Soybeans with combinations of transcriptional regulatory gene mutations

Abstract

The disclosure relates to novel soybean plants, plant parts, and nucleotide sequences in soybean plants comprising: (i) a loss-of-function allele in the endogenous JAG1 gene and a loss-of-function allele in the endogenous JAG2 gene, where at least one of the loss-of-function alleles of the endogenous JAG1 or JAG2 genes is a hypomorphic allele of the JAG1 gene or JAG2 gene; and (ii) a loss-of-function allele in the endogenous BS1 gene and / or a loss-of-function allele in the endogenous BS2 gene, along with methods of using and making the same.

Description

Docket No. P14927WOOOTITLE: SOYBEANS WITH COMBINATIONS OF TRANSCRIPTIONALREGULATORY GENE MUTATIONSCROSS REFERENCE TO RELATED APPLICATIONS

[0001] This international patent application claims the benefit of U.S. provisional patent application Ser. No. 63 / 829,367, filed June 24, 2025, and U.S. provisional patent application Ser. No. 63 / 698,196, filed September 24, 2024, which are each incorporated herein by reference in their entireties.SEQUENCE LISTING XML

[0002] The instant application contains a sequence listing named “P14927US01.xml,” which was created on June 22, 2025, which is 13,529,807 bytes in size, and which has been filed in XML file format by electronic submission. The aforementioned P14927US01.xml sequence listing is incorporated herein by reference in its entirety.TECHNICAL FIELD

[0003] Disclosed herein are novel plants, plant parts, and nucleotide sequences in soybean varieties comprising an amorphic or hypomorphic allele of a JAG1 and a JAG2 gene, and a loss-of-function allele of the BS1 and / or BS2 gene 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.Docket No. P14927WOOOSUMMARY

[0006] Soybean plants comprising: (i) a loss-of-function allele in the endogenous JAG1 gene and a loss-of-function allele in the endogenous JAG2 gene, wherein at least one of the loss- of-function alleles of the endogenous JAG1 or JAG2 genes is a hypomorphic allele of the JAG1 gene or JAG2 gene; and (ii) a loss-of-function allele in the endogenous BS1 gene and / or a loss-of-function allele in the endogenous BS2 gene; wherein the soybean plant exhibits increased yield in comparison to a control plant lacking the loss-of-function alleles of: (i) the JAG1 and JAG2 genes; and (ii) the BS1 and / or BS2 genes are provided. Also provided are soybean plant cells and plant parts of the soybean plants (e.g., a stem, root, leaf, flower, pod, seed, or grain).

[0007] Use of any of the aforementioned soybean plant cells, soybean plant parts, or soybean plants to produce soybean seed, grow a soybean crop, and / or obtain a soybean by-product are provided herein.

[0008] Biological samples comprising one or more nucleic acids containing: : (i) a loss-of- function allele in the endogenous JAG1 gene and a loss-of-function allele in the endogenous JAG2 gene, wherein at least one of the loss-of-function alleles of the endogenous JAG1 or JAG2 genes is a hypomorphic allele of the JAG1 gene or JAG2 gene; and (ii) a loss-of- function allele in the endogenous BS1 gene and / or a loss-of-function allele in the endogenous BS2 gene are also provided.

[0009] Methods of producing a soybean seed lot comprising: (i) growing a population of soybean plants comprising the aforementioned soybean plants; and (ii) harvesting seed from the population of soybean plants of step (i) at maturity are also provided.

[0010] Methods of producing a soybean crop comprising planting a plurality of the seed of the aforementioned soybean plants are provided.

[0011] 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 grain obtained from the aforementioned soybean plants are provided.

[0012] Methods for determining whether a soybean plant cell, plant part, or plant comprises: (i) a loss-of-function allele in the endogenous JAG1 gene and a loss-of-function allele in the endogenous JAG2 gene, wherein at least one of the loss-of-function alleles of the endogenous JAG1 or JAG2 genes is a hypomorphic allele of the JAG1 gene or JAG2 gene; and (ii) a loss- of-function allele in the endogenous BS1 gene and / or a loss-of-function allele in the endogenous BS2 gene comprising analyzing polynucleotides from the plant cell, plant part, orDocket No. P14927WOOO plant comprising a portion of SEQ ID NO: 1 or an allelic variant thereof, a polynucleotide comprising a portion of SEQ ID NO: 18 or an allelic variant thereof, and a polynucleotide comprising a portion of SEQ ID NO: 49, 50, or an allelic variant thereof, wherein an insertion, deletion, and / or substitution of one or more nucleotides in the polynucleotide is indicative of the presence of the loss-of-function alleles.

[0013] Methods for determining whether a soybean seed lot comprises soybean seed comprising at (i) a loss-of-function allele in the endogenous JAG1 gene and a loss-of- function allele in the endogenous JAG2 gene, wherein at least one of the loss-of-function alleles of the endogenous JAG1 or JAG2 genes is a hypomorphic allele of the JAG1 gene or JAG2 gene; and (ii) a loss-of-function allele in the endogenous BS1 gene and / or a loss-of- function allele in the endogenous BS2 gene comprising analyzing polynucleotides from the seed lot comprising a portion of SEQ ID NO: 1 or an allelic variant thereof, a polynucleotide comprising a portion of SEQ ID NO: 18 or an allelic variant thereof, and a polynucleotide comprising a portion of SEQ ID NO: 49, 50, or an allelic variant thereof, wherein an insertion, deletion, and / or substitution of one or more nucleotides in the polynucleotide is indicative of the presence of the seed comprising the loss-of-function alleles are provided.

[0014] Soybean genomes characterized by the fact that they comprise: (i) a loss-of-function allele in the endogenous JAG1 gene and a loss-of-function allele in the endogenous JAG2 gene, wherein at least one of the loss-of-function alleles of the endogenous JAG1 or JAG2 genes is a hypomorphic allele of the JAG1 gene or JAG2 gene; and (ii) a loss-of-function allele in the endogenous BS1 gene and / or a loss-of-function allele in the endogenous BS2 gene are provided.

[0015] Methods of making the aforementioned soybean plants comprising: (i) introducing at least one mutation comprising a hypomorphic allele of a JAG1 or JAG2 gene into at least one of an endogenous wild-type JAG1 and / or JAG2 gene of a soybean plant; and (iii) selecting a soybean plant for a hypomorphic allele of the JAG1 and / or JAG2 gene of the soybean plant, wherein the hypomorphic allele of the JAG1 and / or JAG2 gene is combined in the selected soybean plant or in progeny of the selected soybean plant with a loss-of-function allele of a BS1 and / or BS2 gene and with an amorphic allele of the JAG1 or JAG2 gene when both of the JAG1 or JAG2 genes of the selected soybean plant do not comprise hypomorphic alleles of the JAG1 or JAG2 genes are provided.

[0016] Soybean plants comprising a hypomorphic allele of the endogenous JAG1 gene which comprises an insertion, deletion, and / or substitution (INDELS) of 1, 2, 3, 5, 10, or moreDocket No. P14927WOOO nucleotides in a coding or non-coding region of the JAG1 gene comprising the JAG1 promoter, 5’ untranslated region (UTR), exons, intron, and / or 3’ UTR of SEQ ID NO: 18 or an allelic variant thereof are provided. Also provided are soybean plant cells and plant parts (e.g., a stem, root, leaf, flower, pod, seed, or grain). Also provided are biological samples obtained from the soybean plant parts.

[0017] Methods of making an elite soybean plant variety comprising: (i) crossing an aforementioned soybean plant or a plant comprising one or more of the loss-of-function alleles of the JAG1, JAG2, BS1, and / or BS2 genes to elite soybean germplasm lacking one or more of the loss-of-function alleles of the JAG1, JAG2, BS1, and / or BS2 genes; (ii) selecting progeny comprising the loss-of-function alleles of the: (i) JAG1 and JAG2 genes; and (ii) BS1 and / or BS2 genes; and (iii) backcrossing the selected progeny to the elite soybean germplasm are provided.DESCRIPTION OF THE DRAWINGS

[0018] Figure 1 A, B, C, D, and E show the coding region of the wild-type JAG2 gene of SEQ ID NO: 1 which encompasses the 5’ untranslated region, protein coding region, and 3 ’UTR. The guide RNA target sites for the spacer RNA molecules encoded by SEQ ID NO: 9-13 are indicated.

[0019] Figure 2 shows the wild-type reference sequences for a segment of the soybean JAG1 gene (SEQ ID NO: 73) and the corresponding deletions found in an amorphic jagl alleles (SEQ ID NO: 30). The type V Cas nuclease used to generate the deletions cuts 19 bases from the 3' end of the PAM site (PAM sequence is TTTA and the cut site is shown as “ / ”). The nucleotide residue 20 nucleotides from the PAM site adjacent to the JAG1 gRNA protospacers used to generate the deletions is -1 and nucleotide residue 19 nucleotides from that PAM site is +1. The JAG1 gRNA protospacer is encoded by SEQ ID NO: 29.

[0020] Figure 3 shows the wild-type reference sequences for a segment of the wild-type soybean gene (SEQ ID NO: 73) and the corresponding deletions found in an amorphic jagl allele (SEQ ID NO: 31). The type V Cas nuclease used to generate the deletions cuts 19 bases from the 3' end of the PAM site (PAM sequence is TTTA and the cut site is shown as “ / ”). The nucleotide residue 20 nucleotides from the PAM site adjacent to the JAG1 gRNA protospacers used to generate the deletions PAM site is -1 and nucleotide residue 19 from the PAM site is +1. The JAG1 gRNA protospacer is encoded by SEQ ID NO: 29.Docket No. P14927WOOO

[0021] Figure 4 shows JAGlhet+JAG2KO+BS2hetTO event. Left: Wild-type control plant obtained via the same transformation experiment that gave rise to the TO event shown here. Right: TO plant, homozygous for frameshift (“knock-out” (KO)) edited amorphic allele of JAG2 and heterozygous for frameshift (KO) edited amorphic alleles at JAGland BS2.

[0022] Figure 5 shows JAG1KO+JAG2KOT1 plant (homozygous for amorphic alleles of JAG1 and JAG2).

[0023] Figure 6 shows a comparison of wild-type control plants and plants with various combinations of JAG1, JAG2, and BS2 loss-of-function alleles. On the left bench are a set of NING1295 (WT) plants and the right bench shows a segregating population of plants with the following genotypes: (1) JAGlHet+JAG2KO+BS2KO, (2) JAGlKO+JAG2Het+BS2KO, (3) JAGlHet+JAG2KO+BS2Het, and (4) JAGlKO+JAG2Het+BS2HetTl plants derived from three independent TO events. Plant developmental stage: R3. Growth conditions: 14 / 10 light / dark photoperiod regime. The terms “JAGlHet,” “JAG2het,” and “BS2Het” refer to heterozygous amorphic alleles of JAG1, JAG2, or BS2, respectively. The terms “JAG1KO,” “JAG2KO,” and “BS2KO” refer to homozygous amorphic alleles of JAG1, JAG2, and BS2, respectively.

[0024] Figure 7 shows the canopy of a segregating population of plants with the following genotypes: (1) JAGlHet+JAG2KO+BS2KO, (2) JAGlKO+JAG2Het+BS2KO, (3) JAGlHet+JAG2KO+BS2Het, and (4) JAGlKO+JAG2Het+BS2HetTl plants derived from three independent TO events. Note the dark-green foliage and sparse, and 4SPP pods in the foliage. Plant developmental stage: R5-6. The terms “JAGlHet,” “JAG2het,” and “BS2Het” refer to heterozygous amorphic alleles of JAG1, JAG2, or BS2, respectively. The terms “JAG1KO,” “JAG2KO,” and “BS2KO” refer to homozygous amorphic alleles of JAG1, JAG2, and BS2, respectively.

[0025] Figure 8 shows the seeds-per-pod distribution on a JAGlHet+JAG2KO+BS2KOfloral raceme.

[0026] Figure 9 shows the seeds-per-pod distribution comparison of WT (left) and JAGlHet+JAG2KO+BS2KO(right).

[0027] Figure 10A, B, C show trifoliate leaves of a JAGlHet+JAG2KOplant (Fig. 10A), a JAGlHet+JAG2KO+BS2KOplant (Fig. 10B), and a BS2KOplant (Fig. 10B).Docket No. P14927WOOODETAILED DESCRIPTION

[0028] 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.

[0029] 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.

[0030] 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).

[0031] 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” (z.e., incapable of being regenerated into a soybean plant or soybean plant part).

[0032] As used herein, the terms “correspond,” “corresponding,” and “equivalent,” 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 sequence (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).

[0033] As used herein, the terms “Cpfl” and “Casl2a” are used interchangeably to refer to the same RNA dependent DNA endonuclease (RdDe).

[0034] 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 developmentDocket No. P14927WOOO can be found in “Principles of Cultivar Development” by Fehr, Macmillan Publishing Company (1993), which is incorporated herein by reference in its entirety.

[0035] 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 Fl plants). Elite crop plants can include inbred lines which are selfed to produce non-hybrid cultivars or varieties. Elite crop plants can include hybrid Fl progeny of a cross between two distinct elite inbred or doubled haploid plant lines.

[0036] 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.

[0037] As used herein, the term “expression” refers to the production of a functional endproduct (e.g, an mRNA, guide RNA, or a protein) in either precursor or mature form.

[0038] 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. In certain embodiments, a hypomorphic allele will have 70%, 60%, 50%, 40%, 30%, 20%, or 10% or less expression (e.g., as measured by encoded RNA accumulation or by encoded protein accumulation) than the wild-type control gene. In certain embodiments, a hypomorphic allele will exhibit a phenotypic effect that is absent from plants comprising the wild-type allele but less pronounced than the phenotypic effect exhibited by an amorphic allele.

[0039] 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.Docket No. P14927WOOO

[0040] As used herein, the term “isomorphic allele” refers to an allele of a gene having wildtype gene activity.

[0041] The term “isolated” as used herein means having been removed from its natural environment.

[0042] 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).

[0043] As used herein, a “loss-of-function allele” can include an amorphic allele or a hypomorphic allele of a gene.

[0044] As used herein in the specification, the phrase “JAG1 and / or JAG2 gene” is understood to include: (i) a JAG1 gene alone or an amorphic or hypomorphic allele thereof; (ii) a JAG2 gene alone or an amorphic or hypomorphic allele thereof; (iii) both a JAG1 and a JAG2 gene or amorphic and / or hypomorphic alleles of a JAG1 and a JAG2 gene; or (iv) any one of a JAG1 gene alone or an amorphic or hypomorphic allele thereof; a JAG2 gene alone or an amorphic or hypomorphic allele thereof; or both a JAG1 and a JAG2 gene or amorphic and / or or hypomorphic alleles of both a JAG1 and a JAG2 gene, wherein any one or both of the JAG1 and / or JAG2 genes or amorphic and / or or hypomorphic alleles can in certain embodiments be combined in a soybean plant cell, plant, or part thereof such as a seed, or biological sample, or used in a related method, with additional hypomorphic or amorphic alleles of a distinct soybean gene, including an AlPlOa, AlPlOb, AML4, CRN, RIC1 gene, RIC2 gene, FTla gene, BS1 gene, BS2 gene, Tflb gene, and / or NF-YC4 gene. In certain embodiments, the phrase “JAG1 and / or JAG2 gene” is thus understood to include: (i) a loss- of-function allele in the endogenous JAG1 gene and a loss-of-function allele in the endogenous JAG2 gene, wherein at least one of the loss-of-function alleles of the endogenousDocket No. P14927WOOOJAG1 or JAG2 genes is a hypomorphic allele of the JAG1 gene or JAG2 gene; and (ii) a loss- of-function allele in the endogenous BS1 gene and / or a loss-of-function allele in the endogenous BS2 gene.

[0045] 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).

[0046] 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 been removed.

[0047] 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.

[0048] The phrase “triple or quadruple mutant” as used herein refers to a set of soybean gene mutations comprising: (i) a loss-of-function allele in the endogenous JAG1 gene and a loss- of-function allele in the endogenous JAG2 gene, wherein at least one of the loss-of-function alleles of the endogenous JAG1 or JAG2 genes is a hypomorphic allele of the JAG1 gene or JAG2 gene; and (ii) a loss-of-function allele in the endogenous BS1 gene and / or a loss-of- function allele in the endogenous BS2 gene.Docket No. P14927WOOO

[0049] As used herein, the term “variety” refers to 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.

[0050] 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.

[0051] The present disclosure provides for soybean plant cells, plant parts including seed, plants, seed lots, and biological samples comprising an amorphic and / or hypomorphic allele of a JAG1 and / or of a JAG2 gene (e.g., comprising at least one mutation in the endogenous JAG1 and / or JAG2 gene or a triple or quadruple mutant). In certain embodiments, soybean plant cells, plant parts including seed, plants, seed lots, and biological samples comprise: (i) a loss-of-function allele in the endogenous JAG1 gene and a loss-of-function allele in the endogenous JAG2 gene, wherein at least one of the loss-of-function alleles of the endogenous JAG1 or JAG2 genes is a hypomorphic allele of the JAG1 gene or JAG2 gene; and (ii) a loss- of-function allele in the endogenous BS1 gene and / or a loss-of-function allele in the endogenous BS2 gene (i.e., a triple or quadruple mutant). These soybean plants and 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.

[0052] The target endogenous soybean transcription factor JAG2 gene comprises the genomic DNA of SEQ ID NO: 1 and allelic variants thereof located on soybean chromosome 10 and depicted in Figure 1A-E. The endogenous soybean JAG2 gene has the unique identifier Glyma.l0g273800 in the sequenced Williams 82 soybean genome (Wm82.a4.vl), is located at nucleotides 49718688 to 49722581 of chromosome 10 of the Glycine max Williams 82 genome assembly version 4 (Wm82.a4.vl; Glyma.l0g273800 on the world wide web internet site “legacy.soybase.org”; Grant et al. Nucl. Acids Res. (2010) 38 (suppl 1): D843-D846. doi: 10.1093 / nar / gkp798). The JAG2 protein contains zinc finger motifs characteristic of DNA binding proteins, a nuclear localization sequence, a proline rich domain, and an EAR motif which is characteristic of transcriptional repressor proteins (JeongDocket No. P14927WOOO et al., 2012, doi.org / 10.1105 / tpc.112.104968). Allelic variants of an endogenous soybean JAG2 gene include variants which encode JAG2 proteins 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: 8. Allelic variants of an endogenous soybean JAG2 gene also 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. In certain embodiments, allelic variants of the endogenous soybean JAG2 gene are isomorphic alleles of the endogenous soybean JAG2 gene.

[0053] Soybean plant cells, plant parts, and plants comprising at least one mutation in the soybean JAG2 gene of SEQ ID NO: 1 or an allelic variant thereof are provided. In certain embodiments, the at least one mutation is a non-natural mutation. In certain embodiments, the at least one mutation comprises a loss-of-function allele (i.e., an amorphic or hypomorphic allele) of the JAG2 gene of SEQ ID NO: 1 or allelic variant thereof. Examples of mutations can include a deletion, an insertion, and / or a substitution of one or more nucleotides of the endogenous JAG2 gene. The insertion, deletion, and / or substitution can be made anywhere in the JAG2 gene including, for example, in the promoter region, an exon, an intron, and / or the untranslated regions (5’ UTR or 3’ UTR). In certain embodiments, the at least one mutation comprises, consists essentially of, or consists of a deletion, insertion, and / or substitution of at least one nucleotide (e.g., at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 50, 45, 50, 65, 70, 75, 80, 85, 95, 100, 125, 150, 175, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2500, 3000, 3500, 4000, 4500, 5000, 5500, or 5894 nucleotides) of the JAG2 gene of SEQ ID NO: 1 or allelic variant thereof. In certain embodiments, the at least one mutation comprises, consists essentially of, or consists of a deletion, insertion, and / or substitution in the coding region (z.e., nucleotides 2380-4241 of SEQ ID NO: 1 or in an equivalent position of an allelic variant of SEQ ID NO: 1) of the JAG2 gene. In certain embodiments, the at least one mutation in the JAG2 gene can comprise a deletion of the entire coding region or any portion of the coding region required for biological activity. In certain embodiments, the at least one mutation in the JAG2 gene comprises, consists essentially of, or consists of a deletion, insertion, and / or substitution of one or more nucleotides of: (i) an N-terminal JAG2 protein coding region (e g., nucleotides 2380-2383 or 2513-2608 of SEQ ID NO: 1 or in an equivalent position of an allelic variant of SEQ ID NO: 1) or in an equivalent position of an allelic variant of SEQ ID NO: 1). In certain embodiments, the at least one mutation comprises, consists essentially of,Docket No. P14927WOOO or consists of a deletion, insertion, and / or substitution of at least one nucleotide (e.g., at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 50, 45, 50, 65, 70, 75, 80, 85, 95, 100, 125, 150, 175, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, or 1861 nucleotides) corresponding to nucleotides 2380-4241 (z.e., within the protein and intron coding region) of the JAG2 gene of SEQ ID NO: 1 or in an equivalent position of an allelic variant of SEQ ID NO: 1. In certain embodiments, the at least one mutation comprises, consists essentially of, or consists of a deletion, insertion, and / or substitution of at least one nucleotide (e.g., at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides) corresponding to: (i) nucleotides 2558 to 2583; (ii) nucleotides 2579 to 2604; (iii) nucleotides 3204 to 3229; (iv) nucleotides 3489 to 3514; or (v) nucleotides 3539 to 3564; all of the JAG2 gene of SEQ ID NO: 1 or in an equivalent position of an allelic variant of SEQ ID NO: 1.

[0054] In certain embodiments, the at least one mutation comprises, consists essentially of, or consists of a deletion, an insertion, and / or substitution that results in a frameshift mutation and / or a nonsense mutation in the coding region of the JAG2 gene. In certain embodiments, mutations of the JAG2 gene can comprise a deletion of any number of nucleotides that are not divisible by 3 in an exon of the JAG2 gene (e.g., the exons located between nucleotides 2380-4241 of SEQ ID NO: 1 or in an equivalent position of an allelic variant of SEQ ID NO: 1). In certain embodiments, mutations of the JAG2 gene can comprise, consist essentially of, or consist of a deletion of 1, 2, 4, 5, 7, 8, 10, 11, 13, 14, 16, 17, 19, 20, 22, 23, 25, 26, 28, 29, 31, 32, 34, 35, 37, 38, 40, 41, 43, 44, 46, 47, 49, 50, 52, 53, 55, 56, 58, 59, 61, 62, 64, 65, 67, 68, 70, 71, 73, 74, 76, 77, 79, 80, 82, 83, 85, 86, 88, 89, 91, 92, 94, 95, 97, 98, 100, 101, 103, 104, 106, 107, 109, 110, 112, 113, 115, 116, 118, 119, 121, 122, 124, 125, 127, 128, 130, 131, 133, 134, 136, 137, 139, 140, 142, 143, 145, 146, 148, 149, 151, 152, 154, 155, 157, 158, 160, 161, 163, 164, 166, 167, 169, 170, 172, 173, 175, 176, 178, 179, 181, 182, 184, 185, 187, 188, 190, 191, 193, 194, 196, 197, 199, 200, 202, 203, 205, 206, 208, 209, 211, 212, 214, 215, 217, 218, 220, 221, 223, 224, 226, 227, 229, 230, 232, 233, 235, 236, 238, 239, 241, 242, 244, 245, 247, 248, 250, 251, 253, 254, 256, 257, 259, 260, 262, 263, 265, 266, 268, 269, 271, 272, 274, 275, 277, 278, 280, 281, 283, 284, 286, 287, 289, 290, 292, 293, 295, 296, 298, 299, 301, 302, 304, 305, 307, 308, 310, 311, 313, 314, 316, 317, 319, 320, 322, 323, 325, 326, 328, 329, 331, 332, 334, 335, 337, 338, 340, 341, 343, 344, 346, 347, 349, 350, 352, 353, 355, 356, 358, 359, 361, 362, 364, 365, 367, 368, 370, 371, 373,Docket No. P14927WOOO374, 376, 377, 379, 380, 382, 383, 385, 386, 388, 389, 391, 392, 394, 395, 397, 398, 400,401, 403, 404, 406, 407, 409, 410, 412, 413, 415, 416, 418, 419, 421, 422, 424, 425, 427,428, 430, 431, 433, 434, 436, 437, 439, 440, 442, 443, 445, 446, 448, 449, 451, 452, 454,455, 457, 458, 460, 461, 463, 464, 466, 467, 469, 470, 472, 473, 475, 476, 478, 479, 481,482, 484, 485, 487, 488, 490, 491, 493, 494, 496, 497, 499, 500, 502, 503, 505, 506, 508,509, 511, 512, 514, 515, 517, 518, 520, 521, 523, 524, 526, 527, 529, 530, 532, 533, 535,536, 538, 539, 541, 542, 544, 545, 547, 548, 550, 551, 553, and 554 nucleotides of an exon located in the endogenous soybean JAG2 gene of SEQ ID NO: 1 or in an equivalent position of an allelic variant of SEQ ID NO: 1 and result in a frameshift mutation and / or a nonsense mutation. In certain embodiments, the frameshift mutation and / or a nonsense mutation occurs at nucleotides corresponding to: (i) nucleotides 2558 to 2583; (ii) nucleotides 2579 to 2604; (iii) nucleotides 3204 to 3229; (iv) nucleotides 3489 to 3514; or (v) nucleotides 3539 to 3564; all of the JAG2 gene of SEQ ID NO: 1 or in an equivalent position of an allelic variant of SEQ ID NO: 1.

[0055] In certain embodiments, the at least one mutation comprises, consists essentially of, or consists of an internal deletion that preserves the reading frame of the encoded JAG2 protein while removing at least one, two, three codons, thus resulting in a mutant JAG2 protein lacking at least one, two, or three amino acid residues. In certain embodiments, mutations of the JAG2 gene can comprise a deletion of any number of nucleotides that are divisible by 3 in a protein coding region of an exon of the JAG2 gene. In certain embodiments, the at least one mutation of the JAG2 gene can comprise, consist essentially of, or consist of a deletion of 3, 6, 9, 12, 15, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45, 48, 51, 54, 57, 60, 63, 66, 69, 72, 75, 78, 81, 84, 87, 90, 93, 96, 99, 102, 105, 108, 111, 114, 117, 120, 123, 126, 129, 132, 135, 138, 141, 144, 147, 150, 153, 156, 159, 162, 165, 168, 171, 174, 177, 180, 183, 186, 189, 192,195, 198, 201, 204, 207, 210, 213, 216, 219, 222, 225, 228, 231, 234, 237, 240, 243, 246,249, 252, 255, 258, 261, 264, 267, 270, 273, 276, 279, 282, 285, 288, 291, 294, 297, 300,303, 306, 309, 312, 315, 318, 321, 324, 327, 330, 333, 336, 339, 342, 345, 348, 351, 354,357, 360, 363, 366, 369, 372, 375, 378, 381, 384, 387, 390, 393, 396, 399, 402, 405, 408,411, 414, 417, 420, 423, 426, 429, 432, 435, 438, 441, 444, 447, 450, 453, 456, 459, 462,465, 468, 471, 474, 477, 480, 483, 486, 489, 492, 495, 498, 501, 504, 507, 510, 513, 516,519, 522, 525, 528, 531, 534, 537, 540, 543, 546, 549, 552, and 555 in a protein coding region of an exon of SEQ ID NO: 1 or at an equivalent position in an allelic variant of SEQ ID NO: 1 and preserve the reading frame. In certain embodiments, the at least one mutationDocket No. P14927WOOO comprises an internal deletion of at least 3, 6, or 9 nucleotides corresponding to nucleotides 2558 to 2583, 2579 to 2604, 3204 to 3229, 3489 to 3514, or 3539 to 3564 of SEQ ID NO: 1 or an allelic variant thereof which preserves the reading frame. In certain embodiments, the at least one mutation comprises an internal deletion of at least 3 nucleotides encoding one or more amino acids corresponding to amino acids 13, 15, 18, or 20 to 22, 25, 28 or 30 , or amino acids 60, 62, 64 to 66, 68, or 70, or amino acids 78, 80, or 82 to 84, 86, or 88 of SEQ ID NO: 8 or an allelic variant thereof which preserves the reading frame. In certain embodiments, the at least one mutation comprises an internal deletion of at least 3 nucleotides encoding one or more amino acids corresponding to amino acids 94, 96, or 98 to 100, 102, or 104 of SEQ ID NO: 8 or an allelic variant thereof which preserves the reading frame. In certain embodiments, the hypomorphic allele of the endogenous JAG2 gene comprises, consists essentially of, or consists of an INDELS of one or more nucleotides in a non-coding region of SEQ ID NO: 1 or an allelic variant thereof, optionally wherein the noncoding region comprises the promoter, 5’ untranslated region (UTR), intron, 3’ UTR, or terminator region of SEQ ID NO: 1 or an allelic variant thereof. In certain embodiments, the hypomorphic allele of the endogenous JAG2 gene comprises a deletion in the promoter, 5’ UTR, first intron, 3’ UTR, and / or the terminator of the JAG2 gene comprising a deletion of at least 10 base pairs located 5’ and / or 3’ to a cleavage site specified by a Casl2 nuclease and one or two Casl2 gRNAs comprising a gRNA spacer molecule set forth in Table 8 which target the JAG2 promoter, 5’ UTR, first intron, 3’ UTR, and / or terminator or to a cleavage site specified by a Cas9 nuclease and one or two Cas9 gRNAs comprising one or two gRNA spacer molecule(s) set forth in Table 8 which target the JAG2 promoter, 5’ UTR, first intron, 3’ UTR, and / or terminator.

[0056] The present disclosure provides for the soybean plant cells, plant parts including seed, plants, and biological samples comprising a mutated JAG1 (mJAGl) gene comprising a loss-of-function mutation (e.g., an amorphic or hypomorphic allele) of that gene. In certain embodiments, one or more of the loss-of-function mutation is a non-natural mutation or allele. These loss-of-function mutations in the mJAGl gene can be amorphic (null) or hypomorphic alleles of the JAG1 gene, can be homozygous, and include JAG1 mutations disclosed in WO2023 / 183772 and U.S. Provisional Application 63 / 269,663, which are each incorporated herein by reference in their entireties. The target endogenous JAG1 gene comprises the genomic DNA of SEQ ID NO: 18 and allelic variants thereof located on soybean chromosome 20. The endogenous soybean JAG1 gene has the unique identifierDocket No. P14927WOOOGlyma.20Gl 16200 in the sequenced Williams 82 soybean genome (Wm82.a4.vl), is located at nucleotides 35827671 to 35830107 of chromosome 20 of the Glycine max Wm82.a2.vl set forth in the https internet site “phytozome- next.jgi. doe. gov / report / transcript / Gmax_Wm82_a2_vl / Glyma.20Gl 16200.1 ” The JAG1 protein contains zinc finger motifs characteristic of DNA binding proteins, a nuclear localization sequence, a proline rich domain, and an EAR motif which is characteristic of transcriptional repressor proteins (Jeong et al., 2012, doi.org / 10.1105 / tpc.112.104968). Point mutations in the EAR motif of JAG1 result in loss of JAG activity (Jeong et al., 2012, doi.org / 10.1105 / tpc.112.104968). Allelic variants of an endogenous soybean JAG1 gene include variants which encode JAG1 proteins having at least 95%, 96%, 98%, 99%, or 99.5% sequence identity to the JAG1 protein encoded by SEQ ID NO: 18. Allelic variants of an endogenous soybean JAG1 gene also include variants which comprise genomic DNA having at least 95%, 96%, 98%, 99%, or 99.5% sequence identity to SEQ ID NO: 18 or comprising SEQ ID NO: 15. In certain embodiments, the mJAGl genes can comprise a nucleic acid sequence comprising, consisting essentially of, or consisting of the deletions in the JAG1 gene set forth in Table 3 or an allelic variant thereof (e.g., an mJAGl gene having the deletion in SEQ ID NO: 18 set forth in Table 3 where the remainder of the mJAGl gene sequence has at least at least 95%, 96%, 98%, 99%, or 99.5% sequence identity to SEQ ID NO: 18). In certain embodiments, mJAGl genes can encode the polypeptide encoded by the mutated jagl gene of SEQ ID NO: 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, or an allelic variant thereof. In certain embodiments, allelic variants of the mJAGl genes of SEQ ID NO: 21, 22, 23, 24, 25, 26, 27, 28, 32, or 33 can comprise an nucleic acid sequence comprising, consisting essentially of, or consisting of the deletions in the JAG1 gene set forth in Table 3 and have at least 95%, 96%, 98%, 99%, or 99.5% sequence identity across the entire length of SEQ ID NO: 21, 22, 23, 24, 25, 26, 27, 28, 32, or 33. In certain embodiments, the mJAGl gene comprises a deletion corresponding to nucleotides 426 to 430 , 424 to 430, or 423 to 430 of the endogenous soybean JAG1 gene of SEQ ID NO: 18 and allelic variants thereof comprising the deletion and having at least at least 95%, 96%, 98%, 99%, or 99.5% sequence identity thereto. In certain embodiments, the mJAGl gene can comprise a JAG1 gene or an aforementioned allelic variant thereof which comprises a deletion corresponding to nucleotides 426 to 430, 426 to 431, 417 to 429, 424 to 430, or 423 to 430 of the endogenous soybean JAG1 gene of SEQ ID NO: 18. In certain embodiments, the mJAGl deletion is a null mutation (z.e., an amorphic allele) that comprises, consists essentially of, or consists of aDocket No. P14927WOOO deletion corresponding to at least nucleotides 421 to 436, 426 to 431, or 417 to 429 of SEQ ID NO: 18 or an allelic variant thereof comprising, consisting essentially of, or consisting of the deletion and having at least at least 95%, 96%, 98%, 99%, or 99.5% sequence identity thereto. In certain embodiments, the loss-of-function alleles of the JAG1 gene can comprise a deletion of an JAG1 gene set forth in SEQ ID NO: 30, 31, or an allelic variant thereof comprising the deletion and 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: 30 or 31. In certain embodiments, loss-of-function alleles of the JAG1 gene can comprise a deletion of an JAG1 gene set forth in Table 3. In certain embodiments, loss-of-function alleles of the JAG1 gene can comprise a deletion in an JAG1 gene corresponding to deleted nucleotides of SEQ ID NO: 18 set forth in column 3 of Table 3. In certain embodiments, loss-of-function alleles of the JAG1 gene can comprise a deletion in an allelic variant of SEQ ID NO: 18 having at least 90%, 95%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 18, wherein the deletion corresponds to a deletion of nucleotides in SEQ ID NO: 18 set forth in Table 3. In certain embodiments, the deletion of nucleotides of SEQ ID NO: 18 set forth in column 3 of Table 3 occurs in genomic DNA of SEQ ID NO: 18 or an allelic variant thereof having at least 90%, 95%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 18. In certain embodiments, any of the aforementioned mJAGl genes (e.g., which comprise amorphic or hypomorphic alleles of the JAG1 gene) are combined with (i) an amorphic or hypomorphic allele of the JAG2 gene; and / or with (ii) a hypomorphic or amorphic allele of at least one of an AlPlOa, AlPlOb, AML4, CRN, RIC1 gene, RIC2 gene, FT la gene, BS1 gene, BS2 gene, Tflb gene, and / or NF -YC4 gene.

[0057] Hypomorphic alleles of the JAG1 gene can comprise an insertion, deletion, and / or substitution (INDELS) of 1, 2, 3, 5, 10, or more nucleotides in a coding or non-coding region of the JAG1 gene comprising the JAG1 promoter, 5’ untranslated region (UTR), exons, intron, and / or 3’ UTR of SEQ ID NO: 18 or an allelic variant thereof. In certain embodiments, hypomorphic alleles of the JAG1 gene can comprise a deletion in the promoter of the JAG1 gene comprising, consisting essentially of, or consisting of at least about 10, 20, 40, 50, 60, 80, 100, 120, 140, 150, 160, 170, 180, 190, 200, 210, or 220 nucleotides located within or including nucleotides corresponding to nucleotides 440 to 616 of the JAG1 promoter of SEQ ID NO: 17 or an allelic variant thereof. In certain embodiments, hypomorphic alleles of the JAG1 gene can comprise a deletion in the promoter of the JAG1 gene comprising, consisting essentially of, or consisting of a deletion including nucleotidesDocket No. P14927WOOO corresponding to any one of nucleotides 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, or 440 to any one of nucleotides 616, 617, 618, 619, 620, 621, 622, 623, 624, 625, 626, 627, or 628 of the JAG1 promoter of SEQ ID NO: 17 or an allelic variant thereof. In certain embodiments, hypomorphic alleles of the JAG1 gene can comprise a deletion in the promoter of the JAG1 gene comprising, consisting essentially of, or consisting of at least about 10, 20, 40, 50, 60, 80, 100, 120, 140, 150, 160, 170, 180, 190, 200, 210, 220, 250, 300, 400, 500, 600, 700, 750, 763, 770, 780, or 800 nucleotides located within or including nucleotides corresponding to nucleotides 617 to 1380 of the JAG1 promoter of SEQ ID NO: 17 or an allelic variant thereof. In certain embodiments, hypomorphic alleles of the JAG1 gene can comprise a deletion in the promoter of the JAG1 gene comprising, consisting essentially of, or consisting of a deletion including nucleotides corresponding to any one of nucleotides 604, 605, 606, 607, 608, 609, 610, 611, 612, 613, 614, 615, or 616 to any one of nucleotides 1380, 1381, 1382, 1383, 1384, 1385, 1386, 1387, 1388, 1389, 1390, or 1391 ofthe JAG1 promoter of SEQ ID NO: 17 or an allelic variant thereof. In certain embodiments, hypomorphic alleles of the JAG1 gene can comprise a deletion in the promoter of the JAG1 gene comprising, consisting essentially of, or consisting of at least about 10, 20, 40, 50, 60, 80, 100, 120, 140, 150, 160, 170, 180, 190, 200, 210, 220, 250, 300, 350, 400, 450, 500, 550, 650, 700, 750, 800, 850, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, or 1000 nucleotides located within or including nucleotides corresponding to nucleotides 440 to 1380 of the JAG1 promoter of SEQ ID NO: 17 or an allelic variant thereof. In certain embodiments, hypomorphic alleles of the JAG1 gene can comprise a deletion in the promoter of the JAG1 gene comprising, consisting essentially of, or consisting of a deletion including nucleotides corresponding to any one of nucleotides 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, or 440 to any one of nucleotides 1380, 1381, 1382, 1383, 1384, 1385, 1386, 1387, 1388, 1389, 1390, or 1391 of the JAG1 promoter of SEQ ID NO: 17 or an allelic variant thereof.

[0058] Identification of hypomorphic alleles of JAG1, JAG2, AlPlOa, AlPlOb, AML4, CRN, RIC1 gene, RIC2 gene, FTla gene, BS1 gene, BS2 gene, Tflb gene, and / or NF-YC4 gene having 70%, 60%, 50%, 40%, 30%, 20%, or 10% or less expression than the wild-type control gene can be achieved by analyzing accumulated RNA content or accumulated protein content for each gene in an equivalent plant tissue sample (e.g., expanded leaf, young leaf, meristem, flower, immature seed pods, leaf primordia, axillary buds, meristems, flowers, or seeds) taken from plants at the same developmental stage and same relative location on the plant. Vegetative stages of soybean development include VE (emergence), VC (cotyledon),Docket No. P14927WOOOVI (first-node), V2 (second-node), V3 (third-node), to Vn (nth-node), where VI is the first- node having unifoliate leaves, and subsequent nodes have trifoliate leaves (Ritchie et al., 1985, How a soybean plant develops, Special Report No. 53, Iowa State University of Science and Technology Cooperative Extension Service, Ames, Iowa). Reproductive stages of soybean development include R1 (beginning bloom), R2 (full bloom), R3 (beginning pod), R4 (full pod), R5 (beginning seed), R6 (full seed), R7 (beginning maturity), and R8 (full maturity). Assays for accumulated protein content include various immunoassays (e.g., ELISAs) and mass spectroscopy-based methods. Assays for accumulated RNA content or accumulated protein content can be normalized to an internal RNA or protein control (e.g., actin or ubiquitin). Accumulated RNA content assays include hybridization-based assays and quantitative reverse transcriptase-PCR (qRT-PCR) analysis. In the case of JAG1 and JAG2, accumulated JAG1 and JAG2 RNA content can be determined by qRT-PCR methods using the primers that include those set forth in Table 1. The ACT11 gene expression can be used to normalize expression levels between different samples (e.g., plants comprising hypomorphic alleles of JAG1 or JAG2 and plants comprising wild-type JAG1 or JAG2 alleles) and can be determined by qRT-PCR methods using primers that include those set forth in Table 1. Representative methods of isolating RNA and performing qRT-PCR analysis to analyze JAG1 and JAG2 RNA accumulation are set forth in Jeong et al., 2012, doi.org / 10.1105 / tpc.l 12.104968. In brief, total RNA is isolated from leaf primordia, axillary buds, meristems, flowers, seeds, or immature pods collected from three plants at the same stage of vegetative development (e.g., VI, V2, V3, V4, or Vn) or reproductive development (e.g., Rl, R2, R3, R4, R5, R6, or R7). Tissues are frozen immediately in liquid nitrogen and then ground with a mortar and pestle. RNA is extracted the RNeasy™ plant mini kit (Qiagen, Germantown, MD, USA). Before cDNA synthesis, all RNA samples are treated using RNase- free RQ DNase™ (Promega, Madison, WI, USA). The PCR products are generated using the primer sets disclosed in Table 1. The soybean Actin 11 gene is used as an internal control for RT-PCR analysis in soybean (Jian et al., 2008, BMC Mol. Biol. 9: 59). For qRT-PCR, first- strand cDNA was synthesized from 1 mg total RNA in a 20-mL reaction mixture using the AccuPower RocketScript™ RT PreMix kit (Bioneer, Inc., Oakland, CA, USA). All qRT- PCR reactions are performed in an ABI 7900 HT sequence detection system (Applied Biosystems, Waltham, MA, USA) or equivalent apparatus using the Power SYBRGreen™ PCR MasterMix kit (Applied Biosystems, Waltham, MA, USA) and the following two-stepDocket No. P14927WOOOPCR profile: 10 min at 95°C, followed by 45 cycles of 15 sec at 95°C, 30 sec at 62°C, and 30 s at 72°C. PCR specificity is subjected to the machine’s standard dissociation curve analysis. Specific gene expression is normalized to the internal control gene Actin 11, and a negative control without cDNA is also performed for each primer set. The gene expression value of the meristem of wild-type plants is used as the control and set to an arbitrary value of 1.0. Experiments are performed in two biological replicates, with three technical replicates.

[0059] Table 1. Probes and Primers for analysis of JAG1, JAG2, and ACT11 RNA accumulation.

[0060] Identification of hypomorphic alleles of the JAG1 and / or JAG2 gene can also be accomplished by comparing the leaf length to width ratio (L / W ratio) of a fully expanded vegetative stage leaf of a candidate soybean plant carrying the hypomorphic allele(s) to the L / W ratio of a fully expanded vegetative stage leaf of one or more control plants comprising (i) wild-type alleles of the JAG1 and / or JAG2 genes; (ii) amorphic alleles of the JAG1 and / or JAG2 genes present in the homozygous state; and / or (iii) an amorphic allele of the JAG1 and / or JAG2 gene present in the heterozygous state (e.g., a plant containing both an amorphic and a wild-type allele of the JAG1 gene). In certain embodiments, the fully expanded vegetative stage leave is a V4, V5, or V6 vegetative stage leaf, where the VI stage is the first- node having unifoliate leaves, where subsequent nodes have trifoliate leaves, and where the V4 stage leaf is a fourth-node leaf, the V5 stage leaf is a fifth-node leaf, and the V6 stage leaf is a sixth-node leaf (Ritchie et al., 1985, How a soybean plant develops, Special Report No. 53, Iowa State University of Science and Technology Cooperative Extension Service, Ames, Iowa). The leaf L / W ratio of a soybean plant which is heterozygous for a loss-of-function mutation in the JAG1 gene (i.e., a mutation encoding an LI OF amino acid substitution in the EAR motif of the JAG1 protein) has been shown to be greater than the leaf L / W ratio of a wild-type control soybean plant (i.e., homozygous for a wild-type JAG1 gene) but less than the leaf L / W ratio of a soybean plant which is homozygous for the same loss-of-function mutation in the JAG1 gene (Sayama et al, 2017; doi: 10.1270 / jsbbs.16201). The leaf L / WDocket No. P14927WOOO ratio of a soybean plant which is heterozygous for an amorphic mutation in the JAG1 gene (i.e., a null mutation where the start codon was altered named ‘EnT-0541’) has been shown to be greater than the leaf L / W ratio of a wild-type control soybean plant (i.e., homozygous for a wild-type JAG1 gene) but less than the leaf L / W ratio of a soybean plant which is homozygous for the same amorphic mutation in the JAG1 gene (Sayama et al, 2017; doi: 10.1270 / jsbbs.16201). In certain embodiments provided herein, it is anticipated that soybean plants homozygous for certain hypomorphic alleles of JAG1 provided herein (e.g., hypomorphic alleles of JAG1 having only about 40% to 60% or about 50% of wild-type JAG1 mRNA and / or protein expression levels) will exhibit a leaf L / W ratio which is: (i) greater than the leaf L / W ratio of a wild-type control soybean plant (i.e., homozygous for a wild-type allele of the JAG1 gene); (ii) equivalent to the leaf L / W ratio of a control soybean plant which is heterozygous for a wild-type and an amorphic allele of the JAG1 gene; and (iii) less than the leaf L / W ratio of a control soybean plant which is homozygous for the amorphic allele of the JAG1 gene. In certain embodiments, the leaf L / W ratio of the fully expanded vegetative stage leaf can be determined by capturing a digital image of the leaf in a scanner and analyzing the image with software which measures the length, width, perimeter, and area of a leaf and calculates the leaf L / W ratio. Non-limiting examples of imaging systems which can be used to determine the leaf L / W ratio include a GT-X970 scanner (EPSON, Tokyo, Japan) which is used to produce a JPEG image and SmartLeaf software (http internet site phenotyping.image.coocan.jp / smartleaf / ), which is an updated image analysis software of SmartGrain (Tanabata et al. 2012; doi: 10.1104 / pp.112.205120 ) adapted for leaf shape analysis (Sayama et al, 2017; doi: 10.1270 / jsbbs.16201). Other leaf image analysis software which can be used include LeafAnalyser (www internet site “quantitative-plant.org / software / leafanalyser” described in Weight et al., 2007; doi. org / 10.1111 / j. l365-313X.2007.03330.x) and WinFOLIA™ (described on the https internet site “regent.qc.ca / assets / winfolia_software.html” Regent Instruments Inc. , Quebec, CA). In certain embodiments disclosed herein, soybean plants comprising hypomorphic allele(s) of the JAG1 and / or JAG2 gene are selected or identified by comparing the leaf L / W ratio of a vegetative stage leaf of a candidate soybean plant carrying the hypomorphic allele(s) to the leaf L / W ratio of a vegetative stage leaf of the same stage from one or more control plants (e.g., a plant comprising wild-type alleles of the JAG1 and / or JAG2 genes, a plant heterozygous for an amorphic allele of the JAG1 and / or JAG2 gene, and / or a plant homozygous for an amorphic allele of the JAG1 and / or JAG2 gene).Docket No. P14927WOOO

[0061] In certain embodiments, leaf thickness, chlorophyll content, seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, numbers of pods on the lower third of the main stem, and / or yield of the soybean plant comprising at least one amorphic or hypomorphic allele of the endogenous soybean JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) is increased in comparison to the leaf thickness, chlorophyll content, seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, numbers of pods on the lower third of the main stem, and / or yield of a wild-type or control soybean plant lacking the at least one amorphic or hypomorphic allele of the JAG1 and / or JAG2 gene. 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 leaf thickness, chlorophyll content, seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or yield of the soybean plant comprising at least one amorphic or hypomorphic allele of the endogenous soybean JAG1 and / or JAG2 gene(e.g., a triple or quadruple mutant) is preserved or further enhanced when the at least one amorphic or hypomorphic allele of the endogenous soybean JAG1 and / or JAG2 gene is combined with least one mutation in a distinct soybean gene (e.g., a hypomorphic or amorphic allele of a soybean AML4 gene, AlPlOa gene, AlPlOb gene, RIC1 gene, RIC2 gene, FT la gene, JAG1 gene, BS1 gene, BS2 gene, CRN gene, Tflb gene, and / or NF-YC4 gene or a triple or quadruple mutant). In certain embodiments disclosed herein, soybean plants comprising hypomorphic allele(s) of the JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) are selected or identified by comparing leaf thickness, chlorophyll content, seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, numbers of pods on the lower third of the main stem, and / or yield of a candidate soybean plant carrying the hypomorphic allele(s) to a control plant comprising wild-type alleles of the JAG1 and / or JAG2 genes.

[0062] In certain embodiments, the seeds per pod for the soybean plant comprising the at least one mutation in the JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) is increased in comparison to the seeds per pod for a wild-type or control soybean plant lacking the at least one mutation. In certain embodiments, the seeds per pod 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 seeds per pod from the corresponding wild-type or control soybean plant lacking the at least one mutation. In certain embodiments, the average number of seeds per pod for the soybean plant comprising the at least one mutation in theDocket No. P14927WOOOJAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) is at least about 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, or 3.8. In certain embodiments, the percentage of 3 seeded pods for the soybean plant comprising the at least one mutation in the JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) is increased in comparison to the percentage of 3 seeded pods for a wild-type or control soybean plant lacking the at least one mutation. In certain embodiments, the percentage of 3 seeded pods 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 percentage of 3 seeded pods from the corresponding wild-type or control soybean plant lacking the at least one mutation. In certain embodiments, the percentage of 3 seeded pods for the soybean plant comprising the at least one mutation in the JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) is at least about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, or 95%. In certain embodiments, the percentage of 4 seeded pods for the soybean plant comprising the at least one mutation in the JAG1 and / or JAG2 gene is increased in comparison to the percentage of 4 seeded pods for a wild-type or control soybean plant lacking the at least one mutation. In certain embodiments, the percentage of 4 seeded pods is increased by at least about 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 12%, 15%, 18%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 60%, 70%, 80%, 90%, 100%, 150%, 200%, 250%, 300%, 350%, 400%, 450%, or 500% in comparison to the percentage of 4 seeded pods from the corresponding wild-type or control soybean plant lacking the at least one mutation. In certain embodiments, the percentage of 4 seeded pods for the soybean plant comprising the at least one mutation in the JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) is at least about 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, or 40%.

[0063] In certain embodiments, the pod count per soybean plant comprising the at least one mutation in the JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) is increased in comparison to the pod count per plant for a wild-type or control soybean plant lacking the at least one mutation. 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 wildtype or control soybean plant lacking the at least one mutation. In certain embodiments, the seed count per plant comprising the at least one mutation in the JAG1 and / or JAG2 geneDocket No. P14927WOOO(e.g., a triple or quadruple mutant) is increased in comparison to the seed count per plant for a wild-type or control soybean plant lacking the at least one mutation. In certain embodiments, the seed count per plant comprising the at least one mutation in the JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) 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 mutation. In certain embodiments, the total harvested seed weight per plant comprising the at least one mutation in the JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) 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 mutation. 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 mutation. In certain embodiments, the total harvested seed weight per unit area for soybean plants comprising the at least one mutation in the JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) is increased in comparison to the total harvested seed weight per unit area for a wild-type or control soybean plant lacking the at least one mutation. In certain embodiments, the total harvested seed weight per unit area for soybean plants comprising the at least one mutation in the JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) 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 unit area from the corresponding wild-type or control soybean plant lacking the at least one mutation. In certain embodiments, the average weight of 1000 seeds obtained from the soybean plant is equivalent to or essentially the same as the average weight of 1000 seeds obtained from a wild-type or control soybean plant lacking the at least one mutation.

[0064] In certain embodiment, the seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, pod count per plant, seed count per plant, total harvested seed weight per plant, and / or total harvested seed weight per unit area for the soybean plant comprising the at least one mutation in the JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) are increased in comparison to seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, pod count per plant, seed count per plant, total harvested seed weight per plant, and / or total harvested seed weight per unit area for a wild-type or control soybean plantDocket No. P14927WOOO lacking the at least one mutation 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 seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, pod count per plant, seed count per plant, total harvested seed weight per plant, and / or total harvested seed weight per unit area can be increased when the plant comprising the at least one mutation in the JAG1 and / or JAG2 gene is grown under abiotic stress in comparison to seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods per plant, pod count per plant, seed count per plant, total harvested seed weight per plant, and / or total harvested seed weight per unit area for a wild-type or control soybean plant lacking the at least one mutation grown under abiotic stress. In certain embodiments, soybean plant seeds comprising the at least one mutation in the JAG1 and / or JAG2 gene (e.g., a soybean plant with: (i) JAG1 and JAG2 genes with LOF alleles where at least one of the LOF alleles is a hypomorphic allele; and (ii) LOF alleles of the BS1 and / or BS2 gene(s)) are planted at a seeding rate (e.g., seeds per hectare or seeds per acre) which is greater than the seeding rate which is optimal for yield of a control plant lacking one or more of the loss-of- function alleles. In certain embodiments, soybean plants comprising the at least one mutation in the JAG1 and / or JAG2 gene (e.g., a soybean plant with: (i) JAG1 and JAG2 genes with LOF alleles where at least one of the LOF alleles is a hypomorphic allele; and (ii) LOF alleles of the BS1 and / or BS2 gene(s)) are grown at a plant density (e.g., plants per hectare or plants per acre) which is greater than the plant density which is optimal for yield of a control plant lacking one or more of the loss-of-function alleles. In certain embodiments, the seeding rate and / or the plant density of the seeds or plants comprising the at least one mutation in the JAG1 and / or JAG2 gene (e.g, a triple or quadruple mutant) is increased by at least 25%. 50%, 100%, 200%, 300%, 400%, or more in comparison to a wild-type control plant lacking the at least one mutation in the JAG1 and / or JAG2 gene. Seeding rates and plant density rates which are optimal for yield of a control plant lacking one or more of the loss-of-function alleles (e.g, a wild-type soybean plant) can be calculated by determining seed yield per unit area planted (e.g., kilograms seed harvested per unit area planted) at different seeding rates or plant densities. Seeding rates and plant density rates which are optimal for yield of a control plant lacking one or more of the loss-of-function alleles (e.g., a wild-type soybean plant) canDocket No. P14927WOOO also be calculated by determining seed yield at different seeding rates or plant densities by the following equations (Carciochi et al., 2019, doi.org / 10.2134 / agronj2018.10.0635).Seed yield = seed number (seeds ha'1) X seed weight (mg seed'1)Seed yield = plant density (plants ha'1) X per-plant yield (g plant'1), where Per-plant yield= per-plant seed number (seeds plant'1) X seed weight (mg seed'1)

[0065] Soybean seed lots comprising the soybean seeds comprising the at least one mutation in the JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) are provided. In certain embodiments, soybean plants comprising the mutated JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) can yield seed lots wherein the average weight of 1000 seeds in the seed lot is equivalent to or essentially the same as the average weight of 1000 seeds in a control seed lot obtained from a wild-type or control plant lacking the at least one mutation in the JAG1 and / or JAG2 gene (e.g., a wild-type soybean plant homozygous for a wild-type JAG1 and / or JAG2 gene). In certain embodiments, the average number of seeds per kilogram of seeds in the seed lot is equivalent to or essentially the same as the average number of seeds per kilogram of seeds in a control seed lot obtained from a wild-type or control soybean plant lacking the at least one mutation in the JAG1 and / or JAG2 gene. 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) of seeds. In certain embodiments, the seed lot is not exclusively obtained by means of an essentially biological process.

[0066] Also provided are polynucleotides comprising any of the aforementioned mutated JAG1 and / or JAG2 genes (e.g, a triple or quadruple mutant) or fragments thereof. In certain embodiments, polynucleotides comprising at least one mutation relative to the endogenous soybean JAG2 gene of SEQ ID NO: 1 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 with the proviso that the sequences are not identical to across their entire length to SEQ ID NO: 1. In certain embodiments, polynucleotides comprising at least one mutation relative to the endogenous soybean JAG1 gene of SEQ ID NO: 16 or 18 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: 16 or 18 with the proviso that the sequences are not identical to across their entire length to SEQ ID NO: 16 or 18. In certain embodiments, the polynucleotide is an isolated polynucleotide.Docket No. P14927WOOO

[0067] 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.

[0068] 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.

[0069] This disclosure is also directed to methods for producing a soybean plant having at least one mutation in the endogenous soybean JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) 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. In certain embodiments, a parent plant comprising a hypomorphic allele of a JAG1 gene (e.g., a plant comprising an insertion, deletion, and / or substitution (INDELS) of 1, 2, 3, 5, 10, or more nucleotides in a coding or non-coding region of the JAG1 gene comprising the JAG1 promoter, 5’ untranslated region (UTR), exons, intron, and / or 3’ UTR of SEQ ID NO: 18 or an allelic variant thereof) is crossed to plants comprising loss-of-function mutations in a JAG2, BS1, and / or BS2 genes. Any such methods using a soybean plant comprising the at least one mutation are part of this disclosure: selfing, backcrosses, hybrid 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 Fi progeny soybean plants produced from the crossing of a soybean plant comprising the at least one mutation with any other soybean plant, Fi seed, and various parts of the Fi 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 forDocket No. P14927WOOO developing a progeny soybean plant in a soybean plant breeding program comprising: obtaining the soybean plant, or its parts, comprising at least one mutation in the endogenous soybean JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) 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.

[0070] 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 crosspollinated 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, z.e., less than one percent of soybean seed formed in an open planting is capable of producing Fi hybrid soybean plants.

[0071] 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.

[0072] In certain embodiments, soybean plant cells, plant parts (e.g., seeds), and plants comprising at least one mutation in the endogenous soybean JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) and a transgenic locus are provided. In certain embodiment, the at least one mutation in the endogenous soybean JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) ) 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 combinedDocket No. P14927WOOO with the mutations disclosed herein include Event EE-GM3 (aka FG-072, MST-FG072-3, described in WO2011063411, USDA-APHIS Petition 09-328-01p), Event SYHTOH2 (aka 0H2, SYN-000H2-5, 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-44406-6, described in WO2012 / 075426 and USDA-APHIS 1 l-234-01p), Event MON87708 (di camba-tol erant event of Roundup Ready 2 Xtend Soybeans, described in WO2011 / 034704 and USDA- APHIS Petition 10-188-01p, MON-87708-9), Event MON89788 (aka Genuity Roundup Ready 2 Yield, described in W02006 / 130436 and USDA-APHIS Petition 06-178-01p), Event 40-3-2 (aka Roundup Ready, GTS 40-3-2, MON-04032-6, described in USDA- APHIS Petition 93-258-01), Event A2704-12 (aka LL27, ACS-GM005-3, described in W02006108674 and USDA-APHIS Petition 96-068-01p), Event 127 (aka BPS-CV127-9, described in WO2010 / 080829), Event A5547-127 (aka LL55, ACS-GM006-4, described in W02006108675 and in USDA-APHIS Petition 96-068-01p), event MON87705 (MON- 87705-6, Vistive Gold, published PCT patent application W02010 / 037016, USDA-APHIS Petition 09-201-01p), or event DP305423 (aka DP-305423-1, published PCT patent application W02008 / 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-87708-9*MON-89788-l), Event HOSxEvent 40-3-2 (aka Plenish High Oleic Soybeans xRoundup Ready Soybeans), Event EE-GM3 xEE-GM2 (aka FG-072xLL55, described in WO2011063413), Event MON 87701 xMON 89788 (aka Intacta RR2 Pro Soybean, MON-87701-2xMON-89788-l), DAS-81419-2xDAS-44406-6 (aka Conkesta™ Enlist E3™ Soybean, DAS-81419-2xDAS-444O6-6), Event DAS-68416- 4xEvent MON 89788 (aka Enlist™ RoundUp Ready® 2 Soybean, DAS-68416-4xMON- 89788-1), Event MON-87769-7xEvent MON-89788-1 (aka Omega-3 x Genuity Roundup Ready 2 Yield Soybeans), Event MON 87705 xEvent MON 89788 (aka Vistive Gold, MON- 877O5-6xMON-89788-l), or Event MON87769 xEvent MON89788 (aka Omega-3 x Genuity Roundup Ready 2 Yield Soybeans, MON-87769-7xMON-89788-l), 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 mutation in the endogenous soybean JAG2 gene of SEQ ID NO: 1 or an allelic variant thereof include those set forth in Table 2. Also provided herein are soybean plant cells, plant parts (e.g., seeds), and plants comprising at least one mutation in the endogenous soybeanDocket No. P14927WOOOJAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) ) and a modification of any of the aforementioned transgenic events or transgenic events set forth in Table 2 below. Modifications of the transgenic events include those disclosed in: WO2022 / 026375, WO2022 / 026379, W02022 / 026390, WO2022 / 026395, W02022 / 026403; US Patent Applic. Pub. Nos. US20220030822, US20230250441, and US20250031653; and U.S. Patent No. 11,242,534, which are each incorporated herein by reference in their entireties.

[0073] Table 2. Transgenic Soybean EventsDocket No. P14927WOOO

[0074] In certain embodiments, soybean plant cells, plant parts (e.g., seeds), and plants comprising the at least one mutation in the endogenous soybean JAG2 gene of SEQ ID NO: 1 or an allelic variant thereof and at least one mutation in a distinct soybean gene are provided. In certain embodiments, soybean plant cells, plant parts (e.g., seeds), and plants comprising the at least one mutation in the endogenous soybean JAG1 and / or JAG2 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 mutation in the endogenous soybean JAG2 gene of the disclosure include mutations in any one or a combination of the soybean AML4 gene, AlPlOa gene, AlPlOb gene, RIC1 gene, RIC2 gene, FTla gene, JAG1 gene, BS1 gene, BS2 gene, CRN gene, Tflb gene, and / or NF-YC4 gene, where the mutation is optionally a loss-of-function mutation (e.g., a hypomorphic or amorphic allele). In certain embodiments, the at least one mutation in the endogenous soybean JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) is combined with a mutation in the soybean AML4 gene located at nucleotides 23,215,077 to 23,222,035 of chromosome 8 of the Glycine max Williams 82 genome assembly version 4 (Wm82.a4.vl; Glyma.08g257400 on the world wide web internet site “soybase.org”; Grant et al. Nucl.Acids Res. (2010) 38 (suppl 1): D843-D846. doi: 10.1093 / nar / gkp798). In certain embodiments, the at least one mutation in the AML4 gene comprises a deletion, insertion, and / or substitution in the coding region (e.g., 5’ UTR, an exon, an intron, and / or a 3’ UTR) of the AML4 gene. In certain embodiments, the at least one mutation in the endogenous soybean JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) is combined with a mutation in the soybean AlPlOa gene. The AlPlOa gene (Glyma.07G021400) is located at nucleotides 1,664,710 to 1,668,114 of chromosome 7 of the Glycine max Wm82.a4.vl genome assembly. In certain embodiments, the mutation (e.g., a deletion) in the AlPlOa gene can be in the AlPlOa gene promoter and / or 5’ UTR. In certain embodiments, the at least one mutation in the endogenous soybean JAG1 and / or JAG2 gene is combined with a mutation in the soybean AlPlOb gene. The AlPlOb gene (Glyma.08G220400) is located at nucleotides 17,985,027 to 17,988,197 of chromosome 8 of the Glycine max Wm82.a4.vl genome assembly. In certain embodiments, the mutation (e.g., a deletion) in the AlPlOb gene can be in the AlPlOb gene promoter and / or 5’ UTR. In certain embodiments, the at least one mutation in the endogenous soybean JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) is combined with a mutation in the soybean RIC1 gene. The RIC1 gene (Glyma. l3g292300) is located at nucleotides 38,587,351 to 38,588,133 of chromosome 13 of the Glycine max Wm82.a4.vlDocket No. P14927WOOO genome assembly. Mutations encoding amorphic or hypomorphic alleles of the RIC1 gene are obtainable with a type V Cas nuclease and a gRNA recognized by the Cas nuclease comprising a spacer region encoded by SEQ ID NO: 66, 67, or 68. In certain embodiments, the at least one mutation in the endogenous soybean JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) is combined with a mutation in the soybean RIC2 gene, where the mutation in the RIC2 gene is optionally a deletion in the promoter region of the gene. The RIC2 gene (Glyma.06g284100) is located at nucleotides 46,845,530 to 46,845,811 of chromosome 6 of the Glycine max Wm82.a4.vl genome assembly. Mutations encoding in the RIC2 gene are obtainable with a type V Cas nuclease and a gRNA recognized by the Cas nuclease comprising a spacer region encoded by SEQ ID NO: 70, 71, or 72. In certain embodiments, the at least one mutation in the endogenous soybean JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) is combined with a mutation in the soybean FT la gene. In certain embodiments, the mutation in the FT la gene contains a deletion set forth in SEQ ID NO: 37, 38, 40, 41, 45, or in an allelic variant thereof comprising the deletion. In certain embodiments, the mutation in the FTla gene encodes a protein set forth in SEQ ID NO: 39, 42, 43 or an allelic variant thereof. The FTla gene (Glyma.l8G298900) is located at nucleotides 57,922,912 to 57,928,648 of chromosome 18 of the Glycine max Wm82.a4.vl genome assembly. In certain embodiments, the at least one mutation in the endogenous soybean JAG2 gene of SEQ ID NO: 1 or an allelic variant thereof is combined with a mutation in the soybean JAG1 gene. The JAG1 gene (Glyma.20Gl 16200) is located at nucleotides 35,791,056 to 35,793,868 of chromosome 20 of the Glycine max Wm82.a4.vl genome assembly. In certain embodiments, the at least one mutation in the endogenous soybean JAG1 and / or JAG2 gene is combined with a mutation in the soybean BS1 gene. In certain embodiments, the mutation in the BS1 gene contains a deletion set forth in SEQ ID NO: 56 or in an allelic variant thereof comprising the deletion. The BS1 gene (Glyma.l0g244400) is located at nucleotides 47,330,160 to 47,335,971 of chromosome 10 of the Glycine max Wm82.a4.vl genome assembly. In certain embodiments, the at least one mutation in the endogenous soybean JAG1 and / or JAG2 gene is combined with a mutation in the soybean BS2 gene. In certain embodiments, the mutation in the BS2 gene contains a deletion set forth in SEQ ID NO: 55, 57, 58, 59, or in an allelic variant thereof comprising the deletion. The BS2 gene (Glyma.20gl 50000) is located at nucleotides 38,879,463 to 38,885,344 of chromosome 20 of the Glycine max Wm82.a4.vl genome assembly. In certain embodiments, the at least one mutation in the endogenous soybean JAG1 and / or JAG2 geneDocket No. P14927WOOO(e.g., a triple or quadruple mutant) is combined with a mutation in the endogenous soybean CRN gene is located at nucleotides 23,254,545 to 23,257,685 of chromosome 8 of the Glycine max Williams 82 genome assembly version 4 (Wm82.a4.vl; Glyma.08g257700 on the world wide web internet site “soybase.org”; Grant et al. Nucl. Acids Res. (2010) 38 (suppl 1): D843-D846. doi: 10.1093 / nar / gkp798), where the mutation in the CRN gene is optionally a loss-of-function mutation (e.g., a hypomorphic or amorphic allele). In certain embodiments, the at least one mutation in the endogenous soybean JAG1 and / or JAG2 gene(e.g., a triple or quadruple mutant) is combined with a mutation (e.g., a deletion) in the Tfl lb gene (Glyma. l9gl94300) which can be a promoter element deletion as described in WO2023086765, which is incorporated herein by reference in its entirety. In certain embodiments, the at least one mutation in the endogenous soybean JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) is combined with a mutation (e.g., a deletion) in the NF- YC4 gene (Glyma06gl7780 and / or Glyma04g37291) which can be a promoter element deletion as described in US20230139093, which is incorporated herein by reference in its entirety.

[0075] Methods of producing a soybean seed lot comprising: (i) growing a population of soybean plants comprising an amorphic and / or hypomorphic allele of a JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) to maturity; and (ii) harvesting seed from the population of soybean plants of step (i) at maturity, thereby producing the soybean seed lot, wherein the soybean plants are homozygous for the amorphic and / or hypomorphic allele of a JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant). 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).

[0076] 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.Docket No. P14927WOOO

[0077] The disclosure also provides a method of making a soybean plant comprising an amorphic or hypomorphic allele of a JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant). In certain embodiments, the methods can comprise making a deletion, an insertion and / or a substitution which results in an amorphic or hypomorphic allele of a JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant). 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 mutation results from introduction of a DSB at a target site in the JAG2 gene (e.g., SEQ ID NO: 1 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 mutation results from introduction of a DSB at a target site in the JAG2 gene (e.g, SEQ ID NO: 1 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. In certain embodiments, the at least one mutation results from introduction of a DSB at a target site in the JAG1 gene (e.g, SEQ ID NO: 18 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 mutation results from introduction of a DSB at a target site in the JAG1 gene (e.g., SEQ ID NO: 18 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. In certain embodiments, the DSB are introduced into the JAG1, JAG2, BS1, and / or BS2 genes with a Cas9 or Cast 2 endonuclease and one or two Cas9 or Cast 2 gRNAs comprising one or two gRNA spacer molecule(s) set forth in Table 8 that target the JAG1, JAG 2, BS1, and / or BS2 promoters, 5’ UTRs, introns, exon, 3’ UTR, and / or terminators. 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 Cas 12a nuclease, a nCasl2a nickase, a Cas 12d (CasY), a Casl2e (CasX), a Casl2b (C2cl), a Casl2c (C2c3), a Casl2i, a Casl2j, a Casl4, an engineered nuclease, aDocket No. P14927WOOO codon-optimized nuclease, a zinc-finger nuclease (ZFN) or nickase, a transcription activatorlike 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 for 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.

[0078] In certain embodiments, the mutated JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) and plant cells, parts including seeds, and plants comprising the mutated JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) 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. Cpfl endonuclease and corresponding guide RNAs and PAM sites are disclosed in US Patent Application Publication 2016 / 0208243 Al. 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 Al (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-Docket No. P14927WOOO end cutting RNA-guided endonucleases include Cast 2a, Cast 2b, Cast 2d, Casl 2e, and Casl2i.

[0079] Guide RNA molecules comprising a spacer RNA molecule which can be used to introduce loss-of-function mutations in the JAG1, JAG2, BS1, and BS2 genes are provided in Table 8. Specific guide RNA spacer molecules which can be used with a Casl2 nuclease to generate loss-of-function alleles of the JAG1 gene are set forth in Table 8 and include the spacer RNA molecules encoded by SEQ ID NOs: 1888, 15226, and 15227. In certain embodiments, the loss-of-function alleles of the JAG1 gene are generated by using a Casl2 nuclease and two guide RNAs comprising spacer RNAs encoded by SEQ ID NOs: 1888 and 15226, SEQ ID NOs: 1888 and 15227, or SEQ ID NOs: 15226 and 15227. Guide RNA molecules comprising a spacer RNA molecule which targets the JAG2 gene of SEQ ID NO: 1 or an allelic variant thereof are provided. In certain embodiments, the spacer RNA molecule targets a portion of the protein and intron coding region (z.e., nucleotides 2380-4241 of SEQ ID NO: 1 or in an equivalent position of an allelic variant of SEQ ID NO: 1) of the JAG2 gene of SEQ ID NO: 1 or an allelic variant thereof. In certain embodiments, the spacer RNA molecule comprises the RNA encoded by SEQ ID NO: 9, 10, 11, 12, 13, and / or 15232. Guide RNAs comprising a spacer RNA molecule encoded by SEQ ID NO: 9, 10, 11, 12, 13, and / or 15232 can be used in conjunction with a type V (e.g., Casl2a of SEQ ID NO: 61 or Casl2i nuclease) to generate mutated JAG2 genes which: (i) comprise, consist essentially of, or consist of a deletion, insertion, and / or substitution of at least one nucleotide (e.g., at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 50, 45, 50, 65, 70, 75, 80, 85, 95, 100, 125, 150, 175, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2500, 3000, 3500, 4000, 4500, 5000, 5500, or 5894 nucleotides) of the JAG2 gene of SEQ ID NO: 1 or allelic variant thereof; (ii) comprise, consist essentially of, or consist of a deletion, insertion, and / or substitution of at least one nucleotide (e.g., at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 50, 45, 50, 65, 70, 75, 80, 85, 95, 100, 125, 150, 175, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, or 1861 nucleotides) corresponding to nucleotides 2380-4241 of the JAG2 gene of SEQ ID NO: 1 or in an equivalent position of an allelic variant of SEQ ID NO: 1; or (iii) comprise, consist essentially of, or consist of a deletion, insertion, and / or substitution of at least one nucleotide (e.g., at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides) corresponding to: (i) nucleotides 2558 toDocket No. P14927WOOO2583; (ii) nucleotides 2579 to 2604; (iii) nucleotides 3204 to 3229; (iv) nucleotides 3489 to 3514; and / or (v) nucleotides 3539 to 3564; all in a JAG2 gene of SEQ ID NO: 1 or in an equivalent position of an allelic variant of SEQ ID NO: 1. Specific guide RNA spacer molecules which can be used with a Cast 2 nuclease to generate loss-of-function alleles of the BS2 gene (SEQ ID NO: 50 or allelic variants thereof) are set forth in Table 8 and include the spacer RNA molecules encoded by SEQ ID NOs: 60, 15233, and 15234. Soybean plants comprising mutated JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) that are generated by any of the aforementioned or otherwise disclosed methods set forth herein are provided.

[0080] 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 RNAs 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 Cpfl-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 forDocket No. P14927WOOO design of crRNAs or sgRNAs used with Cast 2a proteins. In some instances, Cast 2a can also recognize a 5’-CTA PAM motif. Other examples of potential Casl2a 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). Cpfl endonuclease and corresponding guide RNAs and PAM sites are disclosed in US Patent Application Publication 2016 / 0208243 Al, which is incorporated herein by reference for its disclosure of DNA encoding Cpfl endonucleases and guide RNAs and PAM sites. Engineered endonucleases with altered or eliminated PAM recognition sites can also be used.

[0081] 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 target sequences in the genome is approached through a combination of in silico selection and experimental evaluation.

[0082] 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.

[0083] 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 havingDocket No. P14927WOOO 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.

[0084] In certain embodiments, the mutated JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) and plant cells, parts including seeds, and plants comprising the mutated JAG1 and / or JAG2 gene are generated by use of zinc finger nucleases or zinc finger nickases. Zinc-finger nucleases are site-specific endonucleases comprising two protein 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 (Umov 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 multifmger 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 fingerDocket No. P14927WOOO 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; 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.

[0085] In certain embodiments, the mutated JAG1 and / or JAG2 gene (e.g, a triple or quadruple mutant) and plant cells, parts including seeds, and plants comprising the mutated JAG1 and / or JAG2 gene 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 forDocket No. P14927WOOO 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(l):261-6; Luo et al; Scientific Reports 6, Article number: 20657 (2016)).

[0086] 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 to 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 itsDocket No. P14927WOOO 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 et 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.

[0087] 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 mutation in the endogenous soybean JAG2 gene of SEQ ID NO: 1 or an allelic variant thereof; and (ii) isolating a soybean plant cell, soybean plant part, or soybean plant comprising at least one mutation in the soybean JAG2 gene of SEQ ID NO: 1 or an allelic variant thereof.

[0088] In certain embodiments, the population of soybean plant cells, parts, or plants which are screened for the presence of at least one mutation in the endogenous soybean JAG1 and / or JAG2 gene (e.g, a triple or quadruple mutant) are first pre-screened by screening for phenotypic characteristics plants having at least one mutation in a JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant). In certain embodiments, the population of soybean plant cells, parts, or plants which are screened for the presence of at least one mutation in the endogenous soybean JAG2 gene of SEQ ID NO: 1, an allelic variant thereof, and / or at least one mutation in a JAG1 gene are first pre-screened by screening of phenotypic characteristics plants having at least one mutation in a JAG2 gene of SEQ ID NO: 1 or an allelic variant thereof. In certain embodiments, such phenotypic characteristics includeDocket No. P14927WOOO increased leaf length to width ratio (L / W ratio) , numbers of pods on the lower third of the main stem, leaf thickness, chlorophyl content, seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or 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 leaf thickness, chlorophyl content, seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or yield for a wild-type or control soybean plant lacking the at least one mutation(s). In certain embodiments, such phenotypic characteristics include increased leaf length to width ratio (L / W ratio) , numbers of pods on the lower third of the main stem, leaf thickness, chlorophyl content, seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or 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 leaf length to width ratio (L / W ratio) , numbers of pods on the lower third of the main stem leaf thickness, chlorophyl content, seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, and / or yield per plant for a wild-type or control soybean plant lacking the at least one mutation where the screened and wild-type or control plants are grown under nitrogen deficient conditions. 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 mutation in the endogenous soybean JAG1 of SEQ ID NO: 18 or JAG2 gene of SEQ ID NO: 1 and soybean plants comprising at least one mutation in the endogenous JAG1 of SEQ ID NO: 18 or soybean JAG2 gene of SEQ ID NO: 1 are identified and / or selected. 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 mutation in the JAG1 and / or JAG2 gene and soybean plants comprising at least one mutation in the endogenous soybean JAG1 and / or JAG2 (e.g., a triple or quadruple mutant) are identified and / or selected.

[0089] In certain embodiments, the population of soybean plant cells, parts, or plants which are screened for the presence of at least one mutation in the endogenous soybean JAG1 (e.g., of SEQ ID NO: 18 or an allelic variant thereof) and / or JAG2 gene (e.g., of SEQ ID NO: 1 or an allelic variant thereof) have been subjected to one or more mutagenesis treatments. Mutations of the endogenous soybean JAG1 and / or JAG2 gene can be generated by mutagenesis methods known in the art, such as chemical mutagenesis or radiation mutagenesis. Suitable chemical mutagens include ethyl methanesulfonate (EMS), sodiumDocket No. P14927WOOO azide, methylnitrosourea (MNU), and diepoxybutane (DEB). Suitable radiation includes x- rays, fast neutron radiation, and gamma radiation.

[0090] Soybean plant cells, parts, or plants comprising at least one mutation in the endogenous JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) 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 Al, 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 mutation in the endogenous JAG1 and / or JAG2 gene.

[0091] In certain embodiments, the screening comprises analyzing leaf length to width ratio (L / W ratio) , pod count on the lower third of the main stem, 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 wildtype 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 certain 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.

[0092] Methods for determining whether a soybean plant cell, plant part, or plant comprises at least one mutation in the endogenous soybean JAG1 and / or JAG2 gene (e.g., a triple or quadruple mutant) are provided. Methods for determining the presence or absence of the atDocket No. P14927WOOO least one mutation can be used in, for example, breeding programs for identification, selection, introgression, and the like.

[0093] In certain embodiments, the methods comprise analyzing a polynucleotide comprising a portion of a JAG2 gene (e.g., of SEQ ID NO: 1, 3, 7, or an allelic variant thereof) or analyzing an RNA encoded by a portion of SEQ ID NO: 1 or an allelic variant thereof from the plant cell, plant part, or plant. In certain embodiments, the methods comprise analyzing a polynucleotide comprising a portion of a JAG1 gene (e.g., of SEQ ID NO: 14, 16, 18, or an allelic variant thereof) or analyzing an RNA encoded by a portion of SEQ ID NO: 14, 16, 18, or an allelic variant thereof from the plant cell, plant part, or plant. In certain embodiments, the methods comprise analyzing a polynucleotide comprising a portion of a BS1 gene (e.g., of SEQ ID NO: 49, or an allelic variant thereof) or BS2 gene (e.g., of SEQ ID NO: 50, or an allelic variant thereof) or analyzing an RNA encoded by a portion of SEQ ID NO: 49, 50 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 JAG2 gene (e.g., a portion of SEQ ID NO: 1 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 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 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 or an allelic variant thereof) can comprise detectable labels (e.g., fluorescent, radioactive, epitope, and chemiluminescent labels). In certain embodiments, the JAG1 and / or JAG2 gene can be directly sequenced using nucleic acid sequencing technologies, including whole genome sequencing.Docket No. P14927WOOO

[0094] In certain embodiments, the methods comprise analyzing a JAG1, JAG2 polypeptide encoded respectively by SEQ ID NO: 16, SEQ ID NO: 1, 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.

[0095] 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.

[0096] The following numbered embodiments also form part of the present disclosure:

[0097] 1. A soybean plant comprising: (i) a loss-of-function allele in the endogenous JAG1 gene and a loss-of-function allele in the endogenous JAG2 gene, wherein at least one of the loss-of-function alleles of the endogenous JAG1 or JAG2 genes is a hypomorphic allele of the JAG1 gene or JAG2 gene; and (ii) a loss-of-function allele in the endogenous BS1 gene and / or a loss-of-function allele in the endogenous BS2 gene; wherein the soybean plant exhibits increased yield in comparison to a control plant lacking the loss-of-function alleles of: (i) the JAG1 and JAG2 genes; and (ii) the BS1 and / or BS2 genes.

[0098] 2. The soybean plant of embodiment 1, wherein: (i) one of the loss-of-function alleles of the endogenous JAG1 or JAG2 genes comprises an amorphic allele of the JAG1 gene or JAG2 gene and wherein one of the loss-of-function alleles of the endogenous JAG1 or JAG2 genes comprises a hypomorphic allele of the JAG1 gene or JAG2 gene; or (ii) both of the endogenous JAG1 or JAG2 genes comprise a hypomorphic allele of the JAG1 gene and JAG2 gene.Docket No. P14927WOOO

[0099] 3. The soybean plant of embodiment 1 or 2, wherein: (i) the hypomorphic allele of the JAG1 gene reduces expression of the JAG1 mRNA or the JAG1 protein in a vegetative shoot apical meristem of a soybean plant containing the hypomorphic allele of the JAG1 gene in the homozygous state to 20% to 80%, 30% to 70%, 40% to 60%, or 45% to 55% of the expression of the JAG1 mRNA or the JAG1 protein in a control vegetative shoot apical meristem of a wild-type control soybean plant lacking the hypomorphic allele of the JAG1 gene; and / or (ii) the hypomorphic allele of the JAG2 gene reduces expression of the JAG2 mRNA or the JAG2 protein in a vegetative shoot apical meristem of a soybean plant containing the hypomorphic allele of the JAG2 gene in the homozygous state to 20% to 80%, 30% to 70%, 40% to 60%, or 45% to 55% of the expression of the JAG2 mRNA or the JAG2 protein in a control vegetative shoot apical meristem of a wild-type control soybean plant lacking the hypomorphic allele of the JAG2 gene.

[0100] 4. The soybean plant of embodiment 3, wherein expression of the JAG1 and / or JAG2 mRNA is determined in the shoot apical meristem of a vegetative stage 5 (V5) soybean plant using a quantitative reverse transcriptase Polymerase Chain Reaction (qRTPCR) assay.

[0101] 5 The soybean plant of embodiment 4, wherein:(i) expression of the JAG1 gene is determined in the qRTPCR assay with SEQ ID NO: 74 as the forward primer and SEQ ID NO: 75 as the reverse primer for the JAG1 mRNA quantitation and with SEQ ID NO: 78 as the forward primer and SEQ ID NO: 79 as the reverse primer for Actin 11 (Actl 1) mRNA quantitation, wherein the expression of the JAG1 mRNA is normalized to expression of the Actl 1 mRNA; and / or (ii) expression of the JAG2 gene is determined in the qRTPCR assay with SEQ ID NO: 76 as the forward primer and SEQ ID NO: 75 as the reverse primer for the JAG2 mRNA quantitation and with SEQ ID NO: 77 as the forward primer and SEQ ID NO: 79 as the reverse primer for Actin 11 (Actl 1) mRNA quantitation, wherein the expression of the JAG2 mRNA is normalized to expression of the Actl 1 mRNA.

[0102] 6. The soybean plant of any one of embodiments 1 to 5, wherein: (i) the hypomorphic allele of the JAG1 gene in the homozygous state in an otherwise wild-type soybean plant provides a fully expanded vegetative stage 5 (V5) leaf length to width ratio (L / W ratio) which is greater than the L / W ratio of a control V5 leaf of a wild-type control plant having a wildtype JAG1 gene in the homozygous state but less than the L / W ratio of a control V5 leaf of a control plant having an amorphic allele of the JAG1 gene in the homozygous state; and / or (ii) the hypomorphic allele of the JAG2 gene in the homozygous state in an otherwise wild-type soybean plant provides a fully expanded vegetative stage 5 (V5) leaf length to width ratioDocket No. P14927WOOO(L / W ratio) which is greater than the L / W ratio of a control V5 leaf of a wild-type control plant having a wild-type JAG1 gene in the homozygous state but less than the L / W ratio of a control V5 leaf of a control plant having an amorphic allele of the JAG2 gene in the homozygous state.

[0103] 7. The soybean plant of any one of embodiments 1 to 6, wherein: (i) the hypomorphic allele of the endogenous JAG1 gene comprises, consists essentially of, or consists of an insertion, deletion, and / or substitution (INDELS) of 1, 2, 3, 5, 10, or more nucleotides in a coding or non-coding region of SEQ ID NO: 18 or an allelic variant thereof, optionally wherein the non-coding region comprises the promoter, 5’ untranslated region (UTR), intron, 3’ UTR, or terminator region of SEQ ID NO: 18 or an allelic variant thereof; or (ii) the hypomorphic allele of the endogenous JAG2 gene comprises, consists essentially of, or consists of an INDELS of one or more nucleotides in a non-coding region of SEQ ID NO: 1 or an allelic variant thereof, optionally wherein the non-coding region comprises the promoter, 5’ untranslated region (UTR), intron, 3’ UTR, or terminator region of SEQ ID NO: 1 or an allelic variant thereof.

[0104] 8. The soybean plant of any one of embodiments 1 to 7, wherein: (i) the hypomorphic allele of the endogenous JAG1 gene comprises a deletion in the promoter, 5’ UTR, first intron, 3’ UTR, and / or the terminator of the JAG1 gene comprising a deletion of at least 10 base pairs located 5’ and / or 3’ to one or two cleavage sites specified by a Casl2 nuclease and one or two Casl2 gRNAs comprising one or two gRNA spacer molecule(s) set forth in Table 8 that target the JAG1 promoter, 5’ UTR, first intron, 3’ UTR, and / or terminator or to a cleavage site specified by a Cas9 nuclease and one or two Cas9 gRNAs comprising one or two gRNA spacer molecule(s) set forth in Table 8 which target the JAG1 promoter, 5’ UTR, first intron, 3’ UTR, and / or terminator; and / or (ii) the hypomorphic allele of the endogenous JAG2 gene comprises a deletion in the promoter, 5’ UTR, first intron, 3’ UTR, and / or the terminator of the JAG2 gene comprising a deletion of at least 10 base pairs located 5’ and / or 3’ to a cleavage site specified by a Casl2 nuclease and one or two Casl2 gRNAs comprising a gRNA spacer molecule set forth in Table 8 which target the JAG2 promoter, 5’ UTR, first intron, 3’ UTR, and / or terminator or to a cleavage site specified by a Cas9 nuclease and one or two Cas9 gRNAs comprising one or two gRNA spacer molecule(s) set forth in Table 8 which target the JAG2 promoter, 5’ UTR, first intron, 3’ UTR, and / or terminator.

[0105] 9. The soybean plant of any one of embodiments 1 to 8, wherein the hypomorphic allele of the endogenous JAG1 gene contains a deletion in the promoter of the JAG1 geneDocket No. P14927WOOO comprising, consisting essentially of, or consisting of at least about 10, 20, 40, 50, 60, 80, 100, 120, 140, 150, 160, 170, 180, 190, 200, 210, or 220 nucleotides located within or including nucleotides corresponding to nucleotides 440 to 616, 617 to 1380, or 440 to 1380 of the JAG1 promoter of SEQ ID NO: 17 or an allelic variant thereof.

[0106] 10. The soybean plant of any one of embodiments 1 to 9, wherein the hypomorphic allele of the endogenous JAG1 or JAG2 gene comprises a deletion in the promoter, 5’ UTR, first intron, 3’ UTR, and / or the terminator of the JAG1 or JAG2 gene and is obtained by a process comprising: (i) directing to the genome of a target soybean plant cell: (a) one or two Casl2 gRNAs comprising one or two gRNA spacer molecule(s) set forth in Table 8 that target the JAG1 or JAG2 promoter, 5’ UTR, first intron, 3’ UTR, and / or terminator and a Cast 2 nuclease which recognizes the Cast 2 gRNAs; or (b) one or two Cas9 gRNAs comprising one or two gRNA spacer molecule(s) set forth in Table 8 which target the JAG1 or JAG2 promoter, 5’ UTR, first intron, 3’ UTR, and / or terminator; and (ii) isolating a soybean plant cell, soybean plant part, or soybean plant comprising at the hypomorphic allele.

[0107] 11. The soybean plant of embodiment 10, wherein the Casl2 gRNAs comprise two distinct gRNA spacer molecule(s) selected from the spacer molecules encoded by SEQ ID NOs: 1888, 15226, and 15227, optionally wherein the Casl2 nuclease comprises the polypeptide of SEQ ID NO: 15229 or a catalytically active variant thereof and the crRNA direct repeat of the gRNA comprises the RNA of SEQ ID NO: 15231.

[0108] 12. The soybean plant of any one of embodiments 1 to 11, wherein the plant is: (i) homozygous for a hypomorphic allele of the endogenous JAG1 gene;(ii) homozygous for an amorphic allele of the endogenous JAG2 gene; and(iii) homozygous for an amorphic or hypomorphic allele of the endogenous Gm BS2 gene.

[0109] 13. The soybean plant of any one of embodiments 3 to 12, wherein: (i) the expression of the JAG1 mRNA or the JAG1 protein in a vegetative shoot apical meristem is reduced to 20% to 80%, 30% to 70%, 40% to 60%, or 45% to 55% of the expression of the JAG1 mRNA or the JAG1 protein in a control vegetative shoot apical meristem of a wild-type control plant; (ii) the expression of the JAG2 mRNA or the JAG2 protein in a vegetative shoot apical meristem is reduced by at least 90%, 95%, or 99% in comparison to the expression of the JAG2 mRNA or the JAG2 protein in a control vegetative shoot apical meristem of a wild-type control plant; and / or (iii) the expression of the BS2 mRNA or the BS2 protein in a soybean plant tissue is reduced by 20% to 100%, 50% to 100%, or 80% to 100% in comparison to the expression of the JAG2 mRNA or the JAG2 protein in a controlDocket No. P14927WOOO soybean plant tissue of a wild-type control plant, optionally wherein the soybean plant tissue is a vegetative or reproductive shoot apical meristem.

[0110] 14. The soybean plant of any one of embodiments 1 to 13, wherein the plant is: (i) homozygous for an amorphic allele of the endogenous JAG1 gene; (ii) homozygous for a hypomorphic allele of the endogenous JAG2 gene; and (iii) homozygous for an amorphic or hypom orphic allele of the endogenous Gm BS2 gene or homozygous for a hypomorphic allele of both the BS1 and BS2 genes.[OHl] 15. The soybean plant of any one of embodiments 1 to 14, wherein: (i) the loss-of- function allele of the endogenous JAG1 gene contains an INDELS of at least one nucleotide in the coding region of the JAG1 gene, optionally wherein:(a) the loss-of-function allele is an amorphic allele of the endogenous JAG1 gene comprising a deletion of at least one, two, or more nucleotides corresponding to nucleotides 2001 to 4178 of SEQ ID NO: 18 or an allelic variant thereof, optionally wherein the deletion comprises, consists essentially of, or consists of a deletion of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 50, 45, 50, 65, 70, 75, 80, 85, 95, 100, 125, 150, 175, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 1000, 1250, 1500, 1750, or 2000 nucleotides corresponding to nucleotides 2001 to 4178 of SEQ ID NO: 18 or an allelic variant thereof; or optionally wherein the amorphic alleles comprises the DNA molecule of SEQ ID NO: 21, 22, 23, 24, 25, 26. 27, 28, 32, or 33; or (b) the loss-of-function allele of the JAG1 gene contains an INDELS in DNA encoding the JAG1 protein of SEQ ID NO: 15 or an allelic variant thereof, optionally wherein the INDELS is in DNA encoding EAR motif residues corresponding to residue 8 to 14 of SEQ ID NO: 15, and optionally wherein the substitution encodes a D9H or L10F substitution in SEQ ID NO: 15; (ii) the loss-of-function allele of the endogenous JAG2 gene comprises an INDELS of at least one nucleotide of the coding region of the JAG2 gene, optionally wherein: (a) the loss-of-function allele is an amorphic allele of the endogenous JAG2 gene comprising a deletion of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 50, 45, 50, 65, 70, 75, 80, 85, 95, 100, 125, 150, 175, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2500, 3000, 3500, or 3894 nucleotides of the coding region of SEQ ID NO: 1 or an allelic variant thereof; (b) the loss-of-function allele of the JAG2 gene contains an INDELS in DNA encoding the JAG2 protein of SEQ ID NO: 8 or an allelic variant thereof, optionally wherein the INDELS is in DNA encoding EAR motif residues corresponding to residue 8 to 14 of SEQ ID NO: 8, and optionally wherein the substitutionDocket No. P14927WOOO encodes a D9H or L10F substitution in SEQ ID NO: 8; or (iii) the loss-of-function allele is an amorphic allele of the endogenous JAG2 gene containing a deletion in the coding region of the JAG2 gene comprising, consisting essentially of, or consisting of a deletion of at least one, two, or more nucleotides corresponding to nucleotides 2558 to 2583 of the JAG2 gene of SEQ ID NO: 1 or an allelic variant thereof; nucleotides 2579 to 2604 of the JAG2 gene ofSEQ ID NO: 1 or an allelic variant thereof; nucleotides 3204 to 3229 of the JAG2 gene ofSEQ ID NO: 1 or an allelic variant thereof; nucleotides 3489 to 3514 of the JAG2 gene ofSEQ ID NO: 1 or an allelic variant thereof; or nucleotides 3539 to 3564 of the JAG2 gene ofSEQ ID NO: 1 or an allelic variant thereof.

[0112] 16. The soybean plant of any one of embodiments 1 to 15, wherein at least one of the loss-of-function alleles in the: (i) JAG1 and JAG2 genes; and (ii) BS1 and / or BS2 genes is a non-natural mutation.

[0113] 17. The soybean plant of any one of embodiments 1 to 16, wherein the soybean plant is homozygous for the loss-of-function alleles of the: (i) JAG1 and JAG2 genes; and (ii) BS1 and / or BS2 genes.

[0114] 18. The soybean plant of any one of embodiments 1 to 17, wherein the plant has increased leaf thickness, leaf length to width ratio (L / W ratio) , chlorophyll content, seeds per pod, percentage of 3 seeded pods, and / or percentage of 4 seeded pods in comparison to seeds per pod, percentage of 3 seeded pods, increased numbers of pods on the lower third of the main stem, and / or percentage of 4 seeded pods for a wild-type or control soybean plant lacking the loss-of-function alleles of the: (i) JAG1 and JAG2 genes; and (ii) BS1 and / or BS2 genes.

[0115] 19. The soybean plant of any one of embodiments 1 to 18, wherein: (i) the plant exhibits increased yield in comparison to a control plant lacking the loss-of-function alleles, optionally wherein the increased yield comprises increased pod count per plant, increased seed count per plant, increased total harvested seed weight per plant, increased numbers of pods on the lower third of the main stem, and / or increased total harvested seed weight per unit area in comparison to a control plant lacking the loss-of-function alleles; and optionally (ii) the increased yield is exhibited when the plant is grown at a plant density which is greater than the plant density which is optimal for yield of a control plant lacking one or more of the loss-of-function alleles.

[0116] 20. A soybean plant cell of the soybean plant of any one of embodiments 1 to 19.

[0117] 21. A soybean plant part of the soybean plant of any one of embodiments 1 to 19.Docket No. P14927WOOO

[0118] 22. The soybean plant part of embodiment 19, wherein the part is a stem, root, leaf, flower, pod, seed, or grain.

[0119] 23. A biological sample obtained from the soybean plant part of embodiment 21.

[0120] 24. 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 19; and (ii) harvesting seed from the population of soybean plants of step (i) at maturity, thereby producing the soybean seed lot.

[0121] 25. The method of embodiment 24, wherein: (i) the population of soybean plants are grown at a plant density which is greater than the plant density which is optimal for yield of a control plant lacking one or more of the loss-of-function alleles; and / or (ii) the seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, numbers of pods on the lower third of the main stem, and / or yield is increased in comparison to seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, numbers of pods on the lower third of the main stem, and / or yield of wild-type or control soybean plants lacking the at least one mutation, optionally wherein yield comprises pod count per plant, seed count per plant, total harvested seed weight per plant, and / or total harvested seed weight per unit area.

[0122] 26. A method of producing a soybean crop comprising planting a plurality of the seed of embodiment 22.

[0123] 27. The method of embodiment 26, further comprising harvesting seed from soybean crop grown from the planted seed.

[0124] 28. The method of embodiment 27 or 28, wherein: (i) the plurality of seed are planted at a seeding rate which is greater than the seeding rate which is optimal for yield of a control plant lacking one or more of the loss-of-function alleles; and / or (ii) the seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, numbers of pods on the lower third of the main stem, and / or yield is increased in comparison to seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, numbers of pods on the lower third of the main stem, and / or yield of a wild-type or control soybean crop lacking one or more of the loss-of- function alleles, optionally wherein yield comprises pod count per plant, seed count per plant, total harvested seed weight per plant, and / or total harvested seed weight per unit area.

[0125] 29. 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 grain of embodiment 22.Docket No. P14927WOOO

[0126] 30. A method of making the soybean plant of any one of embodiments 1 to 19 comprising:(i) introducing at least one mutation comprising a hypomorphic allele of a JAG1 or JAG2 gene into at least one of an endogenous wild-type JAG1 and / or JAG2 gene of a soybean plant; and (ii) selecting a soybean plant for a hypomorphic allele of the JAG1 and / or JAG2 gene of the soybean plant, wherein the hypomorphic allele of the JAG1 and / or JAG2 gene is combined in the selected soybean plant or in progeny of the selected soybean plant with a loss-of-function allele of a BS1 and / or BS2 gene and with an amorphic allele of the JAG1 or JAG2 gene when both of the JAG1 or JAG2 genes of the selected soybean plant do not comprise hypomorphic alleles of the JAG1 or JAG2 genes.

[0127] 31. The method of embodiment 30, wherein the soybean plant is selected for the hypomorphic allele of the JAG1 and / or JAG2 gene by selecting for: (a) a fully expanded leaf length to width ratio (L / W ratio) which is greater than the L / W ratio of a control V5 leaf of a wild-type control plant having a wild-type JAG1 gene in the homozygous state but less than the L / W ratio of a control V5 leaf of a control plant having an amorphic allele of the JAG1 gene in the homozygous state; (b) increased leaf thickness, chlorophyll content, seeds per pod, percentage of 3 seeded pods, and / or percentage of 4 seeded pods in comparison to seeds per pod, percentage of 3 seeded pods, increased numbers of pods on the lower third of the main stem, and / or percentage of 4 seeded pods in comparison to a wild-type control plant; (c) a decrease in expression of JAG1 and / or JAG2 mRNA or protein of at least 40%, 50%, or 60% in comparison to a control plant have a wild-type JAG1 and / or JAG2 gene; and / or (d) identifying an INDELS in the coding or non-coding region of the JAG1 or JAG2 gene which comprises a hypomorphic allele of the JAG1 or JAG2 gene.

[0128] 32. The method of embodiment 30 or 31, wherein the hypomorphic allele is introduced into the JAG1 gene and combined with an amorphic allele of the JAG2 gene, optionally wherein the hypomorphic allele is combined with the amorphic allele by: (i) introducing the mutations comprising the hypomorphic allele and the amorphic alleles into wild-type JAG1 and JAG2 genes simultaneously or consecutively; (ii) introducing the mutation comprising the hypomorphic allele of JAG1 into a soybean plant comprising the amorphic allele of JAG2 in step (i); or (iii) crossing the selected soybean plant comprising the hypomorphic allele of JAG1 gene with a soybean plant comprising the amorphic allele of the JAG2 gene and recovering progeny soybean plants comprising the hypomorphic and amorphic alleles.Docket No. P14927WOOO

[0129] 33. The method of any one of embodiments 30 to 32, wherein the hypomorphic allele is introduced into the JAG2 gene and combined with an amorphic allele of the JAG1 gene, optionally wherein the hypomorphic allele is combined with the amorphic allele by: (i) introducing the mutations comprising the hypomorphic allele and the amorphic alleles into wild-type JAG1 and JAG2 genes simultaneously or consecutively; (ii) introducing the mutation comprising the hypomorphic allele of JAG2 into a soybean plant comprising the amorphic allele of JAG1 in step (i); or (iii) crossing the selected soybean plant comprising the hypomorphic allele of JAG2 gene with a soybean plant comprising the amorphic allele of the JAG1 gene and recovering progeny soybean plants comprising the hypomorphic and amorphic alleles.

[0130] 34. A method of making an elite soybean plant variety comprising: (i) crossing the soybean plant of any one of embodiments 1 to 19 or a plant comprising one or more of the loss-of-function alleles of the JAG1, JAG2, BS1, and / or BS2 genes to elite soybean germplasm lacking one or more of the loss-of-function alleles of the JAG1, JAG2, BS1, and / or BS2 genes; (ii) selecting progeny comprising the loss-of-function alleles of the: (i) JAG1 and JAG2 genes; and (ii) BS1 and / or BS2 genes; and (iii) backcrossing the selected progeny to the elite soybean germplasm.

[0131] 35. A soybean plant comprising a hypomorphic allele of the endogenous JAG1 gene which comprises an insertion, deletion, and / or substitution (INDELS) of 1, 2, 3, 5, 10, or more nucleotides in a coding or non-coding region of the JAG1 gene comprising the JAG1 promoter, 5’ untranslated region (UTR), exons, intron, and / or 3’ UTR of SEQ ID NO: 18 or an allelic variant thereof.

[0132] 36. The soybean plant of embodiment 35, wherein the hypomorphic allele of the JAG1 gene in the homozygous state in an otherwise wild-type soybean plant provides a fully expanded vegetative stage 5 (V5) leaf length to width ratio (L / W ratio) which is greater than the L / W ratio of a control V5 leaf of a wild-type control plant having a wild-type JAG1 gene in the homozygous state but less than the L / W ratio of a control V5 leaf of a control plant having an amorphic allele of the JAG1 gene in the homozygous state

[0133] 37. The soybean plant of embodiment 35 or 36, wherein the hypomorphic allele of the endogenous JAG1 gene comprises a deletion in the promoter, 5’ UTR, first intron, 3’ UTR, and / or the terminator of the JAG1 gene comprising a deletion of at least 10 base pairs located 5’ and / or 3’ to one or two cleavage sites specified by a Casl2 nuclease and one or two Casl2 gRNAs comprising one or two gRNA spacer molecule(s) set forth in Table 8 that target theDocket No. P14927WOOOJAG1 promoter, 5’ UTR, first intron, 3’ UTR, and / or terminator or to a cleavage site specified by a Cas9 nuclease and one or two Cas9 gRNAs comprising one or two gRNA spacer molecule(s) set forth in Table 8 which target the JAG1 promoter, 5’ UTR, first intron, 3’ UTR, and / or terminator.

[0134] 38. The soybean plant of any one of embodiments 35 to 37, wherein the hypom orphic allele of the endogenous JAG1 gene comprises a deletion in the promoter, 5’ UTR, first intron, 3’ UTR, and / or the terminator of the JAG1 gene and is obtained by a process comprising: (i) directing to the genome of a target soybean plant cell: (a) one or two Casl2 gRNAs comprising one or two gRNA spacer molecule(s) set forth in Table 8 that target the JAG1 promoter, 5’ UTR, first intron, 3’ UTR, and / or terminator and a Casl2 nuclease which recognizes the Cast 2 gRNAs; or (b) one or two Cas9 gRNAs comprising one or two gRNA spacer molecule(s) set forth in Table 8 which target the JAG1 promoter, 5’ UTR, first intron, 3’ UTR, and / or terminator; and (ii) isolating a soybean plant cell, soybean plant part, or soybean plant comprising at the hypomorphic allele.

[0135] 39. The soybean plant of embodiment 38, wherein the Casl2 gRNAs comprise two distinct gRNA spacer molecule(s) selected from the spacer molecules encoded by SEQ ID NOs: 1888, 15226, and 15227, optionally wherein the Casl2 nuclease comprises the polypeptide of SEQ ID NO: 15229 or a catalytically active variant thereof and the crRNA direct repeat of the gRNA comprises the RNA encoded by SEQ ID NO: 15231.

[0136] 40. The soybean plant of any one of embodiments 35 to 39, wherein the hypomorphic allele of the endogenous JAG1 gene contains a deletion in the promoter of the JAG1 gene comprising, consisting essentially of, or consisting of at least about 10, 20, 40, 50, 60, 80, 100, 120, 140, 150, 160, 170, 180, 190, 200, 210, or 220 nucleotides located within or including nucleotides corresponding to nucleotides 440 to 616, 617 to 1380, or 440 to 1380 of the JAG1 promoter of SEQ ID NO: 17 or an allelic variant thereof.

[0137] 41. The soybean plant of any one of embodiments 35 to 40, wherein the deletion in the promoter of the JAG1 gene comprises a deletion of nucleotides 440 to 616, 617 to 1380, or 440 to 1380 of the JAG1 promoter of SEQ ID NO: 17 or an allelic variant thereof.

[0138] 42. The soybean plant of any one of embodiments 35 to 41, wherein the hypomorphic allele of the JAG1 gene reduces expression of the JAG1 mRNA or the JAG1 protein in a vegetative shoot apical meristem of a soybean plant containing the hypomorphic allele of the JAG1 gene in the homozygous state to 20% to 80%, 30% to 70%, 40% to 60%, or 45% to 55% of the expression of the JAG1 mRNA or the JAG1 protein in a control vegetative shootDocket No. P14927WOOO apical meristem of a wild-type control soybean plant lacking the hypomorphic allele of the JAG1 gene.

[0139] 43. The soybean plant of embodiment 42, wherein expression of the JAG1 mRNA is determined in the shoot apical meristem of a vegetative stage 5 (V5) soybean plant using a quantitative reverse transcriptase Polymerase Chain Reaction (qRTPCR) assay.

[0140] 44. The soybean plant of embodiment 43, wherein expression of the JAG1 gene is determined in the qRTPCR assay with SEQ ID NO: 74 as the forward primer and SEQ ID NO: 75 as the reverse primer for the JAG1 mRNA quantitation and with SEQ ID NO: 78 as the forward primer and SEQ ID NO: 79 as the reverse primer for Actin 11 (Actl 1) mRNA quantitation, wherein the expression of the JAG1 mRNA is normalized to expression of the Actl 1 mRNA.

[0141] 45. A soybean plant cell of the soybean plant of any one of embodiments 35 to 44.

[0142] 46. A soybean plant part of the soybean plant of any one of embodiments 35 to 44.

[0143] 47. The soybean plant part of embodiment 46, wherein the part is a stem, root, leaf, flower, pod, seed, or grain.

[0144] 48. A biological sample obtained from the soybean plant part of embodiment 46.EXAMPLESExample 1. Generation of soybean with an amorphic allele of a JAG1 and / or JAG2 gene

[0145] A vector was created to transform soybean plants and disrupt the open reading frame of the JAG2gene (SEQ ID NO: 1) through CRISPR-mediated gene editing. At least one CRISPR guide RNA comprising a crRNA fused to a spacer RNA (encoded by SEQ ID NO: 9, 10, 11, 12, and / or 13) was designed to target the of the Glycine max JAG2 gene (Figure 1).

[0146] The plasmids are transformed into Agrobacterium tumefaciens EHA105 (Hood el al., 1993, Transgenic Research. 2: 208-218. doi: 10.1007 / BF01977351) by electroporation following standard techniques. Frozen glycerol stocks are prepared for use in plant transformation.

[0147] Transgenic TO soybean events are made by Hgrotoctera / m-mediated transformation with plasmids each encoding a single guide RNAs to create deletions in the coding region. Sterilized soybean seeds are imbibed in water overnight, and explants are 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, forDocket No. P14927WOOO example, Li et al, Optimization of ^grotocterzwm-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 / sl 1248-020-00198-8).

[0148] TO plants are grown and genotyped by amplicon sequencing (AmpSeq).Example 2. Generation of additional soybean plants with a mutated JAG1 gene

[0149] Deletions in the soybean JAG1 gene in a variety of different soybean genotypes generated with the gRNA comprising the spacer RNA encoded by SEQ ID NO: 29 and the type V Cas nuclease are provided in Table 3, which is incorporated herein by reference in its entirety. The left-most column of Tables 2 labelled “variant ID” provides the coordinates of the different JAG1 gene deletions relative to the cleavage site in the soy JAG1 gene specified by the gRNA comprising the spacer RNA encoded by SEQ ID NO: 29. The cleavage site for the type V Cas nuclease (e.g., a Casl2 nuclease) is located at a position in the gRNA spacer (c.g, encoded by SEQ ID NO: 29) that is 19 nucleotides away from the PAM site. Different deletions in the target JAG1 genes can fall either 5’ or 3’ to the cleavage site specified by the gRNA. In the variant ID of column 1, the first number represents either the number of deleted nucleotides 5’ of the cleavage site (negative (-) values) or 3’ of the cleavage site (positive values (+)) for deletions which extend either 5’ or 3’ of the cleavage site. The cleavage site in the JAG1 gene specified by the spacer encoded by SEQ ID NO: 29 is located between nucleotides 425 (“-1”) and 426 (“+1”) in the JAG1 SEQ ID NO: 18 reference sequence. The second number in the variant ID represents the total number of nucleotides which have been deleted. This nomenclature used in Table 3 is illustrated in Figures 2 and 3 respectively for the JAG1 “-9:13D” and “1:6D” deletions generated with the gRNA comprising the spacer RNA encoded by SEQ ID NO: 29 and the type V Cas nuclease. The second column (“Deletion size”) indicates the number of deleted nucleotides. For Table 3, the third column indicates the deleted nucleotides which correspond to the deletion in a wild-type JAG1 reference sequence of SEQ ID NO: 18. Since the deletions disclosed in Table 3 were generated in a number of different soybean genotypes, it is anticipated that certain deletions shown in those Tables have been generated in an allelic variant of the soybean JAG1 gene of SEQ ID NO: 18. In certain embodiments, such allelic variants of SEQ ID NO: 18 can have at least 90%, 95%, 97%, 98%, or 99% nucleotide sequence identity to SEQ ID NO: 18.Docket No. P14927WOOO

[0150] Table 3. Additional Deletions in the JAG1 geneDocket No. P14927WOOODocket No. P14927WOOODocket No. P14927WOOODocket No. P14927WOOODocket No. P14927WOOODocket No. P14927WOOODocket No. P14927WOOODocket No. P14927WOOODocket No. P14927WOOODocket No. P14927WOOODocket No. P14927WOOODocket No. P14927WOOO

[0151] Example 3. Performance of soybean with an amorphic allele of a JAG1 and / or JAG2 gene

[0152] Seeds of soybean plants homozygous for the loss-of-function alleles of the JAG1 andJAG2 gene where at least one of the loss-of -function alleles is a hypomorphic allele and homozygous for loss of function allele(s) of the BS1 and / or BS2 genes are increased and planted in rows in the field along with checks (e.g., wild-type control plants an optionally additional controls lacking one or more of the loss-of-function alleles). Data on seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, pod count per plant, seed count per plant, total harvested seed weight per plant, numbers of pods on the lower third of the main stem, and total harvested seed weight per unit area from field trials are collected and compared to adjacently grown checks. Plants homozygous for the loss-of-function alleles of the JAG1 and / or JAG2 gene will have increased leaf thickness, chlorophyl content, seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, numbers of pods on the lower third of the main stem, and / or seed yield in comparison to the checks lacking the loss-of- function alleles of : (i) the JAG1 and (ii) JAG2 gene; and (ii) the BS1 and / or BS2 gene.

[0153] Example 4. Characterization of lines comprising loss-of-function alleles of the JAG1, JAG2,and BS2 genes

[0154] About three to 5 JAGlhet+JAG2KO+BS2hetTO events / plants were obtained via Agrobacterium transformation using a Type V Cas nuclease in a NING1295 genetic background. Each TO plant with this edited allele configuration (heterozygous KO), showed the phenotype shown in Fig. 4: Less foliage than WT (NING1295), dark and thick leaves, and absence of 4-seeds-per-pod (SPP) pods. Phenotypic observations are shown in Table 4.Docket No. P14927WOOO

[0155] Table 4. Phenotypic observation on TO events comprising loss-of-function alleles of the JAG1, JAG2, and BS2 genes.

[0156] T1 progeny from selected TO events were obtained by screening the progeny (>200 seeds per TO plant) from 3 independent transgenic TO events to identify and characterize the following genotypes: (i) JAG1WT+JAG2KO+BS2WT; (ii) JAG1KO+JAG2KO+BS2WT; (iii) JAG1KO+JAG2KO+B S2KO

[0157] Among the T1 progeny examined at the V2 stage of vegetative development, we identified two types of plants: a) plants that developed at a normal rate but had different plant architecture from the WT (NING1295), and b) severely stunted (max height 8cm) and leafless plants (FIG. 5.). Genotypic data (at V2 stage) revealed that every stunted plant shared the JAG1KO+JAG2KOhomozygous genotype; and none of the normally-developed soybeans had this genotype. This suggests that homozygous KO for both JAG1 and JAG2 wasDocket No. P14927WOOO detrimental to plant development, and at least one functional copy of the JAG1 or JAG2 gene was necessary for normal plant development.

[0158] T1 progeny were grown to the R3 stage of reproductive development for the following genotypic categories: (1) JAGlhet+JAG2KO+BS2Het or KO(Fig. 6); (2) JAGlKO+JAG2het+BS2Het or KO; (3) JAGlWT+JAG2KO+BS2Het or KO; (4) JAGlhet+JAG2KO+BS2WT; and (5) JAGlKO+JAG2het+BS2WT. Categories 1 and 2 produced slender plants, with less foliage, dark-green thick leaves; which was in contrasting from the WT NING1295 control plants. A high frequency of 4SPP pods was observed in JAGlhet+JAG2KO+BS2Het or KOand JAGlKO+JAG2het+BS2Het or KOT1 progeny plants at the R5 / 6 stage of reproductive development (Fig. 7 and 8). At senescence (R8 stage of reproductive development), the JAGlhet+JAG2KO+BS2Het or KOand JAGlKO+JAG2het+BS2Hetor KOTl progeny plants (Fig. 9), showed pods formed in the bottom 1 / 3 (third) of the stem. Pod at this plant height (bottom third of stem) were absent from the WT NING1295 (wildtype controls). Phenotypic observations for the T1 progeny plants are summarized in Tables 5 and 6.

[0159] Table 5. Phenotypic observations on JAG1, JAG2, and BS2 T1 genotypic classes segregated from three JAG1HET+ JAG2HET+BS2HETindependent TO events.Docket No. P14927WOOO

[0160] Table 6. Seeds-per-pod distribution on T1 plants: comparison of WT and edited classes.

[0161] Partial knockout (heterozygous for an amorphic allele) of JAG1 in a JAG2KO+BS2Hetor KObackground resulted in higher seed yield per plant (i.e., an increase of 30% under greenhouse conditions compared to controls). Higher yield is a result is a combination of: (i) modified canopy architecture (less and narrow leaves, short petioles and petioles) and leaf shape (indicating higher light penetrance); (ii) increased leaf thickness (potentially thicker spongy mesophyll); (iii) increased frequency of 4SPP pods; and (iv) maintenance of normal seed size, due to BS2Het or KO. The reciprocal genotype of a partial knockout (heterozygous for an amorphic allele) of JAG2 in a JAGlKO+BS2Het or KOis higher yielding than NING1295, as well; but not the highest yielding (based on limited plant numbers), for the reason that in these plants the frequency of 4SPP pods is higher than WT, but they have less 4SPP than JAGlhet+JAG2KO+BS2Het or KOplants. JAGlKO+JAG2hetor JAGlhet+JAG2KOcarrying the WT alleles at BS2 do not have higher yield than NING1295. These plants have (i) very small narrow leaves; and ii) very small seeds. To achieve high yield, loss-of-function alleles at JAG1 and JAG2 (where one of the loss-of-function alleles was heterozygous) and a loss-of- function allele of BS2 were required. BS2 modulates both leaf size and seed size.Docket No. P14927WOOO

[0162] Example 5. Generation of hypomorphic alleles of JAG1 in combination with loss- of-function alleles of JAG2 and BS2

[0163] The following experimental design set forth in Table 7 is used to generate soybean plants having a hypomorphic allele of the JAG1 gene with INDELs in the JAG1 gene promoter and loss-of-function alleles of JAG2 and BS2. INDELs in the JAG1 promoter, JAG2, and BS2 genes are generated by transforming soybean plants with the vectors specified in Table 7 essentially according to the ^grotocterzwm-mediated methods set forth in Example 1. TO and T1 plants with the INDELs in the JAG1 promoter, JAG2, and BS2 genes are characterized for increased leaf thickness, leaf length to width ratio (L / W ratio) , chlorophyll content, seeds per pod, percentage of 3 seeded pods, and / or percentage of 4 seeded pods in comparison to seeds per pod, percentage of 3 seeded pods, increased numbers of pods on the lower third of the main stem, percentage of 4 seeded pods and / or yield in comparison to a wild-type or control soybean plant lacking the loss-of-function alleles of the: (i) JAG1 and JAG2 genes; and (ii) BS1 and / or BS2 genes; essentially as described in Example 4.

[0164] Table 7. Gene Edits for production of loss-of-function alleles in JAG1, JAG2, and BS2Docket No. P14927WOOO1SEQ ID NO of DNA molecules encoding the spacer regions of the guide RNAs and target region are provided. The Casl2i crRNA DR DNA coding sequence is SEQ ID NO: 15231.

[0165] Example 6. Summary of Select Biological Sequences

[0166] Table 8. Select Biological SequencesDocket No. P14927WOOODocket No. P14927WOOODocket No. P14927WOOODocket No. P14927WOOODocket No. P14927WOOOAll 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

Docket No. P14927WOOOWhat is claimed is:

1. A soybean plant comprising:(i) a loss-of-function allele in the endogenous JAG1 gene and a loss-of-function allele in the endogenous JAG2 gene, wherein at least one of the loss-of-function alleles of the endogenous JAG1 or JAG2 genes is a hypomorphic allele of the JAG1 gene or JAG2 gene; and(ii) a loss-of-function allele in the endogenous BS1 gene and / or a loss-of-function allele in the endogenous BS2 gene; wherein the soybean plant exhibits increased yield in comparison to a control plant lacking the loss-of-function alleles of: (i) the JAG1 and JAG2 genes; and (ii) the BS1 and / or BS2 genes.

2. The soybean plant of claim 1, wherein:(i) one of the loss-of-function alleles of the endogenous JAG1 or JAG2 genes comprises an amorphic allele of the JAG1 gene or JAG2 gene and wherein one of the loss-of-function alleles of the endogenous JAG1 or JAG2 genes comprises a hypomorphic allele of the JAG1 gene or JAG2 gene; or(ii) both of the endogenous JAG1 or JAG2 genes comprise a hypomorphic allele of the JAG1 gene and JAG2 gene.

3. The soybean plant of claim 1, wherein:(i) the hypomorphic allele of the JAG1 gene reduces expression of the JAG1 mRNA or the JAG1 protein in a vegetative shoot apical meristem of a soybean plant containing the hypomorphic allele of the JAG1 gene in the homozygous state to 20% to 80%, 30% to 70%, 40% to 60%, or 45% to 55% of the expression of the JAG1 mRNA or the JAG1 protein in a control vegetative shoot apical meristem of a wildtype control soybean plant lacking the hypomorphic allele of the JAG1 gene; and / or(ii) the hypomorphic allele of the JAG2 gene reduces expression of the JAG2 mRNA or the JAG2 protein in a vegetative shoot apical meristem of a soybean plantDocket No. P14927WOOO containing the hypomorphic allele of the JAG2 gene in the homozygous state to 20% to 80%, 30% to 70%, 40% to 60%, or 45% to 55% of the expression of the JAG2 mRNA or the JAG2 protein in a control vegetative shoot apical meristem of a wildtype control soybean plant lacking the hypomorphic allele of the JAG2 gene.

4. The soybean plant of claim 3, wherein expression of the JAG1 and / or JAG2 mRNA is determined in the shoot apical meristem of a vegetative stage 5 (V5) soybean plant using a quantitative reverse transcriptase Polymerase Chain Reaction (qRTPCR) assay.

5. The soybean plant of claim 4, wherein:(i) expression of the JAG1 gene is determined in the qRTPCR assay with SEQ ID NO: 74 as the forward primer and SEQ ID NO: 75 as the reverse primer for the JAG1 mRNA quantitation and with SEQ ID NO: 78 as the forward primer and SEQ ID NO: 79 as the reverse primer for Actin 11 (Actl 1) mRNA quantitation, wherein the expression of the JAG1 mRNA is normalized to expression of the Actl 1 mRNA; and / or(ii) expression of the JAG2 gene is determined in the qRTPCR assay with SEQ ID NO: 76 as the forward primer and SEQ ID NO: 75 as the reverse primer for the JAG2 mRNA quantitation and with SEQ ID NO: 77 as the forward primer and SEQ ID NO: 79 as the reverse primer for Actin 11 (Actl 1) mRNA quantitation, wherein the expression of the JAG2 mRNA is normalized to expression of the Actl 1 mRNA.

6. The soybean plant of claim 1, wherein:(i) the hypomorphic allele of the JAG1 gene in the homozygous state in an otherwise wild-type soybean plant provides a fully expanded vegetative stage 5 (V5) leaf length to width ratio (L / W ratio) which is greater than the L / W ratio of a control V5 leaf of a wild-type control plant having a wild-type JAG1 gene in the homozygous state but less than the L / W ratio of a control V5 leaf of a control plant having an amorphic allele of the JAG1 gene in the homozygous state; and / orDocket No. P14927WOOO(ii) the hypomorphic allele of the JAG2 gene in the homozygous state in an otherwise wild-type soybean plant provides a fully expanded vegetative stage 5 (V5) leaf length to width ratio (L / W ratio) which is greater than the L / W ratio of a control V5 leaf of a wild-type control plant having a wild-type JAG1 gene in the homozygous state but less than the L / W ratio of a control V5 leaf of a control plant having an amorphic allele of the JAG2 gene in the homozygous state.

7. The soybean plant of claim 1, wherein:(i) the hypomorphic allele of the endogenous JAG1 gene comprises, consists essentially of, or consists of an insertion, deletion, and / or substitution (INDELS) of 1, 2, 3, 5, 10, or more nucleotides in a coding or non-coding region of SEQ ID NO: 18 or an allelic variant thereof, optionally wherein the non-coding region comprises the promoter, 5’ untranslated region (UTR), intron, 3’ UTR, or terminator region of SEQ ID NO: 18 or an allelic variant thereof; or(ii) the hypomorphic allele of the endogenous JAG2 gene comprises, consists essentially of, or consists of an INDELS of one or more nucleotides in a non-coding region of SEQ ID NO: 1 or an allelic variant thereof, optionally wherein the noncoding region comprises the promoter, 5’ untranslated region (UTR), intron, 3’ UTR, or terminator region of SEQ ID NO: 1 or an allelic variant thereof.

8. The soybean plant of claim 1, wherein:(i) the hypomorphic allele of the endogenous JAG1 gene comprises a deletion in the promoter, 5’ UTR, first intron, 3’ UTR, and / or the terminator of the JAG1 gene comprising a deletion of at least 10 base pairs located 5’ and / or 3’ to one or two cleavage sites specified by a Cast 2 nuclease and one or two Cast 2 gRNAs comprising one or two gRNA spacer molecule(s) set forth in Table 8 that target the JAG1 promoter, 5’ UTR, first intron, 3’ UTR, and / or terminator or to a cleavage site specified by a Cas9 nuclease and one or two Cas9 gRNAs comprising one or two gRNA spacer molecule(s) set forth in Table 8 which target the JAG1 promoter, 5’ UTR, first intron, 3’ UTR, and / or terminator; and / orDocket No. P14927WOOO(ii) the hypomorphic allele of the endogenous JAG2 gene comprises a deletion in the promoter, 5’ UTR, first intron, 3’ UTR, and / or the terminator of the JAG2 gene comprising a deletion of at least 10 base pairs located 5’ and / or 3’ to a cleavage site specified by a Casl2 nuclease and one or two Casl2 gRNAs comprising a gRNA spacer molecule set forth in Table 8 which target the JAG2 promoter, 5’ UTR, first intron, 3’ UTR, and / or terminator or to a cleavage site specified by a Cas9 nuclease and one or two Cas9 gRNAs comprising one or two gRNA spacer molecule(s) set forth in Table 8 which target the JAG2 promoter, 5’ UTR, first intron, 3’ UTR, and / or terminator.

9. The soybean plant of claim 1, wherein the hypomorphic allele of the endogenous JAG1 gene contains a deletion in the promoter of the JAG1 gene comprising, consisting essentially of, or consisting of at least about 10, 20, 40, 50, 60, 80, 100, 120, 140, 150, 160, 170, 180, 190, 200, 210, or 220 nucleotides located within or including nucleotides corresponding to nucleotides 440 to 616, 617 to 1380, or 440 to 1380 of the JAG1 promoter of SEQ ID NO: 17 or an allelic variant thereof.

10. The soybean plant of claim 1, wherein the hypomorphic allele of the endogenous JAG1 or JAG2 gene comprises a deletion in the promoter, 5’ UTR, first intron, 3’ UTR, and / or the terminator of the JAG1 or JAG2 gene and is obtained by a process comprising:(i) directing to the genome of a target soybean plant cell: (a) one or two Cast 2 gRNAs comprising one or two gRNA spacer molecule(s) set forth in Table 8 that target the JAG1 or JAG2 promoter, 5’ UTR, first intron, 3’ UTR, and / or terminator and a Casl2 nuclease which recognizes the Cast 2 gRNAs; or (b) one or two Cas9 gRNAs comprising one or two gRNA spacer molecule(s) set forth in Table 8 which target the JAG1 or JAG2 promoter, 5’ UTR, first intron, 3’ UTR, and / or terminator; and(ii) isolating a soybean plant cell, soybean plant part, or soybean plant comprising at the hypomorphic allele.

11. The soybean plant of claim 10, wherein the Casl2 gRNAs comprise two distinct gRNA spacer molecule(s) selected from the spacer molecules encoded by SEQ ID NOs:Docket No. P14927WOOO1888, 15226, and 15227, optionally wherein the Casl2 nuclease comprises the polypeptide of SEQ ID NO: 15229 or a catalytically active variant thereof and the crRNA direct repeat of the gRNA comprises the RNA of SEQ ID NO: 15231.

12. The soybean plant of claim 1, wherein the plant is:(i) homozygous for a hypomorphic allele of the endogenous JAG1 gene;(ii) homozygous for an amorphic allele of the endogenous JAG2 gene; and(iii) homozygous for an amorphic or hypomorphic allele of the endogenous Gm BS2 gene.

13. The soybean plant of claim 3, wherein:(i) the expression of the JAG1 mRNA or the JAG1 protein in a vegetative shoot apical meristem is reduced to 20% to 80%, 30% to 70%, 40% to 60%, or 45% to 55% of the expression of the JAG1 mRNA or the JAG1 protein in a control vegetative shoot apical meristem of a wild-type control plant;(ii) the expression of the JAG2 mRNA or the JAG2 protein in a vegetative shoot apical meristem is reduced by at least 90%, 95%, or 99% in comparison to the expression of the JAG2 mRNA or the JAG2 protein in a control vegetative shoot apical meristem of a wild-type control plant; and / or(iii) the expression of the BS2 mRNA or the BS2 protein in a soybean plant tissue is reduced by 20% to 100%, 50% to 100%, or 80% to 100% in comparison to the expression of the JAG2 mRNA or the JAG2 protein in a control soybean plant tissue of a wild-type control plant, optionally wherein the soybean plant tissue is a vegetative or reproductive shoot apical meristem .

14. The soybean plant of claim 1, wherein the plant is:(i) homozygous for an amorphic allele of the endogenous JAG1 gene;(ii) homozygous for a hypomorphic allele of the endogenous JAG2 gene; andDocket No. P14927WOOO(iii) homozygous for an amorphic or hypomorphic allele of the endogenous Gm BS2 gene or homozygous for a hypomorphic allele of both the BS1 and BS2 genes.

15. The soybean plant of any one of claims 1 to 14, wherein(i) the loss-of-function allele of the endogenous JAG1 gene contains an INDELS of at least one nucleotide in the coding region of the JAG1 gene, optionally wherein:(a) the loss-of-function allele is an amorphic allele of the endogenous JAG1 gene comprising a deletion of at least one, two, or more nucleotides corresponding to nucleotides 2001 to 4178 of SEQ ID NO: 18 or an allelic variant thereof, optionally wherein the deletion comprises, consists essentially of, or consists of a deletion of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 50, 45, 50, 65, 70, 75, 80, 85, 95, 100, 125, 150, 175, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 1000, 1250, 1500, 1750, or 2000 nucleotides corresponding to nucleotides 2001 to 4178 of SEQ ID NO: 18 or an allelic variant thereof; or optionally wherein the amorphic alleles comprises the DNA molecule of SEQ ID NO: 21, 22, 23, 24, 25, 26. 27, 28, 32, or 33; or(b) the loss-of-function allele of the JAG1 gene contains an INDELS in DNA encoding the JAG1 protein of SEQ ID NO: 15 or an allelic variant thereof, optionally wherein the INDELS is in DNA encoding EAR motif residues corresponding to residue 8 to 14 of SEQ ID NO: 15, and optionally wherein the substitution encodes a D9H or L10F substitution in SEQ ID NO: 15;(ii) the loss-of-function allele of the endogenous JAG2 gene comprises an INDELS of at least one nucleotide of the coding region of the JAG2 gene, optionally wherein:(a) the loss-of-function allele is an amorphic allele of the endogenous JAG2 gene comprising a deletion of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 50, 45, 50, 65, 70, 75, 80, 85, 95, 100, 125, 150, 175, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, 1000, 1250,Docket No. P14927WOOO1500, 1750, 2000, 2500, 3000, 3500, or 3894 nucleotides of the coding region of SEQ ID NO: 1 or an allelic variant thereof;(b) the loss-of-function allele of the JAG2 gene contains an INDELS in DNA encoding the JAG2 protein of SEQ ID NO: 8 or an allelic variant thereof, optionally wherein the INDELS is in DNA encoding EAR motif residues corresponding to residue 8 to 14 of SEQ ID NO: 8, and optionally wherein the substitution encodes a D9H or L10F substitution in SEQ ID NO: 8; or(iii) the loss-of-function allele is an amorphic allele of the endogenous JAG2 gene containing a deletion in the coding region of the JAG2 gene comprising, consisting essentially of, or consisting of a deletion of at least one, two, or more nucleotides corresponding to nucleotides 2558 to 2583 of the JAG2 gene of SEQ ID NO: 1 or an allelic variant thereof; nucleotides 2579 to 2604 of the JAG2 gene of SEQ ID NO: 1 or an allelic variant thereof; nucleotides 3204 to 3229 of the JAG2 gene of SEQ ID NO: 1 or an allelic variant thereof; nucleotides 3489 to 3514 of the JAG2 gene of SEQ ID NO: 1 or an allelic variant thereof; or nucleotides 3539 to 3564 of the JAG2 gene of SEQ ID NO: 1 or an allelic variant thereof.

16. The soybean plant of any one of claims 1 to 14, wherein at least one of the loss-of- function alleles in the: (i) JAG1 and JAG2 genes; and (ii) BS1 and / or BS2 genes is a nonnatural mutation.

17. The soybean plant of any one of claims 1 to 14, wherein the soybean plant is homozygous for the loss-of-function alleles of the: (i) JAG1 and JAG2 genes; and (ii) BS1 and / or BS2 genes.

18. The soybean plant of any one of claims 1 to 14, wherein the plant has increased leaf thickness, leaf length to width ratio (L / W ratio) , chlorophyll content, seeds per pod, percentage of 3 seeded pods, and / or percentage of 4 seeded pods in comparison to seeds per pod, percentage of 3 seeded pods, increased numbers of pods on the lower third of the mainDocket No. P14927WOOO stem, and / or percentage of 4 seeded pods for a wild-type or control soybean plant lacking the loss-of-function alleles of the: (i) JAG1 and JAG2 genes; and (ii) BS1 and / or BS2 genes.

19. The soybean plant of any one of claims 1 to 14, wherein:(i) the plant exhibits increased yield in comparison to a control plant lacking the loss- of-function alleles, optionally wherein the increased yield comprises increased pod count per plant, increased seed count per plant, increased total harvested seed weight per plant, increased numbers of pods on the lower third of the main stem, and / or increased total harvested seed weight per unit area in comparison to a control plant lacking the loss-of- function alleles; and optionally(ii) the increased yield is exhibited when the plant is grown at a plant density which is greater than the plant density which is optimal for yield of a control plant lacking one or more of the loss-of-function alleles.

20. A soybean plant cell of the soybean plant of any one of claims 1 to 14.

21. A soybean plant part of the soybean plant of any one of claims 1 to 14.

22. The soybean plant part of claim 19, wherein the part is a stem, root, leaf, flower, pod, seed, or grain.

23. A biological sample obtained from the soybean plant part of claim 21.

24. A method of producing a soybean seed lot comprising: (i) growing a population of soybean plants comprising the soybean plant of any one of claims 1 to 14; and (ii) harvesting seed from the population of soybean plants of step (i) at maturity, thereby producing the soybean seed lot.Docket No. P14927WOOO25. The method of claim 24, wherein:(i) the population of soybean plants are grown at a plant density which is greater than the plant density which is optimal for yield of a control plant lacking one or more of the loss- of-function alleles; and / or(ii) the seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, numbers of pods on the lower third of the main stem, and / or yield is increased in comparison to seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, numbers of pods on the lower third of the main stem, and / or yield of wild-type or control soybean plants lacking the at least one mutation, optionally wherein yield comprises pod count per plant, seed count per plant, total harvested seed weight per plant, and / or total harvested seed weight per unit area.

26. A method of producing a soybean crop comprising planting a plurality of the seed of claim 22.

27. The method of claim 26, further comprising harvesting seed from soybean crop grown from the planted seed.

28. The method of claim 27, wherein:(i) the plurality of seed are planted at a seeding rate which is greater than the seeding rate which is optimal for yield of a control plant lacking one or more of the loss-of-function alleles; and / or(ii) the seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, numbers of pods on the lower third of the main stem, and / or yield is increased in comparison to seeds per pod, percentage of 3 seeded pods, percentage of 4 seeded pods, numbers of pods on the lower third of the main stem, and / or yield of a wild-type or control soybean crop lacking one or more of the loss-of-function alleles, optionally wherein yield comprises pod count per plant, seed count per plant, total harvested seed weight per plant, and / or total harvested seed weight per unit area.Docket No. P14927WOOO29. 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 grain of claim 22.

30. A method of making the soybean plant of any one of claims 1 to 14 comprising:(i) introducing at least one mutation comprising a hypomorphic allele of a JAG1 or JAG2 gene into at least one of an endogenous wild-type JAG1 and / or JAG2 gene of a soybean plant; and(ii) selecting a soybean plant for a hypomorphic allele of the JAG1 and / or JAG2 gene of the soybean plant, wherein the hypomorphic allele of the JAG1 and / or JAG2 gene is combined in the selected soybean plant or in progeny of the selected soybean plant with a loss-of-function allele of a BS1 and / or BS2 gene and with an amorphic allele of the JAG1 or JAG2 gene when both of the JAG1 or JAG2 genes of the selected soybean plant do not comprise hypomorphic alleles of the JAG1 or JAG2 genes.

31. The method of claim 30, wherein the soybean plant is selected for the hypomorphic allele of the JAG1 and / or JAG2 gene by selecting for:(a) a fully expanded leaf length to width ratio (L / W ratio) which is greater than the L / W ratio of a control V5 leaf of a wild-type control plant having a wild-type JAG1 gene in the homozygous state but less than the L / W ratio of a control V5 leaf of a control plant having an amorphic allele of the JAG1 gene in the homozygous state;(b) increased leaf thickness, chlorophyll content, seeds per pod, percentage of 3 seeded pods, and / or percentage of 4 seeded pods in comparison to seeds per pod, percentage of 3 seeded pods, increased numbers of pods on the lower third of the main stem, and / or percentage of 4 seeded pods in comparison to a wild-type control plant;(c) a decrease in expression of JAG1 and / or JAG2 mRNA or protein of at least 40%, 50%, or 60% in comparison to a control plant have a wild-type JAG1 and / or JAG2 gene; and / or(d) identifying an INDELS in the coding or non-coding region of the JAG1 or JAG2 gene which comprises a hypomorphic allele of the JAG1 or JAG2 gene.Docket No. P14927WOOO32. The method of claim 30, wherein the hypomorphic allele is introduced into the JAG1 gene and combined with an amorphic allele of the JAG2 gene, optionally wherein the hypomorphic allele is combined with the amorphic allele by: (i) introducing the mutations comprising the hypomorphic allele and the amorphic alleles into wild-type JAG1 and JAG2 genes simultaneously or consecutively; (ii) introducing the mutation comprising the hypomorphic allele of JAG1 into a soybean plant comprising the amorphic allele of JAG2 in step (i); or (iii) crossing the selected soybean plant comprising the hypomorphic allele of JAG1 gene with a soybean plant comprising the amorphic allele of the JAG2 gene and recovering progeny soybean plants comprising the hypomorphic and amorphic alleles.

33. The method of claim 30, wherein the hypomorphic allele is introduced into the JAG2 gene and combined with an amorphic allele of the JAG1 gene, optionally wherein the hypomorphic allele is combined with the amorphic allele by: (i) introducing the mutations comprising the hypomorphic allele and the amorphic alleles into wild-type JAG1 and JAG2 genes simultaneously or consecutively; (ii) introducing the mutation comprising the hypomorphic allele of JAG2 into a soybean plant comprising the amorphic allele of JAG1 in step (i); or (iii) crossing the selected soybean plant comprising the hypomorphic allele of JAG2 gene with a soybean plant comprising the amorphic allele of the JAG1 gene and recovering progeny soybean plants comprising the hypomorphic and amorphic alleles.

34. A method of making an elite soybean plant variety comprising:(i) crossing the soybean plant of any one of claims 1 to 14 or a plant comprising one or more of the loss-of-function alleles of the JAG1, JAG2, BS1, and / or BS2 genes to elite soybean germplasm lacking one or more of the loss-of-function alleles of the JAG1, JAG2, BS1, and / or BS2 genes;(ii) selecting progeny comprising the loss-of-function alleles of the: (i) JAG1 and JAG2 genes; and (ii) BS1 and / or BS2 genes; and(iii) backcrossing the selected progeny to the elite soybean germplasm.Docket No. P14927WOOO35. A soybean plant comprising a hypomorphic allele of the endogenous JAG1 gene which comprises an insertion, deletion, and / or substitution (INDELS) of 1, 2, 3, 5, 10, or more nucleotides in a coding or non-coding region of the JAG1 gene comprising the JAG1 promoter, 5’ untranslated region (UTR), exons, intron, and / or 3’ UTR of SEQ ID NO: 18 or an allelic variant thereof.

36. The soybean plant of claim 35, wherein the hypomorphic allele of the JAG1 gene in the homozygous state in an otherwise wild-type soybean plant provides a fully expanded vegetative stage 5 (V5) leaf length to width ratio (L / W ratio) which is greater than the L / W ratio of a control V5 leaf of a wild-type control plant having a wild-type JAG1 gene in the homozygous state but less than the L / W ratio of a control V5 leaf of a control plant having an amorphic allele of the JAG1 gene in the homozygous state37. The soybean plant of claim 35, wherein the hypomorphic allele of the endogenous JAG1 gene comprises a deletion in the promoter, 5’ UTR, first intron, 3’ UTR, and / or the terminator of the JAG1 gene comprising a deletion of at least 10 base pairs located 5’ and / or 3’ to one or two cleavage sites specified by a Cast 2 nuclease and one or two Cast 2 gRNAs comprising one or two gRNA spacer molecule(s) set forth in Table 8 that target the JAG1 promoter, 5’ UTR, first intron, 3’ UTR, and / or terminator or to a cleavage site specified by a Cas9 nuclease and one or two Cas9 gRNAs comprising one or two gRNA spacer molecule(s) set forth in Table 8 which target the JAG1 promoter, 5’ UTR, first intron, 3’ UTR, and / or terminator.

38. The soybean plant of claim 35, wherein the hypomorphic allele of the endogenous JAG1 gene comprises a deletion in the promoter, 5’ UTR, first intron, 3’ UTR, and / or the terminator of the JAG1 gene and is obtained by a process comprising:(i) directing to the genome of a target soybean plant cell: (a) one or two Cast 2 gRNAs comprising one or two gRNA spacer molecule(s) set forth in Table 8 that target the JAG1 promoter, 5’ UTR, first intron, 3’ UTR, and / or terminator and a Casl2 nuclease which recognizes the Casl2 gRNAs; or (b) one or two Cas9 gRNAs comprising oneDocket No. P14927WOOO or two gRNA spacer molecule(s) set forth in Table 8 which target the JAG1 promoter, 5’ UTR, first intron, 3’ UTR, and / or terminator; and(ii) isolating a soybean plant cell, soybean plant part, or soybean plant comprising at the hypomorphic allele.

39. The soybean plant of claim 38, wherein the Casl2 gRNAs comprise two distinct gRNA spacer molecule(s) selected from the spacer molecules encoded by SEQ ID NOs: 1888, 15226, and 15227, optionally wherein the Casl2 nuclease comprises the polypeptide of SEQ ID NO: 15229 or a catalytically active variant thereof and the crRNA direct repeat of the gRNA comprises the RNA encoded by SEQ ID NO: 15231.

40. The soybean plant of claim 35, wherein the hypomorphic allele of the endogenous JAG1 gene contains a deletion in the promoter of the JAG1 gene comprising, consisting essentially of, or consisting of at least about 10, 20, 40, 50, 60, 80, 100, 120, 140, 150, 160, 170, 180, 190, 200, 210, or 220 nucleotides located within or including nucleotides corresponding to nucleotides 440 to 616, 617 to 1380, or 440 to 1380 of the JAG1 promoter of SEQ ID NO: 17 or an allelic variant thereof.

41. The soybean plant of claim 35, wherein the deletion in the promoter of the JAG1 gene comprises a deletion of nucleotides 440 to 616, 617 to 1380, or 440 to 1380 of the JAG1 promoter of SEQ ID NO: 17 or an allelic variant thereof.

42. The soybean plant of any one of claims 35 to 41, wherein the hypomorphic allele of the JAG1 gene reduces expression of the JAG1 mRNA or the JAG1 protein in a vegetative shoot apical meristem of a soybean plant containing the hypomorphic allele of the JAG1 gene in the homozygous state to 20% to 80%, 30% to 70%, 40% to 60%, or 45% to 55% of the expression of the JAG1 mRNA or the JAG1 protein in a control vegetative shoot apical meristem of a wild-type control soybean plant lacking the hypomorphic allele of the JAG1 gene.Docket No. P14927WOOO43. The soybean plant of claim 42, wherein expression of the JAG1 mRNA is determined in the shoot apical meristem of a vegetative stage 5 (V5) soybean plant using a quantitative reverse transcriptase Polymerase Chain Reaction (qRTPCR) assay.

44. The soybean plant of claim 43, wherein expression of the JAG1 gene is determined in the qRTPCR assay with SEQ ID NO: 74 as the forward primer and SEQ ID NO: 75 as the reverse primer for the JAG1 mRNA quantitation and with SEQ ID NO: 78 as the forward primer and SEQ ID NO: 79 as the reverse primer for Actin 11 (Actl 1) mRNA quantitation, wherein the expression of the JAG1 mRNA is normalized to expression of the Actl 1 mRNA.

45. A soybean plant cell of the soybean plant of any one of claims 35 to 41.

46. A soybean plant part of the soybean plant of any one of claims 35 to 41.

47. The soybean plant part of claim 46, wherein the part is a stem, root, leaf, flower, pod, seed, or grain.

48. A biological sample obtained from the soybean plant part of claim 46.

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