Promoter edited soybean plants

Abstract

The disclosure relates to novel soybean plants, plant cells, plant parts, and nucleotide sequences in soybean plants comprising (i) a mutated endogenous AIP10a gene promoter and / or AIP10a gene 5' untranslated region (5' UTR), and / or (ii) a mutated endogenous AIP10b gene promoter and / or AIP10b gene 5' UTR, along with methods of using and making the same.

Description

MVS Docket No. P14649WO00 TITLE: PROMOTER EDITED SOYBEAN PLANTS CROSS-REFERENCE TO RELATED APPLICATIONSS

[0001] This international patent application claims the benefit of U.S. provisional patent application serial no.63 / 662,895, filed June 21, 2024. SEQUENCE LISTING XML

[0002] The instant application contains a sequence listing, which has been submitted in XML file format by electronic submission and is hereby incorporated by reference in its entirety. The XML file, created on May 24, 2024, is named P14649US00.xml and is 44,300 bytes in size. TECHNICAL FIELD

[0003] Disclosed herein are novel plants, plant parts, and nucleotide sequences in soybean varieties comprising a targeted modification to a AIP10a gene promoter and / or a AIP10b gene promoter, along with methods of making the same by growing a soybean plant or lot, and methods of using the same. BACKGROUND

[0004] Agriculture is an essential industry for the global economy and the United States in particular. Soybean (Glycine max) is an important legume crop worldwide due to its ability to fix atmospheric nitrogen. Soybeans serve as a major source of animal feed protein and soybean oil has uses in a wide variety of industries, including the food and beverage, biodiesel, and other industries.

[0005] Soybean sustainability is a priority for farmers worldwide. Farming practices such as water and nutrient management help farmers improve efficiencies, boost crop productivity, conserve water, enrich soil quality, improve nutrient efficiencies of the soil, and produce sustainable soybean crops. The benefits of bioengineering for soybean farmers include increased yields and extreme weather hardiness. SUMMARY

[0006] Disclosed herein are modified soybean plants comprising at least one targeted modification in (i) an endogenous AIP10a gene promoter and / or AIP10a gene 5’ untranslatedMVS Docket No. P14649WO00 region (5’ UTR), and / or (ii) an endogenous AIP10b gene promoter and / or AIP10b gene 5’ UTR resulting in decreased expression of an endogenous AIP10a and / or AIP10b gene relative to a reference soybean plant lacking the modification.

[0007] Disclosed herein are soybean plants, soybean plant parts, and soybean plant cells comprising at least one targeted modification in (i) an endogenous AIP10a gene promoter and / or AIP10a gene 5’ untranslated region (5’ UTR), and / or (ii) an endogenous AIP10b gene promoter and / or AIP10b gene 5’ UTR resulting in decreased expression of an endogenous AIP10a and / or AIP10b gene relative to a reference soybean plant lacking the modification. In some embodiments, the targeted modification in the AIP10a and / or AIP10b gene promoter comprises a deletion of one or more nucleotides. In some embodiments, the decrease of expression in the AIP10a and / or AIP10b gene results in an increase in yield of at least one of a soybean plant seed number, pod number, hundred-seed weight, leaf area, shoot biomass, and / or root biomass relative to the reference plant lacking the modification. In some embodiments, the decrease of expression in the AIP10a and / or AIP10b gene is about 2-fold to about 46-fold relative to unmodified gene. In some embodiments, the targeted modification in the AIP10a and / or AIP10b gene promoter results in elimination of expression of the AIP10a gene and / or the AIP10b gene. In some embodiments, the endogenous AIP10a gene promoter comprises the DNA molecule set forth in SEQ ID NO: 1 or an allelic variant thereof and the endogenous AIP10b gene promoter comprises the DNA molecule set forth in SEQ ID NO: 2 or an allelic variant thereof. In some embodiments, the target modification(s) located within the AIP10a promoter of SEQ ID NO: 1, or in an allelic variant thereof, comprises, consists essentially of, or consists of a deletion corresponding to at least: (a) a deletion of nucleotides 1685-1981 of SEQ ID NO: 1; (b) a deletion of nucleotides 1680-1721 of SEQ ID NO: 1; (c) a deletion of nucleotides 1684 – 1704 of SEQ ID NO: 1; or (d) a deletion of nucleotides 1679 – 1693 of SEQ ID NO: 1. In some embodiments, the target modification(s) located within the AIP10a promoter of SEQ ID NO: 1, or in an allelic variant thereof, comprises, consists essentially of, or consists of a deletion of at least a portion of (a) nucleotides 1685-1981 of SEQ ID NO: 1; (b) nucleotides 1680-1721 of SEQ ID NO: 1; (c) nucleotides 1684 – 1704 of SEQ ID NO: 1; or (d) nucleotides 1679 – 1693 of SEQ ID NO: 1. In some embodiments, the target modification(s) located within the AIP10a promoter of SEQ ID NO: 1, or in an allelic variant thereof, comprises, consists essentially of, or consists of a deletion of at least 2-19 nucleotides within (a) nucleotides 1685-1981 of SEQ ID NO: 1; (b) nucleotides 1680-1721 of SEQ ID NO: 1; (c) nucleotides 1684 – 1704 of SEQ ID NO: 1; or (d) nucleotides 1679 – 1693 of SEQ IDMVS Docket No. P14649WO00 NO: 1. In some embodiments, the target modification(s) located within the AIP10b promoter of SEQ ID NO: 2, or in an allelic variant thereof, comprises, consists essentially of, or consists of a deletion corresponding to at least: (a) a deletion of nucleotides 1499-1605 of SEQ ID NO: 2; or (b) a deletion of nucleotides 1501-1562 of SEQ ID NO: 2. In some embodiments, the target modification(s) located within the AIP10b promoter of SEQ ID NO: 2, or in an allelic variant thereof, comprises, consists essentially of, or consists of a deletion of at least a portion of (a) nucleotides 1499-1605 of SEQ ID NO: 2; or (b) nucleotides 1501-1562 of SEQ ID NO: 2. In some embodiments, the target modification(s) located within the AIP10b promoter of SEQ ID NO: 2, or in an allelic variant thereof, comprises, consists essentially of, or consists of a deletion of at least 2-19 nucleotides within (a) nucleotides 1499-1605 of SEQ ID NO: 2; or (b) nucleotides 1501-1562 of SEQ ID NO: 2. In some embodiments, reducing expression of the AIP10a and / or AIP10b gene is associated with a trait comprising an increase in plant biomass, pod number, seed weight, leaf area, stem biomass, shoot biomass, root biomass, and / or fruit production relative to a plant lacking the target modification.

[0008] In some embodiments, the soybean plant cell is not exclusively produced by an essentially natural biological method. In some embodiments, the soybean plant cell is homozygous for the at least one targeted modification(s) in the endogenous AIP10a and / or AIP10b gene promoter. Also provided are tissue cultures of regenerable cells comprising the aforementioned soybean plant cells. Also provided are soybean plant parts comprising the aforementioned soybean plant cell, including stems, roots, leaves, flowers, pods, and seeds. Also provided are soybean plants comprising the aforementioned soybean plant cells. In some embodiments, soybean seeds comprise an elite soybean germplasm, a soybean cultivar, a soybean variety, and / or are homozygous for the targeted modification(s). Also provided are soybean seed lots comprising the seed.

[0009] Also provided are biological samples comprising a nucleic acid, such as a DNA molecule, containing the aforementioned targeted modification(s) in the endogenous AIP10a and / or AIP10b gene promoter. Polynucleotides comprising, consisting essentially of, or consisting of the AIP10a promoter deletion in SEQ ID NO: 19, 20, or 21 are provided. Polynucleotides comprising, consisting essentially of, or consisting of the AIP10b promoter deletion in SEQ ID NO: 22, 23, or 24 are provided. In some embodiments, the aforementioned polynucleotides are isolated.

[0010] Also disclosed are soybean plants, soybean plant parts, and soybean plant cells comprising the aforementioned targeted modification(s) in the endogenous AIP10a and / orMVS Docket No. P14649WO00 AIP10b gene promoter that further comprise at least one mutation in the soybean FT1a gene, Ric1 gene, Ric2 gene, NF-YC4 gene, JAG1 gene, BS1 gene, BS2 gene, and / or TFL1b gene.

[0011] Also disclosed are soybean plants, soybean plant parts, and soybean plant cells comprising the aforementioned targeted modification(s) in the endogenous AIP10a and / or AIP10b gene promoter that further comprise one or more transgenes, optionally wherein said transgenes encode proteins or RNAs conferring herbicide tolerance or pest tolerance.

[0012] Also disclosed are soybean plants, soybean plant parts, and soybean plant cells comprising the aforementioned targeted modification(s) in the endogenous AIP10a and / or AIP10b gene promoter that further comprise an A2704-12, A5547-127, BPS-CV127-9, DAS44406-6, DAS68416-4, DAS81419-2, DP305423, GTS 40- 3-2, HOS, A5547-127, MON87701, MON87705, MON87708, MON87769, MON89788, MON98788, MST-FG072- 3, or SYHT0H210 transgenic event or modification thereof.

[0013] Also disclosed are methods of producing soybean seeds comprising the aforementioned targeted modification(s) in the endogenous AIP10a and / or AIP10b gene promoter that optionally further comprise the aforementioned transgenes, transgenic events, and / or mutations. Methods of producing soybean seeds can comprise crossing a modified soybean plant comprising the aforementioned targeted modification(s) in the endogenous AIP10a and / or AIP10b gene promoter that optionally further comprise the aforementioned transgenes, transgenic events, and / or mutations with a second soybean plant to produce soybean seed and optionally harvesting the seed. In some embodiments, the modified soybean plant can self- pollinate to produce plant seed.

[0014] Also disclosed are methods for producing a seed lot comprising: (i) growing a population of soybean plants comprising the aforementioned modified soybean plant; and (ii) harvesting seed from the population of soybean plants of step (i) at maturity. Methods of producing a soybean crop comprising planting the aforementioned seed lot are provided.

[0015] Also disclosed are methods for producing a soybean by-product comprising at least one processing step of cleaning, cracking, flaking, crushing, macerating, pressing, extracting, expelling, and / or extruding the aforementioned seed lot. In some embodiments, the by-product is soybean protein and wherein the soybean seed lot is subjected to processing steps comprising: (i) at least one of a cracking, flaking, crushing, pressing, and / or macerating step; (ii) extracting the cracked, flaked, crushed, pressed, and / or macerated soybean seed product from step (i) with an organic solvent to produce defatted soymeal; and (iii) extracting the defatted soymeal from step (ii) with an aqueous solvent to produce an aqueous fractionMVS Docket No. P14649WO00 comprising soybean protein. In some embodiments, the by-product is soybean oil and wherein the soybean seed lot is subjected to processing steps comprising: (i) at least one of a cracking, flaking, crushing, pressing, and / or macerating step; and (ii) solvent extracting, expelling, and / or extruding step the cracked, flaked, crushed, pressed, and / or macerated soybean seed product from step (i) to produce the oil.

[0016] Also disclosed are methods for producing a commodity soybean plant product, the method comprising processing a modified soybean seed obtained from the aforementioned modified soybean plant and recovering the commodity plant product from the processed plant or seed. In some embodiments, the commodity plant product is seed meal, starch, silage, oil, or protein. In some embodiments, the commodity plant product comprises a detectable amount of a DNA molecule comprising the modified endogenous AIP10a gene promoter and the endogenous AIP10b gene promoter.

[0017] Also disclosed are methods for producing soybean plant material, the method comprising: (a) providing the aforementioned modified soybean plant; and, (b) growing the modified soybean plant under conditions that allow for expression of the endogenous soybean AIP10a gene and / or AIP10b gene at levels that are reduced compared to expression levels of the endogenous AIP10a gene and / or AIP10b gene in a reference soybean plant which lacks the modifications. In some embodiments, the modified soybean plant further comprises at least one of sowing a soybean seed which germinates and forms the soybean plant, irrigating the soybean seed or plant, and / or treating the soybean plant or the soybean seed with a biological agent, herbicide, insecticide, or fungicide. In some embodiments, the soybean plant material comprises a seed, optionally wherein the method further comprises harvesting the seed from the plant.

[0018] Guide RNA molecules comprising a spacer RNA molecule which targets an AIP10a gene promoter of SEQ ID NO: 1 or an allelic variant thereof, optionally wherein the spacer RNA molecule comprises the RNA encoded by SEQ ID NO: 3, 4, or 5 are provided. Guide RNA molecules comprising a spacer RNA molecule which targets an AIP10b gene promoter of SEQ ID NO: 2 or an allelic variant thereof, optionally wherein the spacer RNA molecule comprises the RNA encoded by SEQ ID NO: 6, 7, or 8 are provided. Guide RNA molecules comprising a comprising a Cas12 direct repeat element which is operably linked to the aforementioned RNA spacer molecules are also provided. Gene editing systems comprising a CRISPR-Cas effector protein in association with a guide nucleic acid, wherein the guide nucleic acid comprises a spacer sequence that binds to the endogenous AIP10a gene promoterMVS Docket No. P14649WO00 of SEQ ID NO: 1 or allelic variant thereof; or a CRISPR-Cas effector protein in association with a guide nucleic acid, wherein the guide nucleic acid comprises a spacer sequence that binds to an endogenous AIP10b gene promoter of SEQ ID NO: 2 or allelic variant thereof are provided. Expression cassettes comprising a polynucleotide encoding CRISPR-Cas effector protein comprising a cleavage domain and a guide RNA molecule of the disclosure are also provided.

[0019] Also disclosed are methods for generating a soybean plant, soybean plant part, and / or soybean plant cell comprising the aforementioned targeted modification(s) wherein the at least one targeted modification is introduced by: (i) directing both: (a) a guide RNA (gRNA) molecule which targets the endogenous AIP10a gene promoter of SEQ ID NO: 1 or an allelic variant thereof and / or the endogenous AIP10b gene promoter of SEQ ID NO: 2 or an allelic variant thereof, and (b) an RNA dependent endonuclease (RDE) which recognizes the gRNA molecule, to the genome of a target soybean plant cell; and (ii) isolating a soybean plant cell, soybean plant part, or soybean plant comprising the at least one targeted modification in the endogenous soybean AIP10a gene promoter of SEQ ID NO: 1 or an allelic variant thereof and / or the endogenous AIP10b gene promoter of SEQ ID NO: 2 or an allelic variant thereof. In some embodiments, the endogenous AIP10a gene promoter is targeted and the gRNA comprises a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 3, 4, or 5. In some embodiments, the endogenous AIP10b gene promoter is targeted and the gRNA comprises a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 6, 7, or 8.

[0020] Methods for identifying soybean plant cells, plant parts, or plants that comprise the aforementioned targeted modification(s) in the endogenous AIP10a gene promoter of SEQ ID NO: 1 or an allelic variant thereof and / or the endogenous AIP10b gene promoter of SEQ ID NO: 2 or an allelic variant thereof are provided. In certain embodiments, the methods comprise analyzing a polynucleotide comprising a portion of SEQ ID NO: 1 or an allelic variant thereof and / or at least a portion of SEQ ID NO: 2 or an allelic variant thereof or analyzing an RNA encoded by a portion of SEQ ID NO: 1 or an allelic variant thereof and / or at least a portion of SEQ ID NO: 2 or an allelic variant thereof from the plant cell, plant part, or plant, wherein an insertion, deletion, and / or substitution of one or more nucleotides in said polynucleotide or RNA is indicative of the presence of the aforementioned targeted modification(s). In certain embodiments, the methods comprise analyzing a polypeptide encoded by SEQ ID NO: 1 and / or SEQ ID NO: 2, a portion thereof, or an allelic variant thereof from the soybean plant cell, plant part, or plant, wherein an insertion, deletion, and / or substitution of one or more amino acidMVS Docket No. P14649WO00 residues of the polypeptide or a change in the biologic or biochemical activity of the polypeptide is indicative of the presence of the at least one targeted modification(s).

[0021] Uses of the aforementioned soybean plant cells, soybean plant parts, soybean seed lots, and soybean plants to produce soybean seed or to grow a soybean crop are provided are provided. Uses of the aforementioned soybean plant cells, soybean plant parts, soybean seed lots, and soybean plants to obtain a soybean by-product are also provided.

[0022] Uses of the aforementioned guide RNA molecules, gene editing systems, and expression cassettes to introduce at least one targeted modification(s) in the endogenous soybean endogenous AIP10a gene promoter or an allelic variant thereof are provided. DESCRIPTION OF THE DRAWINGS

[0023] Fig. 1 shows the wild-type AIP10a gene promoter (SEQ ID NO: 1) upstream and including the ATG transcriptional start site of the AIP10a gene (Glyma.07G021400) of SEQ ID NO:15. The guide RNA target sites are indicated by arrow lines under the sequence and SEQ ID NOs are shown. Example deletions are indicated below the sequence and SEQ ID NOs are shown. The 5’-UTR is indicated.

[0024] Fig.2 shows the wild-type AIP10b gene promoter (SEQ ID NO: 2) upstream and including the ATG transcriptional start site of the AIP10b gene (Glyma.08G220400) of SEQ ID NO:17. The guide RNA target sites are indicated by arrow lines under the sequence and SEQ ID NOs are shown. Example deletions are indicated below the sequence and SEQ ID NOs are shown. The 5’-UTR is indicated.

[0025] Fig. 3 shows the wild-type AIP10a genomic sequence (SEQ ID NO:15). The ATG transcriptional start site, 5’-UTR, and 3’-UTR are indicated.

[0026] Fig.4: shows the wild-type AIP10a amino acid sequence (SEQ ID NO:16).

[0027] Fig. 5: shows the wild-type AIP10b genomic sequence (SEQ ID NO:17). The ATG transcriptional start site, 5’-UTR, and 3’-UTR are indicated.

[0028] Fig.6 shows the wild-type AIP10b amino acid sequence (SEQ ID NO:18).

[0029] Various embodiments of the present disclosure will be described in detail with reference to the drawings, wherein like reference numerals represent like parts throughout the several views. Reference to various embodiments does not limit the scope of the disclosure. Figures represented herein are not limitations to the various embodiments according to the disclosure and are presented for exemplary illustration of the invention. An artisan of ordinary skill in the art need not view, within isolated figure(s), the near infinite number of distinctMVS Docket No. P14649WO00 permutations of features described in the following detailed description to facilitate an understanding of the present invention. DETAILED DESCRIPTION Definitions

[0030] Unless otherwise stated, nucleic acid sequences in the text of this specification are given, when read from left to right, in the 5’ to 3’ direction. Nucleic acid sequences may be provided as DNA or as RNA, as specified; disclosure of one necessarily defines the other, as well as necessarily defines the exact complements, as is known to one of ordinary skill in the art. Where a term is provided in the singular, the inventors also contemplate aspects of the disclosure described by the plural of that term.

[0031] The phrase “allelic variant” as used herein refers to a polynucleotide or polypeptide sequence variant that occurs in a particular gene at particular locus in a different strain, variety, or isolate of a given organism.

[0032] As used herein, the phrase “amorphic allele” refers to an allele of a gene having no gene activity in comparison to the wild-type allele of the gene. Amorphic alleles are also known as null alleles.

[0033] The term “and / or” where used herein is to be taken as specific disclosure of each of the two specified features or components with or without the other. Thus, the term “and / or” as used in a phrase such as “A and / or B” herein is intended to include “A and B,” “A or B,” “A” (alone), and “B” (alone). Likewise, the term “and / or” as used in a phrase such as “A, B, and / or C” is intended to encompass each of the following embodiments: A, B, and C; A, B, or C; A or C; A or B; B or C; A and C; A and B; B and C; A (alone); B (alone); and C (alone).

[0034] As used herein, the phrase “biological sample” refers to either intact or non-intact (e.g., milled soybean seed or soybean plant tissue, chopped soybean plant tissue, lyophilized tissue) soybean plant tissue. It may also be an extract comprising intact or non-intact seed or soybean plant tissue. The biological sample can comprise flour, meal, syrup, oil, starch, and cereals manufactured in whole or in part to contain soybean plant by-products. In certain embodiments, the biological sample is “non-regenerable” (i.e., incapable of being regenerated into a soybean plant or soybean plant part).

[0035] As used herein, the terms “correspond,” “corresponding,” and the like, when used in the context of an nucleotide position, mutation, and / or substitution in any given polynucleotide (e.g., an allelic variant of SEQ ID NO: 1) with respect to the reference polynucleotide sequenceMVS Docket No. P14649WO00 (e.g., SEQ ID NO: 1) all refer to the position of the nucleotide in the given sequence that has identity to the nucleotide in the reference nucleotide sequence when the given polynucleotide is aligned to the reference polynucleotide sequence using a pairwise alignment algorithm (e.g., CLUSTAL O 1.2.4 with default parameters).

[0036] As used herein, the terms “Cpf1” and “Cas12a” are used interchangeably to refer to the same RNA dependent DNA endonuclease (RdDe).

[0037] As used herein, a “cultivar” refers to a cultivated variety. A cultivar is generally developed using crossing, selfing, and / or selection and is maintained by any suitable method of propagation, through open pollination, selfing, or the like. Details of cultivar development can be found in “Principles of Cultivar Development” by Fehr, Macmillan Publishing Company (1993), which is incorporated herein by reference in its entirety.

[0038] As used herein, the phrases “elite soybean line” or “elite soybean plant” refer to any line or plant which has undergone breeding to provide one or more trait improvements (e.g., desirable agronomic performance (typically commercial production) or superior grain quality). In some cases, an elite line can be an agronomically or otherwise superior line or variety that has resulted from several or many cycles of breeding and selection for one or more trait improvements (e.g., superior agronomic performance or superior grain quality). Similarly, “elite germplasm” is a germplasm resulting from breeding and selection for desirable agronomic performance (typically commercial production). Such germplasm may be agronomically superior germplasm, derived from and / or capable of giving rise to a plant with superior agronomic performance, such as an existing or newly developed elite line of soybean. Elite crop plant lines include plants which are an essentially homozygous, e.g., inbred or doubled haploid. Elite crop plants can include inbred lines used as is or used as pollen donors or pollen recipients in breeding (e.g., used to produce F1 plants). Elite crop plants can include inbred lines which are selfed to produce non-hybrid cultivars or varieties. Elite crop plants can include hybrid F1 progeny of a cross between two distinct elite inbred or doubled haploid plant lines.

[0039] As used herein, the phrase “endogenous gene” refers to the native form of a gene unit in its natural location in the genome of an organism.

[0040] As used herein, the term “expression” refers to the production of a functional end- product (e.g., an mRNA, guide RNA, or a protein) in either precursor or mature form.

[0041] As used herein, the phrase “hypomorphic allele” refers to an allele of a gene with less gene activity than a wild-type allele but more gene activity than an amorphic allele.MVS Docket No. P14649WO00

[0042] As used herein, the terms “include,” “includes,” and “including” are to be construed as at least having the features to which they refer while not excluding any additional unspecified features.

[0043] As used herein, the term “isomorphic allele” refers to an allele of a gene having wild- type gene activity.

[0044] The term “isolated” as used herein means having been removed from its natural environment.

[0045] As used herein, the term “introduced” means providing a nucleic acid (e.g., expression construct) or protein into a cell. Introduced includes reference to the incorporation of a nucleic acid into a eukaryotic or prokaryotic cell where the nucleic acid may be incorporated into the genome of the cell and includes reference to the transient provision of a nucleic acid or protein to the cell. Introduced includes reference to stable or transient transformation methods. Thus, “introduced” in the context of inserting a nucleic acid fragment (e.g., a recombinant DNA construct / expression construct) into a cell, means “transfection” or “transformation” or “transduction” and includes reference to the incorporation of a nucleic acid fragment into a eukaryotic or prokaryotic cell where the nucleic acid fragment may be incorporated into the genome of the cell (e.g., nuclear chromosome, plasmid, plastid, chloroplast, or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (e.g., transfected mRNA).

[0046] As used herein, a “loss-of-function allele” can include an amorphic allele or a hypomorphic allele of a gene.

[0047] As used herein, “nitrogen deficient conditions” refers to less than optimal amounts of available and / or applied nitrogen.

[0048] As used herein, a “non-natural” or “non-naturally occurring” mutation refers to a mutation in a gene which is generated via human intervention or descended from the mutation generated via human intervention. Non-limiting examples of human intervention which can be used to generate a non-naturally occurring mutation include mutagenesis (e.g., chemical mutagenesis, ionizing radiation mutagenesis), mutagenesis followed by DNA sequence-based screening and selection (TILLING), and targeted genetic modifications (e.g., CRISPR-based methods, TALEN-based methods, zinc finger-based methods).

[0049] As used herein, the term “plant” includes a whole soybean plant and any descendant, cell, tissue, part, or parts of the plant. The term “plant” thus includes reference to an immature or mature whole soybean plant, including a plant from which seed or grain or anthers have beenMVS Docket No. P14649WO00 removed. Any seed or embryo that will produce the plant is also considered to be the soybean plant.

[0050] The term “plant part” include any part(s) of a plant, including, for example and without limitation: seed (including mature seed and immature seed); grain; stover; a plant cutting; a plant cell; a plant cell culture; or a plant organ (e.g., pollen, embryos, pods; flowers, fruits, shoots, leaves, roots, stems, and explants). A plant tissue or plant organ may be a seed, protoplast, callus, or any other group of plant cells that is organized into a structural or functional unit. A plant cell or tissue culture may be capable of regenerating a plant having the physiological and morphological characteristics of the plant from which the cell or tissue was obtained, and of regenerating a plant having substantially the same genotype as the plant. Regenerable cells in a plant cell or tissue culture may be embryos, protoplasts, meristematic cells, callus, pollen, leaves, anthers, roots, root tips, flowers, or stalks. In contrast, some plant cells are not capable of being regenerated to produce plants and are referred to herein as “non- regenerable” plant cells.

[0051] As used herein, the phrase “targeted modification” as it pertains to an AIP10a or AIP10b promoter and / or 5’ UTR refers to at least one insertion, deletion, and / or substitution of one or more nucleotides in: (i) an endogenous AIP10a gene promoter and / or in an AIP10a gene 5’ untranslated region (5’ UTR); or (ii) an endogenous AIP10b gene promoter and / or an AIP10b gene 5’ UTR. In certain embodiments, such targeted modification(s) can be in a polynucleotide located in a soybean cell, soybean plant, soybean plant part, and / or in a biological sample or commodity product obtained therefrom.

[0052] As used herein, the term “variety” refers a group of similar plants that by one or more structural features, genetic features, and / or performance can be distinguished from other varieties within the same species. In certain embodiments, the term variety refers to the botanical taxonomic designation whereby variety is ranked below species or subspecies, as well as the legal definition whereby the term “variety” refers to a commercial plant that is protected under the terms outlined in the International Convention for the Protection of New Varieties of Plants.

[0053] To the extent to which any of the preceding definitions is inconsistent with definitions provided in any patent or non-patent reference incorporated herein by reference, any patent or non-patent reference cited herein, or in any patent or non-patent reference found elsewhere, it is understood that the preceding definition will be used herein.MVS Docket No. P14649WO00

[0054] The present disclosure describes soybean plant cells, plant parts including seed, plants, seed lots, and biological samples comprising at least one targeted modification in (i) an endogenous AIP10a gene promoter and / or AIP10a gene 5’ untranslated region (5’ UTR), and / or (ii) an endogenous AIP10b gene promoter and / or AIP10b gene 5’ UTR. The targeted modification(s) can include any mutation that decreases expression of the endogenous AIP10a and / or AIP10b gene relative to a reference soybean plant lacking the targeted modification(s). For example, targeted modification can include deletions, insertions, and / or substitutions of nucleic acids. These soybean plants and plant parts can be utilized for human food, livestock feed, as a raw material in industry, or as breeding material for development of other soybean varieties. As described herein, a decrease in expression of the AIP10a gene and / or the AIP10b gene increases plant biomass and / or yield, increases growth of the soybean plant as a whole, increases seed yield, and increases drought tolerance.

[0055] The endogenous AIP10a gene promoter and 5’ UTR comprises the genomic DNA of SEQ ID NO: 1 and allelic variants thereof. The endogenous soybean AIP10a gene of SEQ ID NO: 15 is located at nucleotides 1,664,710 to 1,668,114 of chromosome 7 of the Glycine max Williams 82 genome assembly version 4 (Wm82.a4.v1; Glyma.07G021400 on the world wide web internet site “soybase.org”).

[0056] The endogenous AIP10b gene promoter and 5’ UTR comprises the genomic DNA of SEQ ID NO: 2 and allelic variants thereof. The endogenous soybean AIP10b gene of SEQ ID NO: 17 is located at nucleotides 17,985,027 to 17,988,197 of chromosome 8 of the Glycine max Williams 82 genome assembly version 4 (Wm82.a4.v1; Glyma.08G220400 on the world wide web internet site “soybase.org”).

[0057] Allelic variants of an endogenous soybean AIP10a gene promoter and an endogenous AIP10b gene promoter include variants which comprise genomic DNA having at least 95%, 96%, 97%, 98%, 99%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% sequence identity to SEQ ID NO: 1 or SEQ ID NO: 2, respectively. In certain embodiments, allelic variants of the endogenous soybean AIP10a and AIP10b gene promoters are isomorphic alleles of the endogenous soybean AIP10a and AIP10b gene promoters.

[0058] Soybean plant cells, plant parts, and plants comprising at least one targeted modification in (i) an endogenous AIP10a gene promoter and / or AIP10a gene 5’ untranslated region (5’ UTR), and / or (ii) an endogenous AIP10b gene promoter and / or AIP10b gene 5’ UTR are provided. The least one targeted modification results in decreased expression of an endogenous AIP10a and / or AIP10b gene relative to a reference soybean plant lacking theMVS Docket No. P14649WO00 modification. In certain embodiments, the at least one mutation is a non-natural mutation. Examples of mutations can include a deletion, an insertion, and / or a substitution of one or more nucleotides of the endogenous AIP10a gene promoter, the AIP10a gene 5’UTR, the endogenous AIP10b gene promoter, and / or the AIP10b gene 5’UTR that result in decreased expression of the AIP10a gene and / or the AIP10b gene.

[0059] In certain embodiments, the at least one targeted modification comprises a deletion. In certain embodiments, the deletion in the AIP10a gene promoter can range from 369 nucleotides upstream of the ATG transcriptional start site of the AIP10a gene to a few bases upstream of the ATG. In some embodiments, the deletion in the AIP10a gene promoter of SEQ ID NO: 1 can be a deletion of nucleotides 1685-1981, a deletion of nucleotides 1680-1721, a deletion of nucleotides 1684 – 1704, or a deletion of nucleotides 1679 – 1693. In some embodiments, the deletion in the AIP10a gene promoter of SEQ ID NO: 1 can be at least a portion of nucleotides 1685-1981, nucleotides 1680-1721, nucleotides 1684 – 1704, or nucleotides 1679 – 1693. In some embodiments, the deletion in the AIP10a gene promoter of SEQ ID NO: 1 can be at least 2-19 nucleotides within nucleotides 1685-1981, nucleotides 1680-1721, nucleotides 1684 – 1704, or nucleotides 1679 – 1693.

[0060] In certain embodiments, the deletion in the AIP10b gene promoter can range from 502 nucleotides upstream of the ATG transcriptional start site of the AIP10b gene to about 395 nucleotides upstream of the ATG. In some embodiments, the deletion in the AIP10b gene promoter of SEQ ID NO: 2 can be a deletion of nucleotides 1499-1605 or nucleotides 1501- 1562. In some embodiments, the deletion in the AIP10b gene promoter of SEQ ID NO: 2 can be a deletion of at least a portion of nucleotides 1499-1605 or nucleotides 1501-1562. In some embodiments, the deletion in the AIP10b gene promoter of SEQ ID NO: 2 can be a deletion of at least 2-19 nucleotides within nucleotides 1499-1605 or nucleotides 1501-1562.

[0061] In certain embodiments, the yield comprising least one of a soybean plant seed number, pod number, hundred-seed weight, leaf area, shoot biomass, or root biomass is increased in comparison to a wild-type or control soybean plant lacking the at least one targeted modification. Increased yield of the soybean plant can be measured in a number of ways, including pod count per plant, seed count per plant, total harvested seed weight per plant, or total harvested seed weight per unit area (e.g., seed weight per acre or seed weight per hectare). In certain embodiments, the increased yield can result from an improved response to stress, including an abiotic stress (e.g., drought, heat, cold, salt stress, and / or nutrient deficiency).MVS Docket No. P14649WO00

[0062] In certain embodiments, the pod count per soybean plant comprising the at least one targeted modification in the endogenous AIP10a gene promoter, the AIP10a gene 5’UTR, the endogenous AIP10b gene promoter, and / or the AIP10b gene 5’UTR is increased in comparison to the pod count per plant for a wild-type or control soybean plant lacking the at least one targeted modification. In certain embodiments, the pod count per plant is increased by at least about 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 12%, 15%, 18%, 20%, 25%, 30%, 35%, 40%, 45%, or 50% in comparison to the pod count per plant from the corresponding wild-type or control soybean plant lacking the at least one targeted modification. In certain embodiments, the seed count per plant comprising the at least one targeted modification in the endogenous AIP10a gene promoter, the AIP10a gene 5’UTR, the endogenous AIP10b gene promoter, and / or the AIP10b gene 5’UTR is increased in comparison to the seed count per plant for a wild-type or control soybean plant lacking the at least one targeted modification. In certain embodiments, the seed count per plant comprising the at least one targeted modification in the endogenous AIP10a gene promoter, the AIP10a gene 5’UTR, the endogenous AIP10b gene promoter, and / or the AIP10b gene 5’UTR is increased by at least about 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 12%, 15%, 18%, 20%, 25%, 30%, 35%, 40%, 45%, or 50% in comparison to the seed count per plant from the corresponding wild-type or control soybean plant lacking the at least one targeted modification. In certain embodiments, the total harvested seed weight per plant comprising the at least one targeted modification in the endogenous AIP10a gene promoter, the AIP10a gene 5’UTR, the endogenous AIP10b gene promoter, and / or the AIP10b gene 5’UTR is increased in comparison to the total harvested seed weight per plant for a wild- type or control soybean plant lacking the at least one targeted modification. In certain embodiments, the total harvested seed weight per plant is increased by at least about 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 12%, 15%, 18%, 20%, 25%, 30%, 35%, 40%, 45%, or 50% in comparison to the total harvested seed weight per plant from the corresponding wild-type or control soybean plant lacking the at least one targeted modification. In certain embodiments, the total leaf area for soybean plants comprising the at least one targeted modification in the endogenous AIP10a gene promoter, the AIP10a gene 5’UTR, the endogenous AIP10b gene promoter, and / or the AIP10b gene 5’UTR is increased in comparison to the total leaf area for a wild-type or control soybean plant lacking the at least one targeted modification. In certain embodiments, the total leaf area for the soybean plants is increased by at least about 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 12%, 15%, 18%, 20%, 25%, 30%, 35%, 40%, 45%, or 50% in comparison to the total leaf area from the corresponding wild-type or control soybean plantMVS Docket No. P14649WO00 lacking the at least one targeted modification. In certain embodiments, the shoot biomass for soybean plants comprising the at least one targeted modification in the endogenous AIP10a gene promoter, the AIP10a gene 5’UTR, the endogenous AIP10b gene promoter, and / or the AIP10b gene 5’UTR is increased in comparison to the shoot biomass for a wild-type or control soybean plant lacking the at least one targeted modification. In certain embodiments, the shoot biomass for the soybean plants is increased by at least about 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 12%, 15%, 18%, 20%, 25%, 30%, 35%, 40%, 45%, or 50% in comparison to the shoot biomass from the corresponding wild-type or control soybean plant lacking the at least one targeted modification. In certain embodiments, the root biomass for soybean plants comprising the at least one targeted modification in the endogenous AIP10a gene promoter, the AIP10a gene 5’UTR, the endogenous AIP10b gene promoter, and / or the AIP10b gene 5’UTR is increased in comparison to the root biomass for a wild-type or control soybean plant lacking the at least one targeted modification. In certain embodiments, the root biomass for the soybean plants is increased by at least about 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 12%, 15%, 18%, 20%, 25%, 30%, 35%, 40%, 45%, or 50% in comparison to the root biomass from the corresponding wild-type or control soybean plant lacking the at least one targeted modification.

[0063] In certain embodiments, the seed number, pod number, hundred-seed weight, leaf area, shoot biomass, and / or root biomass for the soybean plant comprising the at least one targeted modification in the endogenous AIP10a gene promoter, the AIP10a gene 5’UTR, the endogenous AIP10b gene promoter, and / or the AIP10b gene 5’UTR are increased in comparison to seed number, pod number, hundred-seed weight, leaf area, shoot biomass, and / or root biomass for a wild-type or control soybean plant lacking the at least one targeted modification when grown under stress or specific agronomic practices. Non-limiting examples of stresses include drought, cold, heat, salt, shade, nutrient deficiency (e.g., nitrogen deficiency), high planting density, and the presence of pests or pathogens. In certain embodiments, the stress comprises an abiotic stress. In certain embodiments, the abiotic stress comprises drought, cold, heat, salt stress, or nutrient deficiency (e.g., nitrogen deficiency). In these embodiments, the seed number, pod number, hundred-seed weight, leaf area, shoot biomass, and / or root biomass can be increased when the soybean plant comprising the at least one targeted modification in the endogenous AIP10a gene promoter, the AIP10a gene 5’UTR, the endogenous AIP10b gene promoter, and / or the AIP10b gene 5’UTR is grown under abiotic stress in comparison to seed number, pod number, hundred-seed weight, leaf area, shootMVS Docket No. P14649WO00 biomass, and / or root biomass for a wild-type or control soybean plant lacking the at least one targeted modification grown under abiotic stress.

[0064] Also provided are polynucleotides comprising any of the aforementioned targeted modifications in the endogenous AIP10a gene promoter, the AIP10a gene 5’UTR, the endogenous AIP10b gene promoter, and / or the AIP10b gene 5’UTR or fragments thereof. In certain embodiments, polynucleotides comprising at least one targeted modification relative to the endogenous soybean AIP10a gene promoter of SEQ ID NO: 1 and the endogenous soybean AIP10b gene promoter of SEQ ID NO: 2 are provided. In certain embodiments, the polynucleotide comprises a sequence having at least 95%, 96, 97%, 98%, 99%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% sequence identity across the entire length of SEQ ID NO: 1 and SEQ ID NO: 2, with the proviso that the sequences are not identical across their entire length. In certain embodiments, the polynucleotide is an isolated polynucleotide.

[0065] Biological samples and soybean by-products comprising any of the aforementioned polynucleotides are also provided. In certain embodiments, the by-products are processed products are made from the soybean plants of the disclosure or their seeds, including: (a) soybean seed meal (defatted or non-defatted); (b) extracted soybean proteins, oils, sugars, syrups, and starches; (c) soy fermentation products; (d) soybean based animal feed or human food products (e.g., feed and food comprising soybean seed meal (defatted or non-defatted) and other ingredients (e.g., other cereal grains, other seed meal, other protein meal, other oil, other starch, other sugar, a binder, a preservative, a humectant, a vitamin, and / or mineral); (e) a pharmaceutical; (f) raw or processed biomass (e.g., cellulosic and / or lignocellulosic material; silage); and (g) various industrial products.

[0066] Methods of using the soybean plants, seeds, and seed lots of the disclosure to produce soybean by-products are also provided. Such methods will typically include at least one processing step of cleaning, cracking, flaking, crushing, macerating, pressing, extracting, expelling, and / or extruding the seed.

[0067] This disclosure is also directed to methods for producing a soybean plant having at least one targeted modification in the endogenous AIP10a gene promoter, the AIP10a gene 5’UTR, the endogenous AIP10b gene promoter, and / or the AIP10b gene 5’UTR by crossing a first parent soybean plant with a second parent soybean plant wherein the first or second parent soybean plant comprises the at least one mutation. Further, both the first and second parent soybean plants can comprise the at least one mutation. Any such methods using a soybean plant comprising the at least one mutation are part of this disclosure: selfing, backcrosses, hybridMVS Docket No. P14649WO00 production, crosses to populations, and the like. All plants produced using a soybean plant comprising the at least one mutation as a parent are within the scope of this disclosure, including plants derived from a soybean plant having the at least one mutation. Also provided are the F1progeny soybean plants produced from the crossing of a soybean plant comprising the at least one mutation with any other soybean plant, F1 seed, and various parts of the F1 soybean plant. The following describes breeding methods that can be used with soybean plants of the disclosure in the development of further soybean plants. One such embodiment is a method for developing a progeny soybean plant in a soybean plant breeding program comprising: obtaining the soybean plant, or its parts, comprising at least one targeted modification in the endogenous AIP10a gene promoter, the AIP10a gene 5’UTR, the endogenous AIP10b gene promoter, and / or the AIP10b gene 5’UTR and utilizing said plant or plant parts as a source of breeding material; and selecting a progeny plant having the at least one mutation. Breeding steps that can be used in the soybean plant breeding program include pedigree breeding, backcrossing, mutation breeding, and recurrent selection. In conjunction with these steps, techniques such as restriction fragment polymorphism enhanced selection, genetic marker enhanced selection (for example SNP or SSR markers), and the making of double haploids can be utilized.

[0068] Field crops are bred through techniques that take advantage of the plant's method of pollination. A soybean plant of the disclosure can be self-pollinated, sib-pollinated, or cross pollinated to create a pedigree soybean plant. A plant is self-pollinated if pollen from one flower is transferred to the same or another flower of the same plant. A plant is sib-pollinated when individuals within the same family or variety are used for pollination. A plant is cross- pollinated if the pollen comes from a flower on a different plant from a different family or variety. The terms “cross-pollination” and “out-cross” as used herein do not include self- pollination or sib-pollination. Soybean plants (Glycine max) are recognized to be naturally self- pollinated plants which, while capable of undergoing cross-pollination, rarely do so in nature. Insects are reported by some researchers to carry pollen from one soybean plant to another and it generally is estimated that less than one percent of soybean seed formed in an open planting can be traced to cross-pollination, i.e., less than one percent of soybean seed formed in an open planting is capable of producing F1 hybrid soybean plants.

[0069] Any other suitable breeding, selection, or growing methods may be used. Choice of the particular breeding or selection method will vary depending on environmental factors, population size, and the like.MVS Docket No. P14649WO00

[0070] In certain embodiments, soybean plant cells, plant parts (e.g., seeds), and plants comprising at least one targeted modification in the endogenous AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQ ID NO: 1 or an allelic variant thereof and / or the endogenous AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 or an allelic variant thereof and a transgenic locus are provided. In certain embodiments, the at least one targeted modification in the endogenous soybean AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQ ID NO: 1 or an allelic variant thereof and / or the endogenous AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 or an allelic variant thereof is combined with one or more soybean GM events providing tolerance to any one or a combination of glyphosate- based, glufosinate-based, HPPD inhibitor-based, sulfonylurea- or imidazolinone-based, AHAS- or ALS-inhibiting and / or auxin-type (e.g., dicamba, 2,4-D) herbicides and / or an insect resistance trait. GM events that can be combined with the mutations disclosed herein include Event EE-GM3 (aka FG-072, MST-FGØ72-3, described in WO2011063411, USDA-APHIS Petition 09-328-01p), Event SYHTOH2 (aka 0H2, SYN-ØØØH2-5, described in WO2012 / 082548 and 12-215-01p), Event DAS-68416-4 (aka Enlist Soybean, described in WO2011 / 066384 and WO2011 / 066360, USDA-APHIS Petition 09-349-01p), Event DAS- 44406-6 (aka Enlist E3, DAS-444Ø6-6, described in WO2012 / 075426 and USDA-APHIS 11- 234-01p), Event MON87708 (dicamba-tolerant event of Roundup Ready 2 Xtend Soybeans, described in WO2011 / 034704 and USDA-APHIS Petition 10-188-01p, MON-877Ø8-9), Event MON89788 (aka Genuity Roundup Ready 2 Yield, described in WO2006 / 130436 and USDA- APHIS Petition 06-178-01p), Event 40-3-2 (aka Roundup Ready, GTS 40-3-2, MON-Ø4Ø32- 6, described in USDA-APHIS Petition 93-258-01), Event A2704-12 (aka LL27, ACS- GMØØ5-3, described in WO2006108674 and USDA-APHIS Petition 96-068-01p), Event 127 (aka BPS-CV127-9, described in WO2010 / 080829), Event A5547-127 (aka LL55, ACS- GMØØ6-4, described in WO2006108675 and in USDA-APHIS Petition 96-068-01p), event MON87705 (MON-877Ø5-6, Vistive Gold, published PCT patent application WO2010 / 037016, USDA-APHIS Petition 09-201-01p), or event DP305423 (aka DP-3Ø5423- 1, published PCT patent application WO2008 / 054747, USDA-APHIS Petition 06-354-01p), or EE-GM5 is combined with a combination of the following events: Event MON98788×MON87708 (aka Roundup Ready 2 Xtend Soybeans, MON-877Ø8-9×MON- 89788-1), Event HOS×Event 40-3-2 (aka Plenish High Oleic Soybeans×Roundup Ready Soybeans), Event EE-GM3×EE-GM2 (aka FG-072xLL55, described in WO2011063413), Event MON 87701×MON 89788 (aka Intacta RR2 Pro Soybean, MON-877Ø1-2×MON-MVS Docket No. P14649WO00 89788-1), DAS-81419-2×DAS-44406-6 (aka Conkesta™ Enlist E3™ Soybean, DAS-81419- 2×DAS-444Ø6-6), Event DAS-68416-4×Event MON 89788 (aka Enlist™ RoundUp Ready® 2 Soybean, DAS-68416-4×MON-89788-1), Event MON-87769-7×Event MON-89788-1 (aka Omega-3×Genuity Roundup Ready 2 Yield Soybeans), Event MON 87705×Event MON 89788 (aka Vistive Gold, MON-877Ø5-6×MON-89788-1), or Event MON87769×Event MON89788 (aka Omega-3×Genuity Roundup Ready 2 Yield Soybeans, MON-87769- 7×MON-89788-1), where all published PCT patent applications or US national stages thereof are incorporated herein by reference in there entireties. Representative transgenic events that can be combined with the at least one targeted modification of the endogenous AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQ ID NO: 1 or an allelic variant thereof and / or the endogenous AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 or an allelic variant thereof include those set forth in Table 1. Also provided herein are soybean plant cells, plant parts (e.g., seeds), and plants comprising at least AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQ ID NO: 1 or an allelic variant thereof and / or the endogenous AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 or an allelic variant thereof and a modification of any of the aforementioned transgenic events or transgenic events set forth in Table 1 below. Modifications of the transgenic events include those disclosed in: WO2022 / 026375, WO2022 / 026379, WO2022 / 026390, WO2022 / 026395, WO2022 / 026403; US Patent Applic. Pub. Nos. US20220030822 and US20230250441; and U.S. Patent No. 11,242,534, which are each incorporated herein by reference in their entireties.

[0071] Table 1. Transgenic Soybean Events Event Name Patent or Patent ATCC;3NCIMB4Trait (traits)1Application Deposit Number; expression ,MVS Docket No. P14649WO00 MON87701 (IR) US 8049071 PTA-8194 cry1Ac MON87708 US 9447428 PTA-9670 DMO (HT)8,, y p , p p .g., s), and plants comprising the at least one targeted modification of the endogenous AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQ ID NO: 1 or an allelic variant thereof and / or the endogenous AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 or an allelic variant thereof and at least one mutation in a distinct soybean gene are provided. Non- limiting examples of mutations in distinct soybean genes that may be combined with the at least one targeted modification of the endogenous AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQ ID NO: 1 or an allelic variant thereof and / or the endogenous AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 or an allelic variant thereof of the disclosure include mutations in any one or a combination of the soybean FT1a gene, Ric1 gene, Ric2 gene, Tfl1b gene, a NF-YC4 gene, JAG1 gene, BS1 gene, and / or BS2 gene. In certain embodiments, the at least one targeted modification of the endogenous AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQ ID NO: 1 or an allelic variant thereof and / or the endogenous AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 or an allelic variant thereof is combined with a mutation in the soybean FT1a gene. The FT1a gene (Glyma.18G298900) is located at nucleotides 57,922,912 to 57,928,648 of chromosome 18 of the Glycine max Wm82.a4.v1 genome assembly. In certain embodiments, the at least one targeted modification of the endogenous AIP10a gene promoter and / or the AIP10a gene 5’UTRMVS Docket No. P14649WO00 of SEQ ID NO: 1 or an allelic variant thereof and / or the endogenous AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 or an allelic variant thereof is combined with a mutation in the soybean JAG1 gene. In certain embodiments, the at least one targeted modification of the endogenous AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQ ID NO: 1 or an allelic variant thereof and / or the endogenous AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 or an allelic variant thereof is combined with a mutation in the soybean Ric1 and / or Ric2 gene. The endogenous Ric1 gene (Glyma.13g292300) is located at nucleotides 38,587,351 to 38,588,133 of chromosome 13 of the Glycine max Wm82.a4.v1 genome assembly. The endogenous soybean Ric2 gene (Glyma.06g284100) is located at nucleotides 46,845,530 to 46,845,811 of chromosome 6 of the Glycine max Wm82.a4.v1 genome assembly (Grant et al. Nucl. Acids Res. (2010) 38 (suppl 1): D843-D846. doi: 10.1093 / nar / gkp798). The JAG1 gene (Glyma.20G116200) is located at nucleotides 35,791,056 to 35,793,868 of chromosome 20 of the Glycine max Wm82.a4.v1 genome assembly. In certain embodiments, the at least one targeted modification of an endogenous AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQ ID NO: 1 or an allelic variant thereof and / or the endogenous AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 or an allelic variant thereof is combined with a mutation in the soybean BS1 gene. The BS1 gene (Glyma.10g244400) is located at nucleotides 47,330,160 to 47,335,971 of chromosome 10 of the Glycine max Wm82.a4.v1 genome assembly. In certain embodiments, the at least one targeted modification of an endogenous AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQ ID NO: 1 or an allelic variant thereof and / or the endogenous AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 or an allelic variant thereof is combined with a mutation in the soybean BS2 gene. The BS2 gene (Glyma.20g150000) is located at nucleotides 38,879,463 to 38,885,344 of chromosome 20 of the Glycine max Wm82.a4.v1 genome assembly. In certain embodiments, the at least one mutation (e.g., a deletion) in the Tfl1b gene (Glyma.19g194300) can be a promoter deletion as described in WO2023086765, which is incorporated herein by reference in its entirety. In certain embodiments, the at least one mutation in the NF-YC4 gene (Glyma06g17780 and / or Glyma04g37291) can be a promoter element deletion as described in US20230139093, which is incorporated herein by reference in its entirety.

[0073] In certain embodiments, the soybean plant cells, plant parts (e.g., seeds), plants, and / or the biological samples and or commodity products comprise the at least one targeted modification of an endogenous AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQMVS Docket No. P14649WO00 ID NO: 1 or an allelic variant thereof and / or of the endogenous AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 or an allelic variant thereof. In certain embodiments, the soybean plant cells, plant parts (e.g., seeds), plants, and / or the biological samples and or commodity products comprise the at least one targeted modification of an endogenous AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQ ID NO: 1 or an allelic variant thereof and a wild-type AIP10b gene. In certain embodiments, the soybean plant cells, plant parts (e.g., seeds), plants, and / or the biological samples and or commodity products comprise the at least one targeted modification of the endogenous AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 or an allelic variant thereof and a wild-type AIP10a gene. In certain embodiments, the soybean plant cells, plant parts (e.g., seeds), plants, and / or the biological samples and or commodity products comprise the at least one targeted modification of an endogenous AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQ ID NO: 1 or an allelic variant thereof and the at least one targeted modification of endogenous AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 or an allelic variant thereof.

[0074] Methods of producing a soybean seed lot comprising: (i) growing a population of soybean plants comprising at least one targeted modification of an endogenous AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQ ID NO: 1 or an allelic variant thereof and / or the endogenous AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 or an allelic variant thereof to maturity; and (ii) harvesting seed from the population of soybean plants of step (i) at maturity, thereby producing the soybean seed lot. In certain embodiments, the seed lot is packaged in lots comprising about 50 to 60 pounds (i.e., about 22.7 to 27.2 kilograms).

[0075] Also provided herein are methods of treating the soybean seeds and seed lots of the disclosure and the resultant treated seeds and seed lots. Seeds can be treated with such fertilizers, biological agents, nematicides, insecticides, and fungicides by methods including in-furrow applications or by coating (e.g., with a drum coater, rotary coater, tumbling drum, fluidized bed, and / or spouted bed apparatus). Methods and compositions including various binders, fillers, film coats, and active ingredients such as fertilizers, surfactants, plant growth regulators, crop desiccants, fungicides, bacteriocides, bacteriostats, insecticides, and insect repellants for coating seeds that can be adapted for use with seeds provided herein are disclosed in US Patent No.10745578, which is incorporated herein by reference in its entirety.

[0076] The disclosure also provides a method of making a soybean plant comprising a targeted modification of an endogenous AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQMVS Docket No. P14649WO00 ID NO: 1 or an allelic variant thereof and / or the endogenous AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 or an allelic variant thereof. In certain embodiments, the methods can comprise making a deletion in the endogenous AIP10a gene promoter, the AIP10a gene 5’UTR, the AIP10b gene promoter, and / or the AIP10b gene 5’UTR. Gene editing molecules of use in methods provided herein include molecules capable of introducing a double-strand break (“DSB”) or single-strand break (“SSB”) at a specific site or sequence in a double-stranded DNA, such as in genomic DNA or in a target gene located within the genomic DNA as well as accompanying guide RNA. In certain embodiments, the at least one targeted modification results from introduction of a DSB at a target site in the endogenous AIP10a gene promoter and / or the AIP10a gene 5’UTR (e.g., SEQ ID NO: 1 or an allelic variant thereof) and / or the endogenous AIP10b gene promoter and / or the AIP10b gene 5’UTR (e.g., SEQ ID NO: 2 or an allelic variant thereof) to induce non-homologous end joining (NHEJ) at the site of the break followed by recovery of the desired mutation. In certain embodiments, the at least one targeted modification results from introduction of a DSB at a target site in the AIP10a gene promoter and / or the AIP10a gene 5’UTR (e.g., SEQ ID NO: 1 or an allelic variant thereof) and / or AIP10b gene promoter and / or the AIP10b gene 5’UTR (e.g., SEQ ID NO: 2 or an allelic variant thereof) followed by homology-directed repair (HDR), microhomology-mediated end joining (MMEJ), or NHEJ to introduce a desired donor or other DNA template polynucleotide at the DSB, followed by recovery of the desired mutation. Examples of such gene editing molecules include: (a) a nuclease comprising an RNA-guided nuclease, an RNA-guided DNA endonuclease or RNA directed DNA endonuclease (RdDe), a class 1 CRISPR type nuclease system, a class 2 type II Cas nuclease, a Cas9, a nCas9 nickase, a class 2 type V Cas nuclease, a Cas12a nuclease, a nCas12a nickase, a Cas12d (CasY), a Cas12e (CasX), a Cas12b (C2c1), a Cas12c (C2c3), a Cas12i, a Cas12j, a Cas14, an engineered nuclease, a codon-optimized nuclease, a zinc-finger nuclease (ZFN) or nickase, a transcription activator-like effector nuclease (TAL-effector nuclease or TALEN) or nickase (TALE-nickase), an Argonaute, and a meganuclease or engineered meganuclease; (b) a polynucleotide encoding one or more nucleases capable of effectuating site-specific alteration (including introduction of a DSB or SSB) of a target nucleotide sequence; (c) a guide RNA (gRNA) for use with an RNA-guided nuclease, or a DNA encoding a gRNA for use with an RNA-guided nuclease; (d) optionally donor DNA template polynucleotides suitable for insertion at a break in genomic DNA by homology-directed repair (HDR) or microhomology-mediated end joining (MMEJ); and (e) optionally other DNA templates (e.g., dsDNA, ssDNA, or combinations thereof) suitable forMVS Docket No. P14649WO00 insertion at a break in genomic DNA (e.g., by non-homologous end joining (NHEJ). In certain embodiments, the at least one mutation is made with a cytosine and / or adenine base editor, or by a PRIME editing system.

[0077] In certain embodiments, the at least one target modification made in the AIP10a gene promoter, AIP10a gene 5’UTR, AIP10b gene promoter, and / or AIP10b gene 5’UTR and plant cells, parts including seeds, and plants comprising the at least one target modification are generated by CRISPR technology. CRISPR technology for editing the genes of eukaryotes is disclosed in US Patent Application Publications 2016 / 0138008A1 and US2015 / 0344912A1, and in US Patents 8,697,359, 8,771,945, 8,945,839, 8,999,641, 8,993,233, 8,895,308, 8,865,406, 8,889,418, 8,871,445, 8,889,356, 8,932,814, 8,795,965, and 8,906,616. Cpf1 endonuclease and corresponding guide RNAs and PAM sites are disclosed in US Patent Application Publication 2016 / 0208243 A1. Plant RNA promoters for expressing CRISPR guide RNA and plant codon-optimized CRISPR Cas9 endonuclease are disclosed in International Patent Application PCT / US2015 / 018104 (published as WO 2015 / 131101 and claiming priority to US Provisional Patent Application 61 / 945,700). Methods of using CRISPR technology for genome editing in plants are disclosed in US Patent Application Publications US 2015 / 0082478A1 and US 2015 / 0059010A1 and in International Patent Application PCT / US2015 / 038767 A1 (published as WO 2016 / 007347 and claiming priority to US Provisional Patent Application 62 / 023,246). All of the patent publications referenced in this paragraph are incorporated herein by reference in their entirety. In certain embodiments, an RNA-guided endonuclease that leaves a blunt end following cleavage of the target site is used. Blunt-end cutting RNA-guided endonucleases include Cas9. In certain embodiments, an RNA- guided endonuclease that leaves a staggered single stranded DNA overhanging end following cleavage of the target site following cleavage of the target site is used. Staggered-end cutting RNA-guided endonucleases include Cas12a, Cas12b, Cas12d, Cas12e, and Cas12i.

[0078] Guide RNA molecules comprising a spacer RNA molecule which targets the AIP10a gene promoter and / or the AIP10a gene 5’UTR (e.g., SEQ ID NO: 1 or an allelic variant thereof) and / or AIP10b gene promoter and / or the AIP10b gene 5’UTR (e.g., SEQ ID NO: 2 or an allelic variant thereof) are provided. In certain embodiments, the spacer RNA molecule which targets an AIP10a gene promoter of SEQ ID NO: 1 or an allelic variant thereof, comprises the RNA encoded by SEQ ID NO: 3, 4, or 5. In certain embodiments, the spacer RNA molecule which targets an AIP10b gene promoter of SEQ ID NO: 2 or an allelic variant thereof, comprises the RNA encoded by SEQ ID NO: 6, 7, or 8.MVS Docket No. P14649WO00

[0079] Guide RNAs comprising a spacer RNA molecule encoded by SEQ ID NO: 3, 4, or 5 targeting the endogenous soybean AIP10a gene promoter can be used in conjunction with a Cas12a or Cas12i nuclease to generate targeted modifications in the endogenous soybean AIP10a gene promoter and / or the AIP10a gene 5’UTR which: (i) comprise at least one deletion in the endogenous AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQ ID NO: 1 or an allelic variant thereof; (ii) comprise deletions of nucleotides 1685 - 1981, nucleotides 1680- 1721, nucleotides 1684 - 1704, or nucleotides 1679 - 1693 of the endogenous soybean AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQ ID NO: 1 or in an equivalent position of an allelic variant of SEQ ID NO: 1; (iii) comprise deletions of at least a portion of nucleotides 1685-1981, nucleotides 1680-1721, nucleotides 1684 - 1704, or nucleotides 1679 - 1693 of the endogenous soybean AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQ ID NO: 1 or in an equivalent position of an allelic variant of SEQ ID NO: 1; or (iv) comprise deletions of at least at least 2-19 nucleotides within nucleotides 1685-1981, nucleotides 1680-1721, nucleotides 1684 - 1704, or nucleotides 1679 - 1693 of the endogenous soybean AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQ ID NO: 1 or in an equivalent position of an allelic variant of SEQ ID NO: 1.

[0080] Guide RNAs comprising a spacer RNA molecule encoded by SEQ ID NO: 6, 7, or 8 targeting AIP10b gene promoter can be used in conjunction with a Cas12a or Cas12i nuclease to generate targeted modifications in the endogenous soybean AIP10b gene promoter and / or the AIP10b gene 5’UTR which: (i) comprise at least one deletion in the endogenous AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 or an allelic variant thereof; (ii) comprise deletions of nucleotides 1499-1605 or nucleotides 1501-1562 of the endogenous soybean AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 or in an equivalent position of an allelic variant of SEQ ID NO: 2; (iii) comprise deletions of at least a portion of nucleotides 1499-1605 or nucleotides 1501-1562 of the endogenous soybean AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 or in an equivalent position of an allelic variant of SEQ ID NO: 2; or (iv) comprise deletions of at least at least 2- 19 nucleotides within nucleotides 1499-1605 or nucleotides 1501-1562 of the endogenous soybean AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 or in an equivalent position of an allelic variant of SEQ ID NO: 2.

[0081] CRISPR-type genome editing can be adapted for use in the plant cells and methods provided herein in several ways. CRISPR elements, e.g., gene editing molecules comprising CRISPR endonucleases and CRISPR guide RNAs including single guide RNAs or guide RNAsMVS Docket No. P14649WO00 in combination with tracrRNAs or scoutRNA, or polynucleotides encoding the same, are useful in effectuating genome editing without remnants of the CRISPR elements or selective genetic markers occurring in progeny. In certain embodiments, the CRISPR elements are provided directly to the eukaryotic cell (e.g., soybean plant cells), systems, methods, and compositions as isolated molecules, as isolated or semi-purified products of a cell free synthetic process (e.g., in vitro translation), or as isolated or semi-purified products of in a cell-based synthetic process (e.g., such as in a bacterial or other cell lysate). In certain embodiments, soybean plants or soybean plant cells used in the systems, methods, and compositions provided herein can comprise a transgene that expresses a CRISPR endonuclease (e.g., a Cas9, a Cpf1-type or other CRISPR endonuclease). In certain embodiments, one or more CRISPR endonucleases with unique PAM recognition sites can be used. Guide RNAs (sgRNAs or crRNAs and a tracrRNA or scoutRNA) to form an RNA-guided endonuclease / guide RNA complex which can specifically bind sequences in the gDNA target site that are adjacent to a protospacer adjacent motif (PAM) sequence. The type of RNA-guided endonuclease typically informs the location of suitable PAM sites and design of crRNAs or sgRNAs. G-rich PAM sites, e.g., 5’-NGG are typically targeted for design of crRNAs or sgRNAs used with Cas9 proteins. Examples of PAM sequences include 5’-NGG (Streptococcus pyogenes), 5’-NNAGAA (Streptococcus thermophilus CRISPR1), 5’-NGGNG (Streptococcus thermophilus CRISPR3), 5’-NNGRRT or 5’-NNGRR (Staphylococcus aureus Cas9, SaCas9), and 5’-NNNGATT (Neisseria meningitidis). T-rich PAM sites (e.g., 5’-TTN or 5’-TTTV, where “V” is A, C, or G) are typically targeted for design of crRNAs or sgRNAs used with Cas12a proteins. In some instances, Cas12a can also recognize a 5’-CTA PAM motif. Other examples of potential Cas12a PAM sequences include TTN, CTN, TCN, CCN, TTTN, TCTN, TTCN, CTTN, ATTN, TCCN, TTGN, GTTN, CCCN, CCTN, TTAN, TCGN, CTCN, ACTN, GCTN, TCAN, GCCN, and CCGN (wherein N is defined as any nucleotide). Cpf1 endonuclease and corresponding guide RNAs and PAM sites are disclosed in US Patent Application Publication 2016 / 0208243 A1, which is incorporated herein by reference for its disclosure of DNA encoding Cpf1 endonucleases and guide RNAs and PAM sites. Engineered endonucleases with altered or eliminated PAM recognition sites can also be used.

[0082] Identification of a suitable PAM site is only one factor in selecting an efficacious gRNA. Different guides can also have different cutting efficiencies and specificities, which depend on a number of factors. In some embodiments, identification of effective gRNA targetMVS Docket No. P14649WO00 sequences in the genome is approached through a combination of in silico selection and experimental evaluation.

[0083] In some cases, a target sequence that perfectly hybridizes with the gRNA spacer sequence occurs only once in a given plant genome. In some embodiments, the genome comprises additional sequences that imperfectly hybridize with the gRNA spacer sequence, for example, sequences having one or more mismatches (e.g., 1, 2, 3, 4, or 5 mismatches) and / or bulges, relative to the gRNA spacer sequence. In some embodiments, the genome comprises sequences that hybridize the gRNA spacer sequence that are adjacent to a PAM sequence having at least one mismatch relative to the canonical PAM sequence. Such genomic sequences (e.g., target sequences that imperfectly hybridize the gRNA spacer sequence and / or target sequences comprising a non-canonical PAM sequences) are called off-target sites. A favorable off-target profile is typically one that minimizes or eliminates the number of off-target sites and / or the frequency of cutting at these sites.

[0084] The nuclease efficiency and occurrence of off-target activity for a given gRNA / endonuclease combination can be influenced by a number of factors including similarities and dissimilarities between the target site and various off-target sites, as well as the particular endonuclease used. For example, the ability of a given gRNA to promote cleavage at a target sequence in a genomic DNA molecule may relate to the accessibility of the target sequence, which depends on one or more factors that include the chromatin structure of the genomic DNA molecule and / or proximity to transcription factor binding sites. For example, target sequences located within a region of the genomic DNA molecule having a high condensed chromatin structure are less accessible than target sequences located within a region of the genomic DNA molecule having an open chromatin structure. As a further example, target sequences proximal to a region of the genomic DNA molecule bound by a transcription factor or other regulatory protein may be less accessible than target sequences proximal a region of the genomic DNA molecule that is unbound by regulatory proteins. Moreover, the cell state and type of cell may influence the accessibility of target sequences, for example, by influencing the chromatin structure of genomic DNA.

[0085] In certain embodiments, the targeted modifications of the endogenous soybean AIP10a gene promoter, the AIP10a gene 5’UTR, the endogenous AIP10b gene promoter, and / or the AIP10b gene 5’UTR and plant cells, parts including seeds, and plants comprising the aforementioned targeted modifications are generated by use of zinc finger nucleases or zinc finger nickases. Zinc-finger nucleases are site-specific endonucleases comprising two proteinMVS Docket No. P14649WO00 domains: a DNA-binding domain, comprising a plurality of individual zinc finger repeats that each recognize between 9 and 18 base pairs, and a DNA-cleavage domain that comprises a nuclease domain (typically Fokl). The cleavage domain dimerizes in order to cleave DNA; therefore, a pair of ZFNs are required to target non-palindromic target polynucleotides. In certain embodiments, zinc finger nuclease and zinc finger nickase design methods which have been described (Urnov et al. (2010) Nature Rev. Genet., 11:636 – 646; Mohanta et al. (2017) Genes vol.8,12: 399; Ramirez et al. Nucleic Acids Res. (2012); 40(12): 5560–5568; Liu et al. (2013) Nature Communications, 4: 2565) can be adapted for use in the methods set forth herein. The zinc finger binding domains of the zinc finger nuclease or nickase provide specificity and can be engineered to specifically recognize any desired target DNA sequence. The zinc finger DNA binding domains are derived from the DNA-binding domain of a large class of eukaryotic transcription factors called zinc finger proteins (ZFPs). The DNA-binding domain of ZFPs typically contains a tandem array of at least three zinc “fingers” each recognizing a specific triplet of DNA. A number of strategies can be used to design the binding specificity of the zinc finger binding domain. One approach, termed “modular assembly”, relies on the functional autonomy of individual zinc fingers with DNA. In this approach, a given sequence is targeted by identifying zinc fingers for each component triplet in the sequence and linking them into a multifinger peptide. Several alternative strategies for designing zinc finger DNA binding domains have also been developed. These methods are designed to accommodate the ability of zinc fingers to contact neighboring fingers as well as nucleotide bases outside their target triplet. Typically, the engineered zinc finger DNA binding domain has a novel binding specificity, compared to a naturally occurring zinc finger protein. Engineering methods include, for example, rational design and various types of selection. Rational design includes, for example, the use of databases of triplet (or quadruplet) nucleotide sequences and individual zinc finger amino acid sequences, in which each triplet or quadruplet nucleotide sequence is associated with one or more amino acid sequences of zinc fingers which bind the particular triplet or quadruplet sequence. See, e.g., US Patents 6,453,242 and 6,534,261, both incorporated herein by reference in their entirety. Exemplary selection methods (e.g., phage display and yeast two-hybrid systems) can be adapted for use in the methods described herein. In addition, enhancement of binding specificity for zinc finger binding domains has been described in US Patent 6,794,136, incorporated herein by reference in its entirety. In addition, individual zinc finger domains may be linked together using any suitable linker sequences. Examples of linker sequences are publicly known, e.g., see US Patents 6,479,626; 6,903,185;MVS Docket No. P14649WO00 and 7,153,949, incorporated herein by reference in their entirety. The nucleic acid cleavage domain is non-specific and is typically a restriction endonuclease, such as Fokl. This endonuclease must dimerize to cleave DNA. Thus, cleavage by Fokl as part of a ZFN requires two adjacent and independent binding events, which must occur in both the correct orientation and with appropriate spacing to permit dimer formation. The requirement for two DNA binding events enables more specific targeting of long and potentially unique recognition sites. Fokl variants with enhanced activities have been described and can be adapted for use in the methods described herein; see, e.g., Guo et al. (2010) J. Mol. Biol., 400:96 - 107.

[0086] In certain embodiments, the targeted modifications of the endogenous soybean AIP10a gene promoter, the AIP10a gene 5’UTR, the endogenous AIP10b gene promoter, and / or the AIP10b gene 5’UTR and plant cells, parts including seeds, and plants comprising the aforementioned targeted modifications are generated by use of TAL-effector nucleases or TALENs. Transcription activator like effectors (TALEs) are proteins secreted by certain Xanthomonas species to modulate gene expression in host plants and to facilitate the colonization by and survival of the bacterium. TALEs act as transcription factors and modulate expression of resistance genes in the plants. Recent studies of TALEs have revealed the code linking the repetitive region of TALEs with their target DNA-binding sites. TALEs comprise a highly conserved and repetitive region consisting of tandem repeats of mostly 33 or 34 amino acid segments. The repeat monomers differ from each other mainly at amino acid positions 12 and 13. A strong correlation between unique pairs of amino acids at positions 12 and 13 and the corresponding nucleotide in the TALE-binding site has been found. The simple relationship between amino acid sequence and DNA recognition of the TALE binding domain allows for the design of DNA binding domains of any desired specificity. TALEs can be linked to a non- specific DNA cleavage domain to prepare genome editing proteins, referred to as TAL-effector nucleases or TALENs. As in the case of ZFNs, a restriction endonuclease, such as Fokl, can be conveniently used. Methods for use of TALENs in plants have been described and can be adapted for use in the methods described herein, see Mahfouz et al. (2011) Proc. Natl. Acad. Sci. USA, 108:2623 – 2628; Mahfouz (2011) GM Crops, 2:99 – 103; and Mohanta et al. (2017) Genes vol.8,12: 399). TALE nickases have also been described and can be adapted for use in methods described herein (Wu et al.; Biochem Biophys Res Commun. (2014);446(1):261-6; Luo et al; Scientific Reports 6, Article number: 20657 (2016)).

[0087] Various treatments can be used for delivery of gene editing molecules and / or other molecules to a plant cell. In certain embodiments, one or more treatments is employed toMVS Docket No. P14649WO00 deliver the gene editing or other molecules (e.g., comprising a polynucleotide, polypeptide or combination thereof) into a plant cell, e.g., through barriers such as a cell wall, a plasma membrane, a nuclear envelope, and / or other lipid bilayer. In certain embodiments, a polynucleotide-, polypeptide-, or RNP (ribonucleoprotein) -containing composition comprising the molecules are delivered directly, for example by direct contact of the composition with a plant cell. Aforementioned compositions can be provided in the form of a liquid, a solution, a suspension, an emulsion, a reverse emulsion, a colloid, a dispersion, a gel, liposomes, micelles, an injectable material, an aerosol, a solid, a powder, a particulate, a nanoparticle, or a combination thereof can be applied directly to a plant, plant part, plant cell, or plant explant (e.g., through abrasion or puncture or otherwise disruption of the cell wall or cell membrane, by spraying or dipping or soaking or otherwise directly contacting, by microinjection). For example, a plant cell or plant protoplast is soaked in a liquid genome editing molecule-containing composition. In certain embodiments, the composition is delivered using negative or positive pressure, for example, using vacuum infiltration or application of hydrodynamic or fluid pressure. In certain embodiments, the composition is introduced into a plant cell or plant protoplast, e.g., by microinjection or by disruption or deformation of the cell wall or cell membrane, for example by physical treatments such as by application of negative or positive pressure, shear forces, or treatment with a chemical or physical delivery agent such as surfactants, liposomes, or nanoparticles; see, e.g., delivery of materials to cells employing microfluidic flow through a cell-deforming constriction as described in US Published Patent Application 2014 / 0287509, incorporated by reference in its entirety herein. Other techniques useful for delivering the composition to a eukaryotic cell, plant cell or plant protoplast include: ultrasound or sonication; vibration, friction, shear stress, vortexing, cavitation; centrifugation or application of mechanical force; mechanical cell wall or cell membrane deformation or breakage; enzymatic cell wall or cell membrane breakage or permeabilization; abrasion or mechanical scarification (e.g., abrasion with carborundum or other particulate abrasive or scarification with a file or sandpaper) or chemical scarification (e.g., treatment with an acid or caustic agent); and electroporation. In certain embodiments, the composition is provided by bacterially mediated (e.g., Agrobacterium sp., Rhizobium sp., Sinorhizobium sp., Mesorhizobium sp., Bradyrhizobium sp., Azobacter sp., Phyllobacterium sp.) transfection of the plant cell or plant protoplast with a polynucleotide encoding the genome editing molecules (e.g., RNA dependent DNA endonuclease, RNA dependent DNA binding protein, RNA dependent nickase, ABE, or CBE, and / or guide RNA); see, e.g., Broothaerts etMVS Docket No. P14649WO00 al. (2005) Nature, 433:629 – 633). Any of these techniques or a combination thereof are alternatively employed on a plant explant, plant part or tissue or intact plant (or seed) from which a plant cell is optionally subsequently obtained or isolated; in certain embodiments, the composition is delivered in a separate step after the plant cell has been isolated.

[0088] In certain embodiments, the methods for generating the soybean plant cell, soybean plant parts, or soybean plants comprise: (i) screening a population of soybean plant cells, parts, or plants for the presence of at least one targeted modification in the endogenous soybean AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQ ID NO: 1 or an allelic variant thereof and / or the endogenous AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 or an allelic variant thereof; and (ii) isolating a soybean plant cell, soybean plant part, or soybean plant comprising at least one targeted modification in the endogenous soybean AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQ ID NO: 1 or an allelic variant thereof and / or the endogenous AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 or an allelic variant thereof.

[0089] In certain embodiments, the population of soybean plant cells, parts, or plants which are screened for the presence of at least one targeted modification in the endogenous soybean AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQ ID NO: 1 or an allelic variant thereof and / or the endogenous AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 or an allelic variant thereof are first pre-screened by screening of phenotypic characteristics plants having aforementioned targeted modifications. In certain embodiments, such phenotypic characteristics include increased yield (e.g., pod count per plant, seed count per plant, total harvested seed weight per plant, and / or total harvested seed weight per unit area) in comparison to yield for a wild-type or control soybean plant lacking the at least one mutation. In certain embodiments, plants exhibiting one or more of the aforementioned phenotypic characteristics are then subjected to screening for the presence of at least one targeted modification in the endogenous soybean AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQ ID NO: 1 and / or the endogenous AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 and soybean plants comprising the aforementioned targeted modifications are identified and / or selected.

[0090] In certain embodiments, the population of soybean plant cells, parts, or plants which are screened for the presence of at least one targeted modification in the endogenous soybean AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQ ID NO: 1 and / or the endogenous AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 have been subjectedMVS Docket No. P14649WO00 to one or more mutagenesis treatments. Mutations of the endogenous soybean AIP10a gene promoter, the AIP10a gene 5’UTR, the endogenous AIP10b gene promoter, and / or the AIP10b gene 5’UTR can be generated by mutagenesis methods known in the art, such as chemical mutagenesis or radiation mutagenesis. Suitable chemical mutagens include ethyl methanesulfonate (EMS), sodium azide, methylnitrosourea (MNU), and diepoxybutane (DEB). Suitable radiation includes x-rays, fast neutron radiation, and gamma radiation.

[0091] Soybean plant cells, parts, or plants comprising at least one targeted modification in the endogenous AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQ ID NO: 1 and / or the endogenous AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 can be generated using mutagenesis and identified by TILLING (Targeting Induced Local Lesions IN Genomes) or identified using EcoTILLING. TILLING is a general reverse genetics technique that uses mutagenesis methods to create libraries of mutagenized individuals that are later subjected to high throughput screens for the discovery of mutations. In addition to allowing efficient detection of induced mutations, high-throughput TILLING technology is ideal for the detection of natural mutations. EcoTILLING is a method that uses TILLING techniques to look for natural mutations in individuals (Barkley and Wang. Current genomics vol. 9,4 (2008): 212-26. doi:10.2174 / 138920208784533656). Identified mutations can then be introduced into desirable genetic backgrounds by crossing the mutant with a plant of the desired genetic background and performing a suitable number of backcrosses to cross out the originally undesired parent background. A more detailed description of methods and compositions for TILLING are disclosed in US Patent Application Publication 2004 / 0053236 A1, which is incorporated herein by reference in its entirety and can be adapted for use in the methods provided herein for identifying soybean plant cells, parts, or plants comprising at least one targeted modification in the endogenous AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQ ID NO: 1 and / or the endogenous AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2.

[0092] In certain embodiments, the screening comprises analyzing pod count per plant, seed count per plant, total harvested seed weight per plant, and / or total harvested seed weight per unit area in one or more candidate plants or one or more candidate plant populations. In these embodiments, an increase in pod count per plant, seed count per plant, total harvested seed weight per plant, and / or total harvested seed weight per unit area in comparison to a wild-type or control soybean plant lacking the at least one mutation is indicative of a soybean plant cell, soybean plant part, or soybean plant comprising the at least one mutation. In certainMVS Docket No. P14649WO00 embodiments, the screening is conducted on a population of plants grown under stress. Suitable examples of stress conditions include drought, salt, cold, heat, salt, shade, nutrient deficiency, high planting density, and the presence of pests or pathogens.

[0093] Methods for determining whether a soybean plant cell, plant part, or plant comprises a at least one targeted modification in the endogenous AIP10a gene promoter and / or the AIP10a gene 5’UTR of SEQ ID NO: 1 and / or the endogenous AIP10b gene promoter and / or the AIP10b gene 5’UTR of SEQ ID NO: 2 are provided. Methods for determining the presence or absence of the at least one mutation can be used in, for example, breeding programs for identification, selection, introgression, and the like.

[0094] In certain embodiments, the methods comprise analyzing a polynucleotide comprising a portion of SEQ ID NO: 1 and / or SEQ ID NO: 2 or an allelic variant thereof or analyzing an RNA encoded by a portion of SEQ ID NO: 1 and / or SEQ ID NO: 2 and / or an allelic variant thereof from the plant cell, plant part, or plant. In certain embodiments, an insertion, deletion, and / or substitution of one or more nucleotides in the polynucleotide or RNA is indicative of the presence of the at least one mutation. Detection of the at least one mutation in a nucleic acid sample (e.g., DNA, RNA, or cDNA) can be achieved by any combination of nucleic acid amplification (e.g., PCR amplification), hybridization, sequencing, and / or mass-spectrometry based techniques. In certain embodiments, such detection is achieved by amplification and / or hybridization-based detection methods using a primer (e.g., selective amplification primers) and / or probe (e.g., capable of selective hybridization or generation of a specific primer extension product) which specifically recognizes the AIP10a gene promoter, the AIP10a gene 5’UTR, the endogenous AIP10b gene promoter, and / or the AIP10b gene 5’UTR (e.g., a portion of SEQ ID NO: 1 and / or SEQ ID NO: 2 or an allelic variant thereof). Such primers and / or probes can comprise or consist of about 15, 20, 25, 30, 40, 45 or 50 more contiguous nucleotides of SEQ ID NO: 1 and / or SEQ ID NO: 2 or an allelic variant thereof. In certain embodiments, the primers or probes can comprise or consist of about 10 to 50 contiguous nucleotides, about 10 to 40 contiguous nucleotides, about 10 to 30 contiguous nucleotides or about 15 to 30 contiguous nucleotides of SEQ ID NO: 1 and / or SEQ ID NO: 2 or an allelic variant thereof. In certain embodiments, the hybridization probes (e.g., polynucleotides comprising at least about 15 to 30 base pairs of SEQ ID NO: 1 and / or SEQ ID NO: 2 or an allelic variant thereof) can comprise detectable labels (e.g., fluorescent, radioactive, epitope, and chemiluminescent labels). In certain embodiments, the AIP10a gene promoter, the AIP10aMVS Docket No. P14649WO00 gene 5’UTR, the AIP10b gene promoter, and / or the AIP10b gene 5’UTR can be directly sequenced using nucleic acid sequencing technologies, including whole genome sequencing.

[0095] In certain embodiments, the methods comprise analyzing a polypeptide encoded by SEQ ID NO: 1 and / or SEQ ID NO: 2, a portion thereof, or an allelic variant thereof from the soybean plant cell, plant part, or plant. In certain embodiments, an insertion, deletion, and / or substitution of one or more amino acid residues of the polypeptide or a change in the biologic or biochemical activity of the polypeptide is indicative of the presence of the at least one mutation. Detection of the at least one mutation based on the polypeptide can be determined by methods well known in the art such as activity assays, western blots using antibodies capable of specifically binding the polypeptide, enzyme-linked immunosorbent assays (ELISA), radioimmunoassays (RIA), immunohistochemistry, immunocytochemistry, immunofluorescence, and the like.

[0096] In certain optional embodiments, the soybean plant cells disclosed herein are non- regenerable soybean plant cells. In certain optional embodiments provided herein, the soybean plant cells, soybean plant propagules (e.g., a seed, seedling, ovule, embryo, pollen, root, stem, leaf, shoot, explant, or callus), and soybean plants provided herein are not produced by an exclusively biological process. In certain optional embodiments provided herein, the methods for producing soybean plant cells, soybean plant propagules (e.g., a seed, seedling, ovule, embryo, pollen, root, stem, leaf, shoot, explant, or callus), and soybean plants provided herein are not exclusively biological processes.

[0097] The following numbered embodiments also form part of the present disclosure: 1. A modified soybean plant comprising at least one targeted modification in (i) an endogenous AIP10a gene promoter and / or AIP10a gene 5’ untranslated region (5’ UTR), and / or (ii) an endogenous AIP10b gene promoter and / or AIP10b gene 5’ UTR resulting in decreased expression of an endogenous AIP10a and / or AIP10b gene relative to a reference soybean plant lacking the modification. 2. The modified soybean plant of embodiment 1, wherein the targeted modification in the AIP10a and / or AIP10b gene promoter and / or 5’ UTR comprises a deletion of one or more nucleotides. 3. The modified soybean plant of embodiments 1 or 2, wherein the decrease of expression in the AIP10a and / or AIP10b gene results in an increase in yield of at least one of a soybean plant seed number, pod number, hundred-seed weight, leaf area, shoot biomass, and / or root biomass relative to the reference plant lacking the modification.MVS Docket No. P14649WO00 4. The modified soybean plant of any one of embodiments 1 to 3, wherein the decrease of expression in the AIP10a and / or AIP10b gene is about 2-fold to about 46-fold relative to unmodified gene. 5. The modified soybean plant of any one of embodiments 1 to 4, wherein the decrease of expression in the AIP10a and / or AIP10b gene is at least about 2-fold, 4-fold, 6-fold, 8-fold, 10-fold, 12-fold, 14-fold, 16-fold, 18-fold, 20-fold, 22-fold, 24-fold, 26-fold, 28-fold, 30- fold, 32-fold, 34-fold, 36-fold, 38-fold, 40-fold, 42-fold, 44-fold, or 46-fold. 6. The modified soybean plant of any one of embodiments 1 to 5, wherein the targeted modification in the AIP10a and / or AIP10b gene promoter and / or 5’ UTR results in elimination of expression of the AIP10a gene and / or the AIP10b gene. 7. The modified soybean plant of any one of embodiments 1 to 6, wherein said plant comprises at least one targeted modification in an endogenous AIP10a gene promoter. 8. The modified soybean plant of any one of embodiments 1 to 7, wherein said plant comprises at least one targeted modification in an endogenous AIP10b gene promoter. 9. The modified soybean plant of any one of embodiments 1 to 6, comprising at least one targeted modification in both the endogenous AIP10a and AIP10b gene promoters resulting in decreased expression of the endogenous AIP10a and AIP10b gene comprising the promoters relative to a reference soybean plant lacking the modifications, wherein the targeted modification in the AIP10a and AIP10b gene promoter comprises a deletion of one or more nucleotides in each of said promoters. 10. The modified soybean plant of any one of embodiments 1 to 9, wherein the endogenous AIP10a gene promoter comprises the DNA molecule set forth in SEQ ID NO: 1 or an allelic variant thereof and the endogenous AIP10b gene promoter comprises the DNA molecule set forth in SEQ ID NO: 2 or an allelic variant thereof. 11. The modified soybean plant of embodiment 10, wherein the target modification(s) located within the AIP10a promoter of SEQ ID NO: 1, or in an allelic variant thereof, comprises, consists essentially of, or consists of a deletion corresponding to at least: (a) a deletion of nucleotides 1685-1981 of SEQ ID NO: 1; (b) a deletion of nucleotides 1680-1721 of SEQ ID NO: 1; (c) a deletion of nucleotides 1684 – 1704 of SEQ ID NO: 1; or (d) a deletion of nucleotides 1679 – 1693 of SEQ ID NO: 1. 12. The modified soybean plant of embodiment 10, wherein the target modification(s) located within the AIP10a promoter of SEQ ID NO: 1, or in an allelic variant thereof, comprises, consists essentially of, or consists of a deletion of at least a portion of (a) nucleotides 1685-MVS Docket No. P14649WO00 1981 of SEQ ID NO: 1; (b) nucleotides 1680-1721 of SEQ ID NO: 1; (c) nucleotides 1684 – 1704 of SEQ ID NO: 1; or (d) nucleotides 1679 – 1693 of SEQ ID NO: 1. 13. The modified soybean plant of embodiments 10 or 12, wherein the target modification(s) located within the AIP10a promoter and / or 5’ UTR of SEQ ID NO: 1, or in an allelic variant thereof, comprises, consists essentially of, or consists of a deletion of at least 2-19 nucleotides within (a) nucleotides 1685-1981 of SEQ ID NO: 1; (b) nucleotides 1680-1721 of SEQ ID NO: 1; (c) nucleotides 1684 – 1704 of SEQ ID NO: 1; or (d) nucleotides 1679 – 1693 of SEQ ID NO: 1, optionally wherein AIP10a promoter and / or 5’ UTR of SEQ ID NO: 1 or allelic variant thereof comprising the targeted mutation comprises the polynucleotide of SEQ ID NO: 10, 11, or 12 or allelic variant thereof. 14. The modified soybean plant of embodiment 10, wherein the target modification(s) located within the AIP10b promoter of SEQ ID NO: 2, or in an allelic variant thereof, comprises, consists essentially of, or consists of a deletion corresponding to at least: (a) a deletion of nucleotides 1499-1605 of SEQ ID NO: 2; or (b) a deletion of nucleotides 1501-1562 of SEQ ID NO: 2. 15. The modified soybean plant of embodiments 10 or 14, wherein the target modification(s) located within the AIP10b promoter of SEQ ID NO: 2, or in an allelic variant thereof, comprises, consists essentially of, or consists of a deletion of at least a portion of (a) nucleotides 1499-1605 of SEQ ID NO: 2; or (b) nucleotides 1501-1562 of SEQ ID NO: 2. 16. The modified soybean plant of embodiments 10 or 15, wherein the target modification(s) located within the AIP10b promoter of SEQ ID NO: 2, or in an allelic variant thereof, comprises, consists essentially of, or consists of a deletion of at least 2-19 nucleotides within (a) nucleotides 1499-1605 of SEQ ID NO: 2; or (b) nucleotides 1501-1562 of SEQ ID NO: 2, optionally wherein AIP10b promoter of SEQ ID NO: 2 or allelic variant thereof comprising the targeted mutation comprises the polynucleotide of SEQ ID NO: 13, 14, or allelic variant thereof. 17. The modified soybean plant of any one of embodiments 1 to 16, wherein reducing expression of the AIP10a and / or AIP10b gene is associated with a trait comprising an increase in plant biomass, pod number, seed weight, leaf area, stem biomass, shoot biomass, root biomass, and / or fruit production relative to a plant lacking the target modification. 18. A modified soybean plant cell containing a chromosome comprising the targeted modification(s) in the endogenous AIP10a and / or AIP10b gene promoters set forth in any one of embodiments 1 to 17.MVS Docket No. P14649WO00 19. The modified soybean plant cell of embodiment 18, with the proviso that the soybean plant cell is not exclusively produced by an essentially natural biological method. 20. The modified soybean plant cell of embodiments 18 or 19, wherein the soybean plant cell is produced by introducing one or more gene editing molecules into a soybean plant cell and selecting the soybean plant cell comprising the at least one targeted modification(s) in the endogenous AIP10a gene promoter. 21. The modified soybean plant cell of any one of embodiments 18 to 20, wherein the soybean plant cell is homozygous for the at least one targeted modification(s) in the endogenous AIP10a and / or AIP10b gene promoter. 22. A tissue culture of regenerable cells comprising the modified soybean plant cell of embodiments 18 or 21. 23. A modified soybean plant part containing a chromosome comprising the targeted modification(s) in the endogenous AIP10a and / or AIP10b gene promoters set forth in any one of embodiments 1 to 17. 24. The modified soybean plant part of embodiment 23, wherein the plant part is a leaf, stem, root, pod, or seed. 25. The modified soybean plant part of embodiment 24, wherein the soybean seed comprises an elite soybean germplasm, a soybean cultivar, a soybean variety, and / or is homozygous for the targeted modification(s). 26. The modified soybean plant part of embodiments 24 or 25, wherein the soybean seed is heterozygous for the targeted modification(s). 27. The modified soybean plant, plant cell, or plant part of any one of embodiments 1- 21 or 23-26, wherein the at least one targeted modification(s) is a non-natural mutation. 28. A modified soybean seed lot comprising the seed of any one of embodiments 24-26. 29. The modified soybean seed lot of embodiment 28, wherein the seed lot comprises an elite soybean germplasm, a soybean cultivar, a soybean variety, and / or is homozygous for the targeted modification(s) in the endogenous AIP10a and / or AIP10b gene promoter. 30. A DNA molecule containing the targeted modification(s) in the endogenous AIP10a and / or AIP10b gene promoter set forth in any one of embodiments 1 to 17. 31. The DNA molecule of embodiment 30, wherein the DNA molecule comprises, consists essentially of, or consists of the AIP10a promoter deletion in SEQ ID NO: 19, 20, or 21. 32. The DNA molecule of embodiment 30, wherein the DNA molecule comprises, consists essentially of, or consists of the AIP10b promoter deletion in SEQ ID NO: 22, 23, or 24.MVS Docket No. P14649WO00 33. Soybean seed meal comprising the DNA molecule of any one of embodiment 30 to 32, optionally wherein the seed meal is non-regenerable. 34. A biological sample comprising the DNA molecule of any one of embodiments 30 to 32. 35. The modified soybean plant of any of embodiments 1-17, soybean plant cell of any of embodiments 18-21, or the soybean plant part of any of embodiments 23-26, further comprising at least one mutation in the soybean FT1a gene, Ric1 gene, Ric2 gene, NF-YC4, JAG1 gene, BS1 gene, BS2, or TFL1b gene. 36. The modified soybean plant of any of embodiments 1-17, soybean plant cell of any of embodiments 18-21, or the soybean plant part of any of embodiments 23-26, further comprising one or more transgenes, optionally wherein said transgenes encode proteins or RNAs conferring herbicide tolerance or pest tolerance. 37. The modified soybean plant of any of embodiments 1-17, soybean plant cell of any of embodiments 18-21, or the soybean plant part of any of embodiments 23-26, further comprising an A2704-12, A5547-127, BPS-CV127-9, DAS44406-6, DAS68416-4, DAS81419-2, DP305423, GTS 40- 3-2, HOS, A5547-127, MON87701, MON87705, MON87708, MON87769, MON89788, MON98788, MST-FG072-3, or SYHT0H210 transgenic event or modification thereof. 38. A method of soybean seed production comprising crossing the modified soybean plant of any one of embodiments 1 to 17 with a second soybean plant to produce soybean seed and optionally harvesting the seed. 39. A method of soybean seed production comprising allowing the modified soybean plant of any one of embodiments 1 to 17 to self-pollinate to produce plant seed and optionally harvesting the seed. 40. A method of producing a soybean seed lot comprising: (i) growing a population of soybean plants comprising the soybean plant of any one of embodiments 1 to 17; and (ii) harvesting seed from the population of soybean plants of step (i) at maturity, thereby producing the soybean seed lot. 41. A method for producing a soybean by-product comprising at least one processing step of cleaning, cracking, flaking, crushing, macerating, pressing, extracting, expelling, and / or extruding the seed lot of embodiment 40. 42. The method of embodiment 41, wherein the by-product is soybean protein and wherein the soybean seed lot is subjected to processing steps comprising: (i) at least one of a cracking, flaking, crushing, pressing, and / or macerating step; (ii) extracting the cracked, flaked,MVS Docket No. P14649WO00 crushed, pressed, and / or macerated soybean seed product from step (i) with an organic solvent to produce defatted soymeal; and (iii) extracting the defatted soymeal from step (ii) with an aqueous solvent to produce an aqueous fraction comprising soybean protein. 43. The method of embodiment 41, wherein the by-product is soybean oil and wherein the soybean seed lot is subjected to processing steps comprising: (i) at least one of a cracking, flaking, crushing, pressing, and / or macerating step; and (ii) solvent extracting, expelling, and / or extruding step the cracked, flaked, crushed, pressed, and / or macerated soybean seed product from step (i) to produce the oil. 44. A method of producing a commodity soybean plant product, said method comprising processing a modified soybean seed obtained from the modified soybean plant of any one of embodiment 1 to 17 and recovering the commodity plant product from the processed plant or seed. 45. The method of embodiment 44, wherein the commodity plant product is seed meal, starch, silage, oil, or protein. 46. The method of embodiments 44 or 45, wherein the commodity plant product comprises a detectable amount of a DNA molecule comprising the modified endogenous AIP10a gene promoter and the endogenous AIP10b gene promoter. 47. A method of producing soybean plant material, the method comprising: (a) providing the modified soybean plant of any one of embodiments 1 to 17; and, (b) growing the modified soybean plant under conditions that allow for expression of the endogenous soybean AIP10a gene and / or AIP10b gene at levels that are reduced compared to expression levels of the endogenous AIP10a gene and / or AIP10b gene in a reference soybean plant which lacks the modifications. 48. The method of embodiment 47, wherein growing the modified soybean plant further comprises at least one of sowing a soybean seed which germinates and forms the soybean plant, irrigating the soybean seed or plant, and / or treating the soybean plant or the soybean seed with a biological agent, herbicide, insecticide, or fungicide. 49. The method of embodiments 47 or 48, wherein the soybean plant material comprises a seed, optionally wherein the method further comprises harvesting the seed from the plant. 50. A guide RNA molecule comprising a spacer RNA molecule which targets an AIP10a gene promoter of SEQ ID NO: 1 or an allelic variant thereof, optionally wherein the spacer RNA molecule comprises the RNA encoded by SEQ ID NO: 3, 4, or 5.MVS Docket No. P14649WO00 51. A guide RNA molecule comprising a spacer RNA molecule which targets an AIP10b gene promoter of SEQ ID NO: 2 or an allelic variant thereof, optionally wherein the spacer RNA molecule comprises the RNA encoded by SEQ ID NO: 6, 7, or 8. 52. A guide RNA molecule comprising a Cas12 direct repeat element which is operably linked to the spacer RNA of embodiments 50 or 51. 53. A gene editing system comprising: a CRISPR-Cas effector protein and a guide nucleic acid, wherein the guide nucleic acid comprises a spacer sequence that binds to an endogenous AIP10a gene promoter of SEQ ID NO: 1 or allelic variant thereof; or a CRISPR-Cas effector protein and a guide nucleic acid, wherein the guide nucleic acid comprises a spacer sequence that binds to an endogenous AIP10b gene promoter of SEQ ID NO: 2 or allelic variant thereof. 54. An expression cassette comprising: a polynucleotide encoding CRISPR-Cas effector protein comprising a cleavage domain and the guide RNA molecule of embodiments 51 or 52. 55. A method for generating a soybean plant of any of embodiments 1-17, soybean plant cell of any of embodiments 18-21, or the soybean plant part of any of embodiments 23-26, wherein the at least one targeted modification is introduced by: (i) directing both: (a) a guide RNA (gRNA) molecule which targets the endogenous AIP10a gene promoter of SEQ ID NO: 1 or an allelic variant thereof and (b) an RNA dependent endonuclease (RDE) which recognizes the gRNA molecule, to the genome of a target soybean plant cell; and (ii) isolating a soybean plant cell, soybean plant part, or soybean plant comprising the at least one targeted modification in the endogenous soybean AIP10a gene promoter of SEQ ID NO: 1 or an allelic variant thereof. 56. The method of embodiment 55, wherein the endogenous AIP10a gene promoter is targeted and the gRNA comprises a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 3, 4, or 5. 57. The method of embodiment 55, wherein the endogenous AIP10a gene promoter is targeted and the gRNA comprises a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 6, 7, or 8. 58. The method of embodiment 55, wherein the directing of the gRNA and the RDE to the genome of the target soybean plant cell comprises introducing the gRNA, the RDE, aMVS Docket No. P14649WO00 gRNA / RDE complex, a nucleic acid encoding the gRNA, and / or a nucleic acid encoding the RDE into the target soybean plant cell. 59. The method of any of embodiments 55-58, wherein the soybean plant cell, soybean plant part, or soybean plant comprising the at least one targeted modification is identified by: (i) analyzing a polynucleotide comprising at least a portion of SEQ ID NO: 1 or an allelic variant thereof and / or at least a portion of SEQ ID NO: 2 or an allelic variant thereof in one or more candidate plant cells, plant parts, or plants; and / or (ii) analyzing yield of the soybean plant part, soybean plant, or soybean plant grown from the soybean plant cell, wherein the yield comprises least one of a soybean plant seed number, pod number, hundred-seed weight, leaf area, shoot biomass, or root biomass in comparison to a wild-type or control soybean plant lacking the at least one targeted modification, and wherein an increase in the yield indicates that the soybean plant cell, soybean plant part, or soybean plant comprises the at least one targeted modification. 60. Use of the modified soybean plant of any one of embodiments 1 to 17, seed obtained therefrom, or a seed of any of embodiments 24-26 to: (a) grow a soybean plant with improved yield of at least one of a soybean plant seed number, pod number, hundred-seed weight, leaf area, shoot biomass, or root biomass in comparison to a soybean plant lacking the modification; (b) harvest soybean plant seed comprising the targeted modifications; (c) produce a commodity product; or (d) breed soybean plants with improved yield of at least one of a soybean plant seed number, pod number, hundred-seed weight, leaf area, shoot biomass, or root biomass in comparison to a soybean plant lacking the modification. 61. Use of the modified soybean plant cell of any of embodiments 18-21, the modified soybean plant part of any of embodiments 23-26, the modified soybean seed lot of embodiments 28 or 29, or the modified soybean plant of any of embodiments 1-17 to produce a modified soybean seed. 62. Use of the modified soybean plant cell of any of embodiments 18-21, the modified soybean plant part of any of embodiments 23-26, the modified soybean seed lot of embodiments 28 or 29, or the modified soybean plant of any of embodiments 1-17 to grow a modified soybean crop. 63. Use of the soybean plant cell of any of embodiments 18-21, the modified soybean plant part of any of embodiments 23-26, the modified soybean seed lot of embodiments 28 or 29, or the modified soybean plant of any of embodiments 1-17 to obtain a soybean by-product.MVS Docket No. P14649WO00 64. The use of embodiment 63, wherein the soybean by-product comprises soybean flour, meal, protein, oil, syrup, or starch. 65. Use of the guide RNA molecule of any of embodiments 50-52, the gene editing system of embodiment 53, or the expression cassette of embodiment 54 to introduce at least one mutation in the endogenous AIP10a gene promoter of SEQ ID NO: 1 or an allelic variant thereof and / or at least one mutation in the endogenous AIP10b gene promoter of SEQ ID NO: 2 or allelic variant thereof. 66. A method of identifying a biological sample comprising a DNA molecule containing the targeted modification(s) in the endogenous AIP10a and / or AIP10b gene promoter set forth in any one of embodiments 1 to 17, comprising the step of detecting the presence of the DNA molecule in the biological sample. 67. A method of reducing the expression of an endogenous AIP10a gene in a soybean plant, the method comprising introducing the targeted modification(s) in the endogenous AIP10a gene promoter set forth in any one of embodiments 1 to 17. 68. A polynucleotide comprising at least one targeted modification(s) to the endogenous AIP10a gene promoter of any of embodiments 1 to 17, optionally wherein the polynucleotide is isolated. 69. A method of producing a plant comprising an added desired trait, said method comprising introducing a transgene conferring the desired trait into the modified soybean plant of any one of embodiments 1 to 17. 70. A polynucleotide comprising at least one targeted modification(s) to the endogenous AIP10b gene promoter of embodiments 1 to 17, optionally wherein the polynucleotide is isolated. 71. A method of producing a plant comprising an added desired trait, said method comprising introducing a transgene conferring the desired trait into the modified soybean plant of any one of embodiments 1 to 17. 72. A modified soybean plant cell, soybean plant part, or soybean plant comprising at least one targeted modification obtained by the process comprising: (i) directing both: (a) a guide RNA (gRNA) molecule which targets the endogenous AIP10a gene promoter of SEQ ID NO: 1 or an allelic variant thereof and / or a gRNA molecule which targets the endogenous AIP10b gene promoter of SEQ ID NO: 2 or an allelic variant thereof and (b) an RNA dependent endonuclease (RDE) which recognizes the gRNA molecule, to the genome of a target soybean plant cell; andMVS Docket No. P14649WO00 (ii) isolating a soybean plant cell, soybean plant part, or soybean plant comprising the at least one targeted modification in the endogenous soybean AIP10a gene promoter of SEQ ID NO: 1 or an allelic variant thereof; wherein the at least one targeted modification results in decreased expression of an endogenous AIP10a and / or AIP10b gene relative to a reference soybean plant cell, soybean plant part, or soybean plant lacking the modification. 73. The modified soybean plant cell, soybean plant part, or soybean plant of embodiment 72, wherein the endogenous AIP10a gene promoter is targeted and the gRNA comprises a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 3, 4, or 5. 74. The modified soybean plant cell, soybean plant part, or soybean plant of embodiment 72 or 73, wherein the endogenous AIP10a gene promoter is targeted and the gRNA comprises a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 6, 7, or 8. 75. The modified soybean plant cell, soybean plant part, or soybean plant of embodiment 72, 73, or 74, wherein the directing of the gRNA and the RDE to the genome of the target soybean plant cell comprises introducing the gRNA, the RDE, a gRNA / RDE complex, a nucleic acid encoding the gRNA, and / or a nucleic acid encoding the RDE into the target soybean plant cell. 76. The modified soybean plant cell, soybean plant part, or soybean plant of any one of embodiments 72 to 75, wherein the at least one targeted modification is in (i) an endogenous AIP10a gene promoter and / or AIP10a gene 5’ untranslated region (5’ UTR), and / or (ii) an endogenous AIP10b gene promoter and / or AIP10b gene 5’ UTR. EXAMPLES Example 1. Generation of soybean with an AIP10a gene and / or AIP10b gene promoter mutations

[0098] Vectors were created to transform soybean plants and disrupt the promoter of the AIP10a (Glyma.07G021400; SEQ ID NO: 1) or AIP10b (Glyma.08G220400; SEQ ID NO: 2) genes through CRISPR-mediated gene editing. Vectors were created to encode 1) a gRNA for AIP10a, 2) a gRNA for AIP10b, or 3) gRNAs for AIP10a and AIP10b. Vectors were constructed using the strategy and techniques described by Čermák et al., 2017, The Plant Cell. 29 (6) 1196-1217; DOI: 10.1105 / tpc.16.00922). The vectors have the following two functional expression cassettes between the right and left T-DNA border. A dicot ubiquitin gene promoter and 5’ untranslated region (UTR) drives the expression a type V CRISPR-Cas nucleaseMVS Docket No. P14649WO00 transcript. The Cas nuclease encoding gene had a SV40 nuclear localization signal (NLS) fused to the 5’ end and a nucleoplasmin NLS fused to the 3’ end. The coding sequence was followed by an Arabidopsis thaliana heat shock gene terminator. Other expression cassettes comprised an Arabidopsis thaliana U6-26 promoter driving the expression of a CRISPR guide RNA comprising a crRNA fused to a spacer RNA (SEQ ID NOs: 3-8) were designed to target the promoter of the Glycine max AIP10a and AIP10b genes and followed by an RNA polymerase iii termination signal.

[0099] The plasmids were transformed into Agrobacterium tumefaciens EHA105 (Hood et al., 1993, Transgenic Research. 2: 208–218. doi:10.1007 / BF01977351) by electroporation following standard techniques. Frozen glycerol stocks were prepared for use in plant transformation.

[0100] Transgenic T0 soybean events were made by Agrobacterium-mediated transformation with the plasmids and guide RNA’s singularly to create large deletions in the promoter region. Sterilized soybean seeds were imbibed in water overnight, and explants were prepared as mature cotyledon halves with trimmed hypocotyls. The explants went through the typical transformation and regeneration steps of infection and co-cultivation, shoot induction and elongation and selection, rooting, and transplanting to soil to produce T1 seeds (see, for example, Li et al, Optimization of Agrobacterium-Mediated Transformation in Soybean (2017) Frontiers in Plant Science v8 Article 246; Pareddy et al. Transgenic Res.2020 Jun;29(3):267- 281. doi: 10.1007 / s11248-020-00198-8).

[0101] T0 plants were grown and genotyped by amplicon sequencing (AmpSeq).

[0102] A wide range of AIP10a and AIP10b promoter and / or 5’ UTR deletion alleles were created. For AIP10a, these deletions range from 369 bp upstream of the ATG start site to a few bases upstream of the ATG translation initiation codon. For AIP10b, these deletions range from 502 bp upstream of the ATG translation initiation codon to about 395 bp upstream of the ATG translation initiation codon.

[0103] Genotypes recovered included SENG230090, SENG230053, SENG230067, SENG230074, SENG230161, and SENG230202. The SENG230090 genotype has a 15 bp deletion (SEQ ID NO: 9) resulting in a promoter mutation and decreasing AIP10a expression. The SENG230053 genotype has a 21 bp deletion (SEQ ID NO: 10) resulting in a promoter mutation which decreases AIP10a expression. The SENG230067 genotype has a 42 bp deletion (SEQ ID NO: 11) resulting in a promoter mutation which decreases AIP10a expression. The SENG230074 genotype has a 297 bp deletion (SEQ ID NO: 12) resulting in a promoter and 5’MVS Docket No. P14649WO00 UTR mutation and decreasing AIP10a expression. The SENG230161 genotype has a 62 bp deletion (SEQ ID NO: 13) resulting in a promoter mutation and decreasing AIP10b expression. The SENG230202 genotype has a 107 bp deletion (SEQ ID NO: 14) resulting in a promoter mutation and decreasing AIP10b expression. Example 2. Molecular characterization and performance of soybean with a AIP10a gene promoter mutations

[0104] T2 seeds of the homozygous AIP10a mutant lines from Example 1 were increased and planted in plots in the field along with checks and lines having unrelated edits. Each plot was a single row in randomized block design where each genotype was repeated three times with a target density of 140,000 plants per acre.

[0105] Leaf tissue was harvested 35 days after sowing. The quantitative RT-PCR data was generated on gene expression of the youngest partially open trifoliate leaf relative to GMAct11 (Glyma.18G290800). Expression levels are the average of three biological replicates, where each replicate is a different plot, and plot tissue was harvested from 5 individual plants and pooled (Table 2). Values indicated with asterisk are significantly different from wild type (p<0.05, Tukey’s HSD test). SD = standard deviation. N = 3.

[0106] Table 2. Gene Expression in Youngest Partially Open Trifoliate Leaf AIP10a AIP10b

[0107] Leaf tissue was harvested 35 days after sowing. The quantitative RT-PCR data was generated on gene expression of the youngest fully open trifoliate leaf relative to GMAct11. Expression levels are the average of three biological replicates, where each replicate is a different plot, and plot tissue was harvested from 5 individual plants and pooled (Table 3). Values indicated with asterisk are significantly different from wild type (p<0.05, Tukey’s HSD test). SD = standard deviation. N = 3.MVS Docket No. P14649WO00

[0108] Table 3. Gene Expression in Youngest Fully Open Trifoliate Leaf AIP10a AIP10b Average SD Average SD10- 16 plants per plot. Data on total pod count per plant from field trials showed a tendency towards higher pod count per plant per plot for AIP10a compared to adjacently grown checks (e.g., amorphic allele (or “null”) and wild type), means adjusted for effects of block and stand count (Table 4).

[0110] Seed counts were taken at the R8 stage (full maturation) on individual plants, 10-16 plants per plot. Data on total seed count per plant from field trials showed a tendency towards higher seed count per plant per plot for AIP10A compared to adjacently grown checks (e.g., amorphic allele (or “null”) and wild type), means adjusted for effects of block and stand count (Table 4).

[0111] Hundred seed weights (HSW) were measured at the R8 stage (full maturation) on individual plants, 10-16 plants per plot. HSW per plant from field trials did not show a change in HSW per plant per plot for AIP10a compared to adjacently grown checks (e.g., null and wild type), means adjusted for effects of block and stand count (Table 4).

[0112] Seed weights were measured at the R8 stage (full maturation) on individual plants, 10- 16 plants per plot. Data on seed weight per plant from field trials did not show a change in seed weight per plant per plot for AIP10a compared to adjacently grown checks (e.g., null and wild type), means adjusted for effects of block and stand count (Table 4).

[0113] Table 4. Soybean Phenotypes Pod count per Seed count per HSW Seed weightMVS Docket No. P14649WO00 Wild type 77.280 5.561 163.790 13.370 12.753 0.339 21.201 1.868 Null 77.580 4.866 168.858 11.728 12.731 0.299 22.032 1.634 4 1 0 2 Exe promoter mutations

[0114] Seeds of the homozygous AIP10b mutant lines from Example 1 will be increased and planted in plots in the field along with checks and lines having unrelated edits. Each plot will be a single row in randomized block design where each genotype is repeated three times with a target density of about 140,000 plants per acre.

[0115] Leaf tissue will be harvested about 30 to 40 days after sowing. Quantitative RT-PCR data will be generated on gene expression of the youngest partially open trifoliate leaf relative to GMAct11 or another control gene. Expression levels will be calculated from the average of at least three biological replicates, where each replicate is a different plot, and plot tissue will be harvested from about 3-5 individual plants and pooled.

[0116] Leaf tissue will be harvested 30-40 days after sowing. Quantitative RT-PCR data will be generated on gene expression of the youngest fully open trifoliate leaf relative to GMAct11. Expression levels will be calculated from an average of three biological replicates, where each replicate is a different plot, and plot tissue was harvested from 3-5 individual plants and pooled.

[0117] Total pods counts will be taken at the R8 stage (full maturation) on individual plants, 5 plants per plot. Anticipated data on total pod count per plant from field trials will show higher pod count per plant per plot for AIP10b compared to adjacently grown checks (e.g., null and wild type).

[0118] HSWs will be measured at the R8 stage (full maturation) on individual plants, about 5 plants per plot. Anticipated data on total HSW per plant from field trials will show no change in HSW per plant per plot for AIP10b compared to adjacently grown checks (e.g., null and wild type).

[0119] Seed weights will be measured at the R8 stage (full maturation) on individual plants, about 5 plants per plot. Anticipated data on seed weight per plant from field trials will show noMVS Docket No. P14649WO00 change in seed weight per plant per plot for AIP10b compared to adjacently grown checks (e.g., null and wild type)

[0120] All cited patents and patent publications referred to in this application are incorporated herein by reference in their entirety. All of the materials and methods disclosed and claimed herein can be made and used without undue experimentation as instructed by the above disclosure and illustrated by the examples. Although the materials and methods of this disclosure have been described in terms of embodiments and illustrative examples, it will be apparent to those of skill in the art that substitutions and variations can be applied to the materials and methods described herein without departing from the concept, spirit, and scope of the disclosure. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope, and concept of the disclosure as encompassed by the embodiments of the disclosures recited herein and the specification and appended claims.

Claims

MVS Docket No. P14649WO00 CLAIMS What is claimed is:

1. A modified soybean plant comprising at least one targeted modification in (i) an endogenous AIP10a gene promoter and / or AIP10a gene 5’ untranslated region (5’ UTR), and / or (ii) an endogenous AIP10b gene promoter and / or AIP10b gene 5’ UTR resulting in decreased expression of an endogenous AIP10a and / or AIP10b gene relative to a reference soybean plant lacking the modification.

2. The modified soybean plant of claim 1, wherein the targeted modification in the AIP10a and / or AIP10b gene promoter and / or 5’ UTR comprises a deletion of one or more nucleotides.

3. The modified soybean plant of claims 1 or 2, wherein the decrease of expression in the AIP10a and / or AIP10b gene results in an increase in yield of at least one of a soybean plant seed number, pod number, hundred-seed weight, leaf area, shoot biomass, and / or root biomass relative to the reference plant lacking the modification.

4. The modified soybean plant of claims 1 or 2, wherein the decrease of expression in the AIP10a and / or AIP10b gene is about 2-fold to about 46-fold relative to unmodified gene.

5. The modified soybean plant of claim 4, wherein the decrease of expression in the AIP10a and / or AIP10b gene is at least about 2-fold, 4-fold, 6-fold, 8-fold, 10-fold, 12-fold, 14-fold, 16-fold, 18-fold, 20-fold, 22-fold, 24-fold, 26-fold, 28-fold, 30-fold, 32-fold, 34-fold, 36- fold, 38-fold, 40-fold, 42-fold, 44-fold, or 46-fold.

6. The modified soybean plant of claims 1 or 2, wherein the targeted modification in the AIP10a and / or AIP10b gene promoter and / or 5’ UTR results in elimination of expression of the AIP10a gene and / or the AIP10b gene.

7. The modified soybean plant of claims 1 or 2, wherein said plant comprises at least one targeted modification in an endogenous AIP10a gene promoter.

8. The modified soybean plant of claims 1 or 2, wherein said plant comprises at least one targeted modification in an endogenous AIP10b gene promoter.MVS Docket No. P14649WO00 9. The modified soybean plant of claims 1 or 2, comprising at least one targeted modification in both the endogenous AIP10a and AIP10b gene promoters resulting in decreased expression of the endogenous AIP10a and AIP10b gene comprising the promoters relative to a reference soybean plant lacking the modifications, wherein the targeted modification in the AIP10a and AIP10b gene promoter comprises a deletion of one or more nucleotides in each of said promoters.

10. The modified soybean plant of claims 1 or 2, wherein the endogenous AIP10a gene promoter comprises the DNA molecule set forth in SEQ ID NO: 1 or an allelic variant thereof and the endogenous AIP10b gene promoter comprises the DNA molecule set forth in SEQ ID NO: 2 or an allelic variant thereof.

11. The modified soybean plant of claim 10, wherein the target modification(s) located within the AIP10a promoter and / or 5’UTR of SEQ ID NO: 1, or in an allelic variant thereof, comprises, consists essentially of, or consists of a deletion corresponding to at least: (a) a deletion of nucleotides 1685-1981 of SEQ ID NO: 1; (b) a deletion of nucleotides 1680-1721 of SEQ ID NO: 1; (c) a deletion of nucleotides 1684 – 1704 of SEQ ID NO: 1; or (d) a deletion of nucleotides 1679 – 1693 of SEQ ID NO:

1.

12. The modified soybean plant of claim 10, wherein the target modification(s) located within the AIP10a promoter and / or 5’UTR of SEQ ID NO: 1, or in an allelic variant thereof, comprises, consists essentially of, or consists of a deletion of at least a portion of (a) nucleotides 1685-1981 of SEQ ID NO: 1; (b) nucleotides 1680-1721 of SEQ ID NO: 1; (c) nucleotides 1684 – 1704 of SEQ ID NO: 1; or (d) nucleotides 1679 – 1693 of SEQ ID NO:

1.

13. The modified soybean plant of claims 10 or 12, wherein the target modification(s) located within the AIP10a promoter and / or 5’ UTR of SEQ ID NO: 1, or in an allelic variant thereof, comprises, consists essentially of, or consists of a deletion of at least 2-19 nucleotides within (a) nucleotides 1685-1981 of SEQ ID NO: 1; (b) nucleotides 1680-1721 of SEQ ID NO: 1; (c) nucleotides 1684 – 1704 of SEQ ID NO: 1; or (d) nucleotides 1679 – 1693 of SEQ ID NO: 1, optionally wherein AIP10a promoter and / or 5’ UTR of SEQ ID NO: 1 or allelic variant thereof comprising the targeted mutation comprises the polynucleotide of SEQ ID NO: 10, 11, or 12 or allelic variant thereof.MVS Docket No. P14649WO00 14. The modified soybean plant of claim 10, wherein the target modification(s) located within the AIP10b promoter of SEQ ID NO: 2, or in an allelic variant thereof, comprises, consists essentially of, or consists of a deletion corresponding to at least: (a) a deletion of nucleotides 1499-1605 of SEQ ID NO: 2; or (b) a deletion of nucleotides 1501-1562 of SEQ ID NO:

2.

15. The modified soybean plant of claims 10 or 14, wherein the target modification(s) located within the AIP10b promoter of SEQ ID NO: 2, or in an allelic variant thereof, comprises, consists essentially of, or consists of a deletion of at least a portion of (a) nucleotides 1499- 1605 of SEQ ID NO: 2; or (b) nucleotides 1501-1562 of SEQ ID NO:

2.

16. The modified soybean plant of claims 10 or 15, wherein the target modification(s) located within the AIP10b promoter of SEQ ID NO: 2, or in an allelic variant thereof, comprises, consists essentially of, or consists of a deletion of at least 2-19 nucleotides within (a) nucleotides 1499-1605 of SEQ ID NO: 2; or (b) nucleotides 1501-1562 of SEQ ID NO: 2, optionally wherein AIP10b promoter of SEQ ID NO: 2 or allelic variant thereof comprising the targeted mutation comprises the polynucleotide of SEQ ID NO: 13, 14, or allelic variant thereof.

17. The modified soybean plant of claims 1 or 2, wherein reducing expression of the AIP10a and / or AIP10b gene is associated with a trait comprising an increase in plant biomass, pod number, seed weight, leaf area, stem biomass, shoot biomass, root biomass, and / or fruit production relative to a plant lacking the target modification.

18. A modified soybean plant cell containing a chromosome comprising the targeted modification(s) in the endogenous AIP10a and / or AIP10b gene promoters set forth in claims 1 or 2.

19. The modified soybean plant cell of claim 18, with the proviso that the soybean plant cell is not exclusively produced by an essentially natural biological method.

20. The modified soybean plant cell of claims 18 or 19, wherein the soybean plant cell is produced by introducing one or more gene editing molecules into a soybean plant cell and selecting the soybean plant cell comprising the at least one targeted modification(s) in the endogenous AIP10a gene promoter.MVS Docket No. P14649WO00 21. The modified soybean plant cell of claims 18 or 19, wherein the soybean plant cell is homozygous for the at least one targeted modification(s) in the endogenous AIP10a and / or AIP10b gene promoter.

22. A tissue culture of regenerable cells comprising the modified soybean plant cell of claims 18 or 21.

23. A modified soybean plant part containing a chromosome comprising the targeted modification(s) in the endogenous AIP10a and / or AIP10b gene promoters set forth in claims 1 or 2.

24. The modified soybean plant part of claim 23, wherein the plant part is a leaf, stem, root, pod, or seed.

25. The modified soybean plant part of claim 24, wherein the soybean seed comprises an elite soybean germplasm, a soybean cultivar, a soybean variety, and / or is homozygous for the targeted modification(s).

26. The modified soybean plant part of claims 24 or 25, wherein the soybean seed is heterozygous for the targeted modification(s).

27. The modified soybean plant, plant cell, or plant part of claims 1 or 18, wherein the at least one targeted modification(s) is a non-natural mutation.

28. A modified soybean seed lot comprising the seed of claims 24 or 25.

29. The modified soybean seed lot of claim 28, wherein the seed lot comprises an elite soybean germplasm, a soybean cultivar, a soybean variety, and / or is homozygous for the targeted modification(s) in the endogenous AIP10a and / or AIP10b gene promoter.

30. A DNA molecule containing the targeted modification(s) in the endogenous AIP10a and / or AIP10b gene promoter set forth in claims 1 or 2.

31. The DNA molecule of claim 30, wherein the DNA molecule comprises, consists essentially of, or consists of the AIP10a promoter deletion in SEQ ID NO: 19, 20, or 21.

32. The DNA molecule of claim 30, wherein the DNA molecule comprises, consists essentially of, or consists of the AIP10b promoter deletion in SEQ ID NO: 22, 23, or 24.MVS Docket No. P14649WO00 33. Soybean seed meal comprising the DNA molecule of claim 30, optionally wherein the seed meal is non-regenerable.

34. A biological sample comprising the DNA molecule of claim 30.

35. The modified soybean plant of claims 1 or 2, further comprising at least one mutation in the soybean FT1a gene, Ric1 gene, Ric2 gene, JAG1 gene, BS1 gene, BS2, or TFL1b gene.

36. The modified soybean plant of claims 1 or 2, further comprising one or more transgenes, optionally wherein said transgenes encode proteins or RNAs conferring herbicide tolerance or pest tolerance.

37. The modified soybean plant of claims 1 or 2, further comprising an A2704-12, A5547- 127, BPS-CV127-9, DAS44406-6, DAS68416-4, DAS81419-2, DP305423, GTS 40- 3-2, HOS, A5547-127, MON87701, MON87705, MON87708, MON87769, MON89788, MON98788, MST-FG072-3, or SYHT0H210 transgenic event or modification thereof.

38. A method of soybean seed production comprising crossing the modified soybean plant of claims 1 or 2 with a second soybean plant to produce soybean seed and optionally harvesting the seed.

39. A method of soybean seed production comprising allowing the modified soybean plant of claims 1 or 2 to self-pollinate to produce plant seed and optionally harvesting the seed.

40. A method of producing a soybean seed lot comprising: (i) growing a population of soybean plants comprising the soybean plant of claims 1 or 2; and (ii) harvesting seed from the population of soybean plants of step (i) at maturity, thereby producing the soybean seed lot.

41. A method for producing a soybean by-product comprising at least one processing step of cleaning, cracking, flaking, crushing, macerating, pressing, extracting, expelling, and / or extruding the seed lot of claim 40.

42. The method of claim 41, wherein the by-product is soybean protein and wherein the soybean seed lot is subjected to processing steps comprising: (i) at least one of a cracking, flaking, crushing, pressing, and / or macerating step; (ii) extracting the cracked, flaked, crushed, pressed, and / or macerated soybean seed product from step (i) with an organicMVS Docket No. P14649WO00 solvent to produce defatted soymeal; and (iii) extracting the defatted soymeal from step (ii) with an aqueous solvent to produce an aqueous fraction comprising soybean protein.

43. The method of claim 41, wherein the by-product is soybean oil and wherein the soybean seed lot is subjected to processing steps comprising: (i) at least one of a cracking, flaking, crushing, pressing, and / or macerating step; and (ii) solvent extracting, expelling, and / or extruding step the cracked, flaked, crushed, pressed, and / or macerated soybean seed product from step (i) to produce the oil.

44. A method of producing a commodity soybean plant product, said method comprising processing a modified soybean seed obtained from the modified soybean plant of claims 1 or 2 and recovering the commodity plant product from the processed plant or seed.

45. The method of claim 44, wherein the commodity plant product is seed meal, starch, silage, oil, or protein.

46. The method of claim 44 or 45, wherein the commodity plant product comprises a detectable amount of a DNA molecule comprising the modified endogenous AIP10a gene promoter and the endogenous AIP10b gene promoter.

47. A method of producing soybean plant material, the method comprising: (a) providing the modified soybean plant of claims 1 or 2; and, (b) growing the modified soybean plant under conditions that allow for expression of the endogenous soybean AIP10a gene and / or AIP10b gene at levels that are reduced compared to expression levels of the endogenous AIP10a gene and / or AIP10b gene in a reference soybean plant which lacks the modifications.

48. The method of claim 47, wherein growing the modified soybean plant further comprises at least one of sowing a soybean seed which germinates and forms the soybean plant, irrigating the soybean seed or plant, and / or treating the soybean plant or the soybean seed with a biological agent, herbicide, insecticide, or fungicide.

49. The method of claims 47 or 48, wherein the soybean plant material comprises a seed, optionally wherein the method further comprises harvesting the seed from the plant.MVS Docket No. P14649WO00 50. A guide RNA molecule comprising a spacer RNA molecule which targets an AIP10a gene promoter of SEQ ID NO: 1 or an allelic variant thereof, optionally wherein the spacer RNA molecule comprises the RNA encoded by SEQ ID NO: 3, 4, or 5.

51. A guide RNA molecule comprising a spacer RNA molecule which targets an AIP10b gene promoter of SEQ ID NO: 2 or an allelic variant thereof, optionally wherein the spacer RNA molecule comprises the RNA encoded by SEQ ID NO: 6, 7, or 8.

52. A guide RNA molecule comprising a Cas12 direct repeat element which is operably linked to the spacer RNA of claims 50 or 51.

53. A gene editing system comprising: a CRISPR-Cas effector protein and a guide nucleic acid, wherein the guide nucleic acid comprises a spacer sequence that binds to an endogenous AIP10a gene promoter of SEQ ID NO: 1 or allelic variant thereof; or a CRISPR-Cas effector protein and a guide nucleic acid, wherein the guide nucleic acid comprises a spacer sequence that binds to an endogenous AIP10b gene promoter of SEQ ID NO: 2 or allelic variant thereof.

54. An expression cassette comprising: a polynucleotide encoding CRISPR-Cas effector protein comprising a cleavage domain and the guide RNA molecule of claims 51 or 52.

55. A method for generating a modified soybean plant of claim 1 or a modified soybean plant cell of claim 18, wherein the at least one targeted modification is introduced by: (i) directing both: (a) a guide RNA (gRNA) molecule which targets the endogenous AIP10a gene promoter of SEQ ID NO: 1 or an allelic variant thereof and (b) an RNA dependent endonuclease (RDE) which recognizes the gRNA molecule, to the genome of a target soybean plant cell; and (ii) isolating a soybean plant comprising the at least one targeted modification in the endogenous soybean AIP10a gene promoter of SEQ ID NO: 1 or an allelic variant thereof.MVS Docket No. P14649WO00 56. The method of claim 55, wherein the endogenous AIP10a gene promoter is targeted and the gRNA comprises a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 3, 4, or 5.

57. The method of claim 55, wherein the endogenous AIP10a gene promoter is targeted and the gRNA comprises a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 6, 7, or 8.

58. The method of claim 55, wherein the directing of the gRNA and the RDE to the genome of the target soybean plant cell comprises introducing the gRNA, the RDE, a gRNA / RDE complex, a nucleic acid encoding the gRNA, and / or a nucleic acid encoding the RDE into the target soybean plant cell.

59. The method of claim 55, wherein the soybean plant cell or soybean plant comprising the at least one targeted modification is identified by: (i) analyzing a polynucleotide comprising at least a portion of SEQ ID NO: 1 or an allelic variant thereof and / or at least a portion of SEQ ID NO: 2 or an allelic variant thereof in one or more candidate plant cells, plant parts, or plants; and / or (ii) analyzing yield of the soybean plant part, soybean plant, or soybean plant grown from the soybean plant cell, wherein the yield comprises least one of a soybean plant seed number, pod number, hundred-seed weight, leaf area, shoot biomass, or root biomass in comparison to a wild-type or control soybean plant lacking the at least one targeted modification, and wherein an increase in the yield indicates that the soybean plant cell, soybean plant part, or soybean plant comprises the at least one targeted modification.

60. Use of the modified soybean plant of claim 1, seed obtained therefrom, or a seed of claim 24 to: (a) grow a soybean plant with improved yield of at least one of a soybean plant seed number, pod number, hundred-seed weight, leaf area, shoot biomass, or root biomass in comparison to a soybean plant lacking the modification; (b) harvest soybean plant seed comprising the targeted modifications; (c) produce a commodity product; or (d) breed soybean plants with improved yield of at least one of a soybean plant seed number, pod number, hundred-seed weight, leaf area, shoot biomass, or root biomass in comparison to a soybean plant lacking the modification.

61. Use of the modified soybean plant of claim 1 or the modified soybean plant cell of claim 18 to produce a modified soybean seed.MVS Docket No. P14649WO00 62. Use of the modified soybean plant of claim 1 or the modified soybean plant cell of claim 18 to grow a modified soybean crop.

63. Use of the modified soybean plant of claim 1 or the modified soybean plant cell of claim 18 to obtain a soybean by-product.

64. The use of claim 63, wherein the soybean by-product comprises soybean flour, meal, protein, oil, syrup, or starch.

65. Use of the guide RNA molecule of claim 50 or the gene editing system of claim 53 to introduce at least one mutation in the endogenous AIP10a gene promoter of SEQ ID NO: 1 or an allelic variant thereof and / or at least one mutation in the endogenous AIP10b gene promoter of SEQ ID NO: 2 or allelic variant thereof.

66. A method of identifying a biological sample comprising a DNA molecule containing the targeted modification(s) in the endogenous AIP10a and / or AIP10b gene promoter set forth in claims 1 or 2, comprising the step of detecting the presence of the DNA molecule in the biological sample.

67. A method of reducing the expression of an endogenous AIP10a gene in a soybean plant, the method comprising introducing the targeted modification(s) in the endogenous AIP10a gene promoter set forth in claims 1 or 2.

68. A polynucleotide comprising at least one targeted modification(s) to the endogenous AIP10a gene promoter of claims 1 or 2, optionally wherein the polynucleotide is isolated.

69. A method of producing a plant comprising an added desired trait, said method comprising introducing a transgene conferring the desired trait into the modified soybean plant of claims 1 or 2.

70. A polynucleotide comprising at least one targeted modification(s) to the endogenous AIP10b gene promoter of claims 1 or 2, optionally wherein the polynucleotide is isolated.

71. A method of producing a plant comprising an added desired trait, said method comprising introducing a transgene conferring the desired trait into the modified soybean plant of claims 1 or 2.MVS Docket No. P14649WO00 72. A modified soybean plant cell, soybean plant part, or soybean plant comprising at least one targeted modification obtained by the process comprising: (i) directing both: (a) a guide RNA (gRNA) molecule which targets the endogenous AIP10a gene promoter of SEQ ID NO: 1 or an allelic variant thereof and / or a gRNA molecule which targets the endogenous AIP10b gene promoter of SEQ ID NO: 2 or an allelic variant thereof and (b) an RNA dependent endonuclease (RDE) which recognizes the gRNA molecule, to the genome of a target soybean plant cell; and (ii) isolating a soybean plant cell, soybean plant part, or soybean plant comprising the at least one targeted modification in the endogenous soybean AIP10a gene promoter of SEQ ID NO: 1 or an allelic variant thereof; wherein the at least one targeted modification results in decreased expression of an endogenous AIP10a and / or AIP10b gene relative to a reference soybean plant cell, soybean plant part, or soybean plant lacking the modification.

73. The modified soybean plant cell, soybean plant part, or soybean plant of claim 72, wherein the endogenous AIP10a gene promoter is targeted and the gRNA comprises a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 3, 4, or 5.

74. The modified soybean plant cell, soybean plant part, or soybean plant of claim 72, wherein the endogenous AIP10a gene promoter is targeted and the gRNA comprises a spacer RNA molecule comprising the RNA encoded by SEQ ID NO: 6, 7, or 8.

75. The modified soybean plant cell, soybean plant part, or soybean plant of claim 72, wherein the directing of the gRNA and the RDE to the genome of the target soybean plant cell comprises introducing the gRNA, the RDE, a gRNA / RDE complex, a nucleic acid encoding the gRNA, and / or a nucleic acid encoding the RDE into the target soybean plant cell.

76. The modified soybean plant cell, soybean plant part, or soybean plant of claim 72, wherein the at least one targeted modification is in (i) an endogenous AIP10a gene promoter and / or AIP10a gene 5’ untranslated region (5’ UTR), and / or (ii) an endogenous AIP10b gene promoter and / or AIP10b gene 5’ UTR.

77. The modified soybean plant part or soybean plant of claim 72, wherein the decreased expression of the AIP10a and / or AIP10b gene is associated with a trait comprising an increaseMVS Docket No. P14649WO00 in plant biomass, pod number, seed weight, leaf area, stem biomass, shoot biomass, root biomass, and / or fruit production relative to a plant lacking the target modification.

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