Methods and compositions for improving yield and disease resistance

Abstract

The present invention relates to compositions and methods for modifying a desired plant configuration 1 (IPA1) gene encoding a SQUAMOSA promoter binding protein-like (SPL) transcription factor, or ortholog thereof, in a plant. The invention further relates to plants and / or parts thereof comprising one or more mutations in an endogenous IPA1 gene or ortholog thereof produced using the methods and compositions of the invention.

Description

[0001] Statement Regarding Electronic Submission of Sequence Listings

[0002] The disclosed content of the sequence listing in XML format named 1499-101_ST26.xml and with a size of 776,947 bytes, generated and submitted on April 27, 2023, is hereby incorporated by reference into the specification.

[0003] Priority declaration

[0004] This application claims the benefit of U.S. Provisional Application No. 63 / 337,244, filed on May 2, 2022, under 35 U.S.C. §119(e), the entire contents of which are incorporated herein by reference. Technical Field

[0005] The present invention relates to compositions and methods for modifying the IDEAL PLANT ARCHITECTURE 1 (IPA1) gene encoding a SQUAMOSA promoter binding protein-like (SPL) transcription factor or its orthologs in plants. The present invention further relates to plants comprising a modified endogenous IPA1 gene and optionally having improved yield traits and / or disease resistance produced using the methods and compositions of the present invention. Background Art

[0006] There is evidence that growth and defense pathways actively antagonize each other, with salicylic acid (SA)-mediated defense being the main pathway to counteract growth (Butselaar et al. Trends Plant Sci 25, 566–576 (2020)). However, only a few genes that actively regulate growth-SA defense antagonism have been characterized. Therefore, optimizing plant performance for yield may have a negative impact on defense. Vice versa, selection for improved immunity may lead to a reduction in yield and growth.

[0007] Identification of genes that can be engineered to avoid antagonistic effects on yield and defense pathways will lead to improved plant health and performance. Novel strategies for regulating the expression of genes involved in improving yield traits and defense pathways are also needed to improve crop performance. Summary of the invention

[0008] One aspect of the present invention provides a plant or a plant part thereof, comprising at least one mutation in an endogenous ideal plant configuration 1 (IPA1) gene encoding a SQUAMOSA promoter binding protein-like (SPL) transcription factor or its ortholog, optionally wherein the endogenous IPA1 gene encoding the SPL transcription factor is an endogenous SQUAMOSA promoter binding protein-like 9 (SPL9) gene, an endogenous UNBRANCHED2 (UB2) gene or an endogenous UNBRANCHED3 (UB3) gene, optionally wherein at least one mutation may be a non-natural mutation.

[0009] A second aspect of the present invention provides a plant cell comprising an editing system, the editing system comprising: (a) a CRISPR-Cas associated effector protein; and (b) a guide nucleic acid (e.g., gRNA, gDNA, crRNA, crDNA), wherein the guide nucleic acid comprises a spacer sequence complementary to an endogenous ideal plant configuration 1 (IPA1) target gene or its ortholog encoding a SQUAMOSA promoter binding protein-like (SPL) transcription factor.

[0010] A third aspect provides a plant cell comprising at least one mutation in one or more endogenous ideal plant configuration 1 (IPA1) genes or their orthologs encoding a SQUAMOSA promoter binding protein-like (SPL) transcription factor, wherein at least one mutation is a substitution, insertion and / or deletion introduced using an editing system comprising a nucleic acid binding domain that binds to a target site in one or more endogenous IPA1 genes, optionally wherein at least one mutation may be a non-natural mutation.

[0011] In a fourth aspect, a method of providing a plurality of plants exhibiting altered plant architecture, improved yield traits and / or increased tolerance / resistance to abiotic and biotic stresses is provided, the method comprising planting two or more plants of the invention in a growing area, thereby providing a plurality of plants exhibiting altered plant architecture, improved yield traits and / or increased tolerance / resistance to abiotic and biotic stresses compared to a plurality of control plants not comprising at least one mutation, optionally wherein the plurality of plants exhibiting resistance to biotic stresses exhibit increased disease resistance.

[0012] The fifth aspect provides a method for producing / cultivating a transgenic-free genome-edited (e.g., base-edited) plant, the method comprising: (a) crossing a plant of the present invention with a transgenic-free plant, thereby introducing a mutation or modification into the transgenic-free plant; and (b) selecting progeny plants that contain the mutation or modification but are free of transgenes, thereby producing a transgenic-free genome-edited (e.g., base-edited) plant.

[0013] In a sixth aspect, a method for editing a specific site in the genome of a plant cell is provided, the method comprising: cleaving a target site within an endogenous IPA1 gene in the plant cell in a site-specific manner, wherein the endogenous IPA1 gene is: (a) an SPL9 gene having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 72, 73, 75, 76, 78, 79, 81, 82, 143, 144, 182, 183, 222, 223, 255 or 256 and / or comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288, (b) an UB2 gene having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 84 or SEQ ID NO: 85 and / or comprising a region having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: NO:90-96 or 332-393; and / or (c) a UB3 gene having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:87 or SEQ ID NO:88 and / or comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:90, 97-103 or 394-445, thereby producing an edit in the endogenous IPA1 gene of the plant cell.

[0014] The seventh aspect provides a method for preparing a plant, the method comprising: (a) contacting a plant cell population comprising an endogenous IPA1 gene with a nuclease targeted to the endogenous gene, wherein the nuclease is linked to a nucleic acid binding domain that binds to a target site in the endogenous gene, the endogenous IPA1 gene: (i) is a SPL9 gene comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 72, 73, 75, 76, 78, 79, 81, 82, 143, 144, 182, 183, 222, 223, 255 or 256, and / or comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288; (b) a UB2 gene having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 84 or SEQ ID NO:85 has at least 80% sequence identity, and / or comprises a region having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs:90-96 or 332-393; and / or a UB3 gene, which has at least 80% sequence identity with the nucleotide sequence of SEQ ID NO:87 or SEQ ID NO:88, and / or comprises a region having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs:90, 97-103 or 394-445, (b) selecting plant cells from a population comprising a mutation in the endogenous IPA1 gene, wherein the mutation is a substitution and / or a deletion; and (c) growing the selected plant cells into plants comprising a mutation in the endogenous IPA1 gene.

[0015] An eighth aspect of the present invention provides a method for changing plant architecture, improving yield traits and / or increasing tolerance / resistance of plants, the method comprising

[0016] (a) contacting a plant cell comprising an endogenous IPA1 gene with a nuclease that targets the endogenous IPA1 gene, wherein the nuclease is linked to a nucleic acid binding domain that binds to a target site in the endogenous IPA1 gene, wherein the endogenous IPA1 gene is: (i) an SPL9 gene comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 72, 73, 75, 76, 78, 79, 81, 82, 143, 144, 182, 183, 222, 223, 255, or 256, and / or comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254, and / or 258-288; (ii) an UB2 gene having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 84 or SEQ ID NO: 85, and / or comprising a region having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: NO:90-96 or 332-393; and / or (iii) a UB3 gene having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:87 or SEQ ID NO:88, and / or comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:90, 97-103 or 394-445; and (b) growing the plant cell into a plant, thereby changing the plant architecture, improving yield traits and / or increasing the tolerance / resistance of the plant.

[0017] The ninth aspect provides a method for producing a plant or part thereof, the plant or part thereof comprising at least one cell having a mutation in an endogenous ideal plant configuration 1 (IPA1) gene encoding a SQUAMOSA promoter binding protein-like (SPL) transcription factor or its ortholog, the method comprising contacting a target site in the endogenous IPA1 gene in the plant or plant part with a nuclease comprising a cleavage domain and a DNA binding domain, wherein the DNA binding domain of the nuclease binds to the target site in the endogenous IPA1 gene, wherein the endogenous IPA1 gene: (a) is an endogenous SQUAMOSA promoter binding protein-like 9 (SPL9) gene, which (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO: 72, 75, 78, 81, 143, 182, 222 or 255; (ii) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO: 72, 75, 78, 81, 143, 182, 222 or 255; NO:73, 76, 79, 82, 144, 183, 223 or 256; (iii) comprises a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:146-181, 185-221, 225-254 and / or 258-288, and / or (iv) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of any one of SEQ ID NO:74, 77, 80, 83, 145, 184, 224 or 257; (b) is an endogenous unbranched 2 (UB2) gene, which (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:84; (ii) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:85; (iii) comprises a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:146-181, 185-221, 225-254 and / or 258-288, and / or (iv) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of any one of SEQ ID NO:74, 77, 80, 83, 145, 184, 224 or 257. NOs:90-96 or 332-393, and / or (iv) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of SEQ ID NO:86; or (c) is an endogenous UB3 gene, which: (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:87; (ii) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:88; (iii) comprises a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs:90, 97-103 or 394-445, and / or (iv) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of SEQ ID NO:89, thereby producing a plant or part thereof comprising at least one cell having a mutation in an endogenous IPA1 gene.

[0018] In a tenth aspect, a method of producing a plant or part thereof comprising a mutation in an endogenous IPA1 gene and having a phenotype of altered plant architecture, improved yield traits and / or increased tolerance / resistance to abiotic and biotic stresses is provided, the method comprising contacting a target site in an endogenous IPA1 gene in the plant or plant part with a nuclease comprising a cleavage domain and a nucleic acid binding domain, wherein the nucleic acid binding domain of the nuclease binds to the target site in the endogenous IPA1 gene, wherein the endogenous IPA gene: (a) is an endogenous SQUAMOSA promoter binding protein-like 9 (SPL9) gene, which (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 72, 75, 78, 81, 143, 182, 222 or 255; (ii) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: NO:73, 76, 79, 82, 144, 183, 223 or 256; (iii) comprises a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:146-181, 185-221, 225-254 and / or 258-288, and / or (iv) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of any one of SEQ ID NO:74, 77, 80, 83, 145, 184, 224 or 257; (b) is an endogenous unbranched 2 (UB2) gene, which (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:84; (ii) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:85; (iii) comprises a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:146-181, 185-221, 225-254 and / or 258-288, and / or (iv) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of any one of SEQ ID NO:74, 77, 80, 83, 145, 184, 224 or 257. NO:90-96 or 332-393, and / or (iv) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of SEQ ID NO:86; or (c) is an endogenous UB3 gene, which: (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:87; (ii) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:88; (iii) comprises a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:90, 97-103 or 394-445, and / or (iv) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of SEQ ID NO:89, thereby producing a plant or part thereof having a mutated endogenous IPA1 gene and altered plant architecture, improved yield traits and / or increased tolerance / resistance to abiotic and biotic stresses.

[0019] In the eleventh aspect, a guide nucleic acid that binds to a target site in an endogenous IPA1 gene is provided, wherein the endogenous IPA1 gene: (a) is an endogenous SQUAMOSA promoter binding protein-like 9 (SPL9) gene, which (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 72, 75, 78, 81, 143, 182, 222 or 255; (ii) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 73, 76, 79, 82, 144, 183, 223 or 256; (iii) comprises a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288, and / or (iv) encodes a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: NO:74, 77, 80, 83, 145, 184, 224 or 257; (b) is an endogenous unbranched 2 (UB2) gene, which (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:84; (ii) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:85; (iii) comprises a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:90-96 or 332-393, and / or (iv) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of SEQ ID NO:86; or (c) is an endogenous unbranched 3 (UB3) gene, which: (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:87; (ii) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:85; NO:88 has a coding sequence with at least 80% sequence identity; (iii) contains a region with at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs:90, 97-103 or 394-445, and / or (iv) encodes a polypeptide sequence with at least 80% identity to the amino acid sequence of SEQ ID NO:89.

[0020] In a twelfth aspect, a system comprises a guide nucleic acid of the invention and a CRISPR-Cas effector protein associated with the guide nucleic acid.

[0021] The thirteenth aspect provides a gene editing system, which comprises a CRISPR-Cas effector protein associated with a guide nucleic acid, wherein the guide nucleic acid comprises a spacer sequence that binds to the IPA1 gene.

[0022] The fourteenth aspect provides a complex comprising a CRISPR-Cas effector protein containing a cleavage domain and a guide nucleic acid, wherein the guide nucleic acid binds to a target site in an IPA1 gene, wherein the IPA1 gene (a) is an endogenous SQUAMOSA promoter binding protein-like 9 (SPL9) gene, which (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 72, 75, 78, 81, 143, 182, 222 or 255; (ii) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 73, 76, 79, 82, 144, 183, 223 or 256; (iii) comprises a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288, and / or (iv) encodes a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: NO:74, 77, 80, 83, 145, 184, 224 or 257; (b) is an endogenous unbranched 2 (UB2) gene, which (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:84; (ii) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:85; (iii) comprises a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:90-96 or 332-393, and / or (iv) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of SEQ ID NO:86; or (c) is an endogenous unbranched 3 (UB3) gene, which: (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:87; (ii) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:85; NO:88 has a coding sequence with at least 80% sequence identity; (iii) comprises a region with at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs:349-445, and / or (iv) encodes a polypeptide sequence with at least 80% identity to the amino acid sequence of SEQ ID NO:89, wherein the cleavage domain cleaves the target chain in the IPA1 gene.

[0023] The fifteenth aspect provides an expression cassette, comprising (a) a polynucleotide encoding a CRISPR-Cas effector protein comprising a cleavage domain, and (b) a guide nucleic acid that binds to a target site in the IPA1 gene, wherein the guide nucleic acid comprises a spacer sequence that is complementary to and binds to the target site in the IPA1 gene.

[0024] In a sixteenth aspect, a mutant nucleic acid encoding a SPL9 polypeptide is provided, the mutant nucleic acid comprising a sequence having at least 90% sequence identity to any one of SEQ ID NOs: 389-300.

[0025] In a seventeenth aspect, a mutant nucleic acid encoding a UB2 polypeptide is provided, the mutant nucleic acid comprising a sequence having at least 90% sequence identity to any one of SEQ ID NO: 320, 322 or 324.

[0026] In the eighteenth aspect, a mutant nucleic acid encoding a UB3 polypeptide is provided, the mutant nucleic acid comprising a sequence having at least 90% sequence identity to any one of SEQ ID NO: 310, 312, 314, 316 or 318.

[0027] In the nineteenth aspect, a soybean plant or part thereof is provided, comprising at least one mutation in at least one SLP9 gene with a gene identification number (gene ID) of Glyma_02G177500 (SPL9a), Glyma_09G113800 (SPL9b), Glyma_03g143100 (SPL9c) and / or Glyma_19g146000 (SPL9d).

[0028] The twentieth aspect provides a guide nucleic acid, which binds to a target nucleic acid in the SPL9 gene with a gene identification number (gene ID) of Glyma_02G177500 (SPL9a), Glyma_09G113800 (SPL9b), Glyma_03g143100 (SPL9c) and / or Glyma_19g146000 (SPL9d).

[0029] Another aspect provides a mutated endogenous SPL9 gene in a plant cell, wherein the mutated endogenous SPL9 gene comprises a nucleic acid sequence that is at least 90% identical to any one of SEQ ID NOs: 389-300.

[0030] On the other hand, a mutated endogenous unbranched 2 (UB2) gene in a plant cell is provided, wherein the mutated endogenous UB2 gene comprises a nucleic acid sequence that is at least 90% identical to any one of SEQ ID NOs: 320, 322, or 324, and / or a mutated endogenous unbranched 3 (UB3) gene in a plant cell, wherein the mutated endogenous UB3 gene comprises a nucleic acid sequence that is at least 90% identical to any one of SEQ ID NOs: 310, 312, 314, 316, or 318.

[0031] In another aspect, provided is a mutant unbranched 2 (UB2) polypeptide in a plant cell, the mutant UB2 polypeptide having at least 90% identity to any one of SEQ ID NOs: 321, 323 or 325, and / or a mutant endogenous unbranched 3 (UB3) polypeptide in a plant cell, the mutant UB3 polypeptide having at least 90% identity to any one of SEQ ID NOs: 311, 313, 315, 317 or 319.

[0032] Also provided are polypeptides, polynucleotides, nucleic acid constructs, expression cassettes and vectors for making the plants or parts thereof of the present invention.

[0033] These and other aspects of the invention will be described in more detail in the following description of the invention.

[0034] A brief description of the sequence

[0035] SEQ ID NOs: 1-17 are exemplary Cas12a amino acid sequences that can be used in the present invention.

[0036] SEQ ID NOs: 18-20 are exemplary Cas12a nucleotide sequences that can be used in the present invention.

[0037] SEQ ID NOs: 21-22 are exemplary regulatory sequences encoding promoters and introns.

[0038] SEQ ID NOs: 23-29 are exemplary cytosine deaminase sequences that can be used in the present invention.

[0039] SEQ ID NOs: 30-40 are exemplary adenine deaminase amino acid sequences that can be used in the present invention.

[0040] SEQ ID NO: 41 is an exemplary uracil-DNA glycosylase inhibitor (UGI) sequence that can be used in the present invention.

[0041] SEQ ID NOs: 42-44 provide examples of the locations of the protospacer-adjacent motifs of type V CRISPR-Cas12a nucleases.

[0042] SEQ ID NOs:45-47 provide exemplary peptide tags and affinity polypeptides that can be used in the present invention.

[0043] SEQ ID NOs:48-58 provide exemplary RNA recruitment motifs and corresponding affinity polypeptides that can be used in the present invention.

[0044] SEQ ID NOs:59-60 are exemplary Cas9 polypeptide sequences that can be used in the present invention.

[0045] SEQ ID NOs:61-71 are exemplary Cas9 polynucleotide sequences that can be used in the present invention.

[0046] SEQ ID NO:72 is an exemplary SPL9a genomic sequence.

[0047] SEQ ID NO:73 is an exemplary SPL9a coding (cds) sequence.

[0048] SEQ ID NO:74 is an exemplary SPL9a polypeptide sequence.

[0049] SEQ ID NO:75 is an exemplary SPL9b genomic sequence.

[0050] SEQ ID NO:76 is an exemplary SPL9b coding (cds) sequence.

[0051] SEQ ID NO:77 is an exemplary SPL9b polypeptide sequence.

[0052] SEQ ID NO:78 is an exemplary SPL9c genomic sequence.

[0053] SEQ ID NO:79 is an exemplary SPL9c coding (cds) sequence.

[0054] SEQ ID NO:80 is an exemplary SPL9c polypeptide sequence.

[0055] SEQ ID NO:81 is an exemplary SPL9d genomic sequence.

[0056] SEQ ID NO:82 is an exemplary SPL9d coding (cds) sequence.

[0057] SEQ ID NO:83 is an exemplary SPL9d polypeptide sequence.

[0058] SEQ ID NO:84 is an exemplary UB2 genomic sequence.

[0059] SEQ ID NO:85 is an exemplary UB2 coding (cds) sequence.

[0060] SEQ ID NO:86 is an exemplary UB2 polypeptide sequence.

[0061] SEQ ID NO:87 is an exemplary UB3 genomic sequence.

[0062] SEQ ID NO:88 is an exemplary UB3 coding (cds) sequence.

[0063] SEQ ID NO:89 is an exemplary UB3 polypeptide sequence.

[0064] SEQ ID NO:90 is an exemplary UB3 promoter region.

[0065] SEQ ID NO:91, SEQ ID NO:92, and SEQ ID NO:93 are exemplary portions of the 5'UTR region of the UB2 nucleic acid.

[0066] SEQ ID NO:94 and SEQ ID NO:95 are exemplary intron regions of UB2 nucleic acids.

[0067] SEQ ID NO:96 is an exemplary portion of the 3'UTR region of the UB2 nucleic acid.

[0068] SEQ ID NO:97 and SEQ ID NO:98 are exemplary UB3 promoter regions.

[0069] SEQ ID NO:99 is an exemplary portion of the 5'UTR region of a UB3 nucleic acid.

[0070] SEQ ID NO: 100 and SEQ ID NO: 101 are exemplary intron regions of UB3 nucleic acids.

[0071] SEQ ID NO: 102 and SEQ ID NO: 103 are exemplary 3'UTR regions of UB3 nucleic acids.

[0072] SEQ ID NOs: 104-124 and 301 are exemplary spacer sequences of nucleic acid guide sequences that can be used to target SPL9 nucleic acids.

[0073] SEQ ID NOs: 125-142, 326 and 327 are exemplary spacer sequences of nucleic acid guide sequences that can be used to target UB2 and UB3 nucleic acids.

[0074] SEQ ID NO: 144 is an exemplary SPL9a genomic sequence.

[0075] SEQ ID NO: 145 is an exemplary SPL9a coding (cds) sequence.

[0076] SEQ ID NO: 146 is an exemplary SPL9a polypeptide sequence.

[0077] SEQ ID NO: 182 is an exemplary SPL9b genomic sequence.

[0078] SEQ ID NO: 183 is an exemplary SPL9b coding (cds) sequence.

[0079] SEQ ID NO: 184 is an exemplary SPL9b polypeptide sequence.

[0080] SEQ ID NO:222 is an exemplary SPL9c genomic sequence.

[0081] SEQ ID NO:223 is an exemplary SPL9c coding (cds) sequence.

[0082] SEQ ID NO:224 is an exemplary SPL9c polypeptide sequence.

[0083] SEQ ID NO:255 is an exemplary SPL9d genomic sequence.

[0084] SEQ ID NO:256 is an exemplary SPL9d coding (cds) sequence.

[0085] SEQ ID NO:257 is an exemplary SPL9d polypeptide sequence.

[0086] SEQ ID NOs: 146-181, 185-221, 225-254 and 258-288 are exemplary portions or regions of SPL9a, SPL9b, SPL9c and SPL9d genomic sequences.

[0087] SEQ ID NOs:289-300 are exemplary SPL9 sequences edited / modified as described herein.

[0088] SEQ ID NOs: 307-303 are exemplary deletions of SPL9 sequences.

[0089] SEQ ID NOs: 310, 312, 314, 316 and 318 are exemplary UB3 gene sequences edited / modified as described herein.

[0090] SEQ ID NOs: 311, 313, 315, 317 and 319 are exemplary UB3 polypeptide sequences encoded by mutant UB3 gene sequences SEQ ID NOs: 310, 312, 314, 316 and 318, respectively.

[0091] SEQ ID NOs: 320, 322 and 324 are exemplary UB2 gene sequences edited / modified as described herein.

[0092] SEQ ID NOs: 321, 323 and 325 are exemplary UB2 polypeptide sequences encoded by mutant UB3 gene sequences SEQ ID NOs: 320, 322 and 324, respectively.

[0093] SEQ ID NOs: 330-331 are exemplary deletions of UB3 / UB2 sequences.

[0094] SEQ ID NOs: 332-445 are exemplary portions or regions of UB2 and UB3 genomic sequences. DETAILED DESCRIPTION

[0095] The present invention will now be described hereinafter with reference to examples, in which embodiments of the present invention are shown. This specific embodiment is not intended to be a detailed catalog of all different ways in which the present invention can be implemented or all features that can be added to the present invention. For example, the features shown in one embodiment may be incorporated into other embodiments, and the features shown in a specific embodiment may be deleted from the embodiment. Therefore, the present invention contemplates that in some embodiments of the present invention, any feature or combination of features set forth herein may be excluded or omitted. In addition, it will be apparent to those skilled in the art, according to the present disclosure, that many changes and additions to the various embodiments proposed herein will not deviate from the present invention. Therefore, the following description is intended to illustrate some specific embodiments of the present invention, rather than to describe in detail all its permutations, combinations and variations.

[0096] Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the invention belongs. The terms used in the description of the present invention are for the purpose of describing particular embodiments only and are not intended to be limiting of the present invention.

[0097] All publications, patent applications, patents, and other references cited herein are incorporated by reference in their entirety for the teachings relevant to the sentence and / or paragraph in which the reference is presented.

[0098] Unless the context indicates otherwise, it is specifically intended that the various features of the invention described herein may be used in any combination. In addition, the present invention also contemplates that in some embodiments of the present invention, any feature or combination of features set forth herein may be excluded or omitted. For illustration, if the specification states that a composition comprises components A, B, and C, it is specifically intended that any one of A, B, or C or a combination thereof may be omitted and abandoned, either individually or in any combination.

[0099] As used in the description of the invention and the appended claims, the singular forms "a", "an" and "the" are intended to include the plural forms as well, unless the context clearly indicates otherwise.

[0100] Also as used herein, "and / or" refers to and encompasses any and all possible combinations of one or more of the associated listed items, as well as the lack of a combination when interpreted in the alternative ("or").

[0101] As used herein, the term "about" when referring to a measurable value such as an amount or concentration, is intended to encompass variations of ±10%, ±5%, ±1%, ±0.5%, or even ±0.1% of the specified value as well as the specified value. For example, "about X," where X is a measurable value, is intended to include X as well as variations of ±10%, ±5%, ±1%, ±0.5%, or even ±0.1% of X. The ranges of measurable values ​​provided herein may include any other ranges and / or individual values ​​therein.

[0102] As used herein, phrases such as "between X and Y" and "between about X and Y" should be interpreted to include X and Y. As used herein, phrases such as "between about X and Y" mean "between about X and about Y," and phrases such as "from about X to Y" mean "from about X to about Y."

[0103] Recitation of ranges of values ​​herein are merely intended to serve as a shorthand method of referring individually to each separate value falling within the range, unless otherwise indicated herein, and each separate value is incorporated into the specification as if it were individually recited herein. For example, if a range of 10 to 15 is disclosed, 11, 12, 13, and 14 are also disclosed.

[0104] As used herein, the terms “comprising,” “including,” and “having” specify the presence of stated features, integers, steps, operations, elements, and / or components, but do not preclude the presence or addition of one or more other features, integers, steps, operations, elements, components, and / or groups thereof.

[0105] As used herein, the transitional phrase "consisting essentially of" means that the scope of the claim should be interpreted to encompass the specified materials or steps recited in the claim as well as those materials or steps that do not materially affect the basic and novel characteristics of the claimed invention. Therefore, when used in the claims of the present invention, the term "consisting essentially of" is not intended to be interpreted as being equivalent to "comprising".

[0106] As used herein, the terms "increase", "increasing", "increased", "enhance", "enhanced", "enhancing" and "enhancement" (and grammatical variations thereof) describe an increase of at least about 5%, 10%, 15%, 20%, 25%, 50%, 75%, 100%, 150%, 200%, 300%, 400%, 500% or more compared to a control. A control plant is typically the same plant as the edited plant, but the control plant has not been similarly edited and therefore does not contain (lack) the mutation. The control plant can be an isogenic plant and / or a wild-type plant. Thus, the control plant can be the same breeding line, variety or cultivar as the test plant into which the mutation is introgressed as described herein, but the control breeding line, variety or cultivar does not have the mutation. In some embodiments, comparisons between plants of the invention and control plants are performed under identical growing conditions, such as identical environmental conditions (soil, hydration, light, heat, nutrients, etc.).

[0107] As used herein, the terms "reduce", "reduced", "reducing", "reduction", "decrease" and "lower" (and grammatical variations thereof) describe, for example, a decrease of at least about 5%, 10%, 15%, 20%, 25%, 35%, 50%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9% or 100% compared to a control. In certain embodiments, the decrease can result in no or substantially no (i.e., a negligible amount, e.g., less than about 10% or even 5%) detectable activity or amount.

[0108] As used herein, the term "expression" ("express", "expresses", "expressed" or "expression"), etc., with respect to nucleic acid molecules and / or nucleotide sequences (e.g., RNA or DNA) means that the nucleic acid molecules and / or nucleotide sequences are transcribed and optionally translated. Thus, the nucleic acid molecules and / or nucleotide sequences can express a polypeptide of interest or, for example, a functional non-translated RNA.

[0109] A "heterologous" or "recombinant" nucleotide sequence is a nucleotide sequence that is not naturally associated with the host cell into which it is introduced, including non-naturally occurring multiple copies of a naturally occurring nucleotide sequence. A "heterologous" nucleotide / polypeptide may originate from a foreign species or, if from the same species, has been substantially modified from its native form in composition and / or genomic locus by deliberate human intervention.

[0110] A "native" or "wild-type" nucleic acid, nucleotide sequence, polypeptide, or amino acid sequence refers to a naturally occurring or endogenous nucleic acid, nucleotide sequence, polypeptide, or amino acid sequence. Thus, for example, a "wild-type endogenous ideal plant architecture 1 (IPA1) gene" is an IPA2 gene that is naturally occurring in a reference organism (e.g., a plant) or endogenous to the reference organism. As another example, a SQUAMOSA promoter binding protein-like 9 (SPL9) gene is an SPL9 gene (e.g., SPL9a, SPL9b, SPL9c, SPL9d) that is naturally occurring in a reference organism (e.g., a plant, such as a soybean plant) or endogenous to the reference organism; and an endogenous branchless 2 (UB2) gene or an endogenous branchless 3 (UB3) gene is an UB2 / UB3 gene that is naturally occurring in a reference organism (e.g., a plant, such as a corn plant) or endogenous to the reference organism.

[0111] As used herein, the term "heterozygous" refers to a genetic state in which different alleles are located at corresponding loci on homologous chromosomes.

[0112] As used herein, the term "homozygous" refers to a genetic state in which identical alleles are located at corresponding loci on homologous chromosomes.

[0113] As used herein, the term "allele" refers to one of two or more different nucleotides or nucleotide sequences occurring at a particular locus.

[0114] A "null allele" is a non-functional allele caused by a gene mutation that results in no production of the corresponding protein or production of a non-functional protein.

[0115] A "knockout mutation" is a mutation that produces a nonfunctional protein, but it may have a detectable transcript or protein. A "recessive mutation" is a genetic mutation that produces a phenotype when homozygous, but the phenotype is not observable when the locus is heterozygous.

[0116] A "dominant mutation" is a gene mutation that produces a mutant phenotype in the presence of a non-mutated copy of the gene. A dominant mutation can be a loss-of-function or gain-of-function mutation, a hypomorphic mutation, a hypermorphic mutation, or a weak loss-of-function or weak gain-of-function.

[0117] A "dominant negative mutation" is a mutation that produces an altered gene product (e.g., one that has an abnormal function relative to the wild type) that adversely affects the function of the wild type allele or gene product. For example, a "dominant negative mutation" can block the function of a wild type gene product. A dominant negative mutation may also be referred to as a "reversal allele mutation."

[0118] A "semidominant mutation" is a mutation in which the penetrance of the phenotype in a heterozygous organism is less than the penetrance of the phenotype observed in a homozygous organism.

[0119] A "weak loss-of-function mutation" is a mutation that results in a gene product that has partial function or reduced function (partial inactivation) compared to the wild-type gene product.

[0120] A "hypofunctional allele mutation" is a mutation that results in a partial loss of gene function, which may occur through reduced expression (e.g., reduced protein and / or reduced RNA) or reduced functional performance (e.g., reduced activity), but not a complete loss of function / activity. A "hypofunctional" allele is a semi-functional allele caused by a gene mutation that results in the production of a corresponding protein that functions at anywhere between 1% and 99% of normal efficiency.

[0121] A "hyperallelic mutation" is a mutation that results in increased expression of a gene product and / or increased activity of a gene product.

[0122] A "gain of function" allele or mutation is a mutation that confers a new function to the encoded gene product and / or confers a new gene expression pattern. In some embodiments, a gain of function mutation may be a dominant or semi-dominant mutation.

[0123] As used herein, "non-natural mutation" refers to a mutation produced by human intervention that is different from a naturally occurring (e.g., naturally occurring) mutation found in the same gene. As used herein, a "non-natural" mutation does not include a mutation produced in a gene by human intervention, but it is a mutation identical to a naturally occurring mutation in the gene.

[0124] A "locus" is the location on a chromosome where a gene or marker or allele is located. In some embodiments, a locus may encompass one or more nucleotides.

[0125] As used herein, the terms "desired allele," "target allele," and / or "allele of interest" are used interchangeably to refer to an allele associated with a desired trait. In some embodiments, a desired allele may be associated with an increase or decrease (relative to a control) in a given trait, depending on the nature of the desired phenotype.

[0126] A marker is "associated with" a trait when it is linked to the marker and when the presence of the marker is an indication of whether and / or to what extent the desired trait or trait form occurs in the plant / germplasm containing the marker. Similarly, a marker is "associated with" an allele or chromosomal interval when it is linked to the allele or chromosomal interval and when the presence of the marker is an indication of whether the allele or chromosomal interval is present in the plant / germplasm containing the marker.

[0127] As used herein, the terms "backcross" and "backcrossing" refer to the process of crossing a progeny plant back to one of its parents one or more times (e.g., 1, 2, 3, 4, 5, 6, 7, 8 times, etc.). In a backcrossing protocol, the "donor" parent refers to the parent plant that has the desired gene or locus to be introgressed. The "recipient" parent (used one or more times) or the "recurrent" parent (used two or more times) refers to the parent plant into which the gene or locus is introgressed. For example, see Ragot, M. et al., Marker-assisted Backcrossing: A Practical Example, in TECHNIQUES ETUTILISATIONS DE MARQUEURS MOLECULAIRES LES COLLOQUES, Vol. 72, pp. 45-56 (1995); and Openshaw et al., Marker-assisted Selection in Backcross Breeding, in PROCEEDINGS OF THE SYMPOSIUM "ANALYSIS OF MOLECULAR MARKER DATA," pp. 41-43 (1994). The initial cross produces the F1 generation. The term "BC1" refers to the second use of the recurrent parent, "BC2" refers to the third use of the recurrent parent, and so on.

[0128] As used herein, the term "cross" or "crossed" refers to the production of offspring (e.g., cells, seeds, or plants) by the fusion of gametes through pollination. The term encompasses sexual crossing (pollination of one plant to another) and selfing (self-pollination, e.g., when pollen and ovules are from the same plant). The term "crossing" refers to the act of fusion of gametes through pollination to produce offspring.

[0129] As used herein, the term "introgression" ("introgression", "introgressing" and "introgressed") refers to the natural and artificial transmission of a desired allele or combination of desired alleles of one or more genetic loci from one genetic background to another genetic background. For example, the desired allele at a given locus can be transmitted to at least one progeny by sexual hybridization between two parents of the same species, wherein at least one parent has the desired allele in its genome. Alternatively, for example, the transmission of the allele can occur by recombination between two donor genomes, such as in fused protoplasts, wherein at least one donor protoplast has the desired allele in its genome. The desired allele can be a selected allele of a marker, QTL, transgenic, etc. The offspring containing the desired allele can be backcrossed one or more times (e.g., 1, 2, 3, 4 or more times) with a strain having a desired genetic background, selecting the desired allele, with the result that the desired allele is fixed in the desired genetic background. For example, a marker associated with increased yield under non-water stress conditions can be introgressed from a donor into a recurrent parent that does not contain the marker and does not exhibit increased yield under non-water stress conditions. The resulting offspring can then be backcrossed one or more times and selected until the progeny possess the genetic marker associated with increased yield under non-water stress conditions in the recurrent parent background.

[0130] A "genetic map" is a description of the genetic linkage relationships between loci on one or more chromosomes within a given species, usually depicted in a graphical or tabular form. For each genetic map, the distances between loci are measured by the frequencies of recombination between them. A variety of markers can be used to detect recombination between loci. A genetic map is a product of the mapping population, the type of markers used, and the polymorphic potential of each marker between different populations. The order and genetic distance between loci can vary from genetic map to genetic map.

[0131] As used herein, the term "genotype" refers to the genetic constitution of an individual (or individual population) at one or more genetic loci, in contrast to observable and / or detectable and / or phenotype traits (phenotypes). Genotype is defined by the alleles of one or more known loci inherited by an individual from its parents. The term genotype can be used to refer to the genetic constitution of an individual at a single locus, a plurality of loci, or more generally, the term genotype can be used to refer to the genetic constitution of all genes in an individual genome. Genotype can be, for example, indirectly characterized using a mark and / or directly characterized by nucleic acid sequencing.

[0132] As used herein, the term "germplasm" refers to the genetic material of an individual (e.g., plant), a group of individuals (e.g., plant strains, varieties or families), or clones derived from strains, varieties, species or cultures, or from an individual (e.g., plant), a group of individuals (e.g., plant strains, varieties or families), or clones derived from strains, varieties, species or cultures. Germplasm can be a part of an organism or cell or can be separated from an organism or cell. In general, germplasm provides genetic material with a specific genetic composition, providing a basis for some or all of the genetic qualities of an organism or cell culture. As used herein, germplasm includes cells, seeds or tissues that can grow new plants, and plant parts (e.g., leaves, stems, buds, roots, pollen, cells, etc.) that can be cultured into complete plants.

[0133] As used herein, the terms "cultivar" and "variety" refer to a group of similar plants distinguishable from other varieties within the same species by structural or genetic characteristics and / or performance.

[0134] As used herein, the terms "exotic", "exotic strains" and "exotic germplasm" refer to any plant, strain or germplasm that is not superior. Generally speaking, the exotic plant / germplasm is not derived from any known superior plant or germplasm, but is selected to introduce one or more desired genetic elements into a breeding program (e.g., introducing new alleles into a breeding program).

[0135] As used herein, the term "hybrid" in the context of plant breeding refers to a plant that is the offspring of genetically distinct parents produced by crossing plants of different lines or varieties or species, including but not limited to a cross between two inbred lines.

[0136] As used herein, the term "inbred" refers to a substantially homozygous plant or variety. The term can refer to a plant or plant variety that is substantially homozygous throughout the genome, or a plant or plant variety that is substantially homozygous for a portion of the genome of particular interest.

[0137] A "haplotype" is the genotype of an individual at multiple genetic loci, i.e., a combination of alleles. Typically, the genetic loci that define a haplotype are physically and genetically linked, i.e., on the same chromosome segment. The term "haplotype" may refer to a polymorphism at a specific locus, such as a single marker locus, or a polymorphism at multiple loci along a chromosome segment.

[0138] As used herein, the term "heterologous" refers to a nucleotide / polypeptide derived from a foreign species, or, if derived from the same species, a nucleotide / polypeptide that is substantially modified from its native form in composition and / or genomic locus by deliberate human intervention.

[0139] Plants in which at least one orthologous IPA1 gene encoding a SPL transcription factor is modified as described herein (e.g., comprises a modification as described herein) can have altered plant architecture, improved yield traits, and / or increased tolerance / resistance to abiotic and biotic stresses compared to a plant or plant part lacking the same modification (e.g., mutation) in at least one orthologous IPA1 gene. As used herein, "improved yield trait" refers to any plant trait associated with growth, such as biomass, yield, nitrogen use efficiency (NUE), inflorescence size / weight, fruit yield, fruit quality, fruit size, seed size, seed number, leaf tissue weight, nodule number, nodule quality, nodulation activity, seed ear number, tiller number, number of branches, flower number, tuber number, tuber quality, bulb quality, seed number, total seed mass, leaf emergence rate, tiller / branch emergence rate, seedling emergence rate, root length, root number, root mass size and / or weight, or any combination thereof. Thus, in some aspects, "improved yield traits" may include, but are not limited to, increased inflorescence yield, increased fruit yield (e.g., increased number, weight and / or size of fruits; for example, increased number, weight and / or size of ears, for example for corn), increased fruit quality, increased number, size and / or weight of roots, increased meristem size, increased seed size, increased biomass, increased leaf size, improved nitrogen use efficiency, increased height, increased number of internodes and / or increased internode length compared to a control plant or part thereof (e.g., a plant not comprising / lacking a mutated endogenous IPA1 nucleic acid (e.g., a mutant IPA1 gene)). In some embodiments, plant of the present invention or its part can show improved yield trait, wherein improved yield trait includes but is not limited to one or more phenotypes in following phenotype: in any combination, optionally increase the number of grain rows, increase the grain size, increase the ear length, reduce the tiller number, reduce the tassel branch number, reduce the time to flowering, increase the number of seeds per strain plant, increase the number of pods per node and / or increase per strain plant and / or increase the seed weight.Improved yield trait can also be caused by the increase of planting density of plant of the present invention.Therefore, in some aspects, plant of the present invention can be planted with increased density (due to the changed plant configuration caused by endogenous mutation), compared with the control plant planted with the same density, this causes improved yield trait.In some aspects, improved yield trait can be expressed as the quantity of grain produced per unit land area (for example, bushel number per acre of land).

[0140] As used herein, "control plants" means plants that do not contain one or more edited IPA1 genes as described herein, which confers enhanced / improved traits (e.g., yield traits) or altered phenotypes. Control plants are used to identify and select plants edited as described herein, which have enhanced traits or altered phenotypes compared to control plants. Suitable control plants can be parental line plants used to produce plants containing mutated IPA1 genes, for example, wild-type plants lacking editing in endogenous IPA1 genes as described herein. Suitable control plants can also be plants containing recombinant nucleic acids that confer other traits, for example, transgenic plants with enhanced herbicide tolerance. In some cases, suitable control plants can be progeny of heterozygous or hemizygous transgenic plant lines lacking mutated IPA1 genes as described herein, referred to as negative segregants or negative isogenic lines.

[0141] The enhanced traits can be, for example, reduced days from planting to maturity, increased stem size, increased leaf number, increased vegetative stage plant height growth rate, increased ear size, increased dry weight per plant ear, increased number of grains per ear, increased per grain weight, increased number of grains per plant, reduced empty ear grains, extended grain filling period, reduced plant height, increased root branch number, increased total root length, increased yield, improved nitrogen use efficiency, and improved water use efficiency compared to control plants. The altered phenotype can be, for example, plant height, biomass, canopy area, anthocyanin content, chlorophyll content, water application, water content, and water use efficiency.

[0142] As used herein, "properties" are physiology, morphology, biochemistry or physical characteristics of plants or specific plant materials or cells. In some cases, this feature is visible to the human eye and can be measured mechanically, such as the size, weight, shape, form, length, height, growth rate and developmental stage of seeds or plants, or can be measured by biochemical techniques, such as protein, starch, some metabolites or the oil content of detection seeds or leaves, or by observing metabolism or physiological processes, for example, by measuring the tolerance to lack of water or specific salt or sugar concentration, or by measuring the expression level of one or more genes, for example, by adopting Northern analysis, RT-PCR, microarray gene expression array or reporter gene expression system, or by agricultural observations such as high osmotic stress tolerance or yield. However, any technology can be used to measure the amount, comparative level or difference of any selected chemical compound or macromolecule in transgenic plants.

[0143] As used herein, "enhanced traits" refers to plant characteristics caused by mutations in the IPA1 gene as described herein. Such traits include, but are not limited to, enhanced agronomic traits characterized by enhanced plant morphology, physiology, growth and development, yield, nutritional enhancement, disease or pest resistance, or environmental or chemical tolerance. In some embodiments, the enhanced trait / altered phenotype can be, for example, reduced days from planting to maturity, increased stem size, increased number of leaves, increased plant height growth rate in the vegetative stage, increased ear size, increased dry weight per plant ear, increased number of grains per ear, increased weight per grain, increased number of grains per plant, reduced empty grains per ear, extended filling period, reduced plant height, increased number of root branches, increased total root length, drought tolerance, improved water use efficiency, cold tolerance, improved nitrogen use efficiency, and increased yield. In some embodiments, the trait is an increased yield under non-stress conditions or an increased yield under environmental stress conditions. Stress conditions can include biotic and abiotic stresses, such as drought, shading, fungal diseases, viral diseases, bacterial diseases, insect infestation, nematode infestation, low temperature exposure, heat exposure, osmotic stress, nitrogen nutrient availability reduction, phosphorus nutrient availability reduction and high plant density. "Yield" can be affected by many characteristics, including but not limited to plant height, plant biomass, pod number, pod position on plant, internode number, pod cracking incidence, grain size, ear size, ear tip filling degree, grain abortion, nodulation and nitrogen fixation efficiency, nutrient assimilation efficiency, biotic and abiotic stress resistance, carbon assimilation, plant configuration, lodging resistance, seed germination percentage, seedling vigor and juvenile traits. Yield can also be affected by the following factors: germination efficiency (including germination under stress conditions), growth rate (including growth rate under stress conditions), flowering time and duration, ear number, ear size, ear weight, number of seeds per ear or per pod, seed size, composition (starch, oil, protein) of seed and the characteristics of seed filling.

[0144] As also used herein, the term "trait modification" encompasses altering a naturally occurring trait by producing a detectable characteristic difference in a plant comprising a mutation in an endogenous IPA1 gene encoding an SPL transcription factor as described herein relative to a plant not comprising the mutation (such as a wild-type plant, or a negative segregant). In some cases, trait modifications can be evaluated quantitatively. For example, a trait modification can result in an increase or decrease in an observed trait characteristic or phenotype compared to a control plant. It is well known that modified traits may have natural variation. Thus, an observed trait modification results in a normal distribution and a change in magnitude of the trait characteristic or phenotype in a plant compared to a control plant.

[0145] The present disclosure relates to plants with improved economically important characteristics, more specifically increased yield. More specifically, the present disclosure relates to a plant comprising a mutation in an IPA1 gene as described herein, wherein the plant has increased yield compared to a control plant lacking the mutation. In some embodiments, the plants produced as described herein exhibit increased yield or improved yield trait components compared to control plants. In some embodiments, the plants of the present disclosure exhibit improved traits associated with yield, including but not limited to increased nitrogen use efficiency, increased nitrogen stress tolerance, increased water use efficiency, and increased drought tolerance, as defined and discussed below.

[0146] Yield can be defined as a measurable product with economic value from crops. Yield can be defined in the range of quantity and / or quality. Yield can directly depend on several factors, for example, the number and size of organs, plant configuration (such as the number of branches, plant biomass, such as increased root biomass, steeper root angle and / or longer root, etc.), flowering time and duration, filling period. Root configuration and development, photosynthetic efficiency, nutrient absorption, stress tolerance, early vigor, delayed senescence and functional stay-green phenotype may be the factors determining yield. Therefore, optimizing the above factors can help increase crop yield.

[0147] The increase / improvement of the yield correlated traits mentioned herein also can be considered to refer to the increase of the biomass (weight) of one or more parts of plant, and these one or more parts can comprise above-ground and / or underground (can gather in the crops) plant parts.Particularly, this type of part that can gather in the crops is seed, and the execution of the disclosed method produces the plant of the seed yield with the yield of increase, particularly with respect to the seed yield of suitable control plant.The " yield " of term plant can relate to the nutrient biomass (root and / or seedling biomass), reproductive organ and / or propagule (such as seed) of this plant.

[0148] The increased yield of the plants of the present disclosure can be measured in a variety of ways, including test weight, number of seeds per plant, seed weight, number of seeds per unit area (e.g., number of seeds per acre or seed weight), bushels per acre, tons per acre, or kilograms per hectare. The increased yield can be attributed to improved utilization of key biochemical compounds (such as nitrogen, phosphorus, and carbohydrates), or to improved responses to environmental stresses (such as cold, heat, drought, salt, shade, high plant density, and pest or pathogen attack).

[0149] "Increased yield" can be manifested as one or more of the following: (i) increased plant biomass (weight) of one or more parts of the plant, in particular the aboveground (harvestable) parts of the plant, increased root biomass (increased number of roots, increased root thickness, increased root length) or increased biomass of any other harvestable part; or (ii) increased early vigour, defined herein as increased aboveground area of ​​seedlings about three weeks after germination.

[0150] "Early vigor" refers to active and healthy plant growth, especially in the early stages of plant growth, and can be due to, for example, plant better adapting to its environment (for example, optimizing the utilization of energy, nutrient absorption and carbon distribution between seedling and root) caused by the increase in plant fitness. For example, early vigor can be a combination of the ability of seeds to germinate and emerge after planting and the ability of seedlings to grow and develop after emergence. Plants with early vigor also show increased seedling survival rate and better crop planting, which can usually make the field highly uniform, wherein most plants basically reach each development stage at the same time, thereby usually increasing output. Therefore, early vigor can be determined by measuring various factors, such as grain weight, germination percentage, emergence percentage, seedling growth, seedling height, root length, root and seedling biomass, canopy size and color, etc.

[0151] In addition, increased yield can also be manifested as increased total seed yield, which can be attributed to one or more of the following: an increase in seed biomass (seed weight) due to an increase in seed weight per plant and / or individual seed, e.g., an increased number of flowers / panicles per plant; an increased number of pods; an increased number of nodes; an increased number of flowers ("florets") per panicle / plant; an increased seed filling rate; an increased number of filled seeds; an increased seed size (length, width, area, girth), which can also affect seed composition; and / or an increased seed volume, which can also affect seed composition. In one embodiment, the increased yield can be increased seed yield, e.g., increased seed weight; an increased number of filled seeds; and an increased harvest index.

[0152] Increased production may also result in configurational changes or may be due to

[0153] Occurs due to changes in plant architecture.

[0154] Increased yield can also be expressed as an increased harvest index, which is expressed as

[0155] The ratio of the yield of harvestable parts (such as seeds) to the total biomass

[0156] The present disclosure also extends to harvestable parts of plants, such as, but not limited to, seeds, leaves, fruits, flowers, pods, pods, siliques, nuts, stems, rhizomes, tubers and bulbs. The present disclosure also relates to products derived from harvestable parts of such plants, such as dry pellets, powders, oils, fats and fatty acids, starch or proteins.

[0157] The present disclosure provides a method for increasing the "yield" of a plant or the "broadacre yield" of a plant or plant part, which is defined as the harvestable plant part per unit area, such as number of seeds per acre or seed weight, pounds per acre, bushels per acre, tons per acre, tons per acre, kilograms per hectare.

[0158] As used herein, "nitrogen use efficiency" refers to the processes that lead to increased plant yield, biomass, vigor, and growth rate per unit of nitrogen applied. These processes may include plant absorption, assimilation, accumulation, signal transduction, sensing, retransfer (within the plant), and utilization of nitrogen.

[0159] As used herein, "increased nitrogen use efficiency" refers to the ability of a plant to grow, develop or produce faster or better than normal when subjected to the same available / applied amount of nitrogen as under normal or standard conditions; the ability of a plant to grow, develop or produce normally, or the ability to grow, develop or produce faster or better when subjected to less than optimal available / applied amounts of nitrogen or under nitrogen limiting conditions.

[0160] As used herein, "nitrogen limiting conditions" refers to growing conditions or environments that provide less than the optimal amount of nitrogen required for adequate or successful metabolism, growth, reproductive success, and / or survival of a plant.

[0161] As used herein, "increased nitrogen stress tolerance" refers to the ability of a plant to grow, develop or produce normally, or to grow, develop or produce faster or better, when subjected to less than optimal available / applied amounts of nitrogen or under nitrogen limiting conditions.

[0162] The improved plant nitrogen utilization efficiency can be converted into a similar amount of yield in the field while supplying less nitrogen, or an increased yield can be obtained by supplying an optimum / sufficient amount of nitrogen. The improved nitrogen utilization efficiency can improve plant nitrogen stress tolerance, and can also improve the biochemical composition of crop quality and seeds, such as protein yield and oil yield. The terms "improved nitrogen utilization efficiency", "enhanced nitrogen utilization efficiency" and "nitrogen stress tolerance" are used interchangeably in this disclosure and refer to plants with improved productivity under nitrogen limiting conditions.

[0163] As used herein, "water use efficiency" refers to the amount of carbon dioxide assimilated by leaves per unit of transpiration water vapor. It constitutes one of the most important traits controlling plant productivity in dry environments. "Drought tolerance" refers to the degree to which plants adapt to dry or drought conditions. The physiological response of plants to water shortage includes leaf wilting, reduced leaf area, leaf shedding, and stimulating root growth by directing nutrients to the underground parts of the plant. Generally, plants are more susceptible to drought during flowering and seed development (reproduction stage) because the resources of the plant are biased to support root growth. In addition, abscisic acid (ABA) is a plant stress hormone that induces the closure of leaf stomata (microscopic pores involved in gas exchange), thereby reducing water loss caused by transpiration and reducing photosynthesis rate. These reactions improve the water use efficiency of plants in the short term. The terms "improved water use efficiency", "enhanced water use efficiency" and "increased drought tolerance" are used interchangeably in this disclosure and refer to plants with improved productivity under water-limited conditions.

[0164] As used herein, "increased water use efficiency" refers to the ability of a plant to grow, develop or produce faster or better than normal when subjected to the same available / applied amount of water as under normal or standard conditions; the ability of a plant to grow, develop or produce normally, or the ability to grow, develop or produce faster or better when subjected to reduced available / applied amounts of water (water input) or under conditions of water stress or water deficiency stress.

[0165] As used herein, "increased drought tolerance" refers to the ability of a plant to grow, develop or produce normally, or to grow, develop or produce faster or better than normal, when subjected to reduced available / applied amounts of water and / or under conditions of short-term or long-term drought; the ability of a plant to grow, develop or produce normally when subjected to reduced available / applied amounts of water (water input) or under conditions of water stress or under conditions of short-term or long-term drought.

[0166] As used herein, "drought stress" refers to a dry period (short or long / extended) that results in a lack of water and stresses the plant and / or causes damage to plant tissue and / or has a negative impact on grain / crop yield; a dry period (short or long / extended) that results in a lack of water and / or an increase in temperature and stresses the plant and / or causes damage to plant tissue and / or has a negative impact on grain / crop yield.

[0167] As used herein, "water deficit" refers to conditions or circumstances that provide less than the optimal amount of water required for adequate / successful growth and development of plants.

[0168] As used herein, "water stress" refers to a condition or environment that provides an inappropriate amount of water (less / insufficient or more / excessive) relative to the amount of water required for adequate / successful growth and development of the plant / crop, thereby stressing the plant and / or causing damage to plant tissue and / or negatively affecting grain / crop yield.

[0169] As used herein, "water stress" refers to a condition or environment that provides less / insufficient water than required for adequate / successful growth and development of a plant / crop, thereby stressing the plant and / or causing damage to plant tissue and / or negatively affecting grain yield.

[0170] As used herein, the terms "nucleic acid", "nucleic acid molecule", "nucleotide sequence" and "polynucleotide" refer to linear or branched, single-stranded or double-stranded RNA or DNA, or a hybrid thereof. The term also encompasses RNA / DNA hybrids. When synthesizing dsRNA, less common bases such as inosine, 5-methylcytosine, 6-methyladenine, hypoxanthine, etc. can also be used for antisense, dsRNA and ribozyme pairing. For example, polynucleotides containing C-5 propyne analogs of uridine and cytidine have been shown to bind RNA with high affinity and are potent antisense inhibitors of gene expression. Other modifications may also be made, such as modifications to the 2'-hydroxyl in the phosphodiester backbone or the RNA ribose group.

[0171] As used herein, the term "nucleotide sequence" refers to a heteropolymer of nucleotides or a sequence of these nucleotides from the 5' to 3' end of a nucleic acid molecule, and includes DNA or RNA molecules, including cDNA, DNA fragments or parts, genomic DNA, synthetic (e.g., chemically synthesized) DNA, plasmid DNA, mRNA and antisense RNA, any of which can be single-stranded or double-stranded. The terms "nucleotide sequence", "nucleic acid", "nucleic acid molecule", "nucleic acid construct", "oligonucleotide" and "polynucleotide" are also used interchangeably herein to refer to a heteropolymer of nucleotides. Nucleic acid molecules and / or nucleotide sequences provided herein are presented in 5' to 3' directions from left to right herein, and are represented by the standard code for representing nucleotide characters specified in the World Intellectual Property Organization (WIPO) standard ST.26. As used herein, "5' region" can represent the polynucleotide region closest to the 5' end of a polynucleotide. Therefore, for example, the elements in the 5' region of a polynucleotide can be located at any position from the first nucleotide at the 5' end of a polynucleotide to the nucleotide located in the middle of a polynucleotide. As used herein, "3' region" can represent the polynucleotide region closest to the 3' end of a polynucleotide. Thus, for example, elements in the 3' region of a polynucleotide can be located anywhere from the first nucleotide at the 3' end of the polynucleotide to a nucleotide located in the middle of the polynucleotide.

[0172] As used herein with respect to nucleic acids, the terms "fragment" or "portion" refer to a portion of a nucleic acid that is reduced in length (e.g., by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 20, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 400, 450, 500, 550, 660, 670, 680, 690, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800 The nucleic acid fragment may be a nucleic acid having a length of 100, 200, 300, 400, 500, 600, 700, 750, 800, 850 or 900 nucleotides or more, or any range or value therein) and comprising, consisting essentially of and / or consisting of a nucleotide sequence of contiguous nucleotides that are identical or nearly identical (e.g., 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identical) to the corresponding portion of the reference nucleic acid. Where appropriate, such a nucleic acid fragment may be contained in a larger polynucleotide of which the nucleic acid fragment is a component. As an example, the repeat sequence of the guide nucleic acid of the present invention may include a portion of a wild-type CRISPR-Cas repeat sequence (e.g., a wild-type CRISPR-Cas repeat sequence; for example, a repeat sequence from a CRISPR Cas system, such as Cas9, Cas12a (Cpf1), Cas12b, Cas12c (C2c3), Cas12d (CasY), Cas12e (CasX), Cas12g, Cas12h, Cas12i, C2c4, C2c5, C2c8, C2c9, C2c10, Cas14a, Cas14b and / or Cas14c, etc.).

[0173] In some embodiments, the nucleic acid fragment may comprise about 20, 30, 40, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 900, 10 ... 500, 5000, 5500, 6000, 6500, 7000 or more consecutive nucleotides, or any range or value therein.

[0174] In some embodiments, a "sequence-specific nucleic acid binding domain" (e.g., a sequence-specific DNA binding domain) can bind to one or more fragments or portions of an IPA1 nucleic acid (e.g., IPA1 and / or its orthologs) encoding an SPL transcription factor as described herein (e.g., SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288).

[0175] As used herein with respect to polypeptides, the term "fragment" or "portion" may refer to a polypeptide that is reduced in length relative to a reference polypeptide and comprises, consists essentially of, and / or consists of an amino acid sequence of contiguous amino acids that are identical or nearly identical (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identical) to the corresponding portion of the reference polypeptide. Where appropriate, such a polypeptide fragment may be included in a larger polypeptide of which it is a component. In some embodiments, the polypeptide fragment comprises, consists essentially of, or consists of at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 125, 150, 175, 200, 225, 250, 260, 270, 280, 290, or 300 or more contiguous amino acids of a reference polypeptide. In some embodiments, the polypeptide fragment may include a polypeptide encoded by an endogenous IPA1 gene or an ortholog thereof (e.g., SEQ ID NO: 74, SEQ ID NO: 77, SEQ ID NO: 80, SEQ ID NO: 83, SEQ ID NO: 86, SEQ ID NO: 89, SEQ ID NO: 145, SEQ ID NO: 184, SEQ ID NO: 224, and / or SEQ ID NO: 146). 357, 368, 369, 370, 372, or 373 or more consecutive amino acid residues, or any range or value therein, of a fragment or portion of a polypeptide (e.g., a polypeptide having a moiety or a component thereof) of at least one of the foregoing invention. In some embodiments, the deletion can be an in-frame deletion. In some embodiments, such deletions can be null mutations, dominant negative mutations, semi-dominant mutations, hyperallelic mutations, or weak loss-of-function mutations (e.g., hyperallelic mutations), which, when included in a plant, can produce plants that exhibit improved yield traits without reducing disease resistance, plants that exhibit improved yield traits and increased disease resistance, and / or plants with increased disease resistance.In some embodiments, at least one mutation in an endogenous IPA1 gene in a plant can produce a plant with altered plant architecture, improved yield traits, and / or increased tolerance / resistance to abiotic and biotic stresses compared to a plant or plant part lacking the same mutation. Improved yield traits can include, but are not limited to, increased yield (bu / acre), increased number of kernel rows, increased ear length, ears exhibiting increased number of kernel rows without substantially decreasing ear length, increased kernel size, increased number of branches, increased number of flowers, increased number of nodes, increased biomass, increased tassel branch number (TBN), decreased number of tillers, decreased tassel branch number (TBN), increased number of seeds, increased seed size / weight, increased number of pods per node, increased number of pods per plant, etc., compared to a plant not comprising the deletion. In some embodiments, the improved yield traits in plants or parts thereof of the present invention may include one or more of the following phenotypes: increased number of kernel rows, increased kernel size, increased ear length, reduced number of tillers, reduced number of tassel branches, reduced time to flowering, increased number of seeds per plant, increased number of pods per node and / or per plant, and / or increased seed weight, in any combination.

[0176] The IPA1 gene or its ortholog may be edited at more than one position, thereby providing an IPA1 gene or its ortholog comprising more than one mutation. A plant may comprise more than one IPA1 gene or its ortholog, and one or more than one IPA1 gene or its ortholog in a plant may be edited.

[0177] In some embodiments, a “portion” or “region” of a nucleic acid refers to at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75 94, 95, 96, 97, 98, 99, or 100 or more consecutive nucleotides. In some embodiments,63, 64, 65, 66, 67, 68, 69, 70, 75, 80, 81, 82, 83, 84, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 30 , 102, 103, 104, 105, 110, 111, 12, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 140 , 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 170, 171, 172, 173, 174, 175 , 180, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 205, 206, 207, 208, 209, 211, 212, 213, 214, 215, 216, 217, 218, 219 9, 220, 221, 222, 223, 224, 225, 230, 235, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 260, 265, 270, 275, 276, 277, 2 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, or 450 or more consecutive nucleotides, or any range or value therein (e.g.,With reference to the nucleotide numbering from about nucleotide 2001 to about nucleotide 2364 of SEQ ID NO:72, with reference to the nucleotide numbering from about nucleotide 1 to about nucleotide 364 of SEQ ID NO:73, with reference to the nucleotide numbering from about nucleotide 2001 to about nucleotide 2370 of SEQ ID NO:75, with reference to the nucleotide numbering from about nucleotide 1 to about nucleotide 370 of SEQ ID NO:76, with reference to the nucleotide numbering from about nucleotide 2001 to about nucleotide 2347 of SEQ ID NO:78, with reference to the nucleotide numbering from about nucleotide 1 to about nucleotide 347 of SEQ ID NO:79, with reference to the nucleotide numbering from about nucleotide 2001 to about nucleotide 2349 of SEQ ID NO:81, or with reference to the nucleotide numbering from about nucleotide 1 to about nucleotide 349 of SEQ ID NO:82; for example, SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288). In some embodiments, reference to a "portion" or "region" of a polypeptide refers to at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75 1, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 175, 200, 225, 250, 275, 300, 325 or 350 or more consecutive amino acid residues.,

[0178] In some embodiments, a "sequence-specific nucleic acid binding domain" can bind to one or more fragments or portions of a nucleotide sequence encoding a SPL N-containing transcription factor as described herein.

[0179] As used herein with respect to nucleic acids, the term "functional fragment" refers to a nucleic acid encoding a functional fragment of a polypeptide. A "functional fragment" with respect to a polypeptide is a fragment of a polypeptide that retains one or more activities of a native reference polypeptide.

[0180] As used herein, the term "gene" refers to a nucleic acid molecule that can be used to produce mRNA, antisense RNA, miRNA, anti-microRNA antisense oligodeoxyribonucleotides (AMOs), etc. A gene may or may not be used to produce a functional protein or gene product. A gene may include coding regions and non-coding regions (e.g., introns, regulatory elements, promoters, enhancers, termination sequences, and / or 5' and 3' untranslated regions). A gene can be "isolated," which means that the nucleic acid is substantially or substantially free of components that are usually present with the nucleic acid under natural conditions. Such components include other cell materials, culture media from recombinant production, and / or various chemicals for chemically synthesizing nucleic acids.

[0181] The term "mutation" refers to a point mutation (e.g., missense or nonsense, or insertion or deletion of a single base pair that results in a frameshift), insertion, deletion, and / or truncation. When a mutation is a replacement of a residue within an amino acid sequence by another residue, or a deletion or insertion of one or more residues within a sequence, the mutation is typically described by identifying the original residue, followed by identifying the position of the residue within the sequence, and the identity of the newly replaced residue. Truncation may include truncation at the C-terminus of a polypeptide or the N-terminus of a polypeptide. Truncation of a polypeptide may be the result of a corresponding 5' or 3' end deletion of a gene encoding a polypeptide. Frameshift mutations may occur when deletions or insertions of one or more base pairs are introduced into a gene. Frameshift mutations in a gene may result in the production of a polypeptide that is longer, shorter, or the same length as a wild-type polypeptide, depending on when the first stop codon appears after the mutation region of the gene.

[0182] As used herein, the terms "complementary" or "complementarity" refer to the natural binding of polynucleotides by base pairing under permissive salt and temperature conditions. For example, the sequence "AGT" (5' to 3') binds to the complementary sequence "TCA" (3' to 5'). The complementarity between two single-stranded molecules can be "partial", in which only some of the nucleotides bind, or it can be complete when there is complete complementarity between the single-stranded molecules. The degree of complementarity between nucleic acid chains has a significant effect on the efficiency and strength of hybridization between nucleic acid chains.

[0183] As used herein, "complement" can mean 100% complementarity to a compared nucleotide sequence, or it can mean less than 100% complementarity to a compared nucleotide sequence (e.g., about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, etc. complementarity).

[0184] Different nucleic acids or proteins with homology are referred to herein as "homologs". The term homolog includes homologous sequences from the same species and other species and orthologous sequences from the same species and other species." Homology " refers to the level of similarity between two or more nucleic acid and / or amino acid sequences, expressed as a percentage of positional identity (i.e., sequence similarity or identity). Homology also refers to the concept of having similar functional properties between different nucleic acids or proteins. Therefore, the compositions and methods of the present invention also include homologs of the nucleotide sequences and polypeptide sequences of the present invention. As used herein, "orthologs" refer to homologous nucleotide sequences and / or amino acid sequences in different species, which are derived from common ancestral genes during the process of speciation. Homologs of the nucleotide sequences of the invention have substantial sequence identity (e.g., at least about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, or 100%) to the nucleotide sequences of the invention.

[0185] As used herein, "sequence identity" refers to the degree to which two optimally aligned polynucleotide or polypeptide sequences are unchanged over the entire component (e.g., nucleotide or amino acid) comparison window. "Identity" can be readily calculated by known methods, including but not limited to the methods described in the following documents: Computational Molecular Biology (Lesk, AM ed.) Oxford University Press, New York (1988); Biocomputing: Informatics and Genome Projects (Smith, DW ed.) Academic Press, New York (1993); Computer Analysis of Sequence Data, Part I (Griffin, AM and Griffin, HG ed.) Humana Press, New Jersey (1994); Sequence Analysis in Molecular Biology (von Heinje, G. ed.) Academic Press (1987); and Sequence Analysis Primer (Gribskov, M. and Devereux, J. ed.) Stockton Press, New York (1991).

[0186] As used herein, the term "percent sequence identity" or "percent identity" refers to the percentage of identical nucleotides in a linear polynucleotide sequence of a reference ("query") polynucleotide molecule (or its complementary strand) compared to a test ("subject") polynucleotide molecule (or its complementary strand) when the two sequences are optimally aligned. In some embodiments, "percent sequence identity" may refer to the percentage of identical amino acids in an amino acid sequence compared to a reference polypeptide.

[0187] As used herein, the phrases "substantially identical" or "substantial identity" in the context of two nucleic acid molecules, nucleotide sequences, or polypeptide sequences, means that two or more sequences or subsequences have at least about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, or 100% nucleotide or amino acid residue identity when compared and aligned for maximum correspondence as determined using one of the following sequence comparison algorithms, or by visual inspection. In some embodiments of the invention, substantial identity exists over a region of contiguous nucleotides of a nucleotide sequence of the invention, the region being from about 10 nucleotides to about 20 nucleotides, from about 10 nucleotides to about 25 nucleotides, from about 10 nucleotides to about 30 nucleotides, from about 15 nucleotides to about 25 nucleotides, from about 30 nucleotides to about 40 nucleotides, from about 50 nucleotides to about 60 nucleotides, from about 70 nucleotides to about 80 nucleotides, from about 90 nucleotides to about 100 nucleotides, from about 100 nucleotides to about 200 nucleotides, from about 100 nucleotides to about 300 nucleotides, from about 100 nucleotides to about 400 nucleotides, from about 100 nucleotides to about 500 nucleotides, from about 100 nucleotides to about 600 nucleotides, from about 100 nucleotides to about 800 nucleotides, from about 100 nucleotides to about 900 nucleotides, or longer, or any range therein, up to the full length of the sequence. In some embodiments, the nucleotide sequences may be substantially identical over at least about 20 nucleotides (e.g., about 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 60, 70, or 80 nucleotides or more).

[0188] In some embodiments of the invention, substantial identity exists over a region of contiguous amino acid residues of a polypeptide of the invention that is from about 3 amino acid residues to about 20 amino acid residues, from about 5 amino acid residues to about 25 amino acid residues, from about 7 amino acid residues to about 30 amino acid residues, from about 10 amino acid residues to about 25 amino acid residues, from about 15 amino acid residues to about 30 amino acid residues, from about 20 amino acid residues to about 40 amino acid residues, from about 25 amino acid residues to about 40 amino acid residues, from about 25 amino acid residues to about 50 amino acid residues, from about 30 amino acid residues to about 50 amino acid residues, from about 40 amino acid residues to about 50 amino acid residues, from about 40 amino acid residues to about 70 amino acid residues, from about 50 amino acid residues to about 70 amino acid residues, from about 60 amino acid residues to about 80 amino acid residues, from about 70 amino acid residues to about 80 amino acid residues, from about 90 amino acid residues to about 100 amino acid residues, or more, and any ranges therein, up to the full length of the sequence. 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111 150, 175, 200, 225, 250, 300, 350 or more amino acids or more consecutive amino acid residues) are substantially identical to each other.In some embodiments, two or more SPL polypeptides can be identical or substantially identical (e.g., at least 70% to 99.9% identical; for example, about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.9% identical, or any range or value thereof).

[0189] For sequence comparison, usually one sequence acts as a reference sequence compared to a test sequence. When using a sequence comparison algorithm, the test sequence and the reference sequence are input into a computer, subsequence coordinates are specified if necessary, and sequence algorithm program parameters are specified. Then, the sequence comparison algorithm calculates the sequence identity percentage of the test sequence relative to the reference sequence based on the specified program parameters.

[0190] Optimal alignment of sequences for comparison windows is well known to those skilled in the art and can be performed by tools such as the local homology algorithm of Smith and Waterman, the homology alignment algorithm of Needleman and Wunsch, the similarity search method of Pearson and Lipman, and optionally by computerized implementations of these algorithms, such as GAP, BESTFIT, FASTA and TFASTA, which can be used as Wisconsin (Accelrys Inc., San Diego, CA). The "identity score" for the alignment fragment of the test sequence and the reference sequence is the number of identical components shared by the two aligned sequences divided by the total number of components in the reference sequence fragment (e.g., the entire reference sequence or a smaller defined portion of the reference sequence). The percentage of sequence identity is expressed as the identity score multiplied by 100. The comparison of one or more polynucleotide sequences can be a comparison with a full-length polynucleotide sequence or a portion thereof, or a comparison with a longer polynucleotide sequence. For purposes of the present invention, BLASTX version 2.0 can also be used to determine the "identity percentage" for the translated nucleotide sequence, and BLASTN version 2.0 can be used to determine the "identity percentage" for the polynucleotide sequence.

[0191] When two nucleotide sequences hybridize to each other under stringent conditions, the two sequences may also be considered to be substantially complementary. In some embodiments, two nucleotide sequences that are considered to be substantially complementary hybridize to each other under highly stringent conditions.

[0192] In the context of nucleic acid hybridization experiments (such as Southern and Northern hybridizations), "stringent hybridization conditions" and "stringent hybridization wash conditions" are sequence-dependent and are different under different environmental parameters. An extensive guide to nucleic acid hybridization can be found in Tijssen Laboratory Techniques in Biochemistry and Molecular Biology-Hybridization with Nucleic Acid Probes Part I Chapter 2 "Overview of principles of hybridization and the strategy of nucleic acid probe assays" Elsevier, New York (1993). In general, highly stringent hybridization and wash conditions are selected to be higher than the thermal melting point (Tf) for the specific sequence at a defined ionic strength and pH. m ) is about 5℃ lower.

[0193] T m It is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Very stringent conditions are chosen to be equal to the T for a specific probe. m. An example of stringent hybridization conditions for hybridization of complementary nucleotide sequences with more than 100 complementary residues on a filter membrane in a Southern or Northern blot is hybridization overnight with 50% formamide and 1 mg of heparin at 42°C. An example of highly stringent washing conditions is washing with 0.15M NaCl at 72°C for about 15 minutes. An example of stringent washing conditions is washing with 0.2x SSC at 65°C for 15 minutes (for a description of SSC buffer, see Sambrook below). Typically, a low stringency wash is performed before a high stringency wash to remove background probe signals. For example, an example of a medium stringency wash for a duplex of more than 100 nucleotides is washing with 1x SSC at 45°C for 15 minutes. For example, an example of a low stringency wash for a duplex of more than 100 nucleotides is washing with 4-6x SSC at 40°C for 15 minutes. For short probes (e.g., about 10 to 50 nucleotides), stringent conditions typically involve a salt concentration of less than about 1.0 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3, and a temperature of typically at least about 30° C. Stringent conditions may also be achieved by adding a destabilizing agent such as formamide. In general, a signal-to-noise ratio of 2 times (or higher) that observed for an unrelated probe in a particular hybridization assay indicates that specific hybridization has been detected. Nucleotide sequences that do not hybridize to each other under stringent conditions are still substantially identical if the proteins encoded by the nucleotide sequences are substantially identical. This occurs, for example, when a copy of a nucleotide sequence is produced using the maximum codon degeneracy allowed by the genetic code.

[0194] The polynucleotides and / or recombinant nucleic acid constructs (e.g., expression cassettes and / or vectors) of the invention may be codon optimized for expression. In some embodiments, the polynucleotides, nucleic acid constructs, expression cassettes and / or vectors of the editing systems of the invention (e.g., comprising / encoding sequence-specific nucleic acid binding domains (e.g., sequence-specific nucleic acid binding domains from: polynucleotide-guided endonucleases, zinc finger nucleases, transcription activator-like effector nucleases (TALENs), Argonaute proteins and / or CRISPR-Cas endonucleases (e.g., CRISPR-Cas effector proteins) (e.g., type I CRISPR-Cas effector proteins, type II CRISPR-Cas effector proteins, type III CRISPR-Cas effector proteins, type IV CRISPR-Cas s effector protein, type V CRISPR-Cas effector protein or type VI CRISPR-Cas effector protein)), nucleases (e.g., endonucleases (e.g., Fok1), polynucleotide-guided endonucleases, CRISPR-Cas endonucleases (e.g., CRISPR-Cas effector proteins), zinc finger nucleases and / or transcription activator-like effector nucleases (TALENs)), deaminase proteins / domains (e.g., adenine deaminase, cytosine deaminase), polynucleotides encoding reverse transcriptase proteins or domains, polynucleotides encoding 5'-3' exonuclease polypeptides and / or affinity polypeptides, peptide tags, etc.) can be codon-optimized for expression in plants. In some embodiments, a codon-optimized nucleic acid, polynucleotide, expression cassette, and / or vector of the invention has about 70% to about 99.9% (e.g., 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.9%, or 100%) or more identity to a reference nucleic acid, polynucleotide, expression cassette, and / or vector that has not been codon-optimized.

[0195] In any of the embodiments described herein, the polynucleotides or nucleic acid constructs of the present invention may be operably associated with a variety of promoters and / or other regulatory elements for expression in plants and / or plant cells. Therefore, in some embodiments, the polynucleotides or nucleic acid constructs of the present invention may also include one or more promoters, introns, enhancers and / or terminators operably connected to one or more nucleotide sequences. In some embodiments, a promoter may be operably associated with an intron (e.g., Ubil promoter and intron). In some embodiments, a promoter associated with an intron may be referred to as a "promoter region" (e.g., Ubil promoter and intron).

[0196] As used herein, "operably linked" or "operably associated" in relation to a polynucleotide means that the indicated elements are functionally related to each other, and usually also physically related. Thus, as used herein, the term "operably linked" or "operably associated" refers to functionally associated nucleotide sequences on a single nucleic acid molecule. Thus, a first nucleotide sequence that is operably linked to a second nucleotide sequence refers to a situation where the first nucleotide sequence is in a functional relationship with the second nucleotide sequence. For example, if a promoter affects the transcription or expression of a nucleotide sequence, then the promoter is operably associated with the nucleotide sequence. Those skilled in the art will understand that a control sequence (e.g., a promoter) does not have to be adjacent to the nucleotide sequence to which it is operably associated, as long as the function of the control sequence is to direct its expression. Thus, for example, there may be an intervening untranslated but transcribed nucleic acid sequence between a promoter and a nucleotide sequence, and the promoter may still be considered to be "operably linked" to the nucleotide sequence.

[0197] As used herein, the term "linked" in relation to a polypeptide refers to the connection of one polypeptide to another polypeptide. A polypeptide may be linked to another polypeptide (at the N-terminus and / or C-terminus) directly (e.g., via a peptide bond) or via a linker.

[0198] The term "joint" is recognized in the art and refers to a chemical group or molecule that connects two molecules or parts, such as two domains of a fusion protein, such as, for example, a nucleic acid binding polypeptide or domain and a peptide tag and / or a reverse transcriptase and an affinity polypeptide bound to the peptide tag; or a DNA endonuclease polypeptide or domain and a peptide tag and / or a reverse transcriptase and an affinity polypeptide bound to the peptide tag. The joint may consist of a single connecting molecule, or may contain more than one connecting molecule. In some embodiments, the joint may be an organic molecule, a group, a polymer, or a chemical moiety, such as a divalent organic moiety. In some embodiments, the joint may be an amino acid, or may be a peptide. In some embodiments, the joint is a peptide.

[0199] In some embodiments, the length of a peptide linker useful in the invention can be from about 2 to about 100 or more amino acids, for example, about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75 , 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100 or more amino acids (e.g., about 2 to about 40, about 2 to about 50, about 2 to about 60, about 4 to about 40, about 4 to about 50, about 4 to about 60, about 5 to about 40, about 5 to about 50, about 5 to about 60 35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,50,51,52,53,54,55,56,57,58,59,50,51,52,53,54,55,56,57,58,59,50,51,52,53,54,55,56,57,58,59,50,51,52,53,54,55,56,57,58,59,50 In some embodiments, the peptide linker can be a GS linker.

[0200] As used herein, the term "connection" or "fusion" related to polynucleotides refers to the connection of one polynucleotide to another polynucleotide. In some embodiments, two or more polynucleotide molecules can be connected by a joint, which can be an organic molecule, a group, a polymer or a chemical part, such as a divalent organic part. Polynucleotides can be connected or fused to another polynucleotide (at the 5' end or 3' end) by covalent or non-covalent bonds or in conjunction (including, for example, by Watson-Crick base pairing or by one or more connecting nucleotides). In some embodiments, a polynucleotide motif of a certain structure can be inserted into another polynucleotide sequence (for example, an extension of a hairpin structure in a guide RNA). In some embodiments, the connecting nucleotides can be naturally occurring nucleotides. In some embodiments, the connecting nucleotides can be non-naturally occurring nucleotides.

[0201] "Promoter" is a nucleotide sequence that controls or regulates the transcription of a nucleotide sequence (e.g., a coding sequence) operably associated with the promoter. The coding sequence controlled or regulated by the promoter can encode a polypeptide and / or a functional RNA. Generally, "promoter" refers to a nucleotide sequence that contains a binding site for RNA polymerase II and guides transcription initiation. In general, the promoter is located at 5' or upstream of the start of the coding region of the corresponding coding sequence. The promoter may include other elements that act as gene expression regulatory factors; for example, a promoter region. These include a TATA box consensus sequence, and generally also include a CAAT box consensus sequence (Breathnach and Chambon, (1981) Annu. Rev. Biochem. 50: 349). In plants, the CAAT box can be replaced by an AGGA box (Messing et al., (1983) in Genetic Engineering of Plants, T. Kosuge, C. Meredith and A. Hollaender (eds.), Plenum Press, pp. 211-227).

[0202] Promoters useful in the present invention may include, for example, constitutive, inducible, temporally regulated, developmentally regulated, chemically regulated, tissue-preferred and / or tissue-specific promoters for use in preparing recombinant nucleic acid molecules, for example, "synthetic nucleic acid constructs" or "protein-RNA complexes." These different types of promoters are known in the art.

[0203] The selection of promoters may vary depending on the temporal and spatial requirements of expression, and may also vary depending on the host cell to be transformed. Promoters for many different organisms are well known in the art. Based on the extensive knowledge available in the art, appropriate promoters may be selected for a particular host organism of interest. Thus, for example, promoters upstream of genes that are highly constitutively expressed in model organisms are well known, and this knowledge may be easily obtained and implemented in other systems where appropriate.

[0204] In some embodiments, a promoter functional in plants can be used with the construct of the present invention. Non-limiting examples of promoters that can be used to drive expression in plants include the promoter of RubisCo small subunit gene 1 (PrbcS1), the promoter of the actin gene (Pactin), the promoter of the nitrate reductase gene (Pnr), and the promoter of the repeat carbonic anhydrase gene 1 (Pdca1) (see Walker et al., Plant Cell Rep. 23: 727-735 (2005); Li et al., Gene 403: 132-142 (2007); Li et al., Mol Biol. Rep. 37: 1143-1154 (2010)). PrbcS1 and Pactin are constitutive promoters, and Pnr and Pdca1 are inducible promoters. Pnr is induced by nitrate and repressed by ammonium (Li et al., Gene 403: 132-142 (2007)), and Pdca1 is induced by salt (Li et al., Mol Biol. Rep. 37: 1143-1154 (2010)). In some embodiments, the promoter useful in the present invention is an RNA polymerase II (Pol II) promoter. In some embodiments, the U6 promoter or 7SL promoter from corn (Zea mays) can be used in the constructs of the present invention. In some embodiments, the U6c promoter and / or the 7SL promoter from corn can be used to drive the expression of the guide nucleic acid. In some embodiments, the U6c promoter, U6i promoter and / or 7SL promoter from soybean (Glycine max) can be used in the constructs of the present invention. In some embodiments, the U6c promoter, U6i promoter and / or 7SL promoter from soybean can be used to drive the expression of the guide nucleic acid.

[0205] Examples of constitutive promoters useful in plants include, but are not limited to, the cestrum virus promoter (cmp) (U.S. Pat. No. 7,166,770), the rice actin 1 promoter (Wang et al. (1992) Mol. Cell. Biol. 12:3399-3406; and U.S. Pat. No. 5,641,876), the CaMV 35S promoter (Odell et al. (1985) Nature 313:810-812), the CaMV 19S promoter (Lawton et al. (1987) Plant Mol. Biol. 9:315-324), the nos promoter (Ebert et al. (1987) Proc. Natl. Acad. Sci. USA 84:5745-5749), the Adh promoter (Walker et al. (1987) Proc. Natl. Acad. Sci. USA 84:5745-5749), the 84:6624-6629), sucrose synthase promoter (Yang and Russell (1990) Proc. Natl. Acad. Sci. USA 87:4144-4148) and ubiquitin promoter. Constitutive promoters derived from ubiquitin accumulate in many cell types. Ubiquitin promoters have been cloned from several plant species for use in transgenic plants, for example, sunflower (Binet et al., 1991. Plant Science 79:87-94), corn (Christensen et al., 1989. Plant Molec. Biol. 12:619-632) and Arabidopsis thaliana (Norris et al., 1993. Plant Molec. Biol. 21:895-906). The corn ubiquitin promoter (UbiP) has been developed in a transgenic monocot system, and its sequence and vectors constructed for monocot transformation are disclosed in patent publication EP 0 342 926. The ubiquitin promoter is suitable for expressing the nucleotide sequence of the present invention in transgenic plants, especially monocotyledons. In addition, the promoter expression cassette described by McElroy et al. (Mol. Gen. Genet. 231: 150-160 (1991)) can be easily modified for the expression of the nucleotide sequence of the present invention, and is particularly suitable for monocotyledon hosts.

[0206] In some embodiments, tissue-specific / tissue-preferred promoters can be used to express heterologous polynucleotides in plant cells. Tissue-specific or preferred expression patterns include, but are not limited to, green tissue-specific or preferred, root-specific or preferred, stem-specific or preferred, flower-specific or preferred, or pollen-specific or preferred. Promoters suitable for expression in green tissues include many promoters of genes involved in photosynthesis, many of which are cloned from monocots and dicots. In one embodiment, a promoter useful in the present invention is the corn PEPC promoter (Hudspeth and Grula, Plant Molec.Biol.12:579-589 (1989)) from the phosphoenol carboxylase gene. Non-limiting examples of tissue-specific promoters include those associated with genes encoding seed storage proteins (such as β-conglycinin, cruciferin, napin, and phaseolin), zein or oil body proteins (such as oleosin), or proteins involved in fatty acid biosynthesis (including acyl carrier protein, stearoyl-ACP desaturase, and fatty acid desaturase (fad 2-1), as well as other nucleic acids expressed during embryo development (such as Bce4, see, e.g., Kridl et al. (1991) Seed Sci. Res. 1: 209-219; and EP Patent No. 255378). Tissue-specific or tissue-preferred promoters useful for expressing the nucleotide sequences of the present invention in plants, particularly corn, include, but are not limited to, those that direct expression in roots, pith, leaves, or pollen. Such promoters are disclosed, for example, in WO 93 / 07278 (incorporated herein by reference in its entirety).Other non-limiting examples of tissue-specific or tissue-preferred promoters that can be used in the present invention are the cotton rubisco promoter disclosed in U.S. Pat. No. 6,040,504; the rice sucrose synthase promoter disclosed in U.S. Pat. No. 5,604,121; the root-specific promoter described by de Framond (FEBS 290:103-106 (1991); EP 0 452 269 to Ciba-Geigy); the stem-specific promoter described in U.S. Pat. No. 5,625,136 (to Ciba-Geigy), which drives expression of the maize trpA gene; the tuberose yellow leaf curl virus promoter disclosed in WO 01 / 73087; and pollen-specific or -preferred promoters, including but not limited to ProOsLPS10 and ProOsLPS11 from rice (Nguyen et al., Plant Genetics, 1996). Biotechnol. Reports 9(5):297-306 (2015)), ZmSTK2_USP from maize (Wang et al., Genome 60(6):485-495 (2017)), LAT52 and LAT59 from tomato (Twell et al., Development 109(3):705-713 (1990)), Zm13 (U.S. Pat. No. 10,421,972), PLA2-δ promoter from Arabidopsis thaliana (U.S. Pat. No. 7,141,424) and / or ZmC5 promoter from maize (International PCT Publication No. WO1999 / 042587).

[0207] Additional examples of plant tissue-specific / tissue-preferred promoters include, but are not limited to, root hair-specific cis-element (RHE) (Kim et al., The Plant Cell 18:2958-2970 (2006)), root-specific promoters RCc3 (Jeong et al., Plant Physiol. 153:185-197 (2010)) and RB7 (U.S. Pat. No. 5,459,252), lectin promoter (Lindstrom et al. (1990) Der. Genet. 11:160-167; and Vodkin (1983) Prog. Clin. Biol. Res. 138:87-98), corn alcohol dehydrogenase 1 promoter (Dennis et al. (1984) Nucleic Acids Res. 12:3983-4000), S-adenosyl-L-methionine synthetase (SAMS) (Vander Mijnsbrugge et al. (1996) Plant and Cell Physiology, 37 (8): 1108-1115), maize light harvesting complex promoter (Bansal et al. (1992) Proc. Natl. Acad. Sci. USA 89: 3654-3658), maize heat shock protein promoter (O'Dell et al. (1985) EMBO J. 5: 451-458; and Rochester et al. (1986) EMBO J. 5: 451-458), pea small subunit RuBP carboxylase promoter (Cashmore, "Nuclear genes encoding the small subunit of ribulose-1,5-bisphosphate carboxylase" pp. 29-39, in: Genetic Engineering of Plants (Hollaender ed., Plenum Press, 1996), 1983; and Poulsen et al. (1986) Mol. Gen. Genet. 205:193-200), the Ti plasmid mannopine synthase promoter (Langridge et al. (1989) Proc. Natl. Acad. Sci. USA 86:3219-3223), the Ti plasmid nopaline synthase promoter (Langridge et al. (1989), supra), the petunia chalcone isomerase promoter (van Tunen et al. (1988) EMBO J. 7:1257-1263), the legume glycine-rich protein 1 promoter (Keller et al. (1989) Genes Dev.3:1639-1646), truncated CaMV 35S promoter (O'Dell et al. (1985) Nature 313:810-812), potato glycoprotein promoter (Wenzler et al. (1989) Plant Mol. Biol. 13:347-354), root cell promoter (Yamamoto et al. (1990) Nucleic Acids Res. 18:7449), zein promoter (Kriz et al. (1987) Mol. Gen. Genet. 207:90-98; Langridge et al. (1983) Cell 34:1015-1022; Reina et al. (1990) Nucleic Acids Res. 18:6425; Reina et al. (1990) Nucleic Acids Res. 18: 7449; and Wandelt et al. (1989) Nucleic Acids Res. 17: 2354), globulin-1 promoter (Belanger et al. (1991) Genetics 129: 863-872), α-tubulin cab promoter (Sullivan et al. (1989) Mol. Gen. Genet. 215: 431-440), PEPCase promoter (Hudspeth and Grula (1989) Plant Mol. Biol. 12: 579-589), R gene complex-associated promoter (Chandler et al. (1989) Plant Cell 1: 1175-1183) and chalcone synthase promoter (Franken et al. (1991) EMBO J. 10: 2605-2612).

[0208] Useful for seed-specific expression is the vicilin promoter (Czako et al. (1992) Mol. Gen. Genet. 235:33-40; and seed-specific promoters disclosed in U.S. Pat. No. 5,625,136). Useful promoters for expression in mature leaves are those that switch at the onset of senescence, such as the SAG promoter from Arabidopsis thaliana (Gan et al. (1995) Science 270:1986-1988).

[0209] In addition, promoters that are functional in chloroplasts can be used. Non-limiting examples of such promoters include phage T3 gene 9 5'UTR and other promoters disclosed in U.S. Patent No. 7,579,516. Other promoters that can be used in the present invention include, but are not limited to, the S-E9 small subunit RuBP carboxylase promoter and the Kunitz trypsin inhibitor gene promoter (Kti3).

[0210] Additional regulatory elements useful in the present invention include, but are not limited to, introns, enhancers, termination sequences, and / or 5' and 3' untranslated regions.

[0211] Introns that can be used in the present invention can be identified in plants and separated from plants, and then inserted into introns in expression cassettes for plant transformation. As will be appreciated by those skilled in the art, introns can include sequences required for self-excision and are incorporated into nucleic acid constructs / expression cassettes in frame. Introns can be used as spacers to separate multiple protein coding sequences in a nucleic acid construct, or introns can be used in a protein coding sequence, for example, to stabilize mRNA. If they are used in a protein coding sequence, they are inserted "in frame" and include excision sites. Introns can also be associated with promoters to improve or modify expression. As an example, promoter / intron combinations that can be used in the present invention include but are not limited to promoter / intron combinations of corn Ubil promoters and introns (see, for example, SEQ ID NO:21 and SEQ ID NO:22).

[0212] Non-limiting examples of introns that can be used in the present invention include introns from the following genes: ADHI gene (e.g., Adh1-S intron 1, 2 and 6), ubiquitin gene (Ubil), RuBisCO small subunit (rbcS) gene, RuBisCO large subunit (rbcL) gene, actin gene (e.g., actin-1 intron), pyruvate dehydrogenase kinase gene (pdk), nitrate reductase gene (nr), repeated carbonic anhydrase gene 1 (Tdca1), psbA gene, atpA gene, or any combination thereof.

[0213] In some embodiments, the polynucleotides and / or nucleic acid constructs of the present invention may be "expression cassettes", or may be contained within expression cassettes. As used herein, "expression cassettes" refer to recombinant nucleic acid molecules comprising, for example, one or more polynucleotides of the present invention (e.g., polynucleotides encoding sequence-specific nucleic acid (e.g., DNA) binding domains, polynucleotides encoding deaminase proteins or domains, polynucleotides encoding reverse transcriptase proteins or domains, polynucleotides encoding 5'-3' exonuclease polypeptides or domains, guide nucleic acids and / or reverse transcriptase (RT) templates), wherein the polynucleotides are operably associated with one or more control sequences (e.g., promoters, terminators, etc.). Thus, in some embodiments, one or more expression cassettes may be provided, which are designed to express, for example, a nucleic acid construct of the invention (e.g., a polynucleotide encoding a sequence-specific nucleic acid binding domain, a polynucleotide encoding a nuclease polypeptide / domain, a polynucleotide encoding a deaminase protein / domain, a polynucleotide encoding a reverse transcriptase protein / domain, a polynucleotide encoding a 5'-3' exonuclease polypeptide / domain, a polynucleotide encoding a peptide tag, and / or a polynucleotide encoding an affinity polypeptide, etc., or comprising a guide nucleic acid, an extended guide nucleic acid, and / or an RT template, etc.). When the expression cassette of the invention comprises more than one polynucleotide, the polynucleotide may be operably linked to a single promoter that drives expression of all polynucleotides, or the polynucleotide may be operably linked to one or more separate promoters (e.g., three polynucleotides may be driven by one, two, or three promoters in any combination). When two or more separate promoters are used, the promoters may be the same promoter, or they may be different promoters. Thus, when contained in a single expression cassette, a polynucleotide encoding a sequence-specific nucleic acid binding domain, a polynucleotide encoding a nuclease protein / domain, a polynucleotide encoding a CRISPR-Cas effector protein / domain, a polynucleotide encoding a deaminase protein / domain, a polynucleotide encoding a reverse transcriptase polypeptide / domain (e.g., an RNA-dependent DNA polymerase) and / or a polynucleotide encoding a 5'-3' exonuclease polypeptide / domain, a guide nucleic acid, an extended guide nucleic acid and / or an RT template can each be operably linked to a single promoter or separate promoters in any combination.

[0214] The expression cassette comprising the nucleic acid construct of the invention may be chimeric, meaning that at least one of its components is heterologous relative to at least one of its other components (e.g., a promoter from a host organism is operably linked to a polynucleotide of interest to be expressed in the host organism, wherein the polynucleotide of interest is from an organism different from the host, or is not normally associated with the promoter). The expression cassette may also be naturally occurring, but has been obtained in a recombinant form that can be used for heterologous expression.

[0215] The expression cassette may optionally include a transcription and / or translation termination region (i.e., termination region) and / or an enhancer region that is functional in a selected host cell. A variety of transcription terminators and enhancers are known in the art and can be used in expression cassettes. Transcription terminators are responsible for terminating transcription and correcting mRNA polyadenylation. Termination regions and / or enhancer regions may be natural to the transcription initiation region, may be natural to the following: for example, a gene encoding a sequence-specific nucleic acid binding protein, a gene encoding a nuclease, a gene encoding a reverse transcriptase, a gene encoding a deaminase, etc., or may be natural to a host cell, or may be natural to another source (e.g., to a promoter, a gene encoding a sequence-specific nucleic acid binding protein, a gene encoding a nuclease, a gene encoding a reverse transcriptase, a gene encoding a deaminase, etc., or to a host cell, or any combination thereof, exogenous or heterologous).

[0216] The expression cassette of the present invention may also include a polynucleotide encoding a selectable marker that can be used to select transformed host cells. As used herein, a "selectable marker" refers to a polynucleotide sequence that, when expressed, imparts a unique phenotype to the host cell expressing the marker, thereby allowing such transformed cells to be distinguished from cells without the marker. This polynucleotide sequence can encode a selectable or screenable marker, depending on whether the marker imparts a trait that can be selected by chemical means, such as by using a selection agent (e.g., antibiotics, etc.), or whether the marker is simply a trait that can be identified by observation or testing, such as by screening (e.g., fluorescence). Many examples of suitable selectable markers are known in the art and can be used in expression cassettes described herein.

[0217] In addition to expression cassettes, nucleic acid molecules / constructs and polynucleotide sequences described herein can also be used in combination with vectors. The term "vector" refers to a composition for transferring, delivering or introducing nucleic acids (or multiple nucleic acids) into a cell. Vectors include nucleic acid constructs (e.g., expression cassettes) comprising nucleotide sequences to be transferred, delivered or introduced. Vectors for transforming host organisms are well known in the art. Non-limiting examples of general class vectors include viral vectors, plasmid vectors, phage vectors, phagemid vectors, cosmid vectors, fosmid vectors, phages, artificial chromosomes, minicircles or double-stranded or single-stranded linear or circular forms of Agrobacterium binary vectors, which may or may not be self-transferable or removable. In some embodiments, viral vectors may include, but are not limited to, retroviruses, slow viruses, adenoviruses, adeno-associated viruses or herpes simplex virus vectors. Vectors as defined herein can be transformed prokaryotic or eukaryotic hosts by being integrated into the cell genome or being present outside the chromosome (e.g., autonomously replicating plasmids with a replication origin). In addition, shuttle vectors are also included, and shuttle vectors refer to DNA vectors that can be naturally or intentionally replicated in two different host organisms, and host organisms can be selected from actinomycetes and related species, bacteria and eukaryotic organisms (for example, higher plants, mammals, yeast or fungal cells). In some embodiments, the nucleic acid in the vector is controlled by a suitable promoter or other regulatory elements, and is operably connected to a suitable promoter or other regulatory elements so as to be transcribed in a host cell. The vector can be a bifunctional expression vector that works in a variety of hosts. In the case of genomic DNA, this can include its own promoter and / or other regulatory elements, and in the case of cDNA, this can be controlled by a suitable promoter and / or other regulatory elements so as to be expressed in a host cell. Therefore, the nucleic acid or polynucleotide of the present invention and / or the expression cassette comprising the nucleic acid or polynucleotide can be included in a vector as described herein and known in the art.

[0218] As used herein, "contact," "contacting," "contacted," and grammatical variations thereof refer to bringing together the components of a desired reaction under conditions suitable for carrying out the desired reaction (e.g., transformation, transcriptional control, genome editing, nicking and / or cleavage). As an example, a target nucleic acid can be contacted with a sequence-specific nucleic acid binding protein (e.g., a polynucleotide-guided endonuclease, a CRISPR-Cas endonuclease (e.g., a CRISPR-Cas effector protein), a zinc finger nuclease, a transcription activator-like effector nuclease (TALEN) and / or an Argonaute protein)) and a deaminase or a nucleic acid construct encoding these under the following conditions: the sequence-specific nucleic acid binding protein, the reverse transcriptase and / or the deaminase are expressed, the sequence-specific nucleic acid binding protein binds to the target nucleic acid, and the reverse transcriptase and / or the deaminase can be fused to the sequence-specific nucleic acid binding protein or recruited to the sequence-specific nucleic acid binding protein (e.g., by a peptide tag fused to the sequence-specific nucleic acid binding protein and an affinity tag fused to the reverse transcriptase and / or the deaminase), so that the deaminase and / or the reverse transcriptase are located near the target nucleic acid, thereby modifying the target nucleic acid. Other methods of recruiting reverse transcriptases and / or deaminases using other protein-protein interactions can be used, and RNA-protein interactions and chemical interactions can also be used for protein-protein and protein-nucleic acid recruitment.

[0219] As used herein, "modification" ("modifying" or "modification") of a target nucleic acid includes editing (e.g., mutation), covalent modification, exchanging / replacing nucleic acid / nucleotide bases, deletion, cleavage, nicking, and / or altering transcriptional control of a target nucleic acid. In some embodiments, the modification may include any type of one or more single base changes (SNPs).

[0220] "Introducing", "introduce", "introduced" (and grammatical variations thereof) in the context of a polynucleotide of interest refers to presenting a nucleotide sequence of interest (e.g., a polynucleotide, RT template, nucleic acid construct and / or guide nucleic acid) to a plant, a plant part thereof, or a cell thereof in a manner that enables the nucleotide sequence to enter the interior of the cell.

[0221] The terms "transformation" or "transfection" are used interchangeably and as used herein refer to the introduction of a heterologous nucleic acid into a cell. The transformation of a cell can be stable or transient. Thus, in some embodiments, a host cell or host organism (e.g., a plant) can be stably transformed with a polynucleotide / nucleic acid molecule of the present invention. In some embodiments, a host cell or host organism can be transiently transformed with a polynucleotide / nucleic acid molecule of the present invention.

[0222] "Transient transformation" in the context of a polynucleotide means that the polynucleotide is introduced into a cell but is not integrated into the genome of the cell.

[0223] "Stably introduced" or "stably introduced" in the context of a polynucleotide being introduced into a cell means that the introduced polynucleotide is stably incorporated into the genome of the cell, so that the cell is stably transformed with the polynucleotide.

[0224] As used herein, "stable transformation" or "stably transformed" refers to a nucleic acid molecule that is introduced into a cell and integrated into the genome of the cell. Thus, the integrated nucleic acid molecule is capable of being inherited by its progeny, more specifically, by successive generations of progeny. As used herein, "genome" includes nuclear and plastid genomes, and thus includes integration of nucleic acids into, for example, chloroplast or mitochondrial genomes. As used herein, stable transformation may also refer to a transgene that is maintained extrachromosomally, for example, as a minichromosome or plasmid.

[0225] Transient transformation can be detected by, for example, enzyme-linked immunosorbent assay (ELISA) or Western blotting, which can detect the presence of peptides or polypeptides encoded by one or more transgenics introduced into an organism. Stable transformation of cells can be detected by, for example, Southern blot hybridization assays of the genomic DNA of the cells with nucleic acid sequences that specifically hybridize with nucleotide sequences of transgenics introduced into an organism (e.g., a plant). Stable transformation of cells can be detected by, for example, Northern blot hybridization assays of the RNA of the cells with nucleic acid sequences that specifically hybridize with nucleotide sequences of transgenics introduced into a host organism. Stable transformation of cells can also be detected by, for example, polymerase chain reaction (PCR) or other amplification reactions well known in the art, which employ specific primer sequences that hybridize with target sequences of transgenics, resulting in amplification of transgenic sequences, which can be detected according to standard methods. Transformation can also be detected by direct sequencing and / or hybridization protocols well known in the art.

[0226] Thus, in some embodiments, the nucleotide sequences, polynucleotides, nucleic acid constructs and / or expression cassettes of the invention can be transiently expressed and / or they can be stably incorporated into the genome of a host organism. Thus, in some embodiments, the nucleic acid constructs of the invention (e.g., one or more expression cassettes comprising polynucleotides for editing as described herein) can be transiently introduced into a cell along with a guide nucleic acid, and therefore, DNA is not maintained in the cell.

[0227] The nucleic acid construct of the present invention can be introduced into plant cells by any method known to those skilled in the art. The non-limiting examples of transformation methods include conversion by bacterial-mediated nucleic acid delivery (for example, by Agrobacterium), virus-mediated nucleic acid delivery, silicon carbide or nucleic acid whisker-mediated nucleic acid delivery, liposome-mediated nucleic acid delivery, microinjection, microparticle bombardment, calcium phosphate-mediated conversion, cyclodextrin-mediated conversion, electroporation, nanoparticle-mediated conversion, ultrasonic treatment, infiltration, PEG-mediated nucleic acid uptake, and any other electrical, chemical, physical (mechanical) and / or biological mechanism that nucleic acid is introduced into plant cells, including any combination thereof. The program for transforming eukaryotic organisms and prokaryotic organisms is well known in the art and conventional, and is described in the literature (see, for example, Jiang et al., 2013.Nat.Biotechnol.31:233-239; Ran et al., Nature Protocols 8:2281–2308 (2013)). General guides to various plant transformation methods known in the art include Miki et al. ("Procedures for Introducing Foreign DNA into Plants", in Methods in Plant Molecular Biology and Biotechnology, Glick, BR and Thompson, JE, eds. (CRC Press, Inc., Boca Raton, 1993), pp. 67-88) and Rakowoczy-Trojanowska (Cell. Mol. Biol. Lett. 7:849-858 (2002)).

[0228] In some embodiments of the present invention, the transformation of cells may include nuclear transformation. In other embodiments, the transformation of cells may include plastid transformation (e.g., chloroplast transformation). In further embodiments, nucleic acids of the present invention may be introduced into cells by conventional breeding techniques. In some embodiments, one or more of polynucleotides, expression cassettes and / or vectors may be introduced into plant cells by Agrobacterium transformation.

[0229] Therefore, polynucleotide can be introduced into plant, plant part, plant cell in any number of ways known in the art.Method of the present invention does not rely on the ad hoc method for introducing one or more nucleotide sequences into plant, as long as they can enter the interior of the cell.If more than one polynucleotide is to be introduced, they can be assembled as a part of a single nucleic acid construct or assembled as an independent nucleic acid construct, and can be located on the same or different nucleic acid constructs.Therefore, polynucleotide can be introduced into interested cell in a single transformation event, or introduced into interested cell in an independent transformation event, or alternatively, polynucleotide can be incorporated into plant as a part of a breeding scheme.

[0230] The present invention provides methods and compositions for changing plant architecture, improving plant yield traits and / or increasing plant tolerance / resistance to abiotic and biotic stresses, optionally wherein yield traits are improved without loss of defense responses, that is, optimizing plant performance for yield without adversely affecting defense against abiotic and biotic stresses. An example of a gene that regulates growth-defense tradeoff is rice ideal plant architecture 1 (IPA1), which encodes a SQUAMOSA promoter binding protein-like (SPL) transcription factor regulated by microRNA 156 (miR156) (Jiao et al. Nat Genet 42, 541–544 (2010)). IPA1 has been shown to have different binding affinities depending on the immune status of the plant (Wang et al. Science 361, 1026–1028 (2018)). During pathogen infection, IPA1 is phosphorylated and preferentially activates the expression of WRKY45, a key regulator of SA-mediated defense. In the absence of an immune response, IPA1 is not phosphorylated and activates genes essential for growth and yield, such as DENSE AND ERECT PANICLE 1 (DEP1). In rice plants carrying the ipa1-1D allele, mutations in the miR156 binding site increased IPA1 transcript and protein levels in infected and uninfected plants, leading to quantitative improvements in yield and defense.

[0231] In soybean, there are four IPA1 orthologs, which are SPL9 family transcription factors SPL9a-d. These four GmSPL9 genes are negatively regulated by GmmiR156b (Bao, A. et al. BMC Plant Biol 19, 131 (2019); Cao et al. Plant Mol Biol 89, 353-363 (2015)). The maize orthologs of IPA1 are unbranched 2 and unbranched 3 (UB2, UB3) (Chuck et al. Proc National Acad Sci 111, 18775–18780 (2014)). Although reducing SPL activity can increase the activity of stem cell identity genes, resulting in an increase in meristem size, grain row number and yield, the context in which SPL is misregulated is very important. This is because severe loss of SPL function in maize results in dramatic changes in plant architecture, including leaf derepression, changes in homeotic organ identity, increased root number, and increased tiller number, traits that are undesirable for increasing yield (Chuck et al. Nat Genet 39, 544–549 (2007)). It is unclear how any of these developmental phenotypes may determine disease susceptibility, or whether maize SPLs are involved in disease resistance.

[0232] Thus, as described herein, the IPA1 gene in plants is targeted using editing techniques to produce plants with improved yield traits without loss or antagonism of disease resistance. Mutations that can be used to produce such plants include, for example, substitutions, deletions, and insertions, optionally site mutations. In some aspects, the mutations produced by editing techniques can result in dominant negative mutations, semi-dominant mutations, hypomorphic mutations, weak loss-of-function mutations, hypermorphic mutations, or null alleles, optionally wherein the mutations result in null alleles.

[0233] In some embodiments, the present invention provides a plant or plant part thereof, which comprises at least one (e.g., one or more) mutations (e.g., 1, 2, 3, 4, 5 or more mutations) in an endogenous ideal plant configuration 1 (IPA1) gene encoding a SQUAMOSA promoter binding protein-like (SPL) transcription factor or its ortholog. The endogenous IPA1 gene encoding the SPL transcription factor can be an endogenous SQUAMOSA promoter binding protein-like 9 (SPL9) gene, an endogenous unbranched 2 (UB2) gene, or an endogenous unbranched 3 (UB3) gene. The SPL9 gene includes, for example, an SPL9a gene, an SPL9b gene, an SPL9c gene, and / or an SPL9d gene. In some embodiments, the endogenous gene IPA1 gene or its ortholog can be regulated by miR156, optionally, wherein miR156 includes but is not limited to miR156a, miR156b, miR156c, miR156d, miR156e. In some embodiments, miR156 is miR156b.

[0234] In some embodiments, the endogenous IPA1 gene can be an endogenous SPL9 gene, optionally wherein the endogenous SPL9 gene is a SPL9a gene, a SPL9b gene, a SPL9c gene and / or a SPL9d gene, optionally the SPL9 gene is present in the plant or part thereof as two paralogous pairs of (a) a SPL9a gene and a SPL9b gene and / or (b) a SPL9c gene and a SPL9d gene. Exemplary SPL9 genes that can be used in the present invention include, but are not limited to, those genes that: (a) comprise a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs:72, 75, 78, 81, 143, 182, 222, or 255, (b) comprise a coding sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs:73, 76, 79, 82, 144, 183, 223, or 256, (c) comprise a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs:146-181, 185-221, 225-254, and / or 258-288; and / or (d) encode a polypeptide sequence having at least 80% identity to the amino acid sequence of any one of SEQ ID NOs:74, 77, 80, 83, 145, 184, 224, or 257.

[0235] In some embodiments, the endogenous IPA1 gene can be an endogenous UB2 gene and / or an endogenous UB3 gene. Exemplary UB2 genes useful in the present invention (a) comprise a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 84, (b) comprise a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 85, (c) comprise a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 90-96 or 332-393; and / or (d) encode a polypeptide sequence having at least 80% identity to the amino acid sequence of SEQ ID NO: 86. Exemplary UB3 genes useful in the present invention (a) comprise a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:87, (b) comprise a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:88, (c) comprise a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs:90, 97-103, or 394-445; and / or (d) encode a polypeptide sequence having at least 80% identity to the amino acid sequence of SEQ ID NO:89.

[0236] The mutation in the endogenous IPA1 gene or its ortholog in the plant, its plant part or plant cell can be any type of mutation that produces a plant with altered plant architecture, improved yield traits and / or increased tolerance / resistance to abiotic and biotic stresses compared to a plant or plant part lacking the same mutation, optionally wherein these improvements in phenotype occur without loss of disease response. Such mutations include base substitutions, base deletions and / or base insertions. In some embodiments, the mutation may include base substitutions to A, T, G or C. In some embodiments, at least one mutation may be a base substitution from C to T (C>T). In some embodiments, the mutation may be a deletion of one or more base pairs (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 base pairs to about 50, 60, 70, 80, 90 or 100 or more base pairs; for example, 1 base pair to about 100 base pairs or any value or range therein) or an insertion of one or more base pairs. In some embodiments, the deletion or insertion may be an in-frame deletion, an in-frame insertion, an out-of-frame deletion, or an out-of-frame insertion. In some embodiments, the mutation in the IPA1 gene as described herein may result in a dominant negative mutation, a semi-dominant mutation, a hypomorphic mutation, a weak loss-of-function mutation, a hypermorphic mutation, or a null allele, optionally wherein the mutation may result in a null allele. In some embodiments, the mutation in the IPA1 gene as described herein results in a hypomorphic mutation. In some embodiments, the mutation may be a null allele and a hypomorphic mutation. In some embodiments, the mutation in the IPA1 gene as described herein may be a non-natural mutation.

[0237] In some embodiments, the mutation (e.g., at least one mutation, e.g., one or more mutations) in the endogenous IPA1 gene encoding the SPL transcription factor may be in the first exon of the endogenous IPA1 gene encoding the SPL transcription factor, optionally resulting in a premature stop codon and a null allele. In some embodiments, the mutation is in the SPL9 gene and may be present in at least one (e.g., 1, 2, 3, or 4) of the SPL9a gene, the SPL9b gene, the SPL9c gene, and / or the SPL9d gene, wherein at least one mutation is in the first exon, optionally resulting in a premature stop codon and a null allele. In some embodiments, the mutation is in the SPL9 gene and may be present in at least two (e.g., 2, 3, or 4) of the SPL9a gene, SPL9b gene, SPL9c gene, and / or SPL9d gene in any combination, optionally wherein at least one mutation is in the first exon of the SPL9a gene, SPL9b gene, SPL9c gene, and / or SPL9d, optionally resulting in a premature stop codon and a null allele. In some embodiments, the mutation is present in each of the SPL9a gene, SPL9b gene, SPL9c gene, and SPL9d gene. In some embodiments, the first exon of the SPL9a gene may be located at about nucleotide 2001 to about nucleotide 2364 with reference to the nucleotide numbering of SEQ ID NO: 72 and / or at about nucleotide 1 to about nucleotide 364 with reference to the nucleotide numbering of SEQ ID NO: 73. In some embodiments, the first exon of the SPL9b gene may be located at about nucleotide 2001 to about nucleotide 2370 with reference to the nucleotide numbering of SEQ ID NO: 75 and / or at about nucleotide 1 to about nucleotide 370 with reference to the nucleotide numbering of SEQ ID NO: 76. In some embodiments, the first exon of the SPL9c gene may be located at about nucleotide 2001 to about nucleotide 2347 with reference to the nucleotide numbering of SEQ ID NO: 78 and / or at about nucleotide 1 to about nucleotide 347 with reference to the nucleotide numbering of SEQ ID NO: 79. In some embodiments, the first exon of the SPL9d gene may be located at about nucleotide 2001 to about nucleotide 2349 with reference to the nucleotide numbering of SEQ ID NO: 81 and / or at about nucleotide 1 to about nucleotide 349 with reference to the nucleotide numbering of SEQ ID NO: 82.

[0238] In some embodiments, at least one mutation in the SPL9 gene may be (a) in the region from about nucleotide 2053 to about nucleotide 2115 in the first exon of the SPL9a gene with reference to nucleotide numbering of SEQ ID NO:72 or SEQ ID NO:75, (b) in the region from about nucleotide 2015 to about nucleotide 2077 in the first exon of the SPL9b gene with reference to nucleotide numbering of SEQ ID NO:78 or SEQ ID NO:81, (c) in the region from about nucleotide 1 to about nucleotide 115 in the first exon of the SPL9c gene with reference to nucleotide numbering of SEQ ID NO:73 or SEQ ID NO:76, and / or (d) in the region from about nucleotide 1 to about nucleotide 77 in the first exon of the SPL9d gene with reference to nucleotide numbering of SEQ ID NO:79 or SEQ ID NO:82. In some embodiments, at least one mutation in the SPL9 gene can be located in (a) a region in the first exon of the SPL9a gene that has at least 80% sequence identity with the nucleotide sequence of SEQ ID NOs: 161-177, (b) a region in the first exon of the SPL9b gene that has at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs: 201-217, (c) a region in the first exon of the SPL9c gene that has at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs: 240-250, or (d) a region in the first exon of the SPL9d gene that has at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs: 274-284.

[0239] In some embodiments, at least one mutation may be located in a region of the SPL9a gene that has at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-181. In some embodiments, at least one mutation may be located in a region of the SPL9b gene that has at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 185-221. In some embodiments, at least one mutation may be located in a region of the SPL9c gene that has at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 225-254. In some embodiments, at least one mutation may be located in a region of the SPL9d gene that has at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 258-288.

[0240] In some embodiments, the mutation (e.g., at least one mutation, e.g., one or more mutations) in the endogenous IPA1 gene encoding the SPL transcription factor can be in the first exon of the endogenous IPA1 gene encoding the SPL transcription factor, wherein the IPA1 gene is a UB2 gene or a UB3 gene. In some embodiments, the mutation in the UB2 gene can be in the third exon of the endogenous UB2 gene (see, e.g., the third exon of SEQ ID NO: 84; e.g., SEQ ID NOs: 358-376, optionally SEQ ID NOs: 373-376). In some embodiments, the mutation in the UB3 gene can be in the third exon of the endogenous UB3 gene (see, e.g., the third exon of SEQ ID NO: 87; e.g., SEQ ID NOs: 408-426, optionally SEQ ID NOs: 415-416. In some embodiments, the mutation in the first exon or the third exon results in a premature stop codon and a null allele, optionally resulting in a hypomorphic mutation or a knockout mutation.

[0241] In some embodiments, a mutation (e.g., at least one mutation, e.g., one or more mutations) in an endogenous IPA1 gene encoding a SPL transcription factor may be in a miR156 binding site of the endogenous IPA1 gene, optionally wherein the endogenous IPA1 gene is a SPL9 gene, a UB2 gene, and / or a UB3 gene. In some embodiments, the endogenous IPA1 gene can be (a) an SPL9a gene and the miR156 binding site can be located in a region from about nucleotide 6569 to about nucleotide 6588 with reference to nucleotide numbering of SEQ ID NO:72, from about nucleotide 758 to about nucleotide 777 with reference to nucleotide numbering of SEQ ID NO:73, and / or from about nucleotide 6624 to about nucleotide 6847 with reference to nucleotide numbering of SEQ ID NO:143, (b) an SPL9b gene and the miR156 binding site is from about nucleotide 6269 to about nucleotide 6288 with reference to nucleotide numbering of SEQ ID NO:75, from about nucleotide 760 to about nucleotide 780 with reference to nucleotide numbering of SEQ ID NO:76, and / or from about nucleotide 6265 to about nucleotide 6488 with reference to nucleotide numbering of SEQ ID NO:182, (c) an SPL9c gene and the miR156 binding site is from about nucleotide 5388 to about nucleotide 5407 with reference to nucleotide numbering of SEQ ID NO:78, from about nucleotide 5460 to about nucleotide 5510 with reference to nucleotide numbering of SEQ ID NO: The nucleotide numbering of NO:79 is from about nucleotide 761 to about nucleotide 780, and / or the nucleotide numbering of SEQ ID NO:222 is from about nucleotide 5665 to about nucleotide 5887, and / or (d) the SPL9d gene and the miR156 binding site is from about nucleotide 5798 to about nucleotide 5817 with reference to the nucleotide numbering of SEQ ID NO:81, from about nucleotide 737 to about nucleotide 756 with reference to the nucleotide numbering of SEQ ID NO:82, and / or from about nucleotide 6120 to about nucleotide 6342 with reference to the nucleotide numbering of SEQ ID NO:255.

[0242] In some embodiments, (a) the mutation (e.g., at least one mutation, e.g., one or more mutations) in the miR156 binding site of the endogenous SPL9a gene can be located in the region of the SPL9a gene from about nucleotide 6549 to about nucleotide 6608 with reference to nucleotide numbering of SEQ ID NO:72 and / or from about nucleotide 738 to about nucleotide 797 with reference to nucleotide numbering of SEQ ID NO:73, optionally in a region having about 80% sequence identity to any one of the nucleotide sequences of SEQ ID NOs:178-181; (b) the mutation in the miR156 binding site of the endogenous SPL9b gene can be located in the region of the endogenous SPL9b gene from about nucleotide 6250 to about nucleotide 6308 with reference to nucleotide numbering of SEQ ID NO:75 and / or from about nucleotide 741 to about nucleotide 800 with reference to nucleotide numbering of SEQ ID NO:76, optionally in a region having about 80% sequence identity to any one of the nucleotide sequences of SEQ ID NOs:178-181. NO:218-221, (c) the mutation in the miR156 binding site of the endogenous SPL9c gene may be located in the region from about nucleotide 5368 to about nucleotide 5427 with reference to nucleotide numbering of SEQ ID NO:78 and / or from about nucleotide 742 to about nucleotide 800 with reference to nucleotide numbering of SEQ ID NO:79, optionally in a region having about 80% sequence identity with any one of the nucleotide sequences of SEQ ID NO:251-254, and / or (d) the mutation in the miR156 binding site of the endogenous SPL9d gene may be located in the region from about nucleotide 5778 to about nucleotide 5837 with reference to nucleotide numbering of SEQ ID NO:81 and / or from about nucleotide 718 to about nucleotide 775 with reference to nucleotide numbering of SEQ ID NO:82, optionally in a region having about 80% sequence identity with any one of the nucleotide sequences of SEQ ID NO:285-288.

[0243] In some embodiments, the endogenous IPA1 gene can be a UB2 gene and the miR156 binding site in the UB2 gene can be located in the region from about nucleotide 4928 to about nucleotide 4947 with reference to the nucleotide numbering of SEQ ID NO:84 and / or from about nucleotide 815 to about nucleotide 834 with reference to the nucleotide numbering of SEQ ID NO:85, and / or the endogenous IPA1 gene is a UB3 gene and the miR156 binding site in the UB3 gene is located in the region from about nucleotide 5301 to about nucleotide 5320 with reference to the nucleotide numbering of SEQ ID NO:87 and / or from about nucleotide 848 to about nucleotide 866 with reference to the nucleotide numbering of SEQ ID NO:88.

[0244] In some embodiments, the mutation in the miR156 binding site of the endogenous UB2 gene can be located in the region of the UB2 gene from about nucleotide 4894 to about nucleotide 4967 with reference to the nucleotide numbering of SEQ ID NO:84 and / or from about nucleotide 781 to about nucleotide 854 with reference to the nucleotide numbering of SEQ ID NO:85, and / or the mutation in the miR156 binding site of the endogenous UB3 gene can be located in the region of the UB3 gene from about nucleotide 5267 to about nucleotide 5339 with reference to the nucleotide numbering of SEQ ID NO:87 and / or from about nucleotide 814 to about nucleotide 887 with reference to the nucleotide numbering of SEQ ID NO:88.

[0245] In some embodiments, at least one mutation in the miR156 binding site can be a substitution or deletion, optionally an in-frame deletion or an out-of-frame deletion. In some embodiments, at least one mutation in the miR156 binding site is a point mutation, optionally a silent point mutation. In some embodiments, the point mutation can be a substitution, optionally wherein the substitution is C>A, T or G, optionally C>A. In some embodiments, at least one mutation can be a non-natural mutation.

[0246] In some embodiments, a mutation in a miR156 binding site as described herein can upregulate the expression of an endogenous IPA1 gene, for example, the mutation results in upregulation of an endogenous SPL9a gene, an endogenous SPL9b gene, an endogenous SPL9c gene, an endogenous SPL9d gene, an endogenous unbranched 2 (UB2) gene, and / or an endogenous unbranched 3 (UB3) gene.

[0247] In some embodiments, the mutation (e.g., at least one mutation, optionally a non-natural mutation) can be a base substitution in a region of an endogenous UB2 gene or an endogenous UB3 gene that is associated with increased kernel row number (KRN), and / or increased tassel branch number (TBN), optionally without substantially reducing ear length. The region of the endogenous UB2 gene associated with increased KRN can, for example, be located at about nucleotide 4379 to about nucleotide 4800 with reference to nucleotide numbering of SEQ ID NO: 84 and / or at about nucleotide 626 to about nucleotide 688 with reference to nucleotide numbering of SEQ ID NO: 85. In some embodiments, the region of the endogenous UB3 gene associated with increased KRN can, for example, be located at about nucleotide 5094 to about nucleotide 5157 with reference to nucleotide numbering of SEQ ID NO: 87 and / or at about nucleotide 641 to about nucleotide 703 with reference to nucleotide numbering of SEQ ID NO: 88. In some embodiments, the edit associated with increased KRN in the endogenous UB3 gene can be located at about nucleotide 5108 to about nucleotide 5110 with reference to the nucleotide numbering of SEQ ID NO:87 and / or at about nucleotide 655 to about nucleotide 657 with reference to the nucleotide numbering of SEQ ID NO:88.

[0248] In some embodiments, a region of a UB2 gene or UB3 gene associated with increased tassel branch number (TBN) can be targeted for modification as described herein. In some embodiments, a region of an endogenous UB2 gene associated with increased TBN can be from about nucleotide 4834 to about nucleotide 4896 with reference to the nucleotide numbering of SEQ ID NO: 84 and / or from about nucleotide 721 to about nucleotide 783 with reference to the nucleotide numbering of SEQ ID NO: 85. In some embodiments, an edit associated with increased TBN in an endogenous UB2 gene can be located at about nucleotide 4864 to about nucleotide 4866 with reference to the nucleotide numbering of SEQ ID NO: 84 and / or from about nucleotide 751 to about nucleotide 753 with reference to the nucleotide numbering of SEQ ID NO: 85. In some embodiments, a region of an endogenous UB3 gene associated with increased TBN can be from about nucleotide 5204 to about nucleotide 5266 with reference to the nucleotide numbering of SEQ ID NO: 87 or from about nucleotide 751 to about nucleotide 813 with reference to the nucleotide numbering of SEQ ID NO: 88. In some embodiments, the edits in the endogenous UB3 gene associated with increased TBN can be located at about nucleotide 5231 to about nucleotide 5233 with reference to the nucleotide numbering of SEQ ID NO:87 and / or at about nucleotide 778 to about nucleotide 790 with reference to the nucleotide numbering of SEQ ID NO:88.

[0249] In some embodiments, the mutation (e.g., at least one mutation, e.g., one or more mutations, optionally wherein the mutation is a non-natural mutation) in the endogenous IPA1 gene encoding the SPL transcription factor can be a mutation in the 5' untranslated region (UTR) and / or 3'UTR of the endogenous IPA1 gene, optionally wherein the endogenous IPA1 gene is a SPL9 gene (e.g., SPL9a, SPL9b, SPL9c, SPL9d), a UB2 gene and / or a UB3 gene.

[0250] In some embodiments, the endogenous IPA1 gene may be (a) an SPL9a gene and at least one mutation may be in the region of about nucleotide 1826 to about nucleotide 1981 and / or about nucleotide 1846 to about nucleotide 1961 in the 5'UTR with reference to the nucleotide numbering of SEQ ID NO: 72, optionally in a region having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs: 146-160; (b) an SPL9b gene and at least one mutation may be in the region of about nucleotide 1804 to about nucleotide 1973 and / or about nucleotide 1824 to about nucleotide 1953 in the 5'UTR with reference to the nucleotide numbering of SEQ ID NO: 75, optionally in a region having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs: 185-200; (c) an SPL9c gene and at least one mutation may be in the region of about nucleotide 1826 to about nucleotide 1981 and / or about nucleotide 1846 to about nucleotide 1961 in the 5'UTR with reference to the nucleotide numbering of SEQ ID NO: 72, optionally in a region having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs: 185-200; The nucleotide numbering of SEQ ID NO: 78 is located in the region from about nucleotide 1593 to about nucleotide 1783 and / or about nucleotide 1613 to about nucleotide 1764, optionally in a region having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs: 225-239; and / or (d) the SPL9d gene and at least one mutation may be in the region from about nucleotide 1555 to about nucleotide 1740 and / or about nucleotide 1574 to about nucleotide 1720 in the 5'UTR with reference to the nucleotide numbering of SEQ ID NO: 81, optionally in a region having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs: 258-273. In some embodiments, at least one mutation may be a non-natural mutation.

[0251] In some embodiments, the endogenous IPA1 gene can be (a) a UB2 gene and the at least one mutation can be in the 5'UTR in a region from about nucleotide 1414 to about nucleotide 1860, from about nucleotide 1414 to about nucleotide 1522, from about nucleotide 1454 to about nucleotide 1481, from about nucleotide 1553 to about nucleotide 1582, from about nucleotide 1597 to about nucleotide 1633, and / or from about nucleotide 1767 to about nucleotide 1819 with reference to the nucleotide numbering of SEQ ID NO:84, optionally wherein the region of the 5'UTR is a promoter or is in a promoter, optionally in a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs:133-136; and / or (b) a UB3 gene and the at least one mutation can be in the 5'UTR with reference to SEQ ID NO: The nucleotide numbering of NO:87 is located in a region from about nucleotide 1327 to about nucleotide 1646, from about nucleotide 1439 to about nucleotide 1467, from about nucleotide 1368 to about nucleotide 1394, from about nucleotide 1549 to about nucleotide 1606, from about nucleotide 1787 to about nucleotide 1855, and / or from about nucleotide 1747 to about nucleotide 1920, optionally wherein the region of the 5'UTR is a promoter or is in a promoter, optionally in a region having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs: 129-132. In some embodiments, at least one mutation may be a non-natural mutation.

[0252] In some embodiments, the endogenous IPA1 gene may be (a) a UB2 gene and at least one mutation may be in the region of the 3'UTR from about nucleotide 5701 to about nucleotide 5882 and / or from about nucleotide 5742 to about nucleotide 5842, with reference to the nucleotide numbering of SEQ ID NO: 84, optionally in a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 140-142; and / or (b) a UB3 gene and at least one mutation may be in the region of the 3'UTR from about nucleotide 5940 to about nucleotide 6109, about nucleotide 5980 to about nucleotide 6069, about nucleotide 6516 to about nucleotide 6643 and / or about nucleotide 6556 to about nucleotide 6603, with reference to the nucleotide numbering of SEQ ID NO: 87, optionally in a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 137-139. In some embodiments, at least one mutation may be a non-natural mutation.

[0253] In some embodiments, a mutation (e.g., at least one mutation, e.g., one or more mutations) in an endogenous IPA1 gene encoding a SPL transcription factor can be a mutation in an intron of the endogenous IPA1 gene, optionally wherein the endogenous IPA1 gene is a SPL9 gene (e.g., SPL9a, SPL9b, SPL9c, SPL9d), a UB2 gene and / or a UB3 gene, optionally wherein at least one mutation can be a non-natural mutation.

[0254] In some embodiments, the endogenous IPA1 gene can be (a) a UB2 gene and at least one mutation (optionally a non-natural mutation) can be in an intron in a region between about nucleotide 2856 to about nucleotide 2971, about nucleotide 2896 to about nucleotide 2931, about nucleotide 3753 to about nucleotide 3893, and / or about nucleotide 3793 to about nucleotide 3853, with reference to the nucleotide numbering of SEQ ID NO: 84; and / or (b) a UB3 gene and at least one mutation (optionally a non-natural mutation) can be in an intron in a region between about nucleotide 2666 to about nucleotide 2784, about nucleotide 2706 to about nucleotide 2744, about nucleotide 4017 to about nucleotide 4147, and / or about nucleotide 4057 to about nucleotide 4107, with reference to the nucleotide numbering of SEQ ID NO: 87.

[0255] In some embodiments, a mutation (e.g., at least one mutation, e.g., one or more mutations) in the first exon, the third exon, the miR156 binding site, the 5'UTR, the 3'UTR, the intron, or a region associated with plant configuration, increased tolerance / resistance to abiotic and biotic stresses, and / or yield traits of the IPA1 gene encoding the SPL transcription factor may be a dominant negative mutation, a semi-dominant mutation, a hyperallelic mutation, a hypomorphic mutation, a weak loss-of-function mutation, or a null allele, optionally wherein the mutation may be a null allele. In some embodiments, at least one mutation may be a non-natural mutation.

[0256] Mutations in the endogenous IPA1 gene encoding an SPL transcription factor as described herein can produce plants that exhibit, for example, altered plant architecture, improved yield traits, and / or increased tolerance / resistance to abiotic and biotic stresses compared to plants or plant parts lacking the same mutation. In some embodiments, the improved yield traits can include, but are not limited to, one or more of the following phenotypes: increased number of rows of kernels, increased kernel size, increased ear length, increased number of rows of kernels without substantially reducing ear length, reduced number of tillers, reduced number of tassel branches, reduced time to flowering, increased number of seeds per plant, increased number of pods per node and / or per plant, and / or increased seed weight compared to plants or plant parts lacking the same mutation.

[0257] In some embodiments, a plant cell comprising an editing system is provided, the editing system comprising: (a) a CRISPR-Cas associated effector protein; and (b) a guide nucleic acid (e.g., gRNA, gDNA, crRNA, crDNA), wherein the guide nucleic acid comprises a spacer sequence complementary to an endogenous ideal plant configuration 1 (IPA1) target gene encoding a SQUAMOSA promoter binding protein-like (SPL) transcription factor or its ortholog, optionally wherein the IPA1 gene is a SQUAMOSA promoter binding protein-like 9 (SPL9) gene, an endogenous branchless 2 (UB2) gene, or an endogenous branchless 3 (UB3) gene, optionally wherein the SPL9 gene is a SPL9a gene, a SPL9b gene, a SPL9c gene, or a SPL9d gene. In some embodiments, the endogenous IPA1 target gene: (a) is a SLP9 gene, which (i) comprises a nucleotide sequence having at least 80% sequence identity to a nucleotide sequence of any one of SEQ ID NOs: 72, 75, 78, 81, 143, 182, 222, or 255; (ii) comprises a coding sequence having at least 80% sequence identity to a nucleotide sequence of any one of SEQ ID NOs: 73, 76, 79, 82, 144, 183, 223, or 256; (iii) comprises a region having at least 80% sequence identity to a nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254, and / or 258-288; and / or (iv) encodes a polypeptide sequence having at least 80% identity to an amino acid sequence of any one of SEQ ID NOs: 74, 77, 80, 83, 145, 184, 224, or 257; (b) a UB2 gene, which comprises a nucleotide sequence having at least 80% sequence identity to a nucleotide sequence of any one of SEQ ID NOs: 73, 76, 79, 82, 144, 183, 223, or 256; (iii) comprises a region having at least 80% sequence identity to a nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254, and / or 258-288; and / or (iv) encodes a polypeptide sequence having at least 80% identity to an amino acid sequence of any one of SEQ ID NOs: 84, (ii) comprising a coding sequence having at least 80% sequence identity with the nucleotide sequence of SEQ ID NO:85; (iii) comprising a region having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs:90-96 or 332-393; and / or (iv) encoding a polypeptide sequence having at least 80% identity with the amino acid sequence of SEQ ID NO:86; and / or (c) a UB3 gene having at least 80% sequence identity with the nucleotide sequence of SEQ ID NO:87, (ii) comprising a coding sequence having at least 80% sequence identity with the nucleotide sequence of SEQ ID NO:88; (iii) comprising a region having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs:90, 97-103 or 394-445; and / or (iv) encoding a polypeptide sequence having at least 80% identity with the amino acid sequence of SEQ ID NO:89.In some embodiments, the guide nucleic acid can comprise a nucleotide sequence (eg, a spacer sequence) of any one of SEQ ID NOs: 104-142, 301, 326, and / or 327. In some embodiments, the plant cell is a corn plant cell or a soybean plant cell.

[0258] In some embodiments, a plant cell is provided, comprising at least one mutation in one or more endogenous ideal plant configuration 1 (IPA1) genes encoding a SQUAMOSA promoter binding protein-like (SPL) transcription factor or its ortholog, wherein at least one mutation is a substitution, insertion and / or deletion introduced using an editing system comprising a nucleic acid binding domain that binds to a target site in one or more endogenous IPA1 genes, optionally wherein the plant cell is from corn or soybean. In some embodiments, the one or more endogenous IPA1 genes may be a SQUAMOSA promoter binding protein-like 9 (SPL9) gene, an endogenous unbranched 2 (UB2) gene, or an endogenous unbranched 3 (UB3) gene, optionally wherein the SPL9 gene is a SPL9a gene, a SPL9b gene, a SPL9c gene, or a SPL9d gene. In some embodiments, at least one mutation is a null allele, a knockout mutation, or a hypomorphic allele mutation. In some embodiments, the target site can be within a region of one or more endogenous SPL9 genes that has at least 80% sequence identity to any one of SEQ ID NOs: 146-181, 185-221, 225-254, and / or 258-288. In some embodiments, the editing system may further comprise a nuclease, and the target site bound to the nucleic acid binding domain may be: (a) in a SPL9 gene having at least 80% sequence identity to a nucleotide sequence of any one of SEQ ID NOs: 72, 73, 75, 76, 78, 79, 81, 82, 143, 144, 182, 183, 222, 223, 255, or 256; and / or in a region of the SPL9 gene having at least 80% sequence identity to a nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254, and / or 258-288; (b) in a UB2 gene having at least 80% sequence identity to a nucleotide sequence of SEQ ID NO: 84 or SEQ ID NO: 85 and / or in a region of the UB2 gene having at least 80% sequence identity to a nucleotide sequence of SEQ ID NO: NO:90-96 or 332-393 has at least 80% sequence identity; and / or (c) is in a UB3 gene having at least 80% sequence identity with the nucleotide sequence of SEQ ID NO:87 or SEQ ID NO:88 and / or is in a UB2 gene having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NO:90, 97-103 or 394-445; and at least one mutation within the endogenous IPA1 gene is generated after nuclease cleavage.In some embodiments, the nuclease may be a zinc finger nuclease, a transcription activator-like effector nuclease (TALEN), an endonuclease (e.g., Fok1), or a CRISPR-Cas effector protein, and / or the nucleic acid binding domain of the editing system may be from a polynucleotide-guided endonuclease, a CRISPR-Cas endonuclease (e.g., a CRISPR-Cas effector protein), a zinc finger nuclease, a transcription activator-like effector nuclease (TALEN), and / or an Argonaute protein. In some embodiments, at least one mutation within one or more endogenous IPA1 genes is an insertion and / or deletion, optionally a point mutation. In some embodiments, at least one mutation is an out-of-frame insertion or out-of-frame deletion, optionally wherein the insertion and / or deletion results in an early stop codon and / or a truncated protein. In some embodiments, at least one mutation may be a non-natural mutation.

[0259] In some embodiments, a plant can be regenerated from a plant part or plant cell of the invention, optionally wherein the regenerated plant exhibits a phenotype of one or more of altered plant architecture, improved yield traits, and / or increased tolerance / resistance to abiotic and biotic stresses compared to a control plant or part thereof lacking at least one mutation.

[0260] Also provided is a method of providing a plurality of plants exhibiting altered plant architecture, improved yield traits and / or increased tolerance / resistance to abiotic and biotic stresses, the method comprising planting two or more plants of the invention (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 100, 200, 300, 400, 500, 1000, 2000, 3000, 400, 5000 or 10,000 or more plants of the invention) in a growing area, thereby providing a plurality of plants exhibiting altered plant architecture, improved yield traits and / or increased tolerance / resistance to abiotic and biotic stresses compared to a plurality of control plants not comprising at least one mutation, optionally wherein the plurality of plants exhibiting resistance to biotic stresses exhibit increased disease resistance.

[0261] In some embodiments, a method for producing / cultivating a transgene-free genome-edited (e.g., base-edited) plant is provided, the method comprising: (a) crossing a plant of the present invention with a transgene-free plant, thereby introducing a mutation or modification into the transgene-free plant; and (b) selecting progeny plants that contain the mutation or modification but are free of transgenes, thereby producing a transgene-free genome-edited (e.g., base-edited) plant.

[0262] In some embodiments, a method for generating a mutation in an endogenous IPA1 gene of a plant is provided, the method comprising: (a) targeting a gene editing system to a portion of the IPA1 gene that: (i) has at least 80% sequence identity to any one of SEQ ID NOs: 146-181, 185-221, 225-254, and / or 258-288; (ii) has at least 80% sequence identity to any one of SEQ ID NOs: 90-96 or 332-393; and / or (iii) has at least 80% sequence identity to any one of SEQ ID NOs: 90, 97-103, or 394-445; and (b) selecting a plant comprising a modification located in a region of the IPA1 gene that: (i) has at least 80% sequence identity to any one of SEQ ID NOs: 146-181, 185-221, 225-254, and / or 258-288; (ii) has at least 80% sequence identity to any one of SEQ ID NOs: 90-96 or 332-393; and / or (iii) has at least 80% sequence identity to any one of SEQ ID NOs: 90, 97-103, or 394-445. and / or (iii) at least 80% sequence identity to any one of SEQ ID NOs: 90, 97-103, or 394-445.

[0263] In some embodiments, a method for generating a variation in an IPA1 polypeptide is provided, the method comprising: introducing an editing system into a plant cell, wherein the editing system is targeted to a region of an endogenous IPA1 gene encoding an IPA1 polypeptide, and contacting the region of the endogenous IPA1 gene with the editing system, thereby introducing a mutation into the endogenous IPA1 gene and generating a variation in the IPA1 polypeptide of the plant cell, optionally wherein the endogenous IPA1 gene comprises: (a) a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 72, 73, 75, 76, 78, 79, 81, 82, 143, 144, 182, 183, 222, 223, 255, or 256; and / or encodes an amino acid sequence having at least 80% sequence identity to any one of SEQ ID NOs: 74, 77, 80, 83, 145, 184, 224, and / or 257, (b) a nucleotide sequence having at least 80% sequence identity to any one of SEQ ID NOs: 84 or 85; NO:85, and / or encodes an amino acid sequence having at least 80% sequence identity to SEQ ID NO:86; and / or (c) a nucleotide sequence having at least 80% sequence identity to a nucleotide sequence of SEQ ID NO:87 or SEQ ID NO:88, and / or encodes an amino acid sequence having at least 80% sequence identity to SEQ ID NO:39. In some embodiments, the targeted region of the endogenous IPA1 gene (a) has at least 80% sequence identity to any one of SEQ ID NOs:146-181, 185-221, 225-254, and / or 258-288; (b) has at least 80% sequence identity to any one of SEQ ID NOs:90-96 or 332-393; and / or (c) has at least 80% sequence identity to any one of SEQ ID NOs:90, 97-103, or 394-445. In some embodiments, the region of the endogenous IPA1 gene in the plant cell is contacted with the editing system to produce a plant cell comprising an edited IPA1 gene in its genome, optionally wherein the method further comprises (a) regenerating a plant from the plant cell; (b) selfing the plant to produce a progeny plant (E1); (c) analyzing the improved yield trait of the progeny plant of (b); and (d) selecting a progeny plant that exhibits improved yield traits compared to a control plant. In some embodiments, the method further comprises (e) selfing the selected progeny plant of (d) to produce a progeny plant (E2); (f) analyzing the improved yield trait of the progeny plant of (e); and (g) selecting a progeny plant that exhibits improved yield traits compared to a control plant, optionally repeating (e) to (g) one or more times.

[0264] In some embodiments, a method for detecting a mutant IPA1 gene in a plant (a mutation in an endogenous IPA1 gene) is provided, the method comprising detecting an IPA1 gene having at least one mutation in the following region in the genome of the plant, the region: (a) having at least 80% sequence identity to any one of SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288; (b) having at least 80% sequence identity to any one of SEQ ID NOs: 90-96 or 332-393; and / or (c) having at least 80% sequence identity to any one of SEQ ID NOs: 90, 97-103 or 394-445, optionally, wherein the detected mutant IPA1 gene comprises a nucleic acid sequence, the nucleic acid sequence: (a) having at least 90% identity to any one of the nucleotide sequences of SEQ ID NOs: 289-300, (b) having at least 80% sequence identity to any one of SEQ ID NOs: 289-300, Any of the nucleotide sequences of SEQ ID NO:320, 322 or 324 has at least 90% identity, or (c) any of the nucleotide sequences of SEQ ID NO:310, 312, 314, 316 or 318 has at least 90% identity.

[0265] In some embodiments, a method for editing a specific site in the genome of a plant cell is provided, the method comprising: cleaving a target site within an endogenous IPA1 gene in the plant cell in a site-specific manner, wherein the endogenous IPA1 gene can be: (a) an SPL9 gene having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 72, 73, 75, 76, 78, 79, 81, 82, 143, 144, 182, 183, 222, 223, 255 or 256 and / or comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288, (b) an UB2 gene having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 84 or SEQ ID NO: 85 and / or comprising a region having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: NO:90-96 or 332-393; and / or (c) a UB3 gene having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:87 or SEQ ID NO:88 and / or comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:90, 97-103 or 394-445, thereby generating an edit in the endogenous IPA1 gene of the plant cell. In some embodiments, the edit in the endogenous IPA1 gene generates a mutation (e.g., a non-natural mutation) that is a null allele. In some embodiments, a plant can be regenerated from a plant cell comprising the edit in the endogenous IPA1 gene to generate a plant comprising the edit in its endogenous IPA1 gene. In some embodiments, a regenerated plant comprising the edit in its endogenous IPA1 gene can exhibit a phenotype of one or more of altered plant architecture, improved yield traits, and / or increased tolerance / resistance to abiotic and biotic stresses compared to a control plant not comprising the edit.

[0266] In some embodiments, editing in the endogenous SPL9 gene can generate a mutant SPL9 gene having at least 90% identity (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to any one of the nucleotide sequences of SEQ ID NOs: 289-300. In some embodiments, editing in the endogenous UB3 gene can generate a mutant UB3 gene having at least 90% identity (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to any one of the nucleotide sequences of SEQ ID NOs: 310, 312, 314, 316, or 318. In some embodiments, editing in the endogenous UB2 gene can produce a mutant UB2 gene that has at least 90% identity (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to any of the nucleotide sequences of SEQ ID NOs: 320, 322, or 324.

[0267] In some embodiments, a method for preparing a plant is provided, the method comprising: (a) contacting a population of plant cells comprising an endogenous IPA1 gene with a nuclease targeted to the endogenous gene, wherein the nuclease is linked to a nucleic acid binding domain that binds to a target site in the endogenous gene, the endogenous IPA1 gene: (i) is a SPL9 gene comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 72, 73, 75, 76, 78, 79, 81, 82, 143, 144, 182, 183, 222, 223, 255, or 256, and / or comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254, and / or 258-288; (b) a UB2 gene having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 84 or SEQ ID NO:85 has at least 80% sequence identity, and / or comprises a region having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs:90-96 or 332-393; and / or a UB3 gene, which has at least 80% sequence identity with the nucleotide sequence of SEQ ID NO:87 or SEQ ID NO:88, and / or comprises a region having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs:90, 97-103 or 394-445, (b) selecting plant cells from a population comprising a mutation in the endogenous IPA1 gene, wherein the mutation is a substitution and / or a deletion; and (c) growing the selected plant cells into plants comprising the mutation in the endogenous IPA1 gene.

[0268] In some embodiments, a method for changing plant architecture, improving yield traits and / or increasing tolerance / resistance of a plant is provided, the method comprising (a) contacting a plant cell comprising an endogenous IPA1 gene with a nuclease that targets the endogenous IPA1 gene, wherein the nuclease is linked to a nucleic acid binding domain that binds to a target site in the endogenous IPA1 gene, wherein the endogenous IPA1 gene is: (i) an SPL9 gene comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 72, 73, 75, 76, 78, 79, 81, 82, 143, 144, 182, 183, 222, 223, 255 or 256, and / or comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288; (ii) an UB2 gene having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: NO:84 or SEQ ID NO:85 has at least 80% sequence identity, and / or comprises a region having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs:90-96 or 332-393; and / or (iii) a UB3 gene having at least 80% sequence identity with the nucleotide sequence of SEQ ID NO:87 or SEQ ID NO:88, and / or comprises a region having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs:90, 97-103 or 394-445; and (b) growing the plant cell into a plant, thereby changing the plant architecture, improving yield traits and / or increasing the tolerance / resistance of the plant.

[0269] In some embodiments, a method for producing a plant or part thereof is provided, the plant or part thereof comprising at least one cell having a mutation in an endogenous ideal plant configuration 1 (IPA1) gene encoding a SQUAMOSA promoter binding protein-like (SPL) transcription factor or an ortholog thereof, the method comprising contacting a target site in the endogenous IPA1 gene in the plant or plant part with a nuclease comprising a cleavage domain and a DNA binding domain, wherein the DNA binding domain of the nuclease binds to the target site in the endogenous IPA1 gene, wherein the endogenous IPA1 gene: (a) is an endogenous SQUAMOSA promoter binding protein-like 9 (SPL9) gene, which (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 72, 75, 78, 81, 143, 182, 222, or 255; (ii) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 72, 75, 78, 81, 143, 182, 222, or 255; NO:73, 76, 79, 82, 144, 183, 223 or 256; (iii) comprises a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:146-181, 185-221, 225-254 and / or 258-288, and / or (iv) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of any one of SEQ ID NO:74, 77, 80, 83, 145, 184, 224 or 257; (b) is an endogenous unbranched 2 (UB2) gene, which (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:84; (ii) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:85; (iii) comprises a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:146-181, 185-221, 225-254 and / or 258-288, and / or (iv) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of any one of SEQ ID NO:74, 77, 80, 83, 145, 184, 224 or 257. NO:90-96 or 332-393 has a region with at least 80% sequence identity, and / or (iv) encodes a polypeptide sequence with at least 80% identity to the amino acid sequence of SEQ ID NO:86; or (c) is an endogenous UB3 gene, which: (i) comprises a nucleotide sequence with at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:87; (ii) comprises a coding sequence with at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:88; (iii) comprises a region with at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:90, 97-103 or 394-445, and / or (iv) encodes a polypeptide sequence with at least 80% identity to the amino acid sequence of SEQ ID NO:89, thereby producing a plant or part thereof comprising at least one cell having a mutation in an endogenous IPA1 gene.

[0270] In some embodiments, a method of producing a plant or part thereof comprising a mutation in an endogenous IPA1 gene and having an altered plant architecture, improved yield traits, and / or increased tolerance / resistance to abiotic and biotic stresses is provided, the method comprising contacting a target site in an endogenous IPA1 gene in the plant or plant part with a nuclease comprising a cleavage domain and a nucleic acid binding domain, wherein the nucleic acid binding domain of the nuclease binds to the target site in the endogenous IPA1 gene, wherein the endogenous IPA gene: (a) is an endogenous SQUAMOSA promoter binding protein-like 9 (SPL9) gene, which (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 72, 75, 78, 81, 143, 182, 222, or 255; (ii) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 72, 75, 78, 81, 143, 182, 222, or 255; NO:73, 76, 79, 82, 144, 183, 223 or 256; (iii) comprises a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:146-181, 185-221, 225-254 and / or 258-288, and / or (iv) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of any one of SEQ ID NO:74, 77, 80, 83, 145, 184, 224 or 257; (b) is an endogenous unbranched 2 (UB2) gene, which (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:84; (ii) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:85; (iii) comprises a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:146-181, 185-221, 225-254 and / or 258-288, and / or (iv) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of any one of SEQ ID NO:74, 77, 80, 83, 145, 184, 224 or 257. ID NO:90-96 or 332-393; and / or (iv) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of SEQ ID NO:86; or (c) is an endogenous UB3 gene, which: (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:87; (ii) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:88; (iii) comprises a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:90, 97-103 or 394-445; and / or (iv) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of SEQ ID NO:89, thereby producing a plant or part thereof having a mutated endogenous IPA1 gene and altered plant architecture, improved yield traits and / or increased tolerance / resistance to abiotic and biotic stresses.

[0271] In some embodiments, the mutations useful in the present invention may be at least one of base pair deletions, base pair substitutions, and / or base pair insertions. In some embodiments, the mutations may be dominant negative mutations, semi-dominant mutations, hyperallelic mutations, hypomorphic mutations, weak loss-of-function mutations, and / or null alleles. In some embodiments, the mutations may be non-natural mutations.

[0272] In some embodiments, mutations in plants or parts thereof as described herein can produce plants with altered plant architecture, improved yield traits, and / or increased tolerance / resistance to abiotic and biotic stresses compared to plants or plant parts that do not contain the same mutations. In some embodiments, improved yield traits can include, but are not limited to, one or more of the following phenotypes: increased number of kernel rows (about 5% to about 30%, for example, (e.g., about 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29% or 30% or any range or value thereof) in any combination, increased kernel size (about 1% to about 25%; for example, , about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, or 25%, or any range or value thereof), increased ear length (about 2% to about 30%; for example, about 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, or any range or value thereof). , 26%, 27%, 28%, 29% or 30% or any range or value therein), decreased tiller number (from about 2% to about 100%; for example, about 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 3%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% or any range or value thereof, reduced tassel branch number (from about 2% to about 100%);For example, about 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% or any range or value therein), decreased time to flowering (about 5% to about 50%; for example, about 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, %, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 45%, 46%, 47%, 48%, 49%, or 50%, or any range or value therein), increased seed number per plant (from about 10% to about 100%; for example, about 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 45%, 46%, 47%, 48%, 49%, or 50%, or any range or value therein), increased seed number per plant (from about 10% to about 100%; for example, about 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% or any range or value therein), increased number of pods per node (from about 3% to about 50%);For example, about 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 45%, 46%, 47%, 48%, 49%, or 50%, or any range or value thereof) and / or the number of pods per plant (about 3% to about 50%; for example, about 3 %, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, or 30%, or any range or value therein) and / or increased seed weight (about 1% to about 20%; for example, about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, or 20%, or any range or value therein). ;

[0273] In some embodiments, the endogenous SPL9 gene may be present in the plant or part thereof as two paralogous pairs: (a) a SPL9a gene and a SPL9b gene and / or (b) a SPL9c gene and a SPL9d gene, optionally wherein at least one of the SPL9a gene, the SPL9b gene, the SPL9c gene, and the SPL9d gene comprises a mutation in any combination, or wherein each of the SPL9a gene, the SPL9b gene, the SPL9c gene, and the SPL9d gene comprises a mutation.

[0274] In some embodiments, a mutation (optionally a non-natural mutation) in the IPA1 gene may be generated in the first exon of the endogenous SPL9 gene, optionally resulting in a premature stop codon and a null allele. In some embodiments, the first exon of the SPL9a gene may be located at about nucleotide 2001 to about nucleotide 2364 with reference to the nucleotide numbering of SEQ ID NO:72, at about nucleotide 1 to about nucleotide 364 with reference to the nucleotide numbering of SEQ ID NO:73, and / or at about nucleotide 2160 to about nucleotide 2523 with reference to the nucleotide numbering of SEQ ID NO:143, the first exon of the SPL9b gene may be located at about nucleotide 2001 to about nucleotide 2370 with reference to the nucleotide numbering of SEQ ID NO:75, at about nucleotide 1 to about nucleotide 370 with reference to the nucleotide numbering of SEQ ID NO:76, and / or at about nucleotide 2098 to about nucleotide 2467 with reference to the nucleotide numbering of SEQ ID NO:182, the first exon of the SPL9c gene may be located at about nucleotide 2001 to about nucleotide 2347 with reference to the nucleotide numbering of SEQ ID NO:78, at about nucleotide 1 to about nucleotide 347 with reference to the nucleotide numbering of SEQ ID NO:79, and / or at about nucleotide 2160 to about nucleotide 2523 with reference to the nucleotide numbering of SEQ ID NO:143. The nucleotide numbering of NO:222 is located at about nucleotide 2378 to about nucleotide 2724, and / or the first exon of the SPL9d gene can be located at about nucleotide 2001 to about nucleotide 2349 with reference to the nucleotide numbering of SEQ ID NO:81, at about nucleotide 1 to about nucleotide 349 with reference to the nucleotide numbering of SEQ ID NO:82, and / or at about nucleotide 2410 to about nucleotide 2758 with reference to the nucleotide numbering of SEQ ID NO:255.

[0275] In some embodiments, the mutation (optionally a non-natural mutation) in the SPL9 gene may be in the region from about nucleotide 2053 to about nucleotide 2115 in the first exon of the SPL9a gene with reference to nucleotide numbering of SEQ ID NO: 72 or SEQ ID NO: 75, in the region from about nucleotide 2015 to about nucleotide 2077 in the first exon of the SPL9b gene with reference to nucleotide numbering of SEQ ID NO: 78 or SEQ ID NO: 81, in the region from about nucleotide 1 to about nucleotide 115 in the first exon of the SPL9c gene with reference to nucleotide numbering of SEQ ID NO: 73 or SEQ ID NO: 76, and / or in the region from about nucleotide 1 to about nucleotide 77 in the first exon of the SPL9d gene with reference to nucleotide numbering of SEQ ID NO: 79 or SEQ ID NO: 82, optionally in the region from about nucleotide 1 to about nucleotide 77 in the SPL9a gene with reference to SEQ ID NO: 78 or SEQ ID NO: 81. In a region in the SPL9b gene that has at least 80% sequence identity with the nucleotide sequence of any one of NO:161-177, in a region in the SPL9b gene that has at least 80% sequence identity with the nucleotide sequence of any one of 201-217, in a region in the SPL9c gene that has at least 80% sequence identity with the nucleotide sequence of any one of 240-250, or in a region in the SPL9d gene that has at least 80% sequence identity with the nucleotide sequence of any one of 274-284.

[0276] In some embodiments, the mutation in the UB2 gene can be in the region of the third exon of the endogenous UB2 gene (see, e.g., the third exon of SEQ ID NO: 84; e.g., SEQ ID NOs: 358-376, optionally SEQ ID NOs: 373-376), optionally resulting in a premature stop codon and a null allele, optionally a hypomorphic mutation or a knockout mutation. In some embodiments, the mutation in the UB3 gene may be in the region of the third exon of the endogenous UB3 gene (see, e.g., the third exon of SEQ ID NO: 87; e.g., SEQ ID NOs: 408-426, optionally SEQ ID NOs: 415-416, optionally resulting in a premature stop codon and a null allele, optionally a hypomorphic mutation or a knockout mutation. In some embodiments, the mutation may be a non-natural mutation. In some embodiments, the mutation in the IPA1 gene may be generated in a miR156 binding site, e.g., a miRNA binding site of an endogenous SPL9 gene, UB2 gene, and / or UB3 gene. In some embodiments, (a) the endogenous gene is the SPL9a gene and the miR156 binding site may be located at about nucleotide 6569 to about nucleotide 6588 with reference to the nucleotide numbering of SEQ ID NO: 72, at about nucleotide 758 to about nucleotide 777 with reference to the nucleotide numbering of SEQ ID NO: 73, and / or at about nucleotide 760 to about nucleotide 787 with reference to the nucleotide numbering of SEQ ID NO: 74. NO:143 is at about nucleotide 6624 to about nucleotide 6847; (b) the endogenous gene is the SPL9b gene and the miR156 binding site can be located at about nucleotide 6269 to about nucleotide 6288 with reference to the nucleotide numbering of SEQ ID NO:75, at about nucleotide 760 to about nucleotide 780 with reference to the nucleotide numbering of SEQ ID NO:76, and / or at about nucleotide 6265 to about nucleotide 6488 with reference to the nucleotide numbering of SEQ ID NO:182, (c) the endogenous gene is the SPL9c gene and the miR156 binding site can be located at about nucleotide 5388 to about nucleotide 5407 with reference to the nucleotide numbering of SEQ ID NO:78, at about nucleotide 761 to about nucleotide 780 with reference to the nucleotide numbering of SEQ ID NO:79, and / or at about nucleotide 5665 to about nucleotide 5887 with reference to the nucleotide numbering of SEQ ID NO:222, and / or (d) the endogenous gene is the SPL9d gene and the miR156 binding site can be located at about nucleotide 5388 to about nucleotide 5407 with reference to the nucleotide numbering of SEQ ID NO:78, at about nucleotide 761 to about nucleotide 780 with reference to the nucleotide numbering of SEQ ID NO:79, and / or at about nucleotide 5665 to about nucleotide 5887 with reference to the nucleotide numbering of SEQ ID NO:222. The nucleotide numbering of NO:81 is between about nucleotide 5798 and about nucleotide 5817, the nucleotide numbering of reference SEQ ID NO:82 is between about nucleotide 737 and about nucleotide 756, and / or the nucleotide numbering of reference SEQ ID NO:255 is between about nucleotide 6120 and about nucleotide 6342.In some embodiments, the mutation may be a non-natural mutation.

[0277] In some embodiments, the mutation in the miR156 binding site may be located in: (a) in the endogenous SPL9a gene from about nucleotide 6549 to about nucleotide 6608 with reference to nucleotide numbering of SEQ ID NO:72 and / or from about nucleotide 738 to about nucleotide 797 with reference to nucleotide numbering of SEQ ID NO:73, optionally in a region having about 80% sequence identity with any one of the nucleotide sequences of SEQ ID NOs:178-181, (b) in the endogenous SPL9b gene from about nucleotide 6250 to about nucleotide 6308 with reference to nucleotide numbering of SEQ ID NO:75 and / or from about nucleotide 741 to about nucleotide 800 with reference to nucleotide numbering of SEQ ID NO:76, optionally in a region having about 80% sequence identity with any one of the nucleotide sequences of SEQ ID NOs:218-221, (c) in the endogenous SPL9c gene from about nucleotide 5368 to about nucleotide 5427 with reference to nucleotide numbering of SEQ ID NO:78 and / or from about nucleotide 5460 to about nucleotide 5527 with reference to nucleotide numbering of SEQ ID NO:79 In some embodiments, the mutation may be a non-natural mutation.

[0278] In some embodiments, the mutation may be in the miR156 binding site of the UB2 gene, which is located at about nucleotide 4928 to about nucleotide 4947 with reference to the nucleotide numbering of SEQ ID NO: 84 and / or at about nucleotide 815 to about nucleotide 834 with reference to the nucleotide numbering of SEQ ID NO: 85. In some embodiments, the mutation may be in the miR156 binding site of the UB3 gene and the miR156 binding site is located at about nucleotide 5301 to about nucleotide 5320 with reference to the nucleotide numbering of SEQ ID NO: 87 and / or at about nucleotide 848 to about nucleotide 866 with reference to the nucleotide numbering of SEQ ID NO: 88. In some embodiments, (a) the mutation in the miR156 binding site of the endogenous UB2 gene may be located at about nucleotide 4894 to about nucleotide 4967 with reference to the nucleotide numbering of SEQ ID NO: 84 and / or at about nucleotide 781 to about nucleotide 854 with reference to the nucleotide numbering of SEQ ID NO: 85, and / or (b) the mutation in the miR156 binding site of the endogenous UB3 gene may be located at about nucleotide 5267 to about nucleotide 5339 with reference to the nucleotide numbering of SEQ ID NO: 87 and / or at about nucleotide 814 to about nucleotide 887 with reference to the nucleotide numbering of SEQ ID NO: 88. In some embodiments, the mutation may be a non-natural mutation.

[0279] In some embodiments, the mutation in the miR156 binding site of the IPA1 gene can be a substitution or a deletion, optionally wherein the deletion can be an in-frame deletion or an out-of-frame deletion. In some embodiments, at least one mutation in the miR156 binding site can be a point mutation, optionally a silent point mutation. In some embodiments, the mutation can be a non-natural mutation. In some embodiments, the point mutation can be a substitution, optionally wherein the substitution is C>A, T or G, optionally C>A. In some embodiments, the mutation in the miR156 binding site upregulates the expression of an endogenous IPA1 gene, such as an endogenous SPL9a gene, an endogenous SPL9b gene, an endogenous SPL9c gene, an endogenous SPL9d gene, an endogenous unbranched 2 (UB2) gene, and / or an endogenous unbranched 3 (UB3) gene.

[0280] In some embodiments, at least one mutation (optionally a non-natural mutation) is a base substitution in a region of an endogenous UB2 gene or an endogenous UB3 gene associated with increased kernel row number (KRN), and / or increased tassel branch number (TBN), optionally without substantially reducing ear length, optionally wherein the region of the endogenous UB2 gene associated with increased KRN is from about nucleotide 4379 to about nucleotide 4800 with reference to nucleotide numbering of SEQ ID NO:84 and / or from about nucleotide 626 to about nucleotide 688 with reference to nucleotide numbering of SEQ ID NO:85, and / or the region of the endogenous UB3 gene associated with increased KRN is from about nucleotide 5094 to about nucleotide 5157 with reference to nucleotide numbering of SEQ ID NO:87 and / or from about nucleotide 641 to about nucleotide 703 with reference to nucleotide numbering of SEQ ID NO:88, and / or wherein the region of the endogenous UB2 gene associated with increased TBN is from about nucleotide 4834 to about nucleotide 4896 with reference to nucleotide numbering of SEQ ID NO:84 and / or from about nucleotide 626 to about nucleotide 688 with reference to nucleotide numbering of SEQ ID NO:85. The nucleotide numbering of NO:85 is from about nucleotide 721 to about nucleotide 783, and / or the region of the endogenous UB3 gene associated with increased TBN is from about nucleotide 5204 to about nucleotide 5266 with reference to the nucleotide numbering of SEQ ID NO:87 and / or from about nucleotide 751 to about nucleotide 813 with reference to the nucleotide numbering of SEQ ID NO:88.

[0281] In some embodiments, the mutation useful for producing plants with altered plant architecture, improved yield traits and / or increased tolerance / resistance to abiotic and biotic stresses may be in the 5' untranslated region (UTR) and / or 3' UTR of an endogenous SPL9 gene, an endogenous UB2 gene, or an endogenous UB3 gene, optionally wherein the endogenous SPL9 gene is: (a) an endogenous SPL9a gene and the mutation is in the 5'UTR in the region from about nucleotide 1826 to about nucleotide 1981 and / or from about nucleotide 1846 to about nucleotide 1961 with reference to nucleotide numbering of SEQ ID NO:72, optionally in a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-160; (b) an endogenous SPL9b gene and the mutation is in the 5'UTR in the region from about nucleotide 1804 to about nucleotide 1973 and / or from about nucleotide 1824 to about nucleotide 1953 with reference to nucleotide numbering of SEQ ID NO:75, optionally in a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: NO:185-200; (c) an endogenous SPL9c gene and the mutation is in the region of the 5'UTR from about nucleotide 1593 to about nucleotide 1783 and / or from about nucleotide 1613 to about nucleotide 1764 with reference to the nucleotide numbering of SEQ ID NO:78, optionally in a region having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NO:225-239; and / or (d) an endogenous SPL9d gene and the mutation is in the region of the 5'UTR from about nucleotide 1555 to about nucleotide 1740 and / or from about nucleotide 1574 to about nucleotide 1720 with reference to the nucleotide numbering of SEQ ID NO:81, optionally in a region having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NO:258-273. In some embodiments, the mutation may be a non-natural mutation.

[0282] In some embodiments, mutations useful for generating plants with altered plant architecture, improved yield traits and / or increased tolerance / resistance to abiotic and biotic stresses may be in the 5' untranslated region (UTR) of: (a) an endogenous UB2 gene, the 5'UTR of which is located at about nucleotide 1414 to about nucleotide 1860, about nucleotide 1414 to about nucleotide 1522, about nucleotide 1454 to about nucleotide 1481, about nucleotide 1553 to about nucleotide 1582, about nucleotide 1597 to about nucleotide 1633, and / or about nucleotide 1767 to about nucleotide 1819, with reference to the nucleotide numbering of SEQ ID NO: 84, optionally in a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 133-136; and / or (b) an endogenous UB3 gene, the 5'UTR of which is located at about nucleotide 1414 to about nucleotide 1860, about nucleotide 1414 to about nucleotide 1522, about nucleotide 1454 to about nucleotide 1481, about nucleotide 1553 to about nucleotide 1582, about nucleotide 1597 to about nucleotide 1633, and / or about nucleotide 1767 to about nucleotide 1819, with reference to the nucleotide numbering of SEQ ID NO: 84, optionally in a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 133-136; The nucleotide numbering of NO:87 is located at about nucleotide 1327 to about nucleotide 1646, about nucleotide 1439 to about nucleotide 1467, about nucleotide 1368 to about nucleotide 1394, about nucleotide 1549 to about nucleotide 1606, about nucleotide 1787 to about nucleotide 1855 and / or about nucleotide 1747 to about nucleotide 1920, optionally with the nucleotide sequence of any one of SEQ ID NO:129-132, in a region with at least 80% sequence identity. In some embodiments, the mutation can be a non-natural mutation.

[0283] In some embodiments, mutations useful for generating plants with altered plant architecture, improved yield traits, and / or increased tolerance / resistance to abiotic and biotic stresses may be in the 3' untranslated region (UTR) of: (a) an endogenous UB2 gene, the 3'UTR of which is located at about nucleotide 5701 to about nucleotide 5882 and / or about nucleotide 5742 to about nucleotide 5842, with reference to the nucleotide numbering of SEQ ID NO:84, optionally in a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs:140-142; and / or (b) an endogenous UB3 gene, the 3'UTR of which is located at about nucleotide 5940 to about nucleotide 6109, about nucleotide 5980 to about nucleotide 6069, about nucleotide 6516 to about nucleotide 6643, and / or about nucleotide 6556 to about nucleotide 6603, with reference to the nucleotide numbering of SEQ ID NO:87, optionally in a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs:140-142. The nucleotide sequence of any one of NOs: 137-139 has a region of at least 80% sequence identity. In some embodiments, the mutation may be a non-natural mutation.

[0284] In some embodiments, mutations useful for generating plants with altered plant architecture, improved yield traits, and / or increased tolerance / resistance to abiotic and biotic stresses may be in an intron of an endogenous UB2 gene or an endogenous UB3 gene, optionally wherein (a) the region of the intron targeted for mutations in the endogenous UB2 gene is located at about nucleotide 2856 to about nucleotide 2971, about nucleotide 2896 to about nucleotide 2931, about nucleotide 3753 to about nucleotide 3893, and / or about nucleotide 3793 to about nucleotide 3853 with reference to the nucleotide numbering of SEQ ID NO: 84; and / or (b) the region of the intron targeted for mutations in the endogenous UB3 gene is located at about nucleotide 2666 to about nucleotide 2784, about nucleotide 2706 to about nucleotide 2744, about nucleotide 4017 to about nucleotide 4147, and / or about nucleotide 4057 to about nucleotide 4107 with reference to the nucleotide numbering of SEQ ID NO: 87. In some embodiments, the mutation may be a non-natural mutation.

[0285] In some embodiments, at least one mutation is a dominant negative mutation, a semi-dominant mutation, a hyperallelic mutation, a superallelic mutation, a hypomorphic mutation, a weak loss-of-function mutation, or a null allele, optionally wherein the mutation is a non-natural mutation.

[0286] In some embodiments, plants produced by the methods of the invention can exhibit, for example, altered plant architecture, improved yield traits, and / or increased tolerance / resistance to abiotic and biotic stresses compared to plants or plant parts lacking the same mutation. In some embodiments, improved yield traits include, but are not limited to, one or more of the following phenotypes: increased number of kernel rows, increased kernel size, increased ear length, reduced tiller number, reduced number of tassel branches, reduced time to flowering, increased number of seeds per plant, increased number of pods per node and / or per plant, and / or increased seed weight, optionally without substantially reducing ear length.

[0287] Any plant or part thereof comprising an endogenous IPA1 gene encoding an SPL transcription factor can be used with the methods and compositions of the present invention to provide plants or parts thereof comprising an endogenous IPA1 gene modified as described herein and plants exhibiting, for example, altered plant architecture, improved yield traits and / or increased tolerance / resistance to abiotic and biotic stresses compared to plants lacking the same mutation. Plants useful in the present invention can be, for example, monocots or dicots.

[0288] Non-limiting examples of plants that can be modified as described herein can include, but are not limited to, turf grasses (e.g., bluegrass, bentgrass, ryegrass, fescue), feather reed grass, tufted hairgrass, miscanthus, reed, switchgrass, vegetable crops including artichokes, kohlrabi, arugula, leeks, asparagus, lettuce (e.g., cabbage, leaf lettuce, romaine lettuce), yellow taro, melons (e.g., musk melon, watermelon, Crenshaw melon, honeydew melon, cantaloupe), Brassica crops (e.g., Brussels sprouts, cabbage, cauliflower, broccoli, kale, kale, Chinese cabbage, bok choy), cardoons, carrots, sauerkraut, okra, onions, celery, parsley, chickpeas, parsnips, endive, peppers, potatoes, cucurbits (e.g., zucchini, cucumber, zucchini, pumpkin, squash, honeydew melon, watermelon, cantaloupe), radishes, dry bulb onions (e.g., cauliflower, cauliflower, broccoli, kale, kale, Chinese cabbage, pak choi), onion), rutabaga, eggplant, salsify, endive, shallots, endive, garlic, spinach, shallots, pumpkin, leafy greens, beets (sugar and fodder), sweet potatoes, chard, horseradish, tomatoes, carrots, and spices; fruit crops such as apples, apricots, cherries, nectarines, peaches, pears, plums, prunes, cherries, quince, figs, nuts (e.g., chestnuts, pecans, pistachios, hazelnuts, pistachios, peanuts, walnuts, macadamia nuts, almonds etc.), citrus (e.g., clementines, kumquats, oranges, grapefruits, tangerines, mandarins, lemons, limes, etc.), blueberries, black raspberries, boysenberries, cranberries, currants, gooseberries, loganberries, raspberries, strawberries, blackberries, grapes (wine and table grapes), avocados, bananas, kiwis, persimmons, pomegranates, pineapples, tropical fruits, pomegranates, cantaloupe, mangoes, papayas, and lychees, field crops such as clover, alfalfa, timothy, evening primrose, silvergrass, corn / Maize (fodder corn, sweet corn, popcorn), hops, jojoba, buckwheat, safflower, quinoa, wheat, rice, barley, rye, millet, sorghum, oats, triticale, sorghum, tobacco, kapok, legumes (legumes (e.g., green and dry beans), lentils, peas, soybeans), oil plants (rapeseed, canola, mustard, olives, sunflower, coconut, castor oil plants, cocoa beans, peanuts, oil palm), duckweed, Arabidopsis, fiber plants (cotton, flax, , jute), Lauraceae (cinnamon, camphor) or plants such as coffee, sugar cane, tea and natural rubber plants; and / or bedding plants, such as flowering plants, cacti, succulents and / or ornamental plants (e.g., roses, tulips, violets), and trees, such as forest trees (broad-leaved and evergreen trees, such as conifers; e.g., elm, ash, oak, maple, fir, spruce, cedar, pine, birch, cypress, eucalyptus, willow) and shrubs and other nursery stock. In some embodiments, the nucleic acid construct of the invention and / or the expression cassette and / or vector encoding the nucleic acid construct can be used to modify corn, soybean, wheat, canola, rice, tomato, pepper or sunflower.In some embodiments, plants useful in the present invention include, but are not limited to, corn, soybean, canola, wheat, rice, cotton, sugar cane, sugar beet, barley, oats, alfalfa, sunflower, safflower, oil palm, sesame, coconut, tobacco, potato, sweet potato, cassava, coffee tree, apple, plum, apricot, peach, cherry, pear, fig, banana, citrus, cocoa, avocado, olive, almond, walnut, strawberry, watermelon, pepper, grape, tomato, cucumber, or Brassica spp (e.g., B. napus, B. oleracea, B. rapa, B. juncea, and / or B. nigra). In some embodiments, the plant is corn. In some embodiments, the plant is soybean.

[0289] The endogenous IPA1 gene encoding the SPL transcription factor that can be used in the present invention may include, for example, the endogenous SPL9 gene, the endogenous UB2 gene or the endogenous UB3 gene. In some embodiments, the endogenous SPL9 gene that can be used in the present invention: (a) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:72, 75, 78, 81, 143, 182, 222 or 255; (b) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:73, 76, 79, 82, 144, 183, 223 or 256; (c) comprises a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:146-181, 185-221, 225-254 or 258-288, and / or (d) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of any one of SEQ ID NO:74, 77, 80, 83, 145, 184, 224 or 257. In some embodiments, the endogenous UB2 gene useful in the present invention: (a) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:84; (b) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:85; (c) comprises a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs:90-96 or 332-339, and / or (d) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of SEQ ID NO:86. In some embodiments, the endogenous UB3 gene useful in the present invention: (a) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:87; (b) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:88; (c) comprises a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs:90, 97-103, or 394-445, and / or (d) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of SEQ ID NO:89.

[0290] In some embodiments, the nuclease can cleave the endogenous IPA1 gene encoding the SPL transcription factor, thereby introducing mutations into the endogenous IPA1 gene. The nuclease that can be used in the present invention can be any nuclease that can be used to edit / modify the target nucleic acid. Such nucleases include, but are not limited to, zinc finger nucleases, transcription activator-like effector nucleases (TALENs), endonucleases (e.g., Fok1), and / or CRISPR-Cas effector proteins. Similarly, any nucleic acid binding domain (e.g., DNA binding domain, RNA binding domain) that can be used in the present invention can be any nucleic acid binding domain that can be used to edit / modify the target nucleic acid. Such nucleic acid binding domains include, but are not limited to, zinc fingers, transcription activator-like DNA binding domains (TALs), argonautes, and / or CRISPR-Cas effector DNA binding domains.

[0291] In some embodiments, a method for editing an endogenous IPA1 gene in a plant or a plant part is provided, the method comprising contacting a target site in an IPA1 gene in the plant or a plant part with a cytosine base editing system, the cytosine base editing system comprising a cytosine deaminase and a nucleic acid binding domain that binds to a target site in an IPA gene, the IPA gene being (a) a SPL9 gene encoding a sequence having at least 80% sequence identity to an amino acid sequence of SEQ ID NO: 74, 77, 80, 83, 86, 89, 145, 184, 224, or 257 and / or comprising a sequence having at least 80% sequence identity to a nucleotide sequence of SEQ ID NO: 72, 73, 75, 76, 78, 79, 81, 82, 84, 85, 87, 88, 143, 144, 182, 183, 222, 223, 255, or 256; (b) a UB2 gene encoding a sequence having at least 80% sequence identity to a nucleotide sequence of SEQ ID NO: NO:86 having at least 80% sequence identity and / or comprising a sequence having at least 80% sequence identity with the nucleotide sequence of SEQ ID NO:84; and / or (c) a UB3 gene encoding a sequence having at least 80% sequence identity with the amino acid sequence of SEQ ID NO:89 and / or comprising a sequence having at least 80% sequence identity with the nucleotide sequence of SEQ ID NO:87; thereby editing the endogenous IPA1 gene in the plant or part thereof and producing a plant or part thereof comprising at least one cell having a mutation in the endogenous IPA1 gene.

[0292] In some embodiments, a method for editing an endogenous IPA1 gene in a plant or a plant part is provided, the method comprising contacting a target site in an IPA1 gene in the plant or a plant part with an adenosine base editing system, the adenosine base editing system comprising an adenosine deaminase and a nucleic acid binding domain that binds to a target site in an IPA gene, the IPA gene being (a) a SPL9 gene encoding a sequence having at least 80% sequence identity to an amino acid sequence of SEQ ID NO: 74, 77, 80, 83, 86, 89, 145, 184, 224, or 257 and / or comprising a sequence having at least 80% sequence identity to a nucleotide sequence of SEQ ID NO: 72, 73, 75, 76, 78, 79, 81, 82, 84, 85, 87, 88, 143, 144, 182, 183, 222, 223, 255, or 256; (b) a UB2 gene encoding a sequence having at least 80% sequence identity to a nucleotide sequence of SEQ ID NO: NO:86 having at least 80% sequence identity and / or comprising a sequence having at least 80% sequence identity with the nucleotide sequence of SEQ ID NO:84; and / or (c) a UB3 gene encoding a sequence having at least 80% sequence identity with the amino acid sequence of SEQ ID NO:89 and / or comprising a sequence having at least 80% sequence identity with the nucleotide sequence of SEQ ID NO:87; thereby editing the endogenous IPA1 gene in the plant or part thereof and producing a plant or part thereof comprising at least one cell having a mutation in the endogenous IPA1 gene.

[0293] In some embodiments, a method for detecting a mutant IPA1 gene (a mutation in an endogenous IPA1 gene) is provided, the method comprising detecting a deletion in the following nucleic acids in the genome of a plant: (a) a nucleic acid encoding any one of the amino acid sequences of SEQ ID NO: 74, 77, 80, 83, 86, 89, 145, 184, 224 or 257 and / or comprising a sequence having at least 80% sequence identity with the nucleotide sequence of SEQ ID NO: 72, 73, 75, 76, 78, 79, 81, 82, 84, 85, 87, 88, 143, 144, 182, 183, 222, 223, 255 or 256; (b) a nucleic acid encoding the amino acid sequence of SEQ ID NO: 86 and / or comprising a sequence having at least 80% sequence identity with the nucleotide sequence of SEQ ID NO: 84; and / or (c) a nucleic acid encoding the amino acid sequence of SEQ ID NO: 89 and / or comprising a sequence having at least 80% sequence identity with the nucleotide sequence of SEQ ID NO: A nucleic acid having a sequence with at least 80% sequence identity to the nucleotide sequence of NO:87.

[0294] In some embodiments, a method for detecting a mutant IPA1 gene (a mutation in an endogenous IPA1 gene) is provided, the method comprising detecting in the genome of a plant a mutant IPA1 gene of any one of SEQ ID NOs: 289-300 (e.g., a mutant SPL9a gene having a nucleic acid sequence of any one of SEQ ID NOs: 295 or 301; a mutant SPL9b gene having a nucleic acid sequence of SEQ ID NO: 299; a mutant SPL9c gene having a nucleic acid sequence of any one of SEQ ID NOs: 289, 291, 292, 296, or 298; a mutant SPL9d gene having a nucleic acid sequence of any one of SEQ ID NOs: 290, 293, 294, or 297); a mutant IPA1 gene of any one of SEQ ID NOs: 310, 312, 314, 316, or 318 (e.g., a mutant UB3 gene); or a mutant IPA1 gene of any one of SEQ ID NOs: 320, 322, or 324 (e.g., a mutant UB2 gene).

[0295] In some embodiments, the mutation in the endogenous IPA1 gene encoding the SPL transcription factor in the plant can be a substitution, deletion and / or insertion. In some embodiments, the mutation can be a non-natural mutation. In some embodiments, the mutation in the endogenous IPA1 gene of the plant can be a substitution, deletion and / or insertion that results in a dominant negative mutation, a semi-dominant mutation, a weak loss-of-function mutation, a hyperallele mutation, a hypoallele mutation, or a null mutation, and produces a plant that exhibits altered plant architecture, improved yield traits, and / or increased tolerance / resistance to abiotic and biotic stresses compared to a plant or plant part lacking the same mutation. For example, the mutation can be a substitution, deletion and / or insertion of one or more amino acid residues (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more amino acids of the SPL transcription factor), or the mutation can be from at least 1 nucleotide to about 150 consecutive nucleotides (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75 2, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 1, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 110, 111, 12, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134 In some embodiments, the at least one mutation may be a base substitution, deletion, or insertion of about 4, 135, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, or 150 or more consecutive nucleotides, or any range or value therein), optionally wherein the mutation in the IPA1 gene is a deletion, and the deletion may be about 4, 5, 7, 8, 9, 10, 11, 12, 13, 29, 54, 68, or 127 consecutive nucleotides and any combination of deletions thereof. In some embodiments, the deletion may be an in-frame deletion or an out-of-frame deletion. In some embodiments, at least one mutation may be a base substitution for A, T, G, or C.In some embodiments, at least one mutation may be a point mutation, optionally a silent point mutation. The point mutation may be a substitution, optionally wherein the substitution is C>A, T or G, optionally C>A.

[0296] In some embodiments, mutations in an endogenous IPA1 gene encoding an SPL transcription factor can be generated following cleavage by an editing system comprising a nuclease and a nucleic acid binding domain that binds to a target site within a target nucleic acid (e.g., an IPA1 gene), the target nucleic acid comprising a nucleotide sequence having at least 80% identity to any one of the nucleotide sequences of SEQ ID NOs: 72, 73, 75, 76, 78, 79, 81, 82, 85, 87, 88, 143, 144, 182, 183, 222, 223, 255, or 256, or encoding a polypeptide comprising a sequence having at least 80% sequence identity to any one of the amino acid sequences of SEQ ID NOs: 74, 77, 80, 83, 86, 89, 145, 184, 224, or 257. In some embodiments, the nuclease cleaves the endogenous IPA1 gene and introduces the mutation into the endogenous IPA1 gene.

[0297] Also provided herein are guide nucleic acids (e.g., gRNA, gDNA, crRNA, crDNA) that bind to target nucleic acids in the SPL9 gene with a gene identification number (gene ID) of Glyma_02G177500 (SPL9a), Glyma_09G113800 (SPL9b), Glyma_03g143100 (SPL9c) and / or Glyma_19g146000 (SPL9d).

[0298] In some embodiments, the guide nucleic acid of the present invention binds to a target site in an endogenous IPA1 gene, wherein the endogenous IPA1 gene: (a) is an endogenous SQUAMOSA promoter binding protein-like 9 (SPL9) gene, which (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 72, 75, 78, 81, 143, 182, 222, or 255; (ii) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 73, 76, 79, 82, 144, 183, 223, or 256; (iii) comprises a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254, and / or 258-288, and / or (iv) encodes a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: NO:74, 77, 80, 83, 145, 184, 224 or 257; (b) is an endogenous unbranched 2 (UB2) gene, which (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:84; (ii) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:85; (iii) comprises a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:90-96 or 332-393, and / or (iv) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of SEQ ID NO:86; or (c) is an endogenous unbranched 3 (UB3) gene, which: (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:87; (ii) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:85; NO:88 has a coding sequence with at least 80% sequence identity; (iii) contains a region with at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs:90, 97-103 or 394-445, and / or (iv) encodes a polypeptide sequence with at least 80% identity to the amino acid sequence of SEQ ID NO:89.

[0299] In some embodiments, the target site can be in a region of the SPL9 gene that has at least about 80% sequence identity to any of the nucleotide sequences of SEQ ID NOs: 146-181, 185-221, 225-254, and / or 258-288.

[0300] In some embodiments, the target site can be in a region of the UB2 gene that has at least about 80% sequence identity to any of the nucleotide sequences of SEQ ID NOs: 90-96 or 332-393.

[0301] In some embodiments, the target site can be in a region of the UB3 gene that has at least about 80% sequence identity to any of the nucleotide sequences of SEQ ID NOs: 90, 97-103, or 394-445.

[0302] In some embodiments, the guide nucleic acid may comprise a spacer sequence having a nucleotide sequence of any one of SEQ ID NOs: 104-142, 301, 326, and / or 327. In some embodiments, the guide nucleic acid may be directed against the SPL9 gene and may comprise a nucleotide sequence of SEQ ID NOs: 104-124 and 301. In some embodiments, the guide nucleic acid may be directed against the UB3 / UB2 gene and may comprise a nucleotide sequence of SEQ ID NOs: 125-142, 326, and / or 327.

[0303] In some embodiments, a system is provided, comprising a guide nucleic acid of the invention and a CRISPR-Cas effector protein associated with the guide nucleic acid. In some embodiments, the system further comprises a tracr nucleic acid associated with the guide nucleic acid and the CRISPR-Cas effector protein, optionally wherein the tracr nucleic acid and the guide nucleic acid are covalently linked, optionally wherein the guide nucleic acid comprises a spacer having a nucleotide sequence of any one of SEQ ID NOs: 104-124 or 301 or SEQ ID NOs: 125-142, 326 and / or 327.

[0304] The present invention also provides a gene editing system, which comprises a CRISPR-Cas effector protein associated with a guide nucleic acid, and the guide nucleic acid comprises a spacer sequence that binds to an endogenous IPA1 gene encoding an SPL transcription factor, wherein the IPA1 gene (a) is an endogenous SQUAMOSA promoter binding protein-like 9 (SPL9) gene, which (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 72, 75, 78, 81, 143, 182, 222 or 255; (ii) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 73, 76, 79, 82, 144, 183, 223 or 256; (iii) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: NO:146-181, 185-221, 225-254 and / or 258-288, and / or (iv) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of any one of SEQ ID NO:74, 77, 80, 83, 145, 184, 224 or 257; (b) is an endogenous unbranched 2 (UB2) gene, which: (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:84; (ii) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:85; (iii) comprises a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:90-96 or 332-393, and / or (iv) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of any one of SEQ ID NO:74, 77, 80, 83, 145, 184, 224 or 257. NO:86; or (c) is an endogenous unbranched 3 (UB3) gene, which: (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:87; (ii) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:88; (iii) comprises a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs:90, 97-103, or 394-445, and / or (iv) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of SEQ ID NO:89. In some embodiments, the spacer sequence of the guide nucleic acid may comprise a nucleotide sequence of any one of SEQ ID NOs:104-124 or 301 or SEQ ID NOs:125-142, 326, or 327.In some embodiments, the gene editing system can further comprise a tracr nucleic acid associated with a guide nucleic acid and a CRISPR-Cas effector protein, optionally wherein the tracr nucleic acid and the guide nucleic acid are covalently linked, optionally wherein the guide nucleic acid comprises a spacer sequence having a nucleotide sequence of any one of SEQ ID NOs: 104-124 or 301, or a combination thereof, or SEQ ID NOs: 125-142, 326, or 327, or a combination thereof.

[0305] As used herein, “CRISPR-Cas effector protein associated with a guide nucleic acid” refers to a complex formed between the CRISPR-Cas effector protein and the guide nucleic acid to direct the CRISPR-Cas effector protein to a target site in a gene.

[0306] The present invention also provides a complex comprising a CRISPR-Cas effector protein containing a cleavage domain and a guide nucleic acid, wherein the guide nucleic acid binds to a target site in an IPA1 gene, wherein the IPA1 gene (a) is an endogenous SQUAMOSA promoter binding protein-like 9 (SPL9) gene, which (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 72, 75, 78, 81, 143, 182, 222 or 255; (ii) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 73, 76, 79, 82, 144, 183, 223 or 256; (iii) comprises a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288, and / or (iv) encodes a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288, and / or NO:74, 77, 80, 83, 145, 184, 224 or 257; (b) is an endogenous unbranched 2 (UB2) gene, which (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:84; (ii) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:85; (iii) comprises a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:90-96 or 332-393, and / or (iv) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of SEQ ID NO:86; or (c) is an endogenous unbranched 3 (UB3) gene, which: (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:87; (ii) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:85; NO:88 has a coding sequence with at least 80% sequence identity; (iii) comprises a region with at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs:90, 97-103 or 394-445, and / or (iv) encodes a polypeptide sequence with at least 80% identity to the amino acid sequence of SEQ ID NO:89, wherein the cleavage domain cleaves the target strand in the IPA1 gene.

[0307] In some embodiments, an expression cassette is provided, the expression cassette comprising (a) a polynucleotide encoding a CRISPR-Cas effector protein comprising a cleavage domain and (b) a guide nucleic acid that binds to a target site in an IPA1 gene, wherein the guide nucleic acid comprises a spacer sequence that is complementary to and binds to the target site in the IPA1 gene, wherein the IPA1 gene: (a) is an endogenous SQUAMOSA promoter binding protein-like 9 (SPL9) gene, which (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO: 72, 75, 78, 81, 143, 182, 222, or 255; (ii) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO: 73, 76, 79, 82, 144, 183, 223, or 256; (iii) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO: NO:146-181, 185-221, 225-254 and / or 258-288, and / or (iv) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of any one of SEQ ID NO:74, 77, 80, 83, 145, 184, 224 or 257; (b) is an endogenous unbranched 2 (UB2) gene, which (i) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:84; (ii) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:85; (iii) comprises a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:90-96 or 332-393, and / or (iv) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of any one of SEQ ID NO:74, 77, 80, 83, 145, 184, 224 or 257; NO:86; or (c) is an endogenous unbranched 3 (UB3) gene, which: (i) comprises a nucleotide sequence having at least 80% sequence identity with the nucleotide sequence of SEQ ID NO:87; (ii) comprises a coding sequence having at least 80% sequence identity with the nucleotide sequence of SEQ ID NO:88; (iii) comprises a region having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs:90, 97-103 or 394-445, and / or (iv) encodes a polypeptide sequence having at least 80% identity with the amino acid sequence of SEQ ID NO:89.

[0308] In some embodiments, the target site of the system or expression cassette can be (a) in an endogenous SPL9 gene in a region that has at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254, and / or 258-288; (b) in an endogenous UB2 gene in a region between about nucleotide 2000 to about nucleotide 2391 or about nucleotide 2225 to about nucleotide 2537, with reference to the nucleotide numbering of SEQ ID NO: 84, between about nucleotide 1 to about nucleotide 391 or about nucleotide 255 to about nucleotide 357, with reference to the nucleotide numbering of SEQ ID NO: 85, optionally in an endogenous UB2 gene in a region that has at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 90-96 or 332-393, or (c) in an endogenous UB3 gene in a region between about nucleotide 2000 to about nucleotide 2391 or about nucleotide 2225 to about nucleotide 2537, with reference to the nucleotide numbering of SEQ ID NO: 84, The nucleotide numbering of NO:87 is located in the region from about nucleotide 2001 to about nucleotide 2403 or from about nucleotide 2268 to about nucleotide 2370, or with reference to the nucleotide numbering of SEQ ID NO:88, is located in the region from about nucleotide 1 to about nucleotide 403 or from about nucleotide 268 to about nucleotide 371, optionally in a region of the endogenous UB3 gene that has at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs:90, 97-103 or 394-445.

[0309] Also provided herein are nucleic acids encoding mutant IPA1 genes that, when present in a plant or plant part, produce plants having altered plant architecture, improved yield traits, and / or increased tolerance / resistance to abiotic and biotic stresses compared to plants or plant parts lacking the same mutation. In some embodiments, the mutation in the SPL9 gene can be a nucleotide sequence having at least 90% (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) sequence identity to any one of SEQ ID NOs: 289-300. In some embodiments, a plant may comprise two or more mutant SPL9 genes in any combination that have at least 90% sequence identity to any one of SEQ ID NOs: 289-300. In some embodiments, the mutation in the UB3 gene can be a nucleotide sequence having at least 90% (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) sequence identity to any one of SEQ ID NOs: 310, 312, 314, 316, or 318, or can encode an amino acid sequence having at least 90% identity to any one of SEQ ID NOs: 311, 313, 315, 317, or 319. In some embodiments, the mutation in the UB2 gene can be a nucleotide sequence having at least 90% (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%) sequence identity to any one of SEQ ID NOs: 320, 322 or 324, or can encode an amino acid sequence having at least 90% identity to any one of SEQ ID NOs: 321, 323 or 325. Also provided is a soybean plant or part thereof (e.g., a cell) comprising a mutant nucleic acid of any one of SEQ ID NOs: 289-300, optionally wherein the soybean plant or part thereof can comprise two or more mutant SPL9 genes having at least 90% sequence identity to any one of SEQ ID NOs: 289-300 in any combination.

[0310] In some embodiments, a soybean plant or plant part thereof is provided, comprising at least one mutation in at least one endogenous SLP9 gene with gene identification number (Gene ID) Glyma_02G177500 (SPL9a), Glyma_09G113800 (SPL9b), Glyma_03g143100 (SPL9c) and / or Glyma_19g146000 (SPL9d), optionally wherein the soybean plant or plant part thereof comprising at least one mutation in the SPL9 gene exhibits a phenotype of one or more of altered plant architecture, improved yield traits and / or increased tolerance / resistance to abiotic and biotic stresses compared to a plant or plant part not comprising the same mutation.

[0311] In some embodiments, a mutated endogenous SPL9 gene is provided, comprising a nucleic acid sequence at least 90% identical to any one of SEQ ID NOs: 289-300.

[0312] Also provided are corn plants or parts thereof (e.g., cells) comprising a mutant nucleic acid of any one of SEQ ID NOs: 310, 312, 314, 316 or 318 and / or SEQ ID NOs: 320, 322 or 324, optionally wherein the corn plant or part thereof may comprise two or more mutant UB2 / UB3 genes having at least 90% sequence identity to any one of SEQ ID NOs: 310, 312, 314, 316 or 318 and / or SEQ ID NOs: 320, 322 or 324 in any combination, optionally wherein the corn plant or part thereof exhibits a phenotype of one or more of altered plant architecture, improved yield traits, and / or increased tolerance / resistance to abiotic and biotic stresses compared to a plant or plant part not comprising the same mutation.

[0313] In some embodiments, a mutated endogenous UB2 gene is provided, comprising a nucleic acid sequence having at least 90% identity to any one of SEQ ID NOs: 310, 312, 314, 316, or 318. In some embodiments, a mutated endogenous UB3 gene is provided, comprising a nucleic acid sequence having at least 90% identity to any one of SEQ ID NOs: 320, 322, or 324.

[0314] In some embodiments, the present invention provides a method for producing a plant comprising a mutation in an endogenous IPA1 gene encoding an SPL transcription factor and at least one polynucleotide of interest, the method comprising crossing a plant of the present invention (a first plant) comprising at least one mutation in an endogenous IPA1 gene with a second plant comprising at least one polynucleotide of interest to produce progeny plants; and selecting progeny plants comprising at least one mutation in the IPA1 gene and at least one polynucleotide of interest, thereby producing a plant comprising a mutation in the endogenous IPA1 gene and at least one polynucleotide of interest.

[0315] The present invention also provides a method for producing a plant comprising a mutation in an endogenous IPA1 gene encoding an SPL transcription factor and comprising at least one polynucleotide of interest, the method comprising introducing at least one polynucleotide of interest into the plant of the present invention comprising at least one mutation in an endogenous IPA1 gene encoding an SPL transcription factor, thereby producing a plant comprising at least one mutation in the IPA1 gene and comprising at least one polynucleotide of interest.

[0316] In some embodiments, a method of producing a plant comprising a mutation in an endogenous IPA1 gene and exhibiting an improved root architecture phenotype (optionally, exhibiting improved yield traits, increased root biomass, steeper root angles and / or longer roots) is provided, the method comprising crossing a first plant that is a plant of the present invention with a second plant that exhibits an improved root architecture phenotype; and selecting progeny plants that comprise a mutation in the IPA1 gene and comprise the improved root architecture phenotype, thereby producing a plant that comprises a mutation in the endogenous IPA1 gene and exhibits an improved root architecture phenotype compared to a control plant.

[0317] In some embodiments, a method of controlling weeds in a container (e.g., a pot or seed tray, etc.), a growth chamber, a greenhouse, a field, a recreational area, a lawn, or a roadside, the method comprising applying a herbicide to one or more (plural) plants of the present invention growing in a container, a growth chamber, a greenhouse, a field, a recreational area, a lawn, or a roadside, thereby controlling the weeds in the container, growth chamber, greenhouse, field, recreational area, lawn, or roadside where the one or more plants grow.

[0318] In some embodiments, a method of reducing insect predation on plants is provided, the method comprising applying an insecticide to one or more plants of the present invention, thereby reducing insect predation on the one or more plants, optionally wherein the one or more plants are grown in containers, growth chambers, greenhouses, fields, recreational areas, lawns, or roadsides.

[0319] In some embodiments, a method of reducing fungal diseases on plants is provided, the method comprising applying a fungicide to one or more plants of the present invention, thereby reducing fungal diseases on the one or more plants, optionally wherein the one or more plants are grown in containers, growth chambers, greenhouses, fields, recreational areas, lawns, or roadsides.

[0320] The polynucleotide of interest can be any polynucleotide that can confer a desired phenotype on a plant or otherwise alter the phenotype or genotype of a plant. In some embodiments, the polynucleotide of interest can be a polynucleotide that confer herbicide tolerance, insect resistance, disease resistance, increased yield, increased nutrient use efficiency, or abiotic stress resistance.

[0321] Therefore, plants or plant cultivars to be treated preferentially according to the invention include all plants which, by genetic modification, have acquired genetic material which imparts particularly advantageous useful properties ("traits") to these plants. Examples of such properties are better plant growth, vigor, stress tolerance, uprightness, resistance to lodging, nutrient uptake, plant nutrition and / or yield, in particular improved growth, increased tolerance to high or low temperatures, increased tolerance to drought or water or soil salinity levels, enhanced flowering performance, easier harvesting, accelerated maturation, higher yield, higher quality and / or higher nutritional value of the harvested product, better storage life and / or processability of the harvested product.

[0322] A further example of such a property is an increased resistance to animal and microbial pests, such as insects, arachnids, nematodes, mites, slugs and snails, due, for example, to toxins formed in the plant. Among the DNA sequences encoding proteins conferring tolerance properties to such animal and microbial pests, in particular insects, mention will be made in particular of the genetic material encoding the Bt protein from Bacillus thuringiensis, which is widely described in the literature and is well known to the person skilled in the art. Mention will also be made of proteins extracted from bacteria such as Photorhabdus (WO 97 / 17432 and WO 98 / 08932). Specifically, mention will be made of Bt Cry or VIP proteins, which include Cry1A, Cry1Ab, Cry1Ac, CryIIA, CryIIIA, CryIIIB2, Cry9c Cry2Ab, Cry3Bb and CryIF proteins or toxic fragments thereof, and hybrids or combinations thereof, in particular Cry1F protein or hybrids derived from Cry1F protein (e.g., hybrid Cry1A-CrylF protein or toxic fragments thereof), Cry1A-type proteins or toxic fragments thereof, preferably Cry1Ac protein or hybrids derived from Cry1Ac protein (e.g., hybrid Cry1Ab-CrylAc protein) or Cry1Ab or Bt2 protein or toxic fragments thereof, Cry2Ae, Cry2Af or Cry2Ag protein or toxic fragments thereof, Cry1A.105 protein or toxic fragments thereof, VIP3Aa19 protein, VIP3Aa20 protein, VIP3A protein produced in COT202 or COT203 cotton events, as described in Estruch et al. (1996), Proc Natl Acad Sci US A.28; 93 (11): 5389-94 or a toxic fragment thereof, such as the Cry protein described in WO2001 / 47952, an insecticidal protein from a strain of Xenorhabdus (such as described in WO98 / 50427), Serratia (especially from S. entomophila) or Photorhabdus, such as the Tc protein from Photorhabdus described in WO98 / 08932. In addition, any variant or mutant of any of these proteins that differs from any of the above-named sequences in some amino acids (1-10, preferably 1-5) is also included herein, and these sequences are particularly the sequences of their toxic fragments, or are fused to a transit peptide, such as a plastid transit peptide, or another protein or peptide.

[0323] Another particularly emphasized example of such properties is the conferring of tolerance to one or more herbicides, such as imidazolinone, sulfonylurea, glyphosate or glufosinate. Among the DNA sequences (i.e., polynucleotides of interest) encoding proteins that confer the properties of tolerance to certain herbicides on transformed plant cells and plants, particular mention will be made of the bar or PAT gene or the Streptomyces coelicolor gene described in WO2009 / 152359, which confer tolerance to glufosinate herbicides; genes encoding suitable EPSPS (5-enolpyruvylshikimate-3-phosphate-synthetase), which confer tolerance to herbicides targeting EPSPS, in particular herbicides such as glyphosate and its salts; genes encoding glyphosate-n-acetyltransferase, or genes encoding glyphosate oxidoreductase. Additional suitable herbicide tolerance traits include at least one ALS (acetolactate synthase) inhibitor (e.g., WO2007 / 024782); a mutated Arabidopsis ALS / AHAS gene (e.g., U.S. Pat. No. 6,855,533); a gene encoding 2,4-D-monooxygenase, which confers tolerance to 2,4-D (2,4-dichlorophenoxyacetic acid); and a gene encoding dicamba monooxygenase, which confers tolerance to dicamba (3,6-dichloro-2-methoxybenzoic acid).

[0324] Further examples of such traits are increased resistance to phytopathogenic fungi, bacteria and / or viruses due to, for example, systemic acquired resistance (SAR), systemins, phytoalexins, elicitors and resistance genes and correspondingly expressed proteins and toxins.

[0325] Particularly useful transgenic events in transgenic plants or plant cultivars that can be preferentially treated according to the present invention include: event 531 / PV-GHBK04 (cotton, insect control, described in WO2002 / 040677), event 1143-14A (cotton, insect control, not deposited, described in WO2006 / 128569); event 1143-51B (cotton, insect control, not deposited, described in WO2006 / 128570); event 1445 (cotton, herbicide tolerance, not deposited, described in US-A 2002-120964 or WO2002 / 034946); Event 17053 (rice, herbicide tolerance, deposited as PTA-9843, described in WO2010 / 117737); Event 17314 (rice, herbicide tolerance, deposited as PTA-9844, described in WO2010 / 117735); Event 281-24-236 (cotton, insect control-herbicide tolerance, deposited as PTA-6233, described in WO2005 / 103266 or US-A 2005-216969); Event 3006-210-23 (cotton, insect control-herbicide tolerance, deposited as PTA-6233, described in US-A 2007-143876 or WO2005 / 103266); event 3272 (corn, quality traits, deposited as PTA-9972, described in WO2006 / 098952 or US-A 2006-230473); event 33391 (wheat, herbicide tolerance, deposited as PTA-2347, described in WO2002 / 027004), event 40416 (corn, insect control-herbicide tolerance, deposited as ATCC PTA-11508, described in WO 11 / 075593); event 43A47 (corn, insect control-herbicide tolerance, deposited as ATCC PTA-11509, described in WO2011 / 075595); event 5307 (corn, insect control, deposited as ATCC PTA-9561, described in WO2010 / 077816); event ASR-368 (benthgrass, herbicide tolerant, deposited as ATCC PTA-4816, described in US-A 2006-162007 or WO2004 / 053062); event B16 (maize, herbicide tolerant, not deposited, described in US-A 2003-126634); event BPS-CV127-9 (soybean, herbicide tolerant, deposited as NCIMB No. 41603, described in WO2010 / 080829); event BLR1 (canola, male sterility restoration, deposited as NCIMB 41193, described in WO2005 / 074671), event CE43-67B (cotton,insect control, deposited as DSM ACC2724, described in US-A 2009-217423 or WO2006 / 128573); event CE44-69D (cotton, insect control, not deposited, described in US-A 2010-0024077); event CE44-69D (cotton, insect control, not deposited, described in WO2006 / 128571); event CE46-02A (cotton, insect control, not deposited, described in WO2006 / 128572); event COT102 (cotton, insect control, not deposited, described in US-A 2006-130175 or WO2004 / 039986); event COT202 (cotton, insect control, not deposited, described in US-A 2007-067868 or WO2005 / 054479); event COT203 (cotton, insect control, not deposited, described in WO2005 / 054480);); event DAS21606-3 / 1606 (soybean, herbicide tolerance, deposited as PTA-11028, described in WO2012 / 033794), event DAS40278 (corn, herbicide tolerance, deposited as ATCC PTA-10244, described in WO2011 / 022469); event DAS-44406-6 / pDAB8264.44.06.1 (soybean, herbicide tolerance, deposited as PTA-11336, described in WO2012 / 075426), event DAS-14536-7 / pDAB8291.45.36.2 (soybean, herbicide tolerance, deposited as PTA-11335, described in WO2012 / 075429), event DAS-59122-7 (corn, insect control - herbicide tolerance, deposited as ATCC PTA11384, described in US-A 2006-070139); event DAS-59132 (corn, insect control-herbicide tolerance, not deposited, described in WO2009 / 100188); event DAS68416 (soybean, herbicide tolerance, deposited as ATCC PTA-10442, described in WO2011 / 066384 or WO2011 / 066360); event DP-098140-6 (corn, herbicide tolerance, deposited as ATCC PTA-8296, described in US-A 2009-137395 or WO 08 / 112019); event DP-305423-1 (soybean, quality traits, not deposited, described in US-A 2008-312082 or WO2008 / 054747); event DP-32138-1 (maize, hybrid system, deposited as ATCC PTA-9158,described in US-A 2009-0210970 or WO2009 / 103049); event DP-356043-5 (soybean, herbicide tolerance, deposited as ATCC PTA-8287, described in US-A 2010-0184079 or WO2008 / 002872); event EE-I (eggplant, insect control, not deposited, described in WO 07 / 091277); event Fil 17 (corn, herbicide tolerance, deposited as ATCC 209031, described in US-A 2006-059581 or WO98 / 044140); event FG72 (soybean, herbicide tolerance, deposited as PTA-11041, described in WO2011 / 063413), event GA21 (corn, herbicide tolerance, deposited as ATCC 209033, described in US-A 2005-086719 or WO98 / 044140); event GG25 (corn, herbicide tolerance, deposited as ATCC 209032, described in US-A 2005-188434 or WO98 / 044140); event GHB119 (cotton, insect control-herbicide tolerance, deposited as ATCC PTA-8398, described in WO2008 / 151780); event GHB614 (cotton, herbicide tolerant, deposited as ATCC PTA-6878, described in US-A 2010-050282 or WO2007 / 017186); event GJ11 (maize, herbicide tolerant, deposited as ATCC 209030, described in US-A2005-188434 or WO98 / 044140); event GM RZ13 (sugar beet, virus resistant, deposited as NCIMB-41601, described in WO2010 / 076212); event H7-1 (sugar beet, herbicide tolerant, deposited as NCIMB 41158 or NCIMB 41159, described in US-A 2004-172669 or WO 2004 / 074492); event JOPLIN1 (wheat, disease tolerance, not deposited, described in US-A 2008-064032); event LL27 (soybean, herbicide tolerance, deposited as NCIMB 41658, described in WO 2006 / 108674 or US-A 2008-320616); event LL55 (soybean, herbicide tolerance, deposited as NCIMB 41660, described in WO 2006 / 108675 or US-A 2008-196127); event LLcotton25 (cotton, herbicide tolerance, deposited as ATCC PTA-3343,WO2003 / 013224 or US-A2003-097687); event LLRICE06 (rice, herbicide tolerance, deposited as ATCC 203353, described in US 6,468,747 or WO2000 / 026345); event LLRICE62 (rice, herbicide tolerance, deposited as ATCC 203352, described in WO2000 / 026345), event LLRICE601 (rice, herbicide tolerance, deposited as ATCC PTA-2600, described in US-A 2008-2289060 or WO2000 / 026356); event LY038 (maize, quality traits, deposited as ATCC PTA-5623, described in US-A 2007-028322 or WO2005 / 061720); event MIR162 (corn, insect control, deposited as PTA-8166, described in US-A 2009-300784 or WO2007 / 142840); event MIR604 (corn, insect control, not deposited, described in US-A 2008-167456 or WO2005 / 103301); event MON15985 (cotton, insect control, deposited as ATCC PTA-2516, described in US-A 2004-250317 or WO2002 / 100163); event MON810 (corn, insect control, not deposited, described in US-A 2002-102582); event MON863 (corn, insect control, deposited as ATCC PTA-2605, described in WO2004 / 011601 or US-A 2006-095986); event MON87427 (corn, pollination control, deposited as ATCC PTA-7899, described in WO2011 / 062904); event MON87460 (corn, stress tolerance, deposited as ATCC PTA-8910, described in WO2009 / 111263 or US-A 2011-0138504); event MON87701 (soybean, insect control, deposited as ATCC PTA-8194, described in US-A 2009-130071 or WO2009 / 064652); event MON87705 (soybean, quality trait - herbicide tolerance, deposited as ATCC PTA-9241, described in US-A 2010-0080887 or WO2010 / 037016); event MON87708 (soybean, herbicide tolerance, deposited as ATCC PTA-9670, described in WO2011 / 034704); event MON87712 (soybean, yield, deposited as PTA-10296, described in WO2012 / 051199),Event MON87754 (soybean, quality traits, deposited as ATCC PTA-9385, described in WO2010 / 024976); Event MON87769 (soybean, quality traits, deposited as ATCC PTA-8911, described in US-A 2011-0067141 or WO2009 / 102873); Event MON88017 (corn, insect control-herbicide tolerance, deposited as ATCC PTA-5582, described in US-A 2008-028482 or WO2005 / 059103); Event MON88913 (cotton, herbicide tolerance, deposited as ATCC PTA-4854, described in WO2004 / 072235 or US-A 2006-059590); event MON88302 (canola, herbicide tolerant, deposited as PTA-10955, described in WO2011 / 153186), event MON88701 (cotton, herbicide tolerant, deposited as PTA-11754, described in WO2012 / 134808), event MON89034 (maize, insect control, deposited as ATCC PTA-7455, described in WO 07 / 140256 or US-A 2008-260932); event MON89788 (soybean, herbicide tolerant, deposited as ATCC PTA-6708, described in US-A 2006-282915 or WO2006 / 130436); event MS11 (canola, pollination control-herbicide tolerance, deposited as ATCC PTA-850 or PTA-2485, described in WO2001 / 031042); event MS8 (canola, pollination control-herbicide tolerance, deposited as ATCC PTA-730, described in WO2001 / 041558 or US-A 2003-188347); event NK603 (maize, herbicide tolerance, deposited as ATCC PTA-2478, described in US-A 2007-292854); event PE-7 (rice, insect control, not deposited, described in WO2008 / 114282); event RF3 (canola, pollination control-herbicide tolerance, deposited as ATCC PTA-730, described in WO2001 / 041558 or US-A 2003-188347); event RT73 (rapeseed, herbicide tolerant, not deposited, described in WO2002 / 036831 or US-A 2008-070260); event SYHT0H2 / SYN-000H2-5 (soybean, herbicide tolerant, deposited as PTA-11226, described in WO2012 / 082548), event T227-1 (sugar beet, herbicide tolerant, not deposited,described in WO2002 / 44407 or US-A 2009-265817); Event T25 (corn, herbicide tolerance, not deposited, described in US-A2001-029014 or WO2001 / 051654); Event T304-40 (cotton, insect control-herbicide tolerance, deposited as ATCC PTA-8171, described in US-A2010-077501 or WO2008 / 122406); Event T342-142 (cotton, insect control, not deposited, described in WO2006 / 128568); Event TC1507 (corn, insect control-herbicide tolerance, not deposited, described in US-A 2005-039226 or WO2004 / 099447); event VIP1034 (corn, insect control-herbicide tolerance, deposited as ATCC PTA-3925, described in WO2003 / 052073), event 32316 (corn, insect control-herbicide tolerance, deposited as PTA-11507, described in WO2011 / 084632), event 4114 (corn, insect control-herbicide tolerance, deposited as PTA-11506, described in WO2011 / 084621), event EE-GM3 / FG72 (soybean, herbicide tolerance, ATCC accession number PTA -11041), optionally stacked with event EE-GM1 / LL27 or event EE-GM2 / LL55 (WO2011 / 063413A2), event DAS-68416-4 (soybean, herbicide tolerant, ATCC Accession No. PTA-10442, WO2011 / 066360A1), event DAS-68416-4 (soybean, herbicide tolerant, ATCC Accession No. PTA-10442, WO2011 / 066384A 1), event DP-040416-8 (corn, insect control, ATCC accession number PTA-11508, WO2011 / 075593A1), event DP-043A47-3 (corn, insect control, ATCC accession number PTA-11509, WO2011 / 075595A1), event DP-004114-3 (corn, insect control, ATCC accession number PTA-11506, WO2011 / 084621A1), Event DP-032316-8 (corn, insect control, ATCC Accession No. PTA-11507, WO2011 / 084632A1), Event MON-88302-9 (canola, herbicide tolerance, ATCC Accession No. PTA-10955, WO2011 / 153186A1), Event DAS-21606-3 (soybean, herbicide tolerance, ATCC Accession No. PTA-11028, WO2012 / 033794A2),Event MON-87712-4 (soybean, quality traits, ATCC accession number PTA-10296, WO2012 / 051199A2), event DAS-44406-6 (soybean, stacked herbicide tolerance, ATCC accession number PTA-11336, WO2012 / 075426A1), event DAS-14536-7 (soybean, stacked herbicide tolerance, ATCC accession number PTA-11335, WO2012 / 075429 A1), event SYN-000H2-5 (soybean, herbicide tolerance, ATCC accession number PTA-11226, WO2012 / 082548A2), event DP-061061-7 (canola, herbicide tolerance, no deposit number available, WO2012071039A1), event DP-073496-4 (canola, herbicide tolerance, no deposit number available, US2012131692), event 8264.44.06.1 (soybean, added herbicide tolerance, accession number PTA-11336, WO2012075426A2), event 8291.45.36.2 (soybean, superimposed herbicide tolerance, accession number PTA-11335, WO2012075429A2), event SYHT0H2 (soybean, ATCC accession number PTA-11226, WO2012 / 082548A2), event MON88701 (cotton, ATCC accession number PTA-11754, WO 2012 / 134808A1), event KK179-2 (alfalfa, ATCC accession number PTA-11833, WO2013 / 003558A1), event pDAB8264.42.32.1 (soybean, superimposed with herbicide tolerance, ATCC accession number PTA-11993, WO2013 / 010094A1), event MZDT09Y (corn, ATCC accession number PTA-13025, WO2013 / 012775A1). ,

[0326] The genes / events that confer the desired traits in question (e.g., polynucleotides of interest) may also be present in combination with one another in transgenic plants. Examples of transgenic plants that may be mentioned are important crop plants such as cereals (wheat, rice, triticale, barley, rye, oats), corn, soybeans, potatoes, sugar beets, sugar cane, tomatoes, peas and other types of vegetables, cotton, tobacco, rapeseed and fruit plants (fruits are apples, pears, citrus fruits and grapes), with particular emphasis on corn, soybeans, wheat, rice, potatoes, cotton, sugar cane, tobacco and rapeseed. Traits that are particularly emphasized are the increased resistance of the plants to insects, arachnids, nematodes, slugs and snails, and the increased resistance of the plants to one or more herbicides.

[0327] Commercially available examples of such plants, plant parts or plant seeds that may be preferentially treated according to the invention include commercial products such as ROUNDUP VT DOUBLE VT TRIPLE BOLLGARD ROUNDUP READY 2 ROUNDUP 2XTENDTM、INTACTA RR2 VISTIVE and / or XTENDFLEX TM Plant seeds sold or distributed under a trade name.

[0328] The nucleic acid constructs of the present invention (e.g., constructs comprising a sequence-specific nucleic acid binding domain, a CRISPR-Cas effector domain, a deaminase domain, a reverse transcriptase (RT), an RT template and / or a guide nucleic acid, etc.) and expression cassettes / vectors comprising the same can be used as the editing system of the present invention for modifying target nucleic acids (e.g., an endogenous IPA1 gene encoding an SPL transcription factor) and / or their expression.

[0329] Any plant comprising an endogenous IPA1 gene encoding a SPL transcription factor, when modified (e.g., mutated, e.g., base edited, cleaved, nicked, etc.) as described herein using the polypeptides, polynucleotides, RNPs, nucleic acid constructs, expression cassettes and / or vectors of the invention, can confer altered plant architecture, improved yield traits and / or increased tolerance / resistance to abiotic and biotic stresses.

[0330] As used herein, "increased kernel row number" or (e.g., corn plants) refers to an increase in kernel row number by about 5% to about 30% (e.g., about 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 100%, 100%, %, 8%, 29% or 30% or any range or value therein; for example, about 5% to about 10%, about 5% to about 15%, about 5% to about 20%, about 5% to about 25%, about 5% to about 30%, about 10% to about 15%, about 10% to about 20%, about 10% to about 25%, about 10% to about 30%, about 20% to about 30%, about 25% to about 30% and any range or value therein) (e.g., more than about 1 row, 2 rows, 3 rows or 4 rows). In some embodiments, plants that exhibit an increased number of kernel rows as described herein (e.g., plants that produce ears with an increased number of kernel rows) produce ears that are also not substantially reduced in length. By "not substantially reducing" the length of an ear of a plant comprising a mutation as described herein is meant that the length of the ear of the plant is reduced by less than 30% (e.g., reduced by 0% or by about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%) as compared to a plant that does not comprise the same IPA1 mutation.

[0331] As used herein, "altered plant architecture" refers to the structure of a plant that has been altered by modification of the plant genome as described herein. Such structure may include, but is not limited to, the number of branches, the number of nodes, the number of pods (e.g., the number of pods on the main stem and branches), the number of flowers, the plant biomass, increased root biomass, steeper root angles, and / or longer roots.

[0332] As used herein, the term "abiotic stress" refers to an external non-living factor that can cause harmful effects on plants. Therefore, abiotic stress can include, but is not limited to, low temperatures, cold, hot or high temperatures, drought, high light intensity, low light intensity, salinity, osmotic stress, ozone, high plant density, nutrient deficiency / toxicity and / or its combination that cause freezing. The parameters of abiotic stress factors are species-specific and even variety-specific, and therefore vary greatly depending on the species / variety exposed to abiotic stress. Therefore, when one species may be severely affected by 23°C of high temperature, another species may not be affected until at least 30°C, etc. Temperatures above 30°C cause a significant drop in the yield of most important crops. This is due to the reduction of photosynthesis that begins at about 20-25°C, and the increase in carbohydrate requirements of crops grown at higher temperatures. Critical temperature is not absolute, but varies according to factors such as the adaptation of crops to the main environmental conditions. In addition, since most crops are exposed to multiple abiotic stresses at the same time, the interaction between stresses affects the response of plants. For example, damage from excess light can occur at lower light intensities when temperatures rise above the photosynthetic optimum. Water-stressed plants are less able to cool overheated tissues due to reduced transpiration, further exacerbating the effects of excess (high) heat and / or excess (high) light intensity. Thus, the specific parameters of high / low temperature, light intensity, drought, etc. that affect crop productivity will vary with species, variety, degree of adaptation, and exposure to combinations of environmental conditions. By "increased abiotic stress resistance / tolerance" is meant an increase in resistance or tolerance to a stress by about 5% to about 100% (e.g., about 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 50%, 51%, 5 %, 43%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, or any range or value therein).

[0333] As used herein, the term "biotic stress" refers to life or biological factors that have a harmful effect on plants. Such biological factors include, but are not limited to, pathogenic organisms (bacteria, fungi, fungus-like organisms, nematodes, viruses, phytoplasmas, insects, parasitic plants, etc.). By "increased biotic stress resistance / tolerance" is meant an increase in resistance or tolerance to a stress by about 15% to about 200% (about 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, , 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% %, 100%, 101%, 102%, 103%, 104%, 105%, 110%, 111%, 12%, 113%, 114%, 115%, 116%, 117%, 118%, 119%, 120%, 121%, 122%, 123%, 124%, 125%, 126%, 127%, 128%, 129%, 130%, 131%, 132%, 133%, 134%, 135%, 140%, 141%, 142%, 143%, 144%, 145%, 146%, 147%, 148%, 149 %, 150%, 151%, 152%, 153%, 154%, 155%, 156%, 157%, 158%, 159%, 160%, 161%, 162%, 163%, 164%, 165%, 170%, 171%, 172%, 173%, 174%, 175%, 180%, 185%, 186%, 187%, 188%, 189%, 190%, 191%, 192%, 193%, 194%, 195%, 196%, 197%, 198%, 199% or 200%, or any range or value therein).

[0334] As used herein, the term "plant part" includes, but is not limited to, reproductive tissues (e.g., petals, sepals, stamens, pistils, receptacles, anthers, pollen, flowers, fruits, buds, ovules, seeds, and embryos); vegetative tissues (e.g., petioles, stems, roots, root hairs, root tips, pith, coleoptiles, stalks, shoots, branches, bark, apical meristems, axillary buds, cotyledons, hypocotyls, and leaves); vascular tissues (e.g., phloem and xylem); specialized cells, such as epidermal cells, parenchyma cells, collenchyma cells, stomata, guard cells, cuticles, mesophyll cells; callus; and cuttings. The term "plant part" also includes plant cells, including intact plant cells in plants and / or plant parts, plant protoplasts, plant tissues, plant organs, plant cell tissue cultures, plant callus, plant clumps, and the like. As used herein, "shoot" refers to the above-ground parts, including leaves and stems. As used herein, the term "tissue culture" encompasses cultures of tissues, cells, protoplasts, and callus.

[0335] As used herein, "plant cell" refers to the structural and physiological unit of a plant, which generally includes a cell wall, but also includes a protoplast. The plant cell of the present invention can be in the form of an isolated unicellular cell, or can be a cultured cell, or can be a part of a higher organizational unit such as, for example, a plant tissue (including callus) or a plant organ. "Protoplast" is a plant cell that does not have a cell wall or only has a partial cell wall. Therefore, in some embodiments of the present invention, the transgenic cell comprising the nucleic acid molecule of the present invention and / or the nucleotide sequence is a cell of any plant or plant part, including but not limited to root cells, leaf cells, tissue culture cells, seed cells, flower cells, fruit cells, pollen cells, etc. In some aspects of the present invention, a plant part can be a plant germplasm. In some aspects, a plant cell can be a non-breeding plant cell that no longer generates a plant.

[0336] "Plant cell culture" refers to cultures of plant units such as, for example, protoplasts, cell culture cells, cells in plant tissues, pollen, pollen tubes, ovules, embryo sacs, zygotes, and embryos at various stages of development.

[0337] As used herein, a "plant organ" is a distinct and clearly structured and differentiated part of a plant, such as a root, stem, leaf, flower bud, or embryo.

[0338] As used herein, "plant tissue" refers to a group of plant cells organized into a structural and functional unit. Included is any plant tissue in situ or in culture. The term includes, but is not limited to, whole plants, plant organs, plant seeds, tissue cultures, and any group of plant cells organized into a structural and / or functional unit. The term, when used with or without any specific type of plant tissue listed above or included in this definition, is not intended to exclude any other type of plant tissue.

[0339] In some embodiments of the invention, transgenic tissue cultures or transgenic plant cell cultures are provided, wherein the transgenic tissue or cell culture comprises the nucleic acid molecules / nucleotide sequences of the invention. In some embodiments, the transgenic tissue or cell culture is provided, wherein the transgenic tissue or cell culture comprises the nucleic acid molecules / nucleotide sequences of the invention. In some embodiments, the transgenic tissue or cell is provided, wherein the transgenic tissue or cell culture ...

[0340] The editing system that can be used for the present invention can be any site-specific (sequence-specific) genome editing system that is now known or developed later, which can introduce mutations in a target-specific manner. For example, the editing system (e.g., a site-specific or sequence-specific editing system) may include, but is not limited to, a CRISPR-Cas editing system, a meganuclease editing system, a zinc finger nuclease (ZFN) editing system, a transcription activator-like effector nuclease (TALEN) editing system, a base editing system, and / or a lead editing system, each of which may include one or more polypeptides and / or one or more polynucleotides that can modify (mutate) a target nucleic acid in a sequence-specific manner when expressed as a system in a cell. In some embodiments, the editing system (e.g., a site-specific or sequence-specific editing system) may include one or more polynucleotides and / or one or more polypeptides, including but not limited to a nucleic acid binding domain (DNA binding domain), a nuclease, and / or other polypeptides and / or polynucleotides.

[0341] In some embodiments, the editing system may include one or more sequence-specific nucleic acid binding domains (DNA binding domains), which may be derived from, for example, polynucleotide-guided endonucleases, CRISPR-Cas endonucleases (e.g., CRISPR-Cas effector proteins), zinc finger nucleases, transcription activator-like effector nucleases (TALENs), and / or Argonaute proteins. In some embodiments, the editing system may include one or more cleavage domains (e.g., nucleases), including but not limited to endonucleases (e.g., Fok1), polynucleotide-guided endonucleases, CRISPR-Cas endonucleases (e.g., CRISPR-Cas effector proteins), zinc finger nucleases, and / or transcription activator-like effector nucleases (TALENs). In some embodiments, the editing system may include one or more polypeptides, including but not limited to deaminases (e.g., cytosine deaminases, adenine deaminases), reverse transcriptases, Dna2 polypeptides, and / or 5' flap endonucleases (FENs). In some embodiments, the editing system may comprise one or more polynucleotides, including but not limited to a CRISPR array (CRISPR guide sequence) nucleic acid, an extended guide nucleic acid, and / or a reverse transcriptase template.

[0342] In some embodiments, a method of modifying or editing an IPA1 gene encoding an SPL transcription factor may comprise contacting a target nucleic acid (e.g., a nucleic acid encoding an SPL transcription factor) with a base editing fusion protein (e.g., a sequence-specific nucleic acid binding protein, a sequence-specific DNA binding protein (e.g., a CRISPR-Cas effector protein or domain) fused to a deaminase domain (e.g., an adenine deaminase and / or a cytosine deaminase) and a guide nucleic acid, wherein the guide nucleic acid is capable of directing / targeting the base editing fusion protein to the target nucleic acid, thereby editing a locus within the target nucleic acid. In some embodiments, the base editing fusion protein and the guide nucleic acid may be contained in one or more expression cassettes. In some embodiments, the target nucleic acid may be contacted with the base editing fusion protein and an expression cassette containing the guide nucleic acid. In some embodiments, the sequence-specific nucleic acid binding fusion protein and the guide sequence may be provided as a ribonucleoprotein (RNP). In some embodiments, a cell may be contacted with more than one base editing fusion protein and / or one or more guide nucleic acids, which may target one or more target nucleic acids in the cell.

[0343] In some embodiments, a method for modifying or editing an IPA1 gene encoding an SPL transcription factor may include contacting a target nucleic acid (e.g., an IPA1 nucleic acid encoding an SPL transcription factor) with a sequence-specific nucleic acid binding fusion protein (e.g., a sequence-specific DNA binding protein (e.g., a CRISPR-Cas effector protein or domain) fused to a peptide tag, a deaminase fusion protein comprising a deaminase domain (e.g., adenine deaminase and / or cytosine deaminase) fused to an affinity polypeptide capable of binding to the peptide tag, and a guide nucleic acid, wherein the guide nucleic acid is capable of guiding / targeting the sequence-specific nucleic acid binding fusion protein to the target nucleic acid, and the sequence-specific nucleic acid binding fusion protein is capable of binding the deaminase domain to the target nucleic acid through a peptide tag-affinity polypeptide interaction. Aminase fusion protein is recruited to the target nucleic acid, thereby editing the locus within the target nucleic acid. In some embodiments, the sequence-specific nucleic acid binding fusion protein can be fused to an affinity polypeptide that binds a peptide tag, and the deaminase can be fused to the peptide tag, thereby recruiting the deaminase to the sequence-specific nucleic acid binding fusion protein and the target nucleic acid. In some embodiments, the sequence-specific binding fusion protein, the deaminase fusion protein, and the guide nucleic acid can be included in one or more expression cassettes. In some embodiments, the target nucleic acid can be contacted with the sequence-specific binding fusion protein, the deaminase fusion protein, and the expression cassette containing the guide nucleic acid. In some embodiments, the sequence-specific nucleic acid binding fusion protein, the deaminase fusion protein, and the guide sequence can be provided as a ribonucleoprotein (RNP).

[0344] In some embodiments, methods such as lead editing can be used to generate mutations in the endogenous IPA gene encoding the SPL transcription factor. In lead editing, an RNA-dependent DNA polymerase (reverse transcriptase, RT) and a reverse transcriptase template (RT template) are used in combination with a sequence-specific nucleic acid binding domain that confers the ability to recognize and bind to the target in a sequence-specific manner, and can also cause a nick containing the PAM strand within the target. The nucleic acid binding domain can be a CRISPR-Cas effector protein, and in this case, the CRISPR array or guide RNA can be an extended guide sequence comprising an extension that includes a primer binding site (PSB) and an edit to be incorporated into the genome (template). Similar to base editing, lead editing can utilize various methods to recruit proteins for target site editing, including non-covalent and covalent interactions between proteins and nucleic acids used in selected processes of genome editing.

[0345] As used herein, a "CRISPR-Cas effector protein" is a protein or polypeptide or a domain thereof that cleaves or cuts a nucleic acid, binds a nucleic acid (e.g., a target nucleic acid and / or a guide nucleic acid), and / or identifies, recognizes, or binds a guide nucleic acid as defined herein. In some embodiments, a CRISPR-Cas effector protein may be an enzyme (e.g., a nuclease, an endonuclease, a nickase, etc.) or a portion thereof and / or may act as an enzyme. In some embodiments, a CRISPR-Cas effector protein refers to a CRISPR-Cas nuclease polypeptide or a domain thereof that comprises nuclease activity or wherein the nuclease activity has been reduced or eliminated, and / or comprises nickase activity or wherein the nickase activity has been reduced or eliminated, and / or comprises single-stranded DNA cleavage activity (ss DNA enzyme activity) or wherein the ss DNA enzyme activity has been reduced or eliminated, and / or comprises self-processing RNA enzyme activity or wherein the self-processing RNA enzyme activity has been reduced or eliminated. A CRISPR-Cas effector protein may bind to a target nucleic acid.

[0346] In some embodiments, the sequence-specific nucleic acid binding domain (e.g., a sequence-specific DNA binding domain) can be a CRISPR-Cas effector protein. In some embodiments, the CRISPR-Cas effector protein can be from a type I CRISPR-Cas system, a type II CRISPR-Cas system, a type III CRISPR-Cas system, a type IV CRISPR-Cas system, a type V CRISPR-Cas system, or a type VI CRISPR-Cas system. In some embodiments, the CRISPR-Cas effector protein of the present invention can be from a type II CRISPR-Cas system or a type V CRISPR-Cas system. In some embodiments, the CRISPR-Cas effector protein can be a type II CRISPR-Cas effector protein, such as a Cas9 effector protein. In some embodiments, the CRISPR-Cas effector protein can be a type V CRISPR-Cas effector protein, such as a Cas12 effector protein.

[0347] In some embodiments, the CRISPR-Cas effector protein may include, but is not limited to, Cas9, C2c1, C2c3, Cas12a (also known as Cpf1), Cas12b, Cas12c, Cas12d, Cas12e, Cas13a, Cas13b, Cas13c, Cas13d, Cas1, Cas1B, Cas2, Cas3, Cas3', Cas3", Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 (also known as Csn1 and Csx12), Cas10, Csyl, Csy2, Csy3, Csel, Cse2, Cscl, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmrl, Cmr3, Cmr4, Cmr5, Cmr6, Csbl, Csb2, Csb3, Csxl7, Csxl4, CsxlO, Csxl6, CsaX, Csx3, Csxl, Csxl5, Csfl, Csf2, Csf3, Csf4 (dinG) and / or Csf5 nuclease, optionally wherein the CRISPR-Cas effector protein can be a Cas9, Cas12a (Cpf1), Cas12b, Cas12c (C2c3), Cas12d (CasY), Cas12e (CasX), Cas12g, Cas12h, Cas12i, C2c4, C2c5, C2c8, C2c9, C2c10, Cas14a, Cas14b and / or Cas14c effector protein.

[0348] In some embodiments, the CRISPR-Cas effector protein useful in the present invention may comprise a mutation in its nuclease active site (e.g., RuvC, HNH, e.g., a RuvC site of a Cas12a nuclease domain, e.g., a RuvC site and / or a HNH site of a Cas9 nuclease domain). A CRISPR-Cas effector protein has a mutation in its nuclease active site and therefore no longer comprises nuclease activity, and is often referred to as "dead", e.g., dCas. In some embodiments, a CRISPR-Cas effector protein domain or polypeptide having a mutation in its nuclease active site may have impaired activity or reduced activity compared to the same CRISPR-Cas effector protein (e.g., a nickase, e.g., a Cas9 nickase, a Cas12a nickase) without the mutation.

[0349] CRISPR Cas9 effector proteins or CRISPR Cas9 effector domains useful in the present invention can be any known or later identified Cas9 nuclease. In some embodiments, the CRISPR Cas9 polypeptide can be a Cas9 polypeptide from, for example, Streptococcus spp. (e.g., S. pyogenes, S. thermophilus), Lactobacillus spp., Bifidobacterium spp., Kandleria spp., Leuconostoc spp., Oenococcus spp., Pediococcus spp., Weissella spp., and / or Olsenella spp. Example Cas9 sequences include, but are not limited to, the amino acid sequences of SEQ ID NO:59 and SEQ ID NO:60 or the nucleotide sequences of SEQ ID NO:61-71.

[0350] In some embodiments, the CRISPR-Cas effector protein can be a Cas9 polypeptide derived from Streptococcus pyogenes and recognizes the PAM sequence motifs NGG, NAG, NGA (Mali et al., Science 2013; 339(6121): 823-826). In some embodiments, the CRISPR-Cas effector protein can be a Cas9 polypeptide derived from Streptococcus thermophiles and recognizes the PAM sequence motifs NGGNG and / or NNAGAAW (W=A or T) (see, e.g., Horvath et al., Science, 2010; 327(5962): 167-170, and Deveau et al., J Bacteriol 2008; 190(4): 1390-1400). In some embodiments, the CRISPR-Cas effector protein can be a Cas9 polypeptide derived from Streptococcus mutans and recognizes the PAM sequence motifs NGG and / or NAAR (R=A or G) (see, e.g., Deveau et al., J BACTERIOL 2008; 190(4): 1390-1400). In some embodiments, the CRISPR-Cas effector protein can be a Cas9 polypeptide derived from Streptococcus aureus and recognizes the PAM sequence motifs NNGRR (R=A or G). In some embodiments, the CRISPR-Cas effector protein can be a Cas9 polypeptide derived from Streptococcus aureus and recognizes the PAM sequence motifs N GRRT (R=A or G). In some embodiments, the CRISPR-Cas effector protein can be a Cas9 polypeptide derived from Streptococcus aureus that recognizes the PAM sequence motifs N GRRV (R=A or G). In some embodiments, the CRISPR-Cas effector protein can be a Cas9 polypeptide derived from Neisseria meningitidis, and recognizes the PAM sequence motif NGATT or NGCTT (R = A or G, V = A, G or C) (see, e.g., Hou et al., PNAS 2013, 1-6). In the above embodiments, N can be any nucleotide residue, such as any one of A, G, C or T. In some embodiments, the CRISPR-Cas effector protein can be a Cas13a protein derived from Leptotrichia shahii, which recognizes a single 3'A, U or C protospacer flanking sequence (PFS) (or RNA PAM (rPAM)) sequence motif that can be located in the target nucleic acid.

[0351] In some embodiments, the CRISPR-Cas effector protein may be derived from Cas12a, which is a V-type regularly interspaced clustered short palindromic repeats (CRISPR)-Cas nuclease (see, e.g., SEQ ID NO: 1-20). Cas12a differs from the more well-known type II CRISPR Cas9 nuclease in several aspects. For example, Cas9 recognizes a G-rich protospacer adjacent motif (PAM) (3'-NGG) located 3' of its guide RNA (gRNA, sgRNA, crRNA, crDNA, CRISPR array) binding site (protospacer, target nucleic acid, target DNA), while Cas12a recognizes a T-rich PAM (5'-TTN, 5'-TTTN) located 5' of the target nucleic acid. In fact, the orientation of Cas9 and Cas12a binding to their guide RNAs is almost opposite relative to their N and C termini. In addition, the Cas12a enzyme uses a single guide RNA (gRNA, CRISPR array, crRNA), rather than the dual guide RNA (sgRNA (e.g., crRNA and tracrRNA)) found in the natural Cas9 system, and Cas12a processes its own gRNA. In addition, the Cas12a nuclease activity produces staggered DNA double-strand breaks, rather than the flat ends produced by the Cas9 nuclease activity, and Cas12a relies on a single RuvC domain to cleave two DNA chains, while Cas9 utilizes the HNH domain and the RuvC domain to cleave.

[0352] CRISPR Cas12a effector proteins / domains useful in the present invention may be any known or later identified Cas12a polypeptide (formerly known as Cpf1) (see, e.g., U.S. Pat. No. 9,790,490, which is incorporated by reference for its disclosure of Cpf1 (Cas12a) sequences). The term "Cas12a", "Cas12a polypeptide" or "Cas12a domain" refers to an RNA-guided nuclease comprising a Cas12a polypeptide or a fragment thereof, the fragment comprising a guide nucleic acid binding domain of Cas12a and / or an active, inactive or partially active DNA cleavage domain of Cas12a. In some embodiments, Cas12a useful in the present invention may comprise a mutation in a nuclease active site (e.g., a RuvC site of a Cas12a domain). A Cas12a domain or Cas12a polypeptide having a mutation in its nuclease active site and thus no longer comprising nuclease activity is generally referred to as a dead Cas12a (e.g., dCas12a). In some embodiments, a Cas12a domain or Cas12a polypeptide having a mutation in its nuclease active site may have impaired activity, for example, may have nickase activity.

[0353] Any deaminase domain / polypeptide that can be used for base editing can be used in the present invention. In some embodiments, the deaminase domain can be a cytosine deaminase domain or an adenine deaminase domain. The cytosine deaminase (or cytidine deaminase) that can be used in the present invention can be any known or later identified cytosine deaminase from any organism (see, e.g., U.S. Patent No. 10,167,457 and Thuronyi et al., Nat. Biotechnol. 37: 1070–1079 (2019), each of which is incorporated herein by reference for its disclosure of cytosine deaminase). Cytosine deaminase can catalyze the hydrolysis and deamination of cytidine or deoxycytidine to uridine or deoxyuridine, respectively. Therefore, in some embodiments, the deaminase or deaminase domain that can be used in the present invention can be a cytidine deaminase domain that catalyzes the hydrolysis and deamination of cytosine to uracil. In some embodiments, the cytosine deaminase can be a variant of a naturally occurring cytosine deaminase, including but not limited to primates (e.g., humans, monkeys, chimpanzees, gorillas), dogs, cows, rats, or mice. Thus, in some embodiments, the cytosine deaminase useful in the present invention can be about 70% to about 100% identical to a wild-type cytosine deaminase (e.g., about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a naturally occurring cytosine deaminase, and any range or value therein).

[0354] In some embodiments, the cytosine deaminase that can be used in the present invention can be an apolipoprotein B mRNA editing complex (APOBEC) family deaminase. In some embodiments, the cytosine deaminase can be an APOBEC1 deaminase, an APOBEC2 deaminase, an APOBEC3A deaminase, an APOBEC3B deaminase, an APOBEC3C deaminase, an APOBEC3D deaminase, an APOBEC3F deaminase, an APOBEC3G deaminase, an APOBEC3H deaminase, an APOBEC4 deaminase, a human activation-induced deaminase (hAID), rAPOBEC1, FERNY and / or CDA1, optionally pmCDA1, atCDA1 (e.g., At2g19570), and their evolutionary forms (e.g., SEQ ID NO: 27, SEQ ID NO: 28 or SEQ ID NO: 29). In some embodiments, the cytosine deaminase can be an APOBEC1 deaminase having an amino acid sequence of SEQ ID NO: 23. In some embodiments, the cytosine deaminase may be an APOBEC3A deaminase having the amino acid sequence of SEQ ID NO: 24. In some embodiments, the cytosine deaminase may be a CDA1 deaminase, optionally a CDA1 having the amino acid sequence of SEQ ID NO: 25. In some embodiments, the cytosine deaminase may be a FERNY deaminase, optionally a FERNY having the amino acid sequence of SEQ ID NO: 26. In some embodiments, a cytosine deaminase useful in the present invention can be about 70% to about 100% identical (e.g., 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, or 100% identical) to the amino acid sequence of a naturally occurring cytosine deaminase (e.g., an evolved deaminase).In some embodiments, a cytosine deaminase useful in the present invention may be about 70% to about 99.5% identical (e.g., about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical) to the amino acid sequence of SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, or SEQ ID NO: 26 (e.g., about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical) to the amino acid sequence of SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, or SEQ ID NO: NO:29 is at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical). In some embodiments, the polynucleotide encoding the cytosine deaminase can be codon-optimized for expression in plants, and the codon-optimized polypeptide can be about 70% to 99.5% identical to the reference polynucleotide.

[0355] In some embodiments, the nucleic acid constructs of the present invention may also encode uracil glycosylase inhibitor (UGI) (e.g., uracil-DNA glycosylase inhibitor) polypeptides / domains. Thus, in some embodiments, nucleic acid constructs encoding CRISPR-Cas effector proteins and cytosine deaminase domains (e.g., encoding a fusion protein comprising a CRISPR-Cas effector protein domain fused to a cytosine deaminase domain, and / or a CRISPR-Cas effector protein domain fused to a peptide tag or an affinity polypeptide capable of binding a peptide tag, and / or a deaminase protein domain fused to a peptide tag or an affinity polypeptide capable of binding a peptide tag) may also encode uracil-DNA glycosylase inhibitor (UGI), optionally wherein UGI may be codon-optimized for expression in plants. In some embodiments, the present invention provides fusion proteins comprising CRISPR-Cas effector polypeptides, deaminase domains, and UGI and / or one or more polynucleotides encoding them, optionally wherein one or more polynucleotides may be codon-optimized for expression in plants. In some embodiments, the present invention provides fusion proteins, wherein the CRISPR-Cas effector polypeptide, the deaminase domain and the UGI can be fused to any combination of peptide tags and affinity polypeptides as described herein, thereby recruiting the deaminase domain and the UGI to the CRISPR-Cas effector polypeptide and the target nucleic acid. In some embodiments, the guide nucleic acid can be linked to a recruitment RNA motif, and one or more of the deaminase domain and / or the UGI can be fused to an affinity polypeptide capable of interacting with the recruitment RNA motif, thereby recruiting the deaminase domain and the UGI to the target nucleic acid.

[0356] The "uracil glycosylase inhibitor" useful in the present invention may be any protein capable of inhibiting uracil-DNA glycosylase base excision repair enzymes. In some embodiments, the UGI domain comprises a wild-type UGI or a fragment thereof. In some embodiments, the UGI domain useful in the present invention may be about 70% to about 100% identical to the amino acid sequence of a naturally occurring UGI domain (e.g., 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or 100% identical and any range or value therein). In some embodiments, the UGI domain may comprise the amino acid sequence of SEQ ID NO:41, or a polypeptide having about 70% to about 99.5% sequence identity to the amino acid sequence of SEQ ID NO:41 (e.g., at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to the amino acid sequence of SEQ ID NO:41). For example, in some embodiments, the UGI domain may comprise a fragment of the amino acid sequence of SEQ ID NO:41 that is 100% identical to a portion of consecutive nucleotides (e.g., 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80 consecutive nucleotides; e.g., about 10, 15, 20, 25, 30, 35, 40, 45 to about 50, 55, 60, 65, 70, 75, 80 consecutive nucleotides) of the amino acid sequence of SEQ ID NO:41. In some embodiments, the UGI domain can be a variant of a known UGI (e.g., SEQ ID NO: 41) having about 70% to about 99.5% sequence identity (e.g., 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% sequence identity, and any range or value therein) to the known UGI. In some embodiments, the polynucleotide encoding the UGI can be codon-optimized for expression in a plant (e.g., a plant), and the codon-optimized polypeptide can be about 70% to about 99.5% identical to the reference polynucleotide.

[0357] Adenine deaminase (or adenosine deaminase) useful in the present invention can be any known or later identified adenine deaminase from any organism (see, e.g., U.S. Pat. No. 10,113,163, the disclosure of which is incorporated herein by reference for adenine deaminase). Adenine deaminase can catalyze the hydrolytic deamination of adenine or adenosine. In some embodiments, adenine deaminase can catalyze the hydrolytic deamination of adenosine or deoxyadenosine to inosine or deoxyinosine, respectively. In some embodiments, adenosine deaminase can catalyze the hydrolytic deamination of adenine or adenosine in DNA. In some embodiments, adenine deaminase encoded by a nucleic acid construct of the present invention can produce an A→G transition in the sense (e.g., "+"; template) strand of a target nucleic acid or a T→C transition in the antisense (e.g., "-", complementary) strand of a target nucleic acid.

[0358] In some embodiments, the adenosine deaminase may be a variant of a naturally occurring adenine deaminase. Thus, in some embodiments, the adenosine deaminase may be about 70% to 100% identical to a wild-type adenine deaminase (e.g., about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to a naturally occurring adenine deaminase, and any range or value therein). In some embodiments, the deaminase or deaminase is not naturally occurring and may be referred to as an engineered, mutated or evolved adenosine deaminase. Thus,

[0359] For example, an engineered, mutated or evolved adenine deaminase polypeptide or adenine deaminase domain can be about 70% to 99.9% identical to a naturally occurring adenine deaminase polypeptide / domain (e.g., about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 100%, 101%, 102%, 103%, 104%, 105%, 106%, 107%, 108%, 109%, 110%, 111%, 112%, 113%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8% or 99.9% identical, and any range or value therein). In some embodiments, the adenosine deaminase may be from bacteria (e.g., Escherichia coli), Staphylococcus aureus, Haemophilus influenzae, Caulobacter crescentus, etc.). In some embodiments, the polynucleotide encoding the adenine deaminase polypeptide / domain may be codon optimized for expression in plants.

[0360] In some embodiments, the adenine deaminase domain can be a wild-type tRNA-specific adenosine deaminase domain, such as a tRNA-specific adenosine deaminase (TadA), and / or a mutant / evolved adenosine deaminase domain, such as a mutant / evolved tRNA-specific adenosine deaminase domain (TadA*). In some embodiments, the TadA domain can be from Escherichia coli (E. coli). In some embodiments, TadA can be modified, such as truncated, with one or more N-terminal and / or C-terminal amino acids missing relative to full-length TadA (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 6, 17, 18, 19 or 20 N-terminal and / or C-terminal amino acid residues may be missing relative to full-length TadA). In some embodiments, the TadA polypeptide or TadA domain does not include an N-terminal methionine. In some embodiments, the wild-type E. coli TadA comprises the amino acid sequence of SEQ ID NO: 30. In some embodiments, the mutant / evolved E. coli TadA* comprises the amino acid sequence of SEQ ID NO: 31-40 (e.g., SEQ ID NO: 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40). In some embodiments, the polynucleotide encoding TadA / TadA* can be codon-optimized for expression in plants.

[0361] Cytosine deaminase catalyzes the deamination of cytosine and produces thymidine (via a uracil intermediate), causing a C to T transition or a G to A transition in the complementary strand of the genome. Thus, in some embodiments, a cytosine deaminase encoded by a polynucleotide of the invention produces a C→T transition in the sense (e.g., "+"; template) strand of a target nucleic acid or a G→A transition in the antisense (e.g., "-", complementary) strand of a target nucleic acid.

[0362] In some embodiments, an adenine deaminase encoded by a nucleic acid construct of the invention produces an A→G tran...

Claims

1. A plant or plant part thereof comprising at least one mutation in the endogenous ideal plant architecture 1 (IPA1) gene encoding a SQUAMOSA promoter binding protein-like (SPL) transcription factor or an ortholog thereof.

2. The plant or plant part thereof according to claim 1, wherein the endogenous gene is regulated by miR156.

3. The plant or plant part thereof of claim 1 or claim 2, wherein the endogenous IPA1 gene encoding a SPL transcription factor is an endogenous SQUAMOSA promoter binding protein-like 9 (SPL9) gene, an endogenous unbranched 2 (UB2) gene or an endogenous unbranched 3 (UB3) gene.

4. The plant or plant part thereof according to any one of claims 1 to 3, wherein the at least one mutation is a base deletion, a base substitution and / or a base insertion.

5. The plant or part thereof as claimed in any one of the preceding claims, wherein the at least one mutation comprises a base substitution to A, T, G or C.

6. The plant or part thereof as claimed in any one of the preceding claims, wherein the at least one mutation is a base deletion of at least one base pair, optionally a deletion of about 1 base pair to about 150 consecutive base pairs.

7. The plant or part thereof according to any one of claims 1 to 6, wherein the at least one mutation is a base insertion of at least one base pair.

8. The plant or part thereof according to claim 4, 6 or claim 7, wherein the base deletion is an out-of-frame deletion and / or the base insertion is an out-of-frame insertion.

9. The plant or plant part thereof according to any one of the preceding claims, wherein the endogenous SPL9 gene is present in the plant or part thereof as two paralogous pairs of (a) a SPL9a gene and a SPL9b gene and / or (b) a SPL9c gene and a SPL9d gene.

10. The plant or plant part thereof of any one of claims 3 to 9, wherein the endogenous SPL9 gene: (a) comprises a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 72, 75, 78, 81, 143, 182, 222 or 255; (b) comprises a coding sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 73, 76, 79, 82, 144, 183, 223 or 256; (c) comprises a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288; and / or (d) encodes a polypeptide sequence having at least 80% identity to the amino acid sequence of any one of SEQ ID NOs: 74, 77, 80, 83, 145, 184, 224 or 257.

11. The plant or plant part thereof according to any one of claims 3 to 8, wherein the endogenous UB2 gene: (a) comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 84; (b) comprising a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 85; (c) comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 90-96 or 332-393; and / or (d) encodes a polypeptide sequence that is at least 80% identical to the amino acid sequence of SEQ ID NO:86; and The endogenous UB3 gene: a) comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 87; (b) comprising a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 88; (c) comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 90, 97-103 or 394-445; and / or (d) encodes a polypeptide sequence that is at least 80% identical to the amino acid sequence of SEQ ID NO:

89.

12. The plant or plant part thereof according to any one of the preceding claims, wherein the at least one mutation is in the first or third exon of the endogenous IPA1 gene encoding the SPL transcription factor or its ortholog, optionally resulting in a premature stop codon and a null allele, optionally wherein the mutation is a hypomorphic mutation or a knockout mutation.

13. The plant or plant part thereof of any one of claims 3 to 10 or 12, wherein the at least one mutation is present in at least one (e.g., 1, 2, 3 or 4) of the SPL9a gene, the SPL9b gene, the SPL9c gene and / or the SPL9d gene, wherein the at least one mutation is in the first exon, optionally resulting in a premature stop codon and a null allele, optionally a hypomorphic mutation or a knockout mutation.

14. The plant or plant part thereof of any one of claims 3 to 10, 12 or 13, wherein the at least one mutation is present in each of the SPL9a gene, the SPL9b gene, the SPL9c gene and the SPL9d gene.

15. The plant or plant part thereof of any one of claims 12 to 14, wherein the first exon of the SPL9a gene is located at about nucleotide 2001 to about nucleotide 2364 with reference to the nucleotide numbering of SEQ ID NO: 72, at about nucleotide 1 to about nucleotide 364 with reference to the nucleotide numbering of SEQ ID NO: 73, and / or at about nucleotide 2160 to about nucleotide 2523 with reference to the nucleotide numbering of SEQ ID NO: 143, the first exon of the SPL9b gene is located at about nucleotide 2001 to about nucleotide 2370 with reference to the nucleotide numbering of SEQ ID NO: 75, at about nucleotide 1 to about nucleotide 370 with reference to the nucleotide numbering of SEQ ID NO: 76, and / or at about nucleotide 2098 to about nucleotide 2467 with reference to the nucleotide numbering of SEQ ID NO: 182, the first exon of the SPL9c gene is located at about nucleotide 2001 to about nucleotide 2347 with reference to the nucleotide numbering of SEQ ID NO: 78, at about nucleotide 1 to about nucleotide 347 with reference to the nucleotide numbering of SEQ ID NO: 79, and / or at about nucleotide 2160 to about nucleotide 2523 with reference to the nucleotide numbering of SEQ ID NO:

143. The nucleotide numbering of NO:222 is located at about nucleotide 2378 to about nucleotide 2724, and / or the first exon of the SPL9d gene is located at about nucleotide 2001 to about nucleotide 2349 with reference to the nucleotide numbering of SEQ ID NO:81, at about nucleotide 1 to about nucleotide 349 with reference to the nucleotide numbering of SEQ ID NO:82, and / or at about nucleotide 2410 to about nucleotide 2758 with reference to the nucleotide numbering of SEQ ID NO:

255.

16. The plant or plant part thereof of any one of claims 12 to 14, wherein the at least one mutation is in the region from about nucleotide 2053 to about nucleotide 2115 in the first exon of the SPL9a gene with reference to nucleotide numbering of SEQ ID NO:72 or SEQ ID NO:75, in the region from about nucleotide 2015 to about nucleotide 2077 in the first exon of the SPL9b gene with reference to nucleotide numbering of SEQ ID NO:78 or SEQ ID NO:81, in the region from about nucleotide 1 to about nucleotide 115 in the first exon of the SPL9c gene with reference to nucleotide numbering of SEQ ID NO:73 or SEQ ID NO:76, and / or in the region from about nucleotide 1 to about nucleotide 77 in the first exon of the SPL9d gene with reference to nucleotide numbering of SEQ ID NO:79 or SEQ ID NO:82, optionally in a region of the SPL9a gene that has at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 161-177, in a region of the SPL9b gene that has at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 161-177, in a region of the SPL9b gene that has at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 161-177 In a region of the SPL9c gene that has at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs: 201-217, in a region of the SPL9c gene that has at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs: 240-250, or in a region of the SPL9d gene that has at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs: 274-284.

17. The plant or plant part thereof of claim 12, wherein the at least one mutation is located in the third exon of the endogenous UB2 gene, optionally in a region having at least 80% sequence identity to any one of SEQ ID NOs: 358-376, optionally SEQ ID NOs: 373-376.

18. The plant or plant part thereof of claim 12, wherein the at least one mutation is located in the third exon of the endogenous UB3 gene, optionally in a region having at least 80% sequence identity to any one of SEQ ID NOs: 408-426, optionally SEQ ID NOs: 415-416.

19. The plant or plant part thereof of any one of claims 1 to 14, wherein the at least one mutation is in the miR156 binding site of the endogenous IPA1 gene or an ortholog thereof.

20. The plant or plant part thereof according to claim 19, wherein (a) the endogenous gene is the SPL9a gene and the miR156 binding site is from about nucleotide 6569 to about nucleotide 6588 with reference to the nucleotide numbering of SEQ ID NO:72, from about nucleotide 758 to about nucleotide 777 with reference to the nucleotide numbering of SEQ ID NO:73, and / or from about nucleotide 6624 to about nucleotide 6847 with reference to the nucleotide numbering of SEQ ID NO:143, (b) the endogenous gene is the SPL9b gene and the miR156 binding site is from about nucleotide 6269 to about nucleotide 6288 with reference to the nucleotide numbering of SEQ ID NO:75, from about nucleotide 760 to about nucleotide 780 with reference to the nucleotide numbering of SEQ ID NO:76, and / or from about nucleotide 6265 to about nucleotide 6488 with reference to the nucleotide numbering of SEQ ID NO:182, (c) the endogenous gene is the SPL9c gene and the miR156 binding site is from about nucleotide 5388 to about nucleotide 5407 with reference to the nucleotide numbering of SEQ ID NO:78, from about nucleotide 761 to about nucleotide 780 with reference to the nucleotide numbering of SEQ ID NO:79, and / or from about nucleotide 5665 to about nucleotide 5887 with reference to the nucleotide numbering of SEQ ID NO:222, and / or (d) the endogenous gene is the SPL9d gene and the miR156 binding site is from about nucleotide 5798 to about nucleotide 5817 with reference to the nucleotide numbering of SEQ ID NO:81, from about nucleotide 737 to about nucleotide 756 with reference to the nucleotide numbering of SEQ ID NO:82, and / or from about nucleotide 6120 to about nucleotide 6342 with reference to the nucleotide numbering of SEQ ID NO:

255.

21. The plant or plant part thereof of claim 19 or claim 20, wherein the mutation in the miR156 binding site is located at: (a) in the endogenous SPL9a gene, in a region from about nucleotide 6549 to about nucleotide 6608 with reference to nucleotide numbering of SEQ ID NO: 72 and / or from about nucleotide 738 to about nucleotide 797 with reference to nucleotide numbering of SEQ ID NO: 73, optionally in a region having about 80% sequence identity with any one of the nucleotide sequences of SEQ ID NOs: 178-181, (b) in the endogenous SPL9b gene, in a region from about nucleotide 6250 to about nucleotide 6308 with reference to nucleotide numbering of SEQ ID NO: 75 and / or from about nucleotide 741 to about nucleotide 800 with reference to nucleotide numbering of SEQ ID NO: 76, optionally in a region having about 80% sequence identity with any one of the nucleotide sequences of SEQ ID NOs: 218-221, (c) in the region of the endogenous SPL9c gene from about nucleotide 5368 to about nucleotide 5427 with reference to nucleotide numbering of SEQ ID NO: 78 and / or from about nucleotide 742 to about nucleotide 800 with reference to nucleotide numbering of SEQ ID NO: 79, optionally in a region having about 80% sequence identity with any one of the nucleotide sequences of SEQ ID NOs: 251-254, and / or (d) in the endogenous SPL9d gene, in a region from about nucleotide 5778 to about nucleotide 5837 with reference to nucleotide numbering of SEQ ID NO:81 and / or from about nucleotide 718 to about nucleotide 775 with reference to nucleotide numbering of SEQ ID NO:82, optionally in a region having about 80% sequence identity with any one of the nucleotide sequences of SEQ ID NOs:285-288.

22. The plant or plant part thereof of claim 19, wherein the endogenous gene is a UB2 gene and the miR156 binding site is from about nucleotide 4928 to about nucleotide 4947 with reference to the nucleotide numbering of SEQ ID NO:84 and / or from about nucleotide 815 to about nucleotide 834 with reference to the nucleotide numbering of SEQ ID NO:85, and / or the endogenous gene is a UB3 gene and the miR156 binding site is from about nucleotide 5301 to about nucleotide 5320 with reference to the nucleotide numbering of SEQ ID NO:87 and / or from about nucleotide 848 to about nucleotide 866 with reference to the nucleotide numbering of SEQ ID NO:

88.

23. The plant or plant part thereof of claim 19 or claim 22, wherein: (a) the mutation in the miR156 binding site of the endogenous UB2 gene is located at about nucleotide 4894 to about nucleotide 4967 with reference to the nucleotide numbering of SEQ ID NO:84 or at about nucleotide 781 to about nucleotide 854 with reference to the nucleotide numbering of SEQ ID NO:85, and / or (b) the mutation in the miR156 binding site of the endogenous UB3 gene is located at about nucleotide 5267 to about nucleotide 5339 with reference to the nucleotide numbering of SEQ ID NO:87 or at about nucleotide 814 to about nucleotide 887 with reference to the nucleotide numbering of SEQ ID NO:

88.

24. The plant or plant part thereof of any one of claims 19 to 23, wherein the at least one mutation in the miR156 binding site is a substitution or a deletion, optionally an in-frame deletion or an out-of-frame deletion.

25. The plant or plant part thereof of claims 19 to 24, wherein the at least one mutation in the miR156 binding site is a point mutation, optionally a silent point mutation.

26. The plant or plant part thereof of claim 25, wherein the point mutation is a substitution, optionally wherein the substitution is C>A, T or G, optionally C>A.

27. The plant or plant part thereof of any one of claims 19 to 26, wherein the mutation in the miR156 binding site upregulates expression of the endogenous IPA1 gene, e.g., the endogenous SPL9a gene, the endogenous SPL9b gene, the endogenous SPL9c gene, the endogenous SPL9d gene, the endogenous unbranched 2 (UB2) gene and / or the endogenous unbranched 3 (UB3) gene.

28. The plant or plant part thereof of any one of claims 3 to 8 or 11, wherein said at least one mutation is a base substitution in a region of said endogenous UB2 gene or said endogenous UB3 gene associated with increased kernel row number (KRN) and / or increased tassel branch number (TBN).

29. The plant or plant part thereof of claim 28, wherein the region of the endogenous UB2 gene associated with increased KRN is from about nucleotide 4379 to about nucleotide 4800 with reference to nucleotide numbering of SEQ ID NO:84 and / or from about nucleotide 626 to about nucleotide 688 with reference to nucleotide numbering of SEQ ID NO:85, or the region of the endogenous UB3 gene associated with increased KRN is from about nucleotide 5094 to about nucleotide 5157 with reference to nucleotide numbering of SEQ ID NO:87 and / or from about nucleotide 641 to about nucleotide 703 with reference to nucleotide numbering of SEQ ID NO:

88.

30. The plant or plant part thereof of claim 28, wherein the region of the endogenous UB2 gene associated with increased TBN is from about nucleotide 4834 to about nucleotide 4896 with reference to nucleotide numbering of SEQ ID NO:84 and / or from about nucleotide 721 to about nucleotide 783 with reference to nucleotide numbering of SEQ ID NO:85, or the region of the endogenous UB3 gene associated with increased TBN is from about nucleotide 5204 to about nucleotide 5266 with reference to nucleotide numbering of SEQ ID NO:87 and / or from about nucleotide 751 to about nucleotide 813 with reference to nucleotide numbering of SEQ ID NO:

88.

31. The plant or plant part thereof of any one of claims 1 to 11, wherein the at least one mutation is in the 5' untranslated region (UTR) and / or the 3' UTR of the endogenous gene.

32. The plant or plant part thereof of claim 31, wherein the endogenous gene is: (a) an SPL9a gene and the at least one mutation is in the 5'UTR in the region from about nucleotide 1826 to about nucleotide 1981 and / or from about nucleotide 1846 to about nucleotide 1961 with reference to the nucleotide numbering of SEQ ID NO: 72, optionally in a region having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs: 146-160; (b) an SPL9b gene and the at least one mutation is in the 5'UTR in the region from about nucleotide 1804 to about nucleotide 1973 and / or from about nucleotide 1824 to about nucleotide 1953, with reference to the nucleotide numbering of SEQ ID NO: 75, optionally in a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 185-200; (c) an SPL9c gene and the at least one mutation is in the 5'UTR in the region from about nucleotide 1593 to about nucleotide 1783 and / or from about nucleotide 1613 to about nucleotide 1764, with reference to the nucleotide numbering of SEQ ID NO: 78, optionally in a region having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs: 225-239; and / or (d) an SPL9d gene and the at least one mutation is in the 5'UTR from about nucleotide 1555 to about nucleotide 1740 and / or from about nucleotide 1574 to about nucleotide 1720, with reference to the nucleotide numbering of SEQ ID NO: 81, optionally in a region having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs: 258-273.

33. The plant or plant part thereof of claim 31, wherein the endogenous gene is: (a) a UB2 gene and the at least one mutation is in the 5'UTR in a region from about nucleotide 1414 to about nucleotide 1860, from about nucleotide 1414 to about nucleotide 1522, from about nucleotide 1454 to about nucleotide 1481, from about nucleotide 1553 to about nucleotide 1582, from about nucleotide 1597 to about nucleotide 1633, and / or from about nucleotide 1767 to about nucleotide 1819, with reference to the nucleotide numbering of SEQ ID NO: 84, optionally wherein the region of the 5'UTR is or is in a promoter, optionally a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 90-96 or 332-357; and / or (b) a UB3 gene and the at least one mutation is in the 5'UTR in a region between about nucleotide 1327 to about nucleotide 1646, about nucleotide 1439 to about nucleotide 1467, about nucleotide 1368 to about nucleotide 1394, about nucleotide 1549 to about nucleotide 1606, about nucleotide 1787 to about nucleotide 1855 and / or about nucleotide 1747 to about nucleotide 1920 with reference to the nucleotide numbering of SEQ ID NO:87, optionally wherein the region of the 5'UTR is or is in a promoter, optionally a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs:394-407.

34. The plant or plant part thereof of claim 29, wherein the endogenous gene is (a) a UB2 gene and the at least one mutation is in the 3'UTR from about nucleotide 5701 to about nucleotide 5882 and / or from about nucleotide 5742 to about nucleotide 5842, with reference to the nucleotide numbering of SEQ ID NO: 84, optionally in a region having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs: 377-393; and / or (b) a UB3 gene and the at least one mutation is in the 3'UTR within a region from about nucleotide 5940 to about nucleotide 6109, from about nucleotide 5980 to about nucleotide 6069, from about nucleotide 6516 to about nucleotide 6643 and / or from about nucleotide 6556 to about nucleotide 6603, with reference to the nucleotide numbering of SEQ ID NO:87, optionally within a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs:427-445.

35. The plant or plant part thereof of any one of claims 1 to 8, wherein the at least one mutation is in an intron of the endogenous gene.

36. The plant or plant part thereof of claim 35, wherein the endogenous gene (a) is a UB2 gene and the at least one mutation is in the intron in a region from about nucleotide 2856 to about nucleotide 2971, from about nucleotide 2896 to about nucleotide 2931, from about nucleotide 3753 to about nucleotide 3893 and / or from about nucleotide 3793 to about nucleotide 3853, with reference to the nucleotide numbering of SEQ ID NO: 84; and / or (b) is a UB3 gene and the at least one mutation is in the intron in a region from about nucleotide 2666 to about nucleotide 2784, from about nucleotide 2706 to about nucleotide 2744, from about nucleotide 4017 to about nucleotide 4147 and / or from about nucleotide 4057 to about nucleotide 4107, with reference to the nucleotide numbering of SEQ ID NO:

87.

37. A plant or plant part thereof as claimed in any one of the preceding claims, wherein the at least one mutation is a dominant negative mutation, a semi-dominant mutation, a superallelic mutation, a hypomorphic allele mutation, a weak loss-of-function mutation or a null allele.

38. The plant or plant part thereof of any one of the preceding claims, wherein the at least one mutation results in a plant with altered plant architecture, improved yield traits and / or increased tolerance / resistance to abiotic and biotic stresses compared to a plant or plant part lacking the same mutation.

39. The plant of claim 38, or a plant part thereof, wherein the improved yield trait comprises one or more of the following phenotypes: increased number of kernel rows, increased kernel size, increased ear length, reduced tiller number, reduced number of tassel branches, reduced time to flowering, increased number of seeds per plant, increased number of pods per node and / or per plant, and / or increased seed weight, in any combination.

40. The plant or part thereof as claimed in any one of the preceding claims, wherein the plant is a monocot or a dicot.

41. The plant or part thereof of any of the preceding claims, wherein the plant is corn, soybean, canola, wheat, rice, cotton, sugarcane, sugar beet, barley, oats, alfalfa, sunflower, safflower, oil palm, sesame, coconut, tobacco, potato, sweet potato, cassava, coffee, apple, plum, apricot, peach, cherry, pear, fig, banana, citrus, cocoa, avocado, olive, almond, walnut, strawberry, watermelon, pepper, grape, tomato, cucumber, or Brassica species.

42. The plant or part thereof of any one of claims 1 to 41, wherein the plant is corn.

43. The plant or part thereof of any one of claims 1 to 41, wherein the plant is soybean.

44. A plant or part thereof as claimed in any one of the preceding claims, wherein the at least one mutation is a non-natural mutation.

45. The plant or part thereof of any one of the preceding claims, wherein the IPA1 gene is a SPL9 gene and the at least one mutation results in a mutant SPL9 gene having at least 90% identity to any one of the nucleotide sequences of SEQ ID NOs: 289-300, wherein the IPA1 gene is a UB2 gene and the at least one mutation results in a mutant UB2 gene having at least 90% identity to any one of the nucleotide sequences of SEQ ID NOs: 320, 322 or 324, or is a UB3 gene and the at least one mutation results in a mutant UB2 gene having at least 90% identity to any one of the nucleotide sequences of SEQ ID NOs: 310, 312, 314, 316 or 318.

46. ​​The plant or part thereof of any one of the preceding claims, wherein the IPA1 gene is a UB2 gene and the at least one mutation results in a mutant UB2 gene encoding a mutant polypeptide having at least 90% identity to any one of SEQ ID NOs: 321, 323 or 325, or is a UB3 gene and the at least one mutation results in a mutant UB2 gene encoding a mutant polypeptide having at least 90% identity to any one of SEQ ID NOs: 311, 313, 315, 317 or 319.

47. A plant cell, comprising an editing system, wherein the editing system comprises: (a) CRISPR-Cas-associated effector proteins; and (b) a guide nucleic acid (e.g., gRNA, gDNA, crRNA, crDNA) comprising a spacer sequence complementary to an endogenous ideal plant architecture 1 (IPA1) target gene encoding a SQUAMOSA promoter binding protein-like (SPL) transcription factor or an ortholog thereof.

48. The plant cell of claim 47, wherein the IPA1 gene is a SQUAMOSA promoter binding protein-like 9 (SPL9) gene, an endogenous unbranched 2 (UB2) gene, or an endogenous unbranched 3 (UB3) gene, optionally wherein the SPL9 gene is a SPL9a gene, a SPL9b gene, a SPL9c gene, or a SPL9d gene.

49. The plant cell of claim 47 or claim 48, wherein the endogenous IPA1 target gene is: (a) SLP9 gene, which (i) comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO: 72, 75, 78, 81, 143, 182, 222 or 255; (ii) comprising a coding sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO: 73, 76, 79, 82, 144, 183, 223 or 256; (iii) comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288; and / or (iv) encoding a polypeptide sequence that is at least 80% identical to the amino acid sequence of any one of SEQ ID NO: 74, 77, 80, 83, 145, 184, 224 or 257; (b) UB2 gene, which (i) comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 84; (ii) comprising a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 85; (iii) comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 90-96 or 332-393; and / or (iv) encoding a polypeptide sequence that is at least 80% identical to the amino acid sequence of SEQ ID NO: 86; and / or (c) UB3 gene, which (i) comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 87; (ii) comprising a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 88; (iii) comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 90, 97-103, or 394-445; and / or (iv) encodes a polypeptide sequence that has at least 80% identity to the amino acid sequence of any one of SEQ ID NO:

89.

50. The plant cell of any one of claims 47 to 49, wherein the guide nucleic acid comprises the nucleotide sequence (e.g., a spacer sequence) of any one of SEQ ID NOs: 104-142, 301, 326, or 327.

51. The plant cell of any one of claims 47 to 50, wherein the plant cell is a corn plant cell or a soybean plant cell.

52. A plant regenerated from the plant part of any one of claims 1 to 46 or the plant cell of any one of claims 47 to 51.

53. The plant of claim 52, wherein the plant exhibits a phenotype of one or more of altered plant architecture, improved yield traits and / or increased tolerance / resistance to abiotic and biotic stresses compared to a plant or plant part lacking the same mutation.

54. A plant cell comprising at least one mutation in one or more endogenous ideal plant architecture 1 (IPA1) genes encoding a SQUAMOSA promoter binding protein-like (SPL) transcription factor or an ortholog thereof, wherein the at least one mutation is a substitution, insertion and / or deletion introduced using an editing system comprising a nucleic acid binding domain that binds to a target site in the one or more endogenous IPA1 genes.

55. The plant cell of claim 54, wherein the one or more endogenous IPA1 genes are a SQUAMOSA promoter binding protein-like 9 (SPL9) gene, an endogenous unbranched 2 (UB2) gene, or an endogenous unbranched 3 (UB3) gene, optionally wherein the SPL9 gene is a SPL9a gene, a SPL9b gene, a SPL9c gene, or a SPL9d gene.

56. The plant cell of claim 54 or claim 55, wherein the at least one mutation is a non-natural mutation.

57. The plant cell of any one of claims 54 to 56, wherein the at least one mutation is a null allele.

58. The plant cell of any one of claims 54 to 57, wherein the at least one mutation is a knockout mutation or a hypomorphic mutation.

59. The plant cell of any one of claims 54 to 58, wherein the target site is at: (a) within a region of one or more endogenous SPL9 genes, said region having at least 80% sequence identity to any one of SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288; (b) within a region of one or more endogenous UB2 genes, said region having at least 80% sequence identity to any one of SEQ ID NOs: 90-96 or 332-393; and / or (c) within a region of one or more endogenous UB3 genes, said region having at least 80% sequence identity to any one of SEQ ID NOs: 90, 97-103, or 394-445.

60. The plant cell of any one of claims 54 to 59, wherein the editing system further comprises a nuclease and the nucleic acid binding domain binds to a target site in: (a) an SPL9 gene having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 72, 73, 75, 76, 78, 79, 81, 82, 143, 144, 182, 183, 222, 223, 255 or 256; and / or comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288, (b) a UB2 gene having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:84 or SEQ ID NO:85 and / or comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs:90-96 or 332-393; and / or (c) a UB3 gene having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:87 or SEQ ID NO:88 and / or comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:90, 97-103 or 394-445; and said at least one mutation within said endogenous IPA1 gene is generated following cleavage by said nuclease.

61. The plant cell of claim 60, wherein the nuclease is a zinc finger nuclease, a transcription activator-like effector nuclease (TALEN), an endonuclease (e.g., Fok1), or a CRISPR-Cas effector protein.

62. The plant cell of any one of claims 54 to 61, wherein the nucleic acid binding domain of the editing system is from a polynucleotide-guided endonuclease, a CRISPR-Cas endonuclease (e.g., a CRISPR-Cas effector protein), a zinc finger nuclease, a transcription activator-like effector nuclease (TALEN) and / or an Argonaute protein.

63. The plant cell of any one of claims 54 to 62, wherein the at least one mutation within the one or more endogenous IPA1 genes is an insertion and / or a deletion, optionally the at least one mutation is an out-of-frame insertion or an out-of-frame deletion.

64. The plant cell of any one of claims 54 to 63, wherein the at least one mutation within the one or more endogenous IPA1 genes is an insertion and / or deletion resulting in a premature stop codon, optionally wherein the at least one mutation is an out-of-frame insertion or out-of-frame deletion resulting in a premature stop codon, optionally resulting in a truncated protein.

65. The plant cell of any one of claims 54 to 64, wherein the at least one mutation within the one or more endogenous IPA1 genes comprises a point mutation.

66. The plant cell of any one of claims 54 to 65, wherein the endogenous IPA1 gene is a SPL9 gene and the at least one mutation results in a mutant SPL9 gene having at least 90% identity to any one of the nucleotide sequences of SEQ ID NOs: 289-300, wherein the IPA1 gene is a UB2 gene and the at least one mutation results in a mutant UB2 gene having at least 90% identity to any one of the nucleotide sequences of SEQ ID NOs: 320, 322 or 324, or is a UB3 gene and the at least one mutation results in a mutant UB2 gene having at least 90% identity to any one of the nucleotide sequences of SEQ ID NOs: 310, 312, 314, 316 or 318.

67. The plant cell of any one of claims 54 to 66, wherein the IPA1 gene is a UB2 gene and the at least one mutation produces a mutant UB2 gene encoding a mutant polypeptide having at least 90% identity to any one of SEQ ID NOs: 321, 323 or 325, or is a UB3 gene and the at least one mutation produces a mutant UB2 gene encoding a mutant polypeptide having at least 90% identity to any one of SEQ ID NOs: 311, 313, 315, 317 or 319.

68. A plant regenerated from the plant cell of any one of claims 54 to 67, comprising the at least one mutation in the one or more endogenous IPA1 genes and exhibiting a phenotype of one or more of altered plant architecture, improved yield traits and / or increased tolerance / resistance to abiotic and biotic stresses compared to a control plant or part thereof lacking the at least one mutation.

69. The plant of claims 62 to 68, wherein the plant is soybean or corn.

70. A method of providing a plurality of plants exhibiting altered plant architecture, improved yield traits and / or increased tolerance / resistance to abiotic and biotic stresses, the method comprising planting in a growing area two or more plants according to any one of claims 1 to 46, 52, 53, 68 or 69, thereby providing a plurality of plants exhibiting altered plant architecture, improved yield traits and / or increased tolerance / resistance to abiotic and biotic stresses compared to a plurality of control plants not comprising said at least one mutation, optionally wherein said plurality of plants exhibiting resistance to biotic stresses exhibit increased disease resistance.

71. A method of producing / growing a transgene-free genome-edited (e.g., base-edited) plant, the method comprising: (a) crossing the plant of any one of claims 1 to 46, 52, 53, 68 or 69 with a plant without a transgenic plant, thereby introducing the mutation or modification into the plant without a transgenic plant; and (b) selecting progeny plants that comprise the mutation or modification but are free of the transgene, thereby producing genome-edited (e.g., base-edited) plants free of the transgene.

72. A method for generating a mutation in an endogenous IPA1 gene of a plant, the method comprising: (a) targeting a gene editing system to a portion of the IPA1 gene, wherein: (i) having at least 80% sequence identity to any one of SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288; (ii) having at least 80% sequence identity to any one of SEQ ID NOs: 90-96 or 332-393; and / or (iii) having at least 80% sequence identity to any one of SEQ ID NOs: 90, 97-103, or 394-445; and (b) selecting plants comprising a modification in a region of said IPA1 gene, said region: (i) having at least 80% sequence identity to any one of SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288; (ii) having at least 80% sequence identity to any one of SEQ ID NOs: 90-96 or 332-393; and / or (iii) has at least 80% sequence identity to any one of SEQ ID NOs: 90, 97-103, or 394-445.

73. A method for generating a variation in an IPA1 polypeptide, the method comprising: introducing an editing system into a plant cell, wherein the editing system targets a region of an endogenous IPA1 gene encoding the IPA1 polypeptide, and The region of the endogenous IPA1 gene is contacted with the editing system, thereby introducing mutations into the endogenous IPA1 gene and generating variations in the IPA1 polypeptide of the plant cell.

74. The method of claim 73, wherein the endogenous IPA1 gene comprises: (a) a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:72, 73, 75, 76, 78, 79, 81, 82, 143, 144, 182, 183, 222, 223, 255 or 256; and / or encoding an amino acid sequence having at least 80% sequence identity to any one of SEQ ID NO:74, 77, 80, 83, 145, 184, 224 and / or 257, (b) a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:84 or SEQ ID NO:85, and / or encoding an amino acid sequence having at least 80% sequence identity to SEQ ID NO:86; and / or (c) a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:87 or SEQ ID NO:88, and / or encoding an amino acid sequence having at least 80% sequence identity to SEQ ID NO:

39.

75. The method of claim 73 or claim 74, wherein the region of the endogenous IPA1 gene that is targeted (a) having at least 80% sequence identity to any one of SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288; (b) having at least 80% sequence identity to any one of SEQ ID NOs: 90-96 or 332-393; and / or (c) having at least 80% sequence identity to any one of SEQ ID NOs: 90, 97-103, or 394-445.

76. The method of any one of claims 73 to 75, wherein contacting the region of the endogenous IPA1 gene in the plant cell with the editing system produces a plant cell comprising the edited IPA1 gene in its genome, the method further comprising (a) regenerating a plant from the plant cell; (b) selfing the plant to produce a progeny plant (E1); (c) analyzing the progeny plant of (b) for improved yield traits; and (d) selecting the progeny plant that exhibits improved yield traits compared to control plants.

77. The method of claim 76, further comprising (e) selfing the selected progeny plant of (d) to produce a progeny plant (E2); (f) analyzing the progeny plant of (e) for improved yield traits; and (g) selecting the progeny plants exhibiting improved yield traits compared to control plants, optionally repeating (e) to (g) one or more times.

78. A method for detecting a mutant IPA1 gene in a plant (a mutation in an endogenous IPA1 gene), the method comprising detecting in the genome of the plant an IPA1 gene having at least one mutation in a region: (a) having at least 80% sequence identity to any one of SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288; (b) having at least 80% sequence identity to any one of SEQ ID NOs: 90-96 or 332-393; and / or (c) having at least 80% sequence identity to any one of SEQ ID NOs: 90, 97-103, or 394-445.

79. The method of claim 78, wherein the mutant IPA1 gene detected comprises a nucleic acid sequence, wherein: (a) having at least 90% identity to any one of the nucleotide sequences of SEQ ID NOs: 289-300, (b) has at least 90% identity to any one of the nucleotide sequences of SEQ ID NO: 320, 322 or 324, or (c) having at least 90% identity to any one of the nucleotide sequences of SEQ ID NO: 310, 312, 314, 316 or 318.

80. A method for editing a specific site in the genome of a plant cell, the method comprising: cleaving a target site within an endogenous IPA1 gene in the plant cell in a site-specific manner, wherein the endogenous IPA1 gene is: (a) an SPL9 gene having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 72, 73, 75, 76, 78, 79, 81, 82, 143, 144, 182, 183, 222, 223, 255 or 256; and / or comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288, (b) a UB2 gene having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:84 or SEQ ID NO:85 and / or comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs:90-96 or 332-393; and / or (c) a UB3 gene having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:87 or SEQ ID NO:88 and / or comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs:90, 97-103 or 394-445, thereby producing editing in the endogenous IPA1 gene of the plant cell.

81. The method of claim 70, wherein the editing in the endogenous IPA1 gene produces a mutation that is a null allele.

82. The method of claim 80 or claim 81, further comprising regenerating a plant from the plant cell comprising the edit in the endogenous IPA1 gene to produce a plant comprising the edit in its endogenous IPA1 gene.

83. The method of claim 82, wherein said plant comprising said edit in its endogenous IPA1 gene exhibits a phenotype of one or more of altered plant architecture, improved yield traits, and / or increased tolerance / resistance to abiotic and biotic stresses compared to a control plant not comprising said edit.

84. The method of any one of claims 80 to 83, wherein the IPA1 gene is a SPL9 gene and the editing in the endogenous SPL9 gene of the plant cell produces a mutant SPL9 gene having at least 90% identity to any one of the nucleotide sequences of SEQ ID NOs: 289-300.

85. The method of any one of claims 80 to 84, wherein the editing produces a non-natural mutation.

86. The method of any one of claims 80 to 85, wherein the endogenous IPA1 gene is a SPL9 gene and the editing produces a mutant SPL9 gene having at least 90% identity to any one of the nucleotide sequences of SEQ ID NOs: 289-300, wherein the IPA1 gene is a UB2 gene and the at least one mutation produces a mutant UB2 gene having at least 90% identity to any one of the nucleotide sequences of SEQ ID NOs: 320, 322 or 324, or wherein the IPA1 gene is a UB3 gene and the at least one mutation produces a mutant UB2 gene having at least 90% identity to any one of the nucleotide sequences of SEQ ID NOs: 310, 312, 314, 316 or 318.

87. The method of any one of claims 80 to 86, wherein the endogenous IPA1 gene is a UB2 gene and the editing produces a mutant UB2 gene encoding a mutant polypeptide having at least 90% identity to any one of SEQ ID NOs: 321, 323 or 325, or is a UB3 gene and the editing produces a mutant UB2 gene encoding a mutant polypeptide having at least 90% identity to any one of SEQ ID NOs: 311, 313, 315, 317 or 319.

88. A method for preparing a plant, the method comprising: (a) contacting a population of plant cells comprising an endogenous IPA1 gene with a nuclease targeted to the endogenous gene, wherein the nuclease is linked to a nucleic acid binding domain that binds to a target site in the endogenous gene, wherein the endogenous IPA1 gene: (i) is a SPL9 gene comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 72, 73, 75, 76, 78, 79, 81, 82, 143, 144, 182, 183, 222, 223, 255 or 256; and / or comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288; (ii) is a UB2 gene having at least 80% sequence identity with the nucleotide sequence of SEQ ID NO:84 or SEQ ID NO:85 and / or comprising a region having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs:90-96 or 332-393; and / or (iii) is a UB3 gene having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:87 or SEQ ID NO:88 and / or comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:90, 97-103 or 394-445; (b) selecting a plant cell from said population comprising a mutation in said endogenous IPA1 gene, wherein said mutation is a substitution and / or a deletion; and (c) growing the selected plant cell into a plant comprising the mutation in the endogenous IPA1 gene.

89. A method for altering plant architecture, improving yield traits and / or increasing tolerance / resistance of a plant, the method comprising (a) contacting a plant cell comprising an endogenous IPA1 gene with a nuclease that targets the endogenous IPA1 gene, wherein the nuclease is linked to a nucleic acid binding domain that binds to a target site in the endogenous IPA1 gene, wherein the endogenous IPA1 gene is: (i) an SPL9 gene comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 72, 73, 75, 76, 78, 79, 81, 82, 143, 144, 182, 183, 222, 223, 255 or 256; and / or comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288; (ii) a UB2 gene having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:84 or SEQ ID NO:85 and / or comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs:90-96 or 332-393; and / or (iii) a UB3 gene having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:87 or SEQ ID NO:88 and / or comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs:90, 97-103 or 394-445, thereby producing a plant cell comprising a mutation in the endogenous IPA1 gene; and (b) growing the plant cell into a plant, thereby changing the plant architecture, improving yield traits and / or increasing tolerance / resistance of the plant.

90. A method for producing a plant or part thereof comprising at least one cell having a mutation in an endogenous ideal plant architecture 1 (IPA1) gene encoding a SQUAMOSA promoter binding protein-like (SPL) transcription factor, or an ortholog thereof, the method comprising contacting a target site in the endogenous IPA1 gene in the plant or plant part with a nuclease comprising a cleavage domain and a DNA binding domain, wherein the DNA binding domain of the nuclease binds to the target site in the endogenous IPA1 gene, wherein the endogenous IPA1 gene: (a) is the endogenous SQUAMOSA promoter binding protein-like 9 (SPL9) gene, which (i) comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO: 72, 75, 78, 81, 143, 182, 222 or 255; (ii) comprising a coding sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO: 73, 76, 79, 82, 144, 183, 223 or 256; (iii) comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254 or 258-288, and / or (iv) encoding a polypeptide sequence that is at least 80% identical to the amino acid sequence of any one of SEQ ID NO: 74, 77, 80, 83, 145, 184, 224 or 257; (b) is the endogenous unbranched 2 (UB2) gene, which (i) comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 84; (ii) comprising a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 85; (iii) comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 90-96 or 332-393, and / or (iv) encodes a polypeptide sequence that is at least 80% identical to the amino acid sequence of SEQ ID NO:86; or (c) is an endogenous UB3 gene, which: (i) comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 87; (ii) comprising a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 88; (iii) comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 90, 97-103 or 394-445, and / or (iv) encoding a polypeptide region having at least 80% identity to the amino acid sequence of SEQ ID NO: 89, thereby producing a plant or part thereof comprising at least one cell having a mutation in said endogenous IPA1 gene.

91. A method of producing a plant or part thereof comprising a mutation in an endogenous IPA1 gene and having a phenotype of altered plant architecture, improved yield traits and / or increased tolerance / resistance to abiotic and biotic stresses, the method comprising contacting a target site in an endogenous IPA1 gene in the plant or plant part with a nuclease comprising a cleavage domain and a nucleic acid binding domain, wherein the nucleic acid binding domain of the nuclease binds to the target site in the endogenous IPA1 gene, wherein the endogenous IPA gene: (a) is the endogenous SQUAMOSA promoter binding protein-like 9 (SPL9) gene, which ((i) comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:72, 75, 78, 81, 143, 182, 222 or 255; (ii) comprising a coding sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO: 73, 76, 79, 82, 144, 183, 223 or 256; (iii) comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288, and / or (iv) encoding a polypeptide sequence that is at least 80% identical to the amino acid sequence of any one of SEQ ID NO: 74, 77, 80, 83, 145, 184, 224 or 257; (b) is the endogenous unbranched 2 (UB2) gene, which (i) comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 84; (ii) comprising a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 85; (iii) comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 90-96 or 332-393, and / or (iv) encodes a polypeptide sequence that is at least 80% identical to the amino acid sequence of SEQ ID NO:86; or (c) is an endogenous UB3 gene, which: (i) comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 87; (ii) comprising a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 88; (iii) comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 90, 97-103 or 394-445, and / or (iv) encoding a polypeptide sequence having at least 80% identity to the amino acid sequence of SEQ ID NO: 89, thereby producing a plant or part thereof having a mutated endogenous IPA1 gene and altered plant architecture, improved yield traits and / or increased tolerance / resistance to abiotic and biotic stresses.

92. The method of any one of claims 88 to 91, wherein the mutation is at least one of a base pair deletion, a base pair substitution, and / or a base pair insertion.

93. The method of any one of claims 88 to 92, wherein the mutation is a dominant negative mutation, a semi-dominant mutation, a hyperallelic mutation, a hypomorphic mutation, a weak loss-of-function mutation, or a null allele.

94. The method of any one of claims 88 to 93, wherein the mutation results in a plant with altered plant architecture, improved yield traits and / or increased tolerance / resistance to abiotic and biotic stresses compared to a plant or plant part not comprising the same mutation.

95. The method of claim 94, wherein the improved yield trait comprises one or more of the following phenotypes: increased number of kernel rows, increased kernel size, increased ear length, reduced number of tillers, reduced number of tassel branches, reduced time to flowering, increased number of seeds per plant, increased number of pods per node and / or per plant, and / or increased seed weight.

96. The method of any one of claims 88 to 95, wherein the endogenous SPL9 gene is present in the plant or part thereof as two paralogous pairs: (a) a SPL9a gene and a SPL9b gene and / or (b) a SPL9c gene and a SPL9d gene, optionally wherein at least one of the SPL9a gene, the SPL9b gene, the SPL9c gene and the SPL9d gene comprises a mutation in any combination, or wherein each of the SPL9a gene, the SPL9b gene, the SPL9c gene and the SPL9d gene comprises a mutation.

97. The method of any one of claims 80 to 88, wherein the mutation is in the first exon of the endogenous SPL9 gene, optionally generating a premature stop codon and a null allele.

98. The method of claim 97, wherein the first exon of the SPL9a gene is located at about nucleotide 2001 to about nucleotide 2364 with reference to the nucleotide numbering of SEQ ID NO:72, at about nucleotide 1 to about nucleotide 364 with reference to the nucleotide numbering of SEQ ID NO:73, and / or at about nucleotide 2160 to about nucleotide 2523 with reference to the nucleotide numbering of SEQ ID NO:143, the first exon of the SPL9b gene is located at about nucleotide 2001 to about nucleotide 2370 with reference to the nucleotide numbering of SEQ ID NO:75, at about nucleotide 1 to about nucleotide 370 with reference to the nucleotide numbering of SEQ ID NO:76, and / or at about nucleotide 2098 to about nucleotide 2467 with reference to the nucleotide numbering of SEQ ID NO:182, the first exon of the SPL9c gene is located at about nucleotide 2001 to about nucleotide 2347 with reference to the nucleotide numbering of SEQ ID NO:78, at about nucleotide 1 to about nucleotide 347 with reference to the nucleotide numbering of SEQ ID NO:79, and / or at about nucleotide 2160 to about nucleotide 2523 with reference to the nucleotide numbering of SEQ ID NO:143 The nucleotide numbering of IDNO:222 is located at about nucleotide 2378 to about nucleotide 2724, and / or the first exon of the SPL9d gene is located at about nucleotide 2001 to about nucleotide 2349 with reference to the nucleotide numbering of SEQ ID NO:81, at about nucleotide 1 to about nucleotide 349 with reference to the nucleotide numbering of SEQ ID NO:82, and / or at about nucleotide 2410 to about nucleotide 2758 with reference to the nucleotide numbering of SEQ ID NO:

255.

99. The method of claim 97 or claim 98, wherein the mutation is in the region from about nucleotide 2053 to about nucleotide 2115 in the first exon of the SPL9a gene with reference to nucleotide numbering of SEQ ID NO:72 or SEQ ID NO:75, in the region from about nucleotide 2015 to about nucleotide 2077 in the first exon of the SPL9b gene with reference to nucleotide numbering of SEQ ID NO:78 or SEQ ID NO:81, in the region from about nucleotide 1 to about nucleotide 115 in the first exon of the SPL9c gene with reference to nucleotide numbering of SEQ ID NO:73 or SEQ ID NO:76, and / or in the region from about nucleotide 1 to about nucleotide 77 in the first exon of the SPL9d gene with reference to nucleotide numbering of SEQ ID NO:79 or SEQ ID NO:82, optionally in the region from about nucleotide 1 to about nucleotide 77 in the SPL9a gene with reference to SEQ ID NO:78 or SEQ ID NO:

81. In a region in which the nucleotide sequence of any one of NO:161-177 has at least 80% sequence identity, in a region in the SPL9b gene having at least 80% sequence identity with the nucleotide sequence of any one of 201-217, in a region in the SPL9c gene having at least 80% sequence identity with the nucleotide sequence of any one of 240-250, or in a region in the SPL9d gene having at least 80% sequence identity with the nucleotide sequence of any one of 274-284.

100. The method of any one of claims 80 to 88, wherein the mutation is in the third exon of the endogenous UB2 gene or the endogenous UB3 gene, optionally generating a premature stop codon and a null allele.

101. The method of claim 100, wherein the at least one mutation located in the third exon of the endogenous UB2 gene is located in a region having at least 80% sequence identity to any one of SEQ ID NOs: 358-376, optionally SEQ ID NOs: 373-376, and / or the at least one mutation located in the third exon of the endogenous UB3 gene is located in a region having at least 80% sequence identity to any one of SEQ ID NOs: 408-426, optionally SEQ ID NOs: 415-416.

102. The method of any one of claims 88 to 96, wherein the mutation is in the miR156 binding site of the endogenous SPL9 gene, UB2 gene and / or UB3 gene.

103. The method of claim 102, wherein (a) the endogenous gene is the SPL9a gene and the miR156 binding site is from about nucleotide 6569 to about nucleotide 6588 with reference to the nucleotide numbering of SEQ ID NO:72, from about nucleotide 758 to about nucleotide 777 with reference to the nucleotide numbering of SEQ ID NO:73, and / or from about nucleotide 6624 to about nucleotide 6847 with reference to the nucleotide numbering of SEQ ID NO:143, (b) the endogenous gene is the SPL9b gene and the miR156 binding site is from about nucleotide 6269 to about nucleotide 6288 with reference to the nucleotide numbering of SEQ ID NO:75, from about nucleotide 760 to about nucleotide 780 with reference to the nucleotide numbering of SEQ ID NO:76, and / or from about nucleotide 6265 to about nucleotide 6488 with reference to the nucleotide numbering of SEQ ID NO:182, (c) the endogenous gene is the SPL9c gene and the miR156 binding site is from about nucleotide 5388 to about nucleotide 5407 with reference to the nucleotide numbering of SEQ ID NO:78, from about nucleotide 761 to about nucleotide 780 with reference to the nucleotide numbering of SEQ ID NO:79, and / or from about nucleotide 5665 to about nucleotide 5887 with reference to the nucleotide numbering of SEQ ID NO:222, and / or (d) the endogenous gene is the SPL9d gene and the miR156 binding site is from about nucleotide 5798 to about nucleotide 5817 with reference to the nucleotide numbering of SEQ ID NO:81, from about nucleotide 737 to about nucleotide 756 with reference to the nucleotide numbering of SEQ ID NO:82, and / or from about nucleotide 6120 to about nucleotide 6342 with reference to the nucleotide numbering of SEQ ID NO:

255.

104. The method of claim 102 or claim 103, wherein the mutation in the miR156 binding site is located at: (a) in the endogenous SPL9a gene, in a region from about nucleotide 6549 to about nucleotide 6608 with reference to nucleotide numbering of SEQ ID NO: 72 and / or from about nucleotide 738 to about nucleotide 797 with reference to nucleotide numbering of SEQ ID NO: 73, optionally in a region having about 80% sequence identity with any one of the nucleotide sequences of SEQ ID NOs: 178-181, (b) in the endogenous SPL9b gene, in a region from about nucleotide 6250 to about nucleotide 6308 with reference to nucleotide numbering of SEQ ID NO: 75 and / or from about nucleotide 741 to about nucleotide 800 with reference to nucleotide numbering of SEQ ID NO: 76, optionally in a region having about 80% sequence identity with any one of the nucleotide sequences of SEQ ID NOs: 218-221, (c) in the region of the endogenous SPL9c gene from about nucleotide 5368 to about nucleotide 5427 with reference to nucleotide numbering of SEQ ID NO: 78 and / or from about nucleotide 742 to about nucleotide 800 with reference to nucleotide numbering of SEQ ID NO: 79, optionally in a region having about 80% sequence identity with any one of the nucleotide sequences of SEQ ID NOs: 251-254, and / or (d) in the endogenous SPL9d gene, in a region from about nucleotide 5778 to about nucleotide 5837 with reference to nucleotide numbering of SEQ ID NO:81 and / or from about nucleotide 718 to about nucleotide 775 with reference to nucleotide numbering of SEQ ID NO:82, optionally in a region having about 80% sequence identity with any one of the nucleotide sequences of SEQ ID NOs:285-288.

105. The method of claim 102, wherein the endogenous gene is the UB2 gene and the miR156 binding site is from about nucleotide 4928 to about nucleotide 4947 with reference to the nucleotide numbering of SEQ ID NO:84 and / or from about nucleotide 815 to about nucleotide 834 with reference to the nucleotide numbering of SEQ ID NO:85, and / or the endogenous gene is the UB3 gene and the miR156 binding site is from about nucleotide 5301 to about nucleotide 5320 with reference to the nucleotide numbering of SEQ ID NO:87 and / or from about nucleotide 848 to about nucleotide 866 with reference to the nucleotide numbering of SEQ ID NO:

88.

106. The method of claim 102 or claim 105, wherein: (a) the mutation in the miR156 binding site of the endogenous UB2 gene is located at about nucleotide 4894 to about nucleotide 4967 with reference to the nucleotide numbering of SEQ ID NO:84 and / or at about nucleotide 781 to about nucleotide 854 with reference to the nucleotide numbering of SEQ ID NO:85, and / or (b) the mutation in the miR156 binding site of the endogenous UB3 gene is located at about nucleotide 5267 to about nucleotide 5339 with reference to the nucleotide numbering of SEQ ID NO:87 and / or at about nucleotide 814 to about nucleotide 887 with reference to the nucleotide numbering of SEQ ID NO:

88.

107. The method of any one of claims 102 to 106, wherein the mutation in the miR156 binding site is a substitution or a deletion, optionally wherein the deletion is an in-frame deletion or an out-of-frame deletion.

108. The method of claims 102 to 107, wherein the at least one mutation in the miR156 binding site is a point mutation, optionally a silent point mutation.

109. The method of claim 108, wherein the point mutation is a substitution, optionally wherein the substitution is C>A, T or G, optionally C>A.

110. The method of any one of claims 102 to 109, wherein the mutation in the miR156 binding site upregulates expression of the endogenous IPA1 gene, for example, the endogenous SPL9a gene, the endogenous SPL9b gene, the endogenous SPL9c gene, the endogenous SPL9d gene, the endogenous unbranched 2 (UB2) gene and / or the endogenous unbranched 3 (UB3) gene.

111. The method of any one of claims 88 to 95, wherein the at least one mutation is a base substitution in a region of the endogenous UB2 gene or the endogenous UB3 gene associated with increased kernel row number (KRN) and / or increased tassel branch number (TBN).

112. The method of claim 111, wherein the region of the endogenous UB2 gene associated with increased KRN is from about nucleotide 4379 to about nucleotide 4800 with reference to nucleotide numbering of SEQ ID NO:84 and / or from about nucleotide 626 to about nucleotide 688 with reference to nucleotide numbering of SEQ ID NO:85, and / or the region of the endogenous UB3 gene associated with increased KRN is from about nucleotide 5094 to about nucleotide 5157 with reference to nucleotide numbering of SEQ ID NO:87 and / or from about nucleotide 641 to about nucleotide 703 with reference to nucleotide numbering of SEQ ID NO:

88.

113. The method of claim 111, wherein the region of the endogenous UB2 gene associated with increased TBN is from about nucleotide 4834 to about nucleotide 4896 with reference to nucleotide numbering of SEQ ID NO:84 and / or from about nucleotide 721 to about nucleotide 783 with reference to nucleotide numbering of SEQ ID NO:85, and / or the region of the endogenous UB3 gene associated with increased TBN is from about nucleotide 5204 to about nucleotide 5266 with reference to nucleotide numbering of SEQ ID NO:87 and / or from about nucleotide 751 to about nucleotide 813 with reference to nucleotide numbering of SEQ ID NO:

88.

114. The method of any one of claims 88 to 95, wherein the mutation is in the 5' untranslated region (UTR) and / or 3' UTR of the endogenous SPL9 gene, endogenous UB2 gene or endogenous UB3 gene.

115. The method of claim 114, wherein the endogenous SPL9 gene is: (a) an endogenous SPL9a gene and the mutation is in the 5'UTR in a region from about nucleotide 1826 to about nucleotide 1981 and / or from about nucleotide 1846 to about nucleotide 1961 with reference to the nucleotide numbering of SEQ ID NO: 72, optionally in a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-160; (b) an endogenous SPL9b gene and the mutation is in the 5'UTR in a region from about nucleotide 1804 to about nucleotide 1973 and / or from about nucleotide 1824 to about nucleotide 1953, with reference to the nucleotide numbering of SEQ ID NO: 75, optionally in a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 185-200; (c) an endogenous SPL9c gene and the mutation is in the region of the 5'UTR from about nucleotide 1593 to about nucleotide 1783 and / or from about nucleotide 1613 to about nucleotide 1764, with reference to the nucleotide numbering of SEQ ID NO: 78, optionally in a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 225-239; and / or (d) an endogenous SPL9d gene and the mutation is in the 5'UTR from about nucleotide 1555 to about nucleotide 1740 and / or from about nucleotide 1574 to about nucleotide 1720 with reference to the nucleotide numbering of SEQ ID NO: 81, optionally in a region having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs: 258-273.

116. The method of claim 115, wherein the mutation is (a) the 5'UTR of the endogenous UB2 gene is located in a region from about nucleotide 1414 to about nucleotide 1860, from about nucleotide 1414 to about nucleotide 1522, from about nucleotide 1454 to about nucleotide 1481, from about nucleotide 1553 to about nucleotide 1582, from about nucleotide 1597 to about nucleotide 1633, and / or from about nucleotide 1767 to about nucleotide 1819, with reference to the nucleotide numbering of SEQ ID NO:84, optionally in a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs:90-96 or 332-357; and / or (b) the 5'UTR of the endogenous UB3 gene is located in a region from about nucleotide 1327 to about nucleotide 1646, from about nucleotide 1439 to about nucleotide 1467, from about nucleotide 1368 to about nucleotide 1394, from about nucleotide 1549 to about nucleotide 1606, from about nucleotide 1787 to about nucleotide 1855 and / or from about nucleotide 1747 to about nucleotide 1920 with reference to the nucleotide numbering of SEQ ID NO:87, optionally in a region having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs:394-407.

117. The method of claim 115, wherein the mutation is in: (a) the 3' untranslated region (UTR) of the endogenous UB2 gene is located in the region from about nucleotide 5701 to about nucleotide 5882 and / or from about nucleotide 5742 to about nucleotide 5842 with reference to the nucleotide numbering of SEQ ID NO: 84, optionally in a region having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs: 377-393; and / or (b) in the 3'UTR of the endogenous UB3 gene, the nucleotide numbering with reference to SEQ ID NO:87 is located in the region from about nucleotide 5940 to about nucleotide 6109, from about nucleotide 5980 to about nucleotide 6069, from about nucleotide 6516 to about nucleotide 6643, and / or from about nucleotide 6556 to about nucleotide 6603, optionally in a region having at least 80% sequence identity with the nucleotide sequence of any one of SEQ ID NOs:427-445.

118. The method of any one of claims 88 to 95, wherein the mutation is in an intron of the endogenous UB2 gene or the endogenous UB3 gene.

119. The method of claim 118, wherein the mutation is in: (a) the intron of the endogenous UB2 gene is located in a region from about nucleotide 2856 to about nucleotide 2971, from about nucleotide 2896 to about nucleotide 2931, from about nucleotide 3753 to about nucleotide 3893, and / or from about nucleotide 3793 to about nucleotide 3853, as referenced to the nucleotide numbering of SEQ ID NO:84; and / or (b) the intron of the endogenous UB3 gene is located in the region of about nucleotide 2666 to about nucleotide 2784, about nucleotide 2706 to about nucleotide 2744, about nucleotide 4017 to about nucleotide 4147, and / or about nucleotide 4057 to about nucleotide 4107 with reference to the nucleotide numbering of SEQ ID NO:

87.

120. The method of any one of claims 88 to 119, wherein the nuclease is a zinc finger nuclease, a transcription activator-like effector nuclease (TALEN), an endonuclease (e.g., Fok1), or a CRISPR-Cas effector protein.

121. The method of any one of claims 88 to 120, wherein the mutation is a dominant negative mutation, a semi-dominant mutation, a hyperallelic mutation, a superallelic mutation, a hypomorphic mutation, a weak loss-of-function mutation, or a null allele.

122. The method of any one of claims 80 to 121, wherein the mutation is a non-natural mutation.

123. The method of any one of claims 88 to 122, wherein the endogenous IPA1 gene is a SPL9 gene and the mutation produces a mutant SPL9 gene having at least 90% identity to any one of the nucleotide sequences of SEQ ID NOs: 289-300, wherein the IPA1 gene is a UB2 gene and the at least one mutation produces a mutant UB2 gene having at least 90% identity to any one of the nucleotide sequences of SEQ ID NOs: 320, 322 or 324, or is a UB3 gene and the at least one mutation produces a mutant UB2 gene having at least 90% identity to any one of the nucleotide sequences of SEQ ID NOs: 310, 312, 314, 316 or 318.

124. The method of any one of claims 88 to 123, wherein the IPA1 gene is a UB2 gene and the at least one mutation produces a mutant UB2 gene encoding a mutant polypeptide having at least 90% identity to any one of SEQ ID NOs: 321, 323 or 325, or is a UB3 gene and the at least one mutation produces a mutant UB2 gene encoding a mutant polypeptide having at least 90% identity to any one of SEQ ID NOs: 311, 313, 315, 317 or 319.

125. The method of any one of claims 88 to 124, wherein the mutation results in a plant with altered plant architecture, improved yield traits and / or increased tolerance / resistance to abiotic and biotic stresses compared to a plant or plant part not comprising the same mutation.

126. The method of claim 125, wherein the improved yield trait comprises one or more of the following phenotypes: increased number of kernel rows, increased kernel size, increased ear length, reduced number of tillers, reduced number of tassel branches, reduced time to flowering, increased number of seeds per plant, increased number of pods per node and / or per plant, and / or increased seed weight.

127. The method of any one of claims 88 to 126, wherein the plant is a monocot or a dicot.

128. The method of any one of claims 88 to 127, wherein the plant is corn, soybean, canola, wheat, rice, cotton, sugarcane, sugar beet, barley, oats, alfalfa, sunflower, safflower, oil palm, sesame, coconut, tobacco, potato, sweet potato, cassava, coffee, apple, plum, apricot, peach, cherry, pear, fig, banana, citrus, cocoa, avocado, olive, almond, walnut, strawberry, watermelon, pepper, grape, tomato, cucumber, or Brassica species.

129. The method of any one of claims 88 to 128, wherein the plant is corn or soybean.

130. A guide nucleic acid that binds to a target site in an endogenous IPA1 gene, wherein the endogenous IPA1 gene: (a) is the endogenous SQUAMOSA promoter binding protein-like 9 (SPL9) gene, which (i) comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO: 72, 75, 78, 81, 143, 182, 222 or 255; (ii) comprising a coding sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO: 73, 76, 79, 82, 144, 183, 223 or 256; (iii) comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288, and / or (iv) encoding a polypeptide sequence that is at least 80% identical to the amino acid sequence of any one of SEQ ID NO: 74, 77, 80, 83, 145, 184, 224 or 257; (b) is the endogenous unbranched 2 (UB2) gene, which (i) comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 84; (ii) comprising a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 85; (iii) comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 90-96 or 332-393, and / or (iv) encodes a polypeptide sequence that is at least 80% identical to the amino acid sequence of SEQ ID NO:86; or (c) is the endogenous unbranched 3 (UB3) gene, which: (i) comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 87; (ii) comprising a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 88; (iii) comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 90, 97-103 or 394-445, and / or (iv) encodes a polypeptide sequence that is at least 80% identical to the amino acid sequence of SEQ ID NO:

89.

131. The guide nucleic acid of claim 130, wherein the target site is in a region of the SPL9 gene that has at least about 80% sequence identity to any one of the nucleotide sequences of SEQ ID NOs: 146-181, 185-221, 225-254, or 258-288.

132. The guide nucleic acid of claim 130 or claim 131, wherein the guide nucleic acid comprises a spacer sequence having a nucleotide sequence of any one of SEQ ID NOs: 104-142, 301, 326 or 327.

133. A system comprising the guide nucleic acid of any one of claims 130 to 132 and a CRISPR-Cas effector protein associated with the guide nucleic acid.

134. The system of claim 133, further comprising a tracr nucleic acid associated with the guide nucleic acid and a CRISPR-Cas effector protein, optionally wherein the tracr nucleic acid and the guide nucleic acid are covalently linked.

135. A gene editing system comprising a CRISPR-Cas effector protein associated with a guide nucleic acid, wherein the guide nucleic acid comprises a spacer sequence that binds to an IPA1 gene.

136. The gene editing system of claim 135, wherein the IPA1 gene: (a) is the endogenous SQUAMOSA promoter binding protein-like 9 (SPL9) gene, which ((i) comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO:72, 75, 78, 81, 143, 182, 222 or 255; (ii) comprising a coding sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO: 73, 76, 79, 82, 144, 183, 223 or 256; (iii) comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288, and / or (iv) encoding a polypeptide sequence that is at least 80% identical to the amino acid sequence of any one of SEQ ID NO: 74, 77, 80, 83, 145, 184, 224 or 257; (b) is the endogenous unbranched 2 (UB2) gene, which (i) comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 84; (ii) comprising a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 85; (iii) comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 90-96 or 332-393, and / or (iv) encodes a polypeptide sequence that is at least 80% identical to the amino acid sequence of SEQ ID NO:86; or (c) is the endogenous unbranched 3 (UB3) gene, which: (i) comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 87; (ii) comprising a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 88; (iii) comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 90, 97-103 or 394-445, and / or (iv) encodes a polypeptide sequence that is at least 80% identical to the amino acid sequence of SEQ ID NO:

89.

137. The gene editing system of claim 135 or claim 136, wherein the guide nucleic acid comprises a spacer sequence having a nucleotide sequence of any one of SEQ ID NOs: 104-142, 301, 326 or 327.

138. The gene editing system of any one of claims 135 to 137, further comprising a tracr nucleic acid associated with the guide nucleic acid and the CRISPR-Cas effector protein, optionally wherein the tracr nucleic acid and the guide nucleic acid are covalently linked.

139. A complex comprising a CRISPR-Cas effector protein containing a cleavage domain and a guide nucleic acid, wherein the guide nucleic acid binds to a target site in an IPA1 gene, wherein the IPA1 gene (a) is the endogenous SQUAMOSA promoter binding protein-like 9 (SPL9) gene, which (i) comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO: 72, 75, 78, 81, 143, 182, 222 or 255; (ii) comprising a coding sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO: 73, 76, 79, 82, 144, 183, 223 or 256; (iii) comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254 or 258-288, and / or (iv) encoding a polypeptide sequence that is at least 80% identical to the amino acid sequence of any one of SEQ ID NO: 74, 77, 80, 83, 145, 184, 224 or 257; (b) is the endogenous unbranched 2 (UB2) gene, which (i) comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 84; (ii) comprising a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 85; (iii) comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 90-96 or 332-393, and / or (iv) encodes a polypeptide sequence that is at least 80% identical to the amino acid sequence of SEQ ID NO:86; or (c) is the endogenous unbranched 3 (UB3) gene, which: (i) comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 87; (ii) comprising a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 88; (iii) comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 90, 97-103 or 394-445, and / or (iv) encoding a polypeptide sequence having at least 80% identity to the amino acid sequence of SEQ ID NO: 89, wherein the cleavage domain cleaves the target strand in the IPA1 gene.

140. An expression cassette comprising (a) a polynucleotide encoding a CRISPR-Cas effector protein comprising a cleavage domain, and (b) a guide nucleic acid that binds to a target site in an IPA1 gene, wherein the guide nucleic acid comprises a spacer sequence that is complementary to and binds to the target site in the IPA1 gene, wherein the IPA1 gene: (a) is the endogenous SQUAMOSA promoter binding protein-like 9 (SPL9) gene, which (i) comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO: 72, 75, 78, 81, 143, 182, 222 or 255; (ii) comprising a coding sequence having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NO: 73, 76, 79, 82, 144, 183, 223 or 256; (iii) comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288, and / or (iv) encoding a polypeptide sequence that is at least 80% identical to the amino acid sequence of any one of SEQ ID NO: 74, 77, 80, 83, 145, 184, 224 or 257; (b) is the endogenous unbranched 2 (UB2) gene, which (i) comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 84; (ii) comprising a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 85; (iii) comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 90-96 or 332-393, and / or (iv) encodes a polypeptide sequence that is at least 80% identical to the amino acid sequence of SEQ ID NO:86; or (c) is the endogenous unbranched 3 (UB3) gene, which: (i) comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 87; (ii) comprising a coding sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO: 88; (iii) comprising a region having at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 90, 97-103 or 394-445, and / or (iv) encodes a polypeptide sequence that is at least 80% identical to the amino acid sequence of SEQ ID NO:

89.

141. The complex of claim 139 or the expression cassette of claim 140, wherein the target site: (a) in a region of the endogenous SPL9 gene that has at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 146-181, 185-221, 225-254 and / or 258-288, and / or (b) is in a region of the endogenous UB2 gene that has at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 90-96 or 332-393; or (c) is in a region of the endogenous UB3 gene that has at least 80% sequence identity to the nucleotide sequence of any one of SEQ ID NOs: 90, 97-103, or 394-445.

142. A mutant nucleic acid encoding a SPL9 polypeptide, the mutant nucleic acid comprising a sequence having at least 90% sequence identity to any one of SEQ ID NOs: 289-300.

143. A mutant nucleic acid encoding a UB2 polypeptide, said mutant nucleic acid comprising a sequence having at least 90% sequence identity to any one of SEQ ID NOs: 320, 322 or 324.

144. A mutant nucleic acid encoding a UB3 polypeptide, said mutant nucleic acid comprising a sequence having at least 90% sequence identity to any one of SEQ ID NOs: 310, 312, 314, 316 or 318.

145. A soybean plant or part thereof comprising the mutant nucleic acid of claims 142 to 144.

146. A soybean plant or plant part thereof, comprising at least one mutation in at least one endogenous SLP9 gene with gene identification number (Gene ID) Glyma_02G177500 (SPL9a), Glyma_09G113800 (SPL9b), Glyma_03g143100 (SPL9c) and / or Glyma_19g146000 (SPL9d), optionally wherein the mutation is a non-natural mutation.

147. The soybean plant of claim 145 or claim 146, wherein the soybean plant exhibits a phenotype of one or more of altered plant architecture, improved yield traits, and / or increased tolerance / resistance to abiotic and biotic stresses compared to a plant or plant part not comprising the same mutation.

148. A guide nucleic acid that binds to a target nucleic acid in a SPL9 gene with a gene identification number (gene ID) of Glyma_02G177500 (SPL9a), Glyma_09G113800 (SPL9b), Glyma_03g143100 (SPL9c) and / or Glyma_19g146000 (SPL9d).

149. A mutated endogenous SPL9 gene in a plant cell, wherein the mutated endogenous SPL9 gene comprises a nucleic acid sequence at least 90% identical to any one of SEQ ID NOs: 289-300.

150. A mutated endogenous Unbranched 2 (UB2) gene in a plant cell, wherein the mutated endogenous UB2 gene comprises a nucleic acid sequence at least 90% identical to any one of SEQ ID NOs: 320, 322 or 324, and / or a mutated endogenous Unbranched 3 (UB3) gene in a plant cell, wherein the mutated endogenous UB3 gene comprises a nucleic acid sequence at least 90% identical to any one of SEQ ID NOs: 310, 312, 314, 316 or 318.

151. A mutant Unbranched 2 (UB2) polypeptide in a plant cell, the mutant UB2 polypeptide having at least 90% identity to any one of SEQ ID NOs: 321, 323 or 325, and / or a mutant endogenous Unbranched 3 (UB3) polypeptide in a plant cell, the mutant UB3 polypeptide having at least 90% identity to any one of SEQ ID NOs: 311, 313, 315, 317 or 319.

152. A method of producing a plant comprising a mutation in an endogenous IPA1 gene and at least one polynucleotide of interest, the method comprising: hybridizing a first plant that is a plant of any one of claims 1 to 46, 52, 53, 68, 69 or 145 to 148 with a second plant comprising the at least one polynucleotide of interest to produce progeny plants; and Progeny plants are selected that comprise the mutation in the IPA1 gene and the at least one polynucleotide of interest, thereby producing the plant comprising the mutation in the endogenous IPA1 gene and the at least one polynucleotide of interest.

153. A method of producing a plant comprising a mutation in an endogenous IPA1 gene and at least one polynucleotide of interest, the method comprising: Introducing at least one polynucleotide of interest into a plant as described in any one of claims 1 to 46, 52, 53, 68, 69 or 145 to 148, thereby producing a plant comprising a mutation in the IPA1 gene and at least one polynucleotide of interest.

154. A method of producing a plant comprising a mutation in an endogenous IPA1 gene and exhibiting an improved root architecture phenotype (optionally exhibiting improved yield traits, increased root biomass, steeper root angles and / or longer roots), the method comprising crossing a first plant that is a plant of any one of claims 1 to 46, 52, 53, 68, 69, or 145 to 148 with a second plant that exhibits an improved root architecture phenotype; and Progeny plants comprising said mutation in said IPA1 gene and comprising a phenotype of improved root architecture are selected, thereby producing said plants comprising a mutation in the endogenous IPA1 gene and exhibiting a phenotype of improved root architecture as compared to control plants.

155. A method for controlling weeds in a container (e.g., a pot or seed tray, etc.), a growth chamber, a greenhouse, a field, a recreational area, a lawn or a roadside, the method comprising applying a herbicide to one or more (plural) plants as described in any one of claims 1 to 46, 52, 53, 68, 69 or 145 to 148 growing in the container, growth chamber, greenhouse, field, recreational area, lawn or roadside, thereby controlling the weeds in the container, growth chamber, greenhouse, field, recreational area, lawn or roadside where the one or more plants grow.

156. A method of reducing insect predation on a plant, the method comprising applying an insecticide to one or more plants of any one of claims 1 to 46, 52, 53, 68, 69 or 145 to 148, thereby reducing insect predation on the one or more plants.

157. A method of reducing fungal diseases on plants, the method comprising applying a fungicide to one or more plants of any one of claims 1 to 46, 52, 53, 68, 69 or 145 to 148, thereby reducing fungal diseases on the one or more plants.

158. The method of claim 156 or claim 157, wherein the one or more plants are grown in a container, a growth chamber, a greenhouse, a field, a recreational area, a lawn, or a roadside.

159. The method of any one of claims 152 to 158, wherein the polynucleotide of interest is a polynucleotide that confers herbicide tolerance, insect resistance, disease resistance, increased yield, increased nutrient use efficiency, or abiotic stress resistance.

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