AU2015323980A1 - Plants with engineered endogenous genes - Google Patents

Abstract

Genetically engineered plants expressing altered Glucan Water Dikinase and having elevated levels of starch are provided. Methods of genetically engineering plants to express altered Glucan Water Dikinase, and genetic constructs are provided. Methods of breeding genetically engineered plants homozygous for a mutated gene encoding an altered Glucan Water Dikinase are described. Methods of agricultural processing and animal feed using the genetically engineered plants are also provided.

Description

PCT/US2015/052940 WO 2016/054039

PLANTS WITH ENGINEERED ENDOGENOUS GENES

[0001] CROSS REFERENCE TO RELATED APPLICATIONS

[0002] This application claims the benefit of U.S. Provisional Application No. 62/056,852, which was filed September 29, 2014, and is incorporated herein by reference as if fully set forth.

[0003] The sequence listing electronically filed with this application titled “Sequence Listing,” which was created on September 29, 2015 and had a size of 159,500 bytes is incorporated by reference herein as if fully set forth.

[0004] GOVERNMENT SUPPORT STATEMENT

[0005] This invention was made with government support under award number DE-AR0000042 awarded by the Advanced Research Projects Agency-Energy, ARPA-E. The government has certain rights in the invention.

[0006] FIELD

[0007] The disclosure herein relates to genetically improved plants having optimized endogenous nucleic acid sequences encoding altered glucan water dikinase, and having elevated levels of starch. The disclosure also relates to optimized nucleic acids encoding altered glucan water dikinase, methods of optimizing endogenous nucleic acids, methods of increasing starch levels in plants, and methods of making and propagating the genetically improved plants.

[0008] BACKGROUND

[0009] Plants synthesize starch in vegetative tissues during the daytime and degrade the starch at night to mobilize the resulting sugar in order to support the energy needs of the plant. Vegetative plant cells express a series of enzymes to initiate mobilization of transitory starch during the nighttime. Glucan Water Dikinase (“GWD”), which phosphorylates starch is one of these enzymes. GWD transcript levels were shown to undergo diel fluctuation -1- PCT/U S2015/052940 WO 2016/054039 (Smith et al. Plant Phys. Preview, April 29, 2014). Increasing the starch content of biomass can increase the energy content (calories) in animal feed or improve glucose extraction from biomass for the production of ethanol or other biochemicals.

[0010] Different molecular methods exist for manipulating plant characteristics. Almost all of these methods rely on inserting new, synthetic or recombinant nucleic acids into a plant through the process of transformation. The nucleic acids thus inserted may encode a ribonucleic acid (RNA) or protein, which is expressed by the transformed plant and thereby changes the plant phenotype. In many cases, the nucleic acid may encode a heterologous protein or produce more of an endogenous protein. Similarly, the transformed nucleic acids may produce RNA that through a variety of mechanisms (such as RNA interference, antisense RNA, etc.) reduce expression of an endogenous gene thereby “silencing” the gene and production of its product. In all cases the nucleic acid inserted into the plant is expressed in a dominant manner; that is, its presence has a direct effect on the plant’s characteristics. More recently, it has been demonstrated that by expressing nucleic acids that encode deoxyribonucleic acid (DNA) altering proteins (such as nucleases) in an organism, the organism’s genome can be permanently altered, even after the inserted nucleic acids have been removed, and endogenous genes optimized. In this way it is possible to not only generate beneficial dominant traits, but also generate very specific, targeted mutations as the basis to create beneficial recessive traits, which would have been otherwise extremely difficult to find and develop for commercial applications. Currently there are no recessive traits created using nucleases in commercial use in row crops. Recessive traits generated using nucleases have been previously demonstrated in plants and plant cells, but never in fully developed, multicellular corn and sorghum plants, including hybrid corn and sorghum. Like dominant traits, recessive traits may have commercial value and may have specific commercial advantages (security and regulatory benefits in particular) over dominant traits. Such recessive traits will require -2- PCT/US2015/052940 WO 2016/054039 new methods of propagating, tracking, and delivering the trait, particularly in hybrid crops.

[0011] One problem with dominant traits, particularly in hybrid and cross-pollinating crops, such as corn, is that they can be readily transferred to other lines of the same species. In regions of the world where farmers generate at least part of their own seed for planting, this affords the opportunity to breed a dominant trait into a farmer’s existing lines, without paying the technology owner. The established trait business model currently requires seed and trait purchasers to pay the trait provider a royalty and licenses commonly limit use of the trait to a single planting and prohibit breeding. For many traits, monitoring unlicensed breeding is nearly impossible, and substantial unlicensed trait transfer (pirating) of traits occurs in some parts of the world. Depending on the trait, pirating or transferring the trait into a useable line without paying the technology owner can be an easy task and difficult for technology providers to detect. For example, pest resistance or agronomic traits, that do not require any other materials for their use, such as an herbicide resistance or specific fertilizer, are nearly impossible to detect if they have been transferred into a different line. Subsequent generations can be generated and tracked by a breeder using commercially available test strips or phenotypically if the trait confers an easily scorable phenotype. Because the trait is dominant, it may not need to be homozygous in the progeny for farmers to use it, and thereby enables easy continued breeding and use outside of the technology licensor’s awareness.

[0012] In contrast to dominant traits, a recessive trait needs to be homozygous in the crop in order to phenotypically observed or easily scored. Simple test strips may not be available to track the molecular basis of the trait, and accurate breeding of a recessive trait made through the use of a nuclease may require at least polymerase chain reaction (PCR) to detect. In this case, none of the progeny resulting from an outcross of the homozygous parent carrying the trait will display the trait and extended breeding, tracking, and in some cases hybrid crosses will be required to use such a trait. -3- PCT/US2015/052940 WO 2016/054039

This makes pirating of the technology considerably more expensive and difficult than with dominant traits. The process of making, maintaining, and providing a recessive trait requires additional steps not necessary in the production of dominant traits, and therefore requires the use of novel processes in seed and trait production.

[0013] Recessive traits that are based on optimized genes containing a specific genetic mutation may also have regulatory advantages over dominant traits made using transgenic technologies. Because such a recessive trait may not contain any newly introduced heterologous DNA, in many parts of the world it may not be regulated as a transgenic crop.

[0014] SUMMARY

[0015] In as aspect, the invention relates to a genetically engineered plant comprising an engineered nucleic acid encoding an altered Glucan Water Dikinase, wherein the plant has an elevated level of starch in comparison to a plant of the same genetic background comprising a wild type Glucan Water Dikinase.

[0016] In an aspect the invention relates to a method for genetically engineering a plant to comprise an altered Glucan Water Dikinase. The method comprises contacting at least one plant cell comprising a target sequence in an endogenous gene encoding a Glucan Water Dikinase with a vector comprising a first nucleic acid encoding a nuclease capable of inducing a double-strand break at the target sequence. The method also comprises selecting a plant cell that includes an alteration in the target sequence. The method also comprises regenerating a genetically engineered plant including the alteration from the plant cell.

[0017] In an aspect, the invention relates to a method of increasing a starch level in a plant. The method comprises expressing a nucleic acid encoding a nuclease capable of inducing a double-strand break at a target sequence, where the target sequence is a sequence in an endogenous gene encoding a Glucan Water Dikinase. The method also comprises selecting a -4- PCT/US2015/052940 WO 2016/054039 homozygous plant that comprises an alteration in the target sequence and has an elevated level of starch in comparison to a plant of the same genetic background comprising a wild type Glucan Water Dikinase.

[0018] In an aspect, the invention relates to a method of agricultural processing. The method comprises expressing a nucleic acid encoding a nuclease capable of inducing a double-strand break at the target sequence, where the target sequence is a sequence in an endogenous gene encoding a Glucan Water Dikinase. The method may comprise selecting a homozygous plant that includes an alteration in the target sequence and has an elevated level of starch in comparison to a plant of the same genetic background comprising a wild type Glucan Water Dikinase. The method may also comprise processing the homozygous plant.

[0019] In an aspect, the invention relates to a method of preparing animal feed. The method comprises expressing a nucleic acid encoding a nuclease capable of inducing a double-strand break at the target sequence, where the target sequence is a sequence in an endogenous gene encoding a Glucan Water Dikinase. The method may comprise selecting a homozygous plant that includes an alteration in the target sequence and has an elevated level of starch in comparison to a plant of the same genetic background comprising a wild type Glucan Water Dikinase. The method may also comprise performing at least one procedure selected from the group consisting of: harvesting, bailing, shredding, drying, ensiling, pelletizing, combining with a source of edible fiber fiber, and combining with plant biomass.

[0020] In an aspect, the invention relates to a method for producing a genetically engineered plant homozygous for an engineered nucleic acid that encodes an altered Glucan Water Dikinase comprising performing any one of the method for genetically engineering a plant comprising an altered Glucan Water Dikinase described herein.

[0021] In an aspect, the invention relates to a synthetic nucleic acid promoter having a sequence with at least with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 % identity to a reference sequence -5- PCT/US2015/052940 WO 2016/054039 selected from the group consisting of: SEQ ID NO: 78 (MzU3.8), SEQ ID NO: 79 (ZmU3), SEQ ID NO: 82 (ZmU3Pl), SEQ ID NO: 84 (ZmU3P2) and SEQ ID NO: 86 (MzU3.8P).

[0022] In an aspect, the invention relates to a genetic construct comprising a first engineered nucleic acid sequence encoding a Cas9 nuclease. The Cas9 nuclease is capable of cleaving a target sequence included in an endogenous nucleic acid encoding Glucan Water Dikinase in a plant.

[0023] In an aspect, the invention relates to a kit for identifying a modified sequence of an endogenous gene encoding Glucan Water Dikinase in a sample. The kit comprises first primer and a second primer. The first primer and the second primer are capable of amplifying a target sequence included in the endogenous gene encoding Glucan Water Dikinase. The target sequence comprises a nucleic acid sequence with at least 90% identity to a reference sequence selected from SEQ ID NOS: 1 - 4, 75, 170 - 184 186, 187, 189 - 193. The kit may also comprise one or more component for detecting at a modification in the amplified region of the target sequence. The modification may be a modified sequence of an endogenous gene encoding Glucan Water Dikinase in any of genetically engineered plants described herein.

[0024] In an aspect, the invention relates to a method of identifying a modified sequence of an endogenous gene encoding Glucan Water Dikinase in a sample. The method comprises contacting a sample with a first primer and a second primer. The method comprises amplifying a target sequence included in the endogenous gene encoding Glucan Water Dikinase. The target sequence comprises a nucleic acid sequence with at least 90% identity to a reference sequence selected from SEQ ID NOS: 1 - 4, 75, 170 - 184 186, 187, 189 - 193. The method also comprises detecting modification of the target sequence. The modification may be a modified sequence of an endogenous gene encoding Glucan Water Dikinase in any of genetically engineered plants described herein. -6- PCT/US2015/052940 WO 2016/054039

[0025] BRIEF DESCRIPTION OF THE DRAWINGS

[0026] The following detailed description of embodiments of the present invention will be better understood when read in conjunction with the appended drawings. For the purpose of illustration, there are shown in the drawings particular embodiments. It is understood, however, that the invention is not limited to the precise arrangements and instrumentalities shown. In the drawings: [0027] FIG. 1 illustrates the vector pAG4715 for expressing meganuclease. [0028] FIG. 2 illustrates the vector pAG4716 for expressing meganuclease.

[0029] FIG. 3 illustrates PCR detection of mutants.

[0030] FIG. 4 illustrates a chart depicting starch content (mg starch per gram dry weight) across populations of mutant homozygous, heterozygous and hemizygous corn plants produced by using vectors pAG4715 and pAG4716. Lines 195, 20, 19, 18, 9 and 6 are control plants.

[0031] FIG. 5 illustrates starch content in green tissue of gwd knock-out corn mutants: bar 1 is wild type (WT) plant, bar 2 is M17, bar 3 is M18, bar 4 is Ml, bar 5 is M20, bar 6 is M13/M12, bar 7 is M9, bar 8 is M7/M11, bar 9 is M4/M14, bar 10 is M11/M12, bar 11 is M15, bar 12 is M14, bar 13 is Mil, bar 14 is M11/M10 and bar 15 is M13.

[0032] FIG. 6 illustrates starch staining in gwd knock-out (GWDko) meganuclease cobs.

[0033] FIG. 7 illustrates the vector pAG4800 for expressing ZmCas9.

[0034] FIG. 8 illustrates the vector pAG4804 for expressing sgRNA scaffold and ZmCas9.

[0035] FIG. 9 illustrates starch accumulation in the pAG4804 maize events.

[0036] FIG. 10 illustrates starch accumulation in the pAG4806 maize events. -7- PCT/US2015/052940 WO 2016/054039 [0037] FIG. 11 illustrates a schematic drawing of selfing and outcrossing of a targeted mutation M20 derived from the maize event 4716_164.

[0038] FIG. 12 illustrates genotyping of T1 progeny from the selfed TO 4716_164 M20 plant.

[0039] FIG. 13 illustrates genotyping of T1 progeny from the outcrossed TO 4716_164 M20 plant.

[0040] FIG. 14 illustrates genotyping of T1 progeny from the outcrossed 4716_164 M20 plant.

[0041] DETAILED DESCRIPTION

[0042] Certain terminology is used in the following description for convenience only and is not limiting.

[0043] “Engineered nucleic acid sequence,” “engineered polynucleotide,” “engineered oligonucleotide,” “engineered DNA,” or “engineered RNA” as used herein refers to a nucleic acid, polynucleotide, oligonucleotide, DNA, or RNA that differs from one found in nature by having a different sequence than one found in nature or a chemical modification not found in nature. The engineered nucleic acid sequence,” “engineered polynucleotide,” “engineered oligonucleotide,” “engineered DNA,” or “engineered RNA” may be a synthetic nucleic acid sequence, synthetic polynucleotide, synthetic oligonucleotide, synthetic DNA, or synthetic RNA. The definition of engineered nucleic acid includes but is not limited to a DNA sequence created using biotechnology tools. Such tools include but are not limited to recombinant DNA technology, chemical synthesis, or directed use of nucleases (so called "genome editing" or “gene optimizing” technologies).

[0044] “Endogenous nucleic acid” as used herein refers to a nucleic acid, polynucleotide, oligonucleotide, DNA, or RNA naturally occurring in the organism or the genome. An endogenous nucleic acid may be an endogenous gene.

[0045] “Altered protein” as used herein refers to a protein, polypeptide, oligopeptide or peptide that contains at least one amino acid change, or -8- PCT/US2015/052940 WO 2016/054039 deletion compared to the amino acid sequence contained in a naturally occurring organism, e.g., a parent organism. An altered protein may retain or lack the biological activity of the original sequence.

[0046] As used herein, “operably linked” refers to the association of two or more biomolecules in a configuration relative to one another such that the function of the biomolecules can be performed. In relation to two or more nucleotide sequences, “operably linked” refers to the association of the nucleic acid sequences in a configuration relative to one another such that the function of the sequences can be performed. For example, a nucleotide sequence encoding a presequence or secretory leader is operably linked to a nucleotide sequence for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide; a promoter or enhancer sequence is operably linked to a coding sequence if it affects the transcription of the coding sequence; and a nucleic acid ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate binding of the ribosome to the nucleic acid.

[0047] As used herein, genetic background is defined as the sum of all genes, or a collection of specific genes (e.g., all genes but for an engineered genetic modification) in a plant. Plants of the same species may be referred to as plants having the same genes or the same genetic background. A genetically engineered plant may include an engineered nucleic acid or polynucleotide described herein but otherwise have the same genes as non-genetically engineered plant of the same genetic background.

[0048] The words “a” and “one,” as used in the claims and in the corresponding portions of the specification, are defined as including one or more of the referenced item unless specifically stated otherwise. This terminology includes the words above specifically mentioned, derivatives thereof, and words of similar import. The phrase “at least one” followed by a list of two or more items, such as “A, B, or C,” means any individual one of A, B or C as well as any combination thereof. -9- PCT/US2015/052940 WO 2016/054039 [0049] An embodiment comprises a genetically engineered plant comprising an engineered nucleic acid encoding an altered Glucan Water Dikinase. The genetically engineered plant may have an elevated level of starch in comparison to a plant of the same genetic background but comprising a wild type (wt) GWD. The activity of the altered GWD may be reduced in comparison to wild type (wt) GWD included in a plant of the same genetic background. The level of reduction may be 20, 30, 40, 50, 60, 70, 80, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% based on the level of wt GWD. Activity of GWD may be tested by monitoring starch content in plants, for example, by using Fourier Transform Near-infrared (FT-NIR) Technique as described in Example 3 herein. The altered GWD may be inactive. Increased levels of starch indicate reduced GWD activity.

[0050] In an embodiment, the engineered nucleic acid in the genetically engineered plant may comprise an endogenous nucleic acid that includes at least one allele of a gwd gene encoding a GWD protein but having one or more modifications in comparison to the wild type plant. The modifications may be made made by genetic engineering of the plant or its ancestors. The endogenous nucleic acid may be one or more allele of the gwd gene in the engineered plant. The modifications may be in the gwd coding sequences. The endogenous nucleic acid may comprise, consist essentially of, or consist of a sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% identity to a reference sequence selected from SEQ ID NO: 1 (Zm GWD coding sequence) or SEQ ID NO: 2 (Sb GWD coding sequence). The engineered nucleic acid may include at least one mutation relative to the endogenous nucleic acid. A mutation may include an insertion of one or more nucleotides in comparison to the endogenous nucleic acid. A mutation may include a deletion of nucleotides in comparison to the native nucleic acid. A mutation may include a substitution of one or more nucleotides in comparison to the endogenous nucleic acid. A mutation may be a combination of several mutations. The at least one mutation may be within a target sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% identity to -10- PCT/U S2015/052940 WO 2016/054039 a reference sequence selected from SEQ ID NO: 1 (Zm GWD coding sequence), SEQ ID NO: 2 (Sb GWD coding sequence), SEQ ID NO: 3 (Zm GWD Exon 24 + introns), SEQ ID NO; 4 (SbGWD Exon 24 + introns), SEQ ID NO: 91 (GWDela), SEQ ID NO: 92 (GWDe24b), SEQ ID NO: 93 (GWDe24c), and SEQ ID NO: 94 (GWDe25a), SEQ ID NO: 182 (ZmGWD Exon 24), SEQ ID NO: 183 (Sb GWD Exon 24), SEQ ID NO: 184 (SbGWD Exon 7) and SEQ ID NO: 189 (Zm GWD Exon 25).

[0051] In an embodiment, the engineered nucleic acid in the genetically engineered plant may be an endogenous nucleic acid that includes at least one allele of a gwd gene encoding a GWD protein but having one or more modifications made by genetic engineering of the plant or its ancestors. The endogenous nucleic acid may be one or more allele of the gwd gene in the engineered plant. The modifications may be in the gwd coding sequences. The endogenous nucleic acid may comprise, consist essentially of, or consist of a sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% identity to a reference sequence selected from SEQ ID NO: 1 (Zm GWD coding sequence) or SEQ ID NO: 2 (Sb GWD coding sequence). The engineered nucleic acid may include at least one mutation relative to the endogenous nucleic acid. A mutation may include an insertion of one or more nucleotides in comparison to the endogenous nucleic acid. A mutation may include a deletion of nucleotides in comparison to the native nucleic acid. A mutation may include a substitution of one or more nucleotides in comparison to the endogenous nucleic acid. A mutation may be a combination of several mutations. The at least one mutation may be within a target sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% identity to a reference sequence selected from SEQ ID NO: 1 (Zm GWD coding sequence), SEQ ID NO: 2 (Sb GWD coding sequence), SEQ ID NO: 3 (Zm GWD Exon 24 + introns), SEQ ID NO; 4 (SbGWD Exon 24 + introns), SEQ ID NO: 91 (GWDela), SEQ ID NO: 92 (GWDe24b), SEQ ID NO: 93 (GWDe24c), and SEQ ID NO: 94 (GWDe25a), SEQ ID NO: 182 (ZmGWD Exon 24), SEQ ID NO: 183 -11- PCT/U S2015/052940 WO 2016/054039 (Sb GWD Exon 24), SEQ ID NO: 184 (SbGWD Exon 7) and SEQ ID NO: 189 (Zm GWD Exon 25).

[0052] In an embodiment, the engineered nucleic acid in the genetically engineered plant comprises a modified sequence of Exon 24 of the maize gwd gene. The engineered nucleic acid may comprise, consist essentially of, or consist of a polynucleotide having a sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% identity to a reference sequence selected from SEQ ID NOS: 12 - 40, 114 - 118, 119 - 120 and 131 - 146, which comprise mutations in the maize gwd gene.

[0053] In an embodiment, the engineered nucleic acid in the genetically engineered plant may comprise a modified sequence having one or more modifications within a region of the wild type Zm GWD gene (SEQ ID NO: 1) in the position from 3030 nucleotide (nt) to 3243 nt. In an embodiment, the engineered nucleic acid in the genetically engineered plant may comprise a modified sequence having one or more modifications within a region of the wild type Zm GWD gene (SEQ ID NO: 1) in the position from 3157 nt to 3213 nt. In an embodiment, the engineered nucleic acid in the genetically engineered plant may comprise a modified sequence having one or more modifications within a region of the wild type Zm GWD gene Exon 24 (SEQ ID NO: 3) in the position from 81 nt to 160 nt.

[0054] In an embodiment, the Zm GWD gene in the genetically engineered plant may comprise a modified sequence with changes in the sequence relative to wild type Zm GWD (SEQ ID NO: 1) in one of SEQ ID NOS: 12 - 40, 114 - 118, 119 - 120 and 131 - 146. The sequence of Zm GWD with the changes outside of the positions where the changes are located may have at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% identity to the corresponding regions of SEQ ID NO: 1. The changes may be the same or different from one of SEQ ID NOS: 12 - 40, 114 - 118, 119 - 120 and 131 - 146.

[0055] In an embodiment, the engineered nucleic acid in the genetically engineered plant may comprise a modified sequence of Exon 24 of the -12- PCT/US2015/052940 WO 2016/054039 sorghum gwd gene. The engineered nucleic acid may comprise, consist essentially of, or consist of a polynucleotide having a sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% identity to a reference sequence selected from SEQ ID NO: 106 (Sb4715_l (WT + ins)_Exon 24), and SEQ ID NO: 107 (Sb4715_2 (WT + del)_Exon 24), which are mutations in Exon 24 in the sorghum gwd gene. In an embodiment, the engineered nucleic acid in the genetically engineered plant may comprise a modified sequence having one or more modifications within a region of the wild type Sb GWD gene (SEQ ID NO: 2) in the position from 3030 nt to 3243 nt. The engineered nucleic acid in the genetically engineered plant may comprise a modified sequence having one or more modifications within a region of the wild type Sb GWD gene (SEQ ID NO: 2) in the position from 736 nt to 969 nt. The altered GWD may be encoded by any one of the engineered nucleic acids herein.

[0056] In an embodiment, a genetically engineered plant may comprise an altered Zea mays GWD (Zm GWD). The altered ZmGWD may comprise, consist essentially of, or consist of an amino acid sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% identity to a reference sequence selected from SEQ ID NOS: 45 - 73 (Zm GWD mutant proteins Ml -M29), 121 -125 (Zm GWD mutant proteins M32 - M36), 126 - 127 (Zm GWD mutant proteins M38 - M39) and 147 - 162 (Zm GWD mutant proteins M40 -M55).

[0057] In an embodiment, the altered ZmGWD protein in the genetically engineered plant may comprise a modified sequence having one or more modifications within a region of the wild type Zm GWD protein (SEQ ID NO: 43) in the positions from 1040 amino acid (aa) to 1120 aa. The altered ZmGWD protein in the genetically engineered plant may comprise a modified sequence having one or more modifications within a region of the wild type Zm GWD protein (SEQ ID NO: 43) in the positions from 1054 aa to 1081 aa. The altered ZmGWD protein in the genetically engineered plant may comprise a modified sequence having one or more modifications within a region of the -13- PCT/US2015/052940 WO 2016/054039 wild type Zm GWD protein (SEQ ID NO: 43) in the positions from 1011 aa to 1057 aa. The altered ZmGWD protein in the genetically engineered plant may comprise a modified sequence having one or more modifications within a region of the wild type Zm GWD protein (SEQ ID NO: 43) in the positions from 1082 aa to 1116 aa.

[0058] In an embodiment, the Zm GWD protein in the genetically engineered plant may comprise a modified sequence with changes in the sequence relative to wild type Zm GWD (SEQ ID NO: 43) in one of SEQ ID NOS: 45 - 73 (Zm GWD mutant proteins Ml - M29), 121 -125 (Zm GWD mutant proteins M32 - M36), 126 - 127 (Zm GWD mutant proteins M38 - M39) and 147 - 162 (Zm GWD mutant proteins M40 - M55). The sequence of Zm GWD with the changes outside of the positions where the changes are located may have at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% identity to the corresponding regions of SEQ ID NO: 43. The changes may be the same or different from one of SEQ ID NOS: 45 - 73 (Zm GWD mutant proteins Ml - M29), 121 -125 (Zm GWD mutant proteins M32 - M36), 126 - 127 (Zm GWD mutant proteins M38 - M39) and 147 - 162 (Zm GWD mutant proteins M40 - M55).

[0059] In an embodiment, a genetically engineered plant may comprise an altered Sorghum bicolor GWD (Sb GWD). The altered Sb GWD may comprise, consist essentially of, or consist of an amino acid sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% identity to a reference sequence selected from SEQ ID NO: 194(Sb GWD mutant protein Sb4715_lWT + ins) and SEQ ID NO: 195 (Sb GWD mutant protein Sb4715_2 WT + del). Nucleic acids, nucleotide sequences proteins or amino acid sequences herein can be isolated, purified, synthesized chemically, or produced through recombinant DNA technology. All of these methods are well known in the art.

[0060] In an embodiment, the genetically engineered plant may be any type of plant. The genetically engineered plant may be but is not limited to a monocotyledonous plant, a dicotyledonous plant, a C4 plant, a C3 plant, corn, -14- PCT/US2015/052940 WO 2016/054039 soybean, rice, sugar cane, sugar beet, sorghum, switchgrass, miscanthus, eucalyptus, wheat, alfalfa, willow, or poplar. The genetically engineered plant may be derived from an energy crop plant, a forage crop plant, or a food crop plant. The energy crop plant may be a corn plant, a switchgrass plant, a sorghum plant, a poplar plant, or a miscanthus plant. The forage crop plant may be a corn plant, an alfalfa plant, a sorghum plant or a soybean plant. The food crop plant may be a corn plant, a wheat plant, a soybean plant, a rice plant, or a tomato plant.

[0061] The genetically engineered plant may be a transgenic plant or a mutant plant. The genetically engineered plant may be a progeny of a transgenic plant or a mutant plant, or a descendant of a transgenic plant or a mutant plant.

[0062] The genetically engineered plant may be a conventional mutant having one or more mutations in a nucleic acid sequence of a gene encoding GWD that result in inhibited expression of the GWD or reduced activity of GWD. The mutations may be deletions, insertions or substitutions of nucleic acids in a sequence of the GWD encoding gene. The conventional mutant may have an altered level of vegetative starch compared to a non-mutant plant of the same genetic background but expressing wild type GWD.

[0063] As used herein, the genetically engineered plant may refer to a whole transgenic plant or mutant plant or a part thereof. The part may be but is not limited to one or more of leaves, stems, flowers, buds, petals, ovaries, fruits, or seeds. The part may be callus from a transgenic plant or a mutant plant. A genetically engineered plant may be regenerated from parts of a transgenic plant or a mutant plant or plants. A genetically engineered plant may be a product of sexual crossing of a first transgenic plant and a second transgenic plant or a non-transgenic plant where the product plant retains an engineered nucleic acid introduced to the first transgenic plant. A genetically engineered plant may be a product of sexual crossing of a first mutant plant and a second non-mutant plant where the product plant retains a mutation -15- PCT/US2015/052940 WO 2016/054039 introduced to the first mutant plant. The transgenic plant or the mutant plant may be any one of the transgenic plants or mutant plants described herein.

[0064] In an embodiment, a method for genetically engineering a plant that includes an altered Glucan Water Dikinase is provided. The method may include contacting at least one plant cell that comprises a target sequence in an endogenous gene encoding a Glucan Water Dikinase with a vector. The vector may include a first nucleic acid encoding a nuclease capable of inducing a single-strand break or a double-strand break at the target sequence. The vector may be introduced by transforming or otherwise genetically engineering a plant. Transforming may be Agrobacterium-mediated transformation using a vector that includes a first nucleic acid encoding a nuclease. The nuclease may cleave the target sequence as described previously (Puchta et al. 1993; Wright et al. 2005; Wehrkamp-Richter et al. 2009; Cong et al., 2013; Belhaj et al., 2013, all of which are incorporated herein by reference as if fully set forth). The nuclease may be but is not limited to a meganuclease, Cas9 nuclease, a zinc finger nuclease, or a transcription activator-like effector nuclease.

[0065] As stated, the nuclease may be a meganuclease. Meganucleases may introduce single stranded or double stranded DNA breaks and have recognition sites ranging between 14 to 40 nucleotides in length providing good specificity. For use of meganucleases for targeted modification, see Rosen et al., 2006; Wehrkamp-Richter et al. 2009; Djukanovic et al., 2013, all of which are incorporated herein by reference as if fully set forth. The meganuclease may be a LAGLIDADG homing endonuclease (LHE). LAGLIDADG homing endonucleases (LHEs) are native gene-targeting proteins with their coding sequences found in introns or inteins. See Arnould et al., 2011, which is incorporated herein by reference as if fully set forth. The meganuclease may be a I—Crel homing endonuclease. As used herein, the I— Crel homing endonuclease is a meganuclease naturally occurring in chloroplasts of Chlamydomonas reinhardtii, and is a well characterized protein containing a single sequence motif important for nuclease enzymatic -16- PCT/US2015/052940 WO 2016/054039 activity. See Heath et al., 1997, which is incorporated herein by reference as if fully set forth. The I-Crel endonuclease is suitable for protein engineering and was used for targeted genome modifications in several species including plants. See Rosen et al., 2006; Arnould et al., 2007; Djukanovic et al., 2013, all of which are incorporated herein by reference as if fully set forth. The meganuclease may be I-Dmol, I-Scel, E-Dmel or DmoCre. Other meganucleases may be used.

[0066] The meganuclease may be encoded by a sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% identity to a reference sequence selected from the group consisting of SEQ ID NO: 108 (4715_meganuclease) and SEQ ID NO: 109 (4716_meganuclease).

[0067] In an embodiment, the nuclease may be a Cas9 nuclease. Cas9 nuclease is the nuclease used in the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) systems (Cong et al., 2013; Belhaj et al., 2013, both of which are incorporated herein by reference as if fully set forth. The CRISPR/Cas9 is the genome editing technology that due to its low cost, high efficiency and relative simplicity to engineer has a potential of becoming a technology of choice for genome editing in various species, but has not been demonstrated to work in multi-cellular plants by using stable transformation. The CRISPR/Cas9 system may include a Cas9 nuclease and a single guide RNA (sg RNA). The Cas9 nuclease herein may be encoded with a nucleic acid with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% identity to a reference sequence of SEQ ID NO: 74 (Cas9 nuclease) or SEQ ID NO: 75 (ZmCas9). The nuclease may have affinity for a sequence that enables the nuclease to cleave the target sequence, or it may be guided to the target sequence by using an sgRNA. The vector herein may further include a second nucleic acid sequence encoding an sgRNA. The targeted modification of the endogenous gene may be made by expressing the Cas9 and sgRNA in a plant cell. The sgRNA chimera molecule may contain an untranslated CRISPR RNA (crRNA), a 20 bp spacer sequence complementary to the target genomic DNA sequence with a 3 bp protospacer--17- PCT/U S2015/052940 WO 2016/054039 adjacent motif (PAM) sequence (Jinek et al., 2012, which is incorporated herein by reference as if fully set forth). The Cas9 nuclease may be expressed from PPDK, CaMV 35S, Actin, or Ubiquitin promoters in plants, such as Arabidopsis, corn, tobacco, rice, wheat, and sorghum. The sgRNAs may be expressed from primarily RNA Polymerase III promoters U6 or U3 and from RNA polymerase II promoter CaMV E35S (Belhaj et al., 2013; Upadhyay et al., 2014, both of which are incorporated by reference herein as if fully set forth). The sgRNAs may be expressed from SEQ ID NO: 78 (MzU3.8), SEQ ID NO: 79 (ZmU3), ZmU3Pl (SEQ ID NO: 82), ZmU3P2 (SEQ ID NO: 84), or ZmU3.8 promoter (SEQ ID NO: 86) described herein. The promoter may have 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% identity to one of SEQ ID NO: 78 (MzU3.8), SEQ ID NO: 79 (ZmU3), ZmU3Pl (SEQ ID NO: 82), ZmU3P2 (SEQ ID NO: 84), or ZmU3.8 promoter (SEQ ID NO: 86). The promoter may have a length equal to 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% of the length in nucleotides of one of SEQ ID NO: 78 (MzU3.8), SEQ ID NO: 79 (ZmU3), ZmU3Pl (SEQ ID NO: 82), ZmU3P2 (SEQ ID NO: 84), or ZmU3.8 promoter (SEQ ID NO: 86). The percent identity of promoters shorter than SEQ ID NO: 78 (MzU3.8), SEQ ID NO: 79 (ZmU3), ZmU3Pl (SEQ ID NO: 82), ZmU3P2 (SEQ ID NO: 84), or ZmU3.8 promoter (SEQ ID NO: 86 may be as set forth above along the length of the shorter promoter. Cas9 nuclease may introduce a single stranded break or double stranded DNA break into an endogenous nucleic acid included in genomic DNA. Subsequently, breaks introduced by Cas9 in genomic DNA may be repaired via two distinct mechanisms NHEJ (non homologous ends joining) and HR (homologous recombination) (Symington and Gautier, 2011, which is incorporated herein by reference as if fully set forth).

[0068] In an embodiment, the nuclease may be a transcription activator like effector nucleases (TALEN). As used herein, TALENs refer to proteins derived from Xanthomonas. TALENs are customizable fusion proteins comprising an engineered DNA-binding domain of TAL effectors fused to DNA cleavage domains of FokI endonuclease (Boch and Bonas, 2010; Christian et -18- PCT/US2015/052940 WO 2016/054039 al., 2010; Joung and Sander, 2013; Li et al., 2011, all of which are incorporated herein by reference as if fully set forth). These chimeric proteins may work in pairs of two monomers for targeting FokI endonuclease to a specific DNA sequence within a genome for DNA cleavage. The TAL DNA-binding domain may be modified to recognize different sequences (Cermak et al., 2011, which is incorporated herein by reference as if fully set forth).

[0069] In an embodiment, the nuclease may be a zinc-finger nuclease. (Wright et al. 2005; Shukla et al., 2009, both of which are incorporated herein by reference as if fully set forth).

[0070] In an embodiment, the nuclease may be any other nuclease suitable for targeted modification of the target sequence.

[0071] The target sequence may be a target gene. The target gene may be an endogenous gene that is native to the plant. The target sequence may be a gwd gene of a plant The target sequence may be contained within SEQ ID NO: 1 (Zm GWD coding sequence) or SEQ ID NO: 2 (Sb GWD coding sequence). The target sequence may be any nucleic acid sequence included in an exon of an endogenous nucleic acid encoding GWD. The target sequence may be included in an exon of an endogenous nucleic acid encoding a maize GWD. The target sequence may be included in an exon of an endogenous nucleic acid encoding a sorghum GWD. The target sequence may be included in Exon, 1, Exon 7, Exon 24, or Exon 25 of an endogenous nucleic acid encoding GWD. The target sequence may be a target sequence for the meganuclease. The target sequence may comprise, consist essentially of, or consist of a sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% identity to SEQ ID NO: 41 (Meganuclease GWD-9/10x.272 target sequence (pAG4715)) or SEQ ID NO: 42 (Meganuclease GWD-7/8x target sequence (pAG4716)). The target sequence may be the target sequence for Cas9 nuclease. The target sequence may comprise, consist essentially of, or consist of a sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% identity to SEQ ID NO: 91 (GWDela), SEQ ID NO: 92 (GWDe24b), SEQ ID NO: 93 (GWDe24c), or SEQ ID NO: 94 (GWDe25a). The -19- PCT/US2015/052940 WO 2016/054039 sgRNA may be capable of binding a target sequence selected from the group consisting of SEQ ID NO: 91 (GWDela), SEQ ID NO: 92 (GWDe24b), SEQ ID NO: 93 (GWDe24c), and SEQ ID NO: 94 (GWDe25a). The target sequence may be any sequence that hybridizes with the sgRNA. The nuclease may have affinity for a sequence that enables the nuclease to cleave the target sequence, or it may be guided to the target sequence by using an sgRNA.

[0072] Once expressed, the nuclease will introduce one stranded or double stranded DNA breaks in the target sequence. For example, nuclease may delete a short segment that then may be partially repaired by the cell’s DNA repair mechanisms, but leaving a lesion within the target sequence. The repaired target sequence may include an alteration. The alteration may include a mutation. The mutation may be at least one of an insertion, a deletion, or a substitution of one or more nucleotides in the target sequence. The mutation may be a null mutation. As used herein, the term “null mutation” refers to a mutation in a gene that leads to its not being transcribed into RNA or translated into a functional protein. Because of the mutation in the target sequence, the native nucleic acid sequence may encode an altered GWD. The activity of the altered GWD may be reduced. The level of reduction may be 20, 30, 40, 50, 60, 70, 80, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% of the activity level of wild type GWD and may be tested by monitoring starch content in plants by using Fourier Transform Near-infrared (FT-NIR) Technique as described as described in Example 3 herein. The altered GWD may be inactive. The genetically engineered plant having the alteration or progeny thereof may have an elevated level of starch in comparison to a non-genetically engineered plant of the same genetic background.

[0073] The method may include selecting a plant cell that includes an alteration of the target sequences. The method may include regenerating the plant including the alteration from the plant cell. The genetically engineered plant may be homozygous for the alteration.

[0074] The genetically engineered plant may be heterozygous for the alteration. The genetically engineered plant herein may be heterozygous for -20- PCT/US2015/052940 WO 2016/054039 the gene that includes the mutation. The gene may include the engineered nucleic acid encoding the altered GWD. The heterozygous plants may include alleles of the endogenous gene that encode a wild type, unaltered, GWD. The heterozygous plant may also include hemizygous plants when at least one allele of the gene encoding GWD is missing. A heterozygous plant may be phenotypically indistinguishable from the wild type plants and may not have elevated levels of starch. To produce homozygous plants with elevated levels of starch, a heterozygous genetically engineered plant may be self-crossed. Progeny may be obtained from such crosses. The progeny may include homozygous, heterozygous and wild type plants. A heterozygous plant may be phenotypically indistinguishable from the wild type plants. The method may include analyzing the progeny for the presence of the alteration and selecting a progeny plant that includes the alteration.

[0075] In an embodiment, the method may further include crossing a heterozygous genetically engineered plant to another genetically engineered plant heterozygous for the same alteration. The method may include selecting a first progeny plant that is homozygous for the alteration. The method may further include crossing the genetically engineered plant to a wild type plant of the same genetic background. Progeny may be obtained from such crosses. The progeny may include heterozygous and wild type plants. The method may include selecting a first progeny plant that is heterozygous for the alteration. The method may further include selfing the first heterozygous progeny plant and selecting a second progeny plant that is homozygous for the alteration.

[0076] A genetically engineered plant herein may be homozygous or heterozygous for the gene that includes the mutation and may include a transgene encoding a nuclease. The transgene encoding the nuclease may be segregated away during the above-described crosses.

[0077] An embodiment comprises a method for producing a genetically engineered plant homozygous for an engineered nucleic acid encoding a protein. The engineered nucleic acid may encode a recessive trait. The recessive trait may include a cleaved endogenous target sequence of a gene. -21- PCT/US2015/052940 WO 2016/054039

The recessive trait may only be observed in plants that do not contain an unaltered, wild-type, allele of the gene. The method may comprise making an engineered nucleic acid by modifying a sequence of an endogenous nucleic acid. The method may also comprise breeding the recessive trait into other crop lines. The method may comprise maintaining the trait in the crop lines. The method may comprise generating homozygous progeny. The method may include making hybrid seed with a recessive trait.

[0078] An embodiment comprises a plant genetically engineered by any one of methods described herein is provided.

[0079] An embodiment comprises a method of increasing a starch level in a plant. The method may comprise expressing a nucleic acid encoding a meganuclease in a plant. The method may comprise expressing a nucleic acid that encodes a TALEN in a plant. The method may comprise expressing a first nucleic acid that encodes a Cas9 nuclease and a second nucleic acid that encodes a desired guide RNA that target a specific sequence. Expression of the nucleic acid(s) in the plant may alter the function or coding of an endogenous DNA sequence. Expression of the nucleic acid(s) in the plant may alter the activity of GWD and starch metabolism in the plant. The plant may be any transgenic or mutant plant herein. The plant may be a progeny of the transgenic or mutant plant. The nucleic acid(s) may be included in a genetic construct(s). The method may comprise making any genetically engineered plant herein. The genetically engineered plant or its progeny may be the plant, in which starch levels may be increased by the method herein.

[0080] A genetic construct having a nucleic acid encoding a meganuclease that inactivates or inhibits expression of the GWD protein involved in mobilization of starch in a plant in may be expressed at any point in the methods. The nucleic acid may be expressed prior to the step of processing the plant. The nucleic acid may be expressed during the step of processing the plant. The expression may be induced. Upon the expression of the nucleic acid(s), the genetically engineered plant may have an altered level of vegetative starch compared to the level of starch in a non-genetically -22- PCT/US2015/052940 WO 2016/054039 engineered plant of the same genetic background but lacking the one or more genetic construct.

[0081] Any genetically engineered plant herein may be provided in a method of agricultural processing, a method of preparing animal feed, or a method of feeding an animal. A step of providing the genetically engineered plant may include obtaining it from another party that produced it. A step of providing may include making the genetically engineered plant. The genetically engineered plant may be a transgenic plant or mutant plant. The step of providing may include transforming the plant by contacting the plant with any one of the genetic constructs herein. The step of providing may include stable transformation of the plant by any of the methods described herein, or known methods. The step of providing may include genetically engineering the plant by cleaving a gene encoding a protein involved in starch metabolism at a cleavage site recognized by a nuclease transiently expressed in the plant after contacting the plant with a genetic construct comprising a polynucleotide encoding the nuclease. The step of providing may also include regenerating the plant from a tissue of the genetically engineered plant having an altered level of vegetative starch. The step of providing may include obtaining a progeny of the genetically engineered plant resulted from self-pollination or cross-pollination between the genetically engineered plant and non-genetically engineered plant. The step of providing may include obtaining homozygous progeny. The homozygous progeny may be inbred plants. The homozygous progeny may be hybrid plants. The genetically engineered plant may be used in a variety of subsequent methods or uses. The step of providing may include procuring the genetically engineered plant. The step of providing may include making the genetically engineered plant available for further processing steps. The step of providing may include making the genetically engineered plant available as part of an animal diet.

[0082] In the method of agricultural processing, the genetically engineered plant may be a feedstock engineered with elevated levels of starch and/or expressing one or more polysaccharide degrading enzyme. The -23- PCT/US2015/052940 WO 2016/054039 feedstock may include any genetically engineered plant herein alone or in combination with other components. The other components may include other plant material. Agricultural processing may include manipulating or converting any agricultural feedstock including the genetically engineered plant for a particular product or use. Agricultural processing may comprise drying the genetically engineered plant. Agricultural processing may comprise fermenting the genetically engineered plant. Agricultural processing may comprise hydrolyzing the genetically engineered plant with one or more an exogenous enzymes to obtain a biochemical product. The exogenous enzymes may be lignin degrading enzymes, cellulose degrading enzymes, or hemicellulose degrading enzymes. The exogenous enzymes may be glycosidases, xylanases, cellulases, endoglucanases, exoglucanases, cellobiohydrolases, β-xylosidases, feruloyl esterases, β-glucosidases, and amylases. The exogenous enzymes may be purchased from a vendor and may comprise Accellerase® 1000, Accellerase® 1500, Accelerase® TRIO™, and Accellerase ® XY available from Genencor International (Rochester, NY). Exogenous enzymes may comprise Cellic, CTEC, HTEC available from Novozymes (Denmark). The exogenous enzymes may comprise starch degrading enzymes. The exogenous enzymes may comprise an amylase or an invertase. The method of agricultural processing may include simultaneous saccharification and fermentation of soluble sugars to produce ethanol.

[0083] A method of agricultural processing herein may comprise harvesting the genetically engineered plants having elevated levels of starch for use as a feedstock in agricultural processing. The method may include combining the genetically engineered plant with plant biomass. The plant biomass may include non-genetically engineered plants. The plant biomass may be genetically engineered plant biomass. The genetically engineered plant biomass may express polysaccharide degrading enzymes. By combining the genetically engineered plant with the plant biomass that express polysaccharide degrading enzyme, the method herein may not require harsh pretreatments to improve cellulose cell wall accessibility to exogenous -24- PCT/U S2015/052940 WO 2016/054039 enzymes. The methods herein may utilize any methods and compositions for consolidated pretreatment and hydrolysis of plant biomass expressing cell wall degrading enzymes described in U.S. Patent Application No. 13/414,627, filed March 7, 2012; and International Patent Application No. PCT/US2012/028132, filed March 7, 2012, which are incorporated herein by reference as if fully set forth. Plants with altered levels of elevated starch were described International Patent Application No. PCT/US2011/041991, filed June 27, 2011; and U.S. Patent Application No. 13/806,654, filed March 19, 2013; and U.S. Patent Application No. 13/793,078, filed March 11, 2013, which are incorporated herein by reference as if fully set forth.

[0084] The genetically engineered plant may be provided in a method of preparing animal feed. Preparing animal feed may comprise combining the genetically engineered plant with animal feed stuffs, including but not limited to corn, grain, soybeans, and/or other forage. Preparing animal feed may comprise ensiling the genetically engineered plant to make silage. Preparing animal feed may comprise combining the genetically engineered plant with distillers’ grains. Preparing animal feed may comprise pelletizing the genetically engineered plant into feed pellets. Preparing animal feed may comprise combining the genetically engineered plant with a source of edible fiber. Preparing animal feed may comprise combining the genetically engineered plant with a source of protein. Preparing animal feed may comprise combining the genetically engineered plant with one or more carbohydrates as a source of energy. Preparing animal feed may comprise combining the genetically engineered plant with one or more exogenous enzymes described herein.

[0085] A method of agricultural processing or or a method of preparing animal feed may also comprise at least one of the operations of harvesting, baling, grinding, milling, chopping, size reducing, crushing, extracting a component from the feedstock, purifying a component or portion of the feedstock, extracting or purifying starch, hydrolyzing polysaccharides into -25- PCT/U S2015/052940 WO 2016/054039 oligosaccharides or monosaccharides, chemical conversion, or chemical catalysis of the feedstock.

[0086] In an embodiment, animal feed formulations comprising increased levels of starch in vegetative tissues are provided. Animal feed formulations may be used for increasing milk and beef production by feeding animals plant material with increased levels of starch. Easily-fermentable sugars available in a fermentation process may be provided by embodiments herein. Production of biofuels may be enhanced by providing easily-fermentable sugars. Methods of providing easily fermentable sugars and methods of enhancing production of biofuels are provided as embodiments herein. The animal feed formulations may comprise any one or more of the genetically engineered plants herein. The animal feed formulations may comprise the products of a method of preparing animal feed herein.

[0087] Crops with elevated levels of vegetative starch may have a variety of uses and utilities. In an embodiment, biomass from plants that accumulate elevated levels of vegetative starch relative to wild type plants are provided. The biomass may be from any genetically engineered plant herein or its progeny. These plants may have added value as feedstocks for fermentation processes or animal feed applications. For example, in a typical cellulosic process, polysaccharides, such as cellulose and hemicelluloses that are present in the biomass, are hydrolyzed to simple sugars, which may then be fermented to ethanol, butanol, isobutanol, fatty acids, or other hydrocarbons by microorganisms. Because of the recalcitrance of the biomass, the release of the simple sugars from polymers, such as cellulose and hemicelluloses, often requires the use of harsh pretreatment conditions and hydrolysis with relatively expensive mixtures of enzymes. A similar situation occurs in ruminant animals that eat forage, including corn silage, as a nutrient and an energy source. In ruminant animal, the forage is masticated and moves into the rumen, where the fiber polysaccharides, such as cellulose and hemicellulose, are hydrolyzed and fermented by the microorganisms in the rumen flora. These organisms create fatty acids that are absorbed by the -26- PCT/US2015/052940 WO 2016/054039 animal and metabolized, providing nutrition to the animal. In either ruminant digestion or biofuels processing, any starch that is present in the biomass represents an additional source of readily fermentable sugars (namely, glucose), which are less recalcitrant to hydrolysis and can be released very easily by amylases or mild chemical treatments. As a result, any increase in the amount of starch present in the biomass will simultaneously increase the amount of fermentable sugar that can be recovered. Biomass that contains elevated levels of starch may have greater value in forage applications, where the plant material is fed to livestock or dairy animals. Again, the excess starch present in this material is more easily digested by most animals than is the cellulosic material, providing more energy per unit biomass than biomass with ordinary levels of starch. Embodiments include utilizing a plant as set forth herein for any of these methods.

[0088] Methods herein, including those in the previous paragraph, may include at least one of modifying plants to create genetically engineered plants, growing the genetically engineered plants, harvesting the genetically engineered plants, processing (for example reducing the size of the forage, ensiling, treating with an inoculant, combining with other feed components, or pelleting) them for animal feed applications as one would other forage crops, or fermenting the genetically engineered plants in a manner similar to treatments that are used in cellulosic processing. Cellulosic processing steps used may comprise pretreating and hydrolyzing the polysaccharides into their component sugars by enzymatic or chemical hydrolysis or digestion. Any one step, set of steps, or all the steps set forth in this paragraph may be provided in a method herein.

[0089] An embodiment comprises a genetic construct designed to implement a strategy for modifying levels of vegetative starch in plants. The genetic construct may comprise a first engineered nucleic acid sequence that encodes a nuclease capable of cleaving a target sequence in an endogenous nucleic acid encoding GWD. The first engineered nucleic acid may encode any one of the nucleases described herein. The genetic construct may also include -27- PCT/US2015/052940 WO 2016/054039 a second engineered nucleic acid sequence encoding an sgRNA. The second engineered nucleic acid may encode any one the sgRNAs described herein. The genetic construct may include a promoter operably linked to the first engineered nucleic acid sequence or the second engineered nucleic acid. The operably linked promoter may allow transcription of the first engineered nucleic acid sequence encoding a nuclease, or the second engineered nucleic acid sequence encoding the sgRNA. Transcription and translation of the first engineered nucleic acid sequence may be referred to as expression of the nuclease. Upon expression, the nuclease may cut the target sequence of the endogenous nucleic acid. The endogenous nucleic acid may encode GWD. Transcription of the second nucleic acid sequence may result in production of an sgRNA that recognizes a target sequence within an endogenous nucleic acid and guides Cas9 nuclease to the target for making a break.

[0090] The genetic construct may include regions encoding nuclear localization signals. As used herein, nuclear localization signals (NLS) refers the short motifs of basic amino acid sequences within nuclear proteins. Transport of certain proteins from cytoplasm into the nucleolus to perform their specific functions occurs through the nuclear envelope and involves nuclear pore complex (NPC) (Wagner et al., 1990, which is incorporated herein by reference as if fully set forth). In this process, nuclear localization signals (NLS) play an important role as they are thought to be recognized by NPC receptors to subsequently translocate proteins through the nuclear pore complex. The NLSs fall into one of several defined categories (Garcia-Bustos et al., 1991, which is incorporated herein by reference as if fully set forth). The NLS may be the SV40 NLS from simian virus 40 large T antigen, which has been used intensively in experiments for targeted genome modifications due to its activity in various organisms, including plants (Kalderon et al., 1984; Raikhel, 1992, both of which are incorporated herein by reference as if fully set forth). The SV40 NLS may be encoded by a nucleic acid sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% identity to a reference sequence of SEQ ID NO: 163. The SV NLS may comprise, consist -28- PCT/US2015/052940 WO 2016/054039 essentially of, or consist of an amino acid sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% identity to a reference sequence of SEQ ID NO: 196. The NLS may be plant specific NLS sequences. Plant specific NLS sequences were also described, for example, in maize regulatory proteins opaque-2 and R (Varagona et al, 1992; Shieh et al, 1993, both of which are incorporated herein by reference as if fully set forth). The plant specific NLS may be encoded by a nucleic acid sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% identity to a reference sequence selected from the group of SEQ ID NOS: 164 (NLSl), 165 (NLS3), 166 (NLS4), 167 (NLS5), and 168 (NLS6). The plant specific NLS sequence may comprise, consist essentially of, or consist of an amino acid sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% identity to a reference sequence selected from the group of SEQ ID NOS: 128 (NLSl), 129 (NLS3), 130 (NLS4), 169 (NLS5), and 170 (NLS6). The NLS sequence may be a derivative NLS sequence. The NLS sequences or their derivatives may be used to target meganucleases, ZFNs, TALENs, or Cas9 proteins into plant nucleus for targeted genome modification. One or more NLS sequences may be fused with an amino acid sequence of the nuclease.

[0091] The genetic construct may further include one or more regulatory sequences (also referred to as a regulatory element) operably connected to the nucleic acid encoding the nuclease. The promoter may be any kind of promoter. The promoter may be an inducible promoter. The promoter may be a constitutive promoter. The promoter may be an inducible promoter, which initiates transcription of the nucleic acid encoding the nuclease only when exposed to a particular chemical or environmental stimulus. Examples of inducible promoters include but are not limited to alcohol inducible promoters, tetracycline inducible promoters, steroid inducible promoters, or hormone inducible promoters. The promoter may be a constitutive promoter, which provides transcription of the nucleic acids or polynucleotide sequences throughout the plant in most cells, tissues, and organs, and during many but not necessarily all stages of development. The promoter may be specific to a -29- PCT/U S2015/052940 WO 2016/054039 particular developmental stage, organ, or tissue. A tissue specific promoter may be capable of initiating transcription in a particular plant tissue. Plant tissue that may be targeted by a tissue specific promoter may be but is not limited to a stem, leaves, trichomes, anthers, or seed. A constitutive promoter herein may be the rice Ubiquitin 3 promoter (OsUbi3P) or the maize ubiquitin promoter (ZmUbil). Other known constitutive promoters may be part of the genetic construct herein, and include but are not limited to Cauliflower Mosaic Virus (CAMV) 35S promoter, the Cestrum Yellow Leaf Curling Virus promoter (CMP) or the CMP short version (CMPS), the Rubisco small subunit promoter, the rice actin promoter (OsActlP), and the maize phosphoenolpyruvate carboxylase promoter (ZmPepCP). The promoter may be a synthetic nucleic acid promoter from maize Zea mays. The synthetic nucleic acid promoter from maize may comprise, consist essentially of, or consist of a sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% identity to a reference sequence selected from the group consisting of: SEQ ID NO: 78 (MzU3.8), SEQ ID NO: 79 (ZmU3), ZmU3Pl (SEQ ID NO: 82), ZmU3P2 (SEQ ID NO: 84), or ZmU3.8 promoter (SEQ ID NO: 86). The synthetic nucleic acid promoter may have a length equal to 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% of the length in nucleotides of one of SEQ ID NO: 78 (MzU3.8), SEQ ID NO: 79 (ZmU3), ZmU3Pl (SEQ ID NO: 82), ZmU3P2 (SEQ ID NO: 84), or ZmU3.8 promoter (SEQ ID NO: 86). The percent identity of promoters shorter than SEQ ID NO: 78 (MzU3.8), SEQ ID NO: 79 (ZmU3), ZmU3Pl (SEQ ID NO: 82), ZmU3P2 (SEQ ID NO: 84), or ZmU3.8 promoter (SEQ ID NO: 86 may be as set forth above along the length of the shorter promoter. An embodiment comprises any one of the synthetic nucleic acid promoters described herein. The synthetic nucleic acid promoter may be operably connected with the first engineered nucleic acid or the second engineered nucleic acid molecule and may transcriptionally activate the first or the second engineered nucleic acid. As a result of transcriptional activation, the first or the second engineered nucleic acid may be expressed constitutively in a plant. -30- PCT/U S2015/052940 WO 2016/054039 [0092] A regulatory element in a genetic construct herein may be a terminator. A terminator is capable of terminating transcription. A terminator sequence may be included at the 3’ end of a transcriptional unit of the expression cassette. The transcriptional unit may encode the nuclease. The terminator may be derived from a terminator found in a variety of plant genes. The terminator may be a terminator sequence from the nopaline synthase (NOS) or octopine synthase (OCS) genes of Agrobacterium tumefaciens. The terminator may be the S. pyogenes Cas9 terminator (SEQ ID NO: 88). The terminator may be the ZmU3T terminator (SEQ ID NO: 89). The terminator sequence may be the CaMV 35S terminator from CaMV, or any of the 3’UTR sequences shown to terminate the transgene transcription in plants. For example, the terminator may be the maize PepC terminator (3’UTR). The genetic construct may be included in a vector. The genetic construct may be integrated into a genome of the genetically engineered plant. The genetic construct may be transiently expressed in the genetically engineered plant.

[0093] The genetic construct may be used for transformation of a plant. The genetic construct may be used for Agrobacterium-mediated transformation of a plant. The genetic construct may be used for transforming a plant by any known methods, for example, particle bombardment or direct DNA uptake. The genetic construct may be cloned and included into a vector.

[0094] An embodiment includes a vector comprising a genetic construct herein and appropriate for genetically engineering a plant. The vector may be an intermediate vector. The vector may be a transformation vector. Vectors incorporating a genetic construct herein may also include additional genetic elements such as multiple cloning sites to facilitate molecular cloning and one or more selectable markers to facilitate selection. A selectable marker that may be included in a vector may be a phosphomannose isomerase (PMI) gene from Escherichia coli, which confers to the transformed cell the ability to utilize mannose for growth. Selectable markers that may be included in a vector include but are not limited to a neomycin phosphotransferase (npt) -31- PCT/US2015/052940 WO 2016/054039 gene, conferring resistance to kanamycin, a hygromycin phosphotransferase (hpt) gene, conferring resistance to hygromycin, or an enolpyruvylshikimate-3-phosphate synthase gene, conferring resistance to glyphosate. The vector may be any vector described in US application No. 13/793,078, filed March 11, 2013, which is incorporated herein by reference as if fully set forth. The vector may include a genetic construct encoding any one of the nucleases described herein. The vector may comprise a nucleic acid sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% identity to a reference sequence of SEQ ID NO: 108 (meganuclease 4715) or SEQ ID NO: 109 (meganuclease 4716). The vector may comprise a nucleic acid sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% identity to a reference sequence of SEQ ID NO: 75 (Zm Cas9). The vector may comprise a sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% identity to a reference sequence selected from the group consisting of: SEQ ID NO: 95 (ZmU3Pl:sgRNA_GWDe24b), SEQ ID NO: 96 (ZmU3P2:sgRNA_GWDe24b), SEQ ID NO: 97 (ZmU3.8P:sgRNA_GWDe24b), SEQ ID NO: 98 (ZmU3P2:sgRNA_GWDe24c), SEQ ID NO: 99 (ZmU3P2:sgRNA_GWDe25a) and SEQ ID NO: 100 (ZmU3P2:sgRNA_GWDela). The vector or the genetic construct described herein may include an engineered nucleic acid. The vector may be pAG4715 (FIG.l), pAG4716 (FIG. 2), or a modification thereof replacing any one of the annotated landmarks with a counterpart otherwise described herein. Routine vector elements annotated in FIGS. 1 or 2 may be replaced by counterparts described herein or known in the art.

[0095] An embodiment includes an engineered nucleic acid comprising, consisting essentially of, or consisting of a sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% identity to SEQ ID NO: 41 (Meganuclease GWD-9/10x.272 target sequence (pAG4715)) or SEQ ID NO: 42 (Meganuclease GWD-7/8x target sequence (pAG4716)).

[0096] An embodiment includes an engineered nucleic acid sequence comprising, consisting essentially of, or consisting of a sequence with at least -32- PCT/U S2015/052940 WO 2016/054039 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% identity to a reference sequence selected from the group consisting of SEQ ID NO: 91 (GWDela), SEQ ID NO: 92 (GWDe24b), SEQ ID NO: 93 (GWDe24c), and SEQ ID NO: 94 (GWDe25a).

[0097] An embodiment comprises an engineered nucleic acid having a sequence as set forth in any one of the engineered nucleic acids listed herein or the complement thereof. In an embodiment, an engineered nucleic acid having a sequence that hybridizes to a nucleic acid having the sequence of any nucleic acid listed herein or the complement thereof is provided. In an embodiment, the hybridization conditions are low stringency conditions. In an embodiment, the hybridization conditions are moderate stringency conditions. In an embodiment, the hybridization conditions are high stringency conditions. Examples of hybridization protocols and methods for optimization of hybridization protocols are described in the following books: Molecular Cloning, T. Maniatis, E.F. Fritsch, and J. Sambrook, Cold Spring Harbor Laboratory, 1982; and, Current Protocols in Molecular Biology, F.M. Ausubel, R. Brent, R.E. Kingston, D.D. Moore, J.G. Seidman, J.A. Smith, K. Struhl, Volume 1, John Wiley & Sons, 2000, which are incorporated by reference in their entirety as if fully set forth. Moderate conditions include the following: filters loaded with DNA samples are pretreated for 2-4 hours at 68°C in a solution containing 6 x citrate buffered saline (SSC; Amresco, Inc., Solon, OH), 0.5% sodium dodecyl sulfate (SDS; Amresco, Inc., Solon, OH), 5xDenhardt’s solution (Amresco, Inc., Solon, OH), and denatured salmon sperm DNA (Invitrogen Life Technologies, Inc. Carlsbad, CA). Hybridization is carried in the same solution with the following modifications: 0.01 M EDTA (Amresco, Inc., Solon, OH), 100 pg/ml salmon sperm DNA, and 5 - 20 x 106 cpm 32P-labeled or fluorescently labeled probes. Filters are incubated in hybridization mixture for 16-20 hours and then washed for 15 minutes in a solution containing 2xSSC and 0.1% SDS. The wash solution is replaced for a second wash with a solution containing O.lxSSC and 0.5% SDS and incubated an additional 2 hours at 20°C to 29°C below Tm (melting temperature in °C). Tm -33- PCT/US2015/052940 WO 2016/054039 = 81.5 +16.61Logio([Na+]/(1.0+0.7[Na+]))+0.41(%[G+C])-(500/n)-P-F. [Na+] =

Molar concentration of sodium ions. %[G+C] = percent of G+C bases in DNA sequence. N = length of DNA sequence in bases. P = a temperature correction for % mismatched base pairs (~1°C per 1% mismatch). F = correction for formamide concentration (=0.63°C per 1% formamide). Filters are exposed for development in an imager or by autoradiography. Low stringency conditions refers to hybridization conditions at low temperatures between 37°C and 60°C, and the second wash with higher [Na+] (up to 0.825M) and at a temperature 40°C to 48°C below Tm. High stringency refers to hybridization conditions at high temperatures over 68°C, and the second wash with [Na+] = 0.0165 to 0.0330M at a temperature 5°C to 10°C below Tm.

[0098] An embodiment comprises an engineered nucleic acid having a sequence that has at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% identity along its length to a contiguous portion of a nucleic acid having any one of the sequences set forth herein or the complements thereof. The contiguous portion may be any length up to the entire length of a sequence set forth herein or the complement thereof.

[0099] Determining percent identity of two amino acid sequences or two nucleic acid sequences may include aligning and comparing the amino acid residues or nucleotides at corresponding positions in the two sequences. If all positions in two sequences are occupied by identical amino acid residues or nucleotides then the sequences are said to be 100% identical. Percent identity is measured by the Smith Waterman algorithm (Smith TF, Waterman MS 1981 “Identification of Common Molecular Subsequences,” J Mol Biol 147: 195 -197, which is incorporated herein by reference as if fully set forth).

[0100] An embodiment comprises engineered nucleic acids, engineered polynucleotides, or engineered oligonucleotides having a portion of the sequence as set forth in any one of the nucleic acids listed herein or the complement thereof. Theseengineered nucleic acids, engineered polynucleotides, or engineered oligonucleotides may have a length in the range from 10 to full length, 10 to 5000, 10 to 4900, 10 to 4800, 10 to 4700, 10 to -34- PCT/US2015/052940 WO 2016/054039 4600, 10 to 4500, 10 to 4400, 10 to 4300, 10 to 4200, 10 to 4100, 10 to 4000, 10 to 3900, 10 to 3800, 10 to 3700, 10 to 3600, 10 to 3500, 10 to 3400, 10 to 3300, 10 to 3200, 10 to 3100, 10 to 3000, 10 to 2900, 10 to 2800, 10 to 2700, 10 to 2600, 10 to 2500, 10 to 2400, 10 to 2300, 10 to 2200, 10 to 2100, 10 to 2000, 10 to 1900, 10 to 1800, 10 to 1700, 10 to 1600, 10 to 1500, 10 to 1400, 10 to 1300, 10 to 1200, 10 to 1100, 10 to 1000, 10 to 900, 10 to 800, 10 to 700, 10 to 600, 10 to 500, 10 to 400, 10 to 300, 10 to 200, 10 to 100, 10 to 90, 10 to 80, 10 to 70, 10 to 60, 10 to 50, 10 to 40, 10 to 35, 10 to 30, 10 to 25, 10 to 20, 10 to 15, or 20 to 30 nucleotides, or 10, 15, 20 or 25 nucleotides. An engineered nucleic acid, engineered polynucleotide, or engineered oligonucleotide having a length within one of the above ranges may have any specific length within the range recited, endpoints inclusive. The recited length of nucleotides may start at any single position within a reference sequence (i.e., any one of the nucleic acids herein) where enough nucleotides follow the single position to accommodate the recited length. In an embodiment, a hybridization probe or primer is 85 to 100%, 90 to 100%, 91 to 100%, 92 to 100%, 93 to 100%, 94 to 100%, 95 to 100%, 96 to 100%, 97 to 100%, 98 to 100%, 99 to 100%, or 100% complementary to a nucleic acid with the same length as the probe or primer and having a sequence chosen from a length of nucleotides corresponding to the probe or primer length within a portion of a sequence as set forth in any one of the nucleic acids listed herein. In an embodiment, a hybridization probe or primer hybridizes along its length to a corresponding length of a nucleic acid having the sequence as set forth in any one of the nucleic acids listed herein. In an embodiment, the hybridization conditions are low stringency. In an embodiment, the hybridization conditions are moderate stringency. In an embodiment, the hybridization conditions are high stringency.

[0101] An embodiment comprises a kit for identifying a modified sequence of an endogenous gene encoding Glucan Water Dikinase in a sample. The kit may comprise a first primer and a second primer. The first primer and the second primer may be capable of amplifying a target sequence -35- PCT/US2015/052940 WO 2016/054039 included in an endogenous gene encoding Glucan Water Dikinase. The target sequence may include a nucleic acid with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% identity to a reference sequence selected from SEQ ID NOS: 1 - 4, 75, 170 - 184 186, 187, 189 - 193. The kit may further comprise one or more component for detecting modifications in the amplified region of the target sequence. The kit may comprise the first primer comprising a nucleic acid sequence selected from SEQ ID NOS: 6, 7, 9, 11, 101, 103, 105, 110, and 111. The kit may comprise the second primer comprising a nucleic acid sequence selected from SEQ ID NOS: 5, 8, 10, 102, and 104. The kit may comprise the first primer comprising the nucleic acid sequence of SEQ ID NO: 6 and the second primer comprising the nucleic sequence of SEQ ID NO: 5. The kit may comprise the first primer comprising the nucleic acid sequence of SEQ ID NO: 7 and the second primer comprising the nucleic acid sequence of SEQ ID NO: 8. The kit may comprise the first primer comprising the nucleic acid sequence of SEQ ID NO: 9 and the second primer comprising the nucleic acid sequence of SEQ ID NO: 10. The kit may comprise the first primer comprising the nucleic acid sequence of SEQ ID NO: 11 and the second primer comprising the nucleic acid sequence of SEQ ID NO: 13. The kit may comprise the first primer comprising the nucleic acid sequence of SEQ ID NO: 110 and the second primer comprising the nucleic acid sequence of SEQ ID NO: 13. The kit may comprise the first primer comprising the nucleic acid sequence of SEQ ID NO: 111 and the second primer comprising the nucleic acid sequence of SEQ ID NO: 112. The kit may comprise the first primer comprising the nucleic acid sequence of SEQ ID NO: 105 and the second primer comprising the nucleic acid sequence of SEQ ID NO: 13. The first primer and the second primer may be capable of amplifying the target sequence to produce an amplified product. The amplified product may comprise a modified target sequence. The modified target sequence may be capable of hybridizing to the sequence of the nucleic acid comprising a sequence selected of SEQ ID NO: 12 - 40, 114 - 116, 188 - 189, 19 - 120, and 131 - 162 under conditions of high stringency. The modified target sequence -36- PCT/US2015/052940 WO 2016/054039 may be used as a probe for diagnosing the genetically engineered plants having mutations in an endogenous gene encoding the Glucan Water Dikinase. A sample may include any sample in which nucleic acids from plant matter are present. The sample may include any plant matter. The plant matter may derive from a plant or part thereof. The plant material may derive from an animal feed or food.

[0102] An embodiment provides a method of identifying a modified sequence of an endogenous gene encoding a Glucan Water Dikinase in a sample is provided. The method may include contacting a sample with a first primer and a second primer. The method may include amplifying a synthetic polynucleotide comprising a target sequence included in an endogenous gene encoding a Glucan Water Dikinase. The target sequence may be any target sequence included in the endogenous gene encoding the Glucan Water Dikinase described herein. The first primer and the second primer may be capable of amplifying the target sequence to produce an amplified product. The amplified product may be used to determine whether a plant resulted from a sexual crossing or selfing contains one or more modifications in the target sequence and diagnose specific mutants. The length of the amplified product from the sample of the mutant plant may differ from the length of the amplified product from the sample of wild type plant of the same genetic background. The amplified product from the mutant sample may be further used as probe that hybridizes to a synthetic polynucleotide comprising a specific region encoding a mutant protein under conditions of high stringency. The method may include further detecting hybridization of the at least one probe to the specific region of the target sequence.

[0103] Methods of making a genetically engineered plant, methods of increasing starch levels in plants, methods of agricultural processing, methods of preparing animal feed and methods for producing genetically engineered plants homozygous for an engineered nucleic acid that encodes an altered Glucan Water Dikinase may comprise a method of detection herein as part of -37- PCT/US2015/052940 WO 2016/054039 making genetically engineered plants and/or identifying plants or plant biomass that comprise a genetically engineered nucleic acid herein.

[0104] The following list includes particular embodiments of the present invention. But the list is not limiting and does not exclude alternate embodiments, or embodiments otherwise described herein. Percent identity described in the following embodiments list refers to the identity of the recited sequence along the entire length of the reference sequence.

[0105] EMBODIMENTS 1. A synthetic nucleic acid promoter having a sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 % identity to a reference sequence selected from the group consisting of: SEQ ID NO: 78 (MzU3.8), SEQ ID NO: 79 (ZmU3), SEQ ID NO: 82 (ZmU3Pl), SEQ ID NO: 84 (ZmU3P2) and SEQ ID NO: 86 (MzU3.8P). 2. A genetic construct comprising a first engineered nucleic acid sequence encoding a Cas9 nuclease, wherein the Cas9 nuclease is capable of cleaving a target sequence in an endogenous nucleic acid encoding Glucan Water Dikinase in a plant. 3. The genetic construct of embodiment 2, wherein the first synthetic nucleic acid sequence has at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 % identity to SEQ ID NO: 74 (Cas9 nuclease) or SEQ ID NO: 75 (ZmCas9). 4. The genetic construct of one or both embodiments 2 and 3, wherein the first nucleic acid is fused to a polynucleotide sequence encoding at least one nuclear localization signal (NLS). 5. The genetic construct of any one or more of embodiments 2 - 4, wherein the polynucleotide sequence encoding the nuclear localization signal is selected from SEQ ID NOS: 163 - 168. 6. The genetic construct of any one or more of embodiments 2 - 5 further comprising a second engineered nucleic acid sequence encoding an sgRNA, and the sgRNA is capable of binding the target sequence. -38- PCT/US2015/052940 WO 2016/054039 7. The genetic construct of embodiments 6, wherein the second engineered nucleic acid comprises a sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 % identity to a sequence selected from SEQ ID NO: 135 (ZmU3Pl:sgRNA_GWDe24b), SEQ ID NO: 136 (ZmU3P2:sgRNA_GWDe24b), SEQ ID NO: 137 (ZmU3.8P:sgRNA_GWDe24b), SEQ ID NO: 138 (ZmU3P2:sgRNA_GWDe24c), SEQ ID NO: 139 (ZmU3P2:sgRNA_GWDe25a) and SEQ ID NO: 40 (ZmU3P2: sgRNA_GWDe la). 8. The genetic construct of any one or more of embodiments 2 - 7, wherein the target sequence has at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 % identity to a reference sequence selected from the group consisting of SEQ ID NO: 91 (GWDela), SEQ ID NO: 92 (GWDe24b), SEQ ID NO: 93 (GWDe24c), and SEQ ID NO: 94 (GWDe25a). 9. The genetic construct of any one or more of embodiments 2 - 8 further comprising a first promoter operably linked to the first engineered nucleic acid and a second promoter operably linked to the second engineered nucleic acid. 10. The genetic construct of embodiment 9, wherein the first promoter or the second promoter is a synthetic nucleic acid promoter of embodiment 1. 11. The genetic construct of any one or more of embodiments 2 - 10 further comprising a terminator. 12. The genetic construct of embodiment 11, wherein the terminator comprises a nucleic acid sequence with at least 90% identity to SEQ ID NO: 88. 13. A genetic construct comprising an engineered nucleic acid sequence encoding a nuclease, wherein the nuclease is capable of cleaving a target sequence included in an endogenous nucleic acid encoding Glucan Water Dikinase. 14. The genetic construct of embodiment 13, wherein the nuclease is a meganuclease encoded by a sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 % identity to a reference sequence selected -39- PCT/US2015/052940 WO 2016/054039 from the group consisting of SEQ ID N): 164 (4715_meganuclease) and SEQ ID NO: 165 (4716_meganuclease). 15. The genetic construct of any one or more of embodiments 13 - 14, wherein the target sequence includes a polynucleotide of SEQ ID NO: 41 (Meganuclease GWD-9/10x.272) or SEQ ID NO: 42 (Meganucleas3e GWD-7/8x). 16. The genetic construct of any one or more of embodiments 13 - 15 comprising at least one regulatory element, wherein the regulatory element is selected from a promoter, a terminator, and an enhancer. 17. A vector comprising a genetic construct of any one or more of embodiments 2 - 16. 18. A genetically engineered plant comprising an engineered nucleic acid encoding an altered Glucan Water Dikinase and having an elevated level of starch in comparison to a non-genetically engineered plant of the same genetic background. 19. The genetically engineered plant of embodiment 18, wherein the activity of the altered Glucan Water Dikinase is reduced compared to the activity of the wild type Glucan Water Dikinase in a non-genetically engineered plant of the same genetic background. 20. The genetically engineered plant of embodiment 18, wherein the altered Glucan Water Dikinase is inactive. 21. The genetically engineered plant of any one or more of embodiments 18 - 20, wherein the engineered nucleic acid is a modified sequence of an endogenous nucleic that is one allele of a gene encoding a Glucan Water Dikinase. 22. The genetically engineered plant of any one or embodiments 18 - 21, wherein all alleles of a gene encoding Glucan Water Dikinase in the plant have the sequence of the engineered nucleic acid. 23. The genetically engineered plant of any one or more of embodiments 18 - 22, wherein the endogenous nucleic acid includes a sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 % identity to a -40- PCT/US2015/052940 WO 2016/054039 reference sequence of SEQ ID NO: SEQ ID NO: 1 (Zm GWD coding sequence) or SEQ ID NO: 2 (Sb GWD coding sequence). 24. The genetically engineered plant of any one or more of embodiments 18 - 23, wherein the engineered nucleic acid comprises a mutation selected from at least one of an insertion, a deletion, or substitution of one or more nucleotides in the sequence of the endogenous nucleic acid encoding a wild type GWD. 25. The genetically engineered plant embodiment 24, wherein the mutation is within a target sequence in the endogenous nucleic acid having at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 % identity to a reference sequence selected from the group consisting of SEQ ID NO: 3 (Zm GWD Exon 24 + introns), SEQ ID NO; 4 (SbGWD Exon 24 + introns), SEQ ID NO: 182 (ZmGWD Exon 24 no introns), SEQ ID NO: 183 (Sb GWD Exon 24), SEQ ID NO: 184 (SbGWD Exon 7) and SEQ ID NO: 189 (Zm GWD Exon 25). 26. The genetically engineered plant of any one or more of embodiments 18 - 25, wherein the mutation is within a target sequence in the endogenous nucleic acid having at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 % identity to a reference sequence selected from the group consisting of SEQ ID NO: 91 (GWDela), SEQ ID NO: 92 (GWDe24b), SEQ ID NO: 93 (GWDe24c), and SEQ ID NO: 94 (GWDe25a). 27. The genetically engineered plant of any one or more of embodiments 18 - 26, wherein the engineered nucleic acid comprises a polynucleotide having a sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 % identity to a reference sequence selected from the group of sequences consisting of SEQ ID NOS: 12 - 40 (Zm GWD mutations - Exon 24). 28. The genetically engineered plant of any one or more of embodiments 18 -26, wherein the engineered nucleic acid comprises a polynucleotide having a sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 % identity to a reference sequence selected from the group of sequences consisting of SEQ ID NOS: 114 - 118, 188, 131 - 146 (Zm GWD mutations -Exon 24), and 119 - 120 (Zm GWD mutations - Exon 25). -41- PCT/US2015/052940 WO 2016/054039 29. The genetically engineered plant of any one or more of embodiments 18 - 25, wherein the engineered nucleic acid comprises a polynucleotide having a sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 % identity to a reference sequence selected from the group of sequences consisting of SEQ ID NO: 106 (Sb4715_l (WT + ins)_Exon 24, and SEQ ID NO: 107 (Sb4715_2 (WT + ins)_Exon 24). 30. The genetically engineered plant of any one or more of embodiments 16 - 28, wherein the altered Glucan Water Dikinase comprises an amino acid sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 % identity to a reference sequence selected from the group consisting of SEQ ID NOS: 45 - 73 (Zm GWD mutant proteins Ml - M29). 31. The genetically engineered plant of any one or more of embodiments 16 - 25, wherein the altered Glucan Water Dikinase comprises an amino acid sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 % identity to a reference sequence selected from the group consisting of SEQ ID NOS: 121 - 125 (Zm GWD mutant proteins M32 - M36), 126 -127 (Zm GWD mutant proteins M38 - M39) and 147 - 162 (Zm GWD mutant proteins M40- M55). 32. The genetically engineered plant of any one or more of embodiments 18 - 26, wherein the altered Glucan Water Dikinase comprises an amino acid sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 % identity to a reference sequence selected from SEQ ID NO: 82 (Sb GWD mutant protein Sb4715_lWT + ins) or SEQ ID NO: 83 (Sb GWD mutant protein Sb4715_2 WT + del). 33. The genetically engineered plant of any one or more of embodiments 18 - 33, wherein the plant is selected from the group consisting of: a monocotyledonous plant, a dicotyledonous plant, a C4 plant, a C3 plant, tomato, sugar beet, sugar cane, eucalyptus, willow, poplar, corn, sorghum, wheat, alfalfa, soybean, rice, miscanthus, and switchgrass. 34. A genetically engineered plant comprising a genetic construct of any one or more of embodiments 2 - 16. -42- PCT/U S2015/052940 WO 2016/054039 35. A method for producing a genetically engineered plant comprising: transforming a plant cell with a vector of embodiment 17; selecting a transformed plant cell that expresses nuclease and comprises an engineered nucleic acid encoding an altered Glucan Water Dikinase; and regenerating the genetically engineered plant from the transformed plant cell, wherein the genetically engineered plant or progeny thereof has an elevated level of starch in comparison to a non-genetically engineered plant of the same genetic background. 36. The method of embodiment 35, wherein the nuclease is a meganuclease. 37. The method of embodiment 35, wherein the nuclease is a Cas9 nuclease. 38. A method for genetically engineering a plant comprising an altered Glucan Water Dikinase comprising: contacting at least one plant cell comprising a target sequence in an endogenous gene encoding a Glucan Water Dikinase with a vector comprising a first nucleic acid encoding a nuclease capable of inducing a single-strand or double-strand break at the target sequence; selecting a plant cell that includes an alteration in the target sequence; regenerating a genetically engineered plant including the alteration from the plant cell. 39. The method of embodiment 38, wherein the genetically engineered plant is homozygous for the alteration. 40. The method of embodiment 38, wherein the genetically engineered plant is heterozygous for the alteration. 41. The method of embodiment 40 further comprising selfing the heterozygous genetically engineered plant, or crossing to another genetically engineered plant heterozygous for the same alteration, and selecting a first progeny plant that is homozygous for the alteration. 42. The method of embodiment 40 further comprising crossing the genetically engineered plant to a wild type plant of the same genetic background and selecting a first progeny plant that is heterozygous for the -43- PCT/US2015/052940 WO 2016/054039 alteration. 43. The method of embodiment 42 further comprising selfing the first heterozygous progeny plant and selecting a second progeny plant that is homozygous for the alteration. 44. The method of any one or more of embodiment 38 - 43, wherein the alteration is a mutation selected from at least one of an insertion, a deletion, or a substitution of at least one nucleotide in the target sequence. 45. The method of embodiment 44, wherein the mutation is a null mutation. 46. The method of any one or more of embodiments 38 - 44, wherein the genetically engineered plant or progeny thereof has an elevated level of starch in comparison to a non-genetically engineered plant of the same genetic background. 47. The method of any one or more embodiments 38 - 46, wherein the nuclease is selected from the group consisting of a meganuclease, Cas9 nuclease, a zinc finger nuclease, and a transcription activator-like effector nuclease. 48. The method of embodiment 47, wherein the nuclease is the meganuclease and is encoded by a sequence with at least 90% identity to a reference sequence selected from the group consisting of SEQ ID NO: 108 (4715_meganuclease) and SEQ ID NO: 109 (4716_meganuclease). 49. The method of embodiment 48, wherein the meganuclease is capable of cutting the target sequence that comprises a polynucleotide of SEQ ID NO: 41 (target for 4715_ GWD-9/10x.272) or SEQ ID NO: 42 (target for 4716_3e GWD-7/8x276). 50. The method of embodiment 47, wherein the nuclease is the Cas9 nuclease. 51. The method of embodiment 50, wherein the Cas9 nuclease is encoded by a nucleic acid with at least 90% identity to SEQ ID NO: 74 (Cas9 nuclease) or SEQ ID NO: 75 (ZmCas9). -44- PCT/US2015/052940 WO 2016/054039 52. The method of embodiment 51, wherein the nucleic acid encoding the Cas9 nuclease is fused to at least one nuclear localization signal (NLS), and the NLS has a polynucleotide sequence selected from SEQ ID NOS: 163 -168. 53. The method of any one of embodiments 38 - 47 and 50 - 52, wherein the vector further comprises a second nucleic acid sequence encoding an sgRNA. 54. The method of embodiment 53, wherein the sgRNA is capable of binding the target sequence, and the target sequence is selected from the group consisting of SEQ ID NO: 91 (GWDela), SEQ ID NO: 92 (GWDe24b), SEQ ID NO: 93 (GWDe24c), and SEQ ID NO: 94 (GWDe25a). 55. The method of any one or more of embodiments 53 - 54, wherein the second nucleic acid comprises a sequence with at least 90% identity to SEQ ID NOS: 95 (ZmU3Pl:sgRNA_GWDe24b), SEQ ID NO: 96 (ZmU3P2:sgRNA_GWDe24b), SEQ ID NO: 97 (ZmU3.8P:sgRNA_GWDe24b), SEQ ID NO: 98 (ZmU3P2:sgRNA_GWDe24c), SEQ ID NO: 99 (ZmU3P2:sgRNA_GWDe25a) and SEQ ID NO: 100 (ZmU3P2: sgRNA_GWDe la). 56. The method of any one or more of embodiments 38 - 55, wherein the vector further comprises a nucleic acid promoter operably linked to the first nucleic acid or the second nucleic acid. 57. The method of embodiment 56, wherein the nucleic acid promoter comprises a sequence with at least 90% identity to a reference sequence selected from the group consisting of: SEQ ID NO: 78 (MzU3.8), SEQ ID NO: 79 (ZmU3), SEQ ID NO: 82 (ZmU3Pl), SEQ ID NO: 84 (ZmU3P2) and SEQ ID NO: 86 (MzU3.8). 58. A genetically engineered plant produced by the method of any one of one of embodiments 38 - 57, or a progeny or descendant thereof, wherein the plant, progeny or descendant thereof comprises the alteration. 59. The genetically engineered plant of embodiment 58 having an elevated level of starch in comparison to a plant of the same genetic background comprising wild type Glucan Water Dikinase. -45- PCT/US2015/052940 WO 2016/054039 60. A method of increasing a starch level in a plant comprising expressing a nucleic acid in the plant that encodes a nuclease capable of inducing a doublestrand break at a target sequence and selecting a homozygous plant that includes an alteration in the target sequence and has an elevated level of starch, wherein the target sequence is included in an endogenous gene encoding a Glucan Water Dikinase only. 61. A method of agricultural processing comprising: expressing in a plant a nucleic acid encoding a nuclease capable of inducing a double-strand break at a target sequence, wherein the target sequence is included in an endogenous gene encoding a Glucan Water Dikinase; selecting a homozygous plant that includes an alteration in the target sequence and has an elevated level of starch; and processing the homozygous plant, wherein the processing comprises one or more procedures selected from harvesting, bailing, shredding, drying, fermenting, hydrolyzing with chemicals, hydrolyzing with exogenous enzymes and combining with plant biomass. The method may also comprise the method for producing a genetically engineered plant of any one or more of embodiments 63 - 71. 62. A method of preparing animal feed comprising: expressing in a plant a nucleic acid encoding a nuclease capable of inducing a double-strand break at the target sequence, wherein the target sequence is included in an endogenous gene encoding a Glucan Water Dikinase; selecting a homozygous plant that includes an alteration in the target sequence and has an elevated level of starch; and performing at least one procedure selected from the group consisting of: harvesting, bailing, shredding, drying, ensiling, pelletizing, combining with a source of edible fiber, and combining with plant biomass. The method may also comprise the method for producing a genetically engineered plant of any one or more of embodiments 63 - 71. -46- PCT/US2015/052940 WO 2016/054039 63. A method for producing a genetically engineered plant comprising an engineered nucleic acid that encodes an altered Glucan Water Dikinase comprising modifying a sequence of an endogenous nucleic acid of at least one allele of a gene that encodes a Glucan Water Dikinase in a plant, wherein the modified engineered nucleic acid is an engineered nucleic acid and the modified plant is the genetically engineered plant. 64. The method of embodiment 63, wherein the genetically engineered plant is homozygous for the gene that includes the mutation and all alleles include the sequence of the engineered nucleic acid. 65. The method of embodiment 63, wherein the genetically engineered plant is heterozygous for the gene that includes the mutation. 66. The method of any one or more of embodiments 63 or 65 further comprising self-crossing the genetically engineered plant and obtaining progeny. 67. The method of any one or more of embodiments 63 - 65 further comprising crossing the genetically engineered plant and a non-genetically engineered plant of the same genetic background and obtaining progeny. 68. The method of any one or more of embodiments 66 - 67 comprising analyzing the progeny for the presence of the altered Glucan Water Dikinase and selecting a progeny plant that includes the mutation. 69. The method of embodiment 63 comprising the genetically engineered plant of any one or more of embodiments 18 - 34 and 58 - 59. 70. The method of embodiment 63, wherein the step of modifying is performed by a method of any one of embodiments 35 - 36. 71. The method of embodiment 63, wherein the step of modifying is performed by using a genetic construct of any one of embodiments 2 - 16. 72. A kit for identifying a modified sequence of an endogenous gene encoding Glucan Water Dikinase in a sample, wherein the kit comprises a first primer and a second primer, wherein the first primer and the second primer are capable of amplifying a target sequence in the endogenous gene encoding Glucan Water Dikinase and the target sequence comprises a nucleic -47- PCT/US2015/052940 WO 2016/054039 acid sequence with at least 90% identity to a reference sequence selected from SEQ ID NOS: 1 - 4, 75, 171 - 187, 189 - 193. 73. The kit of embodiment 72 urther comprising one or more component for detecting at a modification in the amplified region of the target sequence. 74. The kit of any one or more of embodiments 72 - 73 wherein, the first primer comprises a nucleic acid sequence selected from SEQ ID NOS: 6, 7, 9, 11, 101, 103, 105, 110, and 111. 75. The kit of any one or more of embodiments 72 - 74, wherein the second primer comprises a nucleic acid sequence selected from SEQ ID NOS: 5, 8, 10, 102, and 104. 76. The kit of any one or more of embodiments 72 - 75, wherein the first primer and the second primer are capable of amplifying the target sequence to produce an amplified product comprising a modified target sequence. 77. The kit of any one or more of embodiments 73 - 76, wherein the amplified target sequence comprises a sequence selected from SEQ ID NOS: 12 - 40, 106 - 107, 114 - 120, 131 - 146, and 188. 78. The kit of any one or more of embodiments 72 - 76, wherein the modified target sequence is capable of hybridizing to the sequence of the nucleic acid comprising a sequence selected from SEQ ID NOS: 12 - 40, 106 -107, 114 - 120, 131 - 146, and 188 under conditions of high stringency. 79. The kit of any one or more of embodiments 72 - 78, wherein the sample comprises plant matter derived from a genetically engineered plant having at least one mutation in an endogenous gene encoding the Glucan Water Dikinase. 80. A method of identifying a modified sequence of an endogenous gene encoding Glucan Water Dikinase in a sample comprising: contacting a sample with a first primer and a second primer; amplifying a target sequence included in the endogenous gene encoding Glucan Water Dikinase and the target sequence comprises a nucleic acid sequence with at least 90% identity to a reference sequence selected from SEQ ID NOS: 1 - 4, 75, 170 - 184 186, 187, 189 - 193; and -48- PCT/US2015/052940 WO 2016/054039 detecting a modification in the target sequence. 81. The method of embodiment 79, wherein the modification in the target sequence comprises a sequence selected from SEQ ID NOS: 12 - 40, 106 - 107, 114 - 120, 131 - 146, and 188. The method of identifying may be added to any one or more of embodiments 60 - 71.

[0106] Further embodiments herein may be formed by supplementing an embodiment with one or more element from any one or more other embodiment herein, and/or substituting one or more element from one embodiment with one or more element from one or more other embodiment herein.

[0107] EXAMPLES

[0108] The following non-limiting examples are provided to illustrate particular embodiments. The embodiments throughout may be supplemented with one or more detail from one or more example below, and/or one or more element from an embodiment may be substituted with one or more detail from one or more example below.

[0109] Example 1. Mesanuclease-based modification of GWD sene in maize and sorshum senomes [0110] Meganuclease constructs were designed that target GWD exon 24, which is near the predicted encoded active site of the enzyme, with the intent of introducing a mutation that inactivates GWD (null mutation). Meganuclease-induced GWD DNA mutants were identified and characterized in maize and sorghum.

[0111] In order to engineer I-Crel homing endonucleases with specificities against GWD genes in maize and sorghum genomes, two nucleotide sequences were selected from the previously annotated full length GWD genes of maize and sorghum. The sequence selection was based on the existence of the high nucleotide sequence identity between maize and sorghum sequences (95% nucleotide sequence identity) and the presence of a sequence -49- PCT/US2015/052940 WO 2016/054039 motif in exons #24 of both crops that is required for GWD protein activity. The goal was to develop two meganuclease constructs in such a way that each of them would be specific for GWD modification in both maize and sorghum. Targeted genome modifications at the selected GWD sequences using the meganuclease approach would lead to expression of GWD protein variants lacking the active site (truncated proteins or modified proteins expressed from the frame shift containing coding sequences) and therefore being catalytically inactive. The selected sequences of ZmGWD (maize) and SbGWD (sorghum) shown below were supplied to Precision Biosciences, Inc. for designing meganucleases GWD9-10x.272 and GWD7-8x.226.

[0112] The target sequence for the meganuclease GWD-9/10x.272 (pAG4715) is: ATCCTTGTGGCAAAGAGTGTCA (SEQ ID NO: 41).

[0113] The target sequence for the meganuclease GWD-7/8x.226 target sequence (pAG4716) is: GTAGTTGGTGTAATTACACCTG (SEQ ID NO: 42).

[0114] The DNA sequences within exon 24 that are recognized by the designed meganucleases are underlined. The sequences in the uppercase letters show exon 24, while the sequences in lowercase letters represent flanking introns. The “CAT” codon that is double-underlined encodes a Histidine residue that is critical for GWD protein activity. >ZmGWD_Exon24 aagtgatactagtgaccctctccacaattttatgcgaaccacagaaattaataatatattctattactctgcacct

gacatctggctcctgctatcagTTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTA

TGTGGTTGTGGTTGATGAGTTACTTGCTGTCCAGAACAAATCTTATGATA

AACCAACCATCCTTGTGGCAAAGAGTGTCAAGGGAGAGGAAGAAATACC

AGATGGAGTAGTTGGTGTAATTACACCTGATATGCCAGATGTTCTGTCTC AIGTGTCAGTCCGAGCAAGGAATAGCAAGgtttatcttcacagctatgttgcaagatttctt gaattttttctcttgtattgatgttgacatactagctttttcctaat (SEQ ID NO: 3) >SbGWD_Exon24 aagtggtactagtgacctctccacagttttatgtgaaccacagaaattaaatatgataatatattctattactctg

cacctgacatctggctcctgataacagTTGGCAGGTTATAAGCCCAGTTGAAGTATCAG

GTTATGTGGTTGTGGTTGATGAGTTACTTGCTGTCCAGAACAAATCTTAT

GATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGGAGAGGAAGAAA

TACCAGATGGAGTAGTTGGTGTAATTACACCTGATATGCCAGATGTTCTG -50- PCT/U S2015/052940 WO 2016/054039 TCCCAIGTGTCAGTCCGAGCAAGGAATAGCAAGgtttattttcacagttatgttgcaag ctttctcagattttttttcttgtatcgatgttgacataccagttttttcctaat (SEQ ID NO: 4) [0115] Clustal software was used to align selected ZmGWD and SbGWD sequences. (Larkin MA et al., 2007; Goujon M et al., 2010, both of which are incorporated herein by reference as if fully set forth). CLUSTAL 2.1 multiple sequence alignment

SbGWD_Exon24 aagtggtactagtgacctctccacagttttatgtgaaccacagaaattaaatatgataa 59

ZmGWD_Exon24 aagtgatactagtgaccctctccacaattttatgcgaaccacagaaatta------ataa 54 ***** *********** ******** ******* *************** ****

SbGWD_Exon24 tatattctattactctgcacctgacatctggctcctgataacagTTGGCAGGTTATAAGC119 ZmGWD_Exon24 tatattctattactctgcacctgacatctggctcctgctatcagTTGGCAGGTTATAAGC114 ************************************* ** *******************

SbGWD_Exon24 CCAGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACTTGCTGTCCAGAACAAAl7 9 ZmGWD_Exon24 CCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACTTGCTGTCCAGAACAAAl7 4 ** *********************************************************

SbGWD_Exon24 TCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGGAGAGGAAGAAATACCA23 9 ZmGWD_Exon2 4 TCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGGAGAGGAAGAAATACA234 ************************************************************

SbGWD_Exon24 GATGGAGTAGTTGGTGTAATTACACCTGATATGCCAGATGTTCTGTCC£££GTGTCAGTC299

ZmGWD_Exon24 GATGGAGTAGTTGGTGTAATTACACCTGATATGCCAGATGTTCTGTCTCATGTGTCAGTC294 *********************************************** ************

SbGWD_Exon24 CGAGCAAGGAATAGCAAGgtttattttcacagttatgttgcaagctttctcagatttttt359 ZmGWD_Exon24 CGAGCAAGGAATAGCAAGgtttatcttcacagctatgttgcaagatttcttgaatttttt354 ************************ ******* *********** ***** *******

SbGWD_Exon24 ttcttgtatcgatgttgacataccagttttttcctaat 397(SEQ ID NO: 4)

ZmGWD_Exon24 ctcttgtattgatgttgacatactagctttttcctaat 392(SEQ ID NO: 3) ******** ************* ** *********** [0116] Development of plant transformation vectors for expressing meganucleases: [0117] The meganuclease sequences GWD-9/10x.272 [SEQ ID NO: 108] and GWD-7/8x.226 [SEQ ID NO: 109], which were provided by Precision Biosciences, Inc., were further modified by adding BamHI restriction site at 5’ and AvrII site at 3’ ends using PCR approach. Subsequently, GWD-9/10x.272 and GWD-7/8x.226 nucleotide sequences were cloned into pAG4500 vector as BamHLAvrII fragments between the maize ubiquitin 1 gene promoter and -51- PCT/US2015/052940 WO 2016/054039

Nos transcriptional terminator sequences to generate respectively plant transformation vectors pAG4715 and pAG4716. FIG. 1 and FIG. 2 illustrate respective maps of pAG4715 and pAG4716 vectors. Referring to FIGS. 1 and 2, pAG4715 and 4716 include a maize ubiquitin promoter (ZmUbil), a maize ubiquitin intron (ZmUbil intron), and a polyadenilation signal NosT serving as the transcription terminator. Both vectors also include a phosphomannose isomerase gene (PMI) as a selectable marker, At NLS (nuclear localization sequence), ZmKozak, mUBQmono, T-DNA right and left borders (RB and LB, respectively), a streptothricin acetyltransferase gene, and an aminoglycoside acetyltransferse (aadA) gene conferring resistance to streptomycin. pAG4715 includes a GWD9-10x.272 meganuclease sequence [SEQ ID NO: 108] and pAG4716 includes a GWD7-8x.226 meganuclease sequence [SEQ ID NO: 109].

[0118] pAG4715 and pAG4716 were used to generate transgenic events and mutants in maize and sorghum.

[0119] Sequences of the target proteins, genes, mutants and vectors used herein are listed in Table 1.

Table 1 Description of Sequences

SEQ ID NO Description Type 1 ZmGWD coding sequence DNA 2 SbGWD coding sequence DNA 3 ZmGWD Exon 24 (includes introns) DNA 4 SbGWD Exon 24 (includes introns) DNA 182 ZmGWD Exon 24 (no introns) DNA 183 SbGWD Exon 24 (no introns) DNA 184 SbGWD Exon 7 (no introns) DNA 5 Mega-1 (4716) PCR Primer Reverse DNA 6 Mega-1 (4716) PCR Primer Forward DNA 7 Mega-2 (4715) PCR Primer Forward DNA 8 Mega-2 (4715) PCR Primer Reverse DNA 9 ZmGWD mega-2 PCR Primer Forward DNA 10 ZmGWD mega-2 PCR Primer Reverse DNA 11 SbGWD mega-2 PCR Primer Forward DNA 13 SbGWD mega-2 PCR Primer Reverse DNA 12 M16 (Zm GWD Exon 24 - no introns) DNA 13 M17 (Zm GWD Exon 24 - no introns) DNA 14 Ml8 (Zm GWD Exon 24 - no introns) DNA 15 M27 (Zm GWD Exon 24 - no introns) DNA -52- WO 2016/054039 PCT/US2015/052940 SEQ ID NO Description Type 16 Ml (Zm GWD Exon 24 - no introns) DNA 17 Mil (Zm GWD Exon 24 - no introns) DNA 18 M10 (Zm GWD Exon 24 - no introns) DNA 19 M3 (Zm GWD Exon 24 - no introns) DNA 20 M8 (Zm GWD Exon 24 - no introns) DNA 21 M14 (Zm GWD Exon 24 - no introns) DNA 22 M13 (Zm GWD Exon 24 - no introns) DNA 23 M12 (Zm GWD Exon 24 - no introns) DNA 24 M22 (Zm GWD Exon 24 - no introns) DNA 25 M23 (Zm GWD Exon 24 - no introns) DNA 26 M24 (Zm GWD Exon 24 - no introns) DNA 27 M20 (Zm GWD Exon 24 - no introns) DNA 28 M21 (Zm GWD Exon 24 - no introns) DNA 29 M4 (Zm GWD Exon 24 - no introns) DNA 30 M19 (Zm GWD Exon 24 - no introns) DNA 31 M26 (Zm GWD Exon 24 - no introns) DNA 32 M25 (Zm GWD Exon 24 - no introns) DNA 33 M15 (Zm GWD Exon 24 - no introns) DNA 34 M5 (Zm GWD Exon 24 - no introns) DNA 35 M2 (Zm GWD Exon 24 - no introns) DNA 36 M28 (Zm GWD Exon 24 - no introns) DNA 37 M6 (Zm GWD Exon 24 - no introns) DNA 38 M9 (Zm GWD Exon 24 - no introns) DNA 39 M7 (Zm GWD Exon 24 - no introns) DNA 40 M29 (Zm GWD Exon 24 - no introns) DNA 106 Mutant Sb4715 1 (Wt+ ins) DNA 107 Mutant Sb4715 2 (WT+del) DNA 41 Meganuclease GWD-9/10x.272 target sequence (pAG4715) DNA 42 Meganuclease GWD-7/8x target sequence (pAG4716) DNA 43 ZmGWD (wild type protein) Amino acid 44 SbGWD (wild type protein) Amino acid 45 ZmGWD Ml (mutant GWD protein) Amino acid 46 ZmGWD M2 (mutant GWD protein) Amino acid 47 ZmGWD M3 (mutant GWD protein) Amino acid 48 ZmGWD M4 (mutant GWD protein) Amino acid 49 ZmGWD M5 (mutant GWD protein) Amino acid 50 ZmGWD M6 (mutant GWD protein) Amino acid 51 ZmGWD M7 (mutant GWD protein) Amino acid 52 ZmGWD M8 (mutant GWD protein) Amino acid 53 ZmGWD M9 (mutant GWD protein) Amino acid 54 ZmGWD M10 (mutant GWD protein) Amino acid 55 ZmGWD Mil (mutant GWD protein) Amino acid 56 ZmGWD M12 (mutant GWD protein) Amino acid -53- WO 2016/054039 PCT/US2015/052940 SEQ ID NO Description Type 57 ZmGWD Ml3 (mutant GWD protein) Amino acid 58 ZmGWD M14 (mutant GWD protein) Amino acid 59 ZmGWD Ml5 (mutant GWD protein) Amino acid 60 ZmGWD Ml6 (mutant GWD protein) Amino acid 61 ZmGWD Ml7 (mutant GWD protein) Amino acid 62 ZmGWD Ml8 (mutant GWD protein) Amino acid 63 ZmGWD Ml9 (mutant GWD protein) Amino acid 64 ZmGWD M20 (mutant GWD protein) Amino acid 65 ZmGWD M21 (mutant GWD protein) Amino acid 66 ZmGWD M22 (mutant GWD protein) Amino acid 67 ZmGWD M23 (mutant GWD protein) Amino acid 68 ZmGWD M24 (mutant GWD protein) Amino acid 69 ZmGWD M25 (mutant GWD protein) Amino acid 70 ZmGWD M26 (mutant GWD protein) Amino acid 71 ZmGWD M27 (mutant GWD protein) Amino acid 72 ZmGWD M2 8 (mutant GWD protein) Amino acid 73 ZmGWD M29 (mutant GWD protein) Amino acid 74 Mutant protein Sb4715 1 (WT + ins) Amino acid 75 Mutant protein Sb4715 2 (WT + del) Amino acid [0120] Example 2. Application of TALENs for targeted modification ofGWD sene in sorghum senome [0121] Two pairs of DNA sequences were selected in each of the exons 7 and 24 of the sorghum GWD gene (SbGWD) for development of four custom TAL DNA-binding domains that will be fused to a truncated FokI nuclease sequence. The sorghum exon 24 was selected because it contains the GWD active site and to compare with other endogenous DNA editing technologies in maize, such as meganuclease and CRISP/Cas9 technologies. The sorghum exon 7 was chosen in the upstream region of the GWD gene sequence for producing shorter truncated versions of the GWD protein. Selection of the sequences for DNA-binding domains was performed on Life Technologies web site using a proprietary program. The two pairs of TAL DNA binding domains fused to truncated FokI endonuclease for targeted sorghum genome modifications in exons 7 and 24 of the GWD gene are being constructed by Life Technologies. Each pair of TALENs will recognize top and bottom strands of -54- PCT/US2015/052940 WO 2016/054039 genomic DNA sequence at the respective GWD sites to target FokI nuclease for DNA cleavage.

[0122] SbGWD nucleotide sequences selected for TALENs-based GWD modification. The SbGWD_exon7 sequence is positioned within nt 736 - 969 the SbGWD coding sequence (SEQ ID NO: 2): >SbGWD_exon7 GAGGAGTATGAAGCTGCACGAGCTGAGTTAATAGAGGAATTAAATAGAG GTGTTTCTTTAGAGAAGCTTCGAGCTAAATTGACAAAAACACCTGAAGCA CCTGAGTCAGATGAACGTAAATCTCCTGCATCTCGAATGCCCGTTGATAA ACTTCCAGAGGACCTTGTACAGGTGCAGGCTTATATAAGGTGGGAGAAAG CGGGCAAGCCAAATTATCCTCCTGAGAAGCAACTG (SEQ ID NO: 184) [0123] The SbGWD_exon24 sequence is positioned within nt 3030 - 3243 the SbGWD coding sequence (SEQ ID NO: 2): >SbGWD_exon24 tTGGCAGGTTATAAGCCCAGTTGAAGTATCAGGTTATGTGGTTGTGGTTG ATGAGTTACTTGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTG TGGCAAAGAGTGTCAAGGGAGAGGAAGAAATACCAGATGGAGTAGTTGG TGTAATTACACCTGATATGCCAGATGTTCTGTCCCAIGTGTCAGTCCGAG CAAGGAATAGCAAG (SEQ ID NO: 183) [0124] Underlined sequences in each exon represent selected TAL DNA binding sites with the left sequence being specific for the upper DNA strand and the right sequence targeting the bottom DNA strand. A codon encoding catalytically important Histidine residue for GWD protein activity is double-underlined and in bold within exon 24. The TALENs specific for exon 7 or exon 24 will be cloned as respective pairs into pAG4500-based plant transformation vector.

[0125] Example 3. Plant Transformation and Analysis [0126] Maize and Sorghum Transformation: DNA from Agrobacterium was extracted using the protocol described in the Plasmid pSBl operating manual. Plant DNA was extracted using Qiagen DNeasy Plant Mini kit

(69140). Maize and sorghum embryos were transformed with GWD meganuclease targeting constructs pAG4715 and/or pAG4716 according to

Negrotto D et al. 2000 Plant Cell Rep 19: 798; Ishida Y et al. 1996 Nat Biotech -55- PCT/US2015/052940 WO 2016/054039 14: 74, which is incorporated herein by reference as if fully set forth. Briefly, embryogenic callus from wild-type AxB maize was inoculated with LBA4404 Agrobacterium cells harboring the appropriate transformation plasmid. Agrobacterium-mediated transformation of immature maize embryos was performed as described on Negrotto D et al. The expression cassettes for GWD meganucleases were cloned into the KpnI-EcoRI sites of an intermediate vector capable of recombining with the pSBl vector in triparental mating in Agrobacterium tumefaciens strain LBA4404 using procedures reported previously (Ishida Y et al. 1996 Nat Biotech 14: 745; Hiei Y et al. 1994 Plant J 6: 271; Hiei Y and Komari T 2006 Plant Cell Tissue Organ Cult. 85: 27; Komari T et al. 1996 Plant J 10: 165). Maize (Zea mays cultivars Hill, A188 or B73) stock plants were grown in a greenhouse under 16 hours of daylight at 28°C. Immature zygotic embryos were isolated from the kernels and inoculated with the Agrobacterium solution containing the genes of interest. After inoculation immature embryos were grown in a tissue culture process for 10 - 12 weeks. Well-developed seedlings with leaves and roots were sampled for PCR analysis to identify transgenic plants containing the genes of interest. PCR positive and rooted plants were rinsed with water to wash off the agar medium, and transplanted to soil and grown in the greenhouse to generate seeds and stover.

[0127] Sorghum transformation was carried according to the protocol of Gao et al., 2005. Regeneration of the transgenic plants was performed according to Elkonin and Pakhomova, 2000.

[0128] DNA from Agrobacterium was extracted using the protocol described in the Plasmid pSBl operating manual. Plant DNA was extracted using Qiagen DNeasy Plant Mini kit (69140).

[0129] ΙΟΧΤΕ+Sarkosyl-Plant DNA Isolation for 96 well plates: Briefly, a COSTAR grinding block was filled with 34 leaf samples, one 5 mm steel bead was added to each well with a sample and the storage mat block was applied using a storage mat applicator to seal the block. Samples were stored at -80°C for at least 30 min before grinding or until processing time. For processing, -56- PCT/US2015/052940 WO 2016/054039 samples were ground for 45 sec using the Klecko Pulverizer & Secure grinder at maximum speed. Sealing was removed and discarded. Three hundred microliters of ΙΟΧΤΕ+Sarkosyl buffer (5 mL 1M Tris, 1 mL 0.5M EDTA, 0.5g sarkosyl, 46 mL ddLLO) was added to each sample using a multichannel pipette and a sterile solution basin. The plate was incubated on a shaker for 10 min at 300 rpm, and spun for 3 min at 4000 rpm. Supernatant was removed and discarded, and the pellets were resuspended in lxTE buffer. One hundred fifty microliter sample aliquots were added to the 96 well PCT plate. The PCR plate was sealed with aluminum foil. For best results, DNA isolation and PCR were performed on the same date.

[0130] Transgenic Diagnostic PCR Reaction Setup: The “complete” PCR reaction mix was as follows: 15 μΐ 2X GoTaq MM (GoTaq Green Master Mix (PROMEGA #M712), 3μ1 of combined forward and reverse primers specific to the gene of interest (each mixed at 10μΜ), 2 μΐ DNA prep, and water to adjust volume to 30 μΐ. Twenty eight microliters of the “complete” PCR reaction mix per well were aliquoted into a PCR plate (FISHER, #14230236). Two microliters plant DNA sample were aliquoted into each well of the PCR plate. Positive control and no template negative control were used in each PCR reaction. Control Agrobacterium DNA was diluted 1:100 in TE buffer to yield clear bands. The PCR plate was sealed with a sealing mat (COSTAR #6555) and roller. PCR was performed at BIORAD PTC-100 thermocycler. The thermocycler programs were as follows: 1) 95°C-3min; 30 cycles 95°C-30sec, 55°C-30sec, 72°C-45sec; 72°C-5min; 10°C (hold), and 2) 90°C for 30 min and 10°C (hold). Twelve microliters of each PCR reaction was loaded onto Ready Agarose 96 Plus gel -3% (BIORAD #161-3062) and ran at approximately 100V for 20 minutes before viewing with a BIORAD gel doc system equipped with Quantity One software. Quick-Load 50bp DNA Ladder (NEB N0473S) was used to identify the size of the PCR fragments. 10X TBE Buffer (Promega V4251) was used.

[0131] In line monitor of starch content in living corn leaf using Fourier Transform Near-infrared (FT-NIR) Technique: The starch content in corn leaf -57- PCT/US2015/052940 WO 2016/054039 tissue is an important factor for animal feed and biofuel production. The commonly used GOPOD assay is not applicable for real-time monitoring in living tissue because the assay is invasive, requiring physical tissue samples, and labor intensive. Predictive models of starch content based on the FT-NIR spectra of dry blends of native and maize leaf starches or corn flour (wet and dry) were developed using partial least squares regression. Three key factors determine a successful application of FT-NIR techniques for fast chemical characterization: accurate and repeatable NIR spectral acquisition, reliable calibration data, and robust chemometric analysis. For analysis, the following materials were used: a spectrophotometer (Perkin Elmer Spectrum One NTS Waltham, MA), Unscrambler® (Version 10.2., Camo Software Inc., Woodbridge, NJ), an oven, Hi-maize resistant starch (Honeyville, Brigham City, UT), and Starch (Product No. S516-500, Fisher Scientific). All blank and test samples were diluted 10X using deionized water and the unreacted starch content was determined using a glucose oxidase-peroxidase (GOPOD) colorimetric assay (Megazyme International, Wicklow, Ireland).

[0132] Sample preparation: A total of 56 dry starch blend samples with 0- 33% starch content were prepared by mixing weight proportions of HI-MAIZE® resistant starch (Honeyville, Brigham City, UT) with starch (Product No. S516-500, Fisher Scientific). The Honeyville product contains HI-MAIZE® 260 (Ingredion, Bridgewater, NJ) resistant starch that has been isolated from high amylose corn hybrids produced through traditional plant breeding, and contains 33% digestible, or glycemic starch.

[0133] One hundred fifty green leaf samples from different living maize plants at certain age or with different starch accumulation were collected. One hundred samples were oven-dried and 50 samples were left undried (“wet”). Leaf samples were ground to 0.5 mm and stored in plastic sample bags for moisture equilibration. Moisture content was measured using standard methods.

[0134] Starch determination: The starch content was analyzed for starch blends, wet and dry green tissue or corn flour sample using GOPOD assay. -58- PCT/US2015/052940 WO 2016/054039 [0135] Scanning, processing and analyses of FT-NIR spectra: Scanning-Approximately a 5 g milled sample was poured in a smaller NIRA cup, leveled, and scanned 16 times with a manual rotation between each scan. This procedure was repeated five times with separate subsamples and the resulting spectral scans were averaged. A total of 56 samples of starch blends were used to create starch models. 36 samples were used in the calibration set, 14 samples were used in the validation set, and six samples were used in the test set. The dry ground green tissue or flour models were made using 100 samples of corn leaf or seeds. For calibration, validation, and testing, 72, 20, and 8 samples were used, respectively. The wet ground corn models were made using 49 samples of corn leaf or corn seeds. 36 samples were used for calibration, 10 samples were used for validation, and three samples were used for the test set.

[0136] Processing and analyses of FT-NIR spectra - Unscrambler® (Version 10.2., Camo Software Inc., Woodbridge, NJ) was used to process and analyze the spectral data, build and validate the calibration, and test the regression models. Multiplicative scatter correction (MSC) and a 2nd derivative-based smoothing technique, such as the Savitzky-Golay (SG) technique, were used for data pretreatment. Partial least squares models using a combination of MSC with SG second derivate pretreated spectral data were developed for starch blends and milled green tissue or ground corn. Examples of measured and predicted (MSC+2nd Derivative Model) starch content of calibration, validation, and test samples are shown in Table 2. -59- PCT/US2015/052940

Table 2 Measured and Predicted (MSC+2nd Derivative Model) Starch Content of Calibration, Validation, and Test Samples

Starch blends Dry corn flour Wet corn: lour Starch Measured Predicted Measured Predicted Measured Predicted content (%) (%) (%) (%) (%) (%) Calibration 2.50 2.52 5.0 6.5 5.0 5.2 5.00 4.89 7.5 7.4 10.0 7.9 10.0 10.1 10.0 10.2 12.5 12.0 15.0 15.6 15.0 14.5 13.2 13.5 20.0 20.0 Validation 4.75 4.7 7.5 7.6 7.5 7.5 10.0 9.8 12.5 12.4 10.0 10.0 15.7 16.0 17.5 17.5 12.0 12.5 18.9 18.9 Test 6.5 6.55 5.0 6.5 7.2 7.3 12.5 12.45 11.5 12.5 11.2 11.5 17.5 18.2 14.5 13.2 12.2 13.5 WO 2016/054039 R2: Starch blends: Calibration: 0.98, Validation: 0.97, Prediction: 0.97 Dry corn flour: Calibration: 0.86, Validation: 0.80, Prediction: 0.80 Wet corn flour: Calibration: 0.94, Validation: 0.80, Prediction: 0.75 [0137] Example 4. Identification and characterization of mesanuclease-induced DNA mutations in the Zea mays and Sorshum bicolor GWD senes [0138] Identification of Gene of Interest (GOT) Positive Maize and Sorghum Transformants: Leaves from maize and sorghum plants transformed with pAG4715 or pAG4716 were sampled, DNA was extracted, and screened for the presence of the meganuclease transgenes included in pAG4715 or pAG4716.

[0139] Screening of Maize and Sorghum Transformants: Plants carrying pAG4715 or pAG4716 transgenes referred to as 4715 or 4716 plants, respectively, were screened for GWD mutations using sequence analysis of PCR-amplified GWD DNA sequences.

[0140] PCR Amplification of GWD: DNA sequences surrounding the meganuclease targeting region on exon 24 were amplified using the ZmGWDmega-2 and SbGWDmega-2 primers shown in Table 3. -60- PCT/US2015/052940

Table 3 Primers for Genotyping 4715 and 4716 Plants

Primer Set Primer Name Forward or Reverse Sequence Product size (bp) Mega-1 (4716) Mega-IR Reverse TGATCTTCAGCACGAG GTTG (SEQ ID NO: 5) 265 Mega-1 (4716) Mega-IF Forward GGCTCCATCTATGCCTG TATC (SEQ ID NO: 6) 265 Mega-2 (4715) Mega-2F Forward GAGCTCAGTTTCGCTGT CTATC (SEQ ID NO: 7 ) 209 Mega-2 (4715) Mega-2R Reverse ATGATCTTCAGCACGA GGTTG (SEQ ID NO: 8) 209 ZmGWD mega-2 ZmGWD mega-2F Forward GGTTATAAGCCCGGTT GAAGTA (SEQ ID NO: 9) 204 ZmGWD mega-2 ZmGWD mega-2R Reverse CTATTCCTTGCTCGGAC TGAC (SEQ ID NO: 10) 204 SbGWD mega-2 SbGWD mega-2f Forward GGCAGGTTATAAGCCC AGTT (SEQ ID NO: 11) 208 ZmGWD mega-2 SbGWD mega-2r Reverse CTATTCCTTGCTCGGAC TGAC (SEQ ID NO: 10) 208 WO 2016/054039 [0141] Primer sets were diluted to a final concentration of 5 μΜ in nuclease-free water. PCR reaction was performed as described above.

[0142] PCR samples were run on an Eppendorf Mastercycler proS (Eppendorf) using our PMI55 program (95°C, 2 min; 30 cycles [95°C, 30 sec; 55°C, 30 sec; 72°C, 45 sec]; 72°C, 8 min) [0143] PCR samples were separated on Bio-Rad ReadyAgarose 96 Plus Gels, TBE (#161-3062) and visualized with a Bio-Rad gel imaging system.

[0144] FIG. 3 illustrates an example of a gel showing bands of 4715 and 4716 events or successful incorporation of transgenes from pAG4715 or pAG4716, respectively. Referring to this figure, shifted GWD bands indicate potential insertions and deletions (indels) at the GWD meganuclease targeting site and are marked by asterisks.

[0145] DNA Sequence Characterization of the GWD Indel Alleles:

[0146] Sequencing of Initial GWD PCR Products - PCR products were sequenced at Beckman Coulter Genomics (36 Cherry Hill Dr, Danvers, MA -61- PCT/US2015/052940 WO 2016/054039 01923) using the same primers used for amplification (ZmGWDmega-2 or SbGWDmega-2). Sequencing allowed differentiation between three different genetic outcomes for the GWD locus, wild type, homozygous mutant, and heterozygous mutant. Wild type had no mutation within the 204 or 208 bp GWD PCR fragment, homozygous carried an indel mutation, and heterozygous carried an unresolvable sequence region (indicating at least one indel) of the GWD PCR fragment.

[0147] Cloning and Sequencing of Individual GWD Alleles. To initiate cloning, GWD was amplified with PCR using the same primer sets as above (ZmGWDmega-2 or SbGWDmega-2) from DNA derived from heterozygous plants to characterize the individual GWD alleles. PCR amplification was confirmed by running 8 μΐ of PCR product on agarose gels as described above and the remaining 22 μΐ of PCR reaction was purified with a Qiagen PCR Purification Kit (28104; Qiagen, MD, USA) and eluted in 30 μΐ of Elution Buffer (EB).

[0148] Purified PCR products were cloned using a TOPO® TA Cloning Kit with One Shot® TOP10 Competent E. coli (K4500-01; Life Technologies) according to the protocol. For cloning procedure, 4 μΐ of purified PCR product was used for the ligation, ligations were incubated on ice for at least 10 min, and 50 μΐ of each transformation reaction was plated on LB carbenicillin (50 pg/ml) X-gal plates.

[0149] Eight E. coli colonies from each reaction were picked using a sterile pipet tip and transferred into 20 μΐ of sterile liquid LB with carbenicillin. GWD was then amplified by PCR using the same primer sets as above (ZmGWDmega-2 or SbGWDmega-2) and 2 μΐ of each diluted E. coli clone culture. PCR products were confirmed and sent for sequencing as described above.

[0150] Table 4 describes ZmGWD meganuclease events zygosity, mutation types and locations. In Table 4, ZmGWD mutations were numbered 1-28. The wild type (WT) plant refers to two GWD wild type alleles. Hemizygous event refers to one GWD mutant allele and one GWD wild type -62- PCT/US2015/052940 WO 2016/054039 allele. Heterozygous event refers to two different GWD mutant alleles. Homozygous event refers to two identical GWD mutant alleles.

Table 4 ZmGWD Meganuclease Event Zygosity and Mutations

Construct/ Event Zygosity Mutation Locus # (1) Mutation Type Locus #(1) Mutation Locus # (2) Mutation Type Locus # (2) 4715_5 Hemi M18 lbp del 4715_6 WT GWD wild type 4715_11 Hemi M17 lObp del 4715_13 Hemi M16 24bp del 4715_14 Hemi M17 lObp del 4715_15 Hemi M18 lbp del 4715_18 WT GWD wild type 4715_20 Homo or Hetero two mutant alleles 4715_25 Hemi M17 lObp del 4715_28 Hemi M2 7 16 bp del 4716_1 Hemi Ml 4bp sub 4716_2 Homo M15 40bp del 4716_3 Hetero M9 15bp del M6 lbp del 4716_4 Hetero Mil 17bp del M12 38bp del 4716_5 Hetero M7 4bp del Mil 17bp del 4716_6 Hetero M4 9bp del M14 25bp del 4716_7 Hemi Ml 4bp sub 4716_8 Homo Mil 17bp del 4716_9 WT GWD wild type 4716_10 Hetero Mil 17bp del M10 lbp ins 4716_11 Hetero Mil 17bp del M10 lbp ins 4716_12 Hetero M3 15bp del M8 6bp del 4716_13 Homo M14 25bp del 4716_14 Homo M13 36bp del 4716_15 Hetero Mil 17bp del M12 38bp del 4716_18 Hemi M20 lbp del 4716_20 WT GWD wild type 4716_22 Hetero M5 21 lbp ins Mil 17bp del 4716_23 Homo M15 40bp del -63- WO 2016/054039 PCT/US2015/052940

Construct/ Event Zygosity Mutation Locus # (1) Mutation Type Locus #(1) Mutation Locus # (2) Mutation Type Locus # (2) 4716_24 Hetero M2 6bp del M14 25bp del 4716_25 Hetero M10 1 bp ins M28 27bp del 4716_26 Hetero Mil 17bp del M12 38bp del 4716_27 Hetero Mil 17bp del M10 lbp ins 4716_151 Hemi M10 1 bp ins 4716_152 Hetero M22 lObp del M23 8bp del+15bp ins(7bp ins) 4716_153 WT GWD wild type 4716_154 Hetero M22 lObp del M23 8bp del+15bp ins(7bp ins) 4716_155 Homo M4 9bp del 4716_157 Hemi M2 4 1 bp del 4716_158 Hemi M20 lbp del 4716_159 Homo M20 lbp del 4716_160 Hemi M10 1 bp ins 4716_161 Hetero M4 9bp del M21 33bp del (57bp del+ 17bp ins) 4716_162 Hetero M20 lbp del M19 4bp del 4716_163 Hemi M26 21 lbp ins 4716_164 Hemi M20 lbp del 4716_165 Homo M4 9bp del 4716_166 Homo M4 9bp del 4716_167 Hetero M13 36bp del M25 2bp del 4716_201 Homo M29 2bp del [0151] DNA sequences for each clone were compared to wild type (WT) GWD using Vector NTI Advance (Version 11.5; Life Technologies). DNA sequences for wild type ZmGWD and SbGWD and transgenic events were compared and shown in the following files: ZmGWD meganuclease mutant DNA sequence alignments; ZmGWD meganuclease mutant protein sequence -64- PCT/US2015/052940 WO 2016/054039 alignments; SbGWD meganuclease mutant DNA sequence alignments; SbGWD meganuclease mutant protein sequence alignments.

[0152] As shown below, an alignment of the sequences from three PCR products demonstrates insertions and deletions that distinguish maize mutants M5 and M26 from wild type sequence ZmGWD Exon24.

[0153] CLUSTAL O (1.2.1) multiple sequence alignment for ZmGWD for maize mutants M5 and M26:

ZmGWDExon24 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT60 M5 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT60 M26 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT60

JrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJr

ZmGWDexon24 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGG120 M5 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGG120 M2 6 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGG120

JrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJr

ZmGWDexon24 AG AG G AAG AAAT AC C AG AT GG AG T A-----------------------------------145 M5 AGAG GAAGAAATAC CAGAT GGAG TAG T T GCAGAAT TAT T GAAT T C T T T CATAAT T GAAC T18 0 M2 6 AGAGGAAGAAATACCAGATGGAGCAGTGTGCTCGGGTACAGCTTCTTATTTCAATGTCTC180

JrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJr Jr

ZmGWDexon24 ------------------------------------------------------------145 M5 CTATGATGATGCTTTACTT—GATTGTATTATATTGATGCTCAATCATATATTGATGATT2 3 8 M2 6 CAGTGGGCGTCTTACCTCTATGTTTGTGTTTTTTT-TTAAGTGCAGAAATAGAGAAAGTT239

ZmGWDexon24 ------------------------------------------------------------145 M5 GTTGGAACTTGCTCTCCGATGCAAGGTGATCCAACGGGGGTGTGTCGCAACGTAAACAGG298 M2 6 C T T GCAAATAT C TAC T C TAT GAAAAGGACAGC TAT T T GGAAATA------TGTGAACAGA2 9 3

ZmGWDexon24 ------------------------------------------------------------145 M5 GTTTTCG-CACGAGATGGCAATAGCTCTGT-T---AACCTAGCCTCTCACGGGCACTGTG353 M26 ACTATCCCCAGTTGCTGGGAAAAACCAAGAAGAAAGTTCCTTCAAATATCTACTCCATGA353

ZmGWDexon24 ---GTTGGTGTAATTACACCTGATATGCCAGATGTTCTGTCTCATGTGTCAGTCCGAGCA202 M5 CGGGGGTATTTAATTACACCTGATATGCCAGATGTTCTGTCTCATGTGTCAGTCCGAGCA413 M2 6 CGACAAGTGTCTATTACACCTGATATGCCAGATGTTCTGTCTCATGTGTCAGTCCGAGCA413

JrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJrJr -65- PCT/US2015/052940 WO 2016/054039

ZmGWDexon24 AGGAATAGCAAG 214 (SEQ ID NO: 182) M5 AGGAATAGCAAG 425 (SEQ ID NO: 34) M26 AGGAATAGCAAG 425 (SEQ ID NO: 31) •k'k'k'k'k'k'k'k'k'k'k'k [0154] The below alignment of the sequences from twenty eight PCR products demonstrates modifications, such as deletions and insertions, that distinguish maize mutants Ml - M4, M6 - M25 and M27 - M29 from the wild type sequence ZmGWDExon24 (nt 3030 3243 of SEQ ID NO: 1 (ZmGWD)): CLUSTAL 0(1.2.1) multiple sequence alignment for maize mutants Ml - M4, M6 - M25 and M27 - M29:

ZmGWDexon24 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60 Ml TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60 M2 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60 M3 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60 M4 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60 M6 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60 M7 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60 M8 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60 M9 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60

Ml 0 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60

Ml1 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60 M12 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60

Ml3 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60

Ml4 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60

Ml5 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60

Ml 6 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60

Ml7 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60

Ml 8 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60

Ml 9 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60 M2 0 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60 M21 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60 M22 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60 M23 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60 M24 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60 M25 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60 M27 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60 M2 8 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60 M2 9 TTGGCAGGTTATAAGCCCGGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60 ir'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k'k -66- PCT/US2015/052940 WO 2016/054039

ZmGWDexon24 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 101 110 119 120 120 120 120 120 120 120 116 120 120 173 173 167 158 164 172 169 167 158 174 156 176 156 148 132 148 163 172 172 172 140 163 180 172 171 157

TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGG Ml TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGG M2 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGG M3 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGG M4 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGG M6 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGG M7 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGG M8 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGG M9 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGG Ml0 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGG Ml1 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGG Ml2 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGG Ml3 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGG Ml4 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGG Ml5 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTAATTACAC

Ml 6 T GC T G T C C AG AAC AAAT C T T AT G AT AAAC C AAGGG AG AGG A-------------------

Ml7 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAGGG----------

Ml 8 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAA-GAGTGTCAAGGG Ml 9 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGG M2 0 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGG M21 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAAAT M22 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGG M2 3 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGG M2 4 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGG M2 5 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGG M27 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAGGGAGAGAT----

M2 8 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGG M2 9 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGAGTGTCAAGGG

ZmGWDexon24

AG AG G AAG AAAT AC C AG AT GG AG TAG TTGGTGTA-------AT T AC AC C T G AT AT GC C AG

Ml M2 M3 M4 M6 M7 M8 M9 M10 Mil M12 Ml 3 Ml 4 M15 Ml 6 M17 Ml 8 Ml 9 M2 0 M21 M2 2 M2 3 M2 4 M2 5 M2 7

AGAGGAAGAAATAC CAGAT GGAG TAG T T GGAAGA-------AATACAC C T GATAT GC CAG

AG AGG AAG AAAT AC C AG AT GG AG TAG T T G T T-------------AC AC C T G AT AT GC C AG

AGAGGAAGAAATACCAGATGGAGCACCT----------------------GATATGCCAG

AG AGG AAG AAAT AC C AG AT GG AG T AA----------------T T AC AC C T GATATGCCAG

AG AGG AAG AAAT AC C AG AT GG AG TAG T T GG T AA--------AT T AC AC C T GATATGCCAG

AG AGG AAG AAAT AC C AG AT GG AG TAG T T GG T-----------T T AC AC C T GATATGCCAG

AG AGG AAG AAAT AC C AG AT GG AG TAG T T GG T-------------ATGCCAGATATGCCAG

AG AGG AAG AAAT AC C AG AT GG AG TAG T T G----------------------GTATGCCAG

AGAGGAAGAAATAC CAGAT GGAG TAG T T GG T G TAA------AT TACAC C T GATATGCCAG AGAGGAAGAAATAC CAGAT GGAG TAG T T GG T G T CAG------------------------ AGAGGAAGAAATACCAGATGGAGTAGTTGGTGTCAGTCCGAGCAAGGAATAGCAAG---- AGAGGAAGAAATACCAGATGTTCTGTCTCATGTGTC------------------------

AGAGGAAGAATTACA--------------------------------CCTGATATGCCAG

CTGATATGC------------------------------------------------CAG

------AGAAATAC CAGAT GGAG TAG T T GG T-------GTAATTACACCTGATATGCCAG

AGAG GAAGAAATAC CAGAT GGAG TAG TTGGTGT-A------AT TACAC C T GATATGCCAG

AGAGGAAGAAATACCAGATGGAGTAGTTGGTGTA-------AT TACAC C T GATATGCCAG

AGAGGAAGAAATACCAGATGGAGTAGTTGGTGT--------ATTACACCTGATATGCCAG

AGAGGAAGAAATAC CAGAT GGAG TAG T T GG T G T--------ATTACACCTGATATGCCAG

CTTATGATAAACC----------------------------------------ATGCCAG

AG AGG AAG AAAT AC CAG AT GG AG TAG T T GG T G T G A-----------------TATGCCAG

AGAGGAAGAAATACCAGATGGAGTAGTTGGCAAAGATAAACCTTGCACCTGATATGCCAG

AGAGGAAGAAATAC CAGAT GGAG TAG T T GG T GA--------ATTACACCTGATATGCCAG

AGAGGAAGAAATAC CAGAT GGAG TAG T T GG---TA------ATTACACCTGATATGCCAG

------------ACCAGATGGAGTAGTTGG-------TGTAATTACACCTGATATGCCAG -67- PCT/U S2015/052940 WO 2016/054039 M2 8 AG AGG AAG AAAC AC C T GAT A----------------------------------TGCCAG 14 6 M29 AGAGGAAGAAATACCAGATGGAGTAGTTGG---TA------ATTACACCTGATATGCCAG 171 182) 16) 35) 19) 29) 37) 39) 20) 38) 18) 17) 23) 22) 21) 33) 12) 13) 14) 30) 27) 28) 24) 25) 26) 32) 15) 36) 40) maize

ZmGWDexon24 ATGTTCTGTCTCATGTGTCAGTCCGAGCAAGGAATAGCAAG 214 (SEQ ID NO

Ml ATGTTCTGTCTCATGTGTCAGTCCGAGCAAGGAATAGCAAG 214 (SEQ ID NO

M2 ATGTTCTGTCTCATGTGTCAGTCCGAGCAAGGAATAGCAAG 208 (SEQ ID NO

M3 ATGTTCTGTCTCATGTGTCAGTCCGAGCAAGGAATAGCAAG 199 (SEQ ID NO

M4 ATGTTCTGTCTCATGTGTCAGTCCGAGCAAGGAATAGCAAG 205 (SEQ ID NO

M6 ATGTTCTGTCTCATGTGTCAGTCCGAGCAAGGAATAGCAAG 213 (SEQ ID NO

M7 ATGTTCTGTCTCATGTGTCAGTCCGAGCAAGGAATAGCAAG 210 (SEQ ID NO

M8 ATGTTCTGTCTCATGTGTCAGTCCGAGCAAGGAATAGCAAG 208 (SEQ ID NO

M9 ATGTTCTGTCTCATGTGTCAGTCCGAGCAAGGAATAGCAAG 199 (SEQ ID NO

M10 ATGTTCTGTCTCATGTGTCAGTCCGAGCAAGGAATAGCAAG 215 (SEQ ID NO

Mil ATGTTCTGTCTCATGTGTCAGTCCGAGCAAGGAATAGCAAG 197 (SEQ ID NO

M12 -----------------------------------------176 (SEQ ID NO

Ml3 AGTCCGAGCAAGGAATAGCAAG 178 (SEQ ID NO

Ml4 ATGTTCTGTCTCATGTGTCAGTCCGAGCAAGGAATAGCAAG 189 (SEQ ID NO

Ml5 ATGTTCTGTCTCATGTGTCAGTCCGAGCAAGGAATAGCAAG 173 (SEQ ID NO

Ml6 ATGTTCTGTCTCATGTGTCAGTCCGAGCAAGGAATAGCAAG 189 (SEQ ID NO

M17 ATGTTCTGTCTCATGTGTCAGTCCGAGCAAGGAATAGCAAG 204 (SEQ ID NO

Ml8 ATGTTCTGTCTCATGTGTCAGTCCGAGCAAGGAATAGCAAG 213 (SEQ ID NO

Ml9 ATGTTCTGTCTCATGTGTCAGTCCGAGCAAGGAATAGCAAG 213 (SEQ ID NO

M20 ATGTTCTGTCTCATGTGTCAGTCCGAGCAAGGAATAGCAAG 213 (SEQ ID NO

M21 ATGTTCTGTCTCATGTGTCAGTCCGAGCAAGGAATAGCAAG 181 (SEQ ID NO

M22 ATGTTCTGTCTCATGTGTCAGTCCGAGCAAGGAATAGCAAG 204 (SEQ ID NO

M23 ATGTTCTGTCTCATGTGTCAGTCCGAGCAAGGAATAGCAAG 221 (SEQ ID NO

M24 ATGTTCTGTCTCATGTGTCAGTCCGAGCAAGGAATAGCAAG 213 (SEQ ID NO

M25 ATGTTCTGTCTCATGTGTCAGTCCGAGCAAGGAATAGCAAG 212 (SEQ ID NO

M27 ATGTTCTGTCTCATGTGTCAGTCCGAGCAAGGAATAGCAAG 198 (SEQ ID NO

M28 ATGTTCTGTCTCATGTGTCAGTCCGAGCAAGGAATAGCAAG 187 (SEQ ID NO

M29 ATGTTCTGTCTCATGTGTCAGTCCGAGCAAGGAATAGCAAG 212 (SEQ ID NO

[0155] The amino acid sequences of GWD from twenty nine transgenic events and a wild type plant were analyzed and showed deletions and insertions in the wild type ZmGW (SEQ ID NO: 185) protein in the positions of amino acids 1040 - 1120 that distinguish this protein from maize mutants

ZmGWD_Ml (SEQ ID NO: 45), ZmGWD_M2 (SEQ ID NO: 46), ZmGWD_M3 (SEQ ID NO: 47), ZmGWD_M4 (SEQ ID NO: 48), ZmGWD_M5 (SEQ ID NO: 49), ZmGWD_M6 (SEQ ID NO: 50), ZmGWD_M7 (SEQ ID NO: 51), ZmGWD_M8 (SEQ ID NO: 52), ZmGWD_M9 (SEQ ID NO: 53), ZmGWD_Ml0 (SEQ ID NO: 54), ZmGWD_Mll (SEQ ID NO: 55), ZmGWD_M12 (SEQ ID NO: 56), ZmGWD_M13 (SEQ ID NO: 57), ZmGWD_M14 (SEQ ID NO: 58),

ZmGWD_M15 (SEQ ID NO: 59), ZmGWD_Ml6 (SEQ ID NO: 60), ZmGWD_M17 (SEQ ID NO: 61), ZmGWD_Ml8 (SEQ ID NO: 62), ZmGWD_M19 (SEQ ID NO: 63), ZmGWD_M20 (SEQ ID NO: 4), -68- PCT/U S2015/052940

ZmGWD_M21 (SEQ ID NO: 65), ZmGWD_M22 (SEQ ID NO: 66), ZmGWD_M23 (SEQ ID NO: 67), ZmGWD_M24 (SEQ ID NO: 68), ZmGWD_M25 (SEQ ID NO: 69), ZmGWD_M26 (SEQ ID NO: 70), ZmGWD_M27 (SEQ ID NO: 71), ZmGWD_M28 (SEQ ID NO: 72), and WO 2016/054039

ZmGWD_M29 (SEQ ID NO: 73).

[0156] CLUSTAL 0(1.2.1) multiple sequence alignment of ZmGWD (SEQ ID NO: 43) amino acids 1040 -1120:

ZmGWD ZmGWD_Ml ZmGWD_M2 ZmGWD_M3 ZmGWD_M4 ZmGWD_M5 ZmGWD_M6 ZmGWD_M7 ZmGWD_M8 ZmGWD_M9 ZmGWD_M10 ZmGWD_Mll ZmGWD_M12 ZmGWD_M13 ZmGWD_M14 ZmGWD_Ml5 ZmGWD_Ml6 ZmGWD_M17 ZmGWD_M18 ZmGWD_M19 ZmGWD_M20 ZmGWD_M21 ZmGWD_M22 ZmGWD_M23 ZmGWD_M24 ZmGWD_M25 ZmGWD_M26 ZmGWD_M27 ZmGWD_M28 ZmGWD M2 9

ZmGWD ZmGWD_Ml ZmGWD_M2 ZmGWD_M3 ZmGWD_M4 ZmGWD_M5 ZmGWD_M6 ZmGWD_M7 ZmGWD_M8 ZmGWD_M9 ZmGWD_M10 ZmGWD_Mll ZmGWD_M12 ZmGWD_M13 ZmGWD_M14 ZmGWD_M15 ZmGWD_Ml6 ZmGWD Ml7 PTILVAKSVKGEEEIPDGWGVITPDMPD----------VLS---HV---------SVR- PTILVAKSVKGEEEIPDGWGRNTPDMPD----------VLS---HV---------SVR- PTILVAKSVKGEEEIPDGV—WTPDMPD----------VLS---HV---------SVR- PT ILVAKSVKGEEE IPDGA-----PDMPD----------VLS---HV---------SVR- PT ILVAKSVKGEEE IPDG---VITPDMPD----------VLS---HV---------SVR-

PTILVAKSVKGEEEIPDGWAELLNSFIIELYDDALLDCIILMLNHILMIVGTCSPMQGD

PTILVAKSVKGEEE IPDGWGKLHLICQM----------FCL---MCQSEQGIARYCLRP

PTILVAKSVKGEEE IPDGWG-LHLICQM----------FCL---MCQSEQGIARYCLRP PTILVAKSVKGEEE IPDGV—VGMPDMPD----------VLS---HV---------SVR- PT ILVAKSVKGEEE IPDGV-----VGMPD----------VLS---HV---------SVR- PTILVAKS VKGEEEIPDGWGVNYT *---------------------------------- PTI LVAKS VKGEEE IPDGWGVRC SVSCVS PSKE*------------------------- PTILVAKSVKGEEE IPDGWGVSPSK-------E *------------------------- PTILVAKSVKGEEE I------------PD----------VLS---HV---------SVR-

PT ILVAKSVKGEEE--------LHLICQM----------FCL---MCQSEQGIARYCLRP PTILVAKSNYT*------------------------------------------------ p--------RERKKYQME*----------------------------------------- PTIL VARERKKYQME *----------------------------------------- PTILVARVSRERKKYQME *-----------------------------------------

PT I LVAKS VKGEEE IPDGWG-VHLI CQM----------FCL---MCQSEQGIARYCLRP

PTILVAKSVKGEEE IPDGWGVLHLI CQM----------FCL---MCQSEQGIARYCLRP PTILVAKSVKIL *-----------------------------------------------

PT I LVAKS VKGEEE IPDGWG---VICQM----------FCL---MCQSEQGIARYCLRP PT I LVAKS VKGEEE IPDGWGKDKPCT*--------------------------------

PT I LVAKS VKGEEE IPDGWGELHLI CQM----------FCL---MCQSEQGIARYCLRP PTILVAKSVKGEEE IPDGWGNYT *-----------------------------------

PTILVAKSVKGEEEIPDGAVCSGTASYFNVSS-GRLTSMFVFFFK-CRNRESSCKYLLYE PT ILVA-----RERYQME *----------------------------------------- PTILVAKSVKGEEE---------TPDMPD----------VLS---HV---------SVR- PT ILVAKSVKGEEE I PDGWGNYT *----------------------------------- SEQ : ID NO: 185) (SEQ ID NO: 45) (SEQ ID NO: 46) (SEQ ID NO: 47) (SEQ ID NO: 48) (SEQ ID NO: 49) (SEQ ID NO: 50) (SEQ ID NO: 51) (SEQ ID NO: 52) (SEQ ID NO: 53) (SEQ ID NO: 54) (SEQ ID NO: 55) (SEQ ID NO: 56) (SEQ ID NO: 57) (SEQ ID NO: 58) (SEQ ID NO: 59) (SEQ ID NO: 60) (SEQ ID NO: 61)

-------ARNSKVLFATCFDHTTLSELEGYDQKLFSFKPTSADiCTYREiCTE

-------ARNSKVLFATCFDHTTLSELEGYDQKLFSFKPTSADITYREITE

-------ARNSKVLFATCFDHTTLSELEGYDQKLFSFKPTSADITYREITE -------arnskvlfaxcfdhxxlselegydqklfsfkptsadixyreixe -------arnskvlfaxcfdhxxlselegydqklfsfkpxsadixyreixe ---PTGVCRNVNRVFARDGNSSVNLASHGHCAGVFNYT*----------- VL-TTPLYLNLKDMIRNCFPSSLLLQI*----------------------- VL-TTPLYLNLKDMIRNCFPSSLLLQI*-----------------------

-------ARNSKVLFATCFDHTTLSELEGYDQKLFSFKPTSADITYREITE

-------ARNSKVLFATCFDHTTLSELEGYDQKLFSFKPTSADITYREITE

-------ARNSKVLFATCFDHTTLSELEGYDQKLFSFKPTSADITYREITE VL-TTPLYLNLKDMIRNCFPSSLLLQI*----------------------- -69- PCT/US2015/052940 WO 2016/054039

ZmGWD_M18 --------------------------------------------------- (SEQ ID NO: 62)

ZmGWD_Ml9 VL-TTPLYLNLKDMIRNCFPSSLLLQI*----------------------- (SEQ ID NO: 63)

ZmGWD_M20 VL-TTPLYLNLKDMIRNCFPSSLLLQI*----------------------- (SEQ ID NO: 64)

ZmGWD_M21 --------------------------------------------------- (SEQ ID NO: 65)

ZmGWD_M22 VL-TTPLYLNLKDMIRNCFPSSLLLQI*----------------------- (SEQ ID NO: 66)

ZmGWD_M23 --------------------------------------------------- (SEQ ID NO: 67)

ZmGWD_M24 VL-TTPLYLNLKDMIRNCFPSSLLLQI*----------------------- (SEQ ID NO: 68)

ZmGWD_M25 --------------------------------------------------- (SEQ ID NO: 69)

ZmGWD_M26 KDSYLEICEQNYPQLLGKTKK—K-----VPSNIYSMTTSV YYT* (SEQ ID NO: 70)

ZmGWD_M27 --------------------------------------------------- (SEQ ID NO: 71)

ZmGWD_M28 -------ARNSKVLFATCFDHTTLSELEGYDQKLFSFKPTSADITYREITE (SEQ ID NO: 72)

ZmGWD_M29 --------------------------------------------------- (SEQ ID NO: 73) [0157] For Sorghum bicolor, two meganuclease constructs were used to create GWD mutations, 4715 and 4716. First generation (TO) transformed plants could result in homozygous GWD mutants, hemizygous (WT + mutation) GWD mutants, or heterozygous (2 different mutations; e.g., allele 1 + allele 2) GWD mutants. The following abbreviations were used: del=deletion; ins=insertion; sub=substitution; SbGWD CDS is wild type sequence. For example, the sequence name “Sb4715_l (WT+ins)” has the following meaning: Sb4715 is the construct in Sorghum bicolor, 1 is the transgenic event: WT+ins indicates that TO event 4715_1 was hemizygous for a GWD mutation, carrying a WT GWD allele and an insertion (ins) GWD allele. The same construct was used for transformation of Zea mays (Zm).

[0158] CLUSTAL nucleic acid alignment between Sorghum bicolor (Sb) GWD sequence and Sorghum bicolor GWD mutants Sb475_l (WT+ins) and Sb4715_2 (WT+del) showed alterations in the sequences of the mutants compared to wild type SbGWD sequence. The SbGWD_exon24 sequence is positioned within nt 3030 - 3243 the SbGWD coding sequence (SEQ ID NO: 2). The sequence of Sb475_l (WT+ins) includes a 13 nucleotide insertion in the position 3139-3149 of SbGWD and a nucleotide substitution in the position 3133-3136 of SbGWD.

[0159] As shown below, an alignment of the sequences from the three PCR products demonstrates insertions and deletions that differentiate Sb4715_l (WT+ins) and Sb4715_2 (WT+del) and SbGWD exon 24 regions. CLUSTAL 0(1.2.1) multiple sequence alignment:

SbGWD Exon24 IIGGCAGGIIAIAAGCCCAGTTGAAGIAICAGGIIATGTGGIIGIGGTTGATGAGIIACI 60 -70- WO 2016/054039 PCT/US2015/052940 TTGGCAGGTTATAAGCCCAGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60 TTGGCAGGTTATAAGCCCAGTTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGTTACT 60 ************************************************************ TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGA---------- 110 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGAGTAGTTGGTGTAGTT 12 0 TGCTGTCCAGAACAAATCTTATGATAAACCAACCATCCTTGTGGCAAAGA---------- 110 ---GTGTCAAGGGAGAGGAAGAAATACCAGATGGAGTAGTTGGTGTAATTACACCTGATA 167 GGTGTATCAAGGGAGAGGAAGAAATACCAGATGGAGTAGTTGGTGTAATTACACCTGATA 180 ---GTGTCAAGGGAGAGGAAGAAATACCAGATGGAG------------TTACACCTGATA 155 ** ****************************** ************

Sb4715_l (WT+ins)

Sb4715_2 (WT+del)

SbGWD_Exon24 Sb4715_l (WT+ins)

Sb4715_2 (WT+del)

SbGWD_Exon24 Sb4715_l (WT+ins)

Sb4715_2 (WT+del)

TGCCAGATGTTCTGTCCCATGTGTCAGTCCGAGC7VAGG7VATAGC7VAG214 (SEQ ID NO TGCCAGATGTTCTGTCCCATGTGTCAGTCCGAGCAAGGAATAGCAAG22 7 (SEQ ID NO IGCCAGAIGIICIGICCCAIGIGICAGICCGAGCAAGGAAIAGCAAG202(SEQ ID NO 183) 106) 107)

SbGWD_Exon24 Sb4715_l (WT+ins)

Sb4715_2 (WT+del) [0160] The prediction of the meganuclease mutant protein amino acid sequences were made using the sequence wild type SbGWD (SEQ ID NO: 44).

[0161] Example 5. Mutant plants accumulate elevated levels of green tissue starch [0162] Starch was assayed in the first generation (TO) transformed maize and sorghum GWD meganuclease plants. Tissues were collected, dried and milled to a fine powder. The starch content was determined by standard methods (Smith AM and Zeeman SC, Quantification of starch in plant tissues (2006) Nat Protocols 1: 11342-1345, which is incorporated herein by reference as if fully set forth). A total starch content was assayed by adapting the protocol from Megazyme International Ireland Ltd. (Megazyme kit and reagents; cat. #K-TSTA). Briefly, 85°C and 50°C heat blocks were set up.

From 5 to 15 mg of dry milled tissue were placed into the 1.5 ml boil-proof microcentrifuge tubes. One milliliter of 70% ethanol was added to each tube and samples were vortexed and pelleted. Four hundred microliters of solution 1 was added to each sample. Solution 1 included 1ml of the thermostable a- amylase and 29 ml of 100 mM sodium acetate buffer, pH5.0. The samples were

re-suspended and vortexed. Samples were incubated for 12 minutes at 85°C for 12 minutes, and cooled for 5 minutes at room temperature. Three hundred microliters of the GOPOD reagent (Megazyme kit, cat. #K-TST>) was preloaded into each well of the flat bottom 96 well assay plate. Ten microliters of

samples were added to each well and compared to 1 pL, 5 pL, 10 pL, and 20 pL of glucose standard (lmg/ml), which were also added to their respective wells. -71- PCT/US2015/052940 WO 2016/054039

The plate was incubated at 50°C for 20 min. Absorbance was assessed at 510 nm. Referring to FIG. 4, elevated starch is shown for mutants 4715_20 (two mutant alleles), 4716_7 (Ml), 4716_1 (Ml), 4716_18 (M20), 4716_12 (M3/M8), 4716_23 (M15), 4716_28 (not characterized), 4716_3 (M9/M6), 4716_22 (M5/M11), 4716_24 (M2/M14), 24716_25 (M10/M28), 4716_15 (M11/M12), 4716_5 (M7/M11), 4716_6 (M4/M14), 4716_27 (M11/M10), 4716_4 (M11/M12), 4716_26 (M11/M12), 4716_2 (M15), 4716_13 (M14), 4716_13 (M14), 4716_11 M11/M10), 4716_8 (Mil), 4716_10 (M11/M10), and 4716_14 (M13) compared to wild type plants WT_195, WT_18 and WT_6. Many of the homozygous and heterozygous events exhibited greater than 20% starch increase by weight in leaves. Based on a weighted average of starch accumulation in different tissues, we estimated total plant starch (not including grain) to be approximately 10% (weight/weight).

[0163] The levels were significantly higher was observed previously in maize using RNA interference technology, despite the low transcript abundance measured in those experiments. This was a surprising result as it was anticipated that RNAi based silencing would be dominant in the plant and have the same effect as a gene deletion or knock-out strategy.

[0164] FIG. 5 illustrates green tissue starch for selected hemizygous, homozygous, and heterozygous events. FIG. 5 shows mutation type and zygosity of transgenic corn events M17 (4715_14), M18 (4715_15), Ml (4716_1), M20 (4716_18), M3/M12 (4716_12), M9 (4716_3), M7/M11 (4716_5), M4/M14 (4716_6), M11/M12 (4716_4), M15 (4716_2), M14 (4716_13), Mil (4716_8), M11/M10 (4716_10) and M13 (4716_14) have elevated levels of starch compared to non-transgenic control WT (4716_9). It was observed that several events (4716_13 (M14), 4715_15 (M11/M12) and 4716_6 (M4/M14) have greater than average biomass.

[0165] Example 6. GWD knock-out (GWDko) cobs have increased starch levels [0166] TO GWDko and wild type (wt) maize mutant lines were selfed, developed to maturity, dried, and cross-sectioned for staining. Cob sections -72- PCT/US2015/052940 WO 2016/054039 were stained with Lugol’s solution (5% KI) for 4 min and destained with H2O overnight.

[0167] Mutant events 4716_13, 4716_26, 4716_167, 4716_164, 4716_9, and 4716-153 were analyzed for starch content. The results are shown in Table 5.

Table 5 Starch Content in Mutant Lines

Construct_Event Zygosity Green Tissue Starch Stover Starch 4716_13 Homo 229.7 38.5 4716_26 Hetero 220.7 35.3 4716_167 Hetero 112.0 31.7 4716_164 Hemi 30.5 4.0 4716_9 WT 18.8 8.4 4716_153 WT 5.7 1.2

Referring to Table 5 and FIG. 6, it was shown that homozygous (4716_13) and heterozygous (4716_26 and 4716_167) cobs had increased starch staining compared with hemizygous (4716_164) and wild type (4716_9 and 4716_153) cobs.

[0168] Example 7. Construction of CRISPR/Cas maize transformation vectors [0169] For constructing Cas9 expression cassette, the S. pyogenes Cas9 protein sequence containing N- and C-terminal At nuclear localization sequences (NLS) as well the 3xFLAG sequence positioned immediately after the first ATG codon (Jiang et al., 2013) (SEQ ID NO: 74) was chosen for expression in maize. The sequence of S. pyogenes Cas9 containing two SV40 nuclear localization sequences (shown in bold letters) and 3xFLAG sequence at N-terminal part (underlined sequence) for expression in maize is as follows:

MDYKDHDGDYKDHDIDYKDDDDKMAPKKKRKVGIHGVPAADKKYSIGLDIGTNSVGWAVITDEYKVPSKKFK

VLGNTDRHSIKKNLIGALLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESF -73- PCT/US2015/052940 WO 2016/054039 LVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPD NSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLT PNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSASM IKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKL NREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWM TRKSEETITPWNFEEWDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKP AFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFLDN EENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILD FLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKWDELVKVMGR HKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVD QELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEWKKMKNYWRQLLNAKLITQRKF DNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKD FQFYKVREINNYHHAHDAYLNAWGTALIKKYPKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSN IMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPK RNSDKLIARKKDWDPKKYGGFDSPTVAYSVLWAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAK GYKEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQL FVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFDT TIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGDRPKKKRKVGG (SEQ ID NO: 74) [0170] The sequence was back translated and maize codon optimized to produce ZmCas9 (SEQ ID NO: 75). The optimized ZmCas9 nucleotide sequence was synthesized by Genscript. The ZmCas9 was cloned as BamHI-Avrll fragment between maize ubiquitin 1 promoter (ZmUbilP) and nopaline synthase transcriptional terminator (NosT) sequences into pAG4500 to produce pAG4800.

[0171] The work on construction of sgRNA cassettes involved: 1) identification and isolation of a maize RNA Polymerase III promoter to drive expression of sgRNA; 2) design and synthesis of sgRNA scaffold; and 3) selection of a target gene and 20 bp specific sequences within this gene for guiding Cas9 endonuclease to its target sites.

[0172] The first description of a maize sequence encoding U3 small nuclear RNA (U3snRNA) was reported by Leader et al. in 1994, who isolated MzU3.8 gene (Genebank Accession No. Z29641) (SEQ ID NO: 76) from a maize genomic DNA library and demonstrated that the MzU3.8 U3snRNA is expressed in maize protoplasts. Using BLASTN algorithm and Z29641 sequence to search the Maize Genetics and Genomics Database (http://www.maizegdb.org/) we identified a homologous sequence of maize U3 that was labeled as ZmU3 (SEQ ID NO: 77).

[0173] The ZmU3 is localized on the maize chromosome 8 and is contained within a sequence with nucleotide coordinates 163620300 - -74- WO 2016/054039 PCT/US2015/052940 163621800. The CLUSTAL 2.1 multiple nucleotide sequence alignment of putative promoter regions of MzU3.8 (SEQ ID NO: 78) and ZmU3 (SEQ ID NO: 79) demonstrated 93.8% identity between the two sequences. CLUSTAL 2.1 multiple sequence alignment:

MzU3.i ZmU3 GAATTCCATCTAAGTATCTTGGTAAAGCATGGATTAATTTGGATGCTCACTTCAGGTCTA GAATTCCATCTAAGTATGTTGGTAAAGCATGGATTAATTTGGATGCCCACTTCAGGTCTA -k-k-k-k-k-k-k-k-k-k-k-k-k-k-k-k-k kkkkkkkkkkkkkkkkkkkkkkkkkkkk kkkkkkkkkkkkk 60 60

MzU3.8 ZmU3

MzU3.8 ZmU3 TGCAGCTCCGGTGCCTTGTGATTGTGAGTTGTGACCGATGCTCATGCTATTTTGCATTTC TGCAGCTCCGGTGCCTTGTGATTGTGAGTTGTGACCGATGCTCATGCTATTCTGCATTTC kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk kkkkkkkk TGCGATGTATGATGCTAGTAGATCTTCAAAACTAACAGCGCATGCCATCATCATCCACTG TGCGATGTATGTAGCTAGTAGATCTTCAAAACTAACACCGCATGCCATCATCATCCACTG kkkkkkkkkkk kkkkkkkkkkkkkkkkkkkkkkkk kkkkkkkkkkkkkkkkkkkkkk 120 120 180 180

MzU3.8 ZmU3 MzU3.8 ZmU3

CTTGATTTTAGTCTCACCGCTGGCCAAAAATGTGATGATGCCAGAAACCTCAACTACCTT CTTGATTTTAGTCTCACCGCTGGCCAAAAATGTGATGATGCCAGAAACCTCAACTACCTT kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk GAATCAACACGGGCCCAGCAGTGTGATGACGACAGAAACCAAAAAAAAATGAGCCAATAG GAATCAACACGGGCCCAACAGTGTGATGACGACAGAAAC-AAAAAAAAATGAGCCAATAG 240 240 300 299 kkkkkkkkkkkkkk·) ^kkkkkkkkkkkkkkkkkkk kkkkkkkkkkkkkkkkkkkk

MzU3.8 ZmU3

TTCAGAAGGAGGCACTATGCAGAAACTACATTTCTGAAGGTGACTAAAAGGTGAGCGTAG TTCAGAAGGAGGCACTATGCAGAAACTACATTTCTGAAGGTGACTAAAAGGTGAGCGTAG 360 359 ^kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk

MzU3.i ZmU3

MzU3.i ZmU3

MzU3.8 ZmU3

MzU3.8 ZmU3 AGTGTACTTACTAGTAGTTTAGCCACCATTACCCAAATGCTTTCGAGCTTGTATTAAGAC AGTGTAATTACTAGTAGTTTAGCCACCATTACCCAAATGCTTTCGAGCTTGTATTAAGAT k k k k k kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk TTCCTAAGCTGAGCATCATCACTGATCTGCAGG—AGGGTCGCTTCGCTGCCAAGATCAA TTCCTAAGCTGAGCATCATCACTGATCTGCAGGCCACCCTCGCTTCGCTGCCAAGATCAA ★ ★★★★★★★★★★-λ'·*''*''*''*''*''*''*''*·'*··*··*··*··*··*··*··*··*··*··*··*··*· ★ ★★★★★★★★★★★★★★★★★★★★★ CAGCAACCATGTGGCGGCAACATCCAGCATTGCACATGGGCTAAAGATTGAGCTCTGTGC CAGCAACCATGTGGCGGCAACATCCAGCATTGCACATGGGCTAAAGATTGAGCTTTGTGC ★ ★★★★★★★'Jr'Jr'Jr'Jr'Jr'Jr'Jr'Jr'Jr'Jr'Jr'Jr'Jr·*··*··*··*··*··*··*··*··*··*··*··*··*··*··*··*··*··*··*··*··*··*··*··*··*··*··*··*··*··*··*··*··*· ★★★★★ CAAGTGTGAGCTGCAACCATCTAGGGATCAGCTGAGTTTATCAGTCTTTCCTTTTTTTCA C---------------TCGTCTAGGGATCAGCTGAGGTTATCAGTCTTTCCTTTTTTTCA k k kkkkkkkkkkkkkkkkk kkkkkkkkkkkkkkkkkkkkkkk 420 419 478 479 538 539 598 584

MzU3.8 ZmU3 TTCTGGTGAGGCATCAAGCTACTACTGCCTCGATCGGTTGGACTTGGACCTGAAGCCCAC TCCAGGTGAGGCATCAAGCTACTACTGCCTCGATTGGCTGGA------CCCGAAGCCCAC -k ·k kkkkkkkkkkkkkkkkkkkkkkkkkkkkkk k k ★★★★ ★★ 658 638

MzU3.8 ZmU3 ATGTAGGATACCAGAATGGACCGACCCAGGACG-------------------------TA ATGTAGGATACCAGAATGGGCCGACCCAGGACGCAGTATGTTGGCCAGTCCCACCGGTTA 'JIr'Jr'Jr'Jr'Jr'Jr'Jr'Jr'Jr'Jr'Jr'Jr'Jr'Jr'Jr'Jr'Jr'Jr'Jr ·**·*·*·*·*·*·*·*·*·*·*·★ -Jr·*· 693 698

MzU3.8 ZmU3 GTGCCACCTCGGTTG-TCACACTGCGTAGAAGCCAGCTTAAAAATTTAGCTTTGGTGACT GTGCCATCTCGGTTGCTCACA-TGCGTAGAAGCCAGCTTAAAAATTTAGCTTTGGTAACT 'Jr'Jr'Jr'Jr'Jr'Jr'Jr'Jr ★★★★★★★★★★★★★★★★★★★★★★★★★★★★★★★★★★ ·*** 752 757

MzU3.8 ZmU3 CACAGCA 759 (SEQ ID NO: 78) CACAGCA 764 (SEQ ID NO: 79) ******* -75- PCT/US2015/052940 WO 2016/054039 [0174] Using a PCR approach with the forward primer ob2297 (SEQ ID NO: 80) and reverse primer ob2299 (SEQ ID NO: 81), the 758 bp ZmU3 promoter (ZmU3Pl) (SEQ ID NO: 82) was subsequently isolated from maize genomic DNA of the maize line AxB. The forward primer ob2297 included AsiSI restriction site at its 5’ end to facilitate cloning an sgRNA cassette into a pAG4500-based vector. Similarly, using a forward primer ob2343 (SEQ ID NO: 83), which contained AsiSI restriction site at its 5’ end, a shorter 398 bp version of the maize U3 promoter (ZmU3P2) (SEQ ID NO: 84) was isolated for testing efficiency of a truncated maize U3 promoter. An additional variant of the ZmU3P2 was amplified with the forward primer ob2351 (SEQ ID NO: 85) that has the Swal restriction enzyme site at its 5’ end. Furthermore, a 308 bp control promoter fragment ZmU3.8P (SEQ ID NO: 86) was PCR synthesized using long primers that were designed on a MzU3.8 sequence published by Leader et al. (1994), which was shown to be expressed in maize protoplasts. The ZmU3.8P sequence also included AsiSI restriction site at the 5’ end. All amplified promoter variants were cloned into pCR-Bluntll-TOPO vector (Life Technologies) and their integrity was confirmed by complete sequencing.

[0175] The sgRNA scaffold design herein is based on the published organization of an sgRNA chimera (Larson et al., 2013) and includes a 42 bp Cas9 handle hairpin (SEQ ID NO: 87) followed by a 41 bp S. pyogenes terminator (SEQ ID NO: 88). In order to improve efficiency of transcriptional termination in maize, a 37 bp putative transcription terminator sequence ZmU3T (SEQ ID NO: 89) was isolated from ZmU3 snRNA (SEQ ID NO: 77) and fused downstream of the S. pyogenes terminator (SEQ ID NO: 88). The 120 bp sgRNA scaffold (SEQ ID NO: 90) was synthesized by PCR using long primers and KOD Xtreme DNA Polymerase with the proof reading activity. The SnaBI or AscI restriction sites were added at the 3’ end of the two PCR-amplified sgRNA backbone DNA fragments to facilitate further cloning. The sgRNA scaffold DNA fragments synthesized in this way were cloned into pCR-BluntII-ΤΟΡΟ vector and sequence validated. -76- PCT/U S2015/052940 WO 2016/054039 [0176] For testing efficiency of the CRISPR/Cas system in maize, a maize gene encoding GWD was selected for the initial targeted modifications.

[0177] The maize GWD gene has been annotated earlier and was screened for the presence of AN19NGG target sequences on both sense and antisense DNA strands. The 5’ end “A” in AN19NGG sequence represents a conserved “Adenine” nucleotide at the transcription start of the U3 RNA Polymerase III promoter, the 3’ end positioned “NGG” sequence corresponds to the required for CRISPR/Cas system activity protospacer-adjacent motif (PAM) sequence. The candidate target sequences identified in exons 1, 24, and 25 as well as in their flanking introns were further screened against Maize GDB in order to eliminate sequences that have multiple identity hits within the maize genome. This work has been done to minimize chances for off-target activity of the CRISPR/Cas system. In this analysis, only the seed sequence (12 bp) of the target sequence plus two adjacent PAM nucleotides were used in BLASTN program as it was proposed by Larson et al. (2013). Exon 1 was selected for producing an almost complete GWD knockout, while exons 24 and 25 were chosen to generate GWD variants lacking an active site that is encoded by exon 24. A list of the final 19 bp GWD target sequences (SEQ ID NOS: 131-134), which were identified for sgRNA development, is compiled in Table 6.

Table 6 GWD Gene Target Sequences With Their Corresponding SEQ ID NOS SEQ ID NO Sequence name Sequence GWD strand 91 GWDela GGCATGAGGTGCTTACGTC antisense 92 GWDe24b CATAACCTGATACTTCAAC antisense 93 GWDe24c TCTGGCTCCTGCTATCAGT sense 94 GWDe25a TCTGCAGAAGTAGGCTTGA antisense [0178] Each of the three variants of the maize U3 promoter, selected GWD target sequences and sgRNA backbone were assembled together by the means of fusion PCR using KOD Xtreme DNA Polymerase to construct six sgRNA expression cassettes (SEQ ID NOS: 135-140). The PCR-amplified -77- PCT/US2015/052940 WO 2016/054039 fragments were cloned into pCR-Bluntll-TOPO vector and the integrity of the synthesized sgRNA expression cassettes was verified through sequencing. The list of the PCR-synthesized sgRNA cassettes is presented in Table 7.

Table 7 The Synthesized sgRNA Expression Cassettes with Their Corresponding SEQ ID NOS

SEQ ID NO sgRNA cassette Flanking restriction sites 95 ZmU3Pl:sgRNA_GWDe24b AsiSI-SnaBI 96 ZmU3P2:sgRNA_GWDe24b AsiSI-SnaBI 97 ZmU3.8P:sgRNA_GWDe24b AsiSI-SnaBI 98 ZmU3P2:sgRNA_GWDe24c AsiSI-SnaBI 99 ZmU3P2:sgRNA_GWDe25a Swal-AscI 100 ZmU3P2:sgRNA_GWDela AsiSI-SnaBI

[0179] Assembled sgRNA cassettes were subsequently cloned as AsiSI-SnaBI fragments into pAG4800 to develop vectors pAG4804-4809 (Table 8).

Table 8 Vectors Developed for Maize CRISPR/Case System with SEQ ID NOS

Plasmid Genetic elements pAG4800 UbilP:Cas9 pAG4804 U3Pl:sgRNA_GWDe24b + UbilP:ZmCas9 pAG4805 U3P2:sgRNA_GWDe24b + UbilP:ZmCas9 PAG4806 U3.8P:sgRNA_GWDe24b + UbilP:ZmCas9 PAG4807 U3P2:sgRNA_GWDe24c + UbilP:ZmCas9 pAG4808 U3P2:sgRNA_GWDela + UbilP:ZmCas9 pAG4809 U3P2:sgRNA_GWDe25a + UbilP:ZmCas9 pAG4817 U3P2:sgRNA_GWDe25a + U3P2:sgRNA_GWDe24c + UbilP:ZmCas9 [0180] One additional vector pAG4817 containing two sgRNA expression cassettes was constructed by cloning ZmU3P2:sgRNA_GWDe25a cassette as

Swal-AscI fragment into pAG4807. This vector was developed for complete -78- PCT/US2015/052940 WO 2016/054039 removal of the GWD exon 24 by targeting Cas9 endonuclease to two different sites that are located 364 bp apart within the maize GWD gene and flank exon 24.

[0181] The maps of the plant transformation vectors pAG4800 and pAG4804, which were constructed for development of CRISP/Cas system for maize are shown on FIGS. 7 - 8. Referring to FIG. 7, the pAG4800 vector includes the Cas9 expression cassette and the PMI expression cassette. The Cas9 expression cassette comprises a nucleotide sequence of ZmCas9 (SEQ ID NO: 75). ZmCas9 is a maize codon optimized sequence of the S. pyogenes gene encoding Cas9 fused to two At NLS at 5’ and 3’ ends and 3xFLAG sequence immediately after the first ATG codon. Zm Cas9 encodes the S. pyogenes Cas9 protein (SEQ ID NO: 74) containing two At nuclear localization sequences and 3xFLAG sequence at N-terminal part for expression in maize. The Cas9 cassette also includes the Zm Ubil promoter, Zm Ubil intron, mUBQMono leader, and the NosT terminator. The PMI cassette includes the PMI gene, ZmUbil promoter, mUBQMono, ZmKozak leaders and the NosT terminator. Referring to FIG. 8, the pAG4804 vector includes the GWDe24b-sgRNA scaffold cassette, the Cas9 expression cassette, and the PMI expression cassette. The GWDe24b-sgRNA scaffold cassette includes ZmU3Pl promoter, GWDed24 sequence, the sgRNA scaffold and ZmU3T terminator. The Cas9 expression cassette comprises ZmCas9 fused to two At NLS at 5’ and 3’ ends and 3xFLAG sequence immediately after the first ATG codon. The Cas9 cassette also includes the Zm Ubil promoter, Zm Ubil intron, mUBQMono leader, and the NosT terminator. The PMI cassette includes the PMI gene, ZmUbil promoter, mUBQMono, ZmKozak leaders and the NosT terminator.

[0182] Example 8. Generation of CRISPR/Cas-induced mutant plants [0183] Identification and Characterization of CRISPR/Cas and Maize NLS Meganuclease-induced Mutations in the Maize GWD Gene [0184] Maize plant transformation was performed according to the protocol described in Example 3. Screening of CRISPR/Cas-induced mutations was similar to screening of meganuclease-induced mutations methods that has -79- PCT/U S2015/052940 WO 2016/054039 been described in Example 3 with the exception of primers for genotyping and identifying mutations.

[0185] Table 9 describes primers for genotyping CRISPR/Cas plants that include 4804-4806, 4804-6 primer set; 4809, 4817, and 4804-6 primer set substituting GWDe24a-F for GWD24b-F and primers for amplifying DNA sequences surrounding the GWD meganuclease targeting region that include 4804-4807, 4804-7mut primers; 4817, 2856/2858 primers; 4837-4839, 371/429 primers.

Table 9 Primers for genotyping 4804, 4805, 4806, 4817, 4837, 4838, and 4839 plants and amplifying DNA sequences surrounding the GWD exon 24 targeting region

Primer Set Primer Name Forward or Reverse Sequence SEQ ID NO Product size (bp) 4804-6 GWDe24b-F Forward CTCACAGCACATAA CCTGATACT 101 100 4804-6 sgRNA-R Reverse CGACTCGGTGCCAC TTT 102 100 4804-6 ZmCas9-F Forward AGAATCAGACCACG CAGAAG 103 186 4804-6 ZmCas9-R Reverse GCTCCTGGTCGACA TACATATC 104 186 4809/4817 GWDe24a-F Forward TGCAGAAGTAGGCT TGAGTTT 110 89 4804-7mut GWDex23-F Forward TGCTCTTCTGAACC GATTTGA 105 560 4804-7mut ZmGWD mega-2R Reverse CTATTCCTTGCTCG GACTGAC 13 560 4817 2856 Forward GAAGGGGATTGGAG AGGAAG 111 613 4817 2858 Reverse CATGACGTTCAAAT AGCCTCA 112 613 4837-4839 371 Forward GGTTATAAGCCCGG TTGAAGTA 12 381 -80- WO 2016/054039 PCT/US2015/052940

Primer Set Primer Name Forward or Reverse Sequence SEQ ID NO Product size (bp) 4837-4839 429 Reverse GCAGAAGTAGGCTT GAAGGAA 113 381 [0186] Similar to previous analyses, DNA sequences for each mutant were compared to WT GWD using Vector NTI Advance (Version 11.5; Life Technologies). Mutant DNA sequences are described in Table 10.

[0187] Transgenic maize plants carrying gene editing constructs that target regions of the GWD gene have been produced and are being analyzed for mutations in the target regions of the GWD gene. GWD mutations and predicted proteins are listed in Tables 11-14. In these tables, events carrying two different GWD mutant alleles (heterozygotes) are labeled with -1 or -2, to indicate the individual alleles. Intronic sequences are presented in lowercase letters and exons 24 or 25 are shown in uppercase letters. Since pAG4817 is targeting two different locations within ZmGWD, two mutations are provided for 4817_2 and 4817_52. The first target sequence is located just upstream of the 5’end of the exon 24 and an extra “T” that is inserted into this target location is shown as a capital letter “T” within lowercase letters specific to intron 23 (see M37 sequence). M37 is an identical modification in 4817_2 and 4817_52.

[0188] All modifications introduced by CRISPR/Cas9 are highlighted (bold black = insertion; gray = deletion) and missing nucleotides are shown by dots. Corresponding numbers of deleted or inserted nucleotides are presented in the last columns of Tables 11 and 12.

[0189] Similarly, all changes to deduced protein sequences for M32-M39 are highlighted. In the cases of translation reading frame shifts and early termination of translation, all amino acids differing from wild type GWD are also highlighted and the end of protein is indicated by an asterisk (*). -81- PCT/US2015/052940

Table 10 CRISPR/Cas9 induced mutations in individual transgenic 4804, 4806, and 4817 events

Mutation Events and alleles M32 4804_2, 4804_3-2, 4804_4-l, 4804_5-2, 4806_1 M33 4804_3-l, 4804_5-l, 4804_7-l M34 4804_4-2 M35 4804_6 M36 4804_7-2 M37, M38 4817_2 M37, M39 4817_52

Table 11 Nucleotide sequences of CRISPR/Cas9 induced mutations in individual 4804 and 4806 events

Sequence Description DNA sequence SEQ ID NO Del/Ins number WT ZmGWD Exon 24* gctcctgctatcagTTGGCAGGTTATAAGCCCGGT TGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGT TACTTG 186 None M32 gctcctgctatcagTTGGCAGGTTATAAGCCCGGT T|GAAGTATCAGGTTATGTGGTTGTGGTTGATGAG TTACTTG 114 +1 M33 gctcctgctatcagTTGGCAGGTTATAAGCCCGGT T..AGTATCAGGTTATGTGGTTGTGGTTGATGAGT TACTTG 115 -2 M34 gctcctgctatcagTTGGCAGGTTATAAGCCCGGT T...GTATCAGGTTATGTGGTTGTGGTTGATGAGT TACTTG 116 -3 M35 gctcctgctatcagTTGGCAGGTTATAAGCCCGGT ,GAAGTATCAGGTTATGTGGTTGTGGTTGATGAGT TACTTG 117 -1 M36 gctcctgctatcagTT|§||§.....1111· · 1111 · · 1 ......iiliilf. . lillllGCTTGTGGTTGATGAGT TACTTG 118 -37 *WT ZmGWD is a region of nt 81-160 of Exon 24 (SEQ ID NO: 3) WO 2016/054039 -82- PCT/US2015/052940

Table 12 Nucleotide sequences of CRISPR/Cas9 induced mutations in individual 4817 events

Sequence Description DNA sequence SEQ ID NO Del/Ins number WtZm GWD Exon 24* gctcctgctatcagTTGGCAGGTTATAAGCCCGGT TGAAGTATCAGGTTATGTGGTTGTGGTTGATGAGT TACTTG 187 None M37 gctcctgctatc||agTTGGCAGGTTATAAGCCCGG TTGAAGTATCAGGTTATGTGGTTGTGGTTGATGAG TTACTTG 188 +1 Wt ZmGWD Exon 25 CAC T C TAT C T GAACT T GAAGGATAT GAT CAGAAAC TGTTTTCCTTCAAGCCTACTTCTGCAGATATA 189 None M38 c ac τ c τ at c τ g...............wmmmmmm ........................CAC-ATATA 119 -48 M39 CAC T C TAT C T GAAC Τ T GAAGGATAT GAT CAGAAAC TGTTTTCCTTCAiAGCCTACTTCTGCAGATATA 120 +1 WO 2016/054039 *WT ZmGWD is a region of nt 81-160 of Exon 24 (SEQ ID NO: 3)

Table 13 Partial deduced protein sequences of exon 24 in CRISPR/Cas9 mutants 4804 and 4806

Sequence Descripition Protein sequence SEQ ID NO WT ZmGWD Exon 24* WQVIS PVEVSGYWWDELLAVQNKS YDKPTILVAKS VKGEEEIPDG 190 M32 WQVISPVl 121 M33 WQVIS PVSIRLCGCG* 122 M34 WQVI S PViVSGYWWDELLAVQNKS YDKPT I LVAKS VKGEEE IPDG 123 M35 WQVIS PVKYQVMWLWLMSYIiSRTNLMINQPSLWQRVSKERKKYQME* 124 M36 WliWLMSYLLSRTNLMINQPSLWQRVSRERKKYQME * 125 *WT ZmGWD Exon 24 is a region of aa 1011-1057 of WT ZmGWD (SEQ ID NO: 43) -83- PCT/U S2015/052940

Table 14 Partial deduced protein sequences of exon 25 in CRISPR/Cas9 mutants 4817

Sequence Description Protein sequence SEQ ID NO WT ZmGWD Exon 25* VLFATCFDHTTLSELEGYDQKLFSFKPTSADIT YR 191 M38 VLFATCFDHTTLS................ADITYR 126 M39 VLFATCFDHTTLSELEGYDQKLFSFTAYFCRY NL* 127 WO 2016/054039 **WT ZmGWD Exon 25 is a region of aa 1082-1116 of WT ZmGWD (SEQ ID NO: 43) [0190] Characterization of maize NLS meganuclease-induced mutations [0191] To develop maize NLS meganuclease constructs pAG4837-4839, the viral SV40 NLS sequence in pAG4716 was replaced with the maize NLS sequences derived from Opaque2 (Hicks et al., PNAS,1995) (Table 15). A large variation of the induced mutations in exon 24 of the maize GWD gene was observed. These mutations included substitutions, deletions, and insertions from 1 to 114 nucleotides (Tables 16-17). Indirectly assessed efficiencies of the NLS variants were estimated as the number of events containing any modifications in the target region of the GWD gene divided by the total number of analyzed events (Table 15). Each evaluated NLS sequence supported production of the induced mutations with the NLS3 and NLS4 being the most efficient.

Table 15 Meganuclease constructs containing plant-derived NLS sequences

Construct Expression cassette NLS number Protein sequence SEQ ID NO Relative efficiency (%) pAG4837 ZmUbilP:NLSl: GWD7-8x.226 NLS1 MPTEERVRKRKES NRESARRSRYRKA AHLKEL 128 59.1 pAG4838 ZmUbilP:NLS3: GWD7-8x.226 NLS 3 MARKRKE SNRE SA RRSRYRKAAHLKE L 129 75.0 pAG4839 ZmUbilP:NLS4: GWD7-8x.226 NLS 4 MARKRKE SNRE SA RRSRRSRYRKV 130 71.4 -84- PCT/US2015/052940

Table 16 List of representative mutations induced by maize NLS meganucleases in exon 24 of the ZmGWD gene in 4837, 4838, and 4839 events

Sequence Description Mutation DNA sequence SEQ ID NO Del/Tns WT ZmGWD* None GAAATAC CAGAT GGAGTAGTTGGTGTAATTA CACCTGATATGCCAGATGTTCTGTCT 192 None 4837_12 M40 GAAATAC CAGAT GGAGTAGTT G. - .TAATTA CACCTGATATGCCAGATGTTCTGTCT 131 -3 4837_12 M41 GAAAT AC C AGAT GGAGTAGTT GGT AT7AAAT T ACAC C T GATAT GC CAGAT GT T C T GT C T 132 -2/+3 4837_16 M42 GAAAT AC C AGAT GGAGT AGT T GGT GT A§§T T A CACCTGATATGCCAGATGTTCTGTCT 133 -1 4837_19 M43 GAAATAC CAGAT GGAGTAGTT GGT GTAGAGT AATAACACCTGATAT GCCAGATGTTCTGTCT 134 -3/ + 8 4837J53 M44 GAAATACCAGATGGAGTAGTTGGTGT..... ...................T C T G T C T 135 -24 4838_1 M45 GAAAT AC C AGAT 136 -36 4838J51 M46 GAAATAC CAGAT GGAGTAGTT GGTGTATGAA CACGTAATTACACCT GATATGCCAGAT GTTC TGTCT 137 + 10 4838_53 M47 GAAATACCAGATGGAGTAGTTGGTGT..... 138 -29 4839_1 M48 gaaataccagatggagtagttggtg|§||§tta CACCTGATATGCCAGATGTTCTGTCT 139 -3 4839_3 M49 GAAAT AC C AGAT GGAGT AGT T GGT GTAilAT T ACACCTGATATGCCAGATGTTCTGTCT" 140 + 1 4839_54 M50 GAAAT ACC AGAT GGlllllllllllllllilllillil lllllliGAT AT GC C AGAT GT T C T GT C T 141 -22 4839_57 M51 GAAATACCAGATGGAGTAGTTGGTGTi|ii| llllillllilillliiAAT T AC AC C T GAT AT GC CAGATGTTCTGTCT 142 + 19 4839_58 M52 GAAAT AC C AGAT GGAGT AGT T GGT Gllllllll .......llililllliATcc τ c τ gt c τ 143 -21 4839_58 M53 GAAAT AC C AGAT GGAGT AGT T GGT GTllllli lllilGAT AT GC C AGAT GT T CTGTCT 144 -9/ + 2 4839_61 M54 GAAATACCAGATGGAGTAGTTGGTGiillll C T C AT ATTfTTC TGTGAT T GAATATTCT TT T C CAGATGGAGT’GTCAAGGGAGAGGAAGAAATA CCAGATQGAGT GTCAAGGGAGAGGAAGAAAT liiililiiiiliiiTACAccTGATAT gc c a GATGTTCTGTCT 145 -4/+114 4839_61 M55 GAAAT ACC AGAT GGAGT............ TA CACCTGATATGCCAGATGT 146 -12 WO 2016/054039 * WT ZmGWD is a region of nt 3157-3213 of SEQ ID NO: 1. -85- PCT/US2015/052940

Table 17 Partial deduced protein sequences of exon 24 in CRISPR/Cas9 mutants 4837, 4838, and 4839

Sequence Decsription Protein sequence SEQ ID NO WT ZmGWD Exon 24* IPDGWGVITPDMPDVLSHVSVRARNSK 193 M40 IPDGWgVITPDMPDVLSHVSVRARNSK 147 M41 IPDGWGINYT* 148 M42 IP D GW G VLHLICQMFGLMCQSEQGIARYCL RPVLTTPLYIJHI.KDMIRNCFPSS LLL* 149 M43 IPDGWGVE* 150 M44 IPDGVVGV........L S H VS VRARNS K 151 M45 I PD............VLSHVSVRARNSK 152 M46 IPDGWGV* 153 M47 IPDGWG SCVSPSKE* 154 M48 IPDGVVGV.TPDMPDVLSHVSVRARNS K 155 M49 IPDGWGVNYT* 156 M50 IPDGICQMFCLMFQSEQGIARYCLRPVLTTP LYLNI.KDMIRNCFPS SKLLQI * 157 M51 I PDGWGVSCQM* 158 M52 i p d gwg!!!!!!!!|dvl s h vs vrarns k 159 M53 IPDGWGVRY&RCSVSCVSPSKE* 160 M54 IP D GWGAFTHIFCD * 161 M55 IPDGV....tpdmpdvlshvsvrarnsk 162 WO 2016/054039 * WT ZmGWD Exon 24 is a region of aa 1054-1081 of SEQ ID NO: 43.

[0192] Green Tissue Starch Assays [0193] CRISPR/Cas and maize NLS meganuclease lines were assayed for starch in green leaf tissue. Leaf tissue harvested from 40 day old events was assayed for starch according to the protocol described in Example 3. These data confirm the efficacy of our CRISPR/Cas targeting system and maize NLS meganuclease gene editing constructs. -86- WO 2016/054039 PCT/US2015/052940

Table 18 Starch Content in CRISPR/Cas and Maize NLS Meganuclease Lines

Vector Event Starch (mg glucose/100 mg DW) [% DW1 SD WT WT 1.0 1.4 4804 58 1.1 0.1 4804 60 1.2 0.1 4804 59 1.3 0.2 4804 61 2.4 0.2 4804 53 9.3 1.9 4804 6 9.6 0.3 4804 4 11.2 1.4 4804 54 11.9 0.5 4804 51 12.4 0.9 4804 57 14.1 1.8 4804 62 16.7 0.4 4804 56 16.7 0.7 4804 7 17.0 0.6 4804 63 17.9 0.4 4804 5 18.0 0.2 4804 52 18.2 0.8 4804 3 18.5 0.9 4804 64 19.0 0.7 4804 2 19.5 1.2 4804 55 20.5 0.9 4804 1 27.8 1.7 4805 1 1.2 0.3 4805 103 11.2 0.7 4805 53 11.5 1.0 4805 56 11.7 0.7 4805 55 13.8 2.3 4805 101 14.2 0.4 4805 104 15.0 1.2 4805 51 15.0 1.2 4805 54 15.6 1.0 4805 2 16.4 0.7 4806 204 0.9 0.1 4806 203 0.9 0.1 4806 202 0.9 0.1 4806 201 1.0 0.1

Vector Event Starch (mg glucose/100 mg DW) r% DW1 SD 4806 2 1.2 0.1 4806 52 1.2 0.6 4806 101 1.4 0.2 4806 53 1.7 0.2 4806 154 2.0 0.3 4806 57 2.2 0.7 4806 152 2.7 0.9 4806 1 3.3 0.3 4806 205 4.0 1.0 4806 207 4.6 0.6 4806 209 5.9 1.0 4806 210 7.1 0.9 4806 208 7.4 0.6 4806 155 7.5 1.0 4806 55 8.6 1.4 4806 56 9.4 1.8 4806 206 10.1 1.4 4806 54 11.0 0.9 4806 151 15.7 1.4 4807 1 0.7 0.0 4807 6 0.7 0.1 4807 5 0.7 0.1 4807 2 0.7 0.0 4807 4 1.0 0.1 4807 3 2.1 0.4 4809 1 10.1 0.8 4809 2 10.6 0.5 4809 4 13.3 0.7 4809 3 17.8 1.3 4817 54 14.2 0.7 4817 55 18.0 1.1 4817 51 19.2 0.8 4817 1 19.4 0.8 4817 53 20.7 0.5 4817 52 20.9 0.8 -87- PCT/US2015/052940 WO 2016/054039

Table 19 Starch Content in CRISPR/Cas and Maize NLS Meganuclease 4837, 4838 and 4839 Lines

Vector Event Starch (mg glucose/100 mg DW [%DW] SD WT 1 1.0 0.2 4837 8 1.3 0.2 4837 51 1.8 0.5 4837 7 1.8 0.3 4837 16 2.2 0.5 4837 4 2.3 0.2 4837 1 2.3 0.2 4837 15 2.5 0.1 4837 53 3.3 0.5 4837 9 3.6 0.5 4837 3 4.7 1.0 4837 12 6.2 1.4 4837 17 16.5 0.5 4837 11 17.0 0.7 4837 14 18.2 0.6 4837 2 18.6 1.1 4837 5 19.3 1.3 4837 19 20.0 1.1 4837 18 20.4 0.4 4837 10 22.7 2.1 4837 6 23.3 0.9 4837 52 24.7 1.4 4838 4 1.2 0.1 4838 3 1.7 0.4 4838 53 1.8 0.7 4838 2 3.3 0.4 4838 54 6.9 1.2 4838 51 19.3 1.4 4838 52 19.9 1.2 4838 1 20.0 1.4 4839 53 1.1 0.1 4839 63 1.1 0.1 4839 62 1.3 0.1 4839 52 1.4 0.2 4839 54 2.1 0.4 4839 56 2.3 0.2 4839 51 2.4 1.1 4839 57 2.7 0.3 4839 58 2.8 0.8 4839 55 22.8 1.7 -88- PCT/U S2015/052940 WO 2016/054039

Vector Event Starch (mg glucose/100 mg DW [%DW| SD 4839 61 23.5 1.1 4839 60 24.5 1.1 4839 59 28.0 3.3 [0194] Referring to Tables 18 and 19, it was observed that many of the events exhibited high starch, which ranged approximately 3%-27.8%.

[0195] Example 10. Green tissue starch assays [0196] All of the CRISPR/Cas lines were assayed for starch in green leaf tissue as well as in dried stover leaves, stalks, and cobs. Leaf tissue harvested from 40 day old CRISPR/Cas events were assayed for starch according to our protocol described in Example 3. FIG. 9 illustrates starch accumulation in the pAG4804 maize events. Referring to FIG. 9, all seven TO maize 4804 events had high starch, which ranged 9.6—27.8%, indicating that all currently unresolved GWD sequences were the result of two different GWD mutations rather than one wild type and one mutant allele (hemizygote). FIG. 10 illustrates starch accumulation in the pAG4806 maize events. Referring to FIG. 10, both TO maize 4806 events had low starch, suggesting that the one unresolved GWD sequence is a hemizygote. These data confirm the efficacy of the CRISPR/Cas targeting system herein, which includes new GWD guide RNA targeting sequences and new U3 promoters used for expression of the guide RNAs.

[0197] Example 11. Breeding recessive mutations for elite inbred introsression and testing [0198] The advent of new methods for precision DNA engineering and mutagenesis provides a means of generating targeted recessive and dominant mutations for the development of new and beneficial plant traits. Some of these methods include targeting specific regions of genes with meganucleases,

Talens, and the CRISPR/Cas system. Tracking and advancing targeted mutations present a new challenge for trait development, because, unlike -89- PCT/US2015/052940 WO 2016/054039 traditional transgenic plant traits, they do not carry dominant T-DNA expression cassettes and selectable markers. Generation of targeted mutations in maize and sorghum using TALENS, ZFN, meganuclease and CRISPR/Cas methods described herein can lead to the creation of new methods for screening and breeding these unique plant traits.

[0199] Example 12. Tracking and breedins targeted mutations [0200] Transformation (TO) Generation Genotypes'. Gene-specific mutations identified using the described methods resulted in first generation transformed (TO) plants with one of three different genotypes: 1) one wild type gene allele and one mutant allele, 2) two different mutant alleles, or 3) two identical mutant alleles. These mutant allele combinations were designated as hemizygous, heterozygous, and homozygous, respectively.

[0201] Molecular Methods for Tracking Targeted Mutations'. The specific sequence characteristics of a targeted DNA mutation (e.g., substitution, deletion, insertion, or combination) relative to the wild type sequence were, and may be, tracked using methods described herein when breeding the mutation into other lines, or expanding the existing lines through breeding. To differentiate wild type, hemizygous, heterozygous, and homozygous lines in a TO and T1+ (progeny derived from TO parental lines and beyond) segregating populations, at least five methods could be used. These methods include: 1) PCR of the mutation site with gel electrophoresis for size separation, 2) PCR with restriction enzyme digestion and gel electrophoresis to generate a mutation specific restriction pattern, 3) PCR with direct sequencing, 4) PCR with cloning and sequencing, and 5) PCR using primers that bind or do not bind to mutation sites.

[0202] Homozygous DNA sequences from either wild type or engineered, altered, or optimized endogenous nucleic acids would be easily analyzed by PCR, size determination, and, or DNA sequencing in the targeted or mutated region. In contrast, DNA sequences that possess different alleles may result in a portion of sequence that would be difficult to analyze using sequencing, PCR or size determination due to differences in the two allelic sequences (e.g., -90- PCT/US2015/052940 WO 2016/054039 a wild type and a mutant or two different mutant sequences). PCR products from these types of targeted events would require cloning to isolate and effectively sequence each allele.

[0203] Once the sequence of the targeted mutation has been confirmed, a mutation-specific molecular strategy for tracking is established. As mentioned previously, this strategy will be dependent on the characteristics of the mutation. In tracking the gwd mutations generated herein, PCR specific reactions were developed for each of the mutations and engineered endogenous (optimized) nucleic acids described herein.

[0204] Breeding Crosses and Selfing: A main goal of developing traits with targeted mutations induced with transgenes is to isolate the mutations by separating the desired mutation from the transgene. This can be accomplished through genetic crosses and is most effective through outcrosses (higher frequency of recovered mutant plants that are transgene negative), which involves crossing TO pollen to the female component of a non-transgenic plant. This can also be accomplished at a lower frequency using selfing, which involves self-pollinating (using TO pollen to pollinate the same TO plant). Sibbing is another option and involves crosses between two genetically identical plants, which would be expected to have the same outcome as a selfcross.

[0205] TO plants carrying targeted mutations can be selfed to generate homozygous plants and would result in different numbers and types of progeny depending on the TO zygosity. Homozygous TO plants would generate 100% homozygous progeny, hemizygous TO plants would segregate 1:2:1 (homozygous: hemizygous: wild type) for the mutant allele, and heterozygous TO plants would segregate 1:2:1 (homozygous targeted allele 1: heterozygous: homozygous targeted allele 2).

[0206] TO plants carrying targeted mutations can also be outcrossed into other lines and would result in different numbers and types of progeny depending on the TO zygosity. Homozygous TO plants would generate 100% hemizygous progeny, hemizygous TO plants would generate 50% hemizygous -91- PCT/US2015/052940 WO 2016/054039 progeny and 50% wild type progeny, and heterozygous TO plants would generate hemizygous progeny, 50% with targeted allele 1 and 50% with targeted allele 2.

[0207] Because all TO plants would be carrying transgenes, the transgene insertion location is most commonly different, and the number of transgene insertions could differ, the segregation patterns for the transgenes have the potential to vary considerably between each TO transformation event/plant. To identify transgene-negative plants, PCR would be applied to the progeny from any cross (self, sib, or outcross) with TO plants. Transgenenegative plants would be identified by the absence of a transgene-specific PCR product. The transgene-negative plants would then be screened for the targeted mutation using the molecular diagnostics approach defined during the initial characterization of the TO plants.

[0208] Targeted mutations isolated from the transgene can then be maintained and bred for testing and introgressions with the continued use of the trait-specific molecular diagnostics protocol.

[0209] An Example Tracking and Breeding Procedure for a Targeted Mutation: The molecular tracking and breeding procedure for a targeted mutation is described herein. Tracking of the GWD gene from maize (M20, ZmGWD_M20 from event 4716_164) is described herein. Generation and initial sequence characterization of this and other meganuclease-induced targeted mutations in maize and sorghum has been described in Examples herein. TO 4716_164 plants were hemizygous for the M20 mutation initially and carried an unknown number of T-DNA insertions. The M20 mutation is a recessive single base pair (bp) deletion in exon 24 of ZmGWD, which results in a mutation at an MluCI restriction enzyme site in the wild type sequence. The small size of this deletion required use of the MluCI RFLP with gel electrophoresis because it could not be differentiated from wild type with gel electrophoresis alone.

[0210] FIG. 11 illustrates a schematic drawing of selfing and outcrossing of a targeted mutation M20 derived from the maize event 4716_164. Referring -92- PCT/US2015/052940 WO 2016/054039 to FIG. 11, TO 4716_164 plants were selfed and outcrossed to generate progeny for efficacy testing and introgressions, respectively. To identify homozygous M20 progeny from the TO selfed parent, PCR with the meganuclease targeting gene and the target region of the GWD gene was performed. FIG. 12 illustrates genotyping of T1 progeny from the selfed TO 4716_164 M20 plant. Referring to FIG. 12, PCR products from meganuclease GOI and ZmGWD target region were digested with MluCI, separated on 5% polyacrylamide and stained with ethidium bromide. This revealed plants that did not carry the T-DNA (Meganuclease) but were homozygous for M20. These plants were maintained for testing.

[0211] To identify hemizygous M20 progeny from the TO outcrossed parent, PCR of the selectable marker gene, PMI, the meganuclease gene, and the target region was performed, followed by 3% agarose gel electrophoresis and ethidium bromide staining. This also allowed identification of T-DNA negative plants. FIG. 13 illustrates genotyping of T1 progeny from the outcrossed TO 4716_164 M20 plant. MluCI restriction digests were then performed on the same PCR products from T-DNA negative plants and separated them on a 5% polyacrylamide gel stained with ethidium bromide. FIG. 14 illustrates genotyping of T1 progeny from the outcrossed 4716_164 M20 plant. These plants were maintained for further introgressions and future testing.

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Claims (60)

1. CLAIMS What is claimed is:

   1. A genetically engineered plant comprising an engineered nucleic acid encoding an altered Glucan Water Dikinase, wherein the plant has an elevated level of starch in comparison to a plant of the same genetic background comprising a wild type Glucan Water Dikinase.
2. 2. The genetically engineered plant of claim 1, wherein the activity of the altered Glucan Water Dikinase is reduced compared to the activity of the wild type Glucan Water Dikinase.
3. 3. The genetically engineered plant of claim 1, wherein the altered Glucan Water Dikinase is inactive.
4. 4. The genetically engineered plant of claim 1, wherein the engineered nucleic acid is a modified sequence of at least one allele of a gene encoding wild type Glucan Water Dikinase compared to an endogenous nucleic acid encoding wild type Glucan Water Dikinase.
5. 5. The genetically engineered plant of claims 1, wherein the endogenous nucleic acid includes a sequence with at least 90% identity to a reference sequence of SEQ ID NO: SEQ ID NO: 1 (Zm GWD coding sequence) or SEQ ID NO: 2 (Sb GWD coding sequence).
6. 6. The genetically engineered plant of claim 4, wherein the modified sequence comprises mutation selected from at least one of an insertion, a deletion, or a substitution of at least one nucleotide in the endogenous nucleic acid.
7. 7. The genetically engineered plant of claim 6, wherein the mutation is within a target sequence with at least 90% identity to a reference sequence selected from the group consisting of SEQ ID NO: 3 (Zm GWD Exon 24 + introns), SEQ ID NO; 4 (SbGWD Exon 24 + introns), SEQ ID NO: 182 (ZmGWD Exon 24 no introns), SEQ ID NO: 183 (Sb GWD Exon 24), and SEQ ID NO: 184 (SbGWD Exon 7).
8. 8. The genetically engineered plant of claim 6, wherein the mutation is within a target sequence with at least 90% identity to a reference sequence selected from the group consisting of SEQ ID NO: 91 (GWDela), SEQ ID NO: 92 (GWDe24b), SEQ ID NO: 93 (GWDe24c), and SEQ ID NO: 94 (GWDe25a).
9. 9. The genetically engineered plant of claim 1, wherein the engineered nucleic acid comprises a polynucleotide having a sequence with at least 90% identity to a sequence selected from the group consisting of SEQ ID NOS: 12 -40, 114 -120, 131 -146, and 188 (Zm GWD mutations - Exon 24) and SEQ ID NOS: 119 and 120 (Zm GWD mutations - Exon 25).
10. 10. The genetically engineered plant of claim 1, wherein the engineered nucleic acid comprises a polynucleotide having a sequence with at least 90% identity to a sequence selected from the group consisting of SEQ ID NO: 106 (Sb4715_l (WT + ins)_Exon 24, and SEQ ID NO: 107 (Sb4715_2 (WT + ins)_Exon 24).
11. 11. The genetically engineered plant of claim 1, wherein the altered Glucan Water Dikinase comprises an amino acid sequence with at least 90% identity to a sequence selected from the group consisting of SEQ ID NOS: 45 - 73 (Zm GWD mutant proteins Ml - M29), 121-124 (Zm GWD mutants M32 - M36), 126 - 127 (ZmGWD mutants M38 and M39), 147 - 162 (Zm GWD mutants M40 - M55).
12. 12. The genetically engineered plant of claim 1, wherein the altered Glucan Water Dikinase comprises an amino acid sequence with at least 90% identity to a sequence of SEQ ID NO: 194 (Sb GWD mutant protein Sb4715_lWT + ins) or SEQ ID NO: 195 (Sb GWD mutant protein Sb4715_2 WT + del).
13. 13. A method for genetically engineering a plant comprising an altered Glucan Water Dikinase comprising: contacting at least one plant cell comprising a target sequence in an endogenous gene encoding a Glucan Water Dikinase with a vector comprising a first nucleic acid encoding a nuclease capable of inducing a double-strand break at the target sequence; selecting a plant cell that includes an alteration in the target sequence; and regenerating a genetically engineered plant comprising the alteration from the plant cell.
14. 14. The method of claim 13, wherein the genetically engineered plant is homozygous for the alteration.
15. 15. The method of claim 13, wherein the genetically engineered plant is heterozygous for the alteration.
16. 16. The method of claim 15 further comprising selfing the heterozygous genetically engineered plant, or crossing to another genetically engineered plant heterozygous for the same alteration, and selecting a first progeny plant that is homozygous for the alteration.
17. 17. The method of claim 15 further comprising crossing the genetically engineered plant to a wild type plant of the same genetic background and selecting a first progeny plant that is heterozygous for the alteration.
18. 18. The method of claim 17 further comprising selfing the first heterozygous progeny plant and selecting a second progeny plant that is homozygous for the alteration.
19. 19. The method of claim 13, wherein the alteration comprises the mutation.
20. 20. The method of claim 19, wherein the mutation comprises at least one of an insertion, a deletion, or a substitution of at least one nucleotide in the target sequence.
21. 21. The method of claim 20, wherein the mutation is a null mutation.
22. 22. The method of claim 13, wherein the genetically engineered plant comprising the alteration or a progeny thereof has an elevated level of starch in comparison to a non-genetically engineered plant of the same genetic background.
23. 23. The method of claim 13, wherein the nuclease is selected from the group consisting of a meganuclease, Cas9 nuclease, a zinc finger nuclease, and a transcription activator-like effector nuclease.
24. 24. The method of claim 23, wherein the nuclease is a meganuclease and is encoded by a sequence with at least 90% identity to a reference sequence selected from the group consisting of SEQ ID NO: 108 (4715_meganuclease) and SEQ ID NO: 109 (4716_meganuclease).
25. 25. The method of claim 24, wherein the meganuclease is capable of cutting the target sequence, and the target sequence comprises a polynucleotide with the sequence of SEQ ID NO: 41 (target for 4715_ GWD-9/10x.272) or SEQ ID NO: 42 (target for 4716_3e GWD-7/8x276).
26. 26. The method of claim 23, wherein the nuclease is Cas9 nuclease.
27. 27. The method of claim 26, wherein the Cas9 nuclease is encoded with a nucleic acid with at least 90% identity to a reference sequence of SEQ ID NO: 74 (Cas9 nuclease) or SEQ ID NO: 75 (ZmCas9).
28. 28. The method of claim 13, wherein the vector further comprises a second nucleic acid encoding an sgRNA.
29. 29. The method of 28, wherein the sgRNA is capable of binding the target sequence selected from the group consisting of SEQ ID NO: 91 (GWDela), SEQ ID NO: 92 (GWDe24b), SEQ ID NO: 93 (GWDe24c), and SEQ ID NO: 94 (GWDe25a).
30. 30. The method of claim 13, wherein the vector further comprises a first nucleic acid promoter operably linked to the first nucleic acid.
31. 31. The method of claim 28, wherein the vector further comprises a second nucleic acid promoter operably linked to the second nucleic acid.
32. 32. The method of any of claims 30 or 31, wherein the first nucleic acid promoter or the second nucleic acid promoter comprises a sequence with at least 90% identity to a reference sequence selected from the group consisting of: SEQ ID NO: 78 (MzU3.8), SEQ ID NO: 79 (ZmU3), SEQ ID NO: 82 (ZmU3Pl), SEQ ID NO: 84 (ZmU3P2) and SEQ ID NO: 86 (MzU3.8).
33. 33. The method of claim 13, wherein the second nucleic acid comprises a sequence with at least 90% identity to a reference sequence selected from the group consisting of: SEQ ID NO: 95 (ZmU3Pl:sgRNA_GWDe24b), SEQ ID NO: 96 (ZmU3P2:sgRNA_GWDe24b), SEQ ID NO: 97 (ZmU3.8P:sgRNA_GWDe24b), SEQ ID NO: 98 (ZmU3P2:sgRNA_GWDe24c), SEQ ID NO: 99 (ZmU3P2:sgRNA_GWDe25a) and SEQ ID NO: 100 (ZmU3P2: sgRNA_GWDe la).
34. 34. A genetically engineered plant produced by the method of any one of claims 13-31 and 33, or a progeny or descendant thereof, wherein the plant, progeny or descendant thereof comprises the alteration.
35. 35. The genetically engineered plant of claim 34 having an elevated level of starch in comparison to a plant of the same genetic background comprising a wild type Glucan Water Dikinase.
36. 36. A method of increasing a starch level in a plant comprising expressing a nucleic acid encoding a nuclease capable of inducing a double-strand break at a target sequence and selecting a homozygous plant that includes an alteration in the target sequence and has an elevated level of starch in comparison to a plant of the same genetic background comprising a wild type sequence.
37. 37. A method of agricultural processing comprising: expressing a nucleic acid encoding a nuclease capable of inducing a double-strand break at the target sequence, wherein the target sequence is included in an endogenous gene encoding a Glucan Water Dikinase; selecting a homozygous plant that includes an alteration in the target sequence and has an elevated level of starch in comparison to a plant of the same genetic background comprising a wild type sequence; and processing the homozygous plant, wherein the processing comprises one or more procedures selected from harvesting, bailing, shredding, drying, fermenting, hydrolyzing with chemicals, hydrolyzing with exogenous enzymes and combining with plant biomass.
38. 38. A method of preparing animal feed comprising: expressing a nucleic acid encoding a nuclease capable of inducing a double-strand break at the target sequence, wherein the target sequence is included in an endogenous gene encoding a Glucan Water Dikinase; selecting a homozygous plant that includes an alteration in the target sequence and has an elevated level of starch in comparison to a plant of the same genetic background comprising a wild type sequence; and performing at least one procedure selected from the group consisting of: harvesting, bailing, shredding, drying, ensiling, pelletizing, combining with a source of edible fiber fiber, and combining with plant biomass.
39. 39. A synthetic nucleic acid promoter having a sequence with at least with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 % identity to a reference sequence selected from the group consisting of: SEQ ID NO: 78 (MzU3.8), SEQ ID NO: 79 (ZmU3), SEQ ID NO: 82 (ZmU3Pl), SEQ ID NO: 84 (ZmU3P2) and SEQ ID NO: 86 (MzU3.8P).
40. 40. A genetic construct comprising a first engineered nucleic acid sequence encoding a Cas9 nuclease, wherein the Cas9 nuclease is capable of cleaving a target sequence included in an endogenous nucleic acid encoding Glucan Water Dikinase in a plant.
41. 41. The genetic construct of claim 40, wherein the first engineered nucleic acid sequence has at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 % identity to a reference sequence of SEQ ID NO: 74 (Cas9 nuclease) or SEQ ID NO: 75 (ZmCas9).
42. 42. The genetic construct of claim 40, wherein the first nucleic acid is fused to a polynucleotide sequence encoding at least one nuclear localization signal (NLS).
43. 43. The genetic construct of claim 42, wherein the polynucleotide sequence is selected from SEQ ID NOS: 163 - 168.
44. 44. The genetic construct of claim 40 further comprising a second engineered nucleic acid sequence encoding an sgRNA.
45. 45. The genetic construct of claim 44, wherein the sgRNA is capable of binding the target sequence.
46. 46. The genetic construct of claim 44, wherein the second engineered nucleic acid comprises a sequence with at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 % identity to one from the SEQ ID NO: 135 (ZmU3P 1:sgRNA_GWDe24b), SEQ ID NO: 136 (ZmU3P2:sgRNA_GWDe24b), SEQ ID NO: 137 (ZmU3.8P:sgRNA_GWDe24b), SEQ ID NO: 138 (ZmU3P2:sgRNA_GWDe24c), SEQ ID NO: 139 (ZmU3P2:sgRNA_GWDe25a) and SEQ ID NO: 40 (ZmU3P2:sgRNA_GWDela).
47. 47. The genetic construct of claim 40, wherein the target sequence has at least 70, 72, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 % identity to a reference sequence selected from the group consisting of SEQ ID NO: 91 (GWDela), SEQ ID NO: 92 (GWDe24b), SEQ ID NO: 93 (GWDe24c), and SEQ ID NO: 94 (GWDe25a).
48. 48. The genetic construct of claims 40 further comprising the first nucleic acid promoter operably linked to the first engineered nucleic acid.
49. 49. The genetic construct of claims 40 further comprising the second nucleic acid promoter operably linked to the second engineered nucleic acid.
50. 50. The genetic construct of any claims 48 or 49, wherein the first nucleic acid promoter or the second nucleic acid promoter is the synthetic nucleic acid promoter of claim 39.
51. 51. A kit for identifying a modified sequence of an endogenous gene encoding Glucan Water Dikinase in a sample, wherein the kit comprises a first primer and a second primer, wherein the first primer and the second primer are capable of amplifying a target sequence included in the endogenous gene encoding Glucan Water Dikinase and the target sequence comprises a nucleic acid sequence with at least 90% identity to a reference sequence selected from SEQ ID NOS: 1 - 4, 75, 170 - 184, 186, 187, 189 - 193.
52. 52. The kit of claim 51 further comprising one or more component for detecting a modification in the amplified region of the target sequence.
53. 53. The kit of claim 52, wherein the modification in the amplified region comprises a sequence of SEQ ID NOS: 12 - 40, 106 - 107, 114 - 120, 131 - 146, and 188.
54. 54. The kit of claim 51, wherein, the first primer comprises a nucleic acid sequence selected from SEQ ID NOS: 6, 7, 9, 11, 101, 103, 105, 110, and 111.
55. 55. The kit of claim 51, wherein the second primer comprises a nucleic acid sequence selected from SEQ ID NOS: 5, 8, 10, 102, and 104.
56. 56. The kit of claim 51, wherein the first primer and the second primer are capable of amplifying the target sequence to produce an amplified product comprising a modified target sequence.
57. 57. The kit of claim 51, wherein the modified target sequence is capable of hybridizing to the sequence of the nucleic acid comprising a sequence selected from SEQ ID NOS: 12 - 40, 106 - 107, 114 - 120, 131 - 146, and 188 under conditions of high stringency.
58. 58. The kit of claim 51, wherein the sample comprises plant matter derived from a genetically engineered plant having at least one mutation in an endogenous gene encoding the Glucan Water Dikinase.
59. 59. A method of identifying a modified sequence of an endogenous gene encoding Glucan Water Dikinase in a sample comprising: contacting a sample with a first primer and a second primer; amplifying a target sequence included in the endogenous gene encoding Glucan Water Dikinase and the target sequence comprises a nucleic acid sequence with at least 90% identity to a reference sequence selected from SEQ ID NOS: 1 - 4, 75, 170 - 184 186, 187, 189 - 193; and detecting a modification in the target sequence.
60. 60. The method of claim 59, wherein the modification in the target sequence comprises a sequence selected from SEQ ID NOS: 12 - 40, 106 - 107, 114 - 120, 131 - 146, and 188.