plant genome, including the genomic sequence of such region, that encodes a pre-mRNA expressed by, and transcribed from, such gene, which may include a 5’ untranslated region (5’UTR), a 3’ untranslated region (3’UTR), one or more exon sequence(s), and / or one or more intron sequence(s).Description

[0056] Most grain producing grasses, such as wheat, rice and sorghum, produce both male and female structures within each floret of the panicle (i.e., they have a single reproductive structure). However, corn or maize is unique among the grain-producing grasses in that it forms separate male (tassel) and female (ear) inflorescences. Corn produces completely sexually dimorphicreproductive structures by selective abortion of male organs (anthers) in florets of the ear, and female organs (ovules) in the florets of the tassel within early stages of development. Precisely regulated gibberellin synthesis and signaling is critical to regulation of this selective abortion process, with the female reproductive ear being most sensitive to disruptions in the GA pathway. Indeed, the “anther ear” phenotype is the most common reproductive phenotype in GA com mutants.

[0057] In contrast to corn, mutations in the gibberellin synthesis or signaling pathways that led to the “Green Revolution” in wheat, rice and sorghum had little impact on their reproductive structures because these crop species do not undergo the selective abortion process of the grain bearing panicle during development, and thus are not sensitive to disruptions in GA levels. The same mutations have not been utilized in corn because disruption of the GA synthesis and signaling pathway has repeatedly led to dramatic distortion and masculinization of the ear (“anther ear”) and sterility (disrupted anther and microspore development) in the tassel, in addition to extreme dwarfing in some cases. See, e.g., Chen, Y. et al., “The Maize DWARF1 Encodes a Gibberellin 3-Oxidase and Is Dual Localized to the Nucleus and Cytosol,” Plant Physiology 166: 2028-2039 (2014). These GA mutant phenotypes (off-types) in corn led to significant reductions in kernel production and a reduction in yield. Furthermore, production of anthers within the ear increases the likelihood of fungal or insect infections, which reduces the quality of the grain that is produced on those mutant ears. Forward breeding to develop semi-dwarf lines of corn has not been successful, and the reproductive off-types (as well as the extreme dwarfing) of GA mutants have been challenging to overcome. Thus, the same mutations in the GA pathway that led to the Green Revolution in other grasses have not yet been successful in corn.

[0058] Despite these prior difficulties in achieving higher grain yields in corn through manipulation of the GA pathway, the present inventors have discovered a way to manipulate GA levels in corn plants in a manner that reduces overall plant height and stem internode length and increases resistance to lodging, but does not cause the reproductive off-types previously associated with mutations of the GA pathway in com. Further evidence indicates that these short stature or semi-dwarf com plants may also have one or more additional traits, including increased stem diameter, reduced green snap, deeper roots, increased leaf area, earlier canopy closure, higher stomatai conductance, lower ear height, increased foliar water content, improved drought tolerance, increased nitrogen use efficiency, increased water use efficiency, reduced anthocyanincontent and area in leaves under normal or nitrogen or water limiting stress conditions, increased ear weight, increased kernel number, increased kernel weight, increased yield, and / or increased harvest index.

[0059] Suppression and / or reduced or lowered expression and / or activity of GA20 or GA3 oxidase gene(s) may be effective in achieving a short stature, semi-dwarf phenotype with increased resistance to lodging, but without reproductive off-types in the ear. It is further proposed, without being limited by theory, that restricting the suppression of GA20 and / or GA3 oxidase gene(s) to certain active GA-producing tissues, such as the vascular and / or leaf tissues of the plant, may be sufficient to produce a short-stature plant with increased lodging resistance, but without significant off-types in reproductive tissues. Expression of a GA20 or GA3 oxidase suppression element in a tissue-specific or tissue-preferred manner may be sufficient and effective at producing plants with the short stature phenotype, while avoiding potential off-types in reproductive tissues that were previously observed with GA mutants in corn (e.g., by avoiding or limiting the suppression of the GA20 oxidase gene(s) in those reproductive tissues). For example, GA20 and / or GA3 oxidase gene(s) may be targeted for suppression using a vascular promoter, such as a rice tungro bacilliform virus (RTBV) promoter, that drives expression in vascular tissues of plants. As supported in the Examples below, the expression pattern of the RTBV promoter is enriched in vascular tissues of corn plants relative to non-vascular tissues, which is sufficient to produce a semi-dwarf phenotype in corn plants when operably linked to a suppression element targeting GA20 and GA3 oxidase gene(s). Lowering of active GA levels in tissue(s) of a com or cereal plant that produce active GAs may reduce plant height and increase lodging resistance, and off-types may be avoided in those plants if active GA levels are not also significantly impacted or lowered in reproductive tissues, such as the developing female organ or ear of the plant. If active GA levels could be reduced in the stalk, stem, or internode(s) of corn or cereal plants, perhaps without significantly affecting GA levels in reproductive tissues (e.g., the female or male reproductive organs or inflorescences), then corn or cereal plants having reduced plant height and increased lodging resistance could be created without off-types in the reproductive tissues of the plant.

[0060] Thus, recombinant DNA constructs and transgenic plants are provided herein comprising a GA20 or GA3 oxidase suppression element or sequence operably linked to a plant expressible promoter, which may be a tissue-specific or tissue-preferred promoter. Such a tissue-specific or tissue-preferred promoter may drive expression of its associated GA oxidasesuppression element or sequence in one or more active GA-producing tissue(s) of the plant to suppress or reduce the level of active GAs produced in those tissue(s). Such a tissue-specific or tissue-preferred promoter may drive expression of its associated GA oxidase suppression construct or transgene during one or more vegetative stage(s) of development. Such a tissue-specific or tissue-preferred promoter may also have little or no expression in one or more cell(s) or tissue(s) of the developing female organ or ear of the plant to avoid the possibility of off-types in those reproductive tissues. According to some embodiments, the tissue-specific or tissue-preferred promoter is a vascular promoter, such as the RTBV promoter. The sequence of the RTBV promoter is provided herein as SEQ ID NO: 65, and a truncated version of the RTBV promoter is further provided herein as SEQ ID NO: 66.

[0061] Active or bioactive gibberellic acids (i.e., “active gibberellins” or “active GAs”) are known in the art for a given plant species, as distinguished from inactive GAs. For example, active GAs in com and higher plants include the following: GAI, GA3, GA4, and GA7. Thus, an “active GA-producing tissue” is a plant tissue that produces one or more active GAs.

[0062] In addition to suppressing GA20 oxidase genes in active GA-producing tissues of the plant with a vascular tissue promoter, suppression of the same GA20 oxidase genes with various constitutive promoters could also cause the short, semi-dwarf stature phenotypes in com, but without any visible off-types in the ear. Given that mutations in the GA pathway have previously been shown to cause off-types in reproductive tissues, it was surprising that constitutive suppression of GA20 oxidase did not cause similar reproductive phenotypes in the ear. Thus, suppression of one or more GA20 oxidase genes could be carried out using a constitutive promoter to create a short stature, lodging-resistant corn or cereal plant without any significant or observable reproductive off-types in the plant. Other surprising observations were made when the same GA20 oxidase suppression construct was expressed in the stem, leaf or reproductive tissues. As described further below, targeted suppression of the same GA20 oxidase genes in the stem or ear tissues of com plants did not cause the short stature, semi-dwarf phenotype. Moreover, directed expression of the GA20 oxidase suppression construct directly in reproductive tissues of the developing ear of corn plants with a female reproductive tissue (ear) promoter did not cause any significant or observable off-types in the ear. However, expression of the same GA20 oxidase suppression construct in leaf tissues was sufficient to cause a moderate short stature phenotype without significant or observable reproductive off-types in the plant.

[0063] Without being limited by theory, short stature, semi-dwarf phenotypes in corn and other cereal plants may result from a sufficient level of expression of a suppression construct targeting certain GA oxidase gene(s) in active GA-producing tissue(s) of the plant. At least for targeted suppression of certain GA20 oxidase genes in corn, restricting the pattern of expression to avoid reproductive ear tissues may not be necessary to avoid reproductive off-types in the developing ear. However, expression of the GA20 or GA3 oxidase suppression construct at low levels, and / or in a limited number of plant tissues, may be insufficient to cause a significant short stature, semi-dwarf phenotype. Given that the observed semi-dwarf phenotype with targeted GA20 oxidase suppression is the result of shortening the stem internodes of the plant, it was surprising that suppression of GA20 oxidase genes in at least some stem tissues was not sufficient to cause shortening of the internodes and reduced plant height. Without being bound by theory, suppression of certain GA oxidase gene(s) in tissue(s) and / or cell(s) of the plant where active GAs are produced, and not necessarily in stem or internode tissue(s), may be sufficient to produce semi-dwarf plants, even though the short stature trait is due to shortening of the stem internodes. Given that GAs can migrate through the vasculature of the plant, it is proposed that manipulating GA oxidase genes in plant tissue(s) where active GAs are produced may result in a short stature, semi-dwarf plant, even though this may be largely achieved by suppressing the level of active GAs produced in non-stem tissues (i.e., away from the site of action in the stem where reduced internode elongation leads to the semi-dwarf phenotype). Indeed, suppression of certain GA20 oxidase genes in leaf tissues was found to cause a moderate semi-dwarf phenotype in corn plants. Given that expression of a GA20 oxidase suppression construct with several different “stem” promoters did not produce the semi-dwarf phenotype in com, it is noteworthy that expression of the same GA20 oxidase suppression construct with a RTBV vascular promoter was effective at consistently producing the semi-dwarf phenotype with a high degree of penetrance across events and germplasms. This semi-dwarf phenotype was also observed with expression of the same GA20 oxidase suppression construct using other vascular promoters.

[0064] According to embodiments of the present disclosure, modified cereal or corn plants are provided that have at least one beneficial agronomic trait and at least one female reproductive organ or ear that is substantially or completely free of off-types. The beneficial agronomic trait may include, for example, shorter plant height, shorter internode length in one or more internode(s), larger (thicker) stem or stalk diameter, increased lodging resistance, improved drought tolerance, increased nitrogen use efficiency, increased water use efficiency, deeper roots,larger leaf area, earlier canopy closure, and / or increased harvestable yield. Off-types may include male (tassel or anther) sterility, reduced kernel or seed number, and / or the presence of one or more masculinized or male (or male-like) reproductive structures in the female organ or ear (e.g., anther ear) of the plant. A modified cereal or corn plant is provided herein that lacks significant off-types in the reproductive tissues of the plant. Such a modified cereal or corn plant may have a female reproductive organ or ear that appears normal relative to a control or wild-type plant. Indeed, modified cereal or corn plants are provided that comprise at least one reproductive organ or ear that does not have or exhibit, or is substantially or completely free of, off-types including male sterility, reduced kernel or seed number, and / or masculinized structure(s) in one or more female organs or ears. As used herein, a female organ or ear of a plant, such as corn, is “substantially free” of male reproductive structures if male reproductive structures are absent or nearly absent in the female organ or ear of the plant based on visual inspection of the female organ or ear at later reproductive stages. A female organ or ear of a plant, such as corn, is “completely free” of mature male reproductive structures if male reproductive structures are absent or not observed or observable in the female organ or ear of the plant, such as a corn plant, by visual inspection of the female organ or ear at later reproductive stages. A female organ or ear of a plant, such as com, without significant off-types and substantially free of male reproductive structures in the ear may have a number of kernels or seeds per female organ or ear of the plant that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, or at least 99.9% of the number of kernels or seeds per female organ or ear of a wild-type or control plant. Likewise, a female organ or ear of a plant, such as corn, without significant off-types and substantially free of male reproductive structures in the ear may have an average kernel or seed weight per female organ or ear of the plant that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, or at least 99.9% of the average kernel or seed weight per female organ or ear of a wild-type or control plant. A female organ or ear of a plant, such as corn, that is completely free of mature male reproductive structures may have a number of kernels or seeds per female organ or ear of the plant that is about the same as a wild-type or control plant. In other words, the reproductive development of the female organ or ear of the plant may be normal or substantially normal. However, the number of seeds or kernels per female organ or ear may depend on other factors that affect resource utilization and development of the plant. Indeed, the number of kernels or seeds per female organ or ear of the plant, and / or the kernel or seed weight per female organ or ear of the plant, may be about the same or greater than a wild-type or control plant.

[0065] The plant hormone gibberellin plays an important role in a number of plant developmental processes including germination, cell elongation, flowering, embryogenesis and seed development. Certain biosynthetic enzymes (e.g., GA20 oxidase and GA3 oxidase) and catabolic enzymes (e.g., GA2 oxidase) in the GA pathway are critical to affecting active GA levels in plant tissues. Thus, in addition to suppression of certain GA20 oxidase genes, it is further proposed that suppression of a GA3 oxidase gene in a constitutive or tissue-specific or tissue-preferred manner may also produce com plants having a short stature phenotype and increased lodging resistance, with possible increased yield, but without off-types in the ear. Thus, according to some embodiments, constructs and transgenes are provided comprising a GA3 oxidase suppression element or sequence operably linked to a constitutive or tissue-specific or tissue-preferred promoter, such as a vascular or leaf promoter. According to some embodiments, the tissue-specific or tissue-preferred promoter is a vascular promoter, such as the RTBV promoter. However, other types of tissue-specific or tissue preferred promoters may potentially be used for GA3 oxidase suppression in active GA-producing tissues of a com or cereal plant to produce a semi-dwarf phenotype without significant off-types.

[0066] Any method known in the art for suppression of a target gene may be used to suppress GA oxidase gene(s) according to embodiments of the present invention including expression of antisense RNAs, double stranded RNAs (dsRNAs) or inverted repeat RNA sequences, or via co-suppression or RNA interference (RNAi) through expression of small interfering RNAs (siRNAs), short hairpin RNAs (shRNAs), trans-acting siRNAs (ta-siRNAs), or micro RNAs (miRNAs). Furthermore, sense and / or antisense RNA molecules may be used that target the coding and / or non-coding genomic sequences or regions within or near a GA oxidase gene to cause silencing of the gene. Accordingly, any of these methods may be used for the targeted suppression of an endogenous GA20 oxidase(s) or GA3 oxidase gene(s) in a tissue-specific or tissue-preferred manner. See, e.g., U.S. Patent Application Publication Nos. 2009 / 0070898, 2011 / 0296555, and 2011 / 0035839, the contents and disclosures of which are incorporated herein by reference.

[0067] The term “suppression” as used herein, refers to a lowering, reduction or elimination of the expression level of a mRNA and / or protein encoded by a target gene in a plant, plant cell or plant tissue at one or more stage(s) of plant development, as compared to the expression level of such target mRNA and / or protein in a wild-type or control plant, cell or tissue at the same stage(s) of plant development. According to some embodiments, a modified or transgenic plant is providedhaving a GA20 oxidase gene expression level that is reduced in at least one plant tissue by at least 5%, at least 10%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, or 100%, as compared to a control plant. According to some embodiments, a modified or transgenic plant is provided having a GA3 oxidase gene expression level that is reduced in at least one plant tissue by at least 5%, at least 10%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, or 100%, as compared to a control plant. According to some embodiments, a modified or transgenic plant is provided having a GA20 oxidase gene expression level that is reduced in at least one plant tissue by 5%-20%, 5%-25%, 5%-30%, 5%-40%, 5%-50%, 5%-60%, 5%-70%, 5%-75%, 5%-80%, 5%-90%, 5%-100%, 75%-100%, 50%-100%, 50%-90%, 50%-75%, 25%-75%, 30%-80%, or 10%-75%, as compared to a control plant. According to some embodiments, a modified or transgenic plant is provided having a GA3 oxidase gene expression level that is reduced in at least one plant tissue by 5%-20%, 5%-25%, 5%-30%, 5%-40%, 5%-50%, 5%-60%, 5%-70%, 5%-75%, 5%-80%, 5%-90%, 5%-100%, 75%-100%, 50%-100%, 50%-90%, 50%-75%, 25%-75%, 30%-80%, or 10%-75%, as compared to a control plant. According to these embodiments, the at least one tissue of a modified or transgenic plant having a reduced expression level of a GA20 oxidase and / or GA3 oxidase gene(s) includes one or more active GA producing tissue(s) of the plant, such as the vascular and / or leaf tissue(s) of the plant, during one or more vegetative stage(s) of development.

[0068] In some embodiments, suppression of an endogenous GA20 oxidase gene or a GA3 oxidase gene is tissue-specific (e.g., only in leaf and / or vascular tissue). Suppression of a GA20 oxidase gene or a GA3 oxidase gene may be constitutive and / or vascular or leaf tissue specific or preferred. In other embodiments, suppression of a GA20 oxidase gene or a GA3 oxidase gene is constitutive and not tissue-specific. According to some embodiments, expression of an endogenous GA20 oxidase gene and / or a GA3 oxidase gene is reduced in one or more tissue types (e.g., in leaf and / or vascular tissue(s)), such as one or more active GA producing tissues, of a modified or transgenic plant as compared to the same tissue(s) of a control plant.

[0069] According to embodiments of the present disclosure, a recombinant DNA molecule, construct or vector is provided comprising a suppression element targeting GA20 oxidase or GA3 oxidase gene(s) that is operably linked to a plant-expressible constitutive or tissue-specific or tissue-preferred promoter. The suppression element may comprise a transcribable DNA sequenceof at least 19 nucleotides in length, such as from about 19 nucleotides in length to about 27 nucleotides in length, or 19, 20, 21, 22, 23, 24, 25, 26, or 27 nucleotides in length, wherein the transcribable DNA sequence corresponds to at least a portion of the target GA oxidase gene to be suppressed, and / or to a DNA sequence complementary thereto. The suppression element may be 19-30, 19-50, 19-100, 19-200, 19-300, 19-500, 19-1000, 19-1500, 19-2000, 19-3000, 19-4000, or 19-5000 nucleotides in length. The suppression element may be at least 19, at least 20, at least 21, at least 22, or at least 23 nucleotides or more in length (e.g., at least 25, at least 30, at least 50, at least 100, at least 200, at least 300, at least 500, at least 1000, at least 1500, at least 2000, at least 3000, at least 4000, or at least 5000 nucleotides in length). Depending on the length and sequence of a suppression element, one or more sequence mismatches or non-complementary bases, such as 1, 2, 3, 4, 5, 6, 7, 8 or more mismatches, may be tolerated without a loss of suppression if the non-coding RNA molecule encoded by the suppression element is still able to sufficiently hybridize and bind to the target mRNA molecule of the GA20 oxidase or GA3 oxidase gene(s). Indeed, even shorter RNAi suppression elements ranging from about 19 nucleotides to about 27 nucleotides in length may have one or more mismatches or non-complementary bases, yet still be effective at suppressing a target GA oxidase gene. Accordingly, a sense or anti-sense suppression element sequence may be at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5% or 100% identical or complementary to a corresponding sequence of at least a segment or portion of the targeted GA oxidase gene, or its complementary sequence, respectively.

[0070] A suppression element or transcribable DNA sequence of the present disclosure for targeted suppression of GA oxidase gene(s) may include one or more of the following: (a) a DNA sequence that includes at least one anti-sense DNA sequence that is anti-sense or complementary to at least one segment or portion of the targeted GA oxidase gene; (b) a DNA sequence that includes multiple copies of at least one anti-sense DNA sequence that is anti-sense or complementary to at least one segment or portion of the targeted GA oxidase gene; (c) a DNA sequence that includes at least one sense DNA sequence that comprises at least one segment or portion of the targeted GA oxidase gene; (d) a DNA sequence that includes multiple copies of at least one sense DNA sequence that each comprise at least one segment or portion of the targeted GA oxidase gene; (e) a DNA sequence that includes an inverted repeat of a segment or portion of a targeted GA oxidase gene and / or transcribes into RNA for suppressing the targeted GA oxidase gene by forming double-stranded RNA, wherein the transcribed RNA includes at least oneanti-sense DNA sequence that is anti-sense or complementary to at least one segment or portion of the targeted GA oxidase gene and at least one sense DNA sequence that comprises at least one segment or portion of the targeted GA oxidase gene; (f) a DNA sequence that is transcribed into RNA for suppressing the targeted GA oxidase gene by forming a single double-stranded RNA and includes multiple serial anti-sense DNA sequences that are each anti-sense or complementary to at least one segment or portion of the targeted GA oxidase gene and multiple serial sense DNA sequences that each comprise at least one segment or portion of the targeted GA oxidase gene; (g) a DNA sequence that is transcribed into RNA for suppressing the targeted GA oxidase gene by forming multiple double strands of RNA and includes multiple anti-sense DNA sequences that are each anti-sense or complementary to at least one segment or portion of the targeted GA oxidase gene and multiple sense DNA sequences that each comprise at least one segment or portion of the targeted GA oxidase gene, wherein the multiple anti-sense DNA segments and multiple sense DNA segments are arranged in a series of inverted repeats; (h) a DNA sequence that includes nucleotides derived from a miRNA, preferably a plant miRNA; (i) a DNA sequence that includes a miRNA precursor that encodes an artificial miRNA complementary to at least one segment or portion of the targeted GA oxidase gene; (j) a DNA sequence that includes nucleotides of a siRNA; (k) a DNA sequence that is transcribed into an RNA aptamer capable of binding to a ligand; and (1) a DNA sequence that is transcribed into an RNA aptamer capable of binding to a ligand and DNA that transcribes into a regulatory RNA capable of regulating expression of the targeted GA oxidase gene, wherein the regulation of the targeted GA oxidase gene is dependent on the conformation of the regulatory RNA, and the conformation of the regulatory RNA is allosterically affected by the binding state of the RNA aptamer by the ligand. Any of these gene suppression elements, whether transcribed into a single stranded or double-stranded RNA, may be designed to suppress more than one GA oxidase target gene, depending on the number and sequence of the suppression element(s).

[0071] Multiple sense and / or anti-sense suppression elements for more than one GA oxidase target may be arranged serially in tandem or arranged in tandem segments or repeats, such as tandem inverted repeats, which may also be interrupted by one or more spacer sequence(s), and the sequence of each suppression element may target one or more GA oxidase gene(s). Furthermore, the sense or anti-sense sequence of the suppression element may not be perfectly matched or complementary to the targeted GA oxidase gene sequence, depending on the sequence and length of the suppression element. Even shorter RNAi suppression elements from about 19 nucleotides to about 27 nucleotides in length may have one or more mismatches or non-complementary bases, yetstill be effective at suppressing the target GA oxidase gene. Accordingly, a sense or anti-sense suppression element sequence may be at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5% or 100% identical to a corresponding sequence of at least a segment or portion of the targeted GA oxidase gene, or its complementary sequence, respectively.

[0072] For anti-sense suppression, the transcribable DNA sequence or suppression element comprises a sequence that is anti-sense or complementary to at least a portion or segment of the targeted GA oxidase gene. The suppression element may comprise multiple anti-sense sequences that are complementary to one or more portions or segments of the targeted GA oxidase gene(s), or multiple copies of an anti-sense sequence that is complementary to a targeted GA oxidase gene. The anti-sense suppression element sequence may be at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5% or 100% identical to a DNA sequence that is complementary to at least a segment or portion of the targeted GA oxidase gene. In other words, the anti-sense suppression element sequence may be at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5% or 100% complementary to the targeted GA oxidase gene or mRNA.

[0073] For suppression of GA oxidase gene(s) using an inverted repeat or a transcribed dsRNA, a transcribable DNA sequence or suppression element may comprise a sense sequence that comprises a segment or portion of a targeted GA oxidase gene and an anti-sense sequence that is complementary to a segment or portion of the targeted GA oxidase gene, wherein the sense and anti-sense DNA sequences are arranged in tandem. The sense and / or anti-sense sequences, respectively, may each be less than 100% identical or complementary to a segment or portion of the targeted GA oxidase gene as described above. The sense and anti-sense sequences may be separated by a spacer sequence, such that the RNA molecule transcribed from the suppression element forms a stem, loop or stem-loop structure between the sense and anti-sense sequences. The suppression element may instead comprise multiple sense and anti-sense sequences that are arranged in tandem, which may also be separated by one or more spacer sequences. Such suppression elements comprising multiple sense and anti-sense sequences may be arranged as a series of sense sequences followed by a series of anti-sense sequences, or as a series of tandemly arranged sense and anti-sense sequences. Alternatively, one or more sense DNA sequences may be expressed separately from the one or more anti-sense sequences (i.e., one or more sense DNAsequences may be expressed from a first transcribable DNA sequence, and one or more anti-sense DNA sequences may be expressed from a second transcribable DNA sequence, wherein the first and second transcribable DNA sequences are expressed as separate transcripts).

[0074] For suppression of GA oxidase gene(s) using a microRNA (miRNA), the transcribable DNA sequence or suppression element may comprise a DNA sequence derived from a miRNA sequence native to a virus or eukaryote, such as an animal or plant, or modified or derived from such a native miRNA sequence. Such native or native-derived miRNA sequences may form a fold back structure and serve as a scaffold for the precursor miRNA (pre-miRNA), and may correspond to the stem region of a native miRNA precursor sequence, such as from a native (or native-derived) primary -miRNA (pri-miRNA) or pre-miRNA sequence. However, in addition to these native or native-derived miRNA scaffold or preprocessed sequences, engineered or synthetic miRNAs of the present embodiments further comprise a sequence corresponding to a segment or portion of the targeted GA oxidase gene(s). Thus, in addition to the pre-processed or scaffold miRNA sequences, the suppression element may further comprise a sense and / or anti-sense sequence that corresponds to a segment or portion of a targeted GA oxidase gene, and / or a sequence that is complementary thereto, although one or more sequence mismatches may be tolerated.

[0075] Engineered miRNAs are useful for targeted gene suppression with increased specificity. See, e.g., Parizotto et al., Genes Dev. 18:2237-2242 (2004), and U.S. Patent Application Publication Nos. 2004 / 0053411, 2004 / 0268441, 2005 / 0144669, and 2005 / 0037988, the contents and disclosures of which are incorporated herein by reference. miRNAs are non-protein coding RNAs. When a miRNA precursor molecule is cleaved, a mature miRNA is formed that is typically from about 19 to about 25 nucleotides in length (commonly from about 20 to about 24 nucleotides in length in plants), such as 19, 20, 21, 22, 23, 24, or 25 nucleotides in length, and has a sequence corresponding to the gene targeted for suppression and / or its complement. The mature miRNA hybridizes to target mRNA transcripts and guides the binding of a complex of proteins to the target transcripts, which may function to inhibit translation and / or result in degradation of the transcript, thus negatively regulating or suppressing expression of the targeted gene. miRNA precursors are also useful in plants for directing in-phase production of siRNAs, trans-acting siRNAs (ta-siRNAs), in a process that requires a RNA-dependent RNA polymerase to cause suppression of a target gene. See, e.g., Allen et al., Cell 121 :207-221 (2005),Vaucheret Science STKE, 2005:pe43 (2005), and Yoshikawa et al. Genes Dev., 19:2164-2175 (2005), the contents and disclosures of which are incorporated herein by reference.

[0076] Plant miRNAs regulate their target genes by recognizing and binding to a complementary or near-perfectly complementary sequence (miRNA recognition site) in the target mRNA transcript, followed by cleavage of the transcript by RNase III enzymes, such as ARGONAUTE1. In plants, certain mismatches between a given miRNA recognition site and the corresponding mature miRNA are typically not tolerated, particularly mismatched nucleotides at positions 10 and 11 of the mature miRNA. Positions within the mature miRNA are given in the 5' to 3' direction. Perfect complementarity between a given miRNA recognition site and the corresponding mature miRNA is usually required at positions 10 and 11 of the mature miRNA. See, for example, Franco-Zorrilla et al. (2007) Nature Genetics, 39: 1033-1037; and Axtell et al. (2006) Cell, 127:565-577.

[0077] Many microRNA genes (MIR genes) have been identified and made publicly available in a database (“miRBase”, available online at microrna.sanger.ac.uk / sequences; also see Griffiths-Jones et al. (2003) Nucleic Acids Res., 31 :439-441). MIR genes have been reported to occur in intergenic regions, both isolated and in clusters in the genome, but can also be located entirely or partially within introns of other genes (both protein-coding and non-protein-coding). For a review of miRNA biogenesis, see Kim (2005) Nature Rev. Mol. Cell. Biol., 6:376-385. Transcription of MIR genes can be, at least in some cases, under promotional control of a MIR gene’s own promoter. The primary transcript, termed a “pri-miRNA”, can be quite large (several kilobases) and can be polycistronic, containing one or more pre-miRNAs (fold-back structures containing a stem-loop arrangement that is processed to the mature miRNA) as well as the usual 5’ “cap” and polyadenylated tail of an mRNA. See, for example, FIG. 1 in Kim (2005) Nature Rev. Mol. Cell. Biol., 6:376-385.

[0078] Transgenic expression of miRNAs (whether a naturally occurring sequence or an artificial sequence) can be employed to regulate expression of the miRNA’ s target gene or genes. Recognition sites of miRNAs have been validated in all regions of a mRNA, including the 5’ untranslated region, coding region, intron region, and 3’ untranslated region, indicating that the position of the miRNA target or recognition site relative to the coding sequence may not necessarily affect suppression (see, e.g., Jones-Rhoades and Bartel (2004). Mol. Cell, 14:787-799, Rhoades et al. (2002) Cell, 110:513-520, Allen et al. (2004) Nat. Genet., 36: 1282-1290, Sunkarand Zhu (2004) Plant Cell, 16:2001-2019). miRNAs are important regulatory elements in eukaryotes, and transgenic suppression with miRNAs is a useful tool for manipulating biological pathways and responses. A description of native miRNAs, their precursors, recognition sites, and promoters is provided in U.S. Patent Application Publication No. 2006 / 0200878, the contents and disclosures of which are incorporated herein by reference.

[0079] Designing an artificial miRNA sequence can be achieved by substituting nucleotides in the stem region of a miRNA precursor with a sequence that is complementary to the intended target, as demonstrated, for example, by Zeng et al. (2002) Mol. Cell, 9: 1327-1333. According to many embodiments, the target may be a sequence of a GA20 oxidase gene or a GA3 oxidase gene. One non-limiting example of a general method for determining nucleotide changes in a native miRNA sequence to produce an engineered miRNA precursor for a target of interest includes the following steps: (a) Selecting a unique target sequence of at least 18 nucleotides specific to the target gene, e.g., by using sequence alignment tools such as BLAST (see, for example, Altschul et al. (1990) J. Mol. Biol., 215:403-410; Altschul et al. (1997) Nucleic Acids Res., 25:3389-3402); cDNA and / or genomic DNA sequences may be used to identify target transcript orthologues and any potential matches to unrelated genes, thereby avoiding unintentional silencing or suppression of non-target sequences; (b) Analyzing the target gene for undesirable sequences (e.g., matches to sequences from non-target species), and score each potential target sequence for GC content, Reynolds score (see Reynolds et al. (2004) Nature Biotechnol., 22:326-330), and functional asymmetry characterized by a negative difference in free energy (“AAG”) (see Khvorova et al. (2003) Cell, 115:209-216). Preferably, target sequences (e.g., 19-mers) may be selected that have all or most of the following characteristics: (1) a Reynolds score > 4, (2) a GC content between about 40% to about 60%, (3) a negative AAG, (4) a terminal adenosine, (5) lack of a consecutive run of 4 or more of the same nucleotide; (6) a location near the 3’ terminus of the target gene; (7) minimal differences from the miRNA precursor transcript. In one aspect, a non-coding RNA molecule used herein to suppress a target gene (e.g., a GA20 or GA3 oxidase gene) is designed to have a target sequence exhibiting one or more, two or more, three or more, four or more, or five or more of the foregoing characteristics. Positions at every third nucleotide of a suppression element may be important in influencing RNAi efficacy; for example, an algorithm, “siExplorer” is publicly available at rna.chem.t.u-tokyo. ac.jp / siexplorer.htm (see Katoh and Suzuki (2007) Nucleic Acids Res., 10.1093 / nar / gkll l20); (c) Determining a reverse complement of the selected target sequence (e.g., 19-mer) to use in making a modified mature miRNA. Relative to a 19-mersequence, an additional nucleotide at position 20 may be matched to the selected target or recognition sequence, and the nucleotide at position 21 may be chosen to either be unpaired to prevent spreading of silencing on the target transcript or paired to the target sequence to promote spreading of silencing on the target transcript; and (d) Transforming the artificial miRNA into a plant.

[0080] According to embodiments of the present disclosure, a recombinant DNA molecule, construct or vector is provided comprising a transcribable DNA sequence or suppression element encoding a miRNA or precursor miRNA molecule for targeted suppression of a GA oxidase gene(s). Such a transcribable DNA sequence and suppression element may comprise a sequence of at least 19 nucleotides in length that corresponds to one or more GA oxidase gene(s) and / or a sequence complementary to one or more GA oxidase gene(s), although one or more sequence mismatches or non-base-paired nucleotides may be tolerated.

[0081] GA oxidase gene(s) may also be suppressed using one or more small interfering RNAs (siRNAs). The siRNA pathway involves the non-phased cleavage of a longer double-stranded RNA intermediate (“RNA duplex”) into small interfering RNAs (siRNAs). The size or length of siRNAs ranges from about 19 to about 25 nucleotides or base pairs, but common classes of siRNAs include those containing 21 or 24 base pairs. Thus, a transcribable DNA sequence or suppression element may encode a RNA molecule that is at least about 19 to about 25 nucleotides (or more) in length, such as at least 19, 20, 21, 22, 23, 24, or 25 nucleotides in length. For siRNA suppression, a recombinant DNA molecule, construct or vector is thus provided comprising a transcribable DNA sequence and suppression element encoding a siRNA molecule for targeted suppression of a GA oxidase gene(s). Such a transcribable DNA sequence and suppression element may be at least 19 nucleotides in length and have a sequence corresponding to one or more GA oxidase gene(s), and / or a sequence complementary to one or more GA oxidase gene(s).

[0082] GA oxidase gene(s) may also be suppressed using one or more trans-acting small interfering RNAs (ta-siRNAs). In the ta-siRNA pathway, miRNAs serve to guide in-phase processing of siRNA primary transcripts in a process that requires an RNA-dependent RNA polymerase for production of a double-stranded RNA precursor. ta-siRNAs are defined by lack of secondary structure, a miRNA target site that initiates production of double-stranded RNA, requirements of DCL4 and an RNA-dependent RNA polymerase (RDR6), and production of multiple perfectly phased ~21-nt small RNAs with perfectly matched duplexes with 2-nucleotide3' overhangs (see Allen et al. (2005) Cell, 121 :207-221). The size or length of ta-siRNAs ranges from about 20 to about 22 nucleotides or base pairs, but are mostly commonly 21 base pairs. Thus, a transcribable DNA sequence or suppression element of the present invention may encode a RNA molecule that is at least about 20 to about 22 nucleotides in length, such as 20, 21, or 22 nucleotides in length. For ta-siRNA suppression, a recombinant DNA molecule, construct or vector is thus provided comprising a transcribable DNA sequence or suppression element encoding a ta-siRNA molecule for targeted suppression of a GA oxidase gene(s). Such a transcribable DNA sequence and suppression element may be at least 20 nucleotides in length and have a sequence corresponding to one or more GA oxidase gene(s) and / or a sequence complementary to one or more GA oxidase gene(s). For methods of constructing suitable ta-siRNA scaffolds, see, e.g., U.S. Patent No. 9,309,512, which is incorporated herein by reference in its entirety.

[0083] According to embodiments of the present invention, a recombinant DNA molecule, vector or construct is provided comprising a transcribable DNA sequence encoding a non-coding RNA molecule that binds or hybridizes to a target mRNA in a plant cell, wherein the target mRNA molecule encodes a GA20 or GA3 oxidase gene, and wherein the transcribable DNA sequence is operably linked to a constitutive or tissue-specific or tissue-preferred promoter. In addition to targeting a mature mRNA sequence, a non-coding RNA molecule may instead target an intronic sequence of a GA oxidase gene or mRNA transcript, or a GA oxidase mRNA sequence overlapping coding and non-coding sequences. According to other embodiments, a recombinant DNA molecule, vector or construct is provided comprising a transcribable DNA sequence encoding a non-coding RNA (precursor) molecule that is cleaved or processed into a mature non-coding RNA molecule that binds or hybridizes to a target mRNA in a plant cell, wherein the target mRNA molecule encodes a GA20 or GA3 oxidase protein, and wherein the transcribable DNA sequence is operably linked to a constitutive or tissue-specific or tissue-preferred promoter. For purposes of the present disclosure, a “non-coding RNA molecule” is a RNA molecule that does not encode a protein. Non-limiting examples of a non-coding RNA molecule include a microRNA (miRNA), a miRNA precursor, a small interfering RNA (siRNA), a siRNA precursor, a small RNA (18-26 nt in length) and precursors encoding the same, a heterochromatic siRNA (hc-siRNA), a Pi wi -interacting RNA (piRNA), a hairpin double strand RNA (hairpin dsRNA), a trans-acting siRNA (ta-siRNA), a naturally occurring antisense siRNA (nat-siRNA), a CRISPR RNA (crRNA), a tracer RNA (tracrRNA), a guide RNA (gRNA), and a single-guide RNA (sgRNA).

[0084] According to embodiments of the present disclosure, suitable tissue-specific or tissue preferred promoters for expression of a GA20 oxidase or GA3 oxidase suppression element may include those promoters that drive or cause expression of its associated suppression element or sequence at least in the vascular and / or leaf tissue(s) of a corn or cereal plant, or possibly other tissues in the case of GA3 oxidase. Expression of the GA oxidase suppression element or construct with a tissue-specific or tissue-preferred promoter may also occur in other tissues of the cereal or corn plant outside of the vascular and leaf tissues, but active GA levels in the developing reproductive tissues of the plant (particularly in the female reproductive organ or ear) are preferably not significantly reduced or impacted (relative to wild type or control plants), such that development of the female organ or ear may proceed normally in the transgenic plant without off-types in the ear and a loss in yield potential.

[0085] Any vascular promoters known in the art may potentially be used as the tissue-specific or tissue-preferred promoter. Examples of vascular promoters include the RTBV promoter (see, e.g., SEQ ID NO: 65), a known sucrose synthase gene promoter, such as a corn sucrose synthase-1 (Susi or Shi) promoter (see, e.g., SEQ ID NO: 67), a corn Shi gene paralog promoter, a barley sucrose synthase promoter (Ssl) promoter, a rice sucrose synthase-1 (RSsl) promoter (see, e.g., SEQ ID NO: 68), or a rice sucrose synthase-2 (RSs2) promoter (see, e.g., SEQ ID NO: 69), a known sucrose transporter gene promoter, such as a rice sucrose transporter promoter (SUT1) (see, e.g., SEQ ID NO: 70), or various known viral promoters, such as a Commelina yellow mottle virus (CoYMV) promoter, a wheat dwarf geminivirus (WDV) large intergenic region (LIR) promoter, a maize streak geminivirus (MSV) coat protein (CP) promoter, or a rice yellow stripe 1 (YSl)-like or OsYSL2 promoter (SEQ ID NO: 71), and any functional sequence portion or truncation of any of the foregoing promoters with a similar pattern of expression, such as a truncated RTBV promoter (see, e.g., SEQ ID NO: 66).

[0086] Any leaf promoters known in the art may potentially be used as the tissue-specific or tissue-preferred promoter. Examples of leaf promoters include a com pyruvate phosphate dikinase or PPDK promoter (see, e.g., SEQ ID NO: 72), a corn fructose 1,6 bisphosphate aldolase or FDA promoter (see, e.g., SEQ ID NO: 73), and a rice Nadh-Gogat promoter (see, e.g., SEQ ID NO: 74), and any functional sequence portion or truncation of any of the foregoing promoters with a similar pattern of expression. Other examples of leaf promoters from monocot plant genes include a ribulose biphosphate carboxylase (RuBisCO) or RuBisCO small subunit (RBCS) promoter, achlorophyll a / b binding protein gene promoter, a phosphoenolpyruvate carboxylase (PEPC) promoter, and a Myb gene promoter, and any functional sequence portion or truncation of any of these promoters with a similar pattern of expression.

[0087] Any other vascular and / or leaf promoters known in the art may also be used, including promoter sequences from related genes (e.g., sucrose synthase, sucrose transporter, and viral gene promoter sequences) from the same or different plant species or virus that have a similar pattern of expression. Further provided are promoter sequences with a high degree of homology to any of the foregoing. For example, a vascular promoter may comprise a DNA sequence that is at least at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5% or 100% identical to one or more of SEQ ID NOs: 65, 66, 67, 68, 69, 70, and 71, any functional sequence portion or truncation thereof, and / or any sequence complementary to any of the foregoing sequences; a leaf promoter may comprise, for example, a DNA sequence that is at least at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5% or 100% identical to one or more of SEQ ID NOs: 72, 73, and 74, any functional sequence portion or truncation thereof, and / or any sequence complementary to any of the foregoing sequences; and a constitutive promoter may comprise a DNA sequence that is at least at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5% or 100% identical to one or more of SEQ ID NOs: 75, 76, 77, 78, 79, 80, 81, 82, and 83, any functional sequence portion or truncation thereof, and / or any sequence complementary to any of the foregoing sequences. Examples of vascular and / or leaf promoters may further include other known, engineered and / or later-identified promoter sequences shown to have a pattern of expression in vascular and / or leaf tissue(s) of a cereal or com plant. Furthermore, any known or later-identified constitutive promoter may also be used for expression of a GA20 oxidase or GA3 oxidase suppression element. Common examples of constitutive promoters are provided below.

[0088] As understood in the art, the term “promoter” may generally refer to a DNA sequence that contains an RNA polymerase binding site, transcription start site, and / or TATA box and assists or promotes the transcription and expression of an associated transcribable polynucleotide sequence and / or gene (or transgene). A promoter may be synthetic or artificial and / or engineered, varied or derived from a known or naturally occurring promoter sequence. A promoter may be a chimeric promoter comprising a combination of two or more heterologous sequences. A promoterof the present invention may thus include variants of promoter sequences that are similar in composition, but not identical to, other promoter sequence(s) known or provided herein. A promoter may be classified according to a variety of criteria relating to the pattern of expression of an associated coding or transcribable sequence or gene (including a transgene) operably linked to the promoter, such as constitutive, developmental, tissue-specific, inducible, etc. Promoters that drive expression in all or nearly all tissues of the plant are referred to as “constitutive” promoters. However, the expression level with a “constitutive promoter” is not necessarily uniform across different tissue types and cells. Promoters that drive expression during certain periods or stages of development are referred to as “developmental” promoters. Promoters that drive enhanced expression in certain tissues of the plant relative to other plant tissues are referred to as “tissue-enhanced” or “tissue-preferred” promoters. Thus, a “tissue-preferred” promoter causes relatively higher or preferential or predominant expression in a specific tissue(s) of the plant, but with lower levels of expression in other tissue(s) of the plant. Promoters that express within a specific tissue(s) of the plant, with little or no expression in other plant tissues, are referred to as “tissue-specific” promoters. A tissue-specific or tissue-preferred promoter may also be defined in terms of the specific or preferred tissue(s) in which it drives expression of its associated transcribable DNA sequence or suppression element. For example, a promoter that causes specific expression in vascular tissues may be referred to as a “vascular-specific promoter”, whereas a promoter that causes preferential or predominant expression in vascular tissues may be referred to as a “vascular-preferred promoter”. Likewise, a promoter that causes specific expression in leaf tissues may be referred to as a “leaf-specific promoter”, whereas a promoter that causes preferential or predominant expression in leaf tissues may be referred to as a “leaf-preferred promoter”. An “inducible” promoter is a promoter that initiates transcription in response to an environmental stimulus such as cold, drought or light, or other stimuli, such as wounding or chemical application. A promoter may also be classified in terms of its origin, such as being heterologous, homologous, chimeric, synthetic, etc. A “heterologous” promoter is a promoter sequence having a different origin relative to its associated transcribable sequence, coding sequence, or gene (or transgene), and / or not naturally occurring in the plant species to be transformed, as defined above.

[0089] Several of the GA oxidases in cereal plants consist of a family of related GA oxidase genes. For example, corn has a family of at least nine GA20 oxidase genes that includes GA20 oxidase_l, GA20 oxidase_2, GA20 oxidase_3, GA20 oxidase_4, GA20 oxidase_5, GA20oxidase_6, GA20 oxidase_7, GA20 oxidase_8, and GA20 oxidase_9. However, there are three known or potential GA3 oxidase genes in corn, GA3 oxidase l, GA3 oxidase_2, and GA3 oxidase_3. The DNA and protein sequences by SEQ ID NOs for each of these GA20 oxidase genes are provided in Table 1, and the DNA and protein sequences by SEQ ID NOs for each of these GA3 oxidase genes are provided in Table 2.Table 1. DNA and protein sequences by sequence identifier for GA20 oxidase genes in corn.Table 2. DNA and protein sequences by sequence identifier for GA3 oxidase genes in corn.

[0090] The genomic DNA sequence of GA20 oxidase_3 is provided in SEQ ID NO: 34, and the genomic DNA sequence of GA20 oxidase_5 is provided in SEQ ID NO: 35. For the GA20 oxidase_3 gene, SEQ ID NO: 34 provides 3000 nucleotides upstream of the GA20 oxidase_35’-UTR (nucleotides 1-3000); nucleotides 3001-3096 correspond to the 5’-UTR; nucleotides 3097-3665 correspond to the first exon; nucleotides 3666-3775 correspond to the first intron; nucleotides 3776-4097 correspond to the second exon; nucleotides 4098-5314 correspond to the second intron; nucleotides 5315-5584 correspond to the third exon; and nucleotides 5585-5800 correspond to the 3’-UTR. SEQ ID NO: 34 also provides 3000 nucleotides downstream of the end of the 3’-UTR (nucleotides 5801-8800). For the GA20 oxidase_5 gene, SEQ ID NO: 35 provides 3000 nucleotides upstream of the GA20 oxidase_5 start codon (nucleotides 1-3000); nucleotides 3001-3791 correspond to the first exon; nucleotides 3792-3906 correspond to the first intron; nucleotides 3907-4475 correspond to the second exon; nucleotides 4476-5197 correspond to the second intron; nucleotides 5198-5473 correspond to the third exon; and nucleotides 5474-5859 correspond to the 3’-UTR. SEQ ID NO: 35 also provides 3000 nucleotides downstream of the end of the 3’-UTR (nucleotides 5860-8859).

[0091] The genomic DNA sequence of GA3 oxidase l is provided in SEQ ID NO: 36, 168 and 174, the genomic DNA sequence of GA3 oxidase_2 is provided in SEQ ID NO: 37, 169 and 175, and the genomic DNA sequence of GA3 oxidase_3 is provided in SEQ ID NO: 170 and 176. While SEQ ID NOs: 36 and 37 provide 5’-UTR, exon, intron and 3’-UTR sequences for the GA3 oxidase l and GA3 oxidase_2 genes, respectively, SEQ ID NOs: 168 and 174 and SEQ ID NOs: 169 and 175 further provide upstream and downstream genomic sequences and additional 5’ and 3’ UTR sequences for the GA3 oxidase l and GA3 oxidase_2 genes, respectively.

[0092] For the GA3 oxidase l gene, nucleotides 1-29 of SEQ ID NO: 36 correspond to the 5’-UTR; nucleotides 30-514 of SEQ ID NO: 36 correspond to the first exon; nucleotides 515-879 of SEQ ID NO: 36 correspond to the first intron; nucleotides 880-1038 of SEQ ID NO: 36 correspond to the second exon; nucleotides 1039-1158 of SEQ ID NO: 36 correspond to the second intron; nucleotides 1159-1663 of SEQ ID NO: 36 correspond to the third exon; and nucleotides 1664-1788 of SEQ ID NO: 36 correspond to the 3’-UTR. Alternatively for the GA3 oxidase l gene, SEQ ID NO: 168 provides 3000 nucleotides upstream of the GA3 oxidase l 5 ’-UTR (nucleotides 1-3000); nucleotides 3001-3161 of SEQ ID NO: 168 correspond to the 5 ’-UTR; nucleotides 3162-3646 of SEQ ID NO: 168 correspond to the first exon; nucleotides 3647-4011 of SEQ ID NO: 168 correspond to the first intron; nucleotides 4012-4170 of SEQ ID NO: 168 correspond to the second exon; nucleotides 4171-4290 of SEQ ID NO: 168 correspond to the second intron; nucleotides 4291-4795 of SEQ ID NO: 168 correspond to the third exon; and nucleotides 4796-5406 of SEQ ID NO: 168 correspond to the 3’-UTR. SEQ ID NO: 168 alsoprovides 3000 nucleotides downstream of the end of the 3’-UTR (nucleotides 5407-8406). Alternatively for the GA3 oxidase l gene, SEQ ID NO: 174 provides 7620 nucleotides upstream of the GA3 oxidase l 5’-UTR (nucleotides 1-5620 of SEQ ID NO: 174 correspond to upstream intergenic sequence, and nucleotides 5621-7620 of SEQ ID NO: 174 correspond to the GA3 oxidase l promoter region); nucleotides 7621-8029 of SEQ ID NO: 174 correspond to the 5’-UTR; nucleotides 8030-8514 of SEQ ID NO: 174 correspond to the first exon; nucleotides 8515-8887 of SEQ ID NO: 174 correspond to the first intron; nucleotides 8888-9046 of SEQ ID NO: 174 correspond to the second exon; nucleotides 9047-9166 of SEQ ID NO: 174 correspond to the second intron; nucleotides 9167-9671 of SEQ ID NO: 174 correspond to the third exon; and nucleotides 9672-10276 of SEQ ID NO: 174 correspond to the 3’-UTR. SEQ ID NO: 174 also provides 3951 nucleotides of intergenic sequence downstream of the end of the 3’-UTR (nucleotides 10277-14227 of SEQ ID NO: 174).

[0093] For the GA3 oxidase_2 gene, nucleotides 1-38 of SEQ ID NO: 37 correspond to the 5-UTR; nucleotides 39-532 of SEQ ID NO: 37 correspond to the first exon; nucleotides 533-692 of SEQ ID NO: 37 correspond to the first intron; nucleotides 693-851 of SEQ ID NO: 37 correspond to the second exon; nucleotides 852-982 of SEQ ID NO: 37 correspond to the second intron; nucleotides 983-1445 of SEQ ID NO: 37 correspond to the third exon; and nucleotides 1446-1698 of SEQ ID NO: 37 correspond to the 3’-UTR. Alternatively for the GA3 oxidase_2 gene, SEQ ID NO: 169 provides 3000 nucleotides upstream of the GA3 oxidase_2 5’-UTR (nucleotides 1-3000); nucleotides 3001-3056 of SEQ ID NO: 169 correspond to the 5’-UTR; nucleotides 3057-3550 of SEQ ID NO: 169 correspond to the first exon; nucleotides 3551-3710 of SEQ ID NO: 169 correspond to the first intron; nucleotides 3711-3869 of SEQ ID NO: 169 correspond to the second exon; nucleotides 3870-3991 of SEQ ID NO: 169 correspond to the second intron; nucleotides 3992-4463 of SEQ ID NO: 169 correspond to the third exon; and nucleotides 4464-4581 of SEQ ID NO: 169 correspond to the 3’-UTR. SEQ ID NO: 169 also provides 3000 nucleotides downstream of the end of the 3’-UTR (nucleotides 4582-7581). Alternatively for the GA3 oxidase_2 gene, SEQ ID NO: 175 provides 7285 nucleotides upstream of the GA3 oxidase_2 5’-UTR (nucleotides 1-5385 of SEQ ID NO: 175 correspond to upstream intergenic sequence, and nucleotides 5386-7385 of SEQ ID NO: 175 correspond to the GA3 oxidase_2 promoter region); nucleotides 7386-7831 of SEQ ID NO: 175 correspond to the 5’-UTR; nucleotides 7832-7926 of SEQ ID NO: 175 correspond to the first exon; nucleotides 7927-8086 of SEQ ID NO: 175 correspond to the first intron; nucleotides 8087-8245 of SEQ ID NO: 175 correspond to the second exon; nucleotides 8246-8371 of SEQ ID NO: 175 correspond to the second intron; nucleotides8372-8861 of SEQ ID NO: 175 correspond to the third exon; and nucleotides 8862-8967 of SEQ ID NO: 175 correspond to the 3’-UTR. SEQ ID NO: 175 also provides 7630 nucleotides of intergenic sequence downstream of the end of the 3’-UTR (nucleotides 8968-16597 of SEQ ID NO: 175).

[0094] For the GA3 oxidase_3 gene, SEQ ID NO: 170 provides 3000 nucleotides upstream of the GA3 oxidase_3 5’-UTR (nucleotides 1-3000); nucleotides 3001-3130 of SEQ ID NO: 170 correspond to the 5’-UTR; nucleotides 3131-3483 of SEQ ID NO: 170 correspond to the first exon; nucleotides 3484-3582 of SEQ ID NO: 170 correspond to the first intron; nucleotides 3583-3907 of SEQ ID NO: 170 correspond to the second exon; nucleotides 3908-3998 of SEQ ID NO: 170 correspond to the second intron; nucleotides 3999-4274 of SEQ ID NO: 170 correspond to the third exon; and nucleotides 4275-4332 of SEQ ID NO: 170 correspond to the 3’-UTR. SEQ ID NO: 170 also provides 3000 nucleotides downstream of the end of the 3’-UTR (nucleotides 4333-7332). Alternatively for the GA3 oxidase_3 gene, SEQ ID NO: 176 provides 7546 nucleotides upstream of the GA3 oxidase_3 5’-UTR (nucleotides 1-5546 of SEQ ID NO: 176 correspond to upstream intergenic sequence, and nucleotides 5547-7546 of SEQ ID NO: 176 correspond to the GA3 oxidase_3 promoter region); nucleotides 7547-7751 of SEQ ID NO: 176 correspond to the 5’-UTR; nucleotides 7752-8104 of SEQ ID NO: 176 correspond to the first exon; nucleotides 8105-8205 of SEQ ID NO: 176 correspond to the first intron; nucleotides 8206-8530 of SEQ ID NO: 176 correspond to the second exon; nucleotides 8531-8621 of SEQ ID NO: 176 correspond to the second intron; nucleotides 8622-8903 of SEQ ID NO: 176 correspond to the third exon; and nucleotides 8904-9178 of SEQ ID NO: 176 correspond to the 3’-UTR. SEQ ID NO: 176 also provides 6176 nucleotides of intergenic sequence downstream of the end of the 3’-UTR (nucleotides 9179-15354 of SEQ ID NO: 176).

[0095] Note that for SEQ ID NOs: 174, 175 and 176, the nucleotide boundary between the upstream promoter and intergenic regions may not be exactly according to the coordinates above and that promoter, expression (e.g., enhancer or repressor) and / or regulatory element(s) for transcription also may be present in the upstream intergenic sequence of the respective gene.

[0096] In addition to phenotypic observations with targeting the GA20 oxidase_3 and / or GA20 oxidase_5 gene(s), or the GA3 oxidase gene(s), for suppression, a semi-dwarf phenotype is also observed with suppression of the GA20 oxidase_4 gene. The genomic DNA sequence of GA20 oxidase_4 is provided in SEQ ID NO: 38. For the GA oxidase_4 gene, SEQ ID NO: 38 provides nucleotides 1-1416 upstream of the 5’-UTR; nucleotides 1417-1543 of SEQ ID NO: 38correspond to the 5’-UTR; nucleotides 1544-1995 of SEQ ID NO: 38 correspond to the first exon; nucleotides 1996-2083 of SEQ ID NO: 38 correspond to the first intron; nucleotides 2084-2411 of SEQ ID NO: 38 correspond to the second exon; nucleotides 2412-2516 of SEQ ID NO: 38 correspond to the second intron; nucleotides 2517-2852 of SEQ ID NO: 38 correspond to the third exon; nucleotides 2853-3066 of SEQ ID NO: 38 correspond to the 3’-UTR; and nucleotides 3067-4465 of SEQ ID NO: 38 corresponds to genomic sequence downstream of to the 3’-UTR.

[0097] According to embodiments of the present disclosure, a recombinant DNA molecule, vector or construct is provided comprising a transcribable DNA sequence encoding a non-coding RNA molecule, wherein the non-coding RNA molecule comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least a segment or portion of a mRNA molecule (i) expressed from an endogenous GA oxidase gene and / or (ii) encoding an endogenous GA oxidase protein in the plant, wherein the transcribable DNA sequence is operably linked to a plant-expressible promoter, and wherein the plant is a cereal or corn plant.

[0098] According to some embodiments, a non-coding RNA molecule targets GA20 oxidase gene(s), such as GA20 oxidase_3 and / or GA20 oxidase_5 gene(s), for suppression and comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of one or more of SEQ ID NOs: 7, 8, 13 and 14. According to some embodiments, a non-coding RNA molecule is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA20 oxidase protein in the plant that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% identical to one or both of SEQ ID NOs: 9 and 15. According to further embodiments, a non-coding RNA molecule may comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA20 oxidase protein inthe plant that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% similar to one or both of SEQ ID NOs: 9 and 15. In addition to targeting a mature mRNA sequence (including either or both of the untranslated or exonic sequences), a non-coding RNA molecule may further target the intronic sequences of a GA20 oxidase gene or transcript.

[0099] According to some embodiments, a non-coding RNA molecule targets GA3 oxidase gene(s) for suppression and comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of one or more of SEQ ID NOs: 28, 29, 31, 32, 171 and 172. According to other embodiments, a non-coding RNA molecule is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA3 oxidase protein in the plant that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% identical to one or both of SEQ ID NOs: 30, 33 and 173. According to further embodiments, a non-coding RNA molecule may comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA3 oxidase protein in the plant that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% similar to one or both of SEQ ID NOs: 30, 33 and 173. In addition to targeting a mature mRNA sequence (including either or both of the untranslated or exonic sequences), a non-coding RNA molecule may further target the intronic sequences of a GA3 oxidase gene or transcript.

[0100] According to some embodiments, a non-coding RNA molecule targets GA20 oxidase_4 gene for suppression and comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides ofone or both of SEQ ID NOs: 10 and 11. According to other embodiments, a non-coding RNA molecule is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA20 oxidase protein in the plant that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% identical to one or both of SEQ ID NO: 12. According to further embodiments, a non-coding RNA molecule may comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA20 oxidase protein in the plant that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% similar to SEQ ID NOs: 12. In addition to targeting a mature mRNA sequence (including either or both of the untranslated or exonic sequences), a non-coding RNA molecule may further target the intronic sequences of a GA20 oxidase gene or transcript.

[0101] According to many embodiments, the non-coding RNA molecule encoded by the transcribable DNA sequence of the recombinant DNA molecule, vector or construct may be a precursor miRNA or siRNA that is processed or cleaved in a plant cell to form a mature miRNA or siRNA that targets a GA20 oxidase or GA3 oxidase gene.

[0102] According to embodiments of the present invention, GA levels may be reduced in the stalk or stem of a cereal or com plant by targeting only a limited subset of genes within a GA oxidase family for suppression, mutagenesis or editing. Without being bound by theory, it is proposed that targeting of a limited number of genes within a GA oxidase family for suppression may produce the short stature phenotype and resistance to lodging in transgenic plants, but without off-types in the reproductive or ear tissues of the plant due to differential expression among GA oxidase genes, sufficient compensation for the suppressed GA oxidase gene(s) by other GA oxidase gene(s) in those reproductive tissues, and / or incomplete suppression of the targeted GA oxidase gene(s). Thus, not only may off-types be avoided by limiting expression or suppression of GA oxidase gene(s) with a tissue-specific or tissue preferred promoter, it is proposed that a limited subset of GA oxidase genes (e.g., a limited number of GA20 oxidase genes) may be targeted forsuppression, such that the other GA oxidase genes within the same gene family (e.g., other GA20 oxidase genes) may compensate for loss of expression of the suppressed GA oxidase gene(s) in those tissues. Incomplete suppression of the targeted GA oxidase gene(s) may also allow for a sufficient level of expression of the targeted GA oxidase gene(s) in one or more tissues to avoid off-types or undesirable traits in the plant that would negatively affect crop yield, such as reproductive off-types or excessive shortening of plant height. Unlike complete loss-of-function mutations in a gene, suppression may allow for partial activity of the targeted gene to persist. Since the different GA20 oxidase genes have different patterns of expression in plants, targeting of a limited subset of GA20 oxidase genes for suppression may allow for modification of certain traits while avoiding off-types previously associated with GA mutants in cereal plants. In other words, the growth, developmental and reproductive traits or off-types previously associated with GA mutants in corn and other cereal crops may be decoupled by targeting only a limited number or subset (i.e., one or more, but not all) of the GA20 or GA3 oxidase genes and / or by incomplete suppression of a targeted GA oxidase gene. By transgenically targeting a subset of one or more endogenous GA3 or GA20 oxidase genes for suppression within a plant, a more pervasive pattern of expression (e.g., with a constitutive promoter) may be used to produce semi-dwarf plants without significant reproductive off-types and / or other undesirable traits in the plant, even with expression of the transgenic construct in reproductive tissue(s). Indeed, suppression elements and constructs are provided herein that selectively target the GA20 oxidase_3 and / or GA20 oxidase_5 genes (identified in Table 1 above) for suppression, which may be operably linked to a vascular, leaf and / or constitutive promoter.

[0103] With a suppression construct that only targets a limited subset of GA20 oxidase genes, such as the GA20 oxidase_3, GA20 oxidase_4, and / or GA20 oxidase_5 gene(s), or which targets the GA3 oxidase l, GA3 oxidase_2, and / or GA3 oxidase_3 gene(s), restricting the pattern of expression of the suppression element may be less crucial for obtaining normal reproductive development of the cereal or corn plant and avoidance of off-types in the female organ or ear due to compensation, etc., from the other GA20 and / or GA3 oxidase genes. Therefore, expression of a suppression construct and element, selectively or preferentially targeting, for instance, the GA20 oxidase_3 and / or GA20 oxidase_5 gene(s), the GA20 oxidase_4 gene, and / or the GA3 oxidase_l, GA3 oxidase_2, and / or GA3 oxidase_3 gene(s) in corn, or similar genes and homologs in other cereal plants, may be driven by a variety of different plant-expressible promoter types including constitutive and tissue-specific or tissue-preferred promoters, such as a vascular or leaf promoter, which may include, for example, the RTBV promoter introduced above e.g., a promotercomprising the RTBV (SEQ ID NO: 65) or truncated RTBV (SEQ ID NO: 66) sequence), and any other promoters that drive expression in tissues encompassing much or all of the vascular and / or leaf tissue(s) of a plant. Any known or later-identified constitutive promoter with a sufficiently high level of expression may also be used for expression of a suppression construct targeting a subset of GA20 and / or GA3 oxidase genes in com, particularly the GA20 oxidase_3 and / or GA20 oxidase_5 gene(s), the GA20 oxidase_4 gene, and / or the GA3 oxidase_l, GA3 oxidase_2, and / or GA3 oxidase_3 gene(s), or similar genes and homologs in other cereal plants.

[0104] Examples of constitutive promoters that may be used in monocot plants, such as cereal or com plants, include, for example, various actin gene promoters, such as a rice Actin 1 promoter (see, e.g., US Patent No. 5,641,876; see also SEQ ID NO: 75 or SEQ ID NO: 76) and a rice Actin 2 promoter (see, e.g., US Patent No. 6,429,357; see also, e.g., SEQ ID NO: 77 or SEQ ID NO: 78), a CaMV 35S or 19S promoter (see, e.g., US Patent No. 5,352,605; see also, e.g., SEQ ID NO: 79 for CaMV 35S), a maize ubiquitin promoter (see, e.g., US Patent No. 5,510,474), a Coix lacryma-jobi polyubiquitin promoter (see, e.g., SEQ ID NO: 80), a rice or maize Gos2 promoter (see, e.g., Pater et al., The Plant Journal, 2(6): 837-44 1992; see also, e.g., SEQ ID NO: 81 for the rice Gos2 promoter), a FMV 35S promoter (see, e.g., US Patent No. 6,372,211), a dual enhanced CMV promoter (see, e.g., US Patent No. 5,322,938), a MMV promoter (see, e.g., US Patent No. 6,420,547; see also, e.g., SEQ ID NO: 82), a PCL SV promoter (see, e.g., US Patent No. 5,850,019; see also, e.g., SEQ ID NO: 83), an Emu promoter (see, e.g., Last et al., Theor. Appl. Genet. 81 : 581 (1991); and Mcelroy et al., Mol. Gen. Genet. 231 : 150 (1991)), a tubulin promoter from maize, rice or other species, a nopaline synthase (nos) promoter, an octopine synthase (ocs) promoter, a mannopine synthase (mas) promoter, or a plant alcohol dehydrogenase (e.g., maize Adhl) promoter, any other promoters including viral promoters known or later-identified in the art to provide constitutive expression in a cereal or corn plant, any other constitutive promoters known in the art that may be used in monocot or cereal plants, and any functional sequence portion or truncation of any of the foregoing promoters.

[0105] A sufficient level of expression of a transcribable DNA sequence encoding a non-coding RNA molecule targeting a GA oxidase gene for suppression may be necessary to produce a short stature, semi-dwarf phenotype that resists lodging, since lower levels of expression may be insufficient to lower active GA levels in the plant to a sufficient extent to cause a significant phenotype. Thus, tissue-specific and tissue-preferred promoters that drive, etc., a moderate or strong level of expression of their associated transcribable DNA sequence in activeGA-producing tissue(s) of a plant may be preferred. Furthermore, such tissue-specific and tissue-preferred should drive, etc., expression of their associated transcribable DNA sequence during one or more vegetative stage(s) of plant development when the plant is growing and / or elongating including one or more of the following vegetative stage(s): VE, VI, V2, V3, V4, V5, V6, V7, V8, V9, V10, VI 1, V12, V13, V14, Vn, VT, such as expression at least during V3-V12, V4-V12, V5-V12, V6-V12, V7-V12, V8-V12, V3-V14, V5-V14, V6-V14, V7-V14, V8-V14, V9-V14, V10-V14, etc., or during any other range of vegetative stages when growth and / or elongation of the plant is occurring.

[0106] According to many embodiments, the plant-expressible promoter may preferably drive expression constitutively or in at least a portion of the vascular and / or leaf tissues of the plant. Different promoters driving expression of a suppression element targeting the endogenous GA20 oxidase_3 and / or GA20 oxidase_5 gene(s), the GA20 oxidase_4 gene, the GA3 oxidase_l, GA3 oxidase_2, and / or GA3 oxidase_3 gene(s) in corn, or similar genes and homologs in other cereal plants, may be effective at reducing plant height and increasing lodging resistance to varying degrees depending on their particular pattern and strength of expression in the plant. However, some tissue-specific and tissue-preferred promoters driving expression of a GA20 or GA3 oxidase suppression element in a plant may not produce a significant short stature or anti-lodging phenotypes due to the spatial-temporal pattern of expression of the promoter during plant development, and / or the amount or strength of expression of the promoter being too low or weak. Furthermore, some suppression constructs may only reduce and not eliminate expression of the targeted GA20 or GA3 oxidase gene(s) when expressed in a plant, and thus depending on the pattern and strength of expression with a given promoter, the pattern and level of expression of the GA20 or GA3 oxidase suppression construct with such a promoter may not be sufficient to produce an observable plant height and lodging resistance phenotype in plants.

[0107] According to present embodiments, a recombinant DNA molecule, vector or construct for suppression of one or more endogenous GA20 or GA3 oxidase gene(s) in a plant is provided comprising a transcribable DNA sequence encoding a non-coding RNA molecule, wherein the non-coding RNA molecule comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least a segment or portion of a mRNA molecule expressed from an endogenous GA oxidase gene and encoding an endogenous GA oxidase protein in the plant, wherein the transcribable DNA sequence is operably linked to a plant-expressible promoter, andwherein the plant is a cereal or com plant. As stated above, in addition to targeting a mature mRNA sequence, a non-coding RNA molecule may further target the intronic sequence(s) of a GA oxidase gene or transcript. According to many embodiments, a non-coding RNA molecule may target a GA20 oxidase_3 gene for suppression and comprise a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of SEQ ID NO: 7 or SEQ ID NO: 8. According to some embodiments, a non-coding RNA molecule targeting a GA20 oxidase_3 gene for suppression may be complementary to at least 19 consecutive nucleotides, but no more than 27 consecutive nucleotides, such as complementary to 19, 20, 21, 22, 23, 24, 25, 26, or 27 consecutive nucleotides, of SEQ ID NO: 7 or SEQ ID NO: 8. According to some embodiments, a non-coding RNA molecule may target a GA20 oxidase gene for suppression and comprise a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA20 oxidase protein in the plant that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% identical to SEQ ID NO: 9. According to further embodiments, a non-coding RNA molecule may comprise a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA20 oxidase protein that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% similar to SEQ ID NO: 9.

[0108] As mentioned above, a non-coding RNA molecule may target an intron sequence of a GA oxidase gene instead of, or in addition to, an exonic, 5’ UTR or 3’ UTR of the GA oxidase gene. Thus, a non-coding RNA molecule targeting the GA20 oxidase_3 gene for suppression may comprise a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of SEQ ID NO: 34, and / or of nucleotides3666-3775 or 4098-5314 of SEQ ID NO: 34. It is important to note that the sequences provided herein for the GA20 oxidase_3 gene may vary across the diversity of corn plants, lines and germplasms due to polymorphisms and / or the presence of different alleles of the gene. Furthermore, a GA20 oxidase_3 gene may be expressed as alternatively spliced isoforms that may give rise to different mRNA, cDNA and coding sequences that can affect the design of a suppression construct and non-coding RNA molecule. Thus, a non-coding RNA molecule targeting a GA20 oxidase_3 gene for suppression may be more broadly defined as comprising a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of SEQ ID NO: 34.

[0109] According to embodiments of the present disclosure, a recombinant DNA molecule, vector or construct for suppression of an endogenous GA20 oxidase_5 gene in a plant is provided comprising a transcribable DNA sequence encoding a non-coding RNA molecule, wherein the non-coding RNA molecule targeting the GA20 oxidase_5 gene for suppression comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of SEQ ID NO: 13 or SEQ ID NO: 14. According to some embodiments, a non-coding RNA molecule targeting the GA20 oxidase_5 gene for suppression may be complementary to at least 19 consecutive nucleotides, but no more than 27 consecutive nucleotides, such as complementary to 19, 20, 21, 22, 23, 24, 25, 26, or 27 consecutive nucleotides, of SEQ ID NO: 13 or SEQ ID NO: 14. According to some embodiments, a non-coding RNA molecule may target a GA20 oxidase gene for suppression comprise a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA20 oxidase protein in the plant that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% identical to SEQ ID NO: 15. According to further embodiments, a non-coding RNA molecule may comprise a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18,at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA20 oxidase protein that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% similar to SEQ ID NO: 15.

[0110] As mentioned above, a non-coding RNA molecule may target an intron sequence of a GA oxidase gene instead of, or in addition to, an exonic or untranslated region of the mature mRNA of the GA oxidase gene. Thus, a non-coding RNA molecule targeting the GA20 oxidase_5 gene for suppression may comprise a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of SEQ ID NO: 35, and / or of nucleotides 3792-3906 or 4476-5197 of SEQ ID NO: 35. The sequences provided herein for GA20 oxidase_5 may vary across the diversity of corn plants, lines and germplasms due to polymorphisms and / or the presence of different alleles of the gene. Furthermore, a GA20 oxidase_5 gene may be expressed as alternatively spliced isoforms that may give rise to different mRNA, cDNA and coding sequences that can affect the design of a suppression construct and non-coding RNA molecule. Thus, a non-coding RNA molecule targeting a GA20 oxidase_3 gene for suppression may be defined more broadly as comprising a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of SEQ ID NO: 35.

[0111] According to further embodiments, a recombinant DNA molecule, vector or construct for joint suppression of endogenous GA20 oxidase_3 and GA20 oxidase_5 genes in a plant is provided comprising a transcribable DNA sequence encoding a non-coding RNA molecule, wherein the non-coding RNA molecule targeting the GA20 oxidase_3 and GA20 oxidase_5 genes for suppression comprises a sequence that is (i) at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of SEQ ID NO: 7 and / or SEQ ID NO: 8, and (ii) at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16,at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of SEQ ID NO: 13 and / or SEQ ID NO: 14. According to some of these embodiments, the non-coding RNA molecule jointly targeting the GA20 oxidase_3 and GA20 oxidase_5 genes for suppression may be complementary to at least 19 consecutive nucleotides, but no more than 27 consecutive nucleotides, such as complementary to 19, 20, 21, 22, 23, 24, 25, 26, or 27 consecutive nucleotides, of (i) SEQ ID NO: 7 (and / or SEQ ID NO: 8) and (ii) SEQ ID NO: 13 (and / or SEQ ID NO: 14). According to many embodiments, the non-coding RNA molecule jointly targeting the GA20 oxidase_3 and GA20 oxidase_5 genes for suppression comprises a sequence that is (i) at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA20 oxidase protein in the plant that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% identical to SEQ ID NO: 9, and (ii) at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA20 oxidase protein in the plant that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% identical to SEQ ID NO: 15. As mentioned above, the non-coding RNA molecule may target an intron sequence of a GA oxidase gene. Thus, the non-coding RNA molecule may target an intron sequence(s) of one or both of the GA20 oxidase_3 and / or GA20 oxidase_5 gene(s) as identified above.

[0112] According to particular embodiments, the non-coding RNA molecule encoded by a transcribable DNA sequence comprises (i) a sequence that is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to SEQ ID NO: 39, 41, 43 or 45, and / or (ii) a sequence or suppression element encoding a non-coding RNA molecule comprising a sequence that is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% identical to SEQ ID NO: 40, 42, 44 or 46. According to some embodiments, the non-coding RNA molecule encoded by a transcribable DNA sequence may comprise a sequence with one or more mismatches, such as 1, 2, 3, 4, 5 or more complementary mismatches, relative to the sequence of a target or recognition site of a targeted GA20 oxidase gene mRNA,such as a sequence that is nearly complementary to SEQ ID NO: 40 but with one or more complementary mismatches relative to SEQ ID NO: 40. According to a particular embodiment, the non-coding RNA molecule encoded by the transcribable DNA sequence comprises a sequence that is 100% identical to SEQ ID NO: 40, which is 100% complementary to a target sequence within the cDNA and coding sequences of the GA20 oxidase_3 (z.e., SEQ ID NOs: 7 and 8, respectively), and / or to a corresponding sequence of a mRNA encoded by an endogenous GA20 oxidase_3 gene. However, the sequence of a non-coding RNA molecule encoded by a transcribable DNA sequence that is 100% identical to SEQ ID NO: 40, 42, 44 or 46 may not be perfectly complementary to a target sequence within the cDNA and coding sequences of the GA20 oxidase_5 gene (z.e., SEQ ID NOs: 13 and 14, respectively), and / or to a corresponding sequence of a mRNA encoded by an endogenous GA20 oxidase_5 gene. For example, the closest complementary match between the non-coding RNA molecule or miRNA sequence in SEQ ID NO: 40 and the cDNA and coding sequences of the GA20 oxidase_5 gene may include one mismatch at the first position of SEQ ID NO: 39 (z.e., the “C” at the first position of SEQ ID NO: 39 is replaced with a “G”; i.e., GTCCATCATGCGGTGCAACTA). However, the non-coding RNA molecule or miRNA sequence in SEQ ID NO: 40 may still bind and hybridize to the mRNA encoded by the endogenous GA20 oxidase_5 gene despite this slight mismatch.

[0113] According to embodiments of the present disclosure, a recombinant DNA molecule, vector or construct for suppression of one or more endogenous GA3 oxidase gene(s) in a plant is provided comprising a transcribable DNA sequence encoding a non-coding RNA molecule, wherein the non-coding RNA molecule comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least a segment or portion of a mRNA molecule expressed from an endogenous GA3 oxidase gene and encoding an endogenous GA3 oxidase protein in the plant, wherein the transcribable DNA sequence is operably linked to a plant-expressible promoter, and wherein the plant is a cereal or corn plant. In addition to targeting a mature mRNA sequence, a non-coding RNA molecule may further target the intronic sequences of a GA3 oxidase gene or transcript.

[0114] According to some embodiments, a non-coding RNA molecule may target a GA3 oxidase l gene for suppression and comprise a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21,at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of SEQ ID NO: 28 or SEQ ID NO: 29. According to some embodiments, a non-coding RNA molecule targeting a GA3 oxidase gene for suppression may be complementary to at least 19 consecutive nucleotides, but no more than 27 consecutive nucleotides, such as complementary to 19, 20, 21, 22, 23, 24, 25, 26, or 27 consecutive nucleotides, of SEQ ID NO: 28 or SEQ ID NO: 29. According to some embodiments, a non-coding RNA molecule targeting a GA3 oxidase gene for suppression comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA3 oxidase protein in the plant that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% identical to SEQ ID NO: 30. According to further embodiments, a non-coding RNA molecule may comprise a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA3 oxidase protein that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% similar to SEQ ID NO: 30.

[0115] As mentioned above, a non-coding RNA molecule may target an intron sequence of a GA3 oxidase gene instead of, or in addition to, an exonic, 5’ UTR or 3’ UTR of the GA oxidase gene. Thus, a non-coding RNA molecule targeting the GA3 oxidase l gene for suppression may comprise a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of SEQ ID NO: 36 and / or 168, of nucleotides 515-879 or 1039-1158 of SEQ ID NO: 36, and / or of nucleotides 3647-4011 or 4171-4290 of SEQ ID NO: 168. The sequences provided herein for GA3 oxidase l may vary across the diversity of corn plants, lines and germplasms due to polymorphisms and / or the presence of different alleles of the gene. Furthermore, a GA3 oxidase l gene may be expressed as alternatively spliced isoforms that may give rise to different mRNA, cDNA and coding sequences that can affect the design of a suppression construct and non-coding RNA molecule. Thus, anon-coding RNA molecule targeting a GA3 oxidase l gene for suppression may be defined more broadly as comprising a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of SEQ ID NO: 36 and / or 168.

[0116] According to some embodiments, a non-coding RNA molecule may target a GA3 oxidase_2 gene for suppression and comprise a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of SEQ ID NO: 31 or SEQ ID NO: 32. According to some embodiments, a non-coding RNA molecule targeting the GA3 oxidase gene for suppression may be complementary to at least 19 consecutive nucleotides, but no more than 27 consecutive nucleotides, such as complementary to 19, 20, 21, 22, 23, 24, 25, 26, or 27 consecutive nucleotides, of SEQ ID NO: 31 or SEQ ID NO: 32. According to some embodiments, a non-coding RNA molecule targeting the GA3 oxidase gene for suppression comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA3 oxidase protein in the plant that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% identical to SEQ ID NO: 33. According to further embodiments, a non-coding RNA molecule may comprise a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA3 oxidase protein that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% similar to SEQ ID NO: 33.

[0117] As mentioned above, a non-coding RNA molecule may target an intron sequence of a GA3 oxidase gene instead of, or in addition to, an exonic, 5’ UTR or 3’ UTR of the GA3 oxidasegene. Thus, a non-coding RNA molecule targeting the GA3 oxidase_2 gene for suppression may comprise a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of SEQ ID NO: 37 and / or 169, of nucleotides 533-692 or 852-982 of SEQ ID NO: 37, and / or of nucleotides 3551-3710 or 3870-3991 of SEQ ID NO: 169. The sequences provided herein for GA3 oxidase_2 may vary across the diversity of corn plants, lines and germplasms due to polymorphisms and / or the presence of different alleles of the gene. Furthermore, a GA3 oxidase_2 gene may be expressed as alternatively spliced isoforms that may give rise to different mRNA, cDNA and coding sequences that can affect the design of a suppression construct and non-coding RNA molecule. Thus, a non-coding RNA molecule targeting a GA3 oxidase_2 gene for suppression may be defined more broadly as comprising a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of SEQ ID NO: 37 and / or 169.

[0118] According to some embodiments, a non-coding RNA molecule may target a GA3 oxidase_3 gene for suppression and comprise a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of SEQ ID NO: 171 or SEQ ID NO: 172. According to some embodiments, a non-coding RNA molecule targeting the GA3 oxidase gene for suppression may be complementary to at least 19 consecutive nucleotides, but no more than 27 consecutive nucleotides, such as complementary to 19, 20, 21, 22, 23, 24, 25, 26, or 27 consecutive nucleotides, of SEQ ID NO: 171 or SEQ ID NO: 172. According to some embodiments, a non-coding RNA molecule targeting the GA3 oxidase gene for suppression comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA3 oxidase protein in the plant that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100%identical to SEQ ID NO: 173. According to further embodiments, a non-coding RNA molecule may comprise a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA3 oxidase protein that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% similar to SEQ ID NO: 173.

[0119] As mentioned above, a non-coding RNA molecule may target an intron sequence of a GA3 oxidase gene instead of, or in addition to, an exonic, 5’ UTR or 3’ UTR of the GA3 oxidase gene. Thus, a non-coding RNA molecule targeting the GA3 oxidase_3 gene for suppression may comprise a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of SEQ ID NO: 170 and / or of nucleotides 3484-3582 or 3908-3998 of SEQ ID NO: 170. The sequences provided herein for GA3 oxidase_3 may vary across the diversity of corn plants, lines and germplasms due to polymorphisms and / or the presence of different alleles of the gene. Furthermore, a GA3 oxidase_3 gene may be expressed as alternatively spliced isoforms that may give rise to different mRNA, cDNA and coding sequences that can affect the design of a suppression construct and non-coding RNA molecule. Thus, a non-coding RNA molecule targeting a GA3 oxidase_3 gene for suppression may be defined more broadly as comprising a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of SEQ ID NO: 170.

[0120] According to particular embodiments, a non-coding RNA molecule encoded by a transcribable DNA sequence for targeting a GA3 oxidase gene comprises (i) a sequence that is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to SEQ ID NO: 57 or 59, and / or (ii) a sequence or suppression element encoding a non-coding RNA molecule comprising a sequence that is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% identical to SEQ ID NO: 58 or 60. According tosome embodiments, the non-coding RNA molecule encoded by a transcribable DNA sequence may comprise a sequence with one or more mismatches, such as 1, 2, 3, 4, 5 or more complementary mismatches, relative to the sequence of a target or recognition site of a targeted GA3 oxidase gene mRNA, such as a sequence that is nearly complementary to SEQ ID NO: 57 or 59 but with one or more complementary mismatches relative to SEQ ID NO: 57 or 59. According to a particular embodiment, the non-coding RNA molecule encoded by the transcribable DNA sequence comprises a sequence that is 100% identical to SEQ ID NO: 58 or 60, which is 100% complementary to a target sequence within the cDNA and coding sequences of a GA3 oxidase l or GA3 oxidase_2 gene in corn (z.e., SEQ ID NOs: 28, 29, 31 and / or 32), and / or to a corresponding sequence of a mRNA encoded by an endogenous GA3 oxidase l or GA3 oxidase_2 gene.

[0121] According to some embodiments, a non-coding RNA molecule may target a GA20 oxidase_4 gene for suppression and comprise a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of SEQ ID NO: 10 or SEQ ID NO: 11. According to some embodiments, a non-coding RNA molecule targeting a GA20 oxidase_4 gene for suppression may be complementary to at least 19 consecutive nucleotides, but no more than 27 consecutive nucleotides, such as complementary to 19, 20, 21, 22, 23, 24, 25, 26, or 27 consecutive nucleotides, of SEQ ID NO: 10 or SEQ ID NO: 11. According to some embodiments, a non-coding RNA molecule targeting the GA20 oxidase gene for suppression comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA20 oxidase protein in the plant that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% identical to SEQ ID NO: 12. According to further embodiments, a non-coding RNA molecule may comprise a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA20 oxidase protein that is at least 80%, at least 85%, at least 90%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% similar to SEQ ID NO: 12.

[0122] As mentioned above, a non-coding RNA molecule may target an intron sequence of a GA20 oxidase gene instead of, or in addition to, an exonic, 5’ UTR or 3’ UTR of the GA20 oxidase gene. Thus, a non-coding RNA molecule targeting a GA20 oxidase_4 gene for suppression may comprise a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of SEQ ID NO: 38, and / or of nucleotides 1996-2083 or 2412-2516 of SEQ ID NO: 38. The sequences provided herein for GA20 oxidase_4 may vary across the diversity of corn plants, lines and germplasms due to polymorphisms and / or the presence of different alleles of the gene. Furthermore, a GA20 oxidase_4 gene may be expressed as alternatively spliced isoforms that may give rise to different mRNA, cDNA and coding sequences that can affect the design of a suppression construct and non-coding RNA molecule. Thus, a non-coding RNA molecule targeting a GA20 oxidase_4 gene for suppression may be defined more broadly as comprising a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of SEQ ID NO: 38.

[0123] According to particular embodiments, a non-coding RNA molecule encoded by a transcribable DNA sequence for targeting a GA20 oxidase_4 gene comprises (i) a sequence that is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to SEQ ID NO: 61, and / or (ii) a sequence or suppression element encoding a non-coding RNA molecule comprising a sequence that is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% identical to SEQ ID NO: 62. According to some embodiments, the non-coding RNA molecule encoded by a transcribable DNA sequence may comprise a sequence with one or more mismatches, such as 1, 2, 3, 4, 5 or more complementary mismatches, relative to the sequence of a target or recognition site of a targeted GA20 oxidase gene mRNA, such as a sequence that is nearly complementary to SEQ ID NO: 61 but with one or more complementary mismatches relative to SEQ ID NO: 61. According to a particular embodiment, the non-coding RNA molecule encoded by the transcribable DNA sequence comprises a sequencethat is 100% identical to SEQ ID NO: 62, which is 100% complementary to a target sequence within the cDNA and coding sequences of a GA20 oxidase_4 gene in corn (z.e., SEQ ID NO: 10 or 11), and / or to a corresponding sequence of a mRNA encoded by an endogenous GA20 oxidase_4 gene.

[0124] According to embodiments of the present disclosure, a recombinant DNA construct is provided comprising a transcribable DNA sequence encoding a non-coding RNA molecule targeting an endogenous GA20 oxidase_3 and / or the GA20 oxidase_5 gene(s) for suppression, wherein the transcribable DNA sequence is operably linked to a constitutive, tissue-specific or tissue-preferred promoter, and wherein the transcribable DNA sequence causes the expression level of an endogenous GA20 oxidase_3 and / or the GA20 oxidase_5 gene(s) to become reduced or lowered in one or more tissue(s) of a plant transformed with the transcribable DNA sequence. Such a non-coding RNA molecule encoded by the transcribable DNA sequence may comprise a sequence that is (i) at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA20 oxidase protein in the plant that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% identical to SEQ ID NO: 9, and / or (ii) at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA20 oxidase protein in the plant that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% identical to SEQ ID NO: 15.

[0125] According to embodiments of the present disclosure, a recombinant DNA construct is provided comprising a transcribable DNA sequence encoding a non-coding RNA molecule targeting an endogenous GA3 oxidase l, GA3 oxidase_2, and / or the GA3 oxidase_3 gene(s) for suppression, wherein the transcribable DNA sequence is operably linked to a constitutive, tissue-specific or tissue-preferred promoter, and wherein the transcribable DNA sequence causes the expression level of an endogenous GA3 oxidase l, GA3 oxidase_2, and / or the GA3 oxidase_3 gene(s) to become reduced or lowered in one or more tissue(s) of a plant transformed with thetranscribable DNA sequence. Such a non-coding RNA molecule encoded by the transcribable DNA sequence may comprise a sequence that is (i) at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA3 oxidase protein in the plant that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% identical to SEQ ID NO: 30, (ii) at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA3 oxidase protein in the plant that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% identical to SEQ ID NO: 33, and / or (iii) at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA3 oxidase protein in the plant that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% identical to SEQ ID NO: 173.

[0126] According to embodiments of the present disclosure, a recombinant DNA construct is provided comprising a transcribable DNA sequence encoding a non-coding RNA molecule targeting an endogenous GA20 oxidase_4 gene for suppression, wherein the transcribable DNA sequence is operably linked to a constitutive, tissue-specific or tissue-preferred promoter, and wherein the transcribable DNA sequence causes the expression level of an endogenous GA20 oxidase_4 gene to become reduced or lowered in one or more tissue(s) of a plant transformed with the transcribable DNA sequence. Such a non-coding RNA molecule encoded by the transcribable DNA sequence may comprise a sequence that is (i) at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA20 oxidase protein in the plant that is at least 80%, at least 85%, atleast 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% identical to SEQ ID NO: 12.

[0127] According to many embodiments, a modified or transgenic plant is provided that is transformed with a recombinant DNA construct comprising a transcribable DNA sequence encoding a non-coding RNA molecule targeting an endogenous GA20 oxidase_3 and / or GA20 oxidase_5 gene(s) for suppression, and / or has an endogenous GA20 oxidase_3 and / or GA20 oxidase_5 gene(s) edited through targeted genome editing techniques, as provided herein, wherein the transcribable DNA sequence is operably linked to a constitutive promoter or a tissue-specific or tissue-preferred promoter, such as a vascular promoter or a leaf promoter, and wherein the expression level of the endogenous GA20 oxidase_3 and / or GA20 oxidase_5 gene(s) is eliminated, reduced or lowered in one or more plant tissue(s), such as one or more vascular and / or leaf tissue(s), of the modified or transgenic plant by at least 5%, at least 10%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, or 100% as compared to a wild type or control plant. According to many embodiments, a modified or transgenic plant is provided that is transformed with a recombinant DNA construct comprising a transcribable DNA sequence encoding a non-coding RNA molecule targeting an endogenous GA20 oxidase_3 and / or GA20 oxidase_5 gene(s) for suppression, and / or has an endogenous GA20 oxidase_3 and / or GA20 oxidase_5 gene(s) edited through targeted genome editing techniques to reduce or eliminate its level of expression and / or activity, wherein the transcribable DNA sequence is operably linked to a constitutive promoter or a tissue-specific or tissue-preferred promoter, such as a vascular promoter or a leaf promoter, and / or wherein the level of one or more active GAs, such as GAI, GA3, GA4, and / or GA7, is reduced or lowered in one or more plant tissue(s), such as one or more stem, internode, vascular and / or leaf tissue(s) or one or more stem and / or internode tissue(s), of the modified or transgenic plant by at least 5%, at least 10%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, or 100% as compared to a wild type or control plant.

[0128] According to many embodiments, a modified or transgenic plant is provided that is transformed with a recombinant DNA construct comprising a transcribable DNA sequence encoding a non-coding RNA molecule targeting an endogenous GA3 oxidase l, GA3 oxidase_2, and / or GA3 oxidase_3 gene(s) for suppression, and / or has an endogenous GA3 oxidase l, GA3 oxidase_2, or GA3 oxidase_3 gene edited through targeted genome editing techniques, as provided herein, wherein the transcribable DNA sequence is operably linked to a constitutive promoter or atissue-specific or tissue-preferred promoter, such as a vascular promoter or a leaf promoter, and / or wherein the expression level of the endogenous GA3 oxidase l, GA3 oxidase_2, and / or GA3 oxidase_3 gene(s) is eliminated, reduced or lowered in one or more plant tissue(s), such as one or more vascular and / or leaf tissue(s), of the modified or transgenic plant by at least 5%, at least 10%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, or 100% as compared to a wild type or control plant. According to many embodiments, a modified or transgenic plant is provided that is transformed with a recombinant DNA construct comprising a transcribable DNA sequence encoding a non-coding RNA molecule targeting an endogenous GA3 oxidase l, GA3 oxidase_2, and / or GA3 oxidase_3 gene(s) for suppression, and / or has an endogenous GA3 oxidase l, GA3 oxidase_2, and / or GA3 oxidase_3 gene edited through targeted genome editing techniques to reduce or eliminate its level of expression and / or activity, wherein the transcribable DNA sequence is operably linked to a constitutive promoter or a tissue-specific or tissue-preferred promoter, such as a vascular promoter or a leaf promoter, and / or wherein the level of one or more active GAs, such as GAI, GA3, GA4, and / or GA7, is reduced or lowered in one or more plant tissue(s), such as one or more stem, internode, vascular and / or leaf tissue(s) or one or more stem and / or internode tissue(s), of the modified or transgenic plant by at least 5%, at least 10%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, or 100% as compared to a wild type or control plant.

[0129] According to many embodiments, a modified or transgenic plant is provided that is transformed with a recombinant DNA construct comprising a transcribable DNA sequence encoding a non-coding RNA molecule targeting an endogenous GA20 oxidase_4 gene for suppression, and / or has an endogenous GA20 oxidase_4 gene edited through targeted genome editing techniques, as provided herein, wherein the transcribable DNA sequence is operably linked to a constitutive promoter or a tissue-specific or tissue-preferred promoter, such as a vascular promoter or a leaf promoter, and / or wherein the expression level of the endogenous GA20 oxidase_4 gene(s) is eliminated, reduced or lowered in one or more plant tissue(s), such as one or more vascular and / or leaf tissue(s), of the modified or transgenic plant by at least 5%, at least 10%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, or 100% as compared to a wild type or control plant. According to many embodiments, a modified or transgenic plant is provided that is transformed with a recombinant DNA construct comprising a transcribable DNA sequence encoding a non-coding RNA molecule targeting an endogenous GA20 oxidase_4 gene(s) for suppression,and / or has an endogenous GA20 oxidase_4 gene edited through targeted genome editing techniques to reduce or eliminate its level of expression and / or activity, wherein the transcribable DNA sequence is operably linked to a constitutive promoter or a tissue-specific or tissue-preferred promoter, such as a vascular promoter or a leaf promoter, and / or wherein the level of one or more active GAs, such as GAI, GA3, GA4, and / or GA7, is reduced or lowered in one or more plant tissue(s), such as one or more stem, internode, vascular and / or leaf tissue(s) or one or more stem and / or internode tissue(s), of the modified or transgenic plant by at least 5%, at least 10%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, or 100% as compared to a wild type or control plant.

[0130] According to many embodiments, a modified or transgenic plant is provided that is transformed with a recombinant DNA construct comprising a transcribable DNA sequence encoding a non-coding RNA molecule targeting an endogenous GA20 oxidase_3, GA20 oxidase_4, and / or GA20 oxidase_5 gene(s) for suppression, is transformed with a recombinant DNA construct comprising a transcribable DNA sequence encoding a non-coding RNA molecule targeting an endogenous GA3 oxidase l, GA3 oxidase_2, and / or the GA3 oxidase_3 gene(s) for suppression, has an endogenous GA20 oxidase_3, GA20 oxidase_4, or the GA20 oxidase_5 gene edited through targeted genome editing techniques, and / or has an endogenous GA3 oxidase l, GA3 oxidase_2, or the GA3 oxidase_3 gene edited through targeted genome editing techniques, to reduce or eliminate its level of expression and / or activity, as provided herein, wherein the transcribable DNA sequence is operably linked to a constitutive promoter or a tissue-specific or tissue-preferred promoter, such as a vascular promoter or a leaf promoter, and / or wherein the modified or transgenic plant has one or more of the following traits: a semi-dwarf or reduced plant height or stature, decreased stem internode length, increased lodging resistance, and / or increased stem or stalk diameter. Such a modified or transgenic plant may not have any significant reproductive off-types. A modified or transgenic plant may have one or more of the following additional traits: reduced green snap, deeper roots, increased leaf area, earlier canopy closure, higher stomatai conductance, lower ear height, increased foliar water content, improved drought tolerance, increased nitrogen use efficiency, increased water use efficiency, reduced anthocyanin content and anthocyanin area in leaves under normal and / or nitrogen or water limiting stress conditions, increased ear weight, increased kernel number, increased kernel weight, increased yield, and / or increased harvest index. According to many of these embodiments, the level of expression and / or activity of an endogenous GA20 oxidase_3, GA20 oxidase_4, and / or GA20 oxidase_5 gene(s), or an endogenous GA3 oxidase l, GA3 oxidase_2, and / or GA3 oxidase_3gene(s), may be eliminated, reduced or lowered in one or more plant tissue(s), such as one or more vascular and / or leaf tissue(s), of the modified or transgenic plant by at least 5%, at least 10%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, or 100% as compared to a wild type or control plant, and / or the level of one or more active GAs, such as GAI, GA3, GA4, and / or GA7, is reduced or lowered in one or more plant tissue(s), such as one or more stem, internode, vascular and / or leaf tissue(s), or one or more stem and / or internode tissue(s), of the modified or transgenic plant by at least 5%, at least 10%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, or 100% as compared to a wild type or control plant.

[0131] According to many of the embodiments described in the above paragraphs, the non-coding RNA molecule encoded by the transcribable DNA sequence of the recombinant DNA molecule, vector or construct may be a precursor miRNA or siRNA that may be subsequently processed or cleaved in a plant cell to form a mature miRNA or siRNA.

[0132] A recombinant DNA molecule, construct or vector of the present disclosure may comprise a transcribable DNA sequence encoding a non-coding RNA molecule that targets an endogenous GA oxidase gene for suppression, wherein the transcribable DNA sequence is operatively linked to a plant-expressible promoter, such as a constitutive or vascular and / or leaf promoter. For purposes of the present disclosure, a non-coding RNA molecule encoded by a transcribable DNA sequence that targets an endogenous GA oxidase gene for suppression may include a mature non-coding RNA molecule that targets an endogenous GA oxidase gene for suppression, and / or a precursor RNA molecule that may become processed in a plant cell into a mature non-coding RNA molecule, such as a miRNA or siRNA, that targets an endogenous GA oxidase gene for suppression. In addition to its associated promoter, a transcribable DNA sequence encoding a non-coding RNA molecule for suppression of an endogenous GA oxidase gene may also be operatively linked to one or more additional regulatory element(s), such as an enhancer(s), leader, transcription start site (TSS), linker, 5’ and 3’ untranslated region(s) (UTRs), intron(s), polyadenylation signal, termination region or sequence, etc., that are suitable, necessary or preferred for strengthening, regulating or allowing expression of the transcribable DNA sequence in a plant cell. Such additional regulatory element(s) may be optional and / or used to enhance or optimize expression of the transgene or transcribable DNA sequence. As provided herein, an “enhancer” may be distinguished from a “promoter” in that an enhancer typically lacks a transcription start site, TATA box, or equivalent sequence and is thus insufficient alone to drivetranscription. As used herein, a “leader” may be defined generally as the DNA sequence of the 5’-UTR of a gene (or transgene) between the transcription start site (TSS) and 5’ end of the transcribable DNA sequence or protein coding sequence start site of the transgene.

[0133] According to further embodiments, methods are provided for transforming a plant cell, tissue or explant with a recombinant DNA molecule(s) or construct(s) comprising a transcribable DNA sequence(s) or transgene(s) each operably linked to a plant-expressible promoter to produce a transgenic or edited plant. The transcribable DNA sequence(s) may encode a non-coding RNA molecule that targets a GA oxidase gene(s) for suppression, or a RNA precursor that is processed into a mature RNA molecule, such as a miRNA or siRNA, that targets one or more GA oxidase gene(s) for suppression. Alternatively, the transcribable DNA sequence(s) may encode a site-specific nuclease and / or a guide RNA for targeted genome editing of a plant or plant gene. Numerous methods for transforming chromosomes or plastids in a plant cell with a recombinant DNA molecule or construct are known in the art, which may be used according to method embodiments of the present invention to produce a transgenic plant cell and plant. Any suitable method or technique for transformation of a plant cell known in the art may be used according to present methods. Effective methods for transformation of plants include bacterially mediated transformation, such as d z zcVc vz / zzz-mediated or A7zzzoZ>zz / zzz-mediated transformation, and microprojectile or particle bombardment-mediated transformation. A variety of methods are known in the art for transforming explants with a transformation vector via bacterially mediated transformation or microprojectile or particle bombardment and then subsequently culturing, etc., those explants to regenerate or develop transgenic plants. Other methods for plant transformation, such as microinjection, electroporation, vacuum infiltration, pressure, sonication, silicon carbide fiber agitation, PEG-mediated transformation, etc., are also known in the art.

[0134] Methods of transforming plant cells and explants are well known by persons of ordinary skill in the art. Methods for transforming plant cells by microprojectile bombardment with particles coated with recombinant DNA are provided, for example, in U.S. Patent Nos. 5,550,318; 5,538,880 6,160,208; 6,399,861; and 6,153,812, and Agrobacterium-mediated transformation is described, for example, in U.S. Patent Nos. 5,159,135; 5,824,877; 5,591,616; 6,384,301; 5,750,871; 5,463,174; and 5,188,958, all of which are incorporated herein by reference. Additional methods for transforming plants can be found in, for example, Compendium of Transgenic Crop Plants (2009) Blackwell Publishing. Any suitable method of plant transformationknown or later developed in the art can be used to transform a plant cell or explant with any of the nucleic acid molecules, constructs or vectors provided herein.

[0135] Transgenic plants produced by transformation methods may be chimeric or non-chimeric for the transformation event depending on the methods and explants used. Methods are further provided for expressing a non-coding RNA molecule that targets an endogenous GA oxidase gene for suppression in one or more plant cells or tissues under the control of a plant-expressible promoter, such as a constitutive, tissue-specific, tissue-preferred, vascular and / or leaf promoter as provided herein. Transformation methods may also be used to deliver editing machinery to a plant cell or explant to make a desirable edit in the plant genome. Transformation methods may be used to create modified, edited or transgenic cereal or corn plants having a shorter, semi-dwarf stature, reduced internode length, increased stalk / stem diameter, and / or improved lodging resistance. Such modified, edited or transgenic cereal or corn plants may further have other traits that may be beneficial for yield, such as reduced green snap, deeper roots, increased leaf area, earlier canopy closure, improved drought tolerance, increased nitrogen use efficiency, increased water use efficiency, higher stomatai conductance, lower ear height, increased foliar water content, reduced anthocyanin content and / or area in leaves under normal or nitrogen or water limiting stress conditions, increased ear weight, increased seed or kernel number, increased seed or kernel weight, increased yield, and / or increased harvest index, relative to a wild type or control plant. As used herein, “harvest index” refers to the mass of the harvested grain divided by the total mass of the above-ground biomass of the plant over a harvested area.

[0136] Transgenic plants expressing a GA oxidase transgene or non-coding RNA molecule that targets an endogenous GA oxidase gene for suppression, or modified plants having one or more mutations or edits in a GA oxidase gene, may have an earlier canopy closure (e.g., approximately one day earlier, or 12-48 hours, 12-36 hours, 18-36 hours, or about 24 hours earlier canopy closure) than a wild type or control plant. Although transgenic plants expressing a GA oxidase transgene or non-coding RNA molecule that targets an endogenous GA oxidase gene for suppression and modified plants having one or more mutations or edits in a GA oxidase gene may have a lower ear height than a wild type or control plant, the height of the ear may generally be at least 18 inches above the ground. Transgenic plants expressing a non-coding RNA molecule that targets an endogenous GA oxidase gene for suppression or modified plants having one or more mutations in a GA oxidase gene may have greater biomass and / or leaf area during one or more late vegetative stages (e.g., V8-V12) than a wild type or control plant. Transgenic plants expressing aGA oxidase transgene or non-coding RNA molecule that targets an endogenous GA oxidase gene for suppression or modified plants having one or more mutations or edits in a GA oxidase gene may have deeper roots during later vegetative stages when grown in the field, than a wild type or control plant, which may be due to an increased root front velocity. These transgenic or modified plants may reach a depth 90 cm below ground sooner (e.g., 10-25 days sooner, 15-25 days sooner, or about 20 days sooner) than a wild type or control plant, which may occur by the vegetative to reproductive transition of the plant (e.g., by V16 / R1 at about 50 days after planting as opposed at about 70 days after planting for control plants).

[0137] Recipient cell(s) or explant or cellular targets for transformation include, but are not limited to, a seed cell, a fruit cell, a leaf cell, a cotyledon cell, a hypocotyl cell, a meristem cell, an embryo cell, an endosperm cell, a root cell, a shoot cell, a stem cell, a pod cell, a flower cell, an inflorescence cell, a stalk cell, a pedicel cell, a style cell, a stigma cell, a receptacle cell, a petal cell, a sepal cell, a pollen cell, an anther cell, a filament cell, an ovary cell, an ovule cell, a pericarp cell, a phloem cell, a bud cell, a callus cell, a chloroplast, a stomatai cell, a trichome cell, a root hair cell, a storage root cell, or a vascular tissue cell, a seed, embryo, meristem, cotyledon, hypocotyl, endosperm, root, shoot, stem, node, callus, cell suspension, protoplast, flower, leaf, pollen, anther, ovary, ovule, pericarp, bud, and / or vascular tissue, or any transformable portion of any of the foregoing. For plant transformation, any target cell(s), tissue(s), explant(s), etc., that may be used to receive a recombinant DNA transformation vector or molecule of the present disclosure may be collectively referred to as an “explant” for transformation. Preferably, a transformable or transformed explant cell or tissue may be further developed or regenerated into a plant. Any cell or explant from which a fertile plant can be grown or regenerated is contemplated as a useful recipient cell or explant for practice of this disclosure (i.e., as a target explant for transformation). Callus can be initiated or created from various tissue sources, including, but not limited to, embryos or parts of embryos, non-embryonic seed tissues, seedling apical meristems, microspores, and the like. Any cells that are capable of proliferating as callus may serve as recipient cells for transformation. Transformation methods and materials for making transgenic plants (e.g., various media and recipient target cells or explants and methods of transformation and subsequent regeneration of into transgenic plants) are known in the art.

[0138] Transformation of a target plant material or explant may be practiced in tissue culture on nutrient media, for example a mixture of nutrients that allow cells to grow in vitro or cell culture. Transformed explants, cells or tissues may be subjected to additional culturing steps, suchas callus induction, selection, regeneration, etc., as known in the art. Transformation may also be carried out without creation or use of a callus tissue. Transformed cells, tissues or explants containing a recombinant DNA sequence insertion or event may be grown, developed or regenerated into transgenic plants in culture, plugs, or soil according to methods known in the art. Transgenic plants may be further crossed to themselves or other plants to produce transgenic seeds and progeny. A transgenic plant may also be prepared by crossing a first plant comprising the recombinant DNA sequence or transformation event with a second plant lacking the insertion. For example, a recombinant DNA construct or sequence may be introduced into a first plant line that is amenable to transformation, which may then be crossed with a second plant line to introgress the recombinant DNA construct or sequence into the second plant line. Progeny of these crosses can be further back crossed into the more desirable line multiple times, such as through 6 to 8 generations or back crosses, to produce a progeny plant with substantially the same genotype as the original parental line, but for the introduction of the recombinant DNA construct or sequence.

[0139] A transgenic, mutant or edited plant, plant part, cell, or explant provided herein may be of an elite variety or an elite line. An elite variety or an elite line refers to a variety that has resulted from breeding and selection for superior agronomic performance. A transgenic, mutant or edited plant, cell, or explant provided herein may be a hybrid plant, cell, or explant. As used herein, a “hybrid” is created by crossing two plants from different varieties, lines, inbreds, or species, such that the progeny comprises genetic material from each parent. Skilled artisans recognize that higher order hybrids can be generated as well. For example, a first hybrid can be made by crossing Variety A with Variety B to create a A x B hybrid, and a second hybrid can be made by crossing Variety C with Variety D to create an C x D hybrid. The first and second hybrids can be further crossed to create the higher order hybrid (A x B) x (C x D) comprising genetic information from all four parent varieties.

[0140] According to embodiments of the present disclosure, a modified plant is provided comprising a GA oxidase suppression element that targets two or more GA oxidase genes for suppression, or a combination of two or more GA oxidase suppression element(s) and / or gene edit(s) or mutation(s). A recombinant DNA construct or vector may comprise a single cassette or suppression element comprising a transcribable DNA sequence designed or chosen to encode a non-coding RNA molecule that is complementary to mRNA recognition or target sequences of two or more GA oxidase genes including at least a first GA oxidase gene and a second GA oxidase gene - z.e., the mRNAs of the targeted GA oxidase genes share an identical or nearly identical (orsimilar) sequence such that a single suppression element and encoded non-coding RNA molecule can target each of the targeted GA oxidase genes for suppression. For example, an expression cassette and suppression construct are provided herein comprising a transcribable DNA sequence that encodes a single non-coding RNA molecule that targets both the GA20 oxidase_3 and GA20 oxidase_5 genes for suppression.

[0141] According to other embodiments, a recombinant DNA construct or vector may comprise two or more suppression elements or sequences that may be stacked together in a construct or vector either in tandem in a single expression cassette or separately in two or more expression cassettes. A recombinant DNA construct or vector may comprise a single expression cassette or suppression element comprising a transcribable DNA sequence that encodes a non-coding RNA molecule comprising two or more targeting sequences arranged in tandem, including at least a first targeting sequence and a second targeting sequence, wherein the first targeting sequence is complementary to a mRNA recognition or target site of a first GA oxidase gene, and the second targeting sequence is complementary to a mRNA recognition or target site of a second GA oxidase gene, and wherein the transcribable DNA sequence is operably linked to a plant-expressible promoter. The plant-expressible promoter may be a constitutive promoter, or a tissue-specific or tissue-preferred promoter, as provided herein. The non-coding RNA molecule may be expressed as a pre-miRNA that becomes processed into two or more mature miRNAs including at least a first mature miRNA and a second miRNA, wherein the first miRNA comprises a targeting sequence that is complementary to the mRNA recognition or target site of the first GA oxidase gene, and the second miRNA comprises a targeting sequence that is complementary to the mRNA recognition or target site of the second GA oxidase gene.

[0142] According to other embodiments, a recombinant DNA construct or vector may comprise two or more expression cassettes including a first expression cassette and a second expression cassette, wherein the first expression cassette comprises a first transcribable DNA sequence operably linked to a first plant-expressible promoter, and the second expression cassette comprises a second transcribable DNA sequence operably linked to a second plant-expressible promoter, wherein the first transcribable DNA sequence encodes a first non-coding RNA molecule comprising a targeting sequence that is complementary to a mRNA recognition or target site of a first GA oxidase gene, and the second transcribable DNA sequence encodes a second non-coding RNA molecule comprising a targeting sequence that is complementary to a mRNA recognition or target site of a second GA oxidase gene. The first and second plant-expressible promoters mayeach be a constitutive promoter, or a tissue-specific or tissue-preferred promoter, as provided herein, and the first and second plant-expressible promoters may be the same or different promoters.

[0143] According to other embodiments, two or more suppression elements or constructs targeting GA oxidase gene(s) and / or GA oxidase gene edit(s) or mutation(s) may be combined in a modified plant by crossing two or more plants together in one or more generations to produce a modified plant having a desired combination of suppression element(s) and / or gene edit(s) or mutation(s). According to these embodiments, a first modified plant comprising a suppression element or construct targeting a GA oxidase gene(s) (or a GA oxidase gene edit or mutation) may be crossed to a second modified plant comprising a suppression element or construct targeting a GA oxidase gene(s) (or a GA oxidase gene edit or mutation), such that a modified progeny plant may be made comprising a first suppression element or construct and a second suppression element or construct, a suppression element or construct and a GA oxidase gene edit or mutation, or a first GA oxidase gene edit or mutation and a second GA oxidase gene edit or mutation. Alternatively, a modified plant comprising two or more suppression elements or constructs targeting GA oxidase gene(s) and / or GA oxidase gene edit(s) or mutation(s) may be made by (i) co-transforming a first suppression element or construct and a second suppression element or construct (each targeting a GA oxidase gene for suppression), (ii) transforming a modified plant with a second suppression element or construct, wherein the modified plant already comprises a first suppression element or construct, (iii) transforming a modified plant with a suppression element or construct, wherein the modified plant already comprises an edited or mutated GA oxidase gene, (iv) transforming a modified plant with a construct(s) for making one or more edits or mutations in GA oxidase gene(s), wherein the modified plant already comprises a suppression element or construct, or (v) transforming with construct(s) for making two or more edits or mutations in GA oxidase gene(s).

[0144] According to embodiments of the present disclosure, modified plants are provided comprising two or more constructs targeting GA oxidase gene(s) for suppression including a first recombinant DNA construct and a second recombinant DNA construct, wherein the first recombinant DNA construct comprises a first transcribable DNA sequence encoding a first non-coding RNA molecule that is complementary to a mRNA recognition or target sequence of a first GA oxidase gene, and the second recombinant DNA construct comprises a second transcribable DNA sequence encoding a second non-coding RNA molecule that is complementaryto a mRNA recognition or target sequence of a second GA oxidase gene. The first and second recombinant DNA constructs may be stacked in a single vector and transformed into a plant as a single event, or present in separate vectors or constructs that may be transformed as separate events. According to these embodiments, the first GA oxidase gene may be a GA20 oxidase_3, GA20 oxidase_5, GA20 oxidase_4, GA3 oxidase_l, GA3 oxidase_2, or GA3 oxidase_3 gene, the first non-coding RNA molecule is complementary to a recognition or target sequence of an mRNA expressed from such GA oxidase gene, and the second GA oxidase gene may be a GA20 oxidase_3, GA20 oxidase_5, GA20 oxidase_4, GA3 oxidase_l, GA3 oxidase_2, or GA3 oxidase_3 gene. According to some embodiments, the first and second GA oxidase genes may be the same or different GA oxidase gene(s). Alternatively, the second GA oxidase gene may be another GA oxidase gene, such as a GA20 oxidase_l, GA20 oxidase_2, GA20 oxidase_6, GA20 oxidase_7, GA20 oxidase_8, or GA20 oxidase_9 gene, and the second non-coding RNA molecule is complementary to a recognition or target sequence of an mRNA expressed from such GA oxidase gene.

[0145] According to embodiments of the present disclosure, modified plants are provided comprising a recombinant DNA construct targeting GA oxidase genes for suppression comprising a transcribable DNA sequence encoding a non-coding RNA molecule that comprises two or more targeting sequences arranged in tandem including at least a first targeting sequence that is complementary to a mRNA recognition or target sequence of a first GA oxidase gene and a second targeting sequence that is complementary to a mRNA recognition or target sequence of a second GA oxidase gene. The non-coding RNA molecule may be expressed as a pre-miRNA that becomes processed into two or more mature miRNAs including at least a first mature miRNA and a second miRNA, wherein the first miRNA comprises the first targeting sequence that is complementary to the mRNA recognition or target site of the first GA oxidase gene, and the second miRNA comprises the second targeting sequence that is complementary to the mRNA recognition or target site of the second GA oxidase gene. According to these embodiments, the first GA oxidase gene may be a GA20 oxidase_3, GA20 oxidase_5, GA20 oxidase_4, GA3 oxidase_l, GA3 oxidase_2, or GA3 oxidase_3 gene, the first non-coding RNA molecule is complementary to a recognition or target sequence of an mRNA expressed from such GA oxidase gene, and the second GA oxidase gene may be a GA20 oxidase_3, GA20 oxidase_5, GA20 oxidase_4, GA3 oxidase_l, GA3 oxidase_2, or GA3 oxidase_3 gene. According to some embodiments, the first and second GA oxidase genes may be the same or different GA oxidase gene(s). Alternatively, the second GA oxidase gene may be another GA oxidase gene, such as a GA20 oxidase l, GA20 oxidase_2,GA20 oxidase_6, GA20 oxidase_7, GA20 oxidase_8, or GA20 oxidase_9 gene, and the second non-coding RNA molecule is complementary to a recognition or target sequence of an mRNA expressed from such GA oxidase gene.

[0146] In the above stacking scenarios, and regardless of whether the targeting sequences are stacked in tandem in a single transcribable DNA sequence (or expression cassette) or in separate transcribable DNA sequences (or expression cassettes), the second GA oxidase gene may be a GA oxidase gene other than a GA20 oxidase_3, GA20 oxidase_5, GA20 oxidase_4, GA3 oxidase_l, GA3 oxidase_2, or GA3 oxidase_3 gene, such as a GA20 oxidase_l, GA20 oxidase_2, GA20 oxidase_6, GA20 oxidase_7, GA20 oxidase_8, or GA20 oxidase_9 gene. According to these embodiments, the second targeting sequence of a non-coding RNA molecule may be at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of any one or more of SEQ ID NOs: 1, 2, 4, 5, 16, 17, 19, 20, 22, 23, 25, and / or 26. According to some embodiments, the second targeting sequence of a non-coding RNA molecule may be complementary to at least 19 consecutive nucleotides, but no more than 27 consecutive nucleotides, such as complementary to 19, 20, 21, 22, 23, 24, 25, 26, or 27 consecutive nucleotides, of any one or more of SEQ ID NOs: 1, 2, 4, 5, 16, 17, 19, 20, 22, 23, 25, and / or 26. According to some embodiments, the second targeting sequence of a non-coding RNA molecule may be at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA oxidase protein in the plant that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% identical to any one or more of SEQ ID NOs: 3, 6, 18, 21, 24, and / or 27. According to further embodiments, the second targeting sequence of a non-coding RNA molecule may comprise a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, or at least 27 consecutive nucleotides of a mRNA molecule encoding an endogenous GA oxidase protein that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% similar to any one or more of SEQ ID NO: 3, 6, 18, 21, 24, and / or 27.

[0147] A recombinant DNA molecule or construct of the present disclosure may comprise or be included within a DNA transformation vector for use in transformation of a target plant cell, tissue or explant. Such a transformation vector may generally comprise sequences or elements necessary or beneficial for effective transformation in addition to at least one transgene, expression cassette and / or transcribable DNA sequence encoding a GA oxidase gene or a non-coding RNA molecule targeting an endogenous GA oxidase gene for suppression or a site-specific nuclease and / or a guide RNA for editing an endogenous GA oxidase gene. For d zYz / izzc / cz'zz / zzz-mediated, AAzzoZ fz-mediated or other bacteria-mediated transformation, the transformation vector may comprise an engineered transfer DNA (or T-DNA) segment or region having two border sequences, a left border (LB) and a right border (RB), flanking at least a transcribable DNA sequence or transgene, such that insertion of the T-DNA into the plant genome will create a transformation event for the transcribable DNA sequence, transgene or expression cassette. Thus, a transcribable DNA sequence, transgene or expression cassette encoding a non-coding RNA molecule targeting an endogenous GA oxidase gene for suppression or a site-specific nuclease and / or a guide RNA for editing an endogenous GA oxidase gene may be located between the left and right borders of the T-DNA, perhaps along with an additional transgene(s) or expression cassette(s), such as a plant selectable marker transgene and / or other gene(s) of agronomic interest that may confer a trait or phenotype of agronomic interest to a plant. According to alternative embodiments, the transcribable DNA sequence, transgene or expression cassette encoding a non-coding RNA molecule targeting an endogenous GA oxidase gene for suppression or a site-specific nuclease and / or a guide RNA for editing an endogenous GA oxidase gene, and the plant selectable marker transgene (or other gene of agronomic interest) may be present in separate T-DNA segments on the same or different recombinant DNA molecule(s), such as for co-transformation. According to some embodiments, a transcribable DNA sequence(s), transgene(s) or expression cassette(s) of a recombinant DNA molecule or construct or a DNA transformation vector for genome editing may encode one or more guide RNA(s) and / or a site-specific nuclease. A transformation vector or construct may further comprise prokaryotic maintenance elements, which may be located in the vector outside of the T-DNA region(s).

[0148] A plant selectable marker transgene in a transformation vector or construct of the present disclosure may be used to assist in the selection of transformed cells or tissue due to the presence of a selection agent, such as an antibiotic or herbicide, wherein the plant selectable marker transgene provides tolerance or resistance to the selection agent. Thus, the selection agent may bias or favor the survival, development, growth, proliferation, etc., of transformed cellsexpressing the plant selectable marker gene, such as to increase the proportion of transformed cells or tissues in the Ro plant. Commonly used plant selectable marker genes include, for example, those conferring tolerance or resistance to antibiotics, such as kanamycin and paromomycin (nptll), hygromycin B (aph IV), streptomycin or spectinomycin (aadA) and gentamycin (aac3 and aacC-l), or those conferring tolerance or resistance to herbicides such as glufosinate (bar or pat), dicamba (DM0) and glyphosate (aroA or EPSPS). Plant screenable marker genes may also be used, which provide an ability to visually screen for transformants, such as luciferase or green fluorescent protein (GFP), or a gene expressing a beta glucuronidase or uidA gene (GUS) for which various chromogenic substrates are known. In some embodiments, a vector or polynucleotide provided herein comprises at least one selectable marker gene selected from the group consisting of nptll, aph IV, aadA, aac3, aacC4, bar, pat, DM0, EPSPS, aroA, GFP, and GUS. Plant transformation may also be carried out in the absence of selection during one or more steps or stages of culturing, developing or regenerating transformed explants, tissues, plants and / or plant parts.

[0149] According to present embodiments, methods for transforming a plant cell, tissue or explant with a recombinant DNA molecule or construct may further include site-directed or targeted integration. According to these methods, a portion of a recombinant DNA donor template molecule (i.e., an insertion sequence) may be inserted or integrated at a desired site or locus within the plant genome. The insertion sequence of the donor template may comprise a transgene or construct, such as a transgene or transcribable DNA sequence encoding a non-coding RNA molecule that targets an endogenous GA oxidase gene for suppression. The donor template may also have one or two homology arms flanking the insertion sequence to promote the targeted insertion event through homologous recombination and / or homology-directed repair. Each homology arm may be at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 2500, or at least 5000 consecutive nucleotides of a target DNA sequence within the genome of a monocot or cereal plant. Thus, a recombinant DNA molecule of the present disclosure may comprise a donor template for site-directed or targeted integration of a transgene or construct, such as a transgene or transcribable DNA sequence encoding a non-coding RNA molecule that targets an endogenous GA oxidase gene for suppression, into the genome of a plant.

[0150] Any site or locus within the genome of a plant may potentially be chosen for site-directed integration of a transgene, construct or transcribable DNA sequence provided herein. For site-directed integration, a double-strand break (DSB) or nick may first be made at a selected genomic locus with a site-specific nuclease, such as, for example, a zinc-finger nuclease, an engineered or native meganuclease, a TALE-endonuclease, or an RNA-guided endonuclease (e.g., Cas9 or Cpfl). Any method known in the art for site-directed integration may be used. In the presence of a donor template molecule with an insertion sequence, the DSB or nick may then be repaired by homologous recombination between homology arm(s) of the donor template and the plant genome, or by non-homologous end joining (NHEJ), resulting in site-directed integration of the insertion sequence into the plant genome to create the targeted insertion event at the site of the DSB or nick. Thus, site-specific insertion or integration of a transgene, construct or sequence may be achieved.

[0151] The introduction of a DSB or nick may also be used to introduce targeted mutations in the genome of a plant. According to this approach, mutations, such as deletions, insertions, inversions and / or substitutions, may be introduced at a target site via imperfect repair of the DSB or nick to produce a knock-out or knock-down of a GA oxidase gene. Such mutations may be generated by imperfect repair of the targeted locus even without the use of a donor template molecule. A “knock-out” of a GA oxidase gene may be achieved by inducing a DSB or nick at or near the endogenous locus of the GA oxidase gene that results in non-expression of the GA oxidase protein or expression of a non-functional protein, whereas a “knock-down” of a GA oxidase gene may be achieved in a similar manner by inducing a DSB or nick at or near the endogenous locus of the GA oxidase gene that is repaired imperfectly at a site that does not affect the coding sequence of the GA oxidase gene in a manner that would eliminate the function of the encoded GA oxidase protein. For example, the site of the DSB or nick within the endogenous locus may be in the upstream or 5’ region of the GA oxidase gene (e.g., a promoter and / or enhancer sequence) to affect or reduce its level of expression. Similarly, such targeted knock-out or knock-down mutations of a GA oxidase gene may be generated with a donor template molecule to direct a particular or desired mutation at or near the target site via repair of the DSB or nick. The donor template molecule may comprise a homologous sequence with or without an insertion sequence and comprising one or more mutations, such as one or more deletions, insertions, inversions and / or substitutions, relative to the targeted genomic sequence at or near the site of the DSB or nick. For example, targeted knock-out mutations of a GA oxidase gene may be achieved by deleting or inverting at least a portion of the gene or by introducing a frame shift or premature stop codon into the codingsequence of the gene. A deletion of a portion of a GA oxidase gene may also be introduced by generating DSBs or nicks at two target sites and causing a deletion of the intervening target region flanked by the target sites.

[0152] A site-specific nuclease provided herein may be selected from the group consisting of a zinc-finger nuclease (ZFN), a meganuclease, an RNA-guided endonuclease, a TALE-endonuclease (TALEN), a recombinase, a transposase, or any combination thereof. See, e.g., Khandagale, K. et al., “Genome editing for targeted improvement in plants,” Plant Biotechnol Rep 10: 327-343 (2016); and Gaj, T. et al., “ZFN, TALEN and CRISPR / Cas-based methods for genome engineering,” Trends Biotechnol. 31(7): 397-405 (2013), the contents and disclosures of which are incorporated herein by reference. A recombinase may be a serine recombinase attached to a DNA recognition motif, a tyrosine recombinase attached to a DNA recognition motif or other recombinase enzyme known in the art. A recombinase or transposase may be a DNA transposase or recombinase attached to a DNA binding domain. A tyrosine recombinase attached to a DNA recognition motif may be selected from the group consisting of a Cre recombinase, a Flp recombinase, and a Tnpl recombinase. According to some embodiments, a Cre recombinase or a Gin recombinase provided herein is tethered to a zinc-finger DNA binding domain. In another embodiment, a serine recombinase attached to a DNA recognition motif provided herein is selected from the group consisting of a PhiC31 integrase, an R4 integrase, and a TP-901 integrase. In another embodiment, a DNA transposase attached to a DNA binding domain provided herein is selected from the group consisting of a TALE-piggyBac and TALE-Mutator.

[0153] According to embodiments of the present disclosure, an RNA-guided endonuclease may be selected from the group consisting of Casl, CaslB, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 (also known as Csnl and Csxl2), CaslO, Csyl, Csy2, Csy3, Csel, Cse2, Cscl, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmrl, Cmr3, Cmr4, Cmr5, Cmr6, Csbl, Csb2, Csb3, Csxl7, Csxl4, CsxlO, Csxl6, CsaX, Csx3, Csxl, Csxl5, Csfl, Csf2, Csf3, Csf4, Cpfl, CasX, CasY, and homologs or modified versions thereof, Argonaute (non-limiting examples of Argonaute proteins include Thermus thermophilus Argonaute (TtAgo), Pyrococcus furiosus Argonaute (PfAgo), Natronobacterium gregoryi Argonaute (NgAgo) and homologs or modified versions thereof. According to some embodiments, an RNA-guided endonuclease may be a Cas9 or Cpfl enzyme.

[0154] In an aspect, a site-specific nuclease provided herein is selected from the group consisting of a zinc-finger nuclease, a meganuclease, an RNA-guided nuclease, a TALE-nuclease,a recombinase, a transposase, or any combination thereof. In another aspect, a site-specific nuclease provided herein is selected from the group consisting of a Cas9 or a Cpfl. In another aspect, a site-specific nuclease provided herein is selected from the group consisting of a Casl, a CaslB, a Cas2, a Cas3, a Cas4, a Cas5, a Cas6, a Cas7, a Cas8, a Cas9, a CaslO, a Csyl, a Csy2, a Csy3, a Csel, a Cse2, a Cscl, a Csc2, a Csa5, a Csn2, a Csm2, a Csm3, a Csm4, a Csm5, a Csm6, a Cmrl, a Cmr3, a Cmr4, a Cmr5, a Cmr6, a Csbl, a Csb2, a Csb3, a Csxl7, a Csxl4, a CsxlO, a Csxl6, a CsaX, a Csx3, a Csxl, a Csxl5, a Csfl, a Csf2, a Csf3, a Csf4, a Cpfl, CasX, CasY, a homolog thereof, or a modified version thereof. In another aspect, an RNA-guided nuclease provided herein is selected from the group consisting of a Cas9 or a Cpfl. In another aspect, an RNA guided nuclease provided herein is selected from the group consisting of a Casl, a CaslB, a Cas2, a Cas3, a Cas4, a Cas5, a Cas6, a Cas7, a Cas8, a Cas9, a CaslO, a Csyl, a Csy2, a Csy3, a Csel, a Cse2, a Cscl, a Csc2, a Csa5, a Csn2, a Csm2, a Csm3, a Csm4, a Csm5, a Csm6, a Cmrl, a Cmr3, a Cmr4, a Cmr5, a Cmr6, a Csbl, a Csb2, a Csb3, a Csxl7, a Csxl4, a CsxlO, a Csxl6, a CsaX, a Csx3, a Csxl, a Csxl5, a Csfl, a Csf2, a Csf3, a Csf4, a Cpfl, CasX, CasY, a homolog thereof, or a modified version thereof. In another aspect, a method and / or a composition provided herein comprises at least one, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, or at least ten site-specific nucleases. In yet another aspect, a method and / or a composition provided herein comprises at least one, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, or at least ten polynucleotides encoding at least one, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, or at least ten site-specific nucleases.

[0155] For RNA-guided endonucleases, a guide RNA (gRNA) molecule is further provided to direct the endonuclease to a target site in the genome of the plant via base-pairing or hybridization to cause a DSB or nick at or near the target site. The gRNA may be transformed or introduced into a plant cell or tissue (perhaps along with a nuclease, or nuclease-encoding DNA molecule, construct or vector) as a gRNA molecule, or as a recombinant DNA molecule, construct or vector comprising a transcribable DNA sequence encoding the guide RNA operably linked to a plant-expressible promoter. As understood in the art, a “guide RNA” may comprise, for example, a CRISPR RNA (crRNA), a single-chain guide RNA (sgRNA), or any other RNA molecule that may guide or direct an endonuclease to a specific target site in the genome. A “single-chain guide RNA” (or “sgRNA”) is a RNA molecule comprising a crRNA covalently linked a tracrRNA by a linker sequence, which may be expressed as a single RNA transcript or molecule. The guide RNA comprises a guide or targeting sequence that is identical or complementary to a target site withinthe plant genome, such as at or near a GA oxidase gene. A protospacer-adjacent motif (PAM) may be present in the genome immediately adjacent and upstream to the 5’ end of the genomic target site sequence complementary to the targeting sequence of the guide RNA - z.e., immediately downstream (3’) to the sense (+) strand of the genomic target site (relative to the targeting sequence of the guide RNA) as known in the art. See, e.g., Wu, X. et al., “Target specificity of the CRISPR-Cas9 system,” Quant Biol. 2(2): 59-70 (2014), the content and disclosure of which is incorporated herein by reference. The genomic PAM sequence on the sense (+) strand adjacent to the target site (relative to the targeting sequence of the guide RNA) may comprise 5’-NGG-3’. However, the corresponding sequence of the guide RNA (z.e., immediately downstream (3’) to the targeting sequence of the guide RNA) may generally not be complementary to the genomic PAM sequence. The guide RNA may typically be a non-coding RNA molecule that does not encode a protein. The guide sequence of the guide RNA may be at least 10 nucleotides in length, such as 12-40 nucleotides, 12-30 nucleotides, 12-20 nucleotides, 12-35 nucleotides, 12-30 nucleotides, 15-30 nucleotides, 17-30 nucleotides, or 17-25 nucleotides in length, or about 12, 13, 14, 15, 16,17, 18, 19, 20, 21, 22, 23, 24, 25 or more nucleotides in length. The guide sequence may be at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, or more consecutive nucleotides of a DNA sequence at the genomic target site.

[0156] For genome editing at or near the GA20 oxidase_3 gene with an RNA-guided endonuclease, a guide RNA may be used comprising a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, or more consecutive nucleotides of SEQ ID NO: 34 or a sequence complementary thereto (e.g., 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25 or more consecutive nucleotides of SEQ ID NO: 34 or a sequence complementary thereto). For genome editing at or near the GA20 oxidase_5 gene with an RNA-guided endonuclease, a guide RNA may be used comprising a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, or more consecutive nucleotides of SEQ ID NO: 35 or a sequence complementary thereto (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more consecutive nucleotides of SEQ ID NO: 35or a sequence complementary thereto). As used herein, the term “consecutive” in reference to a polynucleotide or protein sequence means without deletions or gaps in the sequence.

[0157] For knockdown (and possibly knockout) mutations through genome editing, an RNA-guided endonuclease may be targeted to an upstream or downstream sequence, such as a promoter and / or enhancer sequence, or an intron, 5’UTR, and / or 3’UTR sequence of a GA20 oxidase_3 or GA20 oxidase_5 gene to mutate one or more promoter and / or regulatory sequences of the gene and affect or reduce its level of expression. For knockdown (and possibly knockout) of the GA20 oxidase_3 gene in corn, a guide RNA may be used comprising a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, or more consecutive nucleotides within the nucleotide sequence range 1-3096 of SEQ ID NO:34, the nucleotide sequence range 3666-3775 of SEQ ID NO: 34, the nucleotide sequence range 4098-5314 of SEQ ID NO: 34, the nucleotide sequence range 5585-5800 of SEQ ID NO: 34, or the nucleotide sequence range 5801-8800 of SEQ ID NO: 34, or a sequence complementary thereto (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more consecutive nucleotides within the nucleotide sequence range 1-3096, 3666-3775, 4098-5314, 5585-5800, 5801-8800, or 5585-8800 of SEQ ID NO: 34, or a sequence complementary thereto).

[0158] For knockdown (and possibly knockout) of the GA20 oxidase_5 gene in com, a guide RNA may be used comprising a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, or more consecutive nucleotides within the nucleotide sequence range 1-3000 of SEQ ID NO: 35, the nucleotide sequence range 1-3000 of SEQ ID NO:35, the nucleotide sequence range 3792-3906 of SEQ ID NO: 35, the nucleotide sequence range 4476-5197 of SEQ ID NO: 35, or the nucleotide sequence range 5860-8859 of SEQ ID NO: 35, or a sequence complementary thereto (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more consecutive nucleotides within the nucleotide sequence range 1-3000, 3792-3906, 4476-5197, or 5860-8859 of SEQ ID NO: 35, or a sequence complementary thereto).

[0159] For knockout (and possibly knockdown) mutations through genome editing, an RNA-guided endonuclease may be targeted to a coding and / or intron sequence of a GA20 oxidase_3 or GA20 oxidase_5 gene to potentially eliminate expression and / or activity of afunctional GA oxidase protein from the gene. However, a knockout of a GA oxidase gene expression may also be achieved in some cases by targeting the upstream and / or 5’UTR sequence(s) of the gene, or other sequences at or near the genomic locus of the gene. Thus, a knockout of a GA oxidase gene expression may be achieved by targeting a genomic sequence at or near the site or locus of a targeted GA20 oxidase_3 or GA20 oxidase_5 gene, an upstream or downstream sequence, such as a promoter and / or enhancer sequence, or an intron, 5’UTR, and / or 3’UTR sequence, of a GA20 oxidase_3 or GA20 oxidase_5 gene, as described above for knockdown of a GA20 oxidase_3 or GA20 oxidase_5 gene.

[0160] For knockout (and possibly knockdown) of the GA20 oxidase_3 gene in com, a guide RNA may be used comprising a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, or more consecutive nucleotides within the nucleotide sequence range 3097-5584 of SEQ ID NO: 34, the nucleotide sequence range 3097-3665 of SEQ ID NO: 34, the nucleotide sequence range 3776-4097 of SEQ ID NO: 34, or the nucleotide sequence range 5315-5584 of SEQ ID NO: 34, or a sequence complementary thereto (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more consecutive nucleotides within the nucleotide sequence range 3097-5584, 3097-3665, 3097-3775, 3665-4097, 3776-4097, 3776-5314, 4098-5584, or 5315-5584 of SEQ ID NO: 34, or a sequence complementary thereto).

[0161] For knockout (and possibly knockdown) of the GA20 oxidase_5 gene in com, a guide RNA may be used comprising a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, or more consecutive nucleotides within the nucleotide sequence range 3001-5473 of SEQ ID NO: 35, the nucleotide sequence range 3001-3791 of SEQ ID NO: 35, the nucleotide sequence range 3907-4475 of SEQ ID NO: 35, or the nucleotide sequence range 5198-5473 of SEQ ID NO: 35, or a sequence complementary thereto (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more consecutive nucleotides within the nucleotide sequence range 3001-5473, 3001-3791, 3001-3906, 3792-4475, 3907-4475, 3907-5197, 4476-5473, or 5198-5473 of SEQ ID NO: 35, or a sequence complementary thereto).

[0162] According to some embodiments, a guide RNA for targeting an endogenous GA20 oxidase_3 and / or GA20 oxidase_5 gene is provided comprising a guide sequence that is at least90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 consecutive nucleotides of any one or more of SEQ ID NOs: 138-167.

[0163] For genome editing at or near the GA20 oxidase_4 gene with an RNA-guided endonuclease, a guide RNA may be used comprising a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, or more consecutive nucleotides of SEQ ID NO: 38 or a sequence complementary thereto (e.g., 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more consecutive nucleotides of SEQ ID NO: 38 or a sequence complementary thereto).

[0164] For knockout (and possibly knockdown) mutations through genome editing, an RNA-guided endonuclease may be targeted to a coding and / or intron sequence of a GA20 oxidase_4 gene to potentially eliminate expression and / or activity of a functional GA20 oxidase_4 protein from the gene. For the GA20 oxidase_4 gene in corn, a guide RNA may be used comprising a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, or more consecutive nucleotides within the nucleotide sequence range 1544-2852 of SEQ ID NO: 38, the nucleotide sequence range 1544-1995 of SEQ ID NO: 38, the nucleotide sequence range 2084-2411 of SEQ ID NO: 38, or the nucleotide sequence range 2517-2852 of SEQ ID NO: 38, or a sequence complementary thereto (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more consecutive nucleotides within the nucleotide sequence range 1544-2852, 1544-1995, 1544-2083, 1996-2411, 2084-2411, 2084-2516, 2412-2852, or 2517-2852 of SEQ ID NO: 38, or a sequence complementary thereto).

[0165] For knockdown (and possibly knockout) mutations through genome editing, an RNA-guided endonuclease may be targeted to an upstream or downstream sequence, such as a promoter and / or enhancer sequence, or an intron, 5’UTR, and / or 3’UTR sequence of a GA20 oxidase_4 gene to mutate one or more promoter and / or regulatory sequences of the gene and affect or reduce its level of expression. For knockdown of the GA20 oxidase_4 gene in corn, a guide RNA may be used comprising a guide sequence that is at least 90%, at least 95%, at least 96%, atleast 97%, at least 99% or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, or more consecutive nucleotides within the nucleotide sequence range 1-1416 of SEQ ID NO: 38, the nucleotide sequence range 1417-1543 of SEQ ID NO: 38, the nucleotide sequence range 1996-2083 of SEQ ID NO: 38, the nucleotide sequence range 2412-2516 of SEQ ID NO: 38, the nucleotide sequence range 2853-3066 of SEQ ID NO: 38, or the nucleotide sequence range 3067-4465 of SEQ ID NO: 38, or a sequence complementary thereto (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more consecutive nucleotides within the nucleotide sequence range 1-1416, 1417-1543, 1-1543, 1996-2083, 2412-2516, 2853-3066, 3067-4465 or 2853-4465 of SEQ ID NO: 38, or a sequence complementary thereto).

[0166] For genome editing at or near the GA3 oxidase l gene with an RNA-guided endonuclease, a guide RNA may be used comprising a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, or more consecutive nucleotides of SEQ ID NO: 36, 168 or 174 or a sequence complementary thereto (e.g, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more consecutive nucleotides of SEQ ID NO: 168 or a sequence complementary thereto). For genome editing at or near the GA3 oxidase_2 gene with an RNA-guided endonuclease, a guide RNA may be used comprising a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, or more consecutive nucleotides of SEQ ID NO: 37, 169 or 175 or a sequence complementary thereto (e.g, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more consecutive nucleotides of SEQ ID NO: 169 or a sequence complementary thereto). For genome editing at or near the GA3 oxidase_3 gene with an RNA-guided endonuclease, a guide RNA may be used comprising a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, or more consecutive nucleotides of SEQ ID NO: 170 or 176 or a sequence complementary thereto (e.g., 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more consecutive nucleotides of SEQ ID NO: 170 or a sequence complementary thereto).

[0167] For knockout (and possibly knockdown) mutations through genome editing, an RNA-guided endonuclease may be targeted to a coding and / or intron sequence of a GA3 oxidase l gene to potentially eliminate expression and / or activity of a functional GA3 oxidase l protein from the gene. For the GA3 oxidase l gene in corn, a guide RNA may be used comprising a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, or more consecutive nucleotides within the nucleotide sequence range 3162-4795 of SEQ ID NO: 168, the nucleotide sequence range 3162-3646 of SEQ ID NO: 168, the nucleotide sequence range 4012-4170 of SEQ ID NO: 168, or the nucleotide sequence range 4291-4795 of SEQ ID NO: 168, or a sequence complementary thereto (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more consecutive nucleotides within the nucleotide sequence range 3001-3646, 3162-3646, 3162-4011, 3647-4170, 4012-4170, 4012-4290, 4171-4795, 4291-4795, 4291-5406 or 3162-4795 of SEQ ID NO: 168, or a sequence complementary thereto). For the GA3 oxidase l gene in corn, a guide RNA may be used comprising a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, or more consecutive nucleotides within the nucleotide sequence range 30-1663 of SEQ ID NO: 36, the nucleotide sequence range 30-514 of SEQ ID NO: 36, the nucleotide sequence range 880-1038 of SEQ ID NO: 36, or the nucleotide sequence range 1159-1663 of SEQ ID NO: 36, or a sequence complementary thereto (e.g, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more consecutive nucleotides within the nucleotide sequence range 1-514, 30-514, 30-879, 515-1038, 880-1038, 880-1158, 1039-1663, 1159-1663, 1159-1788 or 30-1663 of SEQ ID NO: 36, or a sequence complementary thereto). For the GA3 oxidase l gene in corn, a guide RNA may be used comprising a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, or more consecutive nucleotides within the nucleotide sequence range 8030-9671 of SEQ ID NO: 174, the nucleotide sequence range of 8030-8514 SEQ ID NO: 174, the nucleotide sequence range 8888-9046 of SEQ ID NO: 174, or the nucleotide sequence range 9167-9671 of SEQ ID NO: 174, or a sequence complementary thereto (e.g, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more consecutive nucleotides within the nucleotidesequence range 7621-8514, 8030-9671, 8030-8887, 8515-9046, 8888-9046, 8888-9166, 9047-9671, 9167-9671, 9167-10276 or 8030-9671 of SEQ ID NO: 174, or a sequence complementary thereto).

[0168] For knockdown (and possibly knockout) mutations through genome editing, an RNA-guided endonuclease may be targeted to an upstream, downstream or non-coding sequence, such as a promoter and / or enhancer sequence, or an intron, 5’UTR, and / or 3’UTR sequence of a GA3 oxidase l gene to mutate one or more promoter and / or regulatory sequences of the gene and affect or reduce its level of expression. For knockdown of the GA3 oxidase l gene in com, a guide RNA may be used comprising a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, or more consecutive nucleotides within the nucleotide sequence range 1-3161 of SEQ ID NO: 168, the nucleotide sequence range 3001-3161 of SEQ ID NO: 168, the nucleotide sequence range 3647-4011 of SEQ ID NO: 168, the nucleotide sequence range 4171-4290 of SEQ ID NO: 168, the nucleotide sequence range 4796-5406 of SEQ ID NO: 168, or the nucleotide sequence range 4796-8406 of SEQ ID NO: 168, or a sequence complementary thereto (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more consecutive nucleotides within the nucleotide sequence range 1-3000, 3001-3161, 1-3161, 3647-4011, 4171-4290, 4796-5406, 5407-8406 or 4796-8406 of SEQ ID NO: 168, or a sequence complementary thereto).

[0169] For knockout (and possibly knockdown) mutations through genome editing, an RNA-guided endonuclease may be targeted to a coding and / or intron sequence of a GA3 oxidase_2 gene to potentially eliminate expression and / or activity of a functional GA3 oxidase_2 protein from the gene. For the GA3 oxidase_2 gene in corn, a guide RNA may be used comprising a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, or more consecutive nucleotides within the nucleotide sequence range 3057-4463 of SEQ ID NO: 169, the nucleotide sequence range 3057-3550 of SEQ ID NO: 169, the nucleotide sequence range 3711-3869 of SEQ ID NO: 169, or the nucleotide sequence range 3992-4463 of SEQ ID NO: 169, or a sequence complementary thereto (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more consecutive nucleotides within the nucleotide sequence range3057-4463, 3057-3550, 3057-3710, 3551-3869, 3711-3869, 3711-3991, 3870-4463, or 3992-4463 of SEQ ID NO: 169, or a sequence complementary thereto). For the GA3 oxidase_2 gene in com, a guide RNA may be used comprising a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, or more consecutive nucleotides within the nucleotide sequence range 39-1445 of SEQ ID NO: 37, the nucleotide sequence range 39-532 of SEQ ID NO: 37, the nucleotide sequence range 693-851 of SEQ ID NO: 37, or the nucleotide sequence range 983-1445 of SEQ ID NO: 37, or a sequence complementary thereto (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more consecutive nucleotides within the nucleotide sequence range 1-532, 39-532, 39-692, 533-851, 693-851, 693-982, 852-1445, 983-1445, 983-1698 or 39-1445 of SEQ ID NO: 37, or a sequence complementary thereto). For the GA3 oxidase_2 gene in corn, a guide RNA may be used comprising a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, or more consecutive nucleotides within the nucleotide sequence range 7832-8861 of SEQ ID NO: 175, the nucleotide sequence range of 7832-7926 SEQ ID NO: 175, the nucleotide sequence range 8087-8245 of SEQ ID NO: 175, or the nucleotide sequence range 8372-8861 of SEQ ID NO: 175, or a sequence complementary thereto (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more consecutive nucleotides within the nucleotide sequence range 7386-7926, 7832-7926, 7832-8086, 7927-8245, 8087-8245, 8087-8371, 8246-8861, 8372-8861, 8372-8967 or 7832-8861 of SEQ ID NO: 175, or a sequence complementary thereto).

[0170] For knockdown (and possibly knockout) mutations through genome editing, an RNA-guided endonuclease may be targeted to an upstream, downstream or non-coding sequence, such as a promoter and / or enhancer sequence, or an intron, 5’UTR, and / or 3’UTR sequence of a GA3 oxidase_2 gene to mutate one or more promoter and / or regulatory sequences of the gene and affect or reduce its level of expression. For knockdown of the GA3 oxidase_2 gene in com, a guide RNA may be used comprising a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, or more consecutive nucleotides within the nucleotide sequence range 1-3056 of SEQ ID NO: 169, the nucleotide sequence range 3001-3056 of SEQ IDNO: 169, the nucleotide sequence range 3551 -3710 of SEQ ID NO: 169, the nucleotide sequence range 3870-3991 of SEQ ID NO: 169, the nucleotide sequence range 4464-4581 of SEQ ID NO: 169, or the nucleotide sequence range 4464-7581 of SEQ ID NO: 169, or a sequence complementary thereto (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more consecutive nucleotides within the nucleotide sequence range 1-3000, 3001-3056, 1-3056, 3551-3710, 3870-3991, 4464-4581, 4464-7581 or 4582-7581 of SEQ ID NO: 169, or a sequence complementary thereto).

[0171] For knockout (and possibly knockdown) mutations through genome editing, an RNA-guided endonuclease may be targeted to a coding and / or intron sequence of a GA3 oxidase_3 gene to potentially eliminate expression and / or activity of a functional GA3 oxidase_3 protein from the gene. For the GA3 oxidase_3 gene in corn, a guide RNA may be used comprising a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, or more consecutive nucleotides within the nucleotide sequence range 3131-4274 of SEQ ID NO: 170, the nucleotide sequence range 3131-3483 of SEQ ID NO: 170, the nucleotide sequence range 3583-3907 of SEQ ID NO: 170, or the nucleotide sequence range 3999-4274 of SEQ ID NO: 170, or a sequence complementary thereto (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more consecutive nucleotides within the nucleotide sequence range 3131-4274, 3131-3483, 3131-3582, 3484-3907, 3583-3907, 3583-3998, 3908-4274, or 3999-4274 of SEQ ID NO: 170, or a sequence complementary thereto). For the GA3 oxidase_3 gene in com, a guide RNA may be used comprising a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, or more consecutive nucleotides within the nucleotide sequence range 7752-8903 of SEQ ID NO: 176, the nucleotide sequence range 7752-8104 of SEQ ID NO: 176, the nucleotide sequence range 8206-8530 of SEQ ID NO: 176, or the nucleotide sequence range 8622-8903 of SEQ ID NO: 36, or a sequence complementary thereto (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more consecutive nucleotides within the nucleotide sequence range 7547-8104, 7752-8104, 7752-8205, 8105-8530, 8206-8530, 8206-8621, 8531-8903, 8622-8903, 8622-9178 or 7752-8903 of SEQ ID NO: 176, or a sequence complementary thereto).

[0172] For knockdown (and possibly knockout) mutations through genome editing, an RNA-guided endonuclease may be targeted to an upstream, downstream or non-coding sequence, such as a promoter and / or enhancer sequence, or an intron, 5’UTR, and / or 3’UTR sequence of a GA3 oxidase_3 gene to mutate one or more promoter and / or regulatory sequences of the gene and affect or reduce its level of expression. For knockdown of the GA3 oxidase_3 gene in com, a guide RNA may be used comprising a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, or more consecutive nucleotides within the nucleotide sequence range 1-3130 of SEQ ID NO: 170, the nucleotide sequence range 3001-3130 of SEQ ID NO: 170, the nucleotide sequence range 3484-3582 of SEQ ID NO: 170, the nucleotide sequence range 3908-3998 of SEQ ID NO: 170, the nucleotide sequence range 4275-4332 of SEQ ID NO: 170, or the nucleotide sequence range 4275-7332 of SEQ ID NO: 170, or a sequence complementary thereto (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more consecutive nucleotides within the nucleotide sequence range 1-3000, 3001-3130, 1-3130, 3484-3582, 3908-3998, 4275-4332, 4275-7332 or 4333-7332 of SEQ ID NO: 170, or a sequence complementary thereto).

[0173] In addition to the guide sequence, a guide RNA may further comprise one or more other structural or scaffold sequence(s), which may bind or interact with an RNA-guided endonuclease. Such scaffold or structural sequences may further interact with other RNA molecules (e.g., tracrRNA). Methods and techniques for designing targeting constructs and guide RNAs for genome editing and site-directed integration at a target site within the genome of a plant using an RNA-guided endonuclease are known in the art.

[0174] According to some embodiments, a mutant allele of an endogenous GA3 oxidase gene of a com plant having reduced mRNA and / or protein expression can be made via a targeted genome editing technique or a mutagenesis technique as provided herein to produce one or more edits or mutations in the upstream and / or promoter region of the endogenous GA3 oxidase gene. Such edit(s) or mutations(s) may include a variety of deletions, insertions, inversions and / or substitutions, or a combination thereof, in the upstream and / or promoter region of the endogenous GA3 oxidase gene to reduce or eliminate the expression and / or activity level of the endogenous GA3 oxidase gene. In some embodiments, mutations or edits in the upstream and / or promoter region of the endogenous GA3 oxidase gene may reduce, but not eliminate, the expression and / oractivity level of the endogenous GA3 oxidase gene, as compared to a wild-type allele of the of the endogenous GA3 oxidase gene, and thus produce a hypomorphic or partial loss-of-function mutant allele of the endogenous GA3 oxidase gene, which may also provide a more intermediate phenotype or trait in a modified corn plant homozygous for the hypomorphic mutant allele, as compared to a null or complete loss-of-function mutant allele of the endogenous GA3 oxidase gene, which may produce a stronger or more severe phenotype or trait in a modified com plant homozygous for the null mutant allele of the endogenous GA3 oxidase gene.

[0175] According to some embodiments, a mutant allele of an endogenous GA3 oxidase gene of a com plant having reduced mRNA and / or protein expression can be made via a targeted genome editing technique or a mutagenesis technique as provided herein to introduce an inverted DNA segment into a non-coding sequence (e.g., untranslated region (UTR) or intron sequence) of a transcribable DNA sequence of the endogenous GA3 oxidase gene, wherein the inverted DNA segment encodes an antisense RNA sequence that is complementary to a transcribable DNA region of a wild-type allele of the endogenous GA3 oxidase gene and / or a mRNA molecule encoded by the wild-type allele of the endogenous GA3 oxidase gene, and wherein the mutant allele of the endogenous GA3 oxidase gene encodes a mRNA transcript comprising the antisense RNA sequence. By having an inverted DNA segment in the transcribable DNA region of the mutant allele of the endogenous GA3 oxidase gene, the antisense RNA sequence encoded by the inverted DNA segment can hybridize to a complementary RNA sense sequence of the mRNA encoded by a wild-type allele of the endogenous GA3 oxidase gene. Thus, in a modified corn plant heterozygous for the mutant allele of the endogenous GA3 oxidase gene comprising the inverted DNA segment, the antisense RNA sequence of the mRNA encoded by the mutant allele of the endogenous GA3 oxidase gene can hybridize to the sense RNA sequence of the mRNA encoded by the wild-type allele of the endogenous GA3 oxidase gene and trigger RNA suppression of the endogenous GA3 oxidase gene to reduce its level of expression and / or activity in the modified corn plant. However, modified com plants homozygous for the mutant allele of the endogenous GA3 oxidase gene comprising the inverted DNA segment would not have a wild-type allele of the endogenous GA3 oxidase gene, and thus there would not be a sense RNA sequence in a mRNA transcript expressed from the endogenous GA3 oxidase gene in the modified corn plant that could hybridize to the antisense RNA sequence expressed by the mutant allele of the endogenous GA3 oxidase gene and trigger suppression. As a result, RNA suppression would not be expected to occur in modified corn plants homozygous for the mutant allele with the inversion but would only be expected to occur in the heterozygote. By having the inverted DNA segment in a non-codingsequence portion of the transcribable DNA region of the mutant allele of the endogenous GA3 oxidase gene, the amino acid coding (exon) sequences of the endogenous GA3 oxidase gene would not be disrupted and the mutant allele of the endogenous GA3 oxidase gene may still be able to express a functional protein without suppression of the gene in the homozygote.

[0176] For example, FIG. 14 illustrates different zygosities for an inversion edit in the 3’ UTR of the Zm.GA3ox_l gene with hybridization between the complementary UTR sequences of the wild-type and inversion edit alleles resulting in RNA suppression or silencing of the Zm.GA3ox_l gene only in heterozygous plants (FIG. 1 C), which may result, for example, from a cross between a modified parent plant carrying the edited allele and another wild type plant. However, when a plant is homozygous for the wild-type allele (FIG. 14A) or the inversion edit allele (FIG. 14B), no hybridization of complementary sequences and RNA suppression or silencing of the Zm.GA3ox_l gene occurs. Inversion edits in the 5’ UTR of the Zm.GA3ox_l gene can also be made to produce a similar effect on expression of the Zm.GA3ox_l gene (not shown).

[0177] This type of gene modification (i.e., an inversion or inverted DNA segment in a non-coding sequence or portion of the transcribable DNA sequence of a gene) may be particularly useful for certain genes that are known to produce a phenotype or trait that is too strong or severe in plants homozygous for a loss-of-function mutant allele of the gene, whether or not a desirable or wild-type phenotype or trait is observed in plants heterozygous for the mutant allele. By contrast, plants heterozygous for a mutant allele containing the antisense inversion, the expression level and / or activity of the gene can be attenuated or reduced to provide a more moderate and desirable phenotype or trait that is not too severe in the heterozygous plant, and plants homozygous for the mutant allele would display a wild-type phenotype without RNA suppression of the gene.

[0178] According to some embodiments, recombinant DNA constructs and vectors are provided comprising a polynucleotide sequence encoding a site-specific nuclease, such as a zinc-finger nuclease (ZFN), a meganuclease, an RNA-guided endonuclease, a TALE-endonuclease (TALEN), a recombinase, or a transposase, wherein the coding sequence is operably linked to a plant expressible promoter. For RNA-guided endonucleases, recombinant DNA constructs and vectors are further provided comprising a polynucleotide sequence encoding a guide RNA, wherein the guide RNA comprises a guide sequence of sufficient length having a percent identity or complementarity to a target site within the genome of a plant, such as at or near a targeted GA oxidase gene. According to some embodiments, a polynucleotide sequence of a recombinant DNA construct and vector that encodes a site-specific nuclease or a guide RNA maybe operably linked to a plant expressible promoter, such as an inducible promoter, a constitutive promoter, a tissue-specific promoter, etc.

[0179] According to some embodiments, a recombinant DNA construct or vector may comprise a first polynucleotide sequence encoding a site-specific nuclease and a second polynucleotide sequence encoding a guide RNA that may be introduced into a plant cell together via plant transformation techniques. Alternatively, two recombinant DNA constructs or vectors may be provided including a first recombinant DNA construct or vector and a second DNA construct or vector that may be introduced into a plant cell together or sequentially via plant transformation techniques, wherein the first recombinant DNA construct or vector comprises a polynucleotide sequence encoding a site-specific nuclease and the second recombinant DNA construct or vector comprises a polynucleotide sequence encoding a guide RNA. According to some embodiments, a recombinant DNA construct or vector comprising a polynucleotide sequence encoding a site-specific nuclease may be introduced via plant transformation techniques into a plant cell that already comprises (or is transformed with) a recombinant DNA construct or vector comprising a polynucleotide sequence encoding a guide RNA. Alternatively, a recombinant DNA construct or vector comprising a polynucleotide sequence encoding a guide RNA may be introduced via plant transformation techniques into a plant cell that already comprises (or is transformed with) a recombinant DNA construct or vector comprising a polynucleotide sequence encoding a site-specific nuclease. According to yet further embodiments, a first plant comprising (or transformed with) a recombinant DNA construct or vector comprising a polynucleotide sequence encoding a site-specific nuclease may be crossed with a second plant comprising (or transformed with) a recombinant DNA construct or vector comprising a polynucleotide sequence encoding a guide RNA. Such recombinant DNA constructs or vectors may be transiently transformed into a plant cell or stably transformed or integrated into the genome of a plant cell.

[0180] In an aspect, vectors comprising polynucleotides encoding a site-specific nuclease, and optionally one or more, two or more, three or more, or four or more gRNAs are provided to a plant cell by transformation methods known in the art (e.g., without being limiting, particle bombardment, PEG-mediated protoplast transfection or ^grotocterzwm-mediated transformation). In an aspect, vectors comprising polynucleotides encoding a Cas9 nuclease, and optionally one or more, two or more, three or more, or four or more gRNAs are provided to a plant cell by transformation methods known in the art (e.g., without being limiting, particle bombardment, PEG-mediated protoplast transfection or ^groZirzcterzz / zzz-mediated transformation). In anotheraspect, vectors comprising polynucleotides encoding a Cpfl and, optionally one or more, two or more, three or more, or four or more crRNAs are provided to a cell by transformation methods known in the art (e.g., without being limiting, viral transfection, particle bombardment, PEG-mediated protoplast transfection or ^grotocterzwm-mediated transformation).

[0181] Several site-specific nucleases, such as recombinases, zinc finger nucleases (ZFNs), meganucleases, and TALENs, are not RNA-guided and instead rely on their protein structure to determine their target site for causing the DSB or nick, or they are fused, tethered or attached to a DNA-binding protein domain or motif. The protein structure of the site-specific nuclease (or the fused / attached / tethered DNA binding domain) may target the site-specific nuclease to the target site. According to many of these embodiments, non-RNA-guided site-specific nucleases, such as recombinases, zinc finger nucleases (ZFNs), meganucleases, and TALENs, may be designed, engineered and constructed according to known methods to target and bind to a target site at or near the genomic locus of an endogenous GA oxidase gene of a corn or cereal plant, such as the GA20 oxidase_3 gene or the GA20 oxidase_5 gene or a GA3 oxidase gene in com, to create a DSB or nick at such genomic locus to knockout or knockdown expression of the GA oxidase gene via repair of the DSB or nick. For example, an engineered site-specific nuclease, such as a recombinase, zinc finger nuclease (ZFN), meganuclease, or TALEN, may be designed to target and bind to (i) a target site within the genome of a plant corresponding to a sequence within SEQ ID NO: 34, or its complementary sequence, to create a DSB or nick at the genomic locus for the GA20 oxidase_3 gene, (ii) a target site within the genome of a plant corresponding to a sequence within SEQ ID NO: 35, or its complementary sequence, to create a DSB or nick at the genomic locus for the GA20 oxidase_5 gene, (iii) a target site within the genome of a plant corresponding to a sequence within SEQ ID NO: 38, or its complementary sequence, to create a DSB or nick at the genomic locus for the GA20 oxidase_4 gene, (iv) a target site within the genome of a plant corresponding to a sequence within SEQ ID NO: 36, 168 and / or 174, or its complementary sequence, to create a DSB or nick at the genomic locus for the GA3 oxidase l gene, (v) a target site within the genome of a plant corresponding to a sequence within SEQ ID NO: 37, 169 and / or 175, or its complementary sequence, to create a DSB or nick at the genomic locus for the GA3 oxidase_2 gene, or (vi) a target site within the genome of a plant corresponding to a sequence within SEQ ID NO: 170 and / or 176, or its complementary sequence, to create a DSB or nick at the genomic locus for the GA3 oxidase_3 gene, which may then lead to the creation of a mutation or insertion of a sequence at the site of the DSB or nick, through cellular repair mechanisms, which may be guided by a donor molecule or template.

[0182] In an aspect, a targeted genome editing technique described herein may comprise the use of a recombinase. In some embodiments, a tyrosine recombinase attached, etc., to a DNA recognition domain or motif may be selected from the group consisting of a Cre recombinase, a Flp recombinase, and a Tnpl recombinase. In an aspect, a Cre recombinase or a Gin recombinase provided herein may be tethered to a zinc-finger DNA binding domain. The Flp-FFT site-directed recombination system may come from the 2p plasmid from the baker’s yeast Saccharomyces cerevisiae. In this system, Flp recombinase (flippase) may recombine sequences between flippase recognition target (FRT) sites. FRT sites comprise 34 nucleotides. Flp may bind to the “arms” of the FRT sites (one arm is in reverse orientation) and cleaves the FRT site at either end of an intervening nucleic acid sequence. After cleavage, Flp may recombine nucleic acid sequences between two FRT sites. Cre-lox is a site-directed recombination system derived from the bacteriophage Pl that is similar to the Flp-FFT recombination system. Cre-lox can be used to invert a nucleic acid sequence, delete a nucleic acid sequence, or translocate a nucleic acid sequence. In this system, Cre recombinase may recombine a pair of lox nucleic acid sequences. Lox sites comprise 34 nucleotides, with the first and last 13 nucleotides (arms) being palindromic. During recombination, Cre recombinase protein binds to two lox sites on different nucleic acids and cleaves at the lox sites. The cleaved nucleic acids are spliced together (reciprocally translocated) and recombination is complete. In another aspect, a lox site provided herein is a loxP, lox 2272, loxN, lox 511, lox 5171, lox71, lox66, M2, M3, M7, or Mi l site.

[0183] ZFNs are synthetic proteins consisting of an engineered zinc finger DNA-binding domain fused to a cleavage domain (or a cleavage half-domain), which may be derived from a restriction endonuclease (e.g., FokT). The DNA binding domain may be canonical (C2H2) or non-canonical (e.g., C3H or C4). The DNA-binding domain can comprise one or more zinc fingers (e.g., 2, 3, 4, 5, 6, 7, 8, 9 or more zinc fingers) depending on the target site. Multiple zinc fingers in a DNA-binding domain may be separated by linker sequence(s). ZFNs can be designed to cleave almost any stretch of double-stranded DNA by modification of the zinc finger DNA-binding domain. ZFNs form dimers from monomers composed of a non-specific DNA cleavage domain (e.g., derived from the FokI nuclease) fused to a DNA-binding domain comprising a zinc finger array engineered to bind a target site DNA sequence. The DNA-binding domain of a ZFN may typically be composed of 3-4 (or more) zinc-fingers. The amino acids at positions -1, +2, +3, and +6 relative to the start of the zinc finger a-helix, which contribute to site-specific binding to the target site, can be changed and customized to fit specific target sequences. The other amino acids may form a consensus backbone to generate ZFNs with different sequence specificities. Methodsand rules for designing ZFNs for targeting and binding to specific target sequences are known in the art. See, e.g., US Patent App. Nos. 2005 / 0064474, 2009 / 0117617, and 2012 / 0142062, the contents and disclosures of which are incorporated herein by reference. The FokI nuclease domain may require dimerization to cleave DNA and therefore two ZFNs with their C-terminal regions are needed to bind opposite DNA strands of the cleavage site (separated by 5-7 bp). The ZFN monomer can cut the target site if the two-ZF -binding sites are palindromic. A ZFN, as used herein, is broad and includes a monomeric ZFN that can cleave double stranded DNA without assistance from another ZFN. The term ZFN may also be used to refer to one or both members of a pair of ZFNs that are engineered to work together to cleave DNA at the same site.

[0184] Without being limited by any scientific theory, because the DNA-binding specificities of zinc finger domains can be re-engineered using one of various methods, customized ZFNs can theoretically be constructed to target nearly any target sequence (e.g., at or near a GA oxidase gene in a plant genome). Publicly available methods for engineering zinc finger domains include Context-dependent Assembly (CoDA), Oligomerized Pool Engineering (OPEN), and Modular Assembly. In an aspect, a method and / or composition provided herein comprises one or more, two or more, three or more, four or more, or five or more ZFNs. In another aspect, a ZFN provided herein is capable of generating a targeted DSB or nick. In an aspect, vectors comprising polynucleotides encoding one or more, two or more, three or more, four or more, or five or more ZFNs are provided to a cell by transformation methods known in the art (e.g., without being limiting, viral transfection, particle bombardment, PEG-mediated protoplast transfection, or Agrobacterium-mediated transformation). The ZFNs may be introduced as ZFN proteins, as polynucleotides encoding ZFN proteins, and / or as combinations of proteins and protein-encoding polynucleotides.

[0185] Meganucleases, which are commonly identified in microbes, such as the LAGLID ADG family of homing endonucleases, are unique enzymes with high activity and long recognition sequences (> 14 bp) resulting in site-specific digestion of target DNA. Engineered versions of naturally occurring meganucleases typically have extended DNA recognition sequences (for example, 14 to 40 bp). According to some embodiments, a meganuclease may comprise a scaffold or base enzyme selected from the group consisting of I-Crel, I-Ceul, I-Msol, I-Scel, I-Anil, and I-Dmol. The engineering of meganucleases can be more challenging than ZFNs and TALENs because the DNA recognition and cleavage functions of meganucleases are intertwined in a single domain. Specialized methods of mutagenesis and high-throughput screening have been used tocreate novel meganuclease variants that recognize unique sequences and possess improved nuclease activity. Thus, a meganuclease may be selected or engineered to bind to a genomic target sequence in a plant, such as at or near the genomic locus of a GA oxidase gene. In an aspect, a method and / or composition provided herein comprises one or more, two or more, three or more, four or more, or five or more meganucleases. In another aspect, a meganuclease provided herein is capable of generating a targeted DSB. In an aspect, vectors comprising polynucleotides encoding one or more, two or more, three or more, four or more, or five or more meganucleases are provided to a cell by transformation methods known in the art (e.g., without being limiting, viral transfection, particle bombardment, PEG-mediated protoplast transfection or A grobacterium -medi ated transformati on) .

[0186] TALENs are artificial restriction enzymes generated by fusing the transcription activator-like effector (TALE) DNA binding domain to a nuclease domain (e.g., FokT). When each member of a TALEN pair binds to the DNA sites flanking a target site, the FokI monomers dimerize and cause a double-stranded DNA break at the target site. Besides the wild-type FokI cleavage domain, variants of the FokI cleavage domain with mutations have been designed to improve cleavage specificity and cleavage activity. The FokI domain functions as a dimer, requiring two constructs with unique DNA binding domains for sites in the target genome with proper orientation and spacing. Both the number of amino acid residues between the TALEN DNA binding domain and the FokI cleavage domain and the number of bases between the two individual TALEN binding sites are parameters for achieving high levels of activity.

[0187] TALENs are artificial restriction enzymes generated by fusing the transcription activator-like effector (TALE) DNA binding domain to a nuclease domain. In some aspects, the nuclease is selected from a group consisting of PvuII, MulH. TevI, FokI, A v I, Mlyl, Sbfl, Sdal, StsI, CleDORF, Clo051, and Pept071. When each member of a TALEN pair binds to the DNA sites flanking a target site, the FokI monomers dimerize and cause a double-stranded DNA break at the target site. The term TALEN, as used herein, is broad and includes a monomeric TALEN that can cleave double stranded DNA without assistance from another TALEN. The term TALEN is also refers to one or both members of a pair of TALENs that work together to cleave DNA at the same site.

[0188] Transcription activator-like effectors (TALEs) can be engineered to bind practically any DNA sequence, such as at or near the genomic locus of a GA oxidase gene in a plant. TALE has a central DNA-binding domain composed of 13-28 repeat monomers of 33-34 amino acids.The amino acids of each monomer are highly conserved, except for hypervariable amino acid residues at positions 12 and 13. The two variable amino acids are called repeat-variable diresidues (RVDs). The amino acid pairs NI, NG, HD, and NN of RVDs preferentially recognize adenine, thymine, cytosine, and guanine / adenine, respectively, and modulation of RVDs can recognize consecutive DNA bases. This simple relationship between amino acid sequence and DNA recognition has allowed for the engineering of specific DNA binding domains by selecting a combination of repeat segments containing the appropriate RVDs.

[0189] Besides the wild-type FokI cleavage domain, variants of the FokI cleavage domain with mutations have been designed to improve cleavage specificity and cleavage activity. The FokI domain functions as a dimer, requiring two constructs with unique DNA binding domains for sites in the target genome with proper orientation and spacing. Both the number of amino acid residues between the TALEN DNA binding domain and the FokI cleavage domain and the number of bases between the two individual TALEN binding sites are parameters for achieving high levels of activity. PvuII, MutH, and TevI cleavage domains are useful alternatives to FokI and FokI variants for use with TALEs. PvuII functions as a highly specific cleavage domain when coupled to a TALE (see Yank etal. 2013. PLoS One. 8: e82539). MulHC capable of introducing strand-specific nicks in DNA (see Gabsalilow et al. 2013. Nucleic Acids Research. 41 : e83). TevI introduces double-stranded breaks in DNA at targeted sites (see Beurdeley et al., 2013. Nature Communications. 4: 1762).

[0190] The relationship between amino acid sequence and DNA recognition of the TALE binding domain allows for designable proteins. Software programs such as DNA Works can be used to design TALE constructs. Other methods of designing TALE constructs are known to those of skill in the art. See Doyle et al., Nucleic Acids Research (2012) 40: W 117-122.; Cermak et al., Nucleic Acids Research (2011). 39:e82; and tale-nt.cac.comell.edu / about. In an aspect, a method and / or composition provided herein comprises one or more, two or more, three or more, four or more, or five or more TALENs. In another aspect, a TALEN provided herein is capable of generating a targeted DSB. In an aspect, vectors comprising polynucleotides encoding one or more, two or more, three or more, four or more, or five or more TALENs are provided to a cell by transformation methods known in the art (e.g., without being limiting, viral transfection, particle bombardment, PEG-mediated protoplast transfection or Hgrotocterzwm-mediated transformation). See, e.g., US Patent App. Nos. 2011 / 0145940, 2011 / 0301073, and 2013 / 0117869, the contents and disclosures of which are incorporated herein by reference.

[0191] As used herein, a “targeted genome editing technique” refers to any method, protocol, or technique that allows the precise and / or targeted editing of a specific location in a genome of a plant (z.e., the editing is largely or completely non-random) using a site-specific nuclease, such as a meganuclease, a zinc-finger nuclease (ZFN), an RNA-guided endonuclease (e.g., the CRISPR / Cas9 system), a TALE-endonuclease (TALEN), a recombinase, or a transposase. As used herein, “editing” or “genome editing” refers to generating a targeted mutation, deletion, inversion or substitution of at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 75, at least 100, at least 250, at least 500, at least 1000, at least 2500, at least 5000, at least 10,000, or at least 25,000 nucleotides of an endogenous plant genome nucleic acid sequence. As used herein, “editing” or “genome editing” also encompasses the targeted insertion or site-directed integration of at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 75, at least 100, at least 250, at least 500, at least 750, at least 1000, at least 1500, at least 2000, at least 2500, at least 3000, at least 4000, at least 5000, at least 10,000, or at least 25,000 nucleotides into the endogenous genome of a plant. An “edit” or “genomic edit” in the singular refers to one such targeted mutation, deletion, inversion, substitution or insertion, whereas “edits” or “genomic edits” refers to two or more targeted mutation(s), deletion(s), inversion(s), substitution(s) and / or insertion(s), with each “edit” being introduced via a targeted genome editing technique.

[0192] Given that suppression of GA20 oxidase_3, GA20 oxidase_4, GA20 oxidase_5, and / or GA3 oxidase l genes in com produces plants having a shorter plant height and internode length in addition to other beneficial traits, it is proposed that expression of one or more of GA20 oxidase and / or GA3 oxidase genes may be reduced or eliminated through genome editing one or more of these gene(s) to provide similar beneficial traits to corn plants. Given further that constitutive expression of suppression constructs targeting these GA20 oxidase or GA3 oxidase genes produces corn plants having the beneficial short height traits without off-types in the ear, and that expression directly in reproductive ear tissues also does not give rise to reproductive off-types, it is proposed that one or more of these gene loci may be edited to knock-down or knock-out their expression to produce similar effects in com plants. Targeted gene editing approaches could be used to modify the sequence of the promoter and / or regulatory region(s) of one or more of the GA20 oxidase_3, GA20 oxidase_4, GA20 oxidase_5, GA3 oxidase_l, GA3 oxidase_2, and / or GA3 oxidase_3 genes to knock-down or knock-out expression of these gene(s), such as throughtargeted deletions, insertions, mutations, or other sequence changes. Indeed, the promoter and / or regulatory region(s) or sequence(s), or the 5’-UTR, 3’UTR, and / or intron sequence(s), of one or more of the GA20 oxidase_3, GA20 oxidase_4, GA20 oxidase_5, GA3 oxidase_l, GA3 oxidase_2, and / or GA3 oxidase_3 genes may be largely deleted or mutated. Alternatively, all or a portion of the coding (exon), 5-UTR, 3’UTR, and / or intron sequence(s) of one or more of the GA20 oxidase_3, GA20 oxidase_4, GA20 oxidase_5, GA3 oxidase_l, GA3 oxidase_2, and / or GA3 oxidase_3 genes may be edited, deleted, mutated, or otherwise modified to knock-down or knock-out expression or activity of these gene(s). Such targeted modifications to the GA20 oxidase_3, GA20 oxidase_4, GA20 oxidase_5, GA3 oxidase_l, GA3 oxidase_2, and / or GA3 oxidase_3 gene loci may be achieved using any suitable genome editing technology known in the art, such as via repair of a double strand break (DSB) or nick introduced by a site-specific nuclease, such as, for example, a zinc-finger nuclease, an engineered or native meganuclease, a TALE-endonuclease, or an RNA-guided endonuclease (e.g., Cas9 or Cpfl). Such repair of the DSB or nick may introduce spontaneous or stochastic deletions, additions, mutations, etc., at the targeted site where the DSB or nick was introduced, or repair of the site may involve the use of a donor template molecule to direct or cause a preferred or specific deletion, addition, mutation, etc., at the targeted site.

[0193] As provided herein, a plant transformed with a recombinant DNA molecule or transformation vector comprising a transgene or a transcribable DNA sequence encoding a non-coding RNA molecule that targets an endogenous GA oxidase gene for suppression or encoding a guide RNA and / or a site specific nuclease for editing an endogenous GA oxidase gene may include a variety of monocot or cereal plants, such as maize / com and other monocot or cereal plants that have separate male and female flowers (similarly to corn) and may thus be susceptible to off-types in female reproductive organs, structures or tissues with mutations to the GA pathway.

[0194] Further provided are methods for introducing or transforming into a cereal plant, plant part, or plant cell any of the foregoing constructs, vectors, or constructs, according to any of the methods described herein, which may be constructed in any suitable manner described herein including different stacking or joint targeting arrangements, as well as modified cereal plants, plant parts, plant tissues, and plant cells made thereby and / or comprising any such recombinant DNA molecule, vector or construct. Since a non-coding RNA molecule expressed from the above constructs would be designed to target an endogenous GA oxidase gene, the cereal plant transformed with such recombinant DNA molecules, vectors or constructs should preferablycorrespond to the species of origin for the target sequence, or closely related species, strains, germplasms, lines, etc.

[0195] Further provided are methods for introducing or transforming into a cereal plant, plant part, or plant cell any guide RNA described above, or any construct, vector, or construct encoding a guide RNA, perhaps in addition to an RNA-guided nuclease, according to any of the methods described herein, as well as modified cereal plants, plant parts, plant tissues, and plant cells made thereby and / or comprising any such recombinant DNA molecule, vector or construct and / or an edited GA oxidase gene. Modified cereal plants having an edited GA oxidase gene, and / or a suppression element targeting a GA oxidase gene, may have one or more beneficial traits provided herein, such as a shorter plant height, shorter internode length, increased stalk / stem diameter, improved lodging resistance, and / or drought tolerance, relative to a wild-type or control plant not having any such edit or suppression element. In addition to genome editing, mutations in a GA oxidase gene may be introduced through other mutagenesis techniques as described herein.

[0196] According to another aspect of the present disclosure, a transgenic plant(s), plant cell(s), seed(s), and plant part(s) are provided comprising a transformation event or insertion into the genome of at least one plant cell thereof, wherein the transformation event or insertion comprises a recombinant DNA sequence, construct or expression cassette comprising a transcribable DNA sequence encoding a non-coding RNA molecule that targets an endogenous GA oxidase gene for suppression or a guide RNA and / or a site specific nuclease for editing an endogenous GA oxidase gene, wherein the transcribable DNA sequence is operably linked to a plant-expressible promoter, such as a constitutive, vascular and / or leaf promoter. Such a transgenic plant may be produced by any suitable transformation method as provided above, to produce a transgenic Ro plant, which may then be selfed or crossed to other plants to generate Ri seed and subsequent progeny generations and seed through additional crosses, etc. Embodiments of the present disclosure further include a plant cell, tissue, explant, plant part, etc., comprising one or more transgenic cells having a transformation event or genomic insertion of a recombinant DNA or polynucleotide sequence comprising a transcribable DNA sequence encoding a non-coding RNA molecule that targets an endogenous GA oxidase gene for suppression.

[0197] Transgenic plants, plant cells, seeds, and plant parts of the present disclosure may be homozygous or hemizygous for a transgenic event or insertion of a transcribable DNA sequence for suppression of a GA oxidase gene into the genome of at least one plant cell thereof, or a targeted genome editing event, and plants, plant cells, seeds, and plant parts of the presentembodiments may contain any number of copies of such transgenic event(s), insertion(s) and / or edit(s). The dosage or amount of expression of a transgene or transcribable DNA sequence or a wild-type or mutant allele of an endogenous gene may be altered by its zygosity and / or number of copies, which may affect the degree or extent of phenotypic changes in the transgenic plant, etc. As introduced above, transgenic plants provided herein may include a variety of monocot or cereal plants, such as corn or maize, already having increased yield and / or lodging resistance due to prior breeding efforts and mutations of the GA pathway in these plants. Advantages of using a transgene or transcribable DNA sequence to express a suppression element targeting a biosynthetic GA oxidase gene include not only the ability to limit expression in a tissue-specific or tissue-preferred manner, but also the potential dominance (e.g., dominant negative effects) of a single or hemizygous copy of the transcribable DNA sequence to cause the beneficial short- stature, semi-dwarf traits or phenotypes in crop plants. Thus, recombinant DNA molecules or constructs of the present disclosure may be used to create beneficial traits in a variety of monocot or cereal plants without off-types using only a single copy of the transgenic event, insertion or construct. Plants transformed with the GA-modifying transgenes and suppression constructs of the present disclosure may improve traits, yield and crop breeding efforts by facilitating the production of hybrid cereal plants since they only require a single or hemizygous copy of the transgene or suppression construct.

[0198] According to some embodiments, a transgenic or modified cereal or corn plant comprising a GA oxidase transgene or transcribable DNA sequence for suppression of an endogenous GA oxidase gene, or a genome edited GA oxidase gene, may be further characterized as having one or more beneficial traits, such as a shorter stature or semi-dwarf plant height, reduced internode length, increased stalk / stem diameter, improved lodging resistance, reduced green snap, deeper roots, increased leaf area, earlier canopy closure, increased foliar water content and / or higher stomatai conductance under water limiting conditions, reduced anthocyanin content and / or area in leaves under normal or nitrogen or water limiting stress conditions, improved yield-related traits including a larger female reproductive organ or ear, an increase in ear weight, harvest index, yield, seed or kernel number, and / or seed or kernel weight, relative to a wild type or control plant. Such a transgenic cereal or corn plant may further have increased stress tolerance, such as increased drought tolerance, nitrogen utilization, and / or tolerance to high density planting.

[0199] For purposes of the present disclosure, a “plant” includes an explant, plant part, seedling, plantlet or whole plant at any stage of regeneration or development. As used herein, a“transgenic plant” refers to a plant whose genome has been altered by the integration or insertion of a recombinant DNA molecule, construct or sequence. A transgenic plant includes an Ro plant developed or regenerated from an originally transformed plant cell(s) as well as progeny transgenic plants in later generations or crosses from the Ro transgenic plant. As used herein, a “plant part” may refer to any organ or intact tissue of a plant, such as a meristem, shoot organ / structure (e.g., leaf, stem or node), root, flower or floral organ / structure (e.g., bract, sepal, petal, stamen, carpel, anther and ovule), seed (e.g., embryo, endosperm, and seed coat), fruit (e.g., the mature ovary), propagule, or other plant tissues (e.g., vascular tissue, dermal tissue, ground tissue, and the like), or any portion thereof. Plant parts of the present disclosure may be viable, nonviable, regenerable, and / or non-regenerable. A “propagule” may include any plant part that can grow into an entire plant.

[0200] According to present embodiments, a plant cell transformed with a construct or molecule comprising a transcribable DNA sequence for suppression of an endogenous GA oxidase gene, or with a construct used for genome editing of a GA oxidase gene, may include any plant cell that is competent for transformation as understood in the art based on the method of transformation, such as a meristem cell, an embryonic cell, a callus cell, etc. As used herein, a “transgenic plant cell” simply refers to any plant cell that is transformed with a stably-integrated recombinant DNA molecule, construct or sequence. A transgenic plant cell may include an originally-transformed plant cell, a transgenic plant cell of a regenerated or developed Ro plant, a transgenic plant cell cultured from another transgenic plant cell, or a transgenic plant cell from any progeny plant or offspring of the transformed Ro plant, including cell(s) of a plant seed or embryo, or a cultured plant cell, callus cell, etc.

[0201] Embodiments of the present disclosure further include methods for making or producing transgenic or modified plants, such as by transformation, genome editing, crossing, etc., wherein the method comprises introducing a recombinant DNA molecule, construct or sequence comprising a GA oxidase transgene or a transcribable DNA sequence for suppression of an endogenous GA oxidase gene into a plant cell, or editing the genomic locus of an endogenous GA oxidase gene, and then regenerating or developing the transgenic or modified plant from the transformed or edited plant cell, which may be performed under selection pressure favoring a transgenic event. Such methods may comprise transforming a plant cell with a recombinant DNA molecule, construct or sequence comprising the transcribable DNA sequence for suppression of an endogenous GA oxidase gene, and selecting for a plant having one or more altered phenotypes ortraits, such as one or more of the following traits at one or more stages of development: shorter or semi-dwarf stature or plant height, shorter internode length in one or more internode(s), increased stalk / stem diameter, improved lodging resistance, reduced green snap, deeper roots, increased leaf area, earlier canopy closure, increased foliar water content and / or higher stomatai conductance under water limiting conditions, reduced anthocyanin content and / or area in leaves under normal or nitrogen or water limiting stress conditions, improved yield-related traits including a larger female reproductive organ or ear, an increase in ear weight, harvest index, yield, seed or kernel number, and / or seed or kernel weight, increased stress tolerance, such as increased drought tolerance, increased nitrogen utilization, and / or increased tolerance to high density planting, as compared to a wild type or control plant.

[0202] According to another aspect of the present disclosure, methods are provided for planting a modified or transgenic plant(s) provided herein at a normal / standard or high density in field. According to some embodiments, the yield of a crop plant per acre (or per land area) may be increased by planting a modified or transgenic plant(s) of the present disclosure at a higher density in the field. As described herein, modified or transgenic plants expressing a transcribable DNA sequence that encodes a non-coding RNA molecule targeting an endogenous GA oxidase gene for suppression, or having a genome-edited GA oxidase gene, may have reduced plant height, shorter internode(s), increased stalk / stem diameter, and / or increased lodging resistance. It is proposed that modified or transgenic plants may tolerate high density planting conditions since an increase in stem diameter may resist lodging and the shorter plant height may allow for increased light penetrance to the lower leaves under high density planting conditions. Thus, modified or transgenic plants provided herein may be planted at a higher density to increase the yield per acre (or land area) in the field. For row crops, higher density may be achieved by planting a greater number of seeds / plants per row length and / or by decreasing the spacing between rows.

[0203] According to some embodiments, a modified or transgenic crop plant may be planted at a density in the field (plants per land / field area) that is at least 5%, 10%, 15%, 20%, 25%, 50%, 75%, 100%, 125%, 150%, 175%, 200%, 225%, or 250% higher than the normal planting density for that crop plant according to standard agronomic practices. A modified or transgenic crop plant may be planted at a density in the field of at least 38,000 plants per acre, at least 40,000 plants per acre, at least 42,000 plants per acre, at least 44,000 plants per acre, at least 45,000 plants per acre, at least 46,000 plants per acre, at least 48,000 plants per acre, 50,000 plants per acre, at least 52,000 plants per acre, at least 54,000 per acre, or at least 56,000 plants per acre. As an example, cornplants may be planted at a higher density, such as in a range from about 38,000 plants per acre to about 60,000 plants per acre, or about 40,000 plants per acre to about 58,000 plants per acre, or about 42,000 plants per acre to about 58,000 plants per acre, or about 40,000 plants per acre to about 45,000 plants per acre, or about 45,000 plants per acre to about 50,000 plants per acre, or about 50,000 plants per acre to about 58,000 plants per acre, or about 52,000 plants per acre to about 56,000 plants per acre, or about 38,000 plants per acre, about 42,000 plant per acre, about 46,000 plant per acre, or about 48,000 plants per acre, about 50,000 plants per acre, or about 52,000 plants per acre, or about 54,000 plant per acre, as opposed to a standard density range, such as about 18,000 plants per acre to about 38,000 plants per acre.

[0204] According to embodiments of the present disclosure, a modified corn plant(s) is / are provided that comprise (i) a plant height of less than 2000 mm, less than 1950 mm, less than 1900 mm, less than 1850 mm, less than 1800 mm, less than 1750 mm, less than 1700 mm, less than 1650 mm, less than 1600 mm, less than 1550 mm, less than 1500 mm, less than 1450 mm, less than 1400 mm, less than 1350 mm, less than 1300 mm, less than 1250 mm, less than 1200 mm, less than 1150 mm, less than 1100 mm, less than 1050 mm, or less than 1000 mm, and / or (ii) an average stem or stalk diameter of at least 18 mm, at least 18.5 mm, at least 19 mm, at least 19.5 mm, at least 20 mm, at least 20.5 mm, at least 21 mm, at least 21.5 mm, or at least 22 mm. Stated a different way, a modified corn plant(s) is / are provided that comprise a plant height of less than 2000 mm, less than 1950 mm, less than 1900 mm, less than 1850 mm, less than 1800 mm, less than 1750 mm, less than1700 mm, less than 1650 mm, less than 1600 mm, less than 1550 mm, less than 1500 mm, less than1450 mm, less than 1400 mm, less than 1350 mm, less than 1300 mm, less than 1250 mm, less than1200 mm, less than 1150 mm, less than 1100 mm, less than 1050 mm, or less than 1000 mm, and / or an average stem or stalk diameter that is greater than 18 mm, greater than 18.5 mm, greater than 19 mm, greater than 19.5 mm, greater than 20 mm, greater than 20.5 mm, greater than 21 mm, greater than 21.5 mm, or greater than 22 mm. Any such plant height trait or range that is expressed in millimeters (mm) may be converted into a different unit of measurement based on known conversions (e.g., one inch is equal to 2.54 cm or 25.4 millimeters, and millimeters (mm), centimeters (cm) and meters (m) only differ by one or more powers of ten). Thus, any measurement provided herein is further described in terms of any other comparable units of measurement according to known and established conversions. However, the exact plant height and / or stem diameter of a modified corn plant may depend on the environment and genetic background. Thus, the change in plant height and / or stem diameter of a modified corn plant may instead be described in terms of a minimum difference or percent change relative to a control plant.A modified corn plant may further comprise at least one ear that is substantially free of male reproductive tissues or structures or other off-types.

[0205] According to embodiments of the present disclosure, modified com plants are provided that comprise a plant height during late vegetative and / or reproductive stages of development (e.g., at R3 stage) of between 1000 mm and 1800mm, between 1000 mm and 1700 mm, between 1050 mm and 1700 mm, between 1100 mm and 1700 mm, between 1150 mm and 1700 mm, between 1200 mm and 1700 mm, between 1250 mm and 1700 mm, between 1300 mm and 1700 mm, between 1350 mm and 1700 mm, between 1400 mm and 1700 mm, between 1450 mm and 1700 mm, between 1000 mm and 1500 mm, between 1050 mm and 1500 mm, between 1100 mm and 1500 mm, between 1150 mm and 1500 mm, between 1200 mm and 1500 mm, between 1250 mm and 1500 mm, between 1300 mm and 1500 mm, between 1350 mm and 1500 mm, between 1400 mm and 1500 mm, between 1450 mm and 1500 mm, between 1000 mm and 1600 mm, between 1100 mm and 1600 mm, between 1200 mm and 1600 mm, between 1300 mm and 1600 mm, between 1350 mm and 1600 mm, between 1400 mm and 1600 mm, between 1450 mm and 1600 mm, of between 1000 mm and 2000 mm, between 1200 mm and 2000 mm, between 1200 mm and 1800 mm, between 1300 mm and 1700 mm, between 1400 mm and 1700 mm, between 1400 mm and 1600 mm, between 1400 mm and 1700 mm, between 1400 mm and 1800 mm, between 1400 mm and 1900 mm, between 1400 mm and 2000 mm, or between 1200 mm and 2500 mm, and / or an average stem diameter of between 17.5 mm and 22 mm, between 18 mm and 22 mm, between 18.5 and 22 mm, between 19 mm and 22 mm, between 19.5 mm and 22 mm, between 20 mm and 22 mm, between 20.5 mm and 22 mm, between 21 mm and 22 mm, between 21.5 mm and 22 mm, between 17.5 mm and 21 mm, between 17.5 mm and 20 mm, between 17.5 mm and 19 mm, between 17.5 mm and 18 mm, between 18 mm and 21 mm, between 18 mm and 20 mm, or between 18 mm and 19 mm. A modified corn plant may be substantially free of off-types, such as male reproductive tissues or structures in one or more ears of the modified corn plant.

[0206] According to embodiments of the present disclosure, modified com plants are provided that have (i) a plant height that is at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, or at least 75% less than the height of a wild-type or control plant, and / or (ii) a stem or stalk diameter that is at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or atleast 100% greater than the stem diameter of the wild-type or control plant. According to embodiments of the present disclosure, a modified com plant may have a reduced plant height that is no more than 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, or 60% shorter than the height of a wild-type or control plant, and / or a stem or stalk diameter that is less than (or not more than) 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% greater than the stem or stalk diameter of a wild-type or control plant. For example, a modified plant may have (i) a plant height that is at least 10%, at least 15%, or at least 20% less or shorter (i.e., greater than or equal to 10%, 15%, or 20% shorter), but not greater or more than 50% shorter, than a wild type or control plant, and / or (ii) a stem or stalk diameter that is that is at least 5%, at least 10%, or at least 15% greater, but not more than 30%, 35%, or 40% greater, than a wild type or control plant. For clarity, the phrases “at least 20% shorter” and “greater than or equal to 20% shorter” would exclude, for example, 10% shorter. Likewise for clarity, the phrases “not greater than 50% shorter”, “no more than 50% shorter” and “not more than 50% shorter” would exclude 60% shorter; the phrase “at least 5% greater” would exclude 2% greater; and the phrases “not more than 30% greater” and “no more than 30% greater” would exclude 40% greater.

[0207] According to embodiments of the present disclosure, modified com plants are provided that comprise a height between 5% and 75%, between 5% and 50%, between 10% and 70%, between 10% and 65%, between 10% and 60%, between 10% and 55%, between 10% and 50%, between 10% and 45%, between 10% and 40%, between 10% and 35%, between 10% and 30%, between 10% and 25%, between 10% and 20%, between 10% and 15%, between 10% and 10%, between 10% and 75%, between 25% and 75%, between 10% and 50%, between 20% and 50%, between 25% and 50%, between 30% and 75%, between 30% and 50%, between 25% and 50%, between 15% and 50%, between 20% and 50%, between 25% and 45%, or between 30% and 45% less than the height of a wild-type or control plant, and / or a stem or stalk diameter that is between 5% and 100%, between 5% and 95%, between 5% and 90%, between 5% and 85%, between 5% and 80%, between 5% and 75%, between 5% and 70%, between 5% and 65%, between 5% and 60%, between 5% and 55%, between 5% and 50%, between 5% and 45%, between 5% and 40%, between 5% and 35%, between 5% and 30%, between 5% and 25%, between 5% and 20%, between 5% and 15%, between 5% and 10%, between 10% and 100%, between 10% and 75%, between 10% and 50%, between 10% and 40%, between 10% and 30%, between 10% and 20%, between 25% and 75%, between 25% and 50%, between 50% and 75%, between 8% and 20%, or between 8% and 15% greater than the stem or stalk diameter of the wild-type or control plant.

[0208] According to embodiments of the present disclosure, modified com plants are provided that comprise an average internode length (or a minus-2 internode length and / or minus-4 internode length relative to the position of the ear) that is at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, or at least 75% less than the same or average internode length of a wild-type or control plant. The “minus-2 internode” of a corn plant refers to the second internode below the ear of the plant, and the “minus-4 internode” of a corn plant refers to the fourth internode below the ear of the plant According to many embodiments, modified corn plants are provided that have an average internode length (or a minus-2 internode length and / or minus-4 internode length relative to the position of the ear) that is between 5% and 75%, between 5% and 50%, between 10% and 70%, between 10% and 65%, between 10% and 60%, between 10% and55%, between 10% and 50%, between 10% and 45%, between 10% and 40%, between 10% and35%, between 10% and 30%, between 10% and 25%, between 10% and 20%, between 10% and15%, between 10% and 10%, between 10% and 75%, between 25% and 75%, between 10% and50%, between 20% and 50%, between 25% and 50%, between 30% and 75%, between 30% and50%, between 25% and 50%, between 15% and 50%, between 20% and 50%, between 25% and45%, or between 30% and 45% less than the same or average internode length of a wild-type or control plant.

[0209] According to embodiments of the present disclosure, modified com plants are provided that comprise an ear weight (individually or on average) that is at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 100% greater than the ear weight of a wild-type or control plant. A modified com plant provided herein may comprise an ear weight that is between 5% and 100%, between 5% and 95%, between 5% and 90%, between 5% and 85%, between 5% and 80%, between 5% and 75%, between 5% and 70%, between 5% and 65%, between 5% and 60%, between 5% and 55%, between 5% and 50%, between 5% and 45%, between 5% and 40%, between 5% and 35%, between 5% and 30%, between 5% and 25%, between 5% and 20%, between 5% and 15%, between 5% and 10%, between 10% and 100%, between 10% and 75%, between 10% and 50%, between 25% and 75%, between 25% and 50%, or between 50% and 75% greater than the ear weight of a wild-type or control plant.

[0210] According to embodiments of the present disclosure, modified corn or cereal plants are provided that have a harvest index of at least 0.57, at least 0.58, at least 0.59, at least 0.60, at least 0.61, at least 0.62, at least 0.63, at least 0.64, or at least 0.65 (or greater). A modified corn plant may comprise a harvest index of between 0.57 and 0.65, between 0.57 and 0.64, between 0.57 and 0.63, between 0.57 and 0.62, between 0.57 and 0.61, between 0.57 and 0.60, between 0.57 and 0.59, between 0.57 and 0.58, between 0.58 and 0.65, between 0.59 and 0.65, or between 0.60 and 0.65. A modified corn plant may have a harvest index that is at least 1%, at least 2%, at least 3%, at least 4%, at least 5%, at least 6%, at least 7%, at least 8%, at least 9%, at least 10%, at least 11%, at least 12%, at least 13%, at least 14%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, or at least 50% greater than the harvest index of a wild-type or control plant. A modified corn plant may have a harvest index that is between 1% and 45%, between 1% and 40%, between 1% and 35%, between 1% and 30%, between 1% and 25%, between 1% and 20%, between 1% and 15%, between 1% and 14%, between 1% and 13%, between 1% and 12%, between 1% and 11%, between 1% and 10%, between 1% and 9%, between 1% and 8%, between 1% and 7%, between 1% and 6%, between 1% and 5%, between 1% and 4%, between 1% and 3%, between 1% and 2%, between 5% and 15%, between 5% and 20%, between 5% and 30%, or between 5% and 40% greater than the harvest index of a wild-type or control plant.

[0211] According to embodiments of the present disclosure, modified corn or cereal plants are provided that have an increase in harvestable yield of at least 1 bushel per acre, at least 2 bushels per acre, at least 3 bushels per acre, at least 4 bushels per acre, at least 5 bushels per acre, at least 6 bushels per acre, at least 7 bushels per acre, at least 8 bushels per acre, at least 9 bushels per acre, or at least 10 bushels per acre, relative to a wild-type or control plant. A modified com plant may have an increase in harvestable yield between 1 and 10, between 1 and 8, between 2 and 8, between 2 and 6, between 2 and 5, between 2.5 and 4.5, or between 3 and 4 bushels per acre. A modified corn plant may have an increase in harvestable yield that is at least 1%, at least 2%, at least 3%, at least 4%, at least 5%, at least 6%, at least 7%, at least 8%, at least 9%, at least 10%, at least 11%, at least 12%, at least 13%, at least 14%, at least 15%, at least 20%, or at least 25% greater than the harvestable yield of a wild-type or control plant. A modified corn plant may have a harvestable yield that is between 1% and 25%, between 1% and 20%, between 1% and 15%, between 1% and 14%, between 1% and 13%, between 1% and 12%, between 1% and 11%, between 1% and 10%, between 1% and 9%, between 1% and 8%, between 1% and 7%, between 1% and 6%, between 1% and 5%, between 1% and 4%, between 1% and 3%, between 1% and 2%, between 5% and 15%, between 5% and 20%, between 5% and 25%, between 2% and 10%, between 2% and 9%, between2% and 8%, between 2% and 7%, between 2% and 6%, between 2% and 5%, or between 2% and 4% greater than the harvestable yield of a wild-type or control plant.

[0212] According to embodiments of the present disclosure, a modified cereal or corn plant is provided that has a lodging frequency that is at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% less or lower than a wild-type or control plant. A modified cereal or corn plant may have a lodging frequency that is between 5% and 100%, between 5% and 95%, between 5% and 90%, between 5% and 85%, between 5% and 80%, between 5% and 75%, between 5% and 70%, between 5% and 65%, between 5% and 60%, between 5% and 55%, between 5% and 50%, between 5% and 45%, between 5% and 40%, between 5% and 35%, between 5% and 30%, between 5% and 25%, between 5% and 20%, between 5% and 15%, between 5% and 10%, between 10% and 100%, between 10% and 75%, between 10% and 50%, between 10% and 40%, between 10% and 30%, between 10% and 20%, between 25% and 75%, between 25% and 50%, or between 50% and 75% less or lower than a wild-type or control plant. Further provided are populations of cereal or corn plants having increased lodging resistance and a reduced lodging frequency. Populations of modified cereal or com plants are provided having a lodging frequency that is at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% less or lower than a population of wild-type or control plants. A population of modified corn plants may comprise a lodging frequency that is between 5% and 100%, between 5% and 95%, between 5% and 90%, between 5 / o and 85%, between 5% and 80%, between 5% and 75%, between 5% and 70%, between 5 / o and 65%, between 5% and 60%, between 5% and 55%, between 5% and 50%, between 5% and 45%, between 5% and 40%, between 5% and 35%, between 5% and 30%, between 5% and 25%, between 5% and 20%, between 5% and 15%, between 5% and 10%, between 10% and 100%, between 10% and 75%, between 10% and 50%, between 10% and 40%, between 10% and 30%, between 10% and 20%, between 25% and 75%, between 25% and 50%, or between 50% and 75% less or lower than a population of wild-type or control plants, which may be expressed as an average over a specified number of plants or crop area of equal density.

[0213] According to embodiments of the present disclosure, modified com plants are provided having a significantly reduced or decreased plant height (e.g., 2000 mm or less) and a significantlyincreased stem diameter (e.g., 18 mm or more), relative to a wild-type or control plant. According to these embodiments, the decrease or reduction in plant height and in...

Claims

CLAIMS1. A modified corn plant comprising a mutant allele of an endogenous GA3 oxidase gene, wherein the mutant allele comprises a mutation or edit in the upstream region of the endogenous GA3 oxidase gene relative to a wild-type allele of the endogenous GA3 oxidase gene, and wherein the expression level of the endogenous GA3 oxidase gene is reduced or eliminated in the modified corn plant relative to a wild-type control plant. The modified corn plant of claim 1, wherein the modified corn plant has a shorter plant height relative to the wild-type control plant.3 The modified corn plant of claim 1 or 2, wherein the modified corn plant has one or more of the following beneficial traits relative to the wild-type control plant: increased stalk / stem diameter, improved lodging resistance, reduced green snap, deeper roots, increased leaf area, earlier canopy closure, higher stomatai conductance, lower ear height, increased foliar water content, improved drought tolerance, improved nitrogen use efficiency, reduced anthocyanin content and area in leaves under normal or nitrogen or water limiting stress conditions, increased ear weight, increased harvest index, increased yield, increased seed number, increased seed weight, and increased prolificacy. The modified com plant of any one of claims 1-3, wherein the height of the modified corn plant is at least 10%, at least 20%, at least 25%, at least 30%, at least 35%, or at least 40% shorter than the wild-type control plant.5 The modified corn plant of any one of claims 1-4, wherein the stalk or stem diameter of the modified corn plant at one or more stem internodes is at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, or at least 40% greater than the wild-type control plant.6 The modified corn plant of any one of claims 1-5, wherein the level of one or more active GAs in at least one internode tissue of the stem or stalk of the modified corn plant is lower than the same internode tissue of the wild-type control plant.7 The modified corn plant of any one of claims 1-6, wherein the mutant allele comprises a mutation in the upstream region of the endogenous GA3 oxidase gene introduced by a mutagenesis technique.

8. The modified com plant of any one of claims 1-6, wherein the mutant allele comprises an edit in the upstream region of the endogenous GA3 oxidase gene introduced by a targeted genome editing technique.

9. The modified com plant of any one of claims 1-8, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase l gene, and wherein (i) the upstream region of the wild-type allele of the GA3 oxidase l gene without the mutation or edit comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to nucleotides 1-3000 of SEQ ID NO:168 or nucleotides 1-7620 of SEQ ID NO: 174, and / or (ii) the upstream region of the mutant allele of the GA3 oxidase l gene comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, at least 3000, at least 4000, or at least 5000 consecutive nucleotides of nucleotides 1-3000 of SEQ ID NO: 168, nucleotides 1-7620 of SEQ ID NO: 174, or SEQ ID NO: 208.

10. The modified com plant of any one of claims 1-9, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase l gene, and wherein the upstream region of the mutant allele of the GA3 oxidase l gene comprises, or comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to, one or more of SEQ ID NOs: 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, and / or 231.

11. The modified com plant of any one of claims 1-8, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase_2 gene, and wherein the upstream region of the wild-type allele of the GA3 oxidase_2 gene without the mutation or edit comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to nucleotides 1-3000 of SEQ ID NO:169 or nucleotides 1-7385 of SEQ ID NO: 175, and / or (ii) the upstream region of the mutant allele of the GA3 oxidase_2 gene comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, atleast 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, at least 3000, at least 4000, or at least 5000 consecutive nucleotides of nucleotides 1-3000 of SEQ ID NO: 169 or nucleotides 1-7385 of SEQ ID NO: 175.

12. The modified com plant of any one of claims 1-8, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase_3 gene, and wherein (i) the upstream region of the wild-type allele of the GA3 oxidase_3 gene without the mutation or edit comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to nucleotides 1-3000 of SEQ ID NO: 170 or nucleotides 1-7546 of SEQ ID NO: 176, and / or (ii) the upstream region of the mutant allele of the GA3 oxidase_3 gene comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, at least 3000, at least 4000, or at least 5000 consecutive nucleotides of nucleotides 1-3000 of SEQ ID NO: 170 or nucleotides 1-7546 of SEQ ID NO: 176.

13. The modified corn plant of any one of claims 1-7 and 9-12, wherein the mutant allele comprises a mutation in the promoter region of the endogenous GA3 oxidase gene introduced by a mutagenesis technique.

14. The modified corn plant of any one of claims 1-6 and 8-12, wherein the edited allele comprises an edit in the promoter region of the endogenous GA3 oxidase gene introduced by a targeted genome editing technique.

15. The modified corn plant of any one of claims 1-10, 13 or 14, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase l gene, and wherein (i) the promoter region of the wild-type allele of the GA3 oxidase l gene without the mutation or edit comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to nucleotides 5621-7620 of SEQ ID NO: 174, and / or (ii) the promoter region of the mutant allele of the GA3 oxidase l gene comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to at least 20, at least 25, atleast 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, or at least 1500 consecutive nucleotides of nucleotides 5621-7620 of SEQ ID NO: 174 or SEQ ID NO: 208.

16. The modified corn plant of any one of claims 1-8, 11, 13 or 14, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase_2 gene, and wherein (i) the promoter region of the wild-type allele of the GA3 oxidase_2 gene without the mutation or edit comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to nucleotides 5386-7385 of SEQ ID NO: 175, and / or (ii) the promoter region of the mutant allele of the GA3 oxidase_2 gene comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, or at least 1500 consecutive nucleotides of nucleotides 5386-7385 of SEQ ID NO: 175.

17. The modified corn plant of any one of claims 1-8, 12, 13 or 14, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase_3 gene, and wherein the promoter region of the wild-type allele of the GA3 oxidase_3 gene without the mutation or edit comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to nucleotides 5547-7546 of SEQ ID NO: 176, and / or (ii) the promoter region of the mutant allele of the GA3 oxidase_2 gene comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, or at least 1500 consecutive nucleotides of nucleotides 5547-7546 of SEQ ID NO: 176.

18. The modified com plant of any one of claims 1-17, wherein the modified corn plant is heterozygous for the mutant allele.

19. The modified com plant of any one of claims 1-17, wherein the modified corn plant is homozygous for the mutant allele.

20. The modified com plant of any one of claims 1-19, wherein the mutant allele of the modified com plant comprises two or more edit(s) and / or mutation(s), three or more edit(s) and / or mutation(s), four or more edit(s) and / or mutation(s), five or more edit(s) and / or mutation(s), six or more edit(s) and / or mutation(s), seven or more edit(s) and / or mutation(s), eight or more edit(s) and / or mutation(s), nine or more edit(s) and / or mutation(s), or ten or more edit(s) and / or mutation(s) in the upstream region and / or the promoter region of the endogenous GA3 oxidase gene.

21. A modified com plant part of the modified corn plant of any one of claims 1-20.

22. A modified corn plant comprising a mutant allele of an endogenous GA3 oxidase gene, wherein the mutant allele comprises an inverted DNA segment in a transcribable DNA region of the endogenous GA3 oxidase gene, wherein the inverted DNA segment encodes an antisense RNA sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, or at least 2500 consecutive nucleotides of a transcribable DNA region of a wild-type allele of the endogenous GA3 oxidase gene and / or a mRNA molecule encoded by the wild-type allele of the endogenous GA3 oxidase gene, and wherein the mutant allele of the endogenous GA3 oxidase gene encodes a mRNA transcript comprising the antisense RNA sequence.

23. The modified corn plant of claim 22, wherein the inverted DNA segment of the mutant allele of the endogenous GA3 oxidase gene is introduced into the endogenous GA3 oxidase gene by a targeted genome editing technique.

24. The modified corn plant of claim 22 or 23, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase l gene, and wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase l gene is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, atleast 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, or at least 2500 consecutive nucleotides of: (i) one or more of SEQ ID NOs: 28, 29 and / or 36, (ii) nucleotides 3001-5406 of SEQ ID NO: 168, (iii) nucleotides 7621-10276 of SEQ ID NO: 174, and / or (iv) SEQ ID NO: 206, or a sequence complementary thereto.

25. The modified corn plant of claim 22, 23 or 24, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase l gene, and wherein the mutant allele of the endogenous GA3 oxidase_l gene comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to SEQ ID NO: 207.

26. The modified corn plant of claim 22 or 23, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase_2 gene, and wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase_2 gene is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, or at least 2500 consecutive nucleotides of: (i) one or more of SEQ ID NOs: 31, 32 and / or 37, (ii) nucleotides 3001-4581 of SEQ ID NO: 169, and / or (iii) nucleotides 7386-8967 of SEQ ID NO: 175.

27. The modified corn plant of claim 22 or 23, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase_3 gene, and wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase_3 gene is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, or at least 2500 consecutive nucleotides of: (i) one or more of SEQ ID NOs: 171 and / or 172, (ii) nucleotides 3001-4332 of SEQ ID NO: 170, and / or (iii) nucleotides 7547-9178 of SEQ ID NO: 176.

28. A modified corn plant comprising a mutant allele of an endogenous GA3 oxidase gene, wherein the mutant allele comprises an inverted DNA segment in an untranslated region (UTR) or intron of the endogenous GA3 oxidase gene, wherein the inverted DNA segment encodes an antisense RNA sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, or at least 2500 consecutive nucleotides of an untranslated region (UTR) or intron of a wild-type allele of the endogenous GA3 oxidase gene and / or a mRNA molecule encoded by the wild-type allele of the endogenous GA3 oxidase gene, and wherein the mutant allele of the endogenous GA3 oxidase gene encodes a mRNA transcript comprising the antisense RNA sequence.

29. The modified corn plant of claim 28, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase l gene, wherein the inverted DNA segment is present in an intron of the mutant allele of the endogenous GA3 oxidase l gene, and wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase l gene is complementary to an intron or untranslated region (UTR) of the wild-type allele of the endogenous GA3 oxidase l gene.

30. The modified corn plant of claim 28, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase l gene, wherein the inverted DNA segment is present in an untranslated region (UTR) of the mutant allele of the endogenous GA3 oxidase l gene, and wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase l gene is complementary to an intron or untranslated region (UTR) of the wild-type allele of the endogenous GA3 oxidase l gene.

31. The modified corn plant of claim 28, 29 or 30, wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase l gene is complementary to a 5’ untranslated region (5’ UTR) of the wild-type allele of the endogenous GA3 oxidase l gene.

32. The modified corn plant of any one of claims 28-31, wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase l gene is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%,or 100% complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, or at least 2500 consecutive nucleotides of (i) nucleotides 1-29 of SEQ ID NO: 36, (ii) nucleotides 3001-3161 of SEQ ID NO: 168, and / or (iii) nucleotides 7621-8029 of SEQ ID NO: 174.

33. The modified corn plant of claim 28, 29 or 30, wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase l gene is complementary to a 3’ untranslated region (3’ UTR) of the wild-type allele of the endogenous GA3 oxidase l gene.

34. The modified corn plant of claim 28, 30 or 33, wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase l gene is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, or at least 2500 consecutive nucleotides of (i) nucleotides 1664-1788 of SEQ ID NO: 36, (ii) nucleotides 4796-5406 of SEQ ID NO: 168, (iii) nucleotides 9672-10276 of SEQ ID NO: 174, and / or (iv) SEQ ID NO: 206.

35. The modified corn plant of claim 28, 29 or 30, wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase l gene is complementary to an intron of the wild-type allele of the endogenous GA3 oxidase l gene.

36. The modified corn plant of any one of claims 28-30 or 35, wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase l gene is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, or at least 2500 consecutive nucleotides of (i) nucleotides 515-879 of SEQ ID NO: 36, (ii) nucleotides 1039-1158 of SEQ ID NO: 36, (iii) nucleotides 3647-4011 of SEQ ID NO: 168, (iv) nucleotides 4171-4290 of SEQ ID NO: 168; (v) nucleotides 8515-8887 of SEQ ID NO: 174, and / or (vi) nucleotides 9047-9166 of SEQ ID NO: 174.

37. The modified corn plant of claim 28-30, 35 or 36, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase l gene, and wherein the mutant allele of the endogenous GA3 oxidase l gene comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to SEQ ID NO: 207.

38. The modified corn plant of claim 28, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase_2 gene, wherein the inverted DNA segment is present in an intron of the mutant allele of the endogenous GA3 oxidase_2 gene, and wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase_2 gene is complementary to an intron or untranslated region (UTR) of the wild-type allele of the endogenous GA3 oxidase_2 gene.

39. The modified corn plant of claim 28, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase_2 gene, wherein the inverted DNA segment is present in an untranslated region (UTR) of the mutant allele of the endogenous GA3 oxidase_2 gene, and wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase_2 gene is complementary to an intron or untranslated region (UTR) of the wild-type allele of the endogenous GA3 oxidase_2 gene.

40. The modified corn plant of claim 28, 38 or 39, wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase_2 gene is complementary to a 5’ untranslated region (5’ UTR) of the wild-type allele of the endogenous GA3 oxidase_2 gene.

41. The modified corn plant of claim 28 or 38-40, wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase_2 gene is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, or at least 2500 consecutive nucleotides of (i) nucleotides 1-38 of SEQ ID NO: 37 (ii) nucleotides 3001-3056 of SEQ ID NO: 169, and / or (iii) nucleotides 7386-7831 of SEQ ID NO: 175.

42. The modified corn plant of claim 28, 38 or 39, wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase_2 gene is complementary to a 3’ untranslated region (3’ UTR) of the wild-type allele of the endogenous GA3 oxidase_2 gene.

43. The modified corn plant of claim 28, 3, 39 or 42, wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase_2 gene is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, or at least 2500 consecutive nucleotides of (i) nucleotides 1446-1698 of SEQ ID NO: 37, (ii) nucleotides 4464-4581 of SEQ ID NO: 169, and / or (iii) nucleotides 8862-8967 of SEQ ID NO: 175.

44. The modified corn plant of claim 28, 38 or 39, wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase_2 gene is complementary to an intron of the wild-type allele of the endogenous GA3 oxidase_2 gene.

45. The modified corn plant of any one of claims 28, 38, 39 or 44, wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase_2 gene is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, or at least 2500 consecutive nucleotides of (i) nucleotides 533-692 of SEQ ID NO: 37, (ii) nucleotides 852-982 of SEQ ID NO: 37, (iii) nucleotides 3551-3710 of SEQ ID NO: 169, (iv) nucleotides 3870-3991 of SEQ ID NO: 169, (v) nucleotides 7927-8086 of SEQ ID NO: 175, and / or (vi) nucleotides 8246-8371 of SEQ ID NO: 175.

46. The modified corn plant of claim 28, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase_3 gene, wherein the inverted DNA segment is present in an intron of the mutant allele of the endogenous GA3 oxidase_3 gene, and wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase_3 gene is complementary to an intron or untranslated region (UTR) of the wild-type allele of the endogenous GA3 oxidase_3 gene.

47. The modified corn plant of claim 28, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase_3 gene, wherein the inverted DNA segment is present in an untranslated region (UTR) of the mutant allele of the endogenous GA3 oxidase_3 gene, and wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase_3 gene is complementary to an intron or untranslated region (UTR) of the wild-type allele of the endogenous GA3 oxidase_3 gene.

48. The modified corn plant of claim 28, 46 or 47, wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase_3 gene is complementary to a 5’ untranslated region (5’ UTR) of the wild-type allele of the endogenous GA3 oxidase_3 gene.

49. The modified corn plant of any one of claims 28, 46, 47 or 48, wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase_3 gene is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, or at least 2500 consecutive nucleotides of (i) nucleotides 3001-3130 of SEQ ID NO: 170, and / or (ii) nucleotides 7547-7751 of SEQ ID NO: 176.

50. The modified corn plant of claim 26, 46 or 47, wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase_3 gene is complementary to a 3’ untranslated region (3’ UTR) of the wild-type allele of the endogenous GA3 oxidase_3 gene.

51. The modified corn plant of any one of claims 26, 46, 47 or 50, wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase_3 gene is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, or at least 2500 consecutive nucleotides of (i) nucleotides 4275-4332 of SEQ ID NO: 170, and / or (ii) nucleotides 8904-9178 of SEQ ID NO: 176.

52. The modified corn plant of claim 26, 46 or 47, wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase_3 gene is complementary to an intron of the wild-type allele of the endogenous GA3 oxidase_3 gene.

53. The modified corn plant of any one of claims 26, 46, 47 or 52, wherein the antisense RNA sequence encoded by the mutant allele of the endogenous GA3 oxidase_3 gene is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, or at least 2500 consecutive nucleotides of (i) nucleotides 3484-3582 of SEQ ID NO: 170, (ii) nucleotides 3908-3998 of SEQ ID NO: 170, (iii) nucleotides 8105-8205 of SEQ ID NO: 176, and / or (iv) nucleotides 8531-8621 of SEQ ID NO: 176.

54. The modified corn plant of any one of claims 22-53, wherein the mutant allele of the endogenous GA3 oxidase gene does not comprise a DNA segment in the transcribable DNA region of the endogenous GA3 oxidase gene encoding a sense RNA sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% complementary to the antisense RNA sequence encoded by the inverted DNA segment of the mutant allele of the endogenous GA3 oxidase gene.

55. The modified corn plant of any one of claims 22-54, wherein the modified corn plant is homozygous for the mutant allele.

56. The modified corn plant of claim 55, wherein the expression level of the endogenous GA3 oxidase gene is the same or similar to a wild-type control com plant.

57. The modified corn plant of claim 55 or 56, wherein the modified com plant has the same or similar plant height relative to a wild-type control plant.

58. The modified corn plant of any one of claims 22-57, wherein the modified corn plant is heterozygous for the mutant allele.

59. The modified corn plant of claim 58, wherein the expression level of the endogenous GA3 oxidase gene is reduced or eliminated in the modified corn plant relative to a wild-type control plant.

60. The modified corn plant of claim 58 or 59, wherein the modified corn plant has a shorter plant height relative to a wild-type control plant.

61. The modified corn plant of any one of claims 58-60, wherein the modified plant has one or more of the following beneficial traits relative to a wild-type control plant: increased stalk / stem diameter, improved lodging resistance, reduced green snap, deeper roots, increased leaf area, earlier canopy closure, higher stomatai conductance, lower ear height, increased foliar water content, improved drought tolerance, improved nitrogen use efficiency, reduced anthocyanin content and area in leaves under normal or nitrogen or water limiting stress conditions, increased ear weight, increased harvest index, increased yield, increased seed number, increased seed weight, and increased prolificacy.

62. The modified com plant of any one of claims 58-61, wherein the height of the modified corn plant is at least 10%, at least 20%, at least 25%, at least 30%, at least 35%, or at least 40% shorter than a wild-type control plant.

63. The modified com plant of any one of claims 58-62, wherein the stalk or stem diameter of the modified corn plant at one or more stem internodes is at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, or at least 40% greater than a wild-type control plant.

64. The modified corn plant of any one of claims 58-63, wherein the level of one or more active GAs in at least one internode tissue of the stem or stalk of the modified corn plant is lower than the same internode tissue of a wild-type control plant.

65. The modified corn plant of any one of claims 58-64, wherein the level of one or more active GAs in at least one internode tissue of the stem or stalk of the modified corn plant is at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, or at least 40% lower than the same internode tissue of a wild-type control plant.

66. The modified corn plant of any one of claims 22-65, wherein the modified corn plant does not have any significant off-types in at least one female organ or ear.

67. A modified com plant part of the modified corn plant of any one of claims 22-66.

68. A modified corn plant comprising a mutant allele of an endogenous GA3 oxidase gene, wherein the mutant allele comprises an edit in a transcribable DNA region of theendogenous GA3 oxidase gene or a deletion of at least a portion of the transcribable DNA region or coding sequence of the endogenous GA3 oxidase gene, relative to a wild-type allele of the endogenous GA3 oxidase gene, and wherein the expression level or activity of the mRNA and / or protein encoded by the mutant allele of the endogenous GA3 oxidase gene is reduced or eliminated in the modified corn plant relative to a wild-type allele of the endogenous GA3 oxidase gene in the modified corn plant or a wild-type control plant.

69. The modified corn plant of claim 68, wherein the mutant allele of the endogenous GA3 oxidase gene comprises a deletion of at least a portion of the transcribable DNA region or coding sequence of the endogenous GA3 oxidase gene relative to the wild-type allele of the endogenous GA3 oxidase gene.

70. The modified corn plant of claim 68 or 69, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase l gene, and wherein the mutant allele of the endogenous GA3 oxidase l gene comprises a deletion of at least a portion of the transcribable DNA region or coding sequence of the endogenous GA3 oxidase l gene relative to the wild-type allele of the endogenous GA3 oxidase l gene.

71. The modified corn plant of claim 70, wherein the deletion in the mutant allele of the endogenous GA3 oxidase l gene comprises a deletion of at least a portion of the transcribable DNA region or coding sequence of the wild-type allele of the endogenous GA3 oxidase l gene, wherein the at least a portion of the transcribable DNA region or coding sequence of the wild-type allele of the endogenous GA3 oxidase l gene that is deleted in the mutant allele of the endogenous GA3 oxidase l gene comprises a sequence that is (a) at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical or complementary to (i) one or more of SEQ ID NOs: 28, 29 and / or 36, (ii) nucleotides 3001-5406 of SEQ ID NO: 168, and / or (iii) nucleotides 7621-10276 of SEQ ID NO: 174, and / or (b) at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical or complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, or at least 2500 consecutive nucleotides of: (i) one or more of SEQ ID NOs: 28, 29 and / or 36, (ii)nucleotides 3001-5406 of SEQ ID NO: 168, (iii) nucleotides 7621-10276 of SEQ ID NO: 174, and / or (iv) SEQ ID NO: 206.

72. The modified corn plant of claim 70 or 71, wherein the deletion in the mutant allele of the endogenous GA3 oxidase l gene comprises a deletion of at least a portion of an exon or intron sequence or a combination of exon and intron sequences of the wild-type allele of the endogenous GA3 oxidase l gene, wherein the at least a portion of the exon or intron sequence or the combination of exon and intron sequences of the wild-type allele of the endogenous GA3 oxidase l gene that is deleted in the mutant allele of the endogenous GA3 oxidase_l gene comprises a sequence that is (a) at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical or complementary to (i) nucleotides 30-514 of SEQ ID NO: 36, (ii) nucleotides 515-879 of SEQ ID NO: 36, (iii) nucleotides 880-1038 of SEQ ID NO: 36, (iv) nucleotides 1039-1158 of SEQ ID NO: 36, (v) nucleotides 1159-1663 of SEQ ID NO: 36, (vi) nucleotides 3162-3646 of SEQ ID NO: 168, (vii) nucleotides 3647-4011 of SEQ ID NO: 168, (viii) nucleotides 4012-4170 of SEQ ID NO: 168, (ix) nucleotides 4171-4290 of SEQ ID NO: 168, (x) nucleotides 4291-4795 of SEQ ID NO: 168, (xi) nucleotides 8030-8514 of SEQ ID NO: 174, (xii) nucleotides 8515-8887 of SEQ ID NO: 174, (xiii) nucleotides 8888-9046 of SEQ ID NO: 174, (xiv) nucleotides 9047-9166 of SEQ ID NO: 174, and / or (xv) nucleotides 9167-9671 of SEQ ID NO: 174, and / or (b) at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical or complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, or at least 2500 consecutive nucleotides of (i) nucleotides 30-514 of SEQ ID NO: 36, (ii) nucleotides 515-879 of SEQ ID NO: 36, (iii) nucleotides 880-1038 of SEQ ID NO: 36, (iv) nucleotides 1039-1158 of SEQ ID NO: 36, (v) nucleotides 1159-1663 of SEQ ID NO: 36, (vi) nucleotides 3162-3646 of SEQ ID NO: 168, (vii) nucleotides 3647-4011 of SEQ ID NO: 168, (viii) nucleotides 4012-4170 of SEQ ID NO: 168, (ix) nucleotides 4171-4290 of SEQ ID NO: 168, (x) nucleotides 4291-4795 of SEQ ID NO: 168, (xi) nucleotides 8030-8514 of SEQ ID NO: 174, (xii) nucleotides 8515-8887 of SEQ ID NO: 174, (xiii) nucleotides 8888-9046 of SEQ ID NO: 174, (xiv) nucleotides 9047-9166 of SEQ ID NO: 174, and / or (xv) nucleotides 9167-9671 of SEQ ID NO: 174.

73. The modified corn plant of claim 68 or 69, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase_2 gene, and wherein the mutant allele of the endogenous GA3 oxidase_2 gene comprises a deletion of at least a portion of the transcribable DNA region or coding sequence of the endogenous GA3 oxidase_2 gene relative to the wild-type allele of the endogenous GA3 oxidase_2 gene.

74. The modified corn plant of claim 73, wherein the deletion in the mutant allele of the endogenous GA3 oxidase_2 gene comprises a deletion of at least a portion of the transcribable DNA region or coding sequence of the wild-type allele of the endogenous GA3 oxidase_2 gene, wherein the at least a portion of the transcribable DNA region or coding sequence of the wild-type allele of the endogenous GA3 oxidase_2 gene that is deleted in the mutant allele of the endogenous GA3 oxidase_2 gene comprises a sequence that is (a) at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical or complementary to (i) one or more of SEQ ID NOs: 31, 32 and / or 37, (ii) nucleotides 3001-4581 of SEQ ID NO: 169, and / or (iii) nucleotides 7386-8967 of SEQ ID NO: 175, and / or (b) at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical or complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, or at least 2500 consecutive nucleotides of: (i) one or more of SEQ ID NOs: 31, 32 and / or 37, (ii) nucleotides 3001-4581 of SEQ ID NO: 169, and / or (iii) nucleotides 7386-8967 of SEQ ID NO: 175.

75. The modified corn plant of claim 73 or 74, wherein the deletion in the mutant allele of the endogenous GA3 oxidase_2 gene comprises a deletion of at least a portion of an exon or intron sequence or a combination of exon and intron sequences of the wild-type allele of the endogenous GA3 oxidase_2 gene, wherein the at least a portion of the exon or intron sequence or the combination of exon and intron sequences of the wild-type allele of the endogenous GA3 oxidase_2 gene that is deleted in the mutant allele of the endogenous GA3 oxidase_2 gene comprises a sequence that is (a) at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical or complementary to (i) nucleotides 39-532 of SEQ ID NO: 37, (ii) nucleotides 533-692 of SEQ ID NO: 37, (iii) nucleotides 693-851 of SEQ ID NO: 37, (iv) nucleotides 852-982 ofSEQ ID NO: 37, (v) nucleotides 983-1445 of SEQ ID NO: 37, (vi) nucleotides 3057-3550 of SEQ ID NO: 169, (vii) nucleotides 3551-3710 of SEQ ID NO: 169, (viii) nucleotides 3711-3869 of SEQ ID NO: 169, (ix) nucleotides 3870-3991 of SEQ ID NO: 169, (x) nucleotides 3992-4463 of SEQ ID NO: 169, (xi) nucleotides 7832-7926 of SEQ ID NO: 175, (xii) nucleotides 7927-8086 of SEQ ID NO: 175, (xiii) nucleotides 8087-8245 of SEQ ID NO: 175, (xiv) nucleotides 8246-8371 of SEQ ID NO: 175, and / or (xv) nucleotides 8372-8861 of SEQ ID NO: 175, and / or (b) at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical or complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, or at least 2500 consecutive nucleotides of (i) nucleotides 39-532 of SEQ ID NO: 37, (ii) nucleotides 533-692 of SEQ ID NO: 37, (iii) nucleotides 693-851 of SEQ ID NO: 37, (iv) nucleotides 852-982 of SEQ ID NO: 37, (v) nucleotides 983-1445 of SEQ ID NO: 37, (vi) nucleotides 3057-3550 of SEQ ID NO: 169, (vii) nucleotides 3551-3710 of SEQ ID NO: 169, (viii) nucleotides 3711-3869 of SEQ ID NO: 169, (ix) nucleotides 3870-3991 of SEQ ID NO: 169, (x) nucleotides 3992-4463 of SEQ ID NO: 169, (xi) nucleotides 7832-7926 of SEQ ID NO: 175, (xii) nucleotides 7927-8086 of SEQ ID NO: 175, (xiii) nucleotides 8087-8245 of SEQ ID NO: 175, (xiv) nucleotides 8246-8371 of SEQ ID NO: 175, and / or (xv) nucleotides 8372-8861 of SEQ ID NO:

175. The modified corn plant of claim 68 or 69, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase_3 gene, and wherein the mutant allele of the endogenous GA3 oxidase_3 gene comprises a deletion of at least a portion of the transcribable DNA region or coding sequence of the endogenous GA3 oxidase_3 gene relative to the wild-type allele of the endogenous GA3 oxidase_3 gene. The modified corn plant of claim 79, wherein the deletion in the mutant allele of the endogenous GA3 oxidase_3 gene comprises a deletion of at least a portion of the transcribable DNA region or coding sequence of the wild-type allele of the endogenous GA3 oxidase_3 gene, wherein the at least a portion of the transcribable DNA region or coding sequence of the wild-type allele of the endogenous GA3 oxidase_3 gene that is deleted in the mutant allele of the endogenous GA3 oxidase_3 gene comprises a sequence that is (a) at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, atleast 98%, at least 99%, or 100% identical or complementary to (i) one or more of SEQ ID NOs: 171 and / or 172, (ii) nucleotides 3001-4332 of SEQ ID NO: 170, and / or (iii) nucleotides 7547-9178 of SEQ ID NO: 176 and / or (b) at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical or complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, or at least 2500 consecutive nucleotides of: (i) one or more of SEQ ID NOs: 171 and / or 172, (ii) nucleotides 3001-4332 of SEQ ID NO: 170, and / or (iii) nucleotides 7547-9178 of SEQ ID NO:

176. The modified corn plant of claim 76 or 77, wherein the deletion in the mutant allele of the endogenous GA3 oxidase_3 gene comprises a deletion of at least a portion of an exon or intron sequence or a combination of exon and intron sequences of the wild-type allele of the endogenous GA3 oxidase_3 gene, wherein the at least a portion of the exon or intron sequence or the combination of exon and intron sequences of the wild-type allele of the endogenous GA3 oxidase_3 gene that is deleted in the mutant allele of the endogenous GA3 oxidase_3 gene comprises a sequence that is (a) at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical or complementary to (i) nucleotides 3131-3483 of SEQ ID NO: 170, (ii) nucleotides 3484-3582 of SEQ ID NO: 170, (iii) nucleotides 3583-3907 of SEQ ID NO: 170, (iv) nucleotides 3908-3998 of SEQ ID NO: 170, (v) nucleotides 3999-4274 of SEQ ID NO: 170, (vi) nucleotides 7752-8104 of SEQ ID NO: 176, (vii) nucleotides 8105-8205 of SEQ ID NO: 176, (viii) nucleotides 8206-8530 of SEQ ID NO: 176, (ix) nucleotides 8531-8621 of SEQ ID NO: 176, and / or (x) nucleotides 8622-8903 of SEQ ID NO: 176, and / or (b) at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical or complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, or at least 2500 consecutive nucleotides of (i) nucleotides 3131-3483 of SEQ ID NO: 170, (ii) nucleotides 3484-3582 of SEQ ID NO: 170, (iii) nucleotides 3583-3907 of SEQ ID NO: 170, (iv) nucleotides 3908-3998 of SEQ ID NO: 170, (v) nucleotides 3999-4274 of SEQ ID NO: 170, (vi) nucleotides 7752-8104 of SEQ ID NO: 176, (vii)nucleotides 8105-8205 of SEQ ID NO: 176, (viii) nucleotides 8206-8530 of SEQ ID NO: 176, (ix) nucleotides 8531-8621 of SEQ ID NO: 176, and / or (x) nucleotides 8622-8903 of SEQ ID NO: 176.

79. The modified corn plant of any one of claims 68-78, wherein the deletion in the mutant allele of the endogenous GA3 oxidase gene comprises (i) a deletion of at least one exon of the endogenous GA3 oxidase gene relative to the wild-type allele of the endogenous GA3 oxidase gene, (ii) a deletion of at least one intron of the endogenous GA3 oxidase gene relative to the wild-type allele of the endogenous GA3 oxidase gene, (iii) a deletion of at least one exon and at least one intron of the endogenous GA3 oxidase gene relative to the wild-type allele of the endogenous GA3 oxidase gene, or (iv) a deletion of the entire coding sequence of the endogenous GA3 oxidase gene relative to the wild-type allele of the endogenous GA3 oxidase gene.

80. The modified corn plant of any one of claims 68-79, wherein the expression level or activity of the mRNA and / or protein encoded by the endogenous GA3 oxidase gene is reduced or eliminated in the modified corn plant relative to a wild-type control plant.

81. The modified com plant of any one of claims 68-80, wherein the modified com plant has a shorter plant height relative to a wild-type control plant.

82. The modified corn plant of any one of claims 68-81, wherein the expression level of the endogenous GA3 oxidase gene is reduced or eliminated in the modified com plant relative to a wild-type control plant.

83. The modified corn plant of any one of claims 68-82, wherein the modified corn plant has one or more of the following beneficial traits relative to a wild-type control plant: increased stalk / stem diameter, improved lodging resistance, reduced green snap, deeper roots, increased leaf area, earlier canopy closure, higher stomatai conductance, lower ear height, increased foliar water content, improved drought tolerance, improved nitrogen use efficiency, reduced anthocyanin content and area in leaves under normal or nitrogen or water limiting stress conditions, increased ear weight, increased harvest index, increased yield, increased seed number, increased seed weight, and increased prolificacy.

84. The modified corn plant of any one of claims 68-83, wherein the height of the modified corn plant is at least 10%, at least 20%, at least 25%, at least 30%, at least 35%, or at least 40% shorter than a wild-type control plant.

85. The modified com plant of any one of claims 68-84, wherein the stalk or stem diameter of the modified corn plant at one or more stem internodes is at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, or at least 40% greater than a wild-type control plant.

86. The modified corn plant of any one of claims 68-85, wherein the level of one or more active GAs in at least one internode tissue of the stem or stalk of the modified corn plant is lower than the same internode tissue of a wild-type control plant.

87. The modified corn plant of any one of claims 68-86, wherein the deletion of the mutant allele is introduced by a targeted genome editing technique.

88. The modified corn plant of any one of claims 68-87, wherein the modified corn plant is heterozygous for the mutant allele.

89. The modified com plant of any one of claims 68-87, wherein the modified corn plant is homozygous for the mutant allele.

90. A modified com plant part of the modified corn plant of any one of claims 68-89.

91. The modified corn plant of any one of claims 8, 14, 23 and 83, wherein the edit is introduced using a meganuclease, a zinc-finger nuclease (ZFN), a RNA-guided endonuclease, a TALE-endonuclease (TALEN), a recombinase, or a transposase.

92. A composition comprising a guide RNA, wherein the guide RNA comprises a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of a target DNA sequence in the upstream region, transcribable DNA region, 5’ untranslated region (5’ UTR), 3’ untranslated region (3’ UTR) and / or downstream region of an endogenous GA3 oxidase gene of a corn plant.

93. The composition of claim 92, wherein the target DNA sequence is in the upstream region and / or the promoter region of the endogenous GA3 oxidase gene.

94. The composition of claim 92 or 93, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase l gene, and wherein the guide RNA comprises a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of (i) nucleotides 1-3000 of SEQ ID NO:168, (ii) nucleotides 1-7620 of SEQ ID NO: 174, (iii) nucleotides 5621-7620 of SEQ ID NO: 174, and / or (iv) SEQ ID NO: 208, or a sequence complementary thereto.

95. The composition of claim 92 or 93, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase_2 gene, and wherein the guide RNA comprises a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of (i) nucleotides 1-3000 of SEQ ID NO:169, (ii) nucleotides 1-7385 of SEQ ID NO: 175, and / or (iii) nucleotides 5386-7385 of SEQ ID NO: 175, or a sequence complementary thereto.

96. The composition of claim 92 or 93, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase_3 gene, and wherein the guide RNA comprises a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of (i) nucleotides 1-3000 of SEQ ID NO:170, (ii) nucleotides 1-7546 of SEQ ID NO: 176, and / or (iii) nucleotides 5547-7546 of SEQ ID NO: 176, or a sequence complementary thereto.

97. The composition of claim 92, wherein the target DNA sequence is in the transcribable DNA region of an endogenous GA3 oxidase gene of a corn plant.

98. The composition of claim 92 or 97, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase l gene, and wherein the guide RNA comprises a guide sequencethat is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of (i) one or more of SEQ ID NOs: 28, 29 and / or 36, (ii) nucleotides 3001-5406 of SEQ ID NO: 168, (iii) nucleotides 7621-10276 of SEQ ID NO: 174, and / or (iv) SEQ ID NO: 206, or a sequence complementary thereto.

99. The composition of claim 92 or 97, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase_2 gene, and wherein the guide RNA comprises a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of (i) one or more of SEQ ID NOs: 31, 32 and / or 37, (ii) nucleotides 3001-4581 of SEQ ID NO: 169, and / or (iii) nucleotides 7386-8967 of SEQ ID NO: 175.

100. The composition of claim 92 or 97, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase_3 gene, and wherein the guide RNA comprises a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of (i) one or more of SEQ ID NOs: 171 and / or 172, (ii) nucleotides 3001-4332 of SEQ ID NO: 170, and / or (iii) nucleotides 7547-9178 of SEQ ID NO: 176.

101. The composition of claim 92, wherein the target DNA sequence is in the 5’ untranslated region (5’ UTR) or the 3’ untranslated region (3’ UTR) of an endogenous GA3 oxidase gene of a corn plant.

102. The composition of claim 92 or 101, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase l gene, and wherein the guide RNA comprises a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of (i) nucleotides 1-29 of SEQ ID NO: 36,(ii) nucleotides 1664-1788 of SEQ ID NO: 36, (iii) nucleotides 3001-3161 of SEQ ID NO: 168, (iv) nucleotides 4796-5406 of SEQ ID NO: 168, (v) nucleotides 7621-8029 of SEQ ID NO: 174, and / or (vi) nucleotides 9672-10276 of SEQ ID NO: 174.

103. The composition of claim 92 or 101, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase_2 gene, and wherein the guide RNA comprises a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of (i) nucleotides 1-38 of SEQ ID NO: 37, (ii) nucleotides 1446-1698 of SEQ ID NO: 37, (iii) nucleotides 3001-3056 of SEQ ID NO:169, (iv) nucleotides 4464-4581 of SEQ ID NO: 169, (v) nucleotides 7386-7831 of SEQ ID NO: 175, and / or (vi) nucleotides 8862-8967 of SEQ ID NO: 175.

104. The composition of claim 92 or 101, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase_3 gene, and wherein the guide RNA comprises a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of (i) nucleotides 3001-3130 of SEQ ID NO:170, (ii) nucleotides 4275-4332 of SEQ ID NO: 170, (iii) nucleotides 7547-7751 of SEQ ID NO: 176, and / or (iv) nucleotides 8904-9178 of SEQ ID NO: 176.

105. The composition of claim 92, wherein the target DNA sequence is in the downstream region of an endogenous GA3 oxidase gene of a corn plant.

106. The composition of claim 92 or 105, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase l gene, and wherein the guide RNA comprises a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of (i) nucleotides 5407-8406 of SEQ ID NO: 168, and / or (ii) nucleotides 10277-14227 of SEQ ID NO: 174.

107. The composition of claim 92 or 105, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase_2 gene, and wherein the guide RNA comprises a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of (i) nucleotides 4582-7581 of SEQ ID NO:169, and / or (ii) nucleotides 8968-16597 of SEQ ID NO: 175.

108. The composition of claim 92 or 105, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase_3 gene, and wherein the guide RNA comprises a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of (i) nucleotides 4333-7332 of SEQ ID NO:170, and / or (ii) nucleotides 9179-15354 of SEQ ID NO: 176.

109. A composition comprising a first guide RNA and a second guide RNA, wherein the first guide RNA and the second guide RNA comprise a first guide sequence and a second guide sequence, respectively, wherein(i) the first guide sequence is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of a first target DNA sequence in the upstream region and / or promoter region of an endogenous GA3 oxidase gene of a corn plant, and(ii) the second guide sequence is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of a second target DNA sequence in the upstream region and / or promoter region of the endogenous GA3 oxidase gene of a com plant, andwherein the first target DNA sequence and the second target DNA sequence are different.

110. A composition comprising a first guide RNA and a second guide RNA, wherein the first guide RNA and the second guide RNA comprise a first guide sequence and a second guide sequence, respectively, wherein(i) the first guide sequence is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of a first target DNA sequence in the 5’ untranslated region (5’ UTR) or the 3’ untranslated region (3’ UTR) of an endogenous GA3 oxidase gene of a corn plant, and(ii) the second guide sequence is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of a second target DNA sequence in the 5’ untranslated region (5’ UTR) or the 3’ untranslated region (3’ UTR) of the endogenous GA3 oxidase gene of a com plant.

111. The composition of claim 110, wherein the first target DNA sequence and the second target DNA sequence are different.

112. The composition of claim 110 or 111, wherein the first target DNA sequence and the second target DNA sequence are in the 5’ untranslated region (5’ UTR) of the endogenous GA3 oxidase gene of a com plant.

113. The composition of claim 110 or 111, wherein the first target DNA sequence and the second target DNA sequence are in the 3’ untranslated region (3’ UTR) of the endogenous GA3 oxidase gene of a com plant.

114. The composition of claim 110, 111 or 112, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase l gene, wherein the first guide sequence of the first guide RNA is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, atleast 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of (i) nucleotides 1-29 of SEQ ID NO: 36, (ii) nucleotides 3001-3161 of SEQ ID NO: 168, and / or (iii) nucleotides 7621-8029 of SEQ ID NO: 174, or a sequence complementary thereto, and wherein the second guide sequence of the second guide RNA is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of (i) nucleotides 1-29 of SEQ ID NO: 36, (ii) nucleotides 3001-3161 of SEQ ID NO: 168, and / or (iii) nucleotides 7621-8029 of SEQ ID NO: 174, or a sequence complementary thereto.

15. The composition of claim 110, 111 or 113, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase l gene, wherein the first guide sequence of the first guide RNA is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of (i) nucleotides 1664-1788 of SEQ ID NO: 36, (ii) nucleotides 4796-5406 of SEQ ID NO: 168, and / or (iii) nucleotides 9672-10276 of SEQ ID NO: 174, or a sequence complementary thereto, and wherein the second guide sequence of the second guide RNA is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of (i) nucleotides 1664-1788 of SEQ ID NO: 36, (ii) nucleotides 4796-5406 of SEQ ID NO: 168, and / or (iii) nucleotides 9672-10276 of SEQ ID NO: 174, or a sequence complementary thereto.

16. The composition of claim 110, 111 or 112, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase_2 gene,wherein the first guide sequence of the first guide RNA is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of (i) nucleotides 1-38 of SEQ ID NO: 37 (ii) nucleotides 3001-3056 of SEQ ID NO: 169, and / or (iii) nucleotides 7386-7831 of SEQ ID NO: 175, or a sequence complementary thereto, and wherein the second guide sequence of the second guide RNA is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of (i) nucleotides 1-38 of SEQ ID NO: 37 (ii) nucleotides 3001-3056 of SEQ ID NO: 169, and / or (iii) nucleotides 7386-7831 of SEQ ID NO: 175, or a sequence complementary thereto.

17. The composition of claim 110, 111 or 113, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase_2 gene, wherein the first guide sequence of the first guide RNA is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of (i) nucleotides 1446-1698 of SEQ ID NO: 37, (ii) nucleotides 4464-4581 of SEQ ID NO: 169, and / or (iii) nucleotides 8862-8967 of SEQ ID NO: 175, or a sequence complementary thereto, and wherein the second guide sequence of the second guide RNA is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of (i) nucleotides 1446-1698 of SEQ ID NO: 37, (ii) nucleotides 4464-4581 of SEQ ID NO: 169, and / or (iii) nucleotides 8862-8967 of SEQ ID NO: 175, or a sequence complementary thereto.

18. The composition of claim 110, 111 or 112, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase_3 gene, wherein the first guide sequence of the first guide RNA is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of (i) nucleotides 3001-3130 of SEQ ID NO: 170, and / or (ii) nucleotides 7547-7751 of SEQ ID NO: 176, or a sequence complementary thereto, and wherein the second guide sequence of the second guide RNA is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of (i) nucleotides 3001-3130 of SEQ ID NO: 170, and / or (ii) nucleotides 7547-7751 of SEQ ID NO: 176, or a sequence complementary thereto.

19. The composition of claim 110, 111 or 113, wherein the endogenous GA3 oxidase gene is an endogenous GA3 oxidase_3 gene, wherein the first guide sequence of the first guide RNA is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of (i) nucleotides 4275-4332 of SEQ ID NO: 170, and / or (ii) nucleotides 8904-9178 of SEQ ID NO: 176, or a sequence complementary thereto, and wherein the second guide sequence of the second guide RNA is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of (i) nucleotides 4275-4332 of SEQ ID NO: 170, and / or (ii) nucleotides 8904-9178 of SEQ ID NO: 176, or a sequence complementary thereto.

120. A composition comprising a first guide RNA and a second guide RNA, wherein the first guide RNA and the second guide RNA comprise a first guide sequence and a second guide sequence, respectively, wherein(i) the first guide sequence is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of a first target DNA sequence in the upstream region or the transcribable DNA region of an endogenous GA3 oxidase gene of a com plant, and(ii) the second guide sequence is at least 90%, at least 95%, at least 96%, at least 97%, at least 99%, or 100% identical or complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of a second target DNA sequence in the transcribable DNA region or the downstream region121. The composition of any one of claims 92-120, further comprising an RNA-guided endonuclease.

122. The composition of claim 121, wherein the RNA-guided endonuclease in the presence of the guide RNA, or the first guide RNA and / or the second guide RNA, causes a double strand break or nick at or near the target DNA sequence, or the first target DNA sequence and / or the second target DNA sequence, in the genome of the corn plant.

123. The composition of claim 121 or 122, further comprising a recombinant DNA donor template comprising at least one homology sequence or homology arm, wherein the at least one homology sequence or homology arm is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, at least 2500, or at least 5000 consecutive nucleotides of a genomic sequence at or near the endogenous GA3 oxidase gene of the corn plant.

124. The composition of claim 123, wherein the genomic sequence at or near the endogenous GA3 oxidase gene of the corn plant is in the upstream region, the transcribable DNA region, 5’ untranslated region (5’ UTR), 3’ untranslated region (3’ UTR), and / or downstream region of the endogenous GA3 oxidase gene.

125. A recombinant DNA construct comprising a transcribable DNA sequence encoding a non-coding guide RNA molecule, wherein the guide RNA molecule comprises a guide sequence that is at least 95%, at least 96%, at least 97%, at least 99% or 100% complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of a target DNA sequence in the upstream region, the promoter region, the transcribable DNA region, 5’ untranslated region (5’ UTR), 3’ untranslated region (3’ UTR), and / or the downstream region of an endogenous GA3 oxidase gene of a com plant.

126. The recombinant DNA construct of claim 125, wherein the guide RNA comprises a guide sequence that is at least 95%, at least 96%, at least 97%, at least 99% or 100% complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of SEQ ID NO: 36, 37, 168, 169, 170, 174, 175, or 176, or a sequence complementary thereto.

127. The recombinant DNA construct of claim 125 or 126, wherein the guide RNA molecule comprises a guide sequence that is at least 95%, at least 96%, at least 97%, at least 99% or 100% complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of SEQ ID NO: 28, 29, 31, 32, 171 or 172, or a sequence complementary thereto.

128. The recombinant DNA construct of claim 125, 126 or 127, wherein the transcribable DNA sequence is operably linked to a plant-expressible promoter.

129. The recombinant DNA construct of any one of claims 125-128, wherein the guide RNA molecule is a CRISPR RNA (crRNA) or a single-chain guide RNA (sgRNA).

130. The recombinant DNA construct of any one of claims 125-129, wherein the guide RNA comprises a sequence complementary to a protospacer adjacent motif (PAM) sequence present in the genome of the cereal plant immediately adjacent to the target DNA sequence at or near the genomic locus of the endogenous GA3 oxidase gene.

131. A recombinant DNA construct comprising a first transcribable DNA sequence encoding a first non-coding guide RNA molecule and a second transcribable DNA sequence encoding a second non-coding guide RNA molecule, wherein the first guide RNA molecule comprises a first guide sequence that is at least 95%, at least 96%, at least 97%, at least 99% or 100% complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of a first target DNA sequence in the upstream region, promoter region, transcribable DNA region, 5’ untranslated region (5’ UTR), 3’ untranslated region (3’ UTR), and / or downstream region of an endogenous GA3 oxidase gene of a corn plant, and wherein the second guide RNA molecule comprises a second guide sequence that is at least 95%, at least 96%, at least 97%, at least 99% or 100% complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of a second target DNA sequence in the upstream region, the promoter region, the transcribable DNA region, 5’ untranslated region (5’ UTR), 3’ untranslated region (3’ UTR) and / or the downstream region of an endogenous GA3 oxidase gene of a com plant, and wherein the first target DNA sequence and the second target DNA sequence are different.

132. The recombinant DNA construct of claim 131, wherein the first transcribable DNA sequence is operably linked to a first plant-expressible promoter, and the second transcribable DNA sequence is operably linked to a second plant-expressible promoter.

133. The composition of any one of claims 92-124 or the recombinant DNA construct of any one of claims 125-132, wherein the endogenous GA3 oxidase gene encodes a protein that is atleast 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, or 100% identical to SEQ ID NO: 30, 33 or 173.

134. A DNA molecule or vector comprising the recombinant DNA construct of any one of claims 125-132.

135. A bacterial or host cell comprising the recombinant DNA construct of any one of claims 125-132.

136. A corn plant, plant part or plant cell comprising the composition of any one of claims 92-124 or the recombinant DNA construct of any one of claim 125-132.

137. A composition comprising the recombinant DNA construct of any one of claims 125-132, wherein the composition further comprises a RNA-guided endonuclease.

138. A composition comprising the recombinant DNA construct of any one of claims 125-132, wherein the composition further comprises a second recombinant DNA construct comprising a second transcribable DNA sequence encoding a RNA-guided endonuclease.

139. The composition of claim 138, comprising a DNA molecule or vector comprising the recombinant DNA construct and the second recombinant DNA construct.

140. A composition comprising a first DNA molecule or vector and a second DNA molecule or vector, wherein the first DNA molecule or vector comprises the recombinant DNA construct of any one of claims 125-132, and the second DNA molecule or vector comprises a second recombinant DNA construct encoding a RNA-guided endonuclease.

141. The composition of claim 138, 139 or 140, further comprising a recombinant DNA donor template comprising at least one homology sequence or homology arm, wherein the at least one homology sequence or homology arm is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, at least 2500, or at least 5000 consecutive nucleotides of a genomic sequence at or near the endogenous GA3 oxidase gene of a corn plant.

142. The composition of claim 141, wherein the genomic sequence at or near the endogenous GA3 oxidase gene of the corn plant is in the upstream region, the transcribable DNA region, 5’ untranslated region (5’ UTR), 3’ untranslated region (3’ UTR), and / or downstream region of the endogenous GA3 oxidase gene.

143. A recombinant DNA donor template comprising at least one homology sequence, wherein the at least one homology sequence is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, at least 2500, or at least 5000 consecutive nucleotides of a genomic sequence at or near the endogenous GA3 oxidase gene of a corn plant, and wherein the homology sequence further comprises an inversion or deletion relative to a corresponding genomic sequence of a wild-type allele of the endogenous GA3 oxidase gene or a complement thereof.

144. The recombinant DNA donor template of claim 143, wherein the at least one homology sequence is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, at least 2500, or at least 5000 consecutive nucleotides of SEQ ID NO: 36, 37, 168, 169, 170, 174, 175, or 176, or a sequence complementary thereto.

145. The recombinant DNA donor template of claim 143 or 144, wherein the at least one homology sequence is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, at least 2500, or at least 5000 consecutive nucleotides of SEQ ID NO: 28, 29, 31, 32, 171 or 172, or a sequence complementary thereto.

146. A recombinant DNA donor template comprising at least one homology sequence and an insertion sequence, wherein the at least one homology sequence is at least 70%, at least75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, at least 2500, or at least 5000 consecutive nucleotides of a genomic sequence at or near an endogenous GA3 oxidase gene of a com plant, and wherein the insertion sequence comprises an inversion relative to a genomic sequence of a transcribable DNA segment of a wild-type allele of the endogenous GA3 oxidase gene or a complement thereof.

147. The recombinant DNA donor template of any one of claims 143-146, further comprising a second homology arm, wherein the second homology arm comprises a second homology sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, at least 2500, or at least 5000 consecutive nucleotides of a second genomic sequence at or near the genomic locus of an endogenous GA3 oxidase gene of a corn plant.

148. The recombinant DNA donor template of claim 147, wherein the second homology sequence is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, at least 2500, or at least 5000 consecutive nucleotides of SEQ ID NO: 36, 37, 168, 169 or 170, or a sequence complementary thereto.

149. The recombinant DNA donor template of claim 147, wherein the second homology sequence is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% identical or complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, at least 2500, or at least 5000 consecutive nucleotides of SEQ ID NO: 28, 29, 31, 32, 171 or 172, or a sequence complementary thereto.

150. A com plant, plant part or plant cell comprising the recombinant DNA donor template of any one of claims 143-149.

151. An engineered site-specific nuclease that binds to a target site in the upstream region, promoter region, transcribable DNA region, 5’ untranslated region (5’ UTR), 3’ untranslated region (3’ UTR), or downstream region of an endogenous GA3 oxidase gene of a corn plant and causes a double-strand break or nick at the target site.

152. The engineered site-specific nuclease of claim 151, wherein the site-specific nuclease is a meganuclease or homing endonuclease, a zinc finger nuclease (ZFN) comprising a DNA binding domain and a cleavage domain, or a transcription activator-like effector nuclease (TALEN) comprising a DNA binding domain and a cleavage domain.

153. A recombinant DNA construct comprising a transcribable DNA sequence encoding a site-specific nuclease, wherein the site-specific nuclease binds to a target site in the upstream region, promoter region, transcribable DNA region, 5’ untranslated region (5’ UTR), 3’ untranslated region (3’ UTR), or downstream region of an endogenous GA3 oxidase gene of a corn plant and causes a double-strand break or nick at the target site.

154. The recombinant DNA construct of claim 153, wherein the transcribable DNA sequence is operably linked to a plant-expressible promoter.

155. The recombinant DNA construct of claim 153 or 154, wherein the site-specific nuclease is a meganuclease or homing endonuclease, a zinc finger nuclease, or a transcription activator-like effector nuclease (TALEN).

156. A corn plant, plant part or plant cell comprising the recombinant DNA construct of claim 153, 154 or 155.

157. A method for producing a modified corn plant, comprising:(a) introducing into at least one cell of an explant of the com plant a site-specific nuclease or a recombinant DNA molecule comprising a transgene encoding the site-specific nuclease, wherein the site-specific nuclease binds to an upstream region or promoter region of an endogenous GA3 oxidase gene and causes a double-strand break or nick at the target site, and(b) regenerating or developing a modified corn plant from the at least one explant cell comprising a mutant allele of the endogenous GA3 oxidase gene comprising a genomic edit in the upstream region or the promoter region of the endogenous GA3 oxidase gene of the modified com plant or a deletion of at least a portion of the transcribable DNA region or coding sequence of the endogenous GA3 oxidase gene relative to a wild-type allele of the endogenous GA3 oxidase gene.

58. The method of claim 157, wherein the introducing step (a) further comprises introducing a non-coding guide RNA molecule or a second recombinant DNA construct comprising a transcribable DNA sequence encoding a non-coding guide RNA molecule, wherein the site-specific nuclease is a RNA-guided endonuclease, and wherein the guide RNA molecule comprises a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of a target DNA sequence in the upstream region or the promoter region of an endogenous GA3 oxidase gene of a corn plant.

59. A method for producing a modified corn plant, comprising:(a) introducing into at least one cell of an explant of a corn plant at least one site-specific nuclease or a recombinant DNA molecule comprising at least one transgene encoding a site-specific nuclease, wherein the site-specific nuclease binds to a target site in the transcribable DNA region or an untranslated region (UTR) of an endogenous GA3 oxidase gene and causes a double-strand break or nick at the target site, and(b) regenerating or developing a modified corn plant from the at least one explant cell comprising a mutant allele of the endogenous GA3 oxidase gene comprising an inverted DNA segment in the transcribable DNA region or the untranslated region (UTR) of the endogenous GA3 oxidase gene of the modified corn plant, wherein the inverted DNA segment encodes an antisense RNA sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% complementary to at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 500, at least 1000, at least 1500, at least 2000, or atleast 2500 consecutive nucleotides of the transcribable DNA region of a wild-type allele of the endogenous GA3 oxidase gene and / or a mRNA molecule encoded by the wild-type allele of the endogenous GA3 oxidase gene, and wherein the mutant allele of the endogenous GA3 oxidase gene encodes a mRNA transcript comprising the antisense RNA sequence.

160. The method of claim 159, wherein the introducing step (a) further comprises introducing into the at least one cell a second site-specific nuclease or a recombinant DNA molecule comprising a second transgene encoding a second site-specific nuclease, wherein the site-specific nuclease binds to a second target site in the transcribable DNA region or the untranslated region (UTR) of an endogenous GA3 oxidase gene and causes a double-strand break or nick at the target site.

161. The method of claim 160, wherein the inverted DNA segment in the mutant allele of the endogenous GA3 oxidase gene of the modified corn plant is between the first target site and the second target site in the transcribable DNA region or the untranslated region (UTR) of the endogenous GA3 oxidase gene.

162. The method of claim 159, wherein the introducing step (a) further comprises introducing into the at least one cell (i) a first non-coding guide RNA molecule or a first recombinant DNA construct comprising a first transcribable DNA sequence encoding a first non-coding guide RNA molecule and (ii) a second non-coding guide RNA molecule or a second recombinant DNA construct comprising a second transcribable DNA sequence encoding a second non-coding guide RNA molecule, wherein the site-specific nuclease is a RNA-guided endonuclease, wherein the first guide RNA molecule comprises a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% complementary to at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of a first target DNA sequence in the transcribable DNA region or the untranslated region (UTR) of an endogenous GA3 oxidase gene of a corn plant, and wherein the second guide RNA molecule comprises a guide sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 99% or 100% complementary to atleast 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 consecutive nucleotides of a second target DNA sequence in the transcribable DNA region or the untranslated region (UTR) of an endogenous GA3 oxidase gene of a corn plant.

163. The method of claim 162, wherein the inverted DNA segment in the mutant allele of the endogenous GA3 oxidase gene of the modified com plant is between the first target DNA sequence and the second target DNA sequence in the transcribable DNA region or the untranslated region (UTR) of the endogenous GA3 oxidase gene.

164. The method of any one of claims 159-163, further comprising:(c) selecting the modified corn plant.

165. The method of claim 164, wherein the selecting step (c) comprises determining if the endogenous GA3 oxidase gene locus of the modified com plant comprises the mutant allele of the endogenous GA3 oxidase gene using a molecular assay.

166. The method of claim 164 or 165, wherein the selecting step (c) comprises determining if the endogenous GA3 oxidase gene locus of the modified com plant comprises the mutant allele of the endogenous GA3 oxidase gene by observing a plant phenotype.

167. The method of claim 164, 165 or 166, wherein the selecting step (c) comprises determining if the modified corn plant has a shorter plant height relative to a wild-type control plant.

168. The method of any one of claims 159-167, wherein the modified corn plant or a progeny plant thereof comprising the mutant allele of the endogenous GA3 oxidase gene has one or more of the following beneficial traits relative to a wild type control plant: increased stalk / stem diameter, improved lodging resistance, reduced green snap, deeper roots, increased leaf area, earlier canopy closure, higher stomatai conductance, lower ear height, increased foliar water content, improved drought tolerance, improved nitrogen use efficiency, reduced anthocyanin content and area in leaves under normal or nitrogen or water limiting stress conditions, increased ear weight, increased harvest index, increased yield, increased seed number, increased seed weight, and / or increased prolificacy.

169. The method of any one of claims 159-167, wherein the level of one or more active GAs in at least one internode tissue of the stem or stalk of the modified com plant or a progenyplant thereof comprising the mutant allele of the endogenous GA3 oxidase gene is lower than the same internode tissue of a wild type control plant.

170. The method of any one of claims 159-169, wherein the site specific nuclease is a meganuclease, a zinc-finger nuclease (ZFN), a RNA-guided endonuclease, a TALE-endonuclease (TALEN), a recombinase, or a transposase.

171. The method of any one of claims 159-170, wherein the activity and / or expression level of a mRNA and / or protein encoded by the mutant allele of the endogenous GA3 oxidase gene is reduced or eliminated in the modified corn plant or a progeny plant thereof comprising the mutant allele of the endogenous GA3 oxidase gene relative to a wild-type allele of the endogenous GA3 oxidase gene.

172. The method of any one of claims 159-171, wherein the modified corn plant or a progeny plant thereof comprising the mutant allele of the endogenous GA3 oxidase gene does not have any significant off-types in at least one female organ or ear.

173. A modified com plant produced by the method of any one of claims 159-172.

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